# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 17:55:40 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: methyl (NZ)-N-[(7R)-6-cyano-7-(4-cyanophenyl)-5-methyl-4-[3-(trifluoromethyl)phenyl]-1,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylidene]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N=C1NN2[C@H](c3ccc(cc3)C#N)C(=C(C)N(c4cccc(c4)C(F)(F)F)C2=N1)C#N
#
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
 VBM  VBM  'methyl (NZ)-N-[(7R)-6-cyano-7-(4-cyanophenyl)-5-methyl-4-[3-(trifluoromethyl)phenyl]-1,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylidene]carbamate'  ligand  51  35  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VBM
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
 VBM  C15   C  CR16  0  -0.303  -4.2878  -0.8864  -0.8954
 VBM  C12   C  CR16  0  -0.218  -5.2733  -1.3121  -0.0199
 VBM  C13   C  CR6   0  -0.002  -4.9050  -1.9488   1.1618
 VBM  C19   C  CSP   0   0.063  -5.9138  -2.3924   2.0702
 VBM  N20   N  NS    0  -0.244  -6.7275  -2.7494   2.8030
 VBM  C14   C  CR16  0  -0.217  -3.5596  -2.1640   1.4642
 VBM  C18   C  CR16  0  -0.275  -2.5887  -1.7413   0.5771
 VBM  C11   C  CR6   0   0.189  -2.9474  -1.0981  -0.6039
 VBM  C9    C  CH1   0  -0.217  -1.8877  -0.6194  -1.5743
 VBM  C8    C  C     0  -0.093  -0.9134  -1.7088  -1.9608
 VBM  C10   C  C     0   0.362   0.3587  -1.7936  -1.5062
 VBM  C17   C  CH3   0  -0.741   1.2877  -2.9030  -1.8544
 VBM  C16   C  CSP   0   0.041  -1.4434  -2.7054  -2.8125
 VBM  N35   N  NS    0  -0.246  -1.9268  -3.4898  -3.5071
 VBM  N3    N  NR5   0  -0.325  -1.0779   0.4452  -1.0193
 VBM  N6    N  NR15  0  -0.469  -1.6262   1.5617  -0.4480
 VBM  C5    C  CR5   0   0.595  -0.6543   2.1214   0.3316
 VBM  N7    N  N     0  -0.566  -0.6749   3.2610   0.9681
 VBM  C31   C  C     0   0.642  -1.7600   4.0574   0.8284
 VBM  O32   O  O     0  -0.529  -2.7491   3.8768   0.1311
 VBM  O33   O  O2    0  -0.462  -1.6193   5.1480   1.5845
 VBM  C34   C  CH3   0  -0.419  -2.6729   6.1019   1.5576
 VBM  N2    N  N     0  -0.519   0.4153   1.2812   0.3759
 VBM  C1    C  CR5   0   0.804   0.1060   0.2948  -0.4196
 VBM  N4    N  NT    0  -0.693   0.8577  -0.8093  -0.6688
 VBM  C21   C  CR6   0   0.258   2.1547  -0.8879  -0.0716
 VBM  C26   C  CR16  0  -0.275   3.2364  -0.3332  -0.7366
 VBM  C22   C  CR16  0  -0.231   2.3024  -1.5079   1.1565
 VBM  C23   C  CR16  0  -0.248   3.5643  -1.5834   1.7281
 VBM  C24   C  CR16  0  -0.249   4.6579  -1.0403   1.0751
 VBM  C25   C  CR6   0  -0.199   4.4930  -0.4157  -0.1576
 VBM  C27   C  CT    0   1.061   5.6918   0.1768  -0.8326
 VBM  F29   F  F     0  -0.311   6.1787   1.2169  -0.1430
 VBM  F30   F  F     0  -0.310   6.6862  -0.7135  -0.9358
