# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:28:41 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C([C@@H]2C[C@H]2C#N)N3C(=O)C=C(Cn4nc(cc4Cl)C(F)(F)F)N=C3C=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
 7H2  7H2  (1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile  ligand  41  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7H2
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
 7H2  C4   C   CR16  0  -0.390   1.2113  -2.1961   0.1734
 7H2  C14  C   CH2   0  -0.448   4.3203   1.7093  -0.6116
 7H2  C5   C   CR66  0   0.564   1.0377  -0.8557   0.5978
 7H2  C7   C   CR6   0   0.255  -0.3099   0.8346   1.2899
 7H2  C8   C   CR16  0  -0.486   0.7477   1.6233   1.6437
 7H2  C9   C   CR6   0   0.570   2.0731   1.1303   1.5369
 7H2  C12  C   CR6   0   0.357   3.4158  -0.5301   0.3359
 7H2  C13  C   CH1   0  -0.290   4.5179   0.4546   0.1524
 7H2  C3   C   CR16  0  -0.119   2.4491  -2.6831  -0.0722
 7H2  C2   C   CR6   0  -0.042   3.5852  -1.8322  -0.0308
 7H2  N6   N   N     0  -0.475  -0.1774  -0.4108   0.8369
 7H2  O10  O   O     0  -0.455   3.0736   1.6279   2.0170
 7H2  N11  N   N     0  -0.669   2.1709  -0.0876   0.7751
 7H2  C15  C   CH1   0  -0.379   5.0812   0.5818  -1.2539
 7H2  C16  C   CSP   0   0.137   6.4995   0.6777  -1.4147
 7H2  N17  N   NS    0  -0.273   7.6422   0.7489  -1.5426
 7H2  C18  C   CH2   0  -0.364  -1.7183   1.3316   1.4893
 7H2  N19  N   NR5   0  -0.283  -2.6495   0.6942   0.5927
 7H2  C20  C   CR5   0   0.373  -2.6952   0.8031  -0.7498
 7H2  C21  C   CR15  0  -0.495  -3.6982  -0.0092  -1.2084
 7H2  C22  C   CR5   0   0.016  -4.1957  -0.5794  -0.0288
 7H2  N23  N   N     0  -0.274  -3.5568  -0.1565   1.0419
 7H2  C24  C   CT    0   1.074  -5.2888  -1.5784   0.0893
 7H2  F25  F   F     0  -0.310  -6.3087  -1.2742  -0.7215
 7H2  F26  F   F     0  -0.314  -4.8785  -2.8066  -0.2569
 7H2  F27  F   F     0  -0.304  -5.7619  -1.6544   1.3327
 7H2  CL1  CL  CL    0  -0.063  -1.6276   1.8114  -1.5970
 7H2  H1   H   HCR6  0   0.292   0.3227  -2.8036   0.0828
 7H2  H2   H   HCH2  0   0.287   3.3500   1.9185  -1.0437
 7H2  H3   H   HCH2  0   0.294   4.8683   2.5831  -0.2883
 7H2  H4   H   HCR6  0   0.280   0.6036   2.6004   2.0846
 7H2  H6   H   HCH1  0   0.329   5.2573   0.4947   0.9444
 7H2  H7   H   HCR6  0   0.285   2.5785  -3.7198  -0.3552
 7H2  H8   H   HCH3  0   0.270   4.9670  -3.4424  -0.2217
 7H2  H9   H   HCH3  0   0.261   5.0591  -2.2829  -1.5334
 7H2  H10  H   HCH3  0   0.260   5.7490  -1.8890   0.0403
 7H2  H11  H   HCH1  0   0.343   4.5843   0.0471  -2.0550
 7H2  H12  H   HCH2  0   0.321  -2.0510   1.1017   2.5015
 7H2  H13  H   HCH2  0   0.300  -1.7668   2.4143   1.3697
 7H2  H14  H   HCR5  0   0.303  -4.0137  -0.1580  -2.2267
 7H2  C1   C   CH3   0  -0.738   4.9143  -2.3795  -0.4554

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
 7H2  C14  C13  single    1.482  0.020  1.482
 7H2  C14  C15  single    1.504  0.020  1.504
 7H2  C13  C12  single    1.489  0.020  1.489
 7H2  C13  C15  single    1.520  0.020  1.520
 7H2  C1   C2   single    1.499  0.020  1.499
 7H2  C12  C2   double    1.363  0.020  1.363
 7H2  C12  N11  single    1.392  0.020  1.392
 7H2  O10  C9   double    1.216  0.020  1.216
 7H2  C2   C3   single    1.420  0.020  1.420
