data_RGM
#
_chem_comp.id RGM
_chem_comp.name
"(3aS,8S,9aS)-2-acetyl-10-methyl-2,3,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrol-4(1H)-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H17 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-02-12
_chem_comp.pdbx_modified_date 2020-04-03
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 259.304
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RGM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 5QXK
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
RGM C10 C1 C 0 1 N N N N N N 27.652 48.288 -10.655 -0.946 -1.242 -0.417 C10 RGM 1
RGM C13 C2 C 0 1 Y N N N N N 29.432 50.223 -10.952 -3.528 -0.962 -0.690 C13 RGM 2
RGM C15 C3 C 0 1 Y N N N N N 31.052 48.984 -11.906 -3.653 1.087 0.208 C15 RGM 3
RGM C17 C4 C 0 1 N N N N N N 24.595 44.352 -11.109 3.847 -0.133 0.046 C17 RGM 4
RGM C01 C5 C 0 1 N N N N N N 29.304 46.165 -9.695 -0.913 -0.524 2.176 C01 RGM 5
RGM C03 C6 C 0 1 N N S N N N 29.767 46.621 -11.923 -1.141 1.468 0.776 C03 RGM 6
RGM C04 C7 C 0 1 N N N N N N 28.841 46.382 -12.881 -0.400 2.005 -0.479 C04 RGM 7
RGM C05 C8 C 0 1 N N S N N N 27.565 46.481 -12.358 0.387 0.799 -1.028 C05 RGM 8
RGM C06 C9 C 0 1 N N N N N N 26.687 45.075 -12.494 1.895 1.088 -0.935 C06 RGM 9
RGM C08 C10 C 0 1 N N N N N N 26.369 46.046 -10.226 1.518 -1.016 0.136 C08 RGM 10
RGM C09 C11 C 0 1 N N S N N N 27.613 46.741 -10.953 0.173 -0.320 0.020 C09 RGM 11
RGM C12 C12 C 0 1 Y N N N N N 28.959 48.922 -11.062 -2.272 -0.601 -0.333 C12 RGM 12
RGM C16 C13 C 0 1 Y N N N N N 29.983 48.112 -11.662 -2.374 0.755 0.260 C16 RGM 13
RGM C18 C14 C 0 1 N N N N N N 23.838 44.567 -9.799 4.792 0.962 -0.377 C18 RGM 14
RGM N02 N1 N 0 1 N N N N N N 28.897 46.066 -10.649 -0.221 0.386 1.254 N02 RGM 15
RGM N07 N2 N 0 1 N N N N N N 25.787 45.099 -11.291 2.531 -0.032 -0.230 N07 RGM 16
RGM N14 N3 N 0 1 Y N N N N N 30.695 50.218 -11.468 -4.358 0.057 -0.364 N14 RGM 17
RGM O11 O1 O 0 1 N N N N N N 26.744 48.893 -10.166 -0.771 -2.380 -0.799 O11 RGM 18
RGM O19 O2 O 0 1 N N N N N N 24.227 43.610 -11.974 4.270 -1.105 0.635 O19 RGM 19
RGM H1 H1 H 0 1 N N N N N N 28.905 51.071 -10.540 -3.816 -1.894 -1.152 H1 RGM 20
RGM H2 H2 H 0 1 N N N N N N 31.995 48.721 -12.362 -4.074 2.017 0.559 H2 RGM 21
RGM H3 H3 H 0 1 N N N N N N 28.606 45.749 -8.953 -1.757 -0.987 1.665 H3 RGM 22
RGM H4 H4 H 0 1 N N N N N N 30.259 45.621 -9.646 -0.221 -1.298 2.509 H4 RGM 23
RGM H5 H5 H 0 1 N N N N N N 29.477 47.230 -9.479 -1.273 0.037 3.039 H5 RGM 24
RGM H6 H6 H 0 1 N N N N N N 30.713 46.069 -12.025 -1.360 2.224 1.530 H6 RGM 25
