# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 07:51:42 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}3-methyl-~{N}5-(4-oxidanylcyclohexyl)-1-[(1~{S})-1-phenylethyl]pyrazole-3,5-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(n(n1)[C@@H](C)c2ccccc2)C(=O)N[C@H]3CC[C@H](O)CC3
#
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
 V9H  V9H  ~{N}3-methyl-~{N}5-(4-oxidanylcyclohexyl)-1-[(1~{S})-1-phenylethyl]pyrazole-3,5-dicarboxamide  ligand  53  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V9H
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
 V9H  N1   N  NH1   0  -0.635  44.4668  17.0342   9.9397
 V9H  N3   N  N     0  -0.280  40.5468  17.3078   7.7057
 V9H  C4   C  CR5   0   0.322  42.5815  17.4431   8.5650
 V9H  C5   C  C     0   0.512  43.6640  17.9771   9.4318
 V9H  C6   C  CH1   0  -0.057  45.5801  17.3228  10.8243
 V9H  C7   C  CH2   0  -0.443  45.1303  17.4241  12.2815
 V9H  C8   C  CH2   0  -0.480  46.3193  17.6962  13.1964
 V9H  C10  C  CH2   0  -0.462  47.8358  16.5234  11.5944
 V9H  C13  C  CH3   0  -0.657  39.2610  19.0804   9.3235
 V9H  C15  C  CR16  0  -0.293  41.3526  19.2367  11.9774
 V9H  C17  C  CR16  0  -0.264  41.3640  17.4674  13.6062
 V9H  O1   O  O     0  -0.473  43.7985  19.1780   9.6160
 V9H  C11  C  CH2   0  -0.455  46.6555  16.2535  10.6678
 V9H  C9   C  CH1   0   0.087  47.3880  16.6191  13.0444
 V9H  O2   O  OH1   0  -0.672  48.5286  16.8773  13.8364
 V9H  C3   C  CR15  0  -0.518  42.6359  16.4993   7.5672
 V9H  N2   N  NR5   0  -0.328  41.3054  17.9017   8.6018
 V9H  C2   C  CR5   0   0.176  41.3321  16.4645   7.0551
 V9H  C1   C  C     0   0.507  40.8379  15.6269   5.9384
 V9H  O    O  O     0  -0.484  41.5703  14.8058   5.4017
 V9H  N    N  NH1   0  -0.637  39.5676  15.8417   5.5758
 V9H  C    C  CH3   0  -0.513  38.9350  15.1209   4.4982
 V9H  C12  C  CH1   0  -0.139  40.7412  18.8403   9.5771
 V9H  C14  C  CR6   0   0.088  40.9830  18.3386  10.9830
 V9H  C19  C  CR16  0  -0.285  40.8029  16.9983  11.3126
 V9H  C18  C  CR16  0  -0.238  40.9952  16.5649  12.6172
 V9H  C16  C  CR16  0  -0.239  41.5390  18.8065  13.2838
 V9H  H1   H  HNH1  0   0.407  44.1978  16.0677   9.8292
 V9H  H2   H  HCH1  0   0.243  46.0009  18.2853  10.5207
 V9H  H3   H  HCH2  0   0.247  44.3828  18.2123  12.3906
 V9H  H4   H  HCH2  0   0.220  44.6453  16.4851  12.5696
 V9H  H5   H  HCH2  0   0.221  46.7580  18.6701  12.9532
 V9H  H6   H  HCH2  0   0.237  45.9815  17.7487  14.2357
 V9H  H7   H  HCH2  0   0.241  48.5803  15.7319  11.4819
 V9H  H8   H  HCH2  0   0.222  48.3190  17.4632  11.3060
 V9H  H10  H  HCH3  0   0.248  39.0836  19.4847   8.3280
 V9H  H11  H  HCH3  0   0.239  38.6730  18.1717   9.4414
 V9H  H12  H  HCR6  0   0.252  41.5036  20.2803  11.7276
 V9H  H13  H  HCR6  0   0.256  41.5183  17.1276  14.6222
 V9H  H14  H  HCH2  0   0.226  46.2250  15.2725  10.8993
 V9H  H15  H  HCH2  0   0.249  46.9949  16.2152   9.6306
 V9H  H16  H  HCH1  0   0.185  46.9359  15.6533  13.3239
 V9H  H17  H  HOH1  0   0.443  48.2477  16.9419  14.7547
