# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:22:31 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (3R)-3-({(4-aminobenzyl)[(4-aminophenyl)acetyl]amino}methyl)-5-(hydroxymethyl)-2,3,4,7-tetrahydro-1H-azepinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(CN(C[C@H]2C[NH2+]CC=C(CO)C2)C(=O)Cc3ccc(N)cc3)cc1
#
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
 NC9  NC9  (3R)-3-({(4-aminobenzyl)[(4-aminophenyl)acetyl]amino}methyl)-5-(hydroxymethyl)-2,3,4,7-tetrahydro-1H-azepinium  ligand  60  29  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NC9
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
 NC9  C1    C  CH2   0  -0.370  -5.6467  -0.3385   0.6553
 NC9  N1    N  NT2   1  -0.648  -4.7663  -0.2222   1.8608
 NC9  O1    O  O     0  -0.477   0.3076  -1.1304   1.2393
 NC9  C2    C  CH2   0  -0.301  -3.5597   0.6360   1.7122
 NC9  O2    O  OH1   0  -0.662  -4.2641  -3.1658  -2.1791
 NC9  C3    C  CH1   0  -0.266  -2.5264   0.1053   0.7312
 NC9  N3    N  NH2   0  -0.858   3.0412   6.2522   0.4615
 NC9  C4    C  CH2   0  -0.291  -1.2959   1.0149   0.8715
 NC9  N4    N  NH2   0  -0.861   4.6656  -5.2743   1.1414
 NC9  C5    C  CH2   0  -0.394   0.1031   1.5947  -1.0846
 NC9  C6    C  CR6   0   0.084   0.8719   2.8167  -0.6383
 NC9  C7    C  C     0   0.559   0.5566  -0.4221   0.2772
 NC9  C8    C  CR6   0   0.156   2.5198  -1.9123  -0.1993
 NC9  C9    C  CH2   0  -0.554  -3.0378   0.0557  -0.7108
 NC9  C10   C  C     0   0.118  -3.9408  -1.1155  -0.9841
 NC9  C11   C  CH2   0  -0.193  -3.3983  -2.0854  -1.9843
 NC9  C14   C  C1    0  -0.310  -5.1037  -1.2914  -0.3614
 NC9  C20   C  CR16  0  -0.293   0.8359   3.9734  -1.4130
 NC9  C21   C  CR16  0  -0.310   1.5630   5.0997  -1.0698
 NC9  C22   C  CR6   0   0.287   2.3592   5.1132   0.0819
 NC9  C23   C  CR16  0  -0.310   2.3901   3.9562   0.8666
 NC9  C24   C  CR16  0  -0.295   1.6594   2.8340   0.5072
 NC9  C25   C  CR16  0  -0.303   2.2269  -3.1886  -0.6678
 NC9  C26   C  CR16  0  -0.313   2.9415  -4.2987  -0.2478
 NC9  C27   C  CR6   0   0.287   3.9875  -4.1676   0.6726
 NC9  C28   C  CR16  0  -0.314   4.2897  -2.8834   1.1414
 NC9  C29   C  CR16  0  -0.300   3.5649  -1.7848   0.7099
 NC9  C30   C  CH2   0  -0.720   1.7302  -0.7211  -0.6480
 NC9  H11   H  HCH2  0   0.312  -6.6106  -0.6803   1.0221
 NC9  H21   H  HCH2  0   0.302  -5.7816   0.6748   0.2731
 NC9  H1N1  H  HNT2  0   0.478  -5.3218   0.1630   2.6252
 NC9  H2N1  H  HNT2  0   0.464  -4.4946  -1.1562   2.1723
 NC9  H12   H  HCH2  0   0.290  -3.9209   1.6213   1.4157
 NC9  H22   H  HCH2  0   0.306  -3.1314   0.7208   2.7102
 NC9  HO2   H  HOH1  0   0.464  -3.8541  -3.7710  -2.8031
 NC9  H3    H  HCH1  0   0.275  -2.2362  -0.9023   1.0407
 NC9  H1N3  H  HNH2  0   0.377   3.2687   6.8865  -0.2881
 NC9  H2N3  H  HNH2  0   0.377   3.8374   6.0962   1.0590