RGM H7 H7 H 0 1 N N N N N N 28.990 45.369 -13.283 -1.122 2.354 -1.216 H7 RGM 26
RGM H8 H8 H 0 1 N N N N N N 28.959 47.118 -13.690 0.283 2.810 -0.205 H8 RGM 27
RGM H9 H9 H 0 1 N N N N N N 26.994 47.271 -12.869 0.068 0.513 -2.030 H9 RGM 28
RGM H10 H10 H 0 1 N N N N N N 26.099 45.068 -13.424 2.315 1.180 -1.936 H10 RGM 29
RGM H11 H11 H 0 1 N N N N N N 27.348 44.196 -12.472 2.059 2.013 -0.381 H11 RGM 30
RGM H12 H12 H 0 1 N N N N N N 25.625 46.797 -9.924 1.676 -1.354 1.160 H12 RGM 31
RGM H13 H13 H 0 1 N N N N N N 26.700 45.482 -9.342 1.561 -1.863 -0.549 H13 RGM 32
RGM H14 H14 H 0 1 N N N N N N 22.931 43.944 -9.792 4.234 1.746 -0.889 H14 RGM 33
RGM H15 H15 H 0 1 N N N N N N 24.482 44.286 -8.953 5.281 1.380 0.502 H15 RGM 34
RGM H16 H16 H 0 1 N N N N N N 23.555 45.626 -9.709 5.544 0.552 -1.052 H16 RGM 35
RGM H18 H18 H 0 1 N N N N N N 31.285 51.024 -11.517 -5.316 0.059 -0.514 H18 RGM 36
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
RGM C04 C05 SING N N 1
RGM C04 C03 SING N N 2
RGM C06 C05 SING N N 3
RGM C06 N07 SING N N 4
RGM C05 C09 SING N N 5
RGM O19 C17 DOUB N N 6
RGM C03 C16 SING N N 7
RGM C03 N02 SING N N 8
RGM C15 C16 DOUB Y N 9
RGM C15 N14 SING Y N 10
RGM C16 C12 SING Y N 11
RGM N14 C13 SING Y N 12
RGM N07 C17 SING N N 13
RGM N07 C08 SING N N 14
RGM C17 C18 SING N N 15
RGM C12 C13 DOUB Y N 16
RGM C12 C10 SING N N 17
RGM C09 C10 SING N N 18
RGM C09 N02 SING N N 19
RGM C09 C08 SING N N 20
RGM C10 O11 DOUB N N 21
RGM N02 C01 SING N N 22
RGM C13 H1 SING N N 23
RGM C15 H2 SING N N 24
RGM C01 H3 SING N N 25
RGM C01 H4 SING N N 26
RGM C01 H5 SING N N 27
RGM C03 H6 SING N N 28
RGM C04 H7 SING N N 29
RGM C04 H8 SING N N 30
RGM C05 H9 SING N N 31
RGM C06 H10 SING N N 32
RGM C06 H11 SING N N 33
RGM C08 H12 SING N N 34
RGM C08 H13 SING N N 35
RGM C18 H14 SING N N 36
RGM C18 H15 SING N N 37
RGM C18 H16 SING N N 38
RGM N14 H18 SING N N 39
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
RGM SMILES ACDLabs 12.01 C1(=O)C43C(CC(c2cncc12)N3C)CN(C(C)=O)C4
RGM InChI InChI 1.03 InChI=1S/C14H17N3O2/c1-8(18)17-6-9-3-12-10-4-15-5-11(10)13(19)14(9,7-17)16(12)2/h4-5,9,12,15H,3,6-7H2,1-2H3/t9-,12-,14+/m0/s1
RGM InChIKey InChI 1.03 CPZLROCUKBXZER-DUFXMDAXSA-N
RGM SMILES_CANONICAL CACTVS 3.385 CN1[C@H]2C[C@H]3CN(C[C@@]13C(=O)c4c[nH]cc24)C(C)=O
RGM SMILES CACTVS 3.385 CN1[CH]2C[CH]3CN(C[C]13C(=O)c4c[nH]cc24)C(C)=O
RGM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC(=O)N1C[C@@H]2C[C@H]3c4c[nH]cc4C(=O)[C@]2(C1)N3C
RGM SMILES "OpenEye OEToolkits" 2.0.6 CC(=O)N1CC2CC3c4c[nH]cc4C(=O)C2(C1)N3C