 V9H  H18  H  HCR5  0   0.282  43.4968  15.9402   7.2400
 V9H  H19  H  HNH1  0   0.407  39.0388  16.5435   6.0678
 V9H  H20  H  HCH3  0   0.251  37.9146  15.4792   4.3982
 V9H  H21  H  HCH3  0   0.238  39.4488  15.2808   3.5496
 V9H  H22  H  HCH3  0   0.238  38.9035  14.0482   4.6927
 V9H  H23  H  HCH1  0   0.287  41.2682  19.7864   9.4474
 V9H  H24  H  HCR6  0   0.256  40.5132  16.2821  10.5522
 V9H  H25  H  HCR6  0   0.256  40.8564  15.5195  12.8606
 V9H  H26  H  HCR6  0   0.256  41.8323  19.5158  14.0470
 V9H  H9   H  HCH3  0   0.252  38.9098  19.8111  10.0507

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
 V9H  C    N    single    1.443  0.020  1.443
 V9H  N    C1   single    1.338  0.020  1.338
 V9H  O    C1   double    1.224  0.020  1.224
 V9H  C1   C2   single    1.481  0.020  1.481
 V9H  C2   C3   aromatic  1.401  0.020  1.401
 V9H  C2   N3   aromatic  1.323  0.020  1.323
 V9H  C3   C4   aromatic  1.375  0.020  1.375
 V9H  N3   N2   aromatic  1.316  0.020  1.316
 V9H  C4   N2   aromatic  1.357  0.020  1.357
 V9H  C4   C5   single    1.486  0.020  1.486
 V9H  N2   C12  single    1.466  0.020  1.466
 V9H  C13  C12  single    1.521  0.020  1.521
 V9H  C12  C14  single    1.512  0.020  1.512
 V9H  C5   N1   single    1.338  0.020  1.338
 V9H  C5   O1   double    1.222  0.020  1.222
 V9H  N1   C6   single    1.451  0.020  1.451
 V9H  C11  C6   single    1.525  0.020  1.525
 V9H  C11  C10  single    1.525  0.020  1.525
 V9H  C6   C7   single    1.528  0.020  1.528
 V9H  C14  C19  aromatic  1.392  0.020  1.392
 V9H  C14  C15  aromatic  1.390  0.020  1.390
 V9H  C19  C18  aromatic  1.388  0.020  1.388
 V9H  C10  C9   single    1.521  0.020  1.521
 V9H  C7   C8   single    1.525  0.020  1.525
 V9H  C18  C17  aromatic  1.389  0.020  1.389
 V9H  C15  C16  aromatic  1.388  0.020  1.388
 V9H  C9   C8   single    1.525  0.020  1.525
 V9H  C9   O2   single    1.412  0.020  1.412
 V9H  C17  C16  aromatic  1.388  0.020  1.388
 V9H  N1   H1   single    0.860  0.020  1.020
 V9H  C6   H2   single    0.970  0.020  1.090
 V9H  C7   H3   single    0.970  0.020  1.090
 V9H  C7   H4   single    0.970  0.020  1.090
 V9H  C8   H5   single    0.970  0.020  1.090
 V9H  C8   H6   single    0.970  0.020  1.090
 V9H  C10  H7   single    0.970  0.020  1.090
 V9H  C10  H8   single    0.970  0.020  1.090
 V9H  C13  H9   single    0.970  0.020  1.090
 V9H  C13  H10  single    0.970  0.020  1.090
 V9H  C13  H11  single    0.970  0.020  1.090
 V9H  C15  H12  single    0.930  0.020  1.080
 V9H  C17  H13  single    0.930  0.020  1.080
 V9H  C11  H14  single    0.970  0.020  1.090
 V9H  C11  H15  single    0.970  0.020  1.090
 V9H  C9   H16  single    0.970  0.020  1.090
 V9H  O2   H17  single    0.850  0.020  0.980
 V9H  C3   H18  single    0.930  0.020  1.080
 V9H  N    H19  single    0.860  0.020  1.020
 V9H  C    H20  single    0.970  0.020  1.090
 V9H  C    H21  single    0.970  0.020  1.090
 V9H  C    H22  single    0.970  0.020  1.090
 V9H  C12  H23  single    0.970  0.020  1.090
