# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:24:06 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCc2n(Cc3ccc(cc3)C(=O)NO)c4ccccc4c2C1
#
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
 N9W  N9W  4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-benzamide  ligand  46  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N9W
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
 N9W  O2   O  O     0  -0.460  -7.9502  19.5687  -19.8626
 N9W  C1   C  C     0   0.498  -6.8753  20.0560  -20.1615
 N9W  N1   N  NH1   0  -0.384  -6.6731  21.3859  -20.3001
 N9W  O1   O  OH1   0  -0.539  -7.7519  22.2186  -20.2733
 N9W  C2   C  CR6   0  -0.074  -5.6547  19.2273  -20.3814
 N9W  C7   C  CR16  0  -0.264  -4.3672  19.7028  -20.1539
 N9W  C6   C  CR16  0  -0.275  -3.2657  18.8831  -20.3591
 N9W  C5   C  CR6   0   0.079  -3.4296  17.5755  -20.7968
 N9W  C4   C  CR16  0  -0.274  -4.7213  17.0979  -21.0122
 N9W  C3   C  CR16  0  -0.253  -5.8211  17.9081  -20.8003
 N9W  C8   C  CH2   0  -0.379  -2.2581  16.6577  -21.0571
 N9W  N2   N  NR5   0  -0.592  -0.9889  17.1991  -20.6602
 N9W  C20  C  CR5   0   0.326  -0.1748  17.9860  -21.4437
 N9W  C19  C  CH2   0  -0.546  -0.3815  18.2676  -22.8877
 N9W  C18  C  CH2   0  -0.323   0.5843  19.3942  -23.2955
 N9W  N3   N  NT    0  -0.400   1.9288  19.2577  -22.7639
 N9W  C17  C  CH3   0  -0.524   2.6168  18.0856  -23.2670
 N9W  C16  C  CH2   0  -0.375   1.9296  19.3305  -21.3094
 N9W  C15  C  CR5   0  -0.062   0.8726  18.4543  -20.7078
 N9W  C14  C  CR56  0   0.062   0.6987  17.9620  -19.3777
 N9W  C9   C  CR56  0   0.337  -0.4847  17.1877  -19.3842
 N9W  C13  C  CR16  0  -0.383   1.4187  18.0959  -18.1867
 N9W  C12  C  CR16  0  -0.270   0.9480  17.4728  -17.0454
 N9W  C11  C  CR16  0  -0.285  -0.2322  16.7149  -17.0711
 N9W  C10  C  CR16  0  -0.315  -0.9641  16.5628  -18.2362
 N9W  H1   H  HNH1  0   0.417  -5.8978  21.7441  -20.8397
 N9W  H2   H  HOH1  0   0.479  -7.7492  22.6283  -19.3989
 N9W  H3   H  HCR6  0   0.266  -4.2008  20.7090  -19.7908
 N9W  H4   H  HCR6  0   0.264  -2.2784  19.2808  -20.1618
 N9W  H5   H  HCR6  0   0.260  -4.8697  16.0778  -21.3466
 N9W  H6   H  HCR6  0   0.264  -6.8151  17.5160  -20.9698
 N9W  H7   H  HCH2  0   0.288  -2.4158  15.7044  -20.5481
 N9W  H8   H  HCH2  0   0.296  -2.2169  16.4160  -22.1212
 N9W  H9   H  HCH2  0   0.259  -1.4086  18.5792  -23.0993
 N9W  H10  H  HCH2  0   0.257  -0.2069  17.3661  -23.4850
 N9W  H11  H  HCH2  0   0.245   0.6362  19.4523  -24.3845
 N9W  H12  H  HCH2  0   0.242   0.1797  20.3488  -22.9466
 N9W  H14  H  HCH3  0   0.235   3.6689  18.1248  -22.9805
 N9W  H15  H  HCH3  0   0.201   2.2146  17.1270  -22.9111
 N9W  H16  H  HCH3  0   0.232   2.5735  18.0779  -24.3572
 N9W  H17  H  HCH2  0   0.238   2.9232  19.0574  -20.9429
 N9W  H18  H  HCH2  0   0.241   1.7749  20.3736  -21.0078
 N9W  H19  H  HCR6  0   0.240   2.3296  18.6816  -18.1564
 N9W  H20  H  HCR6  0   0.245   1.4940  17.5715  -16.1159
 N9W  H21  H  HCR6  0   0.248  -0.5786  16.2396  -16.1625
