# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:48:26 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 7-[[3-(aminomethyl)phenoxy]methyl]quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(OCc2ccc3ccc(N)nc3c2)c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 9M9  9M9  7-[[3-(aminomethyl)phenoxy]methyl]quinolin-2-amine  ligand  38  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9M9
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 9M9  N01   N  N     0  -0.507  -4.1954  -0.9080  -0.8041
 9M9  C02   C  CR6   0   0.440  -5.3755  -0.8778  -0.2289
 9M9  N02   N  NH2   0  -0.835  -6.3786  -1.6022  -0.7820
 9M9  C03   C  CR16  0  -0.376  -5.6496  -0.0836   0.9293
 9M9  C04   C  CR16  0  -0.178  -4.6511   0.6672   1.4579
 9M9  C05   C  CR66  0   0.046  -3.3668   0.6607   0.8562
 9M9  C06   C  CR16  0  -0.305  -2.2822   1.4186   1.3401
 9M9  C07   C  CR16  0  -0.297  -1.0666   1.3786   0.7116
 9M9  C08   C  CR6   0   0.097  -0.8861   0.5690  -0.4314
 9M9  C09   C  CR16  0  -0.371  -1.9307  -0.1809  -0.9110
 9M9  C10   C  CR66  0   0.236  -3.1985  -0.1530  -0.2873
 9M9  C11   C  CH2   0  -0.261   0.4435   0.5509  -1.1227
 9M9  O12   O  O2    0  -0.474   1.4107   0.0906  -0.1939
 9M9  C21   C  CR6   0   0.095   4.9764  -0.4023   0.1223
 9M9  C22   C  CR16  0  -0.330   5.4219  -0.0754  -1.1591
 9M9  C23   C  CR16  0  -0.227   4.5137   0.3055  -2.1316
 9M9  C24   C  CR16  0  -0.397   3.1526   0.3775  -1.8557
 9M9  C25   C  CR6   0   0.408   2.7065   0.0588  -0.5758
 9M9  C26   C  CR16  0  -0.392   3.6209  -0.3273   0.4052
 9M9  N28   N  NH2   0  -0.793   5.5712  -0.4659   2.5100
 9M9  HN02  H  HNH2  0   0.387  -6.1289  -2.3085  -1.4538
 9M9  HN0A  H  HNH2  0   0.397  -7.2001  -1.7954  -0.2357
 9M9  H03   H  HCR6  0   0.274  -6.6397  -0.0896   1.3665
 9M9  H04   H  HCR6  0   0.269  -4.8271   1.2746   2.3376
 9M9  H06   H  HCR6  0   0.257  -2.4234   2.0405   2.2161
 9M9  H07   H  HCR6  0   0.252  -0.2439   1.9741   1.0868
 9M9  H09   H  HCR6  0   0.251  -1.8024  -0.8113  -1.7832
 9M9  H11   H  HCH2  0   0.245   0.4079  -0.0984  -2.0039
 9M9  H11A  H  HCH2  0   0.240   0.7015   1.5596  -1.4661
 9M9  H22   H  HCR6  0   0.243   6.4798  -0.1138  -1.3897
 9M9  H23   H  HCR6  0   0.256   4.8614   0.5620  -3.1241
 9M9  H24   H  HCR6  0   0.278   2.4715   0.6807  -2.6392
 9M9  H26   H  HCR6  0   0.251   3.2635  -0.5665   1.3993
 9M9  H27   H  HCH2  0   0.242   6.0156  -1.9498   1.1405
 9M9  H27A  H  HCH2  0   0.215   6.9619  -0.5050   0.8753
 9M9  HN28  H  HNH2  0   0.354   6.2141  -0.8725   3.1770
 9M9  HN2A  H  HNH2  0   0.344   5.6636   0.5373   2.6100
 9M9  C27   C  CH2   0  -0.333   5.9640  -0.8572   1.1683

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 9M9  N01  C02   aromatic  1.313  0.020  1.313
 9M9  N01  C10   aromatic  1.353  0.020  1.353
 9M9  C02  N02   single    1.355  0.020  1.355
 9M9  C02  C03   aromatic  1.431  0.020  1.431
 9M9  C03  C04   aromatic  1.357  0.020  1.357
 9M9  C04  C05   aromatic  1.418  0.020  1.418
 9M9  C05  C06   aromatic  1.409  0.020  1.409
 9M9  C05  C10   aromatic  1.414  0.020  1.414
 9M9  C06  C07   aromatic  1.369  0.020  1.369
 9M9  C07  C08   aromatic  1.412  0.020  1.412
 9M9  C08  C09   aromatic  1.372  0.020  1.372
 9M9  C08  C11   single    1.499  0.020  1.499
 9M9  C09  C10   aromatic  1.413  0.020  1.413
 9M9  C11  O12   single    1.418  0.020  1.418
 9M9  O12  C25   single    1.351  0.020  1.351
 9M9  C21  C22   aromatic  1.395  0.020  1.395
