# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 18:05:43 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: [(3S)-3-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](naphthalen-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc([C@H]2CCCN(C2)C(=O)c3ccc4ccccc4c3)n5ncnc5n1
#
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
 7OG  7OG  '[(3S)-3-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](naphthalen-2-yl)methanone'  ligand  49  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7OG
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
 7OG  C5   C  CR56  0   0.575  -3.9825   1.4632  -0.3052
 7OG  C8   C  CR15  0   0.044  -4.1611   0.6071  -2.1972
 7OG  C10  C  CH1   0  -0.358  -1.5158  -1.2638   0.5093
 7OG  N12  N  NT    0  -0.450   0.4002  -2.3089  -0.5754
 7OG  C13  C  CH2   0  -0.298  -0.4596  -1.1394  -0.6034
 7OG  C15  C  CH2   0  -0.446  -1.3800  -3.7550   0.2854
 7OG  C20  C  CR66  0   0.131   3.3841   0.9539  -0.7573
 7OG  C21  C  CR66  0   0.114   3.9337   1.2526   0.5160
 7OG  C22  C  CR16  0  -0.306   3.6858   0.3672   1.5913
 7OG  C26  C  CR16  0  -0.257   4.3986   2.9519  -1.6617
 7OG  C28  C  CR16  0  -0.309   4.7163   2.4206   0.6695
 7OG  C27  C  CR16  0  -0.254   4.9429   3.2508  -0.3944
 7OG  C25  C  CR16  0  -0.311   3.6372   1.8293  -1.8395
 7OG  C23  C  CR16  0  -0.272   2.9360  -0.7603   1.4117
 7OG  C19  C  CR16  0  -0.326   2.5930  -0.2074  -0.9096
 7OG  C18  C  CR6   0  -0.079   2.3646  -1.0465   0.1499
 7OG  C2   C  CR16  0  -0.452  -2.4610   0.7087   1.7569
 7OG  C1   C  CR6   0   0.533  -2.3800  -0.0510   0.6263
 7OG  C3   C  CR6   0   0.274  -3.3194   1.8360   1.8162
 7OG  C16  C  C     0   0.520   1.6319  -2.3398  -0.0185
 7OG  C14  C  CH2   0  -0.430  -2.3239  -2.5596   0.3534
 7OG  C11  C  CH2   0  -0.324  -0.3253  -3.5533  -0.7942
 7OG  N7   N  N     0  -0.494  -4.6214   1.6213  -1.4514
 7OG  N9   N  N     0  -0.277  -3.2820  -0.1857  -1.6213
 7OG  N4   N  N     0  -0.456  -4.0659   2.2015   0.8011
 7OG  N6   N  N     0  -0.412  -3.1638   0.3622  -0.4031
 7OG  O17  O  O     0  -0.481   2.1856  -3.3780   0.3172
 7OG  H1   H  HCR5  0   0.281  -4.4795   0.4328  -3.2142
 7OG  H2   H  HCH1  0   0.279  -0.9709  -1.3197   1.4574
 7OG  H3   H  HCH2  0   0.267  -0.9391  -1.0821  -1.5814
 7OG  H4   H  HCH2  0   0.289   0.1209  -0.2312  -0.4675
 7OG  H5   H  HCH2  0   0.236  -0.8867  -3.8985   1.2510
 7OG  H6   H  HCH2  0   0.251  -1.9445  -4.6652   0.0761
 7OG  H11  H  HCR6  0   0.261   4.5875   3.6168  -2.4944
 7OG  H12  H  HCR6  0   0.258   5.1352   2.6489   1.6422
 7OG  H13  H  HCR6  0   0.261   5.5437   4.1419  -0.2677
 7OG  H14  H  HCR6  0   0.258   3.2187   1.5987  -2.8118