#
_pdbx_chem_comp_identifier.comp_id RGM
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 12.01
_pdbx_chem_comp_identifier.identifier
"(3aS,8S,9aS)-2-acetyl-10-methyl-2,3,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrol-4(1H)-one"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RGM 'Create component' 2020-02-12 RCSB
RGM 'Initial release' 2020-04-08 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
RGM C10 C 0.819 -0.584 1
RGM C13 C 0.287 -3.710 2
RGM C15 C -2.295 -3.498 3
RGM C17 C 2.117 3.431 4
RGM C01 C -0.533 -1.321 5
RGM C03 C -1.985 -0.775 6
RGM C04 C -2.511 0.636 7
RGM C05 C -1.209 1.405 8
RGM C06 C -0.430 2.695 9
RGM C08 C 1.161 0.843 10
RGM C09 C -0.225 0.265 11
RGM C12 C 0.002 -2.264 12
RGM C16 C -1.769 -2.116 13
RGM C18 C 1.679 4.888 14
RGM N02 N -0.919 -0.580 15
RGM N07 N 1.039 2.353 16
RGM N14 N -1.081 -4.503 17
RGM O11 O 2.285 -0.264 18
RGM O19 O 3.569 3.098 19
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
RGM C04 C05 SINGLE NONE 1
RGM C04 C03 SINGLE NONE 2
RGM C06 C05 SINGLE NONE 3
RGM C06 N07 SINGLE NONE 4
RGM C05 C09 SINGLE NONE 5
RGM O19 C17 DOUBLE NONE 6
RGM C03 C16 SINGLE NONE 7
RGM C03 N02 SINGLE NONE 8
RGM C15 C16 DOUBLE NONE 9
RGM C15 N14 SINGLE NONE 10
RGM C16 C12 SINGLE NONE 11
RGM N14 C13 SINGLE NONE 12
RGM N07 C17 SINGLE NONE 13
RGM N07 C08 SINGLE NONE 14
RGM C17 C18 SINGLE NONE 15
RGM C12 C13 DOUBLE NONE 16
RGM C12 C10 SINGLE NONE 17
RGM C09 C10 SINGLE NONE 18
RGM C09 N02 SINGLE NONE 19
RGM C09 C08 SINGLE BEGINWEDGE 20
RGM C10 O11 DOUBLE NONE 21
RGM N02 C01 SINGLE NONE 22
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
RGM MurckoScaffold S1 scaffold 'O=C1c2c[nH]cc2[C@@H]2C[C@H]3CNC[C@]13N2' InChI=1S/C11H13N3O/c15-10-8-4-12-3-7(8)9-1-6-2-13-5-11(6,10)14-9/h3-4,6,9,12-14H,1-2,5H2/t6-,9-,11+/m0/s1 VRXBTVFTHJTFLJ-DQBIJJQNSA-N
RGM amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
RGM peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
RGM pyrrole F3 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
RGM C10 S1 1
RGM C13 S1 1
RGM C15 S1 1
RGM C03 S1 1
RGM C04 S1 1
RGM C05 S1 1
RGM C06 S1 1
RGM C08 S1 1
RGM C09 S1 1
RGM C12 S1 1
RGM C16 S1 1
RGM N02 S1 1
RGM N07 S1 1
RGM N14 S1 1
RGM O11 S1 1
RGM N07 F1 1
RGM C17 F1 1
RGM O19 F1 1
RGM C18 F1 1
RGM O11 F2 1
RGM C10 F2 1
RGM C09 F2 1
RGM N02 F2 1
RGM C13 F3 1
RGM C12 F3 1
RGM C16 F3 1
RGM C15 F3 1
RGM N14 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RGM
_pdbe_chem_comp_rdkit_properties.exactmw 259.132
