data_M3B
#
_chem_comp.id M3B
_chem_comp.name
;(1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine
;
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H22 N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-10-02
_chem_comp.pdbx_modified_date 2019-12-20
_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 190.286
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code M3B
_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 6SZP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
M3B C01 C1 C 0 1 N N N N N N -4.481 20.060 4.230 -1.766 -0.427 -0.154 C01 M3B 1
M3B C02 C2 C 0 1 N N N N N N -5.168 18.928 3.445 -2.908 0.555 0.118 C02 M3B 2
M3B C03 C3 C 0 1 N N N N N N -6.645 18.775 3.814 -4.247 -0.133 -0.156 C03 M3B 3
M3B C04 C4 C 0 1 N N N N N N -7.278 17.659 2.975 -5.389 0.849 0.115 C04 M3B 4
M3B C07 C5 C 0 1 N N S N N N -3.524 21.885 2.897 0.642 -0.681 -0.141 C07 M3B 5
M3B C11 C6 C 0 1 N N N N N N -2.088 21.118 1.024 2.968 -0.718 -0.814 C11 M3B 6
M3B C12 C7 C 0 1 N N N N N N -0.880 21.977 1.423 4.250 0.114 -0.882 C12 M3B 7
M3B C14 C8 C 0 1 N N N N N N -0.312 23.971 2.511 5.888 1.196 0.493 C14 M3B 8
M3B N05 N1 N 0 1 N N N N N N -6.945 16.347 3.515 -6.675 0.189 -0.147 N05 M3B 9
M3B N06 N2 N 0 1 N N N N N N -4.686 21.376 3.634 -0.480 0.233 0.109 N06 M3B 10
M3B N08 N3 N 0 1 N N N N N N -3.950 22.766 2.090 0.735 -1.654 0.956 N08 M3B 11
M3B N10 N4 N 0 1 N N N N N N -2.962 20.776 2.149 1.891 0.087 -0.222 N10 M3B 12
M3B O13 O1 O 0 1 N N N N N N -1.323 23.225 1.878 4.690 0.417 0.443 O13 M3B 13
M3B H01 H1 H 0 1 N N N N N N -4.885 20.072 5.253 -1.869 -1.294 0.499 H01 M3B 14
M3B H02 H2 H 0 1 N N N N N N -3.401 19.856 4.265 -1.803 -0.749 -1.194 H02 M3B 15
M3B H04 H3 H 0 1 N N N N N N -4.650 17.982 3.662 -2.871 0.877 1.158 H04 M3B 16
M3B H03 H4 H 0 1 N N N N N N -5.094 19.148 2.370 -2.804 1.422 -0.535 H03 M3B 17
M3B H06 H5 H 0 1 N N N N N N -7.170 19.722 3.618 -4.284 -0.455 -1.196 H06 M3B 18
M3B H05 H6 H 0 1 N N N N N N -6.730 18.522 4.881 -4.350 -1.000 0.497 H05 M3B 19
M3B H08 H7 H 0 1 N N N N N N -6.904 17.729 1.943 -5.352 1.171 1.156 H08 M3B 20
M3B H07 H8 H 0 1 N N N N N N -8.371 17.782 2.978 -5.285 1.716 -0.537 H07 M3B 21
M3B H1 H9 H 0 1 N N N N N N -2.778 22.276 3.605 0.478 -1.208 -1.081 H1 M3B 22
M3B H12 H10 H 0 1 N N N N N N -2.679 21.673 0.281 2.680 -1.025 -1.820 H12 M3B 23
M3B H11 H11 H 0 1 N N N N N N -1.718 20.185 0.575 3.140 -1.602 -0.200 H11 M3B 24
M3B H13 H12 H 0 1 N N N N N N -0.320 21.472 2.224 5.023 -0.452 -1.401 H13 M3B 25
M3B H14 H13 H 0 1 N N N N N N -0.225 22.117 0.550 4.053 1.041 -1.421 H14 M3B 26
M3B H17 H14 H 0 1 N N N N N N -0.722 24.936 2.844 5.725 2.145 -0.017 H17 M3B 27
M3B H15 H15 H 0 1 N N N N N N 0.065 23.413 3.381 6.156 1.384 1.533 H15 M3B 28