 VBM  F28   F  F     0  -0.299   5.4216   0.6130  -2.0648
 VBM  H15   H  HCR6  0   0.284  -4.5716  -0.3905  -1.8149
 VBM  H12   H  HCR6  0   0.290  -6.3165  -1.1515  -0.2532
 VBM  H14   H  HCR6  0   0.290  -3.2795  -2.6623   2.3817
 VBM  H18   H  HCR6  0   0.272  -1.5499  -1.9307   0.8175
 VBM  H9    H  HCH1  0   0.339  -2.3770  -0.2338  -2.4727
 VBM  H171  H  HCH3  0   0.287   0.7978  -3.6479  -2.4742
 VBM  H172  H  HCH3  0   0.290   2.1531  -2.5247  -2.3997
 VBM  H173  H  HCH3  0   0.288   1.6555  -3.4000  -0.9569
 VBM  H6    H  HNR5  0   0.444  -2.3143   2.1044  -0.9557
 VBM  H341  H  HCH3  0   0.245  -2.3592   6.9116   2.2112
 VBM  H342  H  HCH3  0   0.231  -2.8382   6.4986   0.5554
 VBM  H343  H  HCH3  0   0.231  -3.6083   5.6850   1.9327
 VBM  H26   H  HCR6  0   0.292   3.0800   0.1486  -1.6924
 VBM  H22   H  HCR6  0   0.287   1.4439  -1.9333   1.6599
 VBM  H23   H  HCR6  0   0.285   3.6944  -2.0690   2.6849
 VBM  H24   H  HCR6  0   0.288   5.6356  -1.1117   1.5337

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
 VBM  C15  C12   aromatic  1.385  0.020  1.385
 VBM  C15  C11   aromatic  1.388  0.020  1.388
 VBM  C12  C13   aromatic  1.392  0.020  1.392
 VBM  C13  C19   single    1.428  0.020  1.428
 VBM  C13  C14   aromatic  1.396  0.020  1.396
 VBM  C19  N20   triple    1.152  0.020  1.152
 VBM  C14  C18   aromatic  1.381  0.020  1.381
 VBM  C18  C11   aromatic  1.392  0.020  1.392
 VBM  C11  C9    single    1.515  0.020  1.515
 VBM  C9   C8    single    1.512  0.020  1.512
 VBM  C9   N3    single    1.448  0.020  1.448
 VBM  C8   C10   double    1.354  0.020  1.354
 VBM  C8   C16   single    1.414  0.020  1.414
 VBM  C10  C17   single    1.488  0.020  1.488
 VBM  C10  N4    single    1.385  0.020  1.385
 VBM  C16  N35   triple    1.154  0.020  1.154
 VBM  N3   N6    single    1.369  0.020  1.369
 VBM  N3   C1    single    1.336  0.020  1.336
 VBM  N6   C5    single    1.366  0.020  1.366
 VBM  C5   N7    double    1.305  0.020  1.305
 VBM  C5   N2    single    1.361  0.020  1.361
 VBM  N7   C31   single    1.353  0.020  1.353
 VBM  C31  O32   double    1.224  0.020  1.224
 VBM  C31  O33   single    1.335  0.020  1.335
 VBM  O33  C34   single    1.422  0.020  1.422
 VBM  N2   C1    double    1.304  0.020  1.304
 VBM  C1   N4    single    1.359  0.020  1.359
 VBM  N4   C21   single    1.430  0.020  1.430
 VBM  C21  C26   aromatic  1.386  0.020  1.386
 VBM  C21  C22   aromatic  1.384  0.020  1.384
 VBM  C26  C25   aromatic  1.386  0.020  1.386
 VBM  C22  C23   aromatic  1.387  0.020  1.387
 VBM  C23  C24   aromatic  1.385  0.020  1.385
 VBM  C24  C25   aromatic  1.392  0.020  1.392
 VBM  C25  C27   single    1.498  0.020  1.498
