# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:24:47 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncnc1[C@@H]2[C@H](Nc3cc(F)cc4C(=O)NN=C2c34)c5ccc(F)cc5
#
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
 2YQ  2YQ  (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one  ligand  42  28  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2YQ
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
 2YQ  N1   N  N     0  -0.214   0.5937   0.5223   2.3157
 2YQ  N3   N  NR16  0  -0.679   0.3314  -0.1890  -1.6947
 2YQ  C4   C  CR6   0   0.518  -0.4515   2.7126   2.0988
 2YQ  C5   C  CR16  0  -0.504   1.2168  -0.8661   0.4591
 2YQ  C6   C  CR16  0  -0.179   0.4264  -1.3101  -0.7935
 2YQ  C7   C  CR66  0   0.349  -0.0665   1.0297  -1.2405
 2YQ  C8   C  CR16  0  -0.508  -0.5413   2.0255  -2.0888
 2YQ  C10  C  CR16  0  -0.508  -0.9742   3.5034  -0.1954
 2YQ  C13  C  CR16  0  -0.394  -3.3240  -1.9342  -0.3055
 2YQ  C15  C  CR16  0  -0.400  -2.0768  -3.7398   0.7008
 2YQ  C17  C  CR5   0   0.560   2.6348  -0.5491   0.1018
 2YQ  C14  C  CR6   0   0.519  -3.2748  -3.1235   0.3907
 2YQ  C12  C  CR16  0  -0.298  -2.1316  -1.3378  -0.6976
 2YQ  C16  C  CR16  0  -0.280  -0.9003  -3.1281   0.3015
 2YQ  C11  C  CR6   0   0.152  -0.9075  -1.9199  -0.3933
 2YQ  N6   N  N     0  -0.460   3.1511   0.6525  -0.0382
 2YQ  C18  C  CR15  0  -0.019   4.4260   0.3985  -0.3931
 2YQ  N5   N  N     0  -0.261   4.7216  -0.8754  -0.4765
 2YQ  N4   N  NR5   0  -0.304   3.5703  -1.4735  -0.1525
 2YQ  C19  C  CH3   0  -0.541   3.4590  -2.9130  -0.1583
 2YQ  C3   C  CR66  0   0.257   0.5616   0.3505   1.0448
 2YQ  C2   C  C     0   0.038  -0.0069   1.3022   0.1445
 2YQ  C9   C  CR6   0   0.573  -0.9700   3.2253  -1.5457
 2YQ  F1   F  F     0  -0.308  -1.4275   4.1553  -2.3914
 2YQ  C1   C  CR66  0  -0.042  -0.4798   2.5148   0.6467
 2YQ  O    O  O     0  -0.468  -0.8602   3.7143   2.6669
 2YQ  N2   N  NR16  0  -0.518   0.0703   1.6611   2.7933
 2YQ  H1   H  HNR6  0   0.406   0.1564  -0.4020  -2.6639
 2YQ  H2   H  HCR6  0   0.326   1.1994  -1.6660   1.2034
 2YQ  H3   H  HCR6  0   0.307   1.0007  -2.0811  -1.3131
 2YQ  H4   H  HCR6  0   0.296  -0.5988   1.8633  -3.1579
 2YQ  H5   H  HCR6  0   0.284  -1.3440   4.4447   0.1852
 2YQ  H7   H  HCR6  0   0.283  -2.0610  -4.6793   1.2375
 2YQ  H8   H  HCR6  0   0.266  -2.1862  -0.4129  -1.2551
 2YQ  H9   H  HCR6  0   0.261   0.0400  -3.6166   0.5298
 2YQ  H10  H  HCR5  0   0.272   5.1544   1.1700  -0.5911
 2YQ  H11  H  HCH3  0   0.272   3.2291  -3.2826  -1.1566
 2YQ  H12  H  HCH3  0   0.288   4.3987  -3.3423   0.1757
 2YQ  H13  H  HCH3  0   0.262   2.6756  -3.2254   0.5271
 2YQ  H14  H  HNR6  0   0.424   0.1124   1.7421   3.7999
 2YQ  H6   H  HCR6  0   0.283  -4.2745  -1.4754  -0.5433