 NC9  H14   H  HCH2  0   0.267  -0.9550   1.0008   1.9086
 NC9  H24   H  HCH2  0   0.263  -1.5770   2.0465   0.6479
 NC9  H1N4  H  HNH2  0   0.377   4.6555  -6.0803   0.5373
 NC9  H2N4  H  HNH2  0   0.377   5.5868  -5.0986   1.5090
 NC9  H15   H  HCH2  0   0.286   0.6442   1.0758  -1.8755
 NC9  H25   H  HCH2  0   0.275  -0.8366   1.9090  -1.5454
 NC9  H19   H  HCH2  0   0.268  -3.5433   0.9956  -0.9599
 NC9  H29   H  HCH2  0   0.278  -2.1809  -0.0025  -1.3851
 NC9  H111  H  HCH2  0   0.215  -2.4074  -2.4092  -1.6295
 NC9  H211  H  HCH2  0   0.225  -3.2102  -1.5307  -2.9161
 NC9  H14A  H  H     0   0.270  -5.7159  -2.1578  -0.5722
 NC9  H20   H  HCR6  0   0.247   0.2255   3.9997  -2.3091
 NC9  H21A  H  HCR6  0   0.255   1.5105   5.9830  -1.6955
 NC9  H23   H  HCR6  0   0.255   2.9916   3.9349   1.7680
 NC9  H24A  H  HCR6  0   0.243   1.7071   1.9636   1.1508
 NC9  H25A  H  HCR6  0   0.241   1.4244  -3.3248  -1.3843
 NC9  H26   H  HCR6  0   0.252   2.6893  -5.2785  -0.6367
 NC9  H28   H  HCR6  0   0.253   5.0995  -2.7483   1.8490
 NC9  H29A  H  HCR6  0   0.241   3.8281  -0.8037   1.0896
 NC9  H130  H  HCH2  0   0.294   1.3493  -0.8867  -1.6599
 NC9  H230  H  HCH2  0   0.286   2.3748   0.1606  -0.7161
 NC9  N2    N  NT    0  -0.461  -0.2024   0.6639  -0.0162

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
 NC9  C1   N1    single    1.497  0.020  1.497
 NC9  C1   C14   single    1.495  0.020  1.495
 NC9  N1   C2    single    1.488  0.020  1.488
 NC9  C14  C10   double    1.331  0.020  1.331
 NC9  C2   C3    single    1.520  0.020  1.520
 NC9  C28  C29   aromatic  1.385  0.020  1.385
 NC9  C28  C27   aromatic  1.400  0.020  1.400
 NC9  N4   C27   single    1.380  0.020  1.380
 NC9  O1   C7    double    1.220  0.020  1.220
 NC9  C29  C8    aromatic  1.391  0.020  1.391
 NC9  C27  C26   aromatic  1.399  0.020  1.399
 NC9  C9   C10   single    1.504  0.020  1.504
 NC9  C9   C3    single    1.531  0.020  1.531
 NC9  C10  C11   single    1.495  0.020  1.495
 NC9  O2   C11   single    1.398  0.020  1.398
 NC9  C3   C4    single    1.537  0.020  1.537
 NC9  C7   C30   single    1.524  0.020  1.524
 NC9  C7   N2    single    1.357  0.020  1.357
 NC9  C4   N2    single    1.452  0.020  1.452
 NC9  C8   C30   single    1.498  0.020  1.498
 NC9  C8   C25   aromatic  1.391  0.020  1.391
 NC9  C26  C25   aromatic  1.385  0.020  1.385
 NC9  N2   C5    single    1.450  0.020  1.450
 NC9  C5   C6    single    1.511  0.020  1.511
 NC9  C24  C6    aromatic  1.390  0.020  1.390
 NC9  C24  C23   aromatic  1.386  0.020  1.386
 NC9  C6   C20   aromatic  1.393  0.020  1.393
 NC9  C23  C22   aromatic  1.398  0.020  1.398
 NC9  C20  C21   aromatic  1.384  0.020  1.384
 NC9  C22  C21   aromatic  1.400  0.020  1.400
 NC9  C22  N3    single    1.381  0.020  1.381
 NC9  C1   H11   single    0.970  0.020  1.090
 NC9  C1   H21   single    0.970  0.020  1.090