M3B H16 H16 H 0 1 N N N N N N 0.511 24.147 1.803 6.695 0.653 0.002 H16 M3B 29
M3B H18 H18 H 0 1 N N N N N N -7.368 15.637 2.952 -6.766 -0.654 0.399 H18 M3B 30
M3B H19 H19 H 0 1 N N N N N N -5.952 16.227 3.511 -7.445 0.817 0.025 H19 M3B 31
M3B H2 H20 H 0 1 N N N N N N -4.902 22.022 4.366 -0.446 0.598 1.049 H2 M3B 32
M3B H3 H22 H 0 1 N N N N N N -4.338 23.531 2.605 1.459 -2.334 0.776 H3 M3B 33
M3B H2C H24 H 0 1 N N N N N N -3.193 23.094 1.525 0.887 -1.190 1.839 H2C M3B 34
M3B H4 H25 H 0 1 N N N N N N -3.723 20.237 1.789 2.160 0.438 0.685 H4 M3B 35
#
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
M3B C11 C12 SING N N 1
M3B C11 N10 SING N N 2
M3B C12 O13 SING N N 3
M3B O13 C14 SING N N 4
M3B N08 C07 SING N N 5
M3B N10 C07 SING N N 6
M3B C07 N06 SING N N 7
M3B C04 N05 SING N N 8
M3B C04 C03 SING N N 9
M3B C02 C03 SING N N 10
M3B C02 C01 SING N N 11
M3B N06 C01 SING N N 12
M3B C01 H01 SING N N 13
M3B C01 H02 SING N N 14
M3B C02 H04 SING N N 15
M3B C02 H03 SING N N 16
M3B C03 H06 SING N N 17
M3B C03 H05 SING N N 18
M3B C04 H08 SING N N 19
M3B C04 H07 SING N N 20
M3B C07 H1 SING N N 21
M3B C11 H12 SING N N 22
M3B C11 H11 SING N N 23
M3B C12 H13 SING N N 24
M3B C12 H14 SING N N 25
M3B C14 H17 SING N N 26
M3B C14 H15 SING N N 27
M3B C14 H16 SING N N 28
M3B N05 H18 SING N N 29
M3B N05 H19 SING N N 30
M3B N06 H2 SING N N 31
M3B N08 H3 SING N N 32
M3B N08 H2C SING N N 33
M3B N10 H4 SING N N 34
#
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
M3B InChI InChI 1.03 InChI=1S/C8H22N4O/c1-13-7-6-12-8(10)11-5-3-2-4-9/h8,11-12H,2-7,9-10H2,1H3/t8-/m0/s1
M3B InChIKey InChI 1.03 HBYRDDGQNQMGCZ-QMMMGPOBSA-N
M3B SMILES_CANONICAL CACTVS 3.385 COCCN[C@@H](N)NCCCCN
M3B SMILES CACTVS 3.385 COCCN[CH](N)NCCCCN
M3B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 COCCN[C@@H](N)NCCCCN
M3B SMILES "OpenEye OEToolkits" 2.0.7 COCCNC(N)NCCCCN
#
_pdbx_chem_comp_identifier.comp_id M3B
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
;(1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine
;
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
M3B 'Create component' 2019-10-02 PDBE
M3B 'Initial release' 2019-12-25 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
M3B C01 C 12.093 0.142 1
M3B C02 C 13.392 0.892 2
M3B C03 C 14.691 0.142 3
M3B C04 C 15.990 0.892 4
M3B C07 C 9.495 0.142 5
M3B C11 C 6.897 0.142 6
M3B C12 C 5.598 0.892 7
M3B C14 C 3.000 0.892 8
M3B N05 N 17.290 0.142 9
M3B N06 N 10.794 0.892 10
M3B N08 N 9.495 -1.357 11
M3B N10 N 8.196 0.892 12
M3B O13 O 4.299 0.142 13
#
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
M3B C11 C12 SINGLE NONE 1
M3B C11 N10 SINGLE NONE 2
M3B C12 O13 SINGLE NONE 3
M3B O13 C14 SINGLE NONE 4
M3B C07 N08 SINGLE BEGINDASH 5