 2YQ  F2   F  F     0  -0.314  -4.4227  -3.7056   0.7715

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
 2YQ  O    C4   double    1.222  0.020  1.222
 2YQ  C4   N2   single    1.364  0.020  1.364
 2YQ  C4   C1   single    1.466  0.020  1.466
 2YQ  N2   N1   single    1.341  0.020  1.341
 2YQ  C10  C1   aromatic  1.390  0.020  1.390
 2YQ  C10  C9   aromatic  1.379  0.020  1.379
 2YQ  C1   C2   aromatic  1.395  0.020  1.395
 2YQ  F1   C9   single    1.338  0.020  1.338
 2YQ  C9   C8   aromatic  1.385  0.020  1.385
 2YQ  N1   C3   double    1.283  0.020  1.283
 2YQ  C2   C3   single    1.428  0.020  1.428
 2YQ  C2   C7   aromatic  1.413  0.020  1.413
 2YQ  C3   C5   single    1.501  0.020  1.501
 2YQ  C8   C7   aromatic  1.392  0.020  1.392
 2YQ  C7   N3   single    1.360  0.020  1.360
 2YQ  C19  N4   single    1.444  0.020  1.444
 2YQ  C5   C17  single    1.496  0.020  1.496
 2YQ  C5   C6   single    1.546  0.020  1.546
 2YQ  N3   C6   single    1.441  0.020  1.441
 2YQ  N4   C17  aromatic  1.340  0.020  1.340
 2YQ  N4   N5   aromatic  1.337  0.020  1.337
 2YQ  C12  C13  aromatic  1.390  0.020  1.390
 2YQ  C12  C11  aromatic  1.389  0.020  1.389
 2YQ  C17  N6   aromatic  1.315  0.020  1.315
 2YQ  C6   C11  single    1.520  0.020  1.520
 2YQ  C13  C14  aromatic  1.379  0.020  1.379
 2YQ  N5   C18  aromatic  1.310  0.020  1.310
 2YQ  C11  C16  aromatic  1.394  0.020  1.394
 2YQ  N6   C18  aromatic  1.348  0.020  1.348
 2YQ  C14  F2   single    1.342  0.020  1.342
 2YQ  C14  C15  aromatic  1.383  0.020  1.383
 2YQ  C16  C15  aromatic  1.385  0.020  1.385
 2YQ  N3   H1   single    0.890  0.020  1.040
 2YQ  C5   H2   single    0.970  0.020  1.090
 2YQ  C6   H3   single    0.970  0.020  1.090
 2YQ  C8   H4   single    0.930  0.020  1.080
 2YQ  C10  H5   single    0.930  0.020  1.080
 2YQ  C13  H6   single    0.930  0.020  1.080
 2YQ  C15  H7   single    0.930  0.020  1.080
 2YQ  C12  H8   single    0.930  0.020  1.080
 2YQ  C16  H9   single    0.930  0.020  1.080
 2YQ  C18  H10  single    0.930  0.020  1.080
 2YQ  C19  H11  single    0.970  0.020  1.090
 2YQ  C19  H12  single    0.970  0.020  1.090
 2YQ  C19  H13  single    0.970  0.020  1.090
 2YQ  N2   H14  single    0.860  0.020  1.020

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
 2YQ  N2   N1   C3   117.18  3.000
 2YQ  H1   N3   C7   117.37  3.000
 2YQ  H1   N3   C6   116.64  3.000
 2YQ  C7   N3   C6   120.49  3.000
 2YQ  N2   C4   O    121.55  3.000
 2YQ  N2   C4   C1   114.07  3.000
 2YQ  O    C4   C1   124.38  3.000
 2YQ  H2   C5   C3   108.71  3.000
 2YQ  H2   C5   C17  109.44  3.000
 2YQ  C3   C5   C17  109.58  3.000
 2YQ  H2   C5   C6   109.48  3.000
 2YQ  C17  C5   C6   110.60  3.000
 2YQ  C3   C5   C6   109.01  3.000
 2YQ  H3   C6   C11  107.65  3.000
