# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:47:40 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CN2C=C(C=CC2=O)C(N)=O)c(C)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
 IWH  IWH  1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide  ligand  35  19  .  2021-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IWH
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
 IWH  C1    C  CH3   0  -0.724  -5.4093   0.9403  -1.2152
 IWH  N1    N  NR6   0  -0.497   0.7113  -0.7013   0.5407
 IWH  C2    C  CR6   0   0.107  -4.1374   0.5535  -0.5188
 IWH  N2    N  NH2   0  -0.824   5.1122   0.8939  -0.4091
 IWH  O2    O  O     0  -0.488   3.7467   2.0325   0.9710
 IWH  C3    C  CR16  0  -0.313  -3.9579  -0.7281  -0.0068
 IWH  C4    C  CR16  0  -0.259  -2.7630  -1.0785   0.5994
 IWH  C5    C  CR6   0   0.093  -1.7162  -0.1707   0.7233
 IWH  C6    C  CR6   0   0.090  -1.8850   1.1290   0.2298
 IWH  C7    C  CR16  0  -0.348  -3.0920   1.4611  -0.3822
 IWH  C8    C  CH3   0  -0.758  -0.8123   2.1744   0.3379
 IWH  C9    C  CH2   0  -0.439  -0.4556  -0.6026   1.4266
 IWH  C10   C  CR16  0   0.079   1.7465   0.1425   0.7042
 IWH  C11   C  CR6   0  -0.213   2.8641   0.1059  -0.0770
 IWH  C12   C  CR16  0  -0.131   2.8970  -0.8687  -1.1085
 IWH  C13   C  CR16  0  -0.449   1.8689  -1.7352  -1.2744
 IWH  C14   C  CR6   0   0.575   0.7125  -1.7188  -0.4188
 IWH  C15   C  C     0   0.495   3.9379   1.0912   0.2100
 IWH  H1    H  HCH3  0   0.249  -5.3603   0.6952  -2.2783
 IWH  H1A   H  HCH3  0   0.243  -6.2689   0.4125  -0.8028
 IWH  H1B   H  HCH3  0   0.243  -5.5993   2.0105  -1.1393
 IWH  HN2   H  HNH2  0   0.407   5.8803   1.5161  -0.2170
 IWH  HN2A  H  HNH2  0   0.413   5.3268   0.0639  -0.9324
 IWH  H3    H  HCR6  0   0.244  -4.7546  -1.4583  -0.0834
 IWH  H4    H  HCR6  0   0.245  -2.6407  -2.0812   0.9891
 IWH  H7    H  HCR6  0   0.239  -3.2202   2.4709  -0.7581
 IWH  H8    H  HCH3  0   0.252   0.0037   1.9920  -0.3644
 IWH  H8A   H  HCH3  0   0.262  -1.2112   3.1630   0.1154
 IWH  H8B   H  HCH3  0   0.241  -0.3776   2.2190   1.3377
 IWH  H9    H  HCH2  0   0.296  -0.6076  -1.5712   1.9018
 IWH  H9A   H  HCH2  0   0.285  -0.1873   0.0974   2.2179
 IWH  H10   H  HCR6  0   0.316   1.6502   0.8589   1.5073
 IWH  H12   H  HCR6  0   0.270   3.7363  -0.9320  -1.7892
 IWH  H13   H  HCR6  0   0.281   1.8904  -2.4820  -2.0558
 IWH  O1    O  O     0  -0.484  -0.2172  -2.5106  -0.4787

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
 IWH  C2   C1    single    1.501  0.020  1.501
 IWH  C1   H1    single    0.970  0.020  1.090
 IWH  C1   H1A   single    0.970  0.020  1.090
 IWH  C1   H1B   single    0.970  0.020  1.090
 IWH  C10  N1    single    1.345  0.020  1.345
 IWH  C14  N1    single    1.399  0.020  1.399
 IWH  N1   C9    single    1.468  0.020  1.468
 IWH  C14  O1    double    1.223  0.020  1.223
 IWH  C3   C2    aromatic  1.392  0.020  1.392