 NC9  N1   H1N1  single    0.890  0.020  1.040
 NC9  N1   H2N1  single    0.890  0.020  1.040
 NC9  C2   H12   single    0.970  0.020  1.090
 NC9  C2   H22   single    0.970  0.020  1.090
 NC9  O2   HO2   single    0.850  0.020  0.980
 NC9  C3   H3    single    0.970  0.020  1.090
 NC9  N3   H1N3  single    0.890  0.020  1.040
 NC9  N3   H2N3  single    0.890  0.020  1.040
 NC9  C4   H14   single    0.970  0.020  1.090
 NC9  C4   H24   single    0.970  0.020  1.090
 NC9  N4   H1N4  single    0.890  0.020  1.040
 NC9  N4   H2N4  single    0.890  0.020  1.040
 NC9  C5   H15   single    0.970  0.020  1.090
 NC9  C5   H25   single    0.970  0.020  1.090
 NC9  C9   H19   single    0.970  0.020  1.090
 NC9  C9   H29   single    0.970  0.020  1.090
 NC9  C11  H111  single    0.970  0.020  1.090
 NC9  C11  H211  single    0.970  0.020  1.090
 NC9  C14  H14A  single    0.930  0.020  1.080
 NC9  C20  H20   single    0.930  0.020  1.080
 NC9  C21  H21A  single    0.930  0.020  1.080
 NC9  C23  H23   single    0.930  0.020  1.080
 NC9  C24  H24A  single    0.930  0.020  1.080
 NC9  C25  H25A  single    0.930  0.020  1.080
 NC9  C26  H26   single    0.930  0.020  1.080
 NC9  C28  H28   single    0.930  0.020  1.080
 NC9  C29  H29A  single    0.930  0.020  1.080
 NC9  C30  H130  single    0.970  0.020  1.090
 NC9  C30  H230  single    0.970  0.020  1.090

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
 NC9  H21   C1   H11   107.49  3.000
 NC9  H21   C1   C14   113.48  3.000
 NC9  H11   C1   C14   110.56  3.000
 NC9  H21   C1   N1    106.41  3.000
 NC9  H11   C1   N1    105.92  3.000
 NC9  C14   C1   N1    112.54  3.000
 NC9  H2N1  N1   H1N1  105.16  3.000
 NC9  H2N1  N1   C2    110.01  3.000
 NC9  H1N1  N1   C2    107.36  3.000
 NC9  H2N1  N1   C1    109.32  3.000
 NC9  H1N1  N1   C1    108.20  3.000
 NC9  C2    N1   C1    116.18  3.000
 NC9  H22   C2   H12   108.00  3.000
 NC9  H22   C2   C3    110.55  3.000
 NC9  H12   C2   C3    111.41  3.000
 NC9  H22   C2   N1    105.79  3.000
 NC9  H12   C2   N1    106.24  3.000
 NC9  C3    C2   N1    114.46  3.000
 NC9  HO2   O2   C11   108.23  3.000
 NC9  H3    C3   C9    108.99  3.000
 NC9  H3    C3   C4    107.89  3.000
 NC9  C9    C3   C4    111.88  3.000
 NC9  H3    C3   C2    108.63  3.000
 NC9  C4    C3   C2    106.18  3.000
 NC9  C9    C3   C2    113.08  3.000
 NC9  H2N3  N3   H1N3  111.11  3.000
 NC9  H2N3  N3   C22   115.19  3.000
 NC9  H1N3  N3   C22   115.22  3.000
 NC9  H24   C4   H14   106.68  3.000
 NC9  H24   C4   C3    109.53  3.000
 NC9  H14   C4   C3    109.21  3.000
 NC9  H24   C4   N2    107.28  3.000
 NC9  H14   C4   N2    110.04  3.000
 NC9  C3    C4   N2    113.84  3.000
 NC9  H2N4  N4   H1N4  111.57  3.000
 NC9  H2N4  N4   C27   115.68  3.000
 NC9  H1N4  N4   C27   115.66  3.000
 NC9  H25   C5   H15   104.94  3.000
 NC9  H25   C5   C6    109.24  3.000