 V9H  C19  H24  single    0.930  0.020  1.080
 V9H  C18  H25  single    0.930  0.020  1.080
 V9H  C16  H26  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
 V9H  H1   N1   C6   117.50  3.000
 V9H  H1   N1   C5   118.25  3.000
 V9H  C6   N1   C5   123.46  3.000
 V9H  C2   N3   N2   106.28  3.000
 V9H  N2   C4   C3   106.80  3.000
 V9H  N2   C4   C5   123.23  3.000
 V9H  C3   C4   C5   129.89  3.000
 V9H  O1   C5   C4   121.41  3.000
 V9H  O1   C5   N1   124.68  3.000
 V9H  C4   C5   N1   113.89  3.000
 V9H  H2   C6   C11  108.51  3.000
 V9H  H2   C6   C7   108.64  3.000
 V9H  C11  C6   C7   110.60  3.000
 V9H  H2   C6   N1   107.53  3.000
 V9H  C7   C6   N1   111.63  3.000
 V9H  C11  C6   N1   109.82  3.000
 V9H  H4   C7   H3   106.83  3.000
 V9H  H4   C7   C8   109.91  3.000
 V9H  H3   C7   C8   110.19  3.000
 V9H  H4   C7   C6   108.92  3.000
 V9H  H3   C7   C6   110.15  3.000
 V9H  C8   C7   C6   110.76  3.000
 V9H  H6   C8   H5   106.97  3.000
 V9H  H6   C8   C9   110.18  3.000
 V9H  H5   C8   C9   108.98  3.000
 V9H  H6   C8   C7   109.74  3.000
 V9H  H5   C8   C7   109.74  3.000
 V9H  C9   C8   C7   111.14  3.000
 V9H  H8   C10  H7   107.09  3.000
 V9H  H8   C10  C9   109.09  3.000
 V9H  H7   C10  C9   110.15  3.000
 V9H  H8   C10  C11  109.47  3.000
 V9H  H7   C10  C11  109.67  3.000
 V9H  C9   C10  C11  111.27  3.000
 V9H  H11  C13  H10  108.71  3.000
 V9H  H11  C13  H9   108.26  3.000
 V9H  H10  C13  H9   107.99  3.000
 V9H  H11  C13  C12  112.08  3.000
 V9H  H10  C13  C12  111.70  3.000
 V9H  H9   C13  C12  107.96  3.000
 V9H  H12  C15  C16  119.78  3.000
 V9H  H12  C15  C14  119.63  3.000
 V9H  C16  C15  C14  120.58  3.000
 V9H  H13  C17  C16  120.19  3.000
 V9H  H13  C17  C18  120.15  3.000
 V9H  C16  C17  C18  119.66  3.000
 V9H  H15  C11  H14  106.94  3.000
 V9H  H15  C11  C10  110.06  3.000
 V9H  H14  C11  C10  109.52  3.000
 V9H  H15  C11  C6   109.95  3.000
 V9H  H14  C11  C6   109.21  3.000
 V9H  C10  C11  C6   111.07  3.000
 V9H  H16  C9   O2   110.43  3.000
 V9H  H16  C9   C10  107.90  3.000
 V9H  O2   C9   C10  107.96  3.000
 V9H  H16  C9   C8   107.83  3.000
 V9H  O2   C9   C8   112.39  3.000
 V9H  C10  C9   C8   110.24  3.000
 V9H  H17  O2   C9   108.16  3.000
 V9H  H18  C3   C2   128.29  3.000
 V9H  H18  C3   C4   127.47  3.000
 V9H  C2   C3   C4   104.22  3.000
 V9H  C12  N2   C4   126.61  3.000
 V9H  C12  N2   N3   121.34  3.000
 V9H  C4   N2   N3   111.79  3.000
 V9H  C1   C2   C3   126.88  3.000
 V9H  C3   C2   N3   110.90  3.000
 V9H  C1   C2   N3   122.22  3.000
 V9H  N    C1   O    123.83  3.000
 V9H  O    C1   C2   120.69  3.000
 V9H  N    C1   C2   115.49  3.000
 V9H  H19  N    C    118.87  3.000
 V9H  H19  N    C1   118.55  3.000
 V9H  C    N    C1   122.58  3.000
 V9H  H22  C    H21  108.24  3.000
 V9H  H22  C    H20  108.28  3.000
 V9H  H21  C    H20  108.31  3.000
 V9H  H22  C    N    111.77  3.000
 V9H  H21  C    N    111.71  3.000
 V9H  H20  C    N    108.42  3.000
 V9H  H23  C12  C14  108.73  3.000