 9M9  C21  C26   aromatic  1.387  0.020  1.387
 9M9  C21  C27   single    1.509  0.020  1.509
 9M9  C22  C23   aromatic  1.384  0.020  1.384
 9M9  C23  C24   aromatic  1.391  0.020  1.391
 9M9  C24  C25   aromatic  1.392  0.020  1.392
 9M9  C25  C26   aromatic  1.396  0.020  1.396
 9M9  C27  N28   single    1.452  0.020  1.452
 9M9  N02  HN02  single    0.890  0.020  1.040
 9M9  N02  HN0A  single    0.890  0.020  1.040
 9M9  C03  H03   single    0.930  0.020  1.080
 9M9  C04  H04   single    0.930  0.020  1.080
 9M9  C06  H06   single    0.930  0.020  1.080
 9M9  C07  H07   single    0.930  0.020  1.080
 9M9  C09  H09   single    0.930  0.020  1.080
 9M9  C11  H11   single    0.970  0.020  1.090
 9M9  C11  H11A  single    0.970  0.020  1.090
 9M9  C22  H22   single    0.930  0.020  1.080
 9M9  C23  H23   single    0.930  0.020  1.080
 9M9  C24  H24   single    0.930  0.020  1.080
 9M9  C26  H26   single    0.930  0.020  1.080
 9M9  C27  H27   single    0.970  0.020  1.090
 9M9  C27  H27A  single    0.970  0.020  1.090
 9M9  N28  HN28  single    0.890  0.020  1.040
 9M9  N28  HN2A  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 9M9  C10   N01  C02   118.81  3.000
 9M9  C03   C02  N02   119.03  3.000
 9M9  C03   C02  N01   122.65  3.000
 9M9  N02   C02  N01   118.30  3.000
 9M9  HN0A  N02  HN02  115.51  3.000
 9M9  HN0A  N02  C02   119.06  3.000
 9M9  HN02  N02  C02   117.64  3.000
 9M9  H03   C03  C04   121.27  3.000
 9M9  H03   C03  C02   119.94  3.000
 9M9  C04   C03  C02   118.79  3.000
 9M9  H04   C04  C05   119.61  3.000
 9M9  H04   C04  C03   120.47  3.000
 9M9  C05   C04  C03   119.91  3.000
 9M9  C10   C05  C06   119.73  3.000
 9M9  C10   C05  C04   116.98  3.000
 9M9  C06   C05  C04   123.29  3.000
 9M9  H06   C06  C07   120.24  3.000
 9M9  H06   C06  C05   119.09  3.000
 9M9  C07   C06  C05   120.67  3.000
 9M9  H07   C07  C08   119.91  3.000
 9M9  H07   C07  C06   119.97  3.000
 9M9  C08   C07  C06   120.12  3.000
 9M9  C11   C08  C09   120.50  3.000
 9M9  C11   C08  C07   119.58  3.000
 9M9  C09   C08  C07   119.92  3.000
 9M9  H09   C09  C10   118.22  3.000
 9M9  H09   C09  C08   120.59  3.000
 9M9  C10   C09  C08   121.19  3.000
 9M9  C09   C10  C05   118.37  3.000
 9M9  C09   C10  N01   118.78  3.000
 9M9  C05   C10  N01   122.85  3.000
 9M9  H11A  C11  H11   107.53  3.000
 9M9  H11A  C11  O12   110.08  3.000
 9M9  H11   C11  O12   110.90  3.000
 9M9  H11A  C11  C08   110.01  3.000
 9M9  H11   C11  C08   110.45  3.000
 9M9  O12   C11  C08   107.88  3.000
 9M9  C25   O12  C11   118.47  3.000
 9M9  C27   C21  C26   120.98  3.000
 9M9  C27   C21  C22   119.88  3.000
 9M9  C26   C21  C22   119.13  3.000
 9M9  H22   C22  C23   120.06  3.000
 9M9  H22   C22  C21   119.93  3.000
 9M9  C23   C22  C21   120.01  3.000
 9M9  H23   C23  C24   118.95  3.000
 9M9  H23   C23  C22   119.91  3.000
 9M9  C24   C23  C22   121.14  3.000
 9M9  H24   C24  C25   121.89  3.000
 9M9  H24   C24  C23   119.16  3.000
 9M9  C25   C24  C23   118.95  3.000
 9M9  C26   C25  C24   119.97  3.000
 9M9  C26   C25  O12   115.86  3.000
 9M9  C24   C25  O12   124.17  3.000
 9M9  H26   C26  C25   119.35  3.000
 9M9  H26   C26  C21   119.86  3.000
 9M9  C25   C26  C21   120.80  3.000
 9M9  HN2A  N28  HN28  105.97  3.000
 9M9  HN2A  N28  C27   109.49  3.000
 9M9  HN28  N28  C27   109.21  3.000
 9M9  H27A  C27  H27   105.70  3.000
 9M9  H27A  C27  N28   113.95  3.000
 9M9  H27   C27  N28   107.78  3.000