 VBM  C27  F29   single    1.340  0.020  1.340
 VBM  C27  F30   single    1.339  0.020  1.339
 VBM  C27  F28   single    1.335  0.020  1.335
 VBM  C15  H15   single    0.930  0.020  1.080
 VBM  C12  H12   single    0.930  0.020  1.080
 VBM  C14  H14   single    0.930  0.020  1.080
 VBM  C18  H18   single    0.930  0.020  1.080
 VBM  C9   H9    single    0.970  0.020  1.090
 VBM  C17  H171  single    0.970  0.020  1.090
 VBM  C17  H172  single    0.970  0.020  1.090
 VBM  C17  H173  single    0.970  0.020  1.090
 VBM  N6   H6    single    0.890  0.020  1.040
 VBM  C34  H341  single    0.970  0.020  1.090
 VBM  C34  H342  single    0.970  0.020  1.090
 VBM  C34  H343  single    0.970  0.020  1.090
 VBM  C26  H26   single    0.930  0.020  1.080
 VBM  C22  H22   single    0.930  0.020  1.080
 VBM  C23  H23   single    0.930  0.020  1.080
 VBM  C24  H24   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
 VBM  H15   C15  C11   120.09  3.000
 VBM  H15   C15  C12   119.41  3.000
 VBM  C11   C15  C12   120.49  3.000
 VBM  H12   C12  C13   120.43  3.000
 VBM  H12   C12  C15   120.30  3.000
 VBM  C13   C12  C15   119.27  3.000
 VBM  C14   C13  C19   119.69  3.000
 VBM  C14   C13  C12   120.63  3.000
 VBM  C19   C13  C12   119.69  3.000
 VBM  N20   C19  C13   180.00  3.000
 VBM  H14   C14  C18   120.26  3.000
 VBM  H14   C14  C13   120.32  3.000
 VBM  C18   C14  C13   119.42  3.000
 VBM  H18   C18  C11   121.09  3.000
 VBM  H18   C18  C14   118.56  3.000
 VBM  C11   C18  C14   120.34  3.000
 VBM  C9    C11  C18   120.62  3.000
 VBM  C9    C11  C15   119.53  3.000
 VBM  C18   C11  C15   119.84  3.000
 VBM  H9    C9   N3    107.81  3.000
 VBM  H9    C9   C8    109.42  3.000
 VBM  N3    C9   C8    105.50  3.000
 VBM  H9    C9   C11   108.96  3.000
 VBM  N3    C9   C11   112.21  3.000
 VBM  C8    C9   C11   112.77  3.000
 VBM  C16   C8   C10   120.69  3.000
 VBM  C16   C8   C9    114.85  3.000
 VBM  C10   C8   C9    124.40  3.000
 VBM  N4    C10  C17   116.50  3.000
 VBM  N4    C10  C8    119.80  3.000
 VBM  C17   C10  C8    123.70  3.000
 VBM  H173  C17  H172  107.59  3.000
 VBM  H173  C17  H171  108.03  3.000
 VBM  H172  C17  H171  108.09  3.000
 VBM  H173  C17  C10   110.97  3.000
 VBM  H172  C17  C10   110.72  3.000
 VBM  H171  C17  C10   111.30  3.000
 VBM  N35   C16  C8    180.00  3.000
 VBM  C1    N3   N6    105.05  3.000
 VBM  C1    N3   C9    125.80  3.000
 VBM  N6    N3   C9    122.38  3.000
 VBM  H6    N6   C5    123.37  3.000
 VBM  H6    N6   N3    120.00  3.000
 VBM  C5    N6   N3    106.70  3.000
 VBM  N2    C5   N7    122.38  3.000
 VBM  N2    C5   N6    108.96  3.000
 VBM  N7    C5   N6    128.66  3.000
 VBM  C31   N7   C5    118.43  3.000
 VBM  O33   C31  O32   121.93  3.000