 2YQ  H3   C6   C5   108.61  3.000
 2YQ  C11  C6   C5   110.51  3.000
 2YQ  H3   C6   N3   106.62  3.000
 2YQ  C11  C6   N3   114.75  3.000
 2YQ  C5   C6   N3   108.47  3.000
 2YQ  C2   C7   C8   118.29  3.000
 2YQ  C8   C7   N3   122.51  3.000
 2YQ  C2   C7   N3   119.20  3.000
 2YQ  H4   C8   C9   120.03  3.000
 2YQ  H4   C8   C7   120.85  3.000
 2YQ  C9   C8   C7   119.11  3.000
 2YQ  H5   C10  C1   121.88  3.000
 2YQ  H5   C10  C9   121.45  3.000
 2YQ  C1   C10  C9   116.68  3.000
 2YQ  H6   C13  C12  120.65  3.000
 2YQ  H6   C13  C14  120.54  3.000
 2YQ  C12  C13  C14  118.81  3.000
 2YQ  H7   C15  C16  120.95  3.000
 2YQ  H7   C15  C14  120.72  3.000
 2YQ  C16  C15  C14  118.33  3.000
 2YQ  N4   C17  N6   109.64  3.000
 2YQ  N6   C17  C5   126.23  3.000
 2YQ  N4   C17  C5   124.12  3.000
 2YQ  F2   C14  C15  118.96  3.000
 2YQ  C15  C14  C13  121.92  3.000
 2YQ  F2   C14  C13  119.13  3.000
 2YQ  H8   C12  C11  121.06  3.000
 2YQ  H8   C12  C13  117.98  3.000
 2YQ  C11  C12  C13  120.96  3.000
 2YQ  H9   C16  C11  120.01  3.000
 2YQ  H9   C16  C15  118.50  3.000
 2YQ  C11  C16  C15  121.49  3.000
 2YQ  C16  C11  C12  118.49  3.000
 2YQ  C16  C11  C6   118.32  3.000
 2YQ  C12  C11  C6   123.19  3.000
 2YQ  C18  N6   C17  103.13  3.000
 2YQ  H10  C18  N5   122.07  3.000
 2YQ  H10  C18  N6   123.51  3.000
 2YQ  N5   C18  N6   114.42  3.000
 2YQ  N4   N5   C18  103.01  3.000
 2YQ  C19  N4   N5   120.75  3.000
 2YQ  N5   N4   C17  109.79  3.000
 2YQ  C19  N4   C17  129.42  3.000
 2YQ  H13  C19  H12  108.43  3.000
 2YQ  H13  C19  H11  109.18  3.000
 2YQ  H12  C19  H11  109.30  3.000
 2YQ  H13  C19  N4   109.85  3.000
 2YQ  H12  C19  N4   109.04  3.000
 2YQ  H11  C19  N4   111.00  3.000
 2YQ  C2   C3   C5   117.90  3.000
 2YQ  C5   C3   N1   118.96  3.000
 2YQ  C2   C3   N1   123.05  3.000
 2YQ  C1   C2   C3   119.16  3.000
 2YQ  C3   C2   C7   120.42  3.000
 2YQ  C1   C2   C7   120.41  3.000
 2YQ  F1   C9   C10  118.55  3.000
 2YQ  F1   C9   C8   117.40  3.000
 2YQ  C10  C9   C8   124.04  3.000
 2YQ  C2   C1   C10  121.39  3.000
 2YQ  C2   C1   C4   117.87  3.000
 2YQ  C10  C1   C4   120.74  3.000
 2YQ  H14  N2   C4   117.47  3.000
 2YQ  H14  N2   N1   113.99  3.000
 2YQ  C4   N2   N1   128.50  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
 2YQ  CONST_01  C10  C1   C2   C7     0.00   0.0  0
 2YQ  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 2YQ  CONST_03  C1   C10  C9   C8     0.00   0.0  0
 2YQ  CONST_04  C1   C2   C7   C8     0.00   0.0  0
 2YQ  CONST_05  C16  C11  C12  C13    0.00   0.0  0
 2YQ  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 2YQ  CONST_07  C12  C13  C14  C15    0.00   0.0  0
 2YQ  CONST_08  C12  C11  C16  C15    0.00   0.0  0
 2YQ  CONST_09  C18  N5   N4   C17    0.00   0.0  0