 N9W  H22  H  HCR6  0   0.258  -1.8740  15.9757  -18.2431

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
 N9W  C18  C19  single    1.539  0.020  1.539
 N9W  C18  N3   single    1.452  0.020  1.452
 N9W  C17  N3   single    1.449  0.020  1.449
 N9W  C19  C20  single    1.486  0.020  1.486
 N9W  N3   C16  single    1.456  0.020  1.456
 N9W  C20  C15  aromatic  1.363  0.020  1.363
 N9W  C20  N2   aromatic  1.377  0.020  1.377
 N9W  C4   C3   aromatic  1.382  0.020  1.382
 N9W  C4   C5   aromatic  1.394  0.020  1.394
 N9W  C16  C15  single    1.499  0.020  1.499
 N9W  C3   C2   aromatic  1.394  0.020  1.394
 N9W  C8   C5   single    1.511  0.020  1.511
 N9W  C8   N2   single    1.436  0.020  1.436
 N9W  C5   C6   aromatic  1.389  0.020  1.389
 N9W  C15  C14  aromatic  1.429  0.020  1.429
 N9W  N2   C9   aromatic  1.372  0.020  1.372
 N9W  C2   C1   single    1.492  0.020  1.492
 N9W  C2   C7   aromatic  1.391  0.020  1.391
 N9W  C1   O2   double    1.217  0.020  1.217
 N9W  C1   N1   single    1.352  0.020  1.352
 N9W  C6   C7   aromatic  1.388  0.020  1.388
 N9W  N1   O1   single    1.363  0.020  1.363
 N9W  C14  C9   aromatic  1.414  0.020  1.414
 N9W  C14  C13  aromatic  1.398  0.020  1.398
 N9W  C9   C10  aromatic  1.392  0.020  1.392
 N9W  C13  C12  aromatic  1.383  0.020  1.383
 N9W  C10  C11  aromatic  1.384  0.020  1.384
 N9W  C12  C11  aromatic  1.403  0.020  1.403
 N9W  N1   H1   single    0.890  0.020  1.040
 N9W  O1   H2   single    0.850  0.020  0.980
 N9W  C7   H3   single    0.930  0.020  1.080
 N9W  C6   H4   single    0.930  0.020  1.080
 N9W  C4   H5   single    0.930  0.020  1.080
 N9W  C3   H6   single    0.930  0.020  1.080
 N9W  C8   H7   single    0.970  0.020  1.090
 N9W  C8   H8   single    0.970  0.020  1.090
 N9W  C19  H9   single    0.970  0.020  1.090
 N9W  C19  H10  single    0.970  0.020  1.090
 N9W  C18  H11  single    0.970  0.020  1.090
 N9W  C18  H12  single    0.970  0.020  1.090
 N9W  C17  H14  single    0.970  0.020  1.090
 N9W  C17  H15  single    0.970  0.020  1.090
 N9W  C17  H16  single    0.970  0.020  1.090
 N9W  C16  H17  single    0.970  0.020  1.090
 N9W  C16  H18  single    0.970  0.020  1.090
 N9W  C13  H19  single    0.930  0.020  1.080
 N9W  C12  H20  single    0.930  0.020  1.080
 N9W  C11  H21  single    0.930  0.020  1.080
 N9W  C10  H22  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
 N9W  C2   C1   N1   114.14  3.000
 N9W  N1   C1   O2   123.43  3.000
 N9W  C2   C1   O2   122.43  3.000
 N9W  H1   N1   O1   113.66  3.000
 N9W  H1   N1   C1   121.21  3.000
 N9W  O1   N1   C1   118.71  3.000
 N9W  H2   O1   N1   105.95  3.000
 N9W  C3   C2   C7   118.88  3.000
 N9W  C7   C2   C1   122.91  3.000
 N9W  C3   C2   C1   118.19  3.000
 N9W  H3   C7   C6   118.46  3.000
 N9W  H3   C7   C2   120.98  3.000
 N9W  C6   C7   C2   120.55  3.000
 N9W  H4   C6   C5   120.73  3.000
 N9W  H4   C6   C7   118.67  3.000
 N9W  C5   C6   C7   120.59  3.000