 NC9  H15   C5   C6    110.29  3.000
 NC9  H25   C5   N2    108.31  3.000
 NC9  H15   C5   N2    109.50  3.000
 NC9  C6    C5   N2    114.13  3.000
 NC9  C24   C6   C20   117.56  3.000
 NC9  C20   C6   C5    119.62  3.000
 NC9  C24   C6   C5    122.79  3.000
 NC9  C30   C7   N2    117.16  3.000
 NC9  N2    C7   O1    121.39  3.000
 NC9  C30   C7   O1    121.45  3.000
 NC9  C30   C8   C29   121.26  3.000
 NC9  C30   C8   C25   121.19  3.000
 NC9  C29   C8   C25   117.55  3.000
 NC9  H29   C9   H19   105.51  3.000
 NC9  H29   C9   C10   108.51  3.000
 NC9  H19   C9   C10   110.46  3.000
 NC9  H29   C9   C3    108.74  3.000
 NC9  H19   C9   C3    109.90  3.000
 NC9  C10   C9   C3    113.39  3.000
 NC9  C14   C10  C11   122.98  3.000
 NC9  C11   C10  C9    114.13  3.000
 NC9  C14   C10  C9    122.86  3.000
 NC9  H211  C11  H111  105.50  3.000
 NC9  H211  C11  C10   107.55  3.000
 NC9  H111  C11  C10   107.56  3.000
 NC9  H211  C11  O2    112.17  3.000
 NC9  H111  C11  O2    112.02  3.000
 NC9  C10   C11  O2    111.70  3.000
 NC9  H14A  C14  C10   120.61  3.000
 NC9  H14A  C14  C1    115.94  3.000
 NC9  C10   C14  C1    123.45  3.000
 NC9  H20   C20  C21   118.74  3.000
 NC9  H20   C20  C6    119.63  3.000
 NC9  C21   C20  C6    121.63  3.000
 NC9  H21A  C21  C22   119.64  3.000
 NC9  H21A  C21  C20   119.65  3.000
 NC9  C22   C21  C20   120.71  3.000
 NC9  C23   C22  C21   117.78  3.000
 NC9  C21   C22  N3    121.00  3.000
 NC9  C23   C22  N3    121.15  3.000
 NC9  H23   C23  C24   119.48  3.000
 NC9  H23   C23  C22   119.68  3.000
 NC9  C24   C23  C22   120.83  3.000
 NC9  H24A  C24  C23   118.23  3.000
 NC9  H24A  C24  C6    120.29  3.000
 NC9  C23   C24  C6    121.48  3.000
 NC9  H25A  C25  C26   118.77  3.000
 NC9  H25A  C25  C8    119.58  3.000
 NC9  C26   C25  C8    121.64  3.000
 NC9  H26   C26  C27   119.64  3.000
 NC9  H26   C26  C25   119.70  3.000
 NC9  C27   C26  C25   120.65  3.000
 NC9  C28   C27  C26   117.87  3.000
 NC9  C26   C27  N4    121.03  3.000
 NC9  C28   C27  N4    121.05  3.000
 NC9  H28   C28  C29   119.70  3.000
 NC9  H28   C28  C27   119.61  3.000
 NC9  C29   C28  C27   120.68  3.000
 NC9  H29A  C29  C28   118.78  3.000
 NC9  H29A  C29  C8    119.61  3.000
 NC9  C28   C29  C8    121.61  3.000
 NC9  H230  C30  H130  105.64  3.000
 NC9  H230  C30  C8    110.41  3.000
 NC9  H130  C30  C8    109.90  3.000
 NC9  H230  C30  C7    109.47  3.000
 NC9  H130  C30  C7    108.85  3.000
 NC9  C8    C30  C7    112.34  3.000
 NC9  C7    N2   C5    123.74  3.000
 NC9  C5    N2   C4    117.02  3.000
 NC9  C7    N2   C4    118.86  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
 NC9  CONST_01  C22   C23  C24  C6     0.00   0.0  0
 NC9  CONST_02  C22   C21  C20  C6     0.00   0.0  0
 NC9  CONST_03  C27   C28  C29  C8     0.00   0.0  0
 NC9  CONST_04  C27   C26  C25  C8     0.00   0.0  0