 2YQ  CONST_10  N5   C18  N6   C17    0.00   0.0  0
 2YQ  CONST_11  C11  C12  C13  C14    0.00   0.0  0
 2YQ  CONST_12  C11  C16  C15  C14    0.00   0.0  0
 2YQ  CONST_13  N5   N4   C17  N6     0.00   0.0  0
 2YQ  CONST_14  N4   N5   C18  N6     0.00   0.0  0
 2YQ  CONST_15  N4   C17  N6   C18    0.00   0.0  0
 2YQ  CONST_16  C9   C10  C1   C2     0.00   0.0  0
 2YQ  CONST_17  C9   C8   C7   C2     0.00   0.0  0
 2YQ  CONST_18  N5   N4   C17  C5   180.00   0.0  0
 2YQ  CONST_19  C18  N6   C17  C5   180.00   0.0  0
 2YQ  CONST_20  C13  C12  C11  C6   180.00   0.0  0
 2YQ  CONST_21  C15  C16  C11  C6   180.00   0.0  0
 2YQ  CONST_22  C1   C4   N2   N1     0.00   0.0  0
 2YQ  CONST_23  C19  N4   C17  C5     0.00   0.0  0
 2YQ  CONST_24  F1   C9   C8   C7   180.00   0.0  0
 2YQ  CONST_25  C12  C13  C14  F2   180.00   0.0  0
 2YQ  CONST_26  C16  C15  C14  F2   180.00   0.0  0
 2YQ  CONST_27  C19  N4   C17  N6   180.00   0.0  0
 2YQ  CONST_28  C19  N4   N5   C18  180.00   0.0  0
 2YQ  CONST_29  C1   C10  C9   F1   180.00   0.0  0
 2YQ  CONST_30  O    C4   N2   N1   180.00   0.0  0
 2YQ  CONST_31  H4   C8   C7   N3     0.00   0.0  0
 2YQ  CONST_32  H5   C10  C1   C4     0.00   0.0  0
 2YQ  CONST_33  H8   C12  C11  C6     0.00   0.0  0
 2YQ  CONST_34  H9   C16  C11  C6     0.00   0.0  0
 2YQ  CONST_35  H7   C15  C14  C13  180.00   0.0  0
 2YQ  CONST_36  H6   C13  C14  C15  180.00   0.0  0
 2YQ  CONST_37  H10  C18  N6   C17  180.00   0.0  0
 2YQ  CONST_38  H14  N2   C4   C1   180.00   0.0  0
 2YQ  Var_01    N2   N1   C3   C5   175.99   0.0  0
 2YQ  Var_02    C2   C7   N3   C6    18.55  30.0  1
 2YQ  Var_03    H11  C19  N4   C17   92.64  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
 2YQ  chir_01  C5  C3  C17  C6   positiv
 2YQ  chir_02  C6  N3  C5   C11  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
 2YQ  plan-1  C5   0.020
 2YQ  plan-1  C17  0.020
 2YQ  plan-1  N6   0.020
 2YQ  plan-1  C18  0.020
 2YQ  plan-1  N5   0.020
 2YQ  plan-1  N4   0.020
 2YQ  plan-1  C19  0.020
 2YQ  plan-1  H10  0.020
 2YQ  plan-2  C6   0.020
 2YQ  plan-2  C13  0.020
 2YQ  plan-2  C15  0.020
 2YQ  plan-2  C14  0.020
 2YQ  plan-2  C12  0.020
 2YQ  plan-2  C16  0.020
 2YQ  plan-2  C11  0.020
 2YQ  plan-2  H7   0.020
 2YQ  plan-2  H8   0.020
 2YQ  plan-2  H9   0.020
 2YQ  plan-2  H6   0.020
 2YQ  plan-2  F2   0.020
 2YQ  plan-3  N1   0.020
 2YQ  plan-3  N3   0.020
 2YQ  plan-3  C4   0.020
 2YQ  plan-3  C5   0.020
 2YQ  plan-3  C7   0.020
 2YQ  plan-3  C8   0.020
 2YQ  plan-3  C10  0.020
 2YQ  plan-3  C3   0.020
 2YQ  plan-3  C2   0.020
 2YQ  plan-3  C9   0.020
 2YQ  plan-3  F1   0.020
 2YQ  plan-3  C1   0.020
 2YQ  plan-3  O    0.020
 2YQ  plan-3  N2   0.020
 2YQ  plan-3  H4   0.020
 2YQ  plan-3  H5   0.020
 2YQ  plan-3  H14  0.020