 7OG  H15  H  HCR6  0   0.263   2.7655  -1.4344   2.2411
 7OG  H16  H  HCR6  0   0.270   2.1782  -0.4297  -1.8865
 7OG  H17  H  HCR6  0   0.291  -1.8644   0.4393   2.6170
 7OG  H18  H  HCH2  0   0.257  -3.0126  -2.6672   1.1934
 7OG  H19  H  HCH2  0   0.244  -2.9284  -2.5165  -0.5550
 7OG  H20  H  HCH2  0   0.250  -0.8028  -3.4916  -1.7766
 7OG  H21  H  HCH2  0   0.269   0.3749  -4.3832  -0.8236
 7OG  C24  C  CH3   0  -0.735  -3.3733   2.6488   3.0673
 7OG  H7   H  HCR6  0   0.259   4.1057   0.5905   2.5646
 7OG  H8   H  HCH3  0   0.268  -2.4314   3.1829   3.2074
 7OG  H9   H  HCH3  0   0.261  -4.1807   3.3753   3.0258
 7OG  H10  H  HCH3  0   0.261  -3.5106   2.0111   3.9408

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
 7OG  O17  C16  double    1.224  0.020  1.224
 7OG  C11  C15  single    1.523  0.020  1.523
 7OG  C11  N12  single    1.457  0.020  1.457
 7OG  C15  C14  single    1.525  0.020  1.525
 7OG  C16  N12  single    1.352  0.020  1.352
 7OG  C16  C18  single    1.496  0.020  1.496
 7OG  N12  C13  single    1.452  0.020  1.452
 7OG  C14  C10  single    1.535  0.020  1.535
 7OG  C23  C18  aromatic  1.414  0.020  1.414
 7OG  C23  C22  aromatic  1.366  0.020  1.366
 7OG  C18  C19  aromatic  1.371  0.020  1.371
 7OG  C13  C10  single    1.539  0.020  1.539
 7OG  C10  C1   single    1.494  0.020  1.494
 7OG  C22  C21  aromatic  1.415  0.020  1.415
 7OG  C19  C20  aromatic  1.413  0.020  1.413
 7OG  C2   C1   aromatic  1.364  0.020  1.364
 7OG  C2   C3   aromatic  1.418  0.020  1.418
 7OG  C1   N6   aromatic  1.358  0.020  1.358
 7OG  C21  C20  aromatic  1.419  0.020  1.419
 7OG  C21  C28  aromatic  1.414  0.020  1.414
 7OG  C20  C25  aromatic  1.415  0.020  1.415
 7OG  C24  C3   single    1.493  0.020  1.493
 7OG  C28  C27  aromatic  1.368  0.020  1.368
 7OG  C3   N4   aromatic  1.312  0.020  1.312
 7OG  N6   N9   aromatic  1.341  0.020  1.341
 7OG  N6   C5   aromatic  1.376  0.020  1.376
 7OG  N9   C8   aromatic  1.316  0.020  1.316
 7OG  C25  C26  aromatic  1.368  0.020  1.368
 7OG  N4   C5   aromatic  1.333  0.020  1.333
 7OG  C5   N7   aromatic  1.322  0.020  1.322
 7OG  C27  C26  aromatic  1.411  0.020  1.411
 7OG  C8   N7   aromatic  1.340  0.020  1.340
 7OG  C8   H1   single    0.930  0.020  1.080
 7OG  C10  H2   single    0.970  0.020  1.090
 7OG  C13  H3   single    0.970  0.020  1.090
 7OG  C13  H4   single    0.970  0.020  1.090
 7OG  C15  H5   single    0.970  0.020  1.090
 7OG  C15  H6   single    0.970  0.020  1.090
 7OG  C22  H7   single    0.930  0.020  1.080
 7OG  C24  H8   single    0.970  0.020  1.090
 7OG  C24  H9   single    0.970  0.020  1.090
 7OG  C24  H10  single    0.970  0.020  1.090