M3B N10 C07 SINGLE NONE 6
M3B C07 N06 SINGLE NONE 7
M3B C04 N05 SINGLE NONE 8
M3B C04 C03 SINGLE NONE 9
M3B C02 C03 SINGLE NONE 10
M3B C02 C01 SINGLE NONE 11
M3B N06 C01 SINGLE NONE 12
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id M3B
_pdbe_chem_comp_rdkit_properties.exactmw 190.179
_pdbe_chem_comp_rdkit_properties.amw 190.291
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 111.445
_pdbe_chem_comp_rdkit_properties.tpsa 85.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.207
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.145
_pdbe_chem_comp_rdkit_properties.chi0v 6.197
_pdbe_chem_comp_rdkit_properties.chi1v 2.750
_pdbe_chem_comp_rdkit_properties.chi2v 0.583
_pdbe_chem_comp_rdkit_properties.chi3v 0.583
_pdbe_chem_comp_rdkit_properties.chi4v 0.254
_pdbe_chem_comp_rdkit_properties.chi0n 28.197
_pdbe_chem_comp_rdkit_properties.chi1n 13.433
_pdbe_chem_comp_rdkit_properties.chi2n 0.583
_pdbe_chem_comp_rdkit_properties.chi3n 0.583
_pdbe_chem_comp_rdkit_properties.chi4n 0.254
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 1.560
_pdbe_chem_comp_rdkit_properties.kappa2 9.885
_pdbe_chem_comp_rdkit_properties.kappa3 9.716
_pdbe_chem_comp_rdkit_properties.Phi 1.186
#
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
M3B UniChem PDBe M3B
M3B UniChem PubChem 145946078
#
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
M3B C01 1.805 1.265 0.380 ETKDGv3 1
M3B C02 1.992 -0.224 0.704 ETKDGv3 2
M3B C03 3.257 -0.823 0.067 ETKDGv3 3
M3B C04 3.259 -0.834 -1.474 ETKDGv3 4
M3B C07 -0.623 1.637 0.443 ETKDGv3 5
M3B C11 -2.807 0.661 1.001 ETKDGv3 6
M3B C12 -2.519 -0.827 1.262 ETKDGv3 7
M3B C14 -3.320 -2.126 -0.486 ETKDGv3 8
M3B N05 2.139 -1.589 -2.035 ETKDGv3 9
M3B N06 0.670 1.807 1.141 ETKDGv3 10
M3B N08 -0.885 2.797 -0.414 ETKDGv3 11
M3B N10 -1.700 1.526 1.446 ETKDGv3 12
M3B O13 -3.597 -1.620 0.802 ETKDGv3 13
M3B H01 1.665 1.417 -0.712 ETKDGv3 14
M3B H02 2.731 1.808 0.674 ETKDGv3 15
M3B H04 2.080 -0.333 1.807 ETKDGv3 16
M3B H03 1.099 -0.805 0.396 ETKDGv3 17
M3B H06 3.375 -1.867 0.432 ETKDGv3 18
M3B H05 4.146 -0.256 0.420 ETKDGv3 19
M3B H08 3.251 0.202 -1.874 ETKDGv3 20
M3B H07 4.205 -1.302 -1.819 ETKDGv3 21
M3B H1 -0.593 0.722 -0.195 ETKDGv3 22
M3B H12 -3.720 0.945 1.565 ETKDGv3 23
M3B H11 -3.032 0.826 -0.075 ETKDGv3 24
M3B H13 -1.533 -1.127 0.834 ETKDGv3 25
M3B H14 -2.433 -0.980 2.359 ETKDGv3 26
M3B H17 -2.486 -2.861 -0.448 ETKDGv3 27
M3B H15 -3.085 -1.311 -1.206 ETKDGv3 28
M3B H16 -4.220 -2.656 -0.859 ETKDGv3 29
M3B H18 2.041 -2.498 -1.527 ETKDGv3 30
M3B H19 1.257 -1.044 -1.905 ETKDGv3 31
M3B H2 0.836 2.825 1.325 ETKDGv3 32
M3B H3 -1.786 2.642 -0.920 ETKDGv3 33
M3B H2C -0.146 2.843 -1.151 ETKDGv3 34
M3B H4 -1.322 1.159 2.352 ETKDGv3 35
#