 7H2  C15  C16  single    1.431  0.020  1.431
 7H2  C16  N17  triple    1.152  0.020  1.152
 7H2  C9   N11  single    1.440  0.020  1.440
 7H2  C9   C8   single    1.418  0.020  1.418
 7H2  N11  C5   single    1.380  0.020  1.380
 7H2  C3   C4   double    1.353  0.020  1.353
 7H2  C8   C7   double    1.366  0.020  1.366
 7H2  C5   C4   single    1.417  0.020  1.417
 7H2  C5   N6   double    1.316  0.020  1.316
 7H2  CL1  C20  single    1.695  0.020  1.695
 7H2  C7   N6   single    1.332  0.020  1.332
 7H2  C7   C18  single    1.507  0.020  1.507
 7H2  C18  N19  single    1.441  0.020  1.441
 7H2  C20  N19  aromatic  1.348  0.020  1.348
 7H2  C20  C21  aromatic  1.370  0.020  1.370
 7H2  N19  N23  aromatic  1.322  0.020  1.322
 7H2  C21  C22  aromatic  1.401  0.020  1.401
 7H2  N23  C22  aromatic  1.317  0.020  1.317
 7H2  C22  C24  single    1.486  0.020  1.486
 7H2  F25  C24  single    1.338  0.020  1.338
 7H2  F27  C24  single    1.333  0.020  1.333
 7H2  C24  F26  single    1.340  0.020  1.340
 7H2  C4   H1   single    0.930  0.020  1.080
 7H2  C14  H2   single    0.970  0.020  1.090
 7H2  C14  H3   single    0.970  0.020  1.090
 7H2  C8   H4   single    0.930  0.020  1.080
 7H2  C13  H6   single    0.970  0.020  1.090
 7H2  C3   H7   single    0.930  0.020  1.080
 7H2  C1   H8   single    0.970  0.020  1.090
 7H2  C1   H9   single    0.970  0.020  1.090
 7H2  C1   H10  single    0.970  0.020  1.090
 7H2  C15  H11  single    0.970  0.020  1.090
 7H2  C18  H12  single    0.970  0.020  1.090
 7H2  C18  H13  single    0.970  0.020  1.090
 7H2  C21  H14  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
 7H2  H1   C4   C3   122.35  3.000
 7H2  H1   C4   C5   117.16  3.000
 7H2  C3   C4   C5   120.48  3.000
 7H2  H3   C14  H2   114.69  3.000
 7H2  H3   C14  C15  118.50  3.000
 7H2  H2   C14  C15  115.33  3.000
 7H2  H3   C14  C13  117.55  3.000
 7H2  H2   C14  C13  119.26  3.000
 7H2  C15  C14  C13   61.20  3.000
 7H2  N11  C5   N6   123.14  3.000
 7H2  N6   C5   C4   119.17  3.000
 7H2  N11  C5   C4   117.67  3.000
 7H2  C18  C7   N6   116.51  3.000
 7H2  C18  C7   C8   119.94  3.000
 7H2  N6   C7   C8   123.43  3.000
 7H2  H4   C8   C9   117.99  3.000
 7H2  H4   C8   C7   121.60  3.000
 7H2  C9   C8   C7   120.23  3.000
 7H2  N11  C9   O10  119.94  3.000
 7H2  N11  C9   C8   113.41  3.000
 7H2  O10  C9   C8   126.64  3.000
 7H2  N11  C12  C2   119.96  3.000
 7H2  N11  C12  C13  119.37  3.000
 7H2  C2   C12  C13  120.43  3.000
 7H2  H6   C13  C15  114.83  3.000
 7H2  H6   C13  C12  116.05  3.000
 7H2  C15  C13  C12  116.33  3.000
 7H2  H6   C13  C14  115.85  3.000
 7H2  C15  C13  C14   60.11  3.000
 7H2  C12  C13  C14  121.64  3.000
 7H2  H7   C3   C2   119.06  3.000
 7H2  H7   C3   C4   120.12  3.000
 7H2  C2   C3   C4   120.74  3.000
 7H2  C1   C2   C3   118.85  3.000
 7H2  C3   C2   C12  118.73  3.000
 7H2  C1   C2   C12  122.36  3.000
 7H2  C7   N6   C5   118.02  3.000
 7H2  C12  N11  C9   119.76  3.000
 7H2  C9   N11  C5   118.87  3.000
 7H2  C12  N11  C5   121.11  3.000
 7H2  H11  C15  C16  113.86  3.000
 7H2  H11  C15  C13  118.20  3.000
 7H2  C16  C15  C13  118.49  3.000
 7H2  H11  C15  C14  116.97  3.000
 7H2  C16  C15  C14  119.95  3.000
 7H2  C13  C15  C14   58.69  3.000
 7H2  N17  C16  C15  180.00  3.000