 VBM  O33   C31  N7    109.75  3.000
 VBM  O32   C31  N7    128.33  3.000
 VBM  C34   O33  C31   117.35  3.000
 VBM  H343  C34  H342  108.98  3.000
 VBM  H343  C34  H341  108.99  3.000
 VBM  H342  C34  H341  108.99  3.000
 VBM  H343  C34  O33   111.88  3.000
 VBM  H342  C34  O33   111.96  3.000
 VBM  H341  C34  O33   105.94  3.000
 VBM  C1    N2   C5    105.11  3.000
 VBM  N4    C1   N2    126.53  3.000
 VBM  N4    C1   N3    119.97  3.000
 VBM  N2    C1   N3    113.50  3.000
 VBM  C21   N4   C1    118.02  3.000
 VBM  C21   N4   C10   122.69  3.000
 VBM  C1    N4   C10   119.27  3.000
 VBM  C22   C21  C26   121.47  3.000
 VBM  C22   C21  N4    119.48  3.000
 VBM  C26   C21  N4    119.05  3.000
 VBM  H26   C26  C25   121.78  3.000
 VBM  H26   C26  C21   119.31  3.000
 VBM  C25   C26  C21   118.91  3.000
 VBM  H22   C22  C23   120.56  3.000
 VBM  H22   C22  C21   120.28  3.000
 VBM  C23   C22  C21   119.16  3.000
 VBM  H23   C23  C24   119.91  3.000
 VBM  H23   C23  C22   119.91  3.000
 VBM  C24   C23  C22   120.18  3.000
 VBM  H24   C24  C25   120.80  3.000
 VBM  H24   C24  C23   119.19  3.000
 VBM  C25   C24  C23   120.01  3.000
 VBM  C27   C25  C24   118.81  3.000
 VBM  C27   C25  C26   120.91  3.000
 VBM  C24   C25  C26   120.28  3.000
 VBM  F28   C27  F30   107.25  3.000
 VBM  F28   C27  F29   107.16  3.000
 VBM  F30   C27  F29   106.62  3.000
 VBM  F28   C27  C25   112.54  3.000
 VBM  F30   C27  C25   111.48  3.000
 VBM  F29   C27  C25   111.47  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
 VBM  CONST_01  C14   C13  C12  C15     0.00   0.0  0
 VBM  CONST_02  C14   C18  C11  C15     0.00   0.0  0
 VBM  CONST_03  C18   C11  C15  C12     0.00   0.0  0
 VBM  CONST_04  C18   C14  C13  C12     0.00   0.0  0
 VBM  CONST_05  C11   C15  C12  C13     0.00   0.0  0
 VBM  CONST_06  C11   C18  C14  C13     0.00   0.0  0
 VBM  CONST_07  C24   C25  C26  C21     0.00   0.0  0
 VBM  CONST_08  C24   C23  C22  C21     0.00   0.0  0
 VBM  CONST_09  C23   C22  C21  C26     0.00   0.0  0
 VBM  CONST_10  C23   C24  C25  C26     0.00   0.0  0
 VBM  CONST_11  C25   C26  C21  C22     0.00   0.0  0
 VBM  CONST_12  C25   C24  C23  C22     0.00   0.0  0
 VBM  CONST_13  C9    C11  C15  C12   180.00   0.0  0
 VBM  CONST_14  C9    C11  C18  C14   180.00   0.0  0
 VBM  CONST_15  C25   C26  C21  N4    180.00   0.0  0
 VBM  CONST_16  C23   C22  C21  N4    180.00   0.0  0
 VBM  CONST_20  N3    C1   N4   C10     0.00   0.0  0
 VBM  CONST_21  N2    C1   N4   C10   180.00   0.0  0
 VBM  CONST_22  N2    C5   N6   N3      0.00   0.0  0
 VBM  CONST_23  C5    N2   C1   N3      0.00   0.0  0
 VBM  CONST_24  C21   N4   C1   N3    180.00   0.0  0
 VBM  CONST_25  N2    C1   N3   N6      0.00   0.0  0
