# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 21:34:24 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2R,3S,5R)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl]-2-(2,4,5-trifluorophenyl)tetrahydro-2H-pyran-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)n1cc2CN(Cc2n1)[C@H]3CO[C@@H]([C@@H](N)C3)c4cc(F)c(F)cc4F
#
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
 2VH  2VH  (2R,3S,5R)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl]-2-(2,4,5-trifluorophenyl)tetrahydro-2H-pyran-3-amine  ligand  47  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2VH
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
 2VH  F2   F  F     0  -0.299  -8.2137  -0.6777  -0.3850
 2VH  C    C  CR6   0   0.407  -6.9369  -0.3831  -0.1385
 2VH  C5   C  CR6   0   0.410  -5.9471  -1.2759  -0.5148
 2VH  F    F  F     0  -0.305  -6.2949  -2.4173  -1.1183
 2VH  C4   C  CR16  0  -0.434  -4.6229  -0.9927  -0.2707
 2VH  C3   C  CR6   0  -0.115  -4.2542   0.1958   0.3592
 2VH  C2   C  CR6   0   0.525  -5.2705   1.0639   0.7203
 2VH  F1   F  F     0  -0.303  -4.9664   2.2180   1.3321
 2VH  C1   C  CR16  0  -0.555  -6.6084   0.7997   0.4850
 2VH  C6   C  CH1   0   0.014  -2.8009   0.5172   0.5747
 2VH  C10  C  CH1   0  -0.111  -2.1541   1.0646  -0.7144
 2VH  N    N  NH2   0  -0.789  -2.7293   2.3034  -1.1937
 2VH  C9   C  CH2   0  -0.473  -0.6598   1.2459  -0.4787
 2VH  C8   C  CH1   0  -0.065  -0.0193  -0.0404   0.0350
 2VH  C7   C  CH2   0  -0.183  -0.7917  -0.4961   1.2721
 2VH  O    O  O2    0  -0.490  -2.1622  -0.6682   0.9920
 2VH  N1   N  NR5   0  -0.474   1.3762   0.1605   0.3660
 2VH  C14  C  CH2   0  -0.317   2.1785   0.7448  -0.7196
 2VH  C13  C  CR55  0   0.267   3.5429   0.2876  -0.3478
 2VH  N2   N  N     0  -0.282   4.7638   0.5875  -0.6977
 2VH  N3   N  NR5   0  -0.486   5.5058  -0.2817   0.0200
 2VH  S    S  S     0   1.367   7.1972  -0.1385  -0.0383
 2VH  O2   O  OS    0  -0.621   7.5493   0.1054  -1.4183
 2VH  C16  C  CH3   0  -0.786   7.4924   1.3205   0.9166
 2VH  O1   O  OS    0  -0.631   7.6972  -1.3062   0.6577
 2VH  C15  C  CR15  0  -0.006   4.7631  -1.1044   0.8321
 2VH  C12  C  CR55  0  -0.107   3.4731  -0.7484   0.5932
 2VH  C11  C  CH2   0  -0.341   2.0499  -1.0343   0.9103
 2VH  H1   H  HCR6  0   0.297  -3.8700  -1.7083  -0.5747
 2VH  H2   H  HCR6  0   0.316  -7.3775   1.5008   0.7820
 2VH  H3   H  HCH1  0   0.233  -2.6949   1.2879   1.3538
 2VH  H4   H  HCH1  0   0.241  -2.2938   0.3110  -1.4986
 2VH  H5   H  HNH2  0   0.354  -3.6947   2.1741  -1.4685
 2VH  H6   H  HNH2  0   0.342  -2.7227   3.0081  -0.4657
 2VH  H8   H  HCH2  0   0.261  -0.1986   1.5708  -1.4132
 2VH  H9   H  HCH2  0   0.228  -0.4995   2.0419   0.2595
 2VH  H10  H  HCH1  0   0.209  -0.1336  -0.8188  -0.7431
 2VH  H11  H  HCH2  0   0.251  -0.4391  -1.4622   1.6369
 2VH  H12  H  HCH2  0   0.207  -0.6440   0.2420   2.0745