 IWH  C2   C7    aromatic  1.391  0.020  1.391
 IWH  N2   C15   single    1.342  0.020  1.342
 IWH  N2   HN2   single    0.860  0.020  1.020
 IWH  N2   HN2A  single    0.860  0.020  1.020
 IWH  C15  O2    double    1.226  0.020  1.226
 IWH  C4   C3    aromatic  1.385  0.020  1.385
 IWH  C3   H3    single    0.930  0.020  1.080
 IWH  C4   C5    aromatic  1.391  0.020  1.391
 IWH  C4   H4    single    0.930  0.020  1.080
 IWH  C9   C5    single    1.507  0.020  1.507
 IWH  C5   C6    aromatic  1.400  0.020  1.400
 IWH  C6   C7    aromatic  1.393  0.020  1.393
 IWH  C6   C8    single    1.502  0.020  1.502
 IWH  C7   H7    single    0.930  0.020  1.080
 IWH  C8   H8    single    0.970  0.020  1.090
 IWH  C8   H8A   single    0.970  0.020  1.090
 IWH  C8   H8B   single    0.970  0.020  1.090
 IWH  C9   H9    single    0.970  0.020  1.090
 IWH  C9   H9A   single    0.970  0.020  1.090
 IWH  C11  C10   double    1.364  0.020  1.364
 IWH  C10  H10   single    0.930  0.020  1.080
 IWH  C15  C11   single    1.485  0.020  1.485
 IWH  C12  C11   single    1.419  0.020  1.419
 IWH  C12  C13   double    1.355  0.020  1.355
 IWH  C12  H12   single    0.930  0.020  1.080
 IWH  C13  C14   single    1.439  0.020  1.439
 IWH  C13  H13   single    0.930  0.020  1.080

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
 IWH  H1B   C1   H1A  108.17  3.000
 IWH  H1B   C1   H1   107.22  3.000
 IWH  H1A   C1   H1   107.16  3.000
 IWH  H1B   C1   C2   111.63  3.000
 IWH  H1A   C1   C2   111.59  3.000
 IWH  H1    C1   C2   110.85  3.000
 IWH  C14   N1   C10  122.62  3.000
 IWH  C14   N1   C9   117.61  3.000
 IWH  C10   N1   C9   119.73  3.000
 IWH  C7    C2   C3   117.89  3.000
 IWH  C7    C2   C1   120.95  3.000
 IWH  C3    C2   C1   121.16  3.000
 IWH  HN2A  N2   HN2  116.55  3.000
 IWH  HN2A  N2   C15  123.28  3.000
 IWH  HN2   N2   C15  119.25  3.000
 IWH  H3    C3   C4   119.66  3.000
 IWH  H3    C3   C2   119.99  3.000
 IWH  C4    C3   C2   120.35  3.000
 IWH  H4    C4   C5   119.16  3.000
 IWH  H4    C4   C3   119.30  3.000
 IWH  C5    C4   C3   121.54  3.000
 IWH  C9    C5   C6   122.10  3.000
 IWH  C6    C5   C4   118.91  3.000
 IWH  C9    C5   C4   118.95  3.000
 IWH  C8    C6   C7   118.98  3.000
 IWH  C8    C6   C5   122.31  3.000
 IWH  C7    C6   C5   118.71  3.000
 IWH  H7    C7   C6   118.44  3.000
 IWH  H7    C7   C2   118.97  3.000
 IWH  C6    C7   C2   122.58  3.000
 IWH  H8B   C8   H8A  107.22  3.000
 IWH  H8B   C8   H8   107.37  3.000
 IWH  H8A   C8   H8   107.09  3.000
 IWH  H8B   C8   C6   112.27  3.000
 IWH  H8A   C8   C6   110.83  3.000
 IWH  H8    C8   C6   111.79  3.000
 IWH  H9A   C9   H9   106.78  3.000
 IWH  H9A   C9   C5   111.14  3.000
 IWH  H9    C9   C5   109.98  3.000
 IWH  H9A   C9   N1   106.59  3.000
 IWH  H9    C9   N1   108.32  3.000
 IWH  C5    C9   N1   113.73  3.000
 IWH  H10   C10  C11  121.10  3.000