 7OG  C26  H11  single    0.930  0.020  1.080
 7OG  C28  H12  single    0.930  0.020  1.080
 7OG  C27  H13  single    0.930  0.020  1.080
 7OG  C25  H14  single    0.930  0.020  1.080
 7OG  C23  H15  single    0.930  0.020  1.080
 7OG  C19  H16  single    0.930  0.020  1.080
 7OG  C2   H17  single    0.930  0.020  1.080
 7OG  C14  H18  single    0.970  0.020  1.090
 7OG  C14  H19  single    0.970  0.020  1.090
 7OG  C11  H20  single    0.970  0.020  1.090
 7OG  C11  H21  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
 7OG  N6   C5   N4   122.67  3.000
 7OG  N4   C5   N7   128.56  3.000
 7OG  N6   C5   N7   108.77  3.000
 7OG  H1   C8   N9   120.78  3.000
 7OG  H1   C8   N7   123.02  3.000
 7OG  N9   C8   N7   116.20  3.000
 7OG  H2   C10  C14  107.87  3.000
 7OG  H2   C10  C1   105.16  3.000
 7OG  C14  C10  C1   112.88  3.000
 7OG  H2   C10  C13  106.77  3.000
 7OG  C1   C10  C13  112.83  3.000
 7OG  C14  C10  C13  110.86  3.000
 7OG  C11  N12  C16  119.73  3.000
 7OG  C16  N12  C13  124.46  3.000
 7OG  C11  N12  C13  112.97  3.000
 7OG  H4   C13  H3   107.64  3.000
 7OG  H4   C13  N12  110.77  3.000
 7OG  H3   C13  N12  108.66  3.000
 7OG  H4   C13  C10  110.11  3.000
 7OG  H3   C13  C10  110.53  3.000
 7OG  N12  C13  C10  109.11  3.000
 7OG  H6   C15  H5   107.05  3.000
 7OG  H6   C15  C11  109.43  3.000
 7OG  H5   C15  C11  109.33  3.000
 7OG  H6   C15  C14  110.01  3.000
 7OG  H5   C15  C14  110.04  3.000
 7OG  C11  C15  C14  110.89  3.000
 7OG  C19  C20  C25  121.74  3.000
 7OG  C25  C20  C21  119.14  3.000
 7OG  C19  C20  C21  119.11  3.000
 7OG  C28  C21  C22  122.09  3.000
 7OG  C28  C21  C20  119.06  3.000
 7OG  C22  C21  C20  118.85  3.000
 7OG  H7   C22  C23  120.07  3.000
 7OG  H7   C22  C21  119.08  3.000
 7OG  C23  C22  C21  120.85  3.000
 7OG  H11  C26  C25  120.09  3.000
 7OG  H11  C26  C27  119.57  3.000
 7OG  C25  C26  C27  120.34  3.000
 7OG  H12  C28  C27  120.40  3.000
 7OG  H12  C28  C21  119.04  3.000
 7OG  C27  C28  C21  120.55  3.000
 7OG  H13  C27  C28  120.04  3.000
 7OG  H13  C27  C26  119.58  3.000
 7OG  C28  C27  C26  120.38  3.000
 7OG  H14  C25  C26  120.42  3.000
 7OG  H14  C25  C20  119.06  3.000
 7OG  C26  C25  C20  120.52  3.000
 7OG  H15  C23  C18  119.60  3.000
 7OG  H15  C23  C22  119.99  3.000
 7OG  C18  C23  C22  120.41  3.000
 7OG  H16  C19  C18  120.47  3.000
 7OG  H16  C19  C20  118.66  3.000
 7OG  C18  C19  C20  120.86  3.000
 7OG  C16  C18  C19  121.59  3.000
 7OG  C19  C18  C23  119.89  3.000
 7OG  C16  C18  C23  118.24  3.000
 7OG  H17  C2   C3   119.92  3.000
 7OG  H17  C2   C1   119.20  3.000
 7OG  C3   C2   C1   120.88  3.000