 2VH  H14  H  HCH2  0   0.239   1.9093   0.3504  -1.7119
 2VH  H15  H  HCH2  0   0.267   2.0712   1.8298  -0.7563
 2VH  H16  H  HCH3  0   0.307   7.1296   1.1625   1.9290
 2VH  H17  H  HCH3  0   0.319   8.5683   1.4892   0.9233
 2VH  H18  H  HCH3  0   0.308   6.9842   2.1603   0.4498
 2VH  H19  H  HCR5  0   0.314   5.2199  -1.8436   1.4687
 2VH  H20  H  HCH2  0   0.260   1.8536  -1.1429   1.9785
 2VH  H21  H  HCH2  0   0.233   1.7216  -1.9634   0.4193

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
 2VH  N    C10  single    1.448  0.020  1.448
 2VH  C10  C9   single    1.524  0.020  1.524
 2VH  C10  C6   single    1.543  0.020  1.543
 2VH  O1   S    double    1.448  0.020  1.448
 2VH  C9   C8   single    1.526  0.020  1.526
 2VH  C14  C13  single    1.486  0.020  1.486
 2VH  C14  N1   single    1.471  0.020  1.471
 2VH  N2   C13  aromatic  1.305  0.020  1.305
 2VH  N2   N3   aromatic  1.350  0.020  1.350
 2VH  F    C5   single    1.337  0.020  1.337
 2VH  C13  C12  aromatic  1.401  0.020  1.401
 2VH  C5   C4   aromatic  1.376  0.020  1.376
 2VH  C5   C    aromatic  1.385  0.020  1.385
 2VH  C4   C3   aromatic  1.395  0.020  1.395
 2VH  F2   C    single    1.333  0.020  1.333
 2VH  C    C1   aromatic  1.377  0.020  1.377
 2VH  C8   N1   single    1.448  0.020  1.448
 2VH  C8   C7   single    1.528  0.020  1.528
 2VH  C3   C6   single    1.504  0.020  1.504
 2VH  C3   C2   aromatic  1.385  0.020  1.385
 2VH  S    N3   single    1.698  0.020  1.698
 2VH  S    O2   double    1.445  0.020  1.445
 2VH  S    C16  single    1.768  0.020  1.768
 2VH  C1   C2   aromatic  1.384  0.020  1.384
 2VH  C6   O    single    1.410  0.020  1.410
 2VH  N3   C15  aromatic  1.374  0.020  1.374
 2VH  N1   C11  single    1.476  0.020  1.476
 2VH  C2   F1   single    1.341  0.020  1.341
 2VH  C12  C15  aromatic  1.359  0.020  1.359
 2VH  C12  C11  single    1.486  0.020  1.486
 2VH  O    C7   single    1.409  0.020  1.409
 2VH  C4   H1   single    0.930  0.020  1.080
 2VH  C1   H2   single    0.930  0.020  1.080
 2VH  C6   H3   single    0.970  0.020  1.090
 2VH  C10  H4   single    0.970  0.020  1.090
 2VH  N    H5   single    0.890  0.020  1.040
 2VH  N    H6   single    0.890  0.020  1.040
 2VH  C9   H8   single    0.970  0.020  1.090
 2VH  C9   H9   single    0.970  0.020  1.090
 2VH  C8   H10  single    0.970  0.020  1.090
 2VH  C7   H11  single    0.970  0.020  1.090
 2VH  C7   H12  single    0.970  0.020  1.090
 2VH  C14  H14  single    0.970  0.020  1.090
 2VH  C14  H15  single    0.970  0.020  1.090
 2VH  C16  H16  single    0.970  0.020  1.090
 2VH  C16  H17  single    0.970  0.020  1.090
 2VH  C16  H18  single    0.970  0.020  1.090
 2VH  C15  H19  single    0.930  0.020  1.080
 2VH  C11  H20  single    0.970  0.020  1.090
 2VH  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