 IWH  H10   C10  N1   115.95  3.000
 IWH  C11   C10  N1   122.95  3.000
 IWH  C15   C11  C12  125.38  3.000
 IWH  C12   C11  C10  116.98  3.000
 IWH  C15   C11  C10  117.64  3.000
 IWH  H12   C12  C13  118.29  3.000
 IWH  H12   C12  C11  121.00  3.000
 IWH  C13   C12  C11  120.70  3.000
 IWH  H13   C13  C14  116.98  3.000
 IWH  H13   C13  C12  121.01  3.000
 IWH  C14   C13  C12  122.00  3.000
 IWH  C13   C14  O1   125.08  3.000
 IWH  C13   C14  N1   114.65  3.000
 IWH  O1    C14  N1   120.27  3.000
 IWH  C11   C15  O2   121.11  3.000
 IWH  C11   C15  N2   116.49  3.000
 IWH  O2    C15  N2   122.40  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
 IWH  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 IWH  CONST_02  C5    C6   C7   C2     0.00   0.0  0
 IWH  CONST_03  C6    C7   C2   C3     0.00   0.0  0
 IWH  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 IWH  CONST_05  C7    C2   C3   C4     0.00   0.0  0
 IWH  CONST_06  C7    C6   C5   C4     0.00   0.0  0
 IWH  CONST_07  C13   C14  N1   C10    0.00   0.0  0
 IWH  CONST_08  C4    C3   C2   C1   180.00   0.0  0
 IWH  CONST_09  C6    C7   C2   C1   180.00   0.0  0
 IWH  CONST_10  C8    C6   C7   C2   180.00   0.0  0
 IWH  CONST_11  C9    C5   C4   C3   180.00   0.0  0
 IWH  CONST_12  C8    C6   C5   C4   180.00   0.0  0
 IWH  CONST_13  C9    C5   C6   C7   180.00   0.0  0
 IWH  CONST_14  C10   N1   C14  O1   180.00   0.0  0
 IWH  CONST_15  C13   C14  N1   C9   180.00   0.0  0
 IWH  CONST_16  H4    C4   C3   C2   180.00   0.0  0
 IWH  CONST_17  H7    C7   C2   C3   180.00   0.0  0
 IWH  CONST_18  H3    C3   C4   C5   180.00   0.0  0
 IWH  CONST_19  C9    N1   C14  O1     0.00   0.0  0
 IWH  CONST_20  HN2   N2   C15  C11  180.00   0.0  0
 IWH  CONST_21  HN2A  N2   C15  C11    0.00   0.0  0
 IWH  Var_01    C4    C5   C9   N1   112.42  30.0  2
 IWH  Var_02    C10   N1   C9   C5   113.82  30.0  3
 IWH  Var_03    C10   C11  C15  N2   168.92  30.0  2
 IWH  Var_04    H1    C1   C2   C3   -87.25  30.0  2
 IWH  Var_05    H8    C8   C6   C5    73.96  30.0  2

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
 IWH  plan-1  C1    0.020
 IWH  plan-1  C2    0.020
 IWH  plan-1  C3    0.020
 IWH  plan-1  C4    0.020
 IWH  plan-1  C5    0.020
 IWH  plan-1  C6    0.020
 IWH  plan-1  C7    0.020
 IWH  plan-1  C8    0.020
 IWH  plan-1  C9    0.020
 IWH  plan-1  H3    0.020
 IWH  plan-1  H4    0.020
 IWH  plan-1  H7    0.020
 IWH  plan-2  N1    0.020
 IWH  plan-2  C9    0.020
 IWH  plan-2  C10   0.020
 IWH  plan-2  C11   0.020
 IWH  plan-2  C12   0.020
 IWH  plan-2  C13   0.020
 IWH  plan-2  C14   0.020
 IWH  plan-2  C15   0.020
 IWH  plan-2  H10   0.020
 IWH  plan-2  H12   0.020
 IWH  plan-2  H13   0.020
 IWH  plan-2  O1    0.020
 IWH  plan-3  N2    0.020
 IWH  plan-3  O2    0.020
 IWH  plan-3  C11   0.020
 IWH  plan-3  C15   0.020
 IWH  plan-3  HN2   0.020
 IWH  plan-3  HN2A  0.020