 7OG  N6   C1   C2   115.11  3.000
 7OG  N6   C1   C10  121.43  3.000
 7OG  C2   C1   C10  123.46  3.000
 7OG  N4   C3   C2   122.24  3.000
 7OG  N4   C3   C24  118.44  3.000
 7OG  C2   C3   C24  119.32  3.000
 7OG  O17  C16  C18  118.75  3.000
 7OG  C18  C16  N12  118.22  3.000
 7OG  O17  C16  N12  123.00  3.000
 7OG  H19  C14  H18  107.15  3.000
 7OG  H19  C14  C15  109.67  3.000
 7OG  H18  C14  C15  110.35  3.000
 7OG  H19  C14  C10  110.03  3.000
 7OG  H18  C14  C10  109.70  3.000
 7OG  C15  C14  C10  109.90  3.000
 7OG  H21  C11  H20  107.46  3.000
 7OG  H21  C11  C15  111.38  3.000
 7OG  H20  C11  C15  109.99  3.000
 7OG  H21  C11  N12  109.62  3.000
 7OG  H20  C11  N12  107.70  3.000
 7OG  C15  C11  N12  110.58  3.000
 7OG  C8   N7   C5   103.06  3.000
 7OG  N6   N9   C8   102.14  3.000
 7OG  C3   N4   C5   116.89  3.000
 7OG  N9   N6   C1   127.97  3.000
 7OG  N9   N6   C5   109.83  3.000
 7OG  C1   N6   C5   122.21  3.000
 7OG  H10  C24  H9   109.14  3.000
 7OG  H10  C24  H8   106.97  3.000
 7OG  H9   C24  H8   108.59  3.000
 7OG  H10  C24  C3   110.95  3.000
 7OG  H9   C24  C3   111.02  3.000
 7OG  H8   C24  C3   110.05  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
 7OG  CONST_01  C2   C1   N6   C5     0.00   0.0  0
 7OG  CONST_02  C8   N9   N6   C5     0.00   0.0  0
 7OG  CONST_03  C2   C3   N4   C5     0.00   0.0  0
 7OG  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 7OG  CONST_05  C1   N6   N9   C8   180.00   0.0  0
 7OG  CONST_06  N6   C5   N7   C8     0.00   0.0  0
 7OG  CONST_07  N4   C5   N7   C8   180.00   0.0  0
 7OG  CONST_08  C23  C18  C19  C20    0.00   0.0  0
 7OG  CONST_09  C23  C22  C21  C20    0.00   0.0  0
 7OG  CONST_10  C27  C28  C21  C20    0.00   0.0  0
 7OG  CONST_11  C27  C26  C25  C20    0.00   0.0  0
 7OG  CONST_12  C18  C23  C22  C21    0.00   0.0  0
 7OG  CONST_13  C18  C19  C20  C21    0.00   0.0  0
 7OG  CONST_14  C26  C25  C20  C21    0.00   0.0  0
 7OG  CONST_15  C26  C27  C28  C21    0.00   0.0  0
 7OG  CONST_16  C19  C18  C23  C22    0.00   0.0  0
 7OG  CONST_17  C19  C20  C21  C22    0.00   0.0  0
 7OG  CONST_18  C25  C20  C21  C22  180.00   0.0  0
 7OG  CONST_19  C27  C28  C21  C22  180.00   0.0  0
 7OG  CONST_20  C19  C20  C25  C26  180.00   0.0  0
 7OG  CONST_21  C23  C22  C21  C28  180.00   0.0  0
 7OG  CONST_22  C19  C20  C21  C28  180.00   0.0  0
 7OG  CONST_23  C25  C20  C21  C28    0.00   0.0  0
 7OG  CONST_24  C25  C26  C27  C28    0.00   0.0  0
 7OG  CONST_25  C18  C19  C20  C25  180.00   0.0  0
 7OG  CONST_26  N9   N6   C1   C2   180.00   0.0  0
 7OG  CONST_27  N4   C3   C2   C1     0.00   0.0  0
 7OG  CONST_28  N4   C5   N6   C1     0.00   0.0  0