 N9W  C8   C5   C4   118.93  3.000
 N9W  C8   C5   C6   122.34  3.000
 N9W  C4   C5   C6   118.73  3.000
 N9W  H5   C4   C3   119.34  3.000
 N9W  H5   C4   C5   119.81  3.000
 N9W  C3   C4   C5   120.85  3.000
 N9W  H6   C3   C4   119.64  3.000
 N9W  H6   C3   C2   119.98  3.000
 N9W  C4   C3   C2   120.38  3.000
 N9W  H8   C8   H7   105.45  3.000
 N9W  H8   C8   N2   108.64  3.000
 N9W  H7   C8   N2   109.15  3.000
 N9W  H8   C8   C5   109.37  3.000
 N9W  H7   C8   C5   109.75  3.000
 N9W  N2   C8   C5   114.12  3.000
 N9W  C9   N2   C20  108.46  3.000
 N9W  C9   N2   C8   125.37  3.000
 N9W  C20  N2   C8   125.51  3.000
 N9W  C15  C20  C19  124.51  3.000
 N9W  C15  C20  N2   110.09  3.000
 N9W  C19  C20  N2   125.39  3.000
 N9W  H10  C19  H9   106.17  3.000
 N9W  H10  C19  C18  110.98  3.000
 N9W  H9   C19  C18  109.24  3.000
 N9W  H10  C19  C20  110.60  3.000
 N9W  H9   C19  C20  111.87  3.000
 N9W  C18  C19  C20  108.00  3.000
 N9W  H12  C18  H11  106.82  3.000
 N9W  H12  C18  N3   107.92  3.000
 N9W  H11  C18  N3   109.04  3.000
 N9W  H12  C18  C19  108.79  3.000
 N9W  H11  C18  C19  109.46  3.000
 N9W  N3   C18  C19  114.53  3.000
 N9W  C16  N3   C17  112.76  3.000
 N9W  C16  N3   C18  111.19  3.000
 N9W  C17  N3   C18  112.86  3.000
 N9W  H16  C17  H15  107.63  3.000
 N9W  H16  C17  H14  107.51  3.000
 N9W  H15  C17  H14  107.42  3.000
 N9W  H16  C17  N3   109.50  3.000
 N9W  H15  C17  N3   114.80  3.000
 N9W  H14  C17  N3   109.72  3.000
 N9W  H18  C16  H17  105.87  3.000
 N9W  H18  C16  C15  110.25  3.000
 N9W  H17  C16  C15  111.11  3.000
 N9W  H18  C16  N3   108.79  3.000
 N9W  H17  C16  N3   108.83  3.000
 N9W  C15  C16  N3   111.80  3.000
 N9W  C14  C15  C16  131.36  3.000
 N9W  C14  C15  C20  106.90  3.000
 N9W  C16  C15  C20  121.73  3.000
 N9W  C13  C14  C9   119.16  3.000
 N9W  C13  C14  C15  134.21  3.000
 N9W  C9   C14  C15  106.63  3.000
 N9W  C10  C9   C14  122.01  3.000
 N9W  C10  C9   N2   130.10  3.000
 N9W  C14  C9   N2   107.89  3.000
 N9W  H19  C13  C12  120.44  3.000
 N9W  H19  C13  C14  120.57  3.000
 N9W  C12  C13  C14  118.99  3.000
 N9W  H20  C12  C11  119.30  3.000
 N9W  H20  C12  C13  119.73  3.000
 N9W  C11  C12  C13  120.98  3.000
 N9W  H21  C11  C10  119.27  3.000
 N9W  H21  C11  C12  119.42  3.000
 N9W  C10  C11  C12  121.31  3.000
 N9W  H22  C10  C11  120.61  3.000
 N9W  H22  C10  C9   121.83  3.000
 N9W  C11  C10  C9   117.56  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
 N9W  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 N9W  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 N9W  CONST_03  C4   C3   C2   C7     0.00   0.0  0
 N9W  CONST_04  C4   C5   C6   C7     0.00   0.0  0
 N9W  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 N9W  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 N9W  CONST_07  C14  C15  C20  N2     0.00   0.0  0
 N9W  CONST_08  C15  C14  C9   N2     0.00   0.0  0
 N9W  CONST_09  C13  C14  C9   N2   180.00   0.0  0
 N9W  CONST_10  C11  C10  C9   N2   180.00   0.0  0