 2VH  C1   C    C5   120.42  3.000
 2VH  C1   C    F2   120.13  3.000
 2VH  C5   C    F2   119.45  3.000
 2VH  C4   C5   F    120.41  3.000
 2VH  C4   C5   C    120.45  3.000
 2VH  F    C5   C    119.14  3.000
 2VH  H1   C4   C3   120.42  3.000
 2VH  H1   C4   C5   118.92  3.000
 2VH  C3   C4   C5   120.66  3.000
 2VH  C6   C3   C2   122.55  3.000
 2VH  C2   C3   C4   117.25  3.000
 2VH  C6   C3   C4   120.15  3.000
 2VH  C1   C2   F1   117.45  3.000
 2VH  F1   C2   C3   119.47  3.000
 2VH  C1   C2   C3   123.07  3.000
 2VH  H2   C1   C2   121.11  3.000
 2VH  H2   C1   C    120.75  3.000
 2VH  C2   C1   C    118.14  3.000
 2VH  H3   C6   O    109.61  3.000
 2VH  H3   C6   C10  107.61  3.000
 2VH  O    C6   C10  110.84  3.000
 2VH  H3   C6   C3   110.12  3.000
 2VH  O    C6   C3   107.49  3.000
 2VH  C10  C6   C3   111.18  3.000
 2VH  H4   C10  C9   108.51  3.000
 2VH  H4   C10  N    107.50  3.000
 2VH  C9   C10  N    109.83  3.000
 2VH  H4   C10  C6   107.48  3.000
 2VH  C9   C10  C6   108.92  3.000
 2VH  N    C10  C6   114.44  3.000
 2VH  H6   N    H5   106.87  3.000
 2VH  H6   N    C10  110.78  3.000
 2VH  H5   N    C10  111.08  3.000
 2VH  H9   C9   H8   107.35  3.000
 2VH  H9   C9   C8   108.88  3.000
 2VH  H8   C9   C8   111.21  3.000
 2VH  H9   C9   C10  109.49  3.000
 2VH  H8   C9   C10  108.50  3.000
 2VH  C8   C9   C10  111.31  3.000
 2VH  H10  C8   N1   110.96  3.000
 2VH  H10  C8   C7   107.90  3.000
 2VH  N1   C8   C7   110.09  3.000
 2VH  H10  C8   C9   108.23  3.000
 2VH  C7   C8   C9   108.17  3.000
 2VH  N1   C8   C9   111.37  3.000
 2VH  H12  C7   H11  107.86  3.000
 2VH  H12  C7   O    110.94  3.000
 2VH  H11  C7   O    105.82  3.000
 2VH  H12  C7   C8   108.81  3.000
 2VH  H11  C7   C8   111.80  3.000
 2VH  O    C7   C8   111.54  3.000
 2VH  C7   O    C6   113.37  3.000
 2VH  C11  N1   C14  110.17  3.000
 2VH  C11  N1   C8   114.32  3.000
 2VH  C14  N1   C8   114.33  3.000
 2VH  H15  C14  H14  107.57  3.000
 2VH  H15  C14  C13  113.87  3.000
 2VH  H14  C14  C13  109.85  3.000
 2VH  H15  C14  N1   111.49  3.000
 2VH  H14  C14  N1   112.92  3.000
 2VH  C13  C14  N1   101.18  3.000
 2VH  C12  C13  N2   113.36  3.000
 2VH  C12  C13  C14  110.47  3.000
 2VH  N2   C13  C14  136.14  3.000
 2VH  N3   N2   C13  102.93  3.000
 2VH  C15  N3   S    127.52  3.000
 2VH  C15  N3   N2   113.75  3.000
 2VH  S    N3   N2   118.36  3.000
 2VH  O1   S    C16  110.36  3.000
 2VH  C16  S    O2   109.62  3.000
 2VH  O1   S    O2   120.72  3.000
 2VH  C16  S    N3   102.55  3.000
 2VH  O2   S    N3   106.84  3.000
 2VH  O1   S    N3   105.03  3.000
 2VH  H18  C16  H17  110.17  3.000
 2VH  H18  C16  H16  110.87  3.000
 2VH  H17  C16  H16  110.28  3.000
 2VH  H18  C16  S    109.11  3.000
 2VH  H17  C16  S    107.22  3.000
 2VH  H16  C16  S    109.10  3.000
 2VH  H19  C15  C12  133.31  3.000
 2VH  H19  C15  N3   122.07  3.000