_pdbe_chem_comp_rdkit_properties.amw 259.309
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.571
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 135.058
_pdbe_chem_comp_rdkit_properties.tpsa 56.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.695
_pdbe_chem_comp_rdkit_properties.CrippenMR 68.187
_pdbe_chem_comp_rdkit_properties.chi0v 9.158
_pdbe_chem_comp_rdkit_properties.chi1v 5.197
_pdbe_chem_comp_rdkit_properties.chi2v 3.242
_pdbe_chem_comp_rdkit_properties.chi3v 3.242
_pdbe_chem_comp_rdkit_properties.chi4v 2.370
_pdbe_chem_comp_rdkit_properties.chi0n 26.158
_pdbe_chem_comp_rdkit_properties.chi1n 13.644
_pdbe_chem_comp_rdkit_properties.chi2n 3.242
_pdbe_chem_comp_rdkit_properties.chi3n 3.242
_pdbe_chem_comp_rdkit_properties.chi4n 2.370
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.620
_pdbe_chem_comp_rdkit_properties.kappa1 3.337
_pdbe_chem_comp_rdkit_properties.kappa2 3.278
_pdbe_chem_comp_rdkit_properties.kappa3 1.104
_pdbe_chem_comp_rdkit_properties.Phi 0.576
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
RGM UniChem PDBe RGM
RGM UniChem PubChem 146018226
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
RGM C10 0.624 1.191 0.980 ETKDGv3 1
RGM C13 3.070 1.901 1.154 ETKDGv3 2
RGM C15 3.911 0.262 -0.188 ETKDGv3 3
RGM C17 -3.814 -0.340 -0.753 ETKDGv3 4
RGM C01 0.863 -1.758 1.426 ETKDGv3 5
RGM C03 1.658 -0.886 -0.761 ETKDGv3 6
RGM C04 1.000 -0.163 -1.941 ETKDGv3 7
RGM C05 -0.204 0.580 -1.305 ETKDGv3 8
RGM C06 -1.575 0.151 -1.843 ETKDGv3 9
RGM C08 -1.668 0.021 0.581 ETKDGv3 10
RGM C09 -0.192 0.163 0.178 ETKDGv3 11
RGM C12 2.074 1.128 0.760 ETKDGv3 12
RGM C16 2.607 0.078 -0.074 ETKDGv3 13
RGM C18 -4.637 -0.538 0.482 ETKDGv3 14
RGM N02 0.508 -1.146 0.128 ETKDGv3 15
RGM N07 -2.404 -0.067 -0.670 ETKDGv3 16
RGM N14 4.285 1.402 0.590 ETKDGv3 17
RGM O11 0.098 2.072 1.712 ETKDGv3 18
RGM O19 -4.370 -0.426 -1.882 ETKDGv3 19
RGM H1 2.988 2.786 1.772 ETKDGv3 20
RGM H2 4.587 -0.324 -0.796 ETKDGv3 21
RGM H3 -0.055 -2.096 1.948 ETKDGv3 22
RGM H4 1.412 -1.066 2.096 ETKDGv3 23
RGM H5 1.493 -2.657 1.256 ETKDGv3 24
RGM H6 2.164 -1.826 -1.069 ETKDGv3 25
RGM H7 0.681 -0.911 -2.698 ETKDGv3 26
RGM H8 1.696 0.550 -2.437 ETKDGv3 27
RGM H9 -0.092 1.683 -1.422 ETKDGv3 28
RGM H10 -2.007 0.958 -2.474 ETKDGv3 29
RGM H11 -1.530 -0.790 -2.432 ETKDGv3 30
RGM H12 -1.840 -0.890 1.190 ETKDGv3 31
RGM H13 -2.029 0.906 1.146 ETKDGv3 32
RGM H14 -4.531 0.341 1.150 ETKDGv3 33
RGM H15 -4.298 -1.451 1.014 ETKDGv3 34
RGM H16 -5.710 -0.656 0.220 ETKDGv3 35
RGM H18 5.238 1.817 0.682 ETKDGv3 36
#