 N9W  CONST_11  C9   C14  C15  C20    0.00   0.0  0
 N9W  CONST_12  C13  C14  C15  C20  180.00   0.0  0
 N9W  CONST_13  C14  C9   N2   C20    0.00   0.0  0
 N9W  CONST_14  C10  C9   N2   C20  180.00   0.0  0
 N9W  CONST_15  C9   N2   C20  C15    0.00   0.0  0
 N9W  CONST_16  C10  C9   C14  C15  180.00   0.0  0
 N9W  CONST_17  C12  C13  C14  C15  180.00   0.0  0
 N9W  CONST_18  C11  C10  C9   C14    0.00   0.0  0
 N9W  CONST_19  C11  C12  C13  C14    0.00   0.0  0
 N9W  CONST_20  C12  C13  C14  C9     0.00   0.0  0
 N9W  CONST_21  C12  C11  C10  C9     0.00   0.0  0
 N9W  CONST_22  C10  C9   C14  C13    0.00   0.0  0
 N9W  CONST_23  C10  C11  C12  C13    0.00   0.0  0
 N9W  CONST_24  C4   C3   C2   C1   180.00   0.0  0
 N9W  CONST_25  C6   C7   C2   C1   180.00   0.0  0
 N9W  CONST_26  C8   C5   C6   C7   180.00   0.0  0
 N9W  CONST_27  C8   C5   C4   C3   180.00   0.0  0
 N9W  CONST_28  C19  C20  N2   C8     0.00   0.0  0
 N9W  CONST_29  C15  C20  N2   C8   180.00   0.0  0
 N9W  CONST_30  C14  C9   N2   C8   180.00   0.0  0
 N9W  CONST_31  C10  C9   N2   C8     0.00   0.0  0
 N9W  CONST_32  H5   C4   C3   C2   180.00   0.0  0
 N9W  CONST_33  H4   C6   C7   C2   180.00   0.0  0
 N9W  CONST_34  H6   C3   C2   C7   180.00   0.0  0
 N9W  CONST_35  H3   C7   C6   C5   180.00   0.0  0
 N9W  CONST_36  H22  C10  C9   N2     0.00   0.0  0
 N9W  CONST_37  H19  C13  C14  C15    0.00   0.0  0
 N9W  CONST_38  H20  C12  C13  C14  180.00   0.0  0
 N9W  CONST_39  H21  C11  C10  C9   180.00   0.0  0
 N9W  CONST_40  C2   C1   N1   O1   180.00   0.0  0
 N9W  CONST_42  O1   N1   C1   O2     0.00   0.0  0
 N9W  Var_01    C18  C19  C20  N2   169.07  30.0  1
 N9W  Var_02    N3   C18  C19  C20   43.20  30.0  1
 N9W  Var_03    N3   C16  C15  C20  -17.76  30.0  1
 N9W  Var_04    C16  N3   C18  C19  -63.55  30.0  1
 N9W  Var_05    C15  C16  N3   C18   47.48  30.0  1
 N9W  Var_06    N2   C8   C5   C6     7.15  30.0  2
 N9W  Var_07    C20  N2   C8   C5   -87.84  30.0  2
 N9W  Var_08    C3   C2   C1   O2    26.86  30.0  2
 N9W  Var_09    H14  C17  N3   C18  170.05  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
 N9W  plan-1  C1   0.020
 N9W  plan-1  C2   0.020
 N9W  plan-1  C7   0.020
 N9W  plan-1  C6   0.020
 N9W  plan-1  C5   0.020
 N9W  plan-1  C4   0.020
 N9W  plan-1  C3   0.020
 N9W  plan-1  C8   0.020
 N9W  plan-1  H3   0.020
 N9W  plan-1  H4   0.020
 N9W  plan-1  H5   0.020
 N9W  plan-1  H6   0.020
 N9W  plan-2  C8   0.020
 N9W  plan-2  N2   0.020
 N9W  plan-2  C20  0.020
 N9W  plan-2  C19  0.020
 N9W  plan-2  C16  0.020
 N9W  plan-2  C15  0.020
 N9W  plan-2  C14  0.020
 N9W  plan-2  C9   0.020
 N9W  plan-2  C13  0.020
 N9W  plan-2  C12  0.020
 N9W  plan-2  C11  0.020
 N9W  plan-2  C10  0.020
 N9W  plan-2  H19  0.020
 N9W  plan-2  H20  0.020
 N9W  plan-2  H21  0.020
 N9W  plan-2  H22  0.020
 N9W  plan-3  O2   0.020
 N9W  plan-3  C1   0.020
 N9W  plan-3  N1   0.020
 N9W  plan-3  O1   0.020
 N9W  plan-3  C2   0.020
 N9W  plan-3  H1   0.020