 9M9  H27A  C27  C21   108.26  3.000
 9M9  H27   C27  C21   108.32  3.000
 9M9  N28   C27  C21   112.48  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 9M9  CONST_01  C04   C03  C02  N01    0.00   0.0  0
 9M9  CONST_02  C04   C05  C10  N01    0.00   0.0  0
 9M9  CONST_03  C06   C05  C10  N01  180.00   0.0  0
 9M9  CONST_04  C08   C09  C10  N01  180.00   0.0  0
 9M9  CONST_05  C05   C10  N01  C02    0.00   0.0  0
 9M9  CONST_06  C09   C10  N01  C02  180.00   0.0  0
 9M9  CONST_07  C05   C04  C03  C02    0.00   0.0  0
 9M9  CONST_08  C10   N01  C02  C03    0.00   0.0  0
 9M9  CONST_09  C06   C05  C04  C03  180.00   0.0  0
 9M9  CONST_10  C10   C05  C04  C03    0.00   0.0  0
 9M9  CONST_11  C07   C06  C05  C04  180.00   0.0  0
 9M9  CONST_12  C09   C10  C05  C04  180.00   0.0  0
 9M9  CONST_13  C08   C07  C06  C05    0.00   0.0  0
 9M9  CONST_14  C08   C09  C10  C05    0.00   0.0  0
 9M9  CONST_15  C09   C10  C05  C06    0.00   0.0  0
 9M9  CONST_16  C09   C08  C07  C06    0.00   0.0  0
 9M9  CONST_17  C10   C05  C06  C07    0.00   0.0  0
 9M9  CONST_18  C10   C09  C08  C07    0.00   0.0  0
 9M9  CONST_19  C24   C23  C22  C21    0.00   0.0  0
 9M9  CONST_20  C24   C25  C26  C21    0.00   0.0  0
 9M9  CONST_21  C25   C26  C21  C22    0.00   0.0  0
 9M9  CONST_22  C25   C24  C23  C22    0.00   0.0  0
 9M9  CONST_23  C26   C21  C22  C23    0.00   0.0  0
 9M9  CONST_24  C26   C25  C24  C23    0.00   0.0  0
 9M9  CONST_25  C10   N01  C02  N02  180.00   0.0  0
 9M9  CONST_26  C04   C03  C02  N02  180.00   0.0  0
 9M9  CONST_27  C11   C08  C07  C06  180.00   0.0  0
 9M9  CONST_28  C11   C08  C09  C10  180.00   0.0  0
 9M9  CONST_29  C23   C24  C25  O12  180.00   0.0  0
 9M9  CONST_30  C21   C26  C25  O12  180.00   0.0  0
 9M9  CONST_31  C27   C21  C22  C23  180.00   0.0  0
 9M9  CONST_32  C27   C21  C26  C25  180.00   0.0  0
 9M9  CONST_33  H03   C03  C02  N01  180.00   0.0  0
 9M9  CONST_34  H09   C09  C10  N01    0.00   0.0  0
 9M9  CONST_35  H04   C04  C03  C02  180.00   0.0  0
 9M9  CONST_36  H06   C06  C05  C04    0.00   0.0  0
 9M9  CONST_37  H07   C07  C06  C05  180.00   0.0  0
 9M9  CONST_38  H23   C23  C22  C21  180.00   0.0  0
 9M9  CONST_39  H26   C26  C21  C22  180.00   0.0  0
 9M9  CONST_40  H24   C24  C23  C22  180.00   0.0  0
 9M9  CONST_41  H22   C22  C23  C24  180.00   0.0  0
 9M9  Var_01    O12   C11  C08  C07   60.43  30.0  2
 9M9  Var_02    C24   C25  O12  C11   -3.88  30.0  2
 9M9  Var_03    N28   C27  C21  C22  148.27  30.0  2
 9M9  Var_04    HN28  N28  C27  C21  174.39  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 9M9  plan-1  O12   0.020
 9M9  plan-1  C21   0.020
 9M9  plan-1  C22   0.020
 9M9  plan-1  C23   0.020
 9M9  plan-1  C24   0.020
 9M9  plan-1  C25   0.020
 9M9  plan-1  C26   0.020
 9M9  plan-1  H22   0.020
 9M9  plan-1  H23   0.020
 9M9  plan-1  H24   0.020
 9M9  plan-1  H26   0.020
 9M9  plan-1  C27   0.020
 9M9  plan-2  N01   0.020
 9M9  plan-2  C02   0.020
 9M9  plan-2  N02   0.020
 9M9  plan-2  C03   0.020
 9M9  plan-2  C04   0.020
 9M9  plan-2  C05   0.020
 9M9  plan-2  C06   0.020
 9M9  plan-2  C07   0.020
 9M9  plan-2  C08   0.020
 9M9  plan-2  C09   0.020
 9M9  plan-2  C10   0.020
 9M9  plan-2  C11   0.020
 9M9  plan-2  H03   0.020
 9M9  plan-2  H04   0.020
 9M9  plan-2  H06   0.020
 9M9  plan-2  H07   0.020
 9M9  plan-2  H09   0.020
 9M9  plan-3  C02   0.020
 9M9  plan-3  N02   0.020
 9M9  plan-3  HN02  0.020
 9M9  plan-3  HN0A  0.020