 2VH  C12  C15  N3   104.61  3.000
 2VH  C11  C12  C15  145.19  3.000
 2VH  C11  C12  C13  109.47  3.000
 2VH  C15  C12  C13  105.33  3.000
 2VH  H21  C11  H20  107.39  3.000
 2VH  H21  C11  C12  110.66  3.000
 2VH  H20  C11  C12  113.59  3.000
 2VH  H21  C11  N1   112.50  3.000
 2VH  H20  C11  N1   111.06  3.000
 2VH  C12  C11  N1   101.70  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
 2VH  CONST_01  C3   C4   C5   C       0.00   0.0  0
 2VH  CONST_02  C3   C2   C1   C       0.00   0.0  0
 2VH  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 2VH  CONST_04  C2   C1   C    C5      0.00   0.0  0
 2VH  CONST_05  C1   C    C5   C4      0.00   0.0  0
 2VH  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 2VH  CONST_07  C15  N3   N2   C13     0.00   0.0  0
 2VH  CONST_08  N3   C15  C12  C13     0.00   0.0  0
 2VH  CONST_09  C15  C12  C13  N2      0.00   0.0  0
 2VH  CONST_10  C12  C15  N3   N2      0.00   0.0  0
 2VH  CONST_11  C12  C13  N2   N3      0.00   0.0  0
 2VH  CONST_12  C6   C3   C4   C5    180.00   0.0  0
 2VH  CONST_13  C6   C3   C2   C1    180.00   0.0  0
 2VH  CONST_14  C4   C5   C    F2    180.00   0.0  0
 2VH  CONST_15  C2   C1   C    F2    180.00   0.0  0
 2VH  CONST_16  F1   C2   C1   C     180.00   0.0  0
 2VH  CONST_17  C3   C4   C5   F     180.00   0.0  0
 2VH  CONST_18  C1   C    C5   F     180.00   0.0  0
 2VH  CONST_19  F1   C2   C3   C4    180.00   0.0  0
 2VH  CONST_20  C6   C3   C2   F1      0.00   0.0  0
 2VH  CONST_21  S    N3   N2   C13   180.00   0.0  0
 2VH  CONST_22  C12  C15  N3   S     180.00   0.0  0
 2VH  CONST_23  H1   C4   C5   C     180.00   0.0  0
 2VH  CONST_24  H2   C1   C    C5    180.00   0.0  0
 2VH  CONST_25  H19  C15  C12  C13   180.00   0.0  0
 2VH  Var_01    C8   C7   O    C6    -61.53  30.0  1
 2VH  Var_02    C13  C14  N1   C8   -156.42  30.0  1
 2VH  Var_03    C12  C11  N1   C8    156.35  30.0  1
 2VH  Var_04    N2   C13  C14  N1   -166.06  30.0  1
 2VH  Var_05    C13  C12  C11  N1    -15.16  30.0  1
 2VH  Var_06    O1   S    N3   N2   -171.91  30.0  1
 2VH  Var_07    H16  C16  S    N3     60.96  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
 2VH  chir_01  C6   C10  C3  O   negativ
 2VH  chir_02  C10  N    C6  C9  positiv
 2VH  chir_03  C8   N1   C7  C9  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
 2VH  plan-1  F2   0.020
 2VH  plan-1  C    0.020
 2VH  plan-1  C5   0.020
 2VH  plan-1  F    0.020
 2VH  plan-1  C4   0.020
 2VH  plan-1  C3   0.020
 2VH  plan-1  C2   0.020
 2VH  plan-1  F1   0.020
 2VH  plan-1  C1   0.020
 2VH  plan-1  C6   0.020
 2VH  plan-1  H1   0.020
 2VH  plan-1  H2   0.020
 2VH  plan-2  C14  0.020
 2VH  plan-2  C13  0.020
 2VH  plan-2  N2   0.020
 2VH  plan-2  N3   0.020
 2VH  plan-2  S    0.020
 2VH  plan-2  C15  0.020
 2VH  plan-2  C12  0.020
 2VH  plan-2  C11  0.020
 2VH  plan-2  H19  0.020