 NC9  CONST_05  C23   C24  C6   C20    0.00   0.0  0
 NC9  CONST_06  C23   C22  C21  C20    0.00   0.0  0
 NC9  CONST_07  C24   C6   C20  C21    0.00   0.0  0
 NC9  CONST_08  C24   C23  C22  C21    0.00   0.0  0
 NC9  CONST_09  C28   C29  C8   C25    0.00   0.0  0
 NC9  CONST_10  C28   C27  C26  C25    0.00   0.0  0
 NC9  CONST_11  C29   C28  C27  C26    0.00   0.0  0
 NC9  CONST_12  C29   C8   C25  C26    0.00   0.0  0
 NC9  CONST_13  C24   C23  C22  N3   180.00   0.0  0
 NC9  CONST_14  C20   C21  C22  N3   180.00   0.0  0
 NC9  CONST_15  C29   C28  C27  N4   180.00   0.0  0
 NC9  CONST_16  C25   C26  C27  N4   180.00   0.0  0
 NC9  CONST_17  C23   C24  C6   C5   180.00   0.0  0
 NC9  CONST_18  C21   C20  C6   C5   180.00   0.0  0
 NC9  CONST_19  C30   C8   C25  C26  180.00   0.0  0
 NC9  CONST_20  C30   C8   C29  C28  180.00   0.0  0
 NC9  CONST_21  H23   C23  C24  C6   180.00   0.0  0
 NC9  CONST_22  H21A  C21  C20  C6   180.00   0.0  0
 NC9  CONST_23  H28   C28  C29  C8   180.00   0.0  0
 NC9  CONST_24  H26   C26  C25  C8   180.00   0.0  0
 NC9  CONST_25  H24A  C24  C6   C20  180.00   0.0  0
 NC9  CONST_26  H20   C20  C21  C22  180.00   0.0  0
 NC9  CONST_27  H29A  C29  C8   C25  180.00   0.0  0
 NC9  CONST_28  H25A  C25  C26  C27  180.00   0.0  0
 NC9  CONST_33  C4    N2   C7   O1     0.00   0.0  0
 NC9  CONST_34  C5    N2   C7   O1   180.00   0.0  0
 NC9  CONST_35  C30   C7   N2   C4   180.00   0.0  0
 NC9  CONST_36  C30   C7   N2   C5     0.00   0.0  0
 NC9  Var_01    C24   C6   C5   N2    23.90  30.0  2
 NC9  Var_02    C29   C8   C30  C7   -87.57  30.0  2
 NC9  Var_03    C8    C30  C7   O1    -2.10  30.0  3
 NC9  Var_04    C7    N2   C4   C3   -75.45  30.0  3
 NC9  Var_05    C6    C5   N2   C4    77.31  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NC9  chir_01  C3  C2  C9  C4  negativ

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
 NC9  plan-1  N3    0.020
 NC9  plan-1  C5    0.020
 NC9  plan-1  C6    0.020
 NC9  plan-1  C20   0.020
 NC9  plan-1  C21   0.020
 NC9  plan-1  C22   0.020
 NC9  plan-1  C23   0.020
 NC9  plan-1  C24   0.020
 NC9  plan-1  H20   0.020
 NC9  plan-1  H21A  0.020
 NC9  plan-1  H23   0.020
 NC9  plan-1  H24A  0.020
 NC9  plan-2  N4    0.020
 NC9  plan-2  C8    0.020
 NC9  plan-2  C25   0.020
 NC9  plan-2  C26   0.020
 NC9  plan-2  C27   0.020
 NC9  plan-2  C28   0.020
 NC9  plan-2  C29   0.020
 NC9  plan-2  C30   0.020
 NC9  plan-2  H25A  0.020
 NC9  plan-2  H26   0.020
 NC9  plan-2  H28   0.020
 NC9  plan-2  H29A  0.020
 NC9  plan-3  O1    0.020
 NC9  plan-3  C4    0.020
 NC9  plan-3  C5    0.020
 NC9  plan-3  C7    0.020
 NC9  plan-3  C30   0.020
 NC9  plan-3  N2    0.020
 NC9  plan-4  N3    0.020
 NC9  plan-4  C22   0.020
 NC9  plan-4  H1N3  0.020
 NC9  plan-4  H2N3  0.020
 NC9  plan-5  N4    0.020
 NC9  plan-5  C27   0.020
 NC9  plan-5  H1N4  0.020
 NC9  plan-5  H2N4  0.020