 7H2  H13  C18  H12  107.32  3.000
 7H2  H13  C18  N19  110.01  3.000
 7H2  H12  C18  N19  106.69  3.000
 7H2  H13  C18  C7   110.77  3.000
 7H2  H12  C18  C7   109.79  3.000
 7H2  N19  C18  C7   112.07  3.000
 7H2  N23  N19  C20  111.54  3.000
 7H2  N23  N19  C18  121.10  3.000
 7H2  C20  N19  C18  127.28  3.000
 7H2  CL1  C20  C21  130.28  3.000
 7H2  C21  C20  N19  108.08  3.000
 7H2  CL1  C20  N19  121.64  3.000
 7H2  H14  C21  C22  129.49  3.000
 7H2  H14  C21  C20  127.83  3.000
 7H2  C22  C21  C20  102.68  3.000
 7H2  C24  C22  N23  120.56  3.000
 7H2  C24  C22  C21  127.00  3.000
 7H2  N23  C22  C21  112.43  3.000
 7H2  C22  N23  N19  105.27  3.000
 7H2  F27  C24  F26  107.30  3.000
 7H2  F26  C24  F25  106.57  3.000
 7H2  F27  C24  F25  107.93  3.000
 7H2  F26  C24  C22  111.74  3.000
 7H2  F27  C24  C22  111.95  3.000
 7H2  F25  C24  C22  111.09  3.000
 7H2  H10  C1   H9   107.95  3.000
 7H2  H10  C1   H8   107.76  3.000
 7H2  H9   C1   H8   106.96  3.000
 7H2  H10  C1   C2   112.75  3.000
 7H2  H9   C1   C2   111.40  3.000
 7H2  H8   C1   C2   109.78  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
 7H2  CONST_01  C22  C21  C20  N19    0.00   0.0  0
 7H2  CONST_02  C21  C22  N23  N19    0.00   0.0  0
 7H2  CONST_03  C22  N23  N19  C20    0.00   0.0  0
 7H2  CONST_04  N23  C22  C21  C20    0.00   0.0  0
 7H2  CONST_05  N23  N19  C20  C21    0.00   0.0  0
 7H2  CONST_06  C12  N11  C5   C4     0.00   0.0  0
 7H2  CONST_08  C7   N6   C5   C4   180.00   0.0  0
 7H2  CONST_10  N11  C5   N6   C7     0.00   0.0  0
 7H2  CONST_11  C12  N11  C9   C8   180.00   0.0  0
 7H2  CONST_12  N6   C5   N11  C9     0.00   0.0  0
 7H2  CONST_13  N6   C5   N11  C12  180.00   0.0  0
 7H2  CONST_14  C21  C20  N19  C18  180.00   0.0  0
 7H2  CONST_15  C22  N23  N19  C18  180.00   0.0  0
 7H2  CONST_16  C24  C22  N23  N19  180.00   0.0  0
 7H2  CONST_17  C24  C22  C21  C20  180.00   0.0  0
 7H2  CONST_18  CL1  C20  C21  C22  180.00   0.0  0
 7H2  CONST_19  CL1  C20  N19  N23  180.00   0.0  0
 7H2  CONST_21  O10  C9   N11  C12    0.00   0.0  0
 7H2  CONST_22  H14  C21  C20  N19  180.00   0.0  0
 7H2  Var_01    C2   C12  C13  C14  124.97  30.0  3
 7H2  Var_02    C12  C13  C15  C14  112.99  30.0  1
 7H2  Var_03    C20  N19  C18  C7   -65.89  30.0  2
 7H2  Var_04    N19  C18  C7   C8   155.24  30.0  3
 7H2  Var_05    F25  C24  C22  C21  -42.61  30.0  2
 7H2  Var_06    H8   C1   C2   C12  151.56  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
 7H2  chir_01  C13  C14  C12  C15  both
 7H2  chir_02  C15  C14  C13  C16  both

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
 7H2  plan-1  C18  0.020
 7H2  plan-1  N19  0.020
 7H2  plan-1  C20  0.020
 7H2  plan-1  C21  0.020
 7H2  plan-1  C22  0.020
 7H2  plan-1  N23  0.020
 7H2  plan-1  C24  0.020
 7H2  plan-1  CL1  0.020
 7H2  plan-1  H14  0.020
 7H2  plan-2  C4   0.020
 7H2  plan-2  C5   0.020
 7H2  plan-2  C7   0.020
 7H2  plan-2  C8   0.020
 7H2  plan-2  C9   0.020
 7H2  plan-2  C12  0.020
 7H2  plan-2  C13  0.020
 7H2  plan-2  C3   0.020
 7H2  plan-2  C2   0.020
 7H2  plan-2  N6   0.020
 7H2  plan-2  O10  0.020
 7H2  plan-2  N11  0.020
 7H2  plan-2  C18  0.020
 7H2  plan-2  H1   0.020
 7H2  plan-2  H4   0.020
 7H2  plan-2  H7   0.020
 7H2  plan-2  C1   0.020