 7OG  CONST_29  N7   C5   N6   C1   180.00   0.0  0
 7OG  CONST_30  N6   C1   C2   C3     0.00   0.0  0
 7OG  CONST_31  N6   C5   N4   C3     0.00   0.0  0
 7OG  CONST_32  N7   C5   N4   C3   180.00   0.0  0
 7OG  CONST_33  N9   N6   C5   N7     0.00   0.0  0
 7OG  CONST_34  N6   N9   C8   N7     0.00   0.0  0
 7OG  CONST_35  N4   C5   N6   N9   180.00   0.0  0
 7OG  CONST_36  C10  C1   N6   C5   180.00   0.0  0
 7OG  CONST_37  C3   C2   C1   C10  180.00   0.0  0
 7OG  CONST_38  N9   N6   C1   C10    0.00   0.0  0
 7OG  CONST_39  C24  C3   N4   C5   180.00   0.0  0
 7OG  CONST_40  C16  C18  C19  C20  180.00   0.0  0
 7OG  CONST_41  C16  C18  C23  C22  180.00   0.0  0
 7OG  CONST_42  C1   C2   C3   C24  180.00   0.0  0
 7OG  CONST_44  C11  N12  C16  C18  180.00   0.0  0
 7OG  CONST_45  H1   C8   N7   C5   180.00   0.0  0
 7OG  CONST_46  H17  C2   C1   C10    0.00   0.0  0
 7OG  CONST_47  H7   C22  C21  C20  180.00   0.0  0
 7OG  CONST_48  H12  C28  C21  C20  180.00   0.0  0
 7OG  CONST_49  H11  C26  C25  C20  180.00   0.0  0
 7OG  CONST_50  H15  C23  C22  C21  180.00   0.0  0
 7OG  CONST_51  H16  C19  C20  C21  180.00   0.0  0
 7OG  CONST_52  H14  C25  C20  C21  180.00   0.0  0
 7OG  CONST_53  H13  C27  C28  C21  180.00   0.0  0
 7OG  CONST_55  O17  C16  N12  C11    0.00   0.0  0
 7OG  Var_01    C11  C15  C14  C10  -53.23  30.0  1
 7OG  Var_02    C11  N12  C13  C10   60.38  30.0  1
 7OG  Var_03    C14  C15  C11  N12   55.66  30.0  1
 7OG  Var_04    C15  C11  N12  C13  -60.30  30.0  1
 7OG  Var_05    C23  C18  C16  N12  130.79  30.0  2
 7OG  Var_06    H8   C24  C3   C2    68.83  30.0  2

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
 7OG  chir_01  C10  C14  C13  C1  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
 7OG  plan-1  C5   0.020
 7OG  plan-1  C8   0.020
 7OG  plan-1  C10  0.020
 7OG  plan-1  C2   0.020
 7OG  plan-1  C1   0.020
 7OG  plan-1  C3   0.020
 7OG  plan-1  N7   0.020
 7OG  plan-1  N9   0.020
 7OG  plan-1  N4   0.020
 7OG  plan-1  N6   0.020
 7OG  plan-1  H1   0.020
 7OG  plan-1  H17  0.020
 7OG  plan-1  C24  0.020
 7OG  plan-2  C20  0.020
 7OG  plan-2  C21  0.020
 7OG  plan-2  C22  0.020
 7OG  plan-2  C26  0.020
 7OG  plan-2  C28  0.020
 7OG  plan-2  C27  0.020
 7OG  plan-2  C25  0.020
 7OG  plan-2  C23  0.020
 7OG  plan-2  C19  0.020
 7OG  plan-2  C18  0.020
 7OG  plan-2  C16  0.020
 7OG  plan-2  H11  0.020
 7OG  plan-2  H12  0.020
 7OG  plan-2  H13  0.020
 7OG  plan-2  H14  0.020
 7OG  plan-2  H15  0.020
 7OG  plan-2  H16  0.020
 7OG  plan-2  H7   0.020
 7OG  plan-3  N12  0.020
 7OG  plan-3  C13  0.020
 7OG  plan-3  C18  0.020
 7OG  plan-3  C16  0.020
 7OG  plan-3  C11  0.020
 7OG  plan-3  O17  0.020