 VBM  CONST_26  N4    C1   N3   N6    180.00   0.0  0
 VBM  CONST_27  C1    N2   C5   N6      0.00   0.0  0
 VBM  CONST_28  C1    N3   N6   C5      0.00   0.0  0
 VBM  CONST_29  N4    C1   N2   C5    180.00   0.0  0
 VBM  CONST_30  C21   N4   C1   N2      0.00   0.0  0
 VBM  CONST_31  C19   C13  C12  C15   180.00   0.0  0
 VBM  CONST_32  C18   C14  C13  C19   180.00   0.0  0
 VBM  CONST_33  C27   C25  C26  C21   180.00   0.0  0
 VBM  CONST_34  C27   C25  C24  C23   180.00   0.0  0
 VBM  CONST_35  N7    C5   N6   N3    180.00   0.0  0
 VBM  CONST_36  C1    N2   C5   N7    180.00   0.0  0
 VBM  CONST_37  H18   C18  C11  C15   180.00   0.0  0
 VBM  CONST_38  H14   C14  C13  C12   180.00   0.0  0
 VBM  CONST_39  H15   C15  C12  C13   180.00   0.0  0
 VBM  CONST_40  H12   C12  C13  C14   180.00   0.0  0
 VBM  CONST_41  H26   C26  C21  N4      0.00   0.0  0
 VBM  CONST_42  H22   C22  C21  N4      0.00   0.0  0
 VBM  CONST_43  H23   C23  C22  C21   180.00   0.0  0
 VBM  CONST_44  H24   C24  C25  C26   180.00   0.0  0
 VBM  CONST_46  C31   N7   C5   N6      0.00   0.0  0
 VBM  CONST_47  N2    C5   N7   C31   180.00   0.0  0
 VBM  Var_01    N4    C10  C8   C9     -2.60  30.0  1
 VBM  Var_02    C1    N4   C10  C8     -6.35  30.0  1
 VBM  Var_03    C26   C21  N4   C10    91.03  30.0  2
 VBM  Var_04    F29   C27  C25  C26   112.87  30.0  2
 VBM  Var_05    H171  C17  C10  C8     -2.71  30.0  3
 VBM  Var_06    O32   C31  N7   C5     -2.56  30.0  3
 VBM  Var_07    H341  C34  O33  C31  -178.74  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
 VBM  chir_01  C9  C11  C8  N3  positiv

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
 VBM  plan-1  C15  0.020
 VBM  plan-1  C12  0.020
 VBM  plan-1  C13  0.020
 VBM  plan-1  C19  0.020
 VBM  plan-1  N20  0.020
 VBM  plan-1  C14  0.020
 VBM  plan-1  C18  0.020
 VBM  plan-1  C11  0.020
 VBM  plan-1  C9   0.020
 VBM  plan-1  H15  0.020
 VBM  plan-1  H12  0.020
 VBM  plan-1  H14  0.020
 VBM  plan-1  H18  0.020
 VBM  plan-2  N4   0.020
 VBM  plan-2  C21  0.020
 VBM  plan-2  C26  0.020
 VBM  plan-2  C22  0.020
 VBM  plan-2  C23  0.020
 VBM  plan-2  C24  0.020
 VBM  plan-2  C25  0.020
 VBM  plan-2  C27  0.020
 VBM  plan-2  H26  0.020
 VBM  plan-2  H22  0.020
 VBM  plan-2  H23  0.020
 VBM  plan-2  H24  0.020
 VBM  plan-3  C9   0.020
 VBM  plan-3  C10  0.020
 VBM  plan-3  N3   0.020
 VBM  plan-3  N6   0.020
 VBM  plan-3  C5   0.020
 VBM  plan-3  N7   0.020
 VBM  plan-3  C31  0.020
 VBM  plan-3  N2   0.020
 VBM  plan-3  C1   0.020
 VBM  plan-3  N4   0.020
 VBM  plan-3  C21  0.020
 VBM  plan-3  H6   0.020
 VBM  plan-4  N7   0.020
 VBM  plan-4  C31  0.020
 VBM  plan-4  O32  0.020
 VBM  plan-4  O33  0.020