 V9H  H23  C12  N2   106.87  3.000
 V9H  C14  C12  N2   110.15  3.000
 V9H  H23  C12  C13  108.27  3.000
 V9H  C14  C12  C13  111.29  3.000
 V9H  N2   C12  C13  111.38  3.000
 V9H  C19  C14  C12  121.26  3.000
 V9H  C19  C14  C15  119.16  3.000
 V9H  C12  C14  C15  119.56  3.000
 V9H  H24  C19  C18  119.34  3.000
 V9H  H24  C19  C14  120.31  3.000
 V9H  C18  C19  C14  120.35  3.000
 V9H  H25  C18  C19  119.68  3.000
 V9H  H25  C18  C17  120.11  3.000
 V9H  C19  C18  C17  120.22  3.000
 V9H  H26  C16  C17  120.16  3.000
 V9H  H26  C16  C15  119.80  3.000
 V9H  C17  C16  C15  120.04  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
 V9H  CONST_01  C4   C3   C2   N3      0.00   0.0  0
 V9H  CONST_02  C3   C4   N2   N3      0.00   0.0  0
 V9H  CONST_03  C2   N3   N2   C4      0.00   0.0  0
 V9H  CONST_04  C18  C19  C14  C15     0.00   0.0  0
 V9H  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 V9H  CONST_06  C14  C19  C18  C17     0.00   0.0  0
 V9H  CONST_07  C14  C15  C16  C17     0.00   0.0  0
 V9H  CONST_08  N2   N3   C2   C3      0.00   0.0  0
 V9H  CONST_09  C2   C3   C4   N2      0.00   0.0  0
 V9H  CONST_10  C16  C15  C14  C19     0.00   0.0  0
 V9H  CONST_11  C16  C17  C18  C19     0.00   0.0  0
 V9H  CONST_12  C5   C4   N2   N3    180.00   0.0  0
 V9H  CONST_13  C1   C2   C3   C4    180.00   0.0  0
 V9H  CONST_14  C2   C3   C4   C5    180.00   0.0  0
 V9H  CONST_15  C12  N2   C4   C3    180.00   0.0  0
 V9H  CONST_16  C1   C2   N3   N2    180.00   0.0  0
 V9H  CONST_17  C12  N2   N3   C2    180.00   0.0  0
 V9H  CONST_18  C18  C19  C14  C12   180.00   0.0  0
 V9H  CONST_19  C16  C15  C14  C12   180.00   0.0  0
 V9H  CONST_20  H18  C3   C2   N3    180.00   0.0  0
 V9H  CONST_21  H24  C19  C14  C15   180.00   0.0  0
 V9H  CONST_22  H13  C17  C16  C15   180.00   0.0  0
 V9H  CONST_23  H12  C15  C16  C17   180.00   0.0  0
 V9H  CONST_24  H25  C18  C19  C14   180.00   0.0  0
 V9H  CONST_25  H26  C16  C15  C14   180.00   0.0  0
 V9H  CONST_26  C6   N1   C5   C4    180.00   0.0  0
 V9H  CONST_27  O1   C5   N1   C6      0.00   0.0  0
 V9H  CONST_28  C    N    C1   C2    180.00   0.0  0
 V9H  CONST_29  H1   N1   C5   C4      0.00   0.0  0
 V9H  CONST_30  H19  N    C1   C2      0.00   0.0  0
 V9H  CONST_31  C    N    C1   O       0.00   0.0  0
 V9H  Var_01    C9   C10  C11  C6     56.49  30.0  1
 V9H  Var_02    C9   C8   C7   C6    -56.94  30.0  1
 V9H  Var_03    C3   C4   C5   N1    -45.50  30.0  2
 V9H  Var_04    N    C1   C2   N3      4.09  30.0  3
 V9H  Var_05    H20  C    N    C1   -179.64  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
 V9H  chir_01  C6   N1  C11  C7   positiv
 V9H  chir_02  C9   O2  C10  C8   positiv
 V9H  chir_03  C12  N2  C13  C14  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
 V9H  plan-1  N3   0.020
 V9H  plan-1  C4   0.020
 V9H  plan-1  C5   0.020
 V9H  plan-1  C3   0.020
 V9H  plan-1  N2   0.020
 V9H  plan-1  C2   0.020
 V9H  plan-1  C1   0.020
 V9H  plan-1  C12  0.020
 V9H  plan-1  H18  0.020
 V9H  plan-2  C15  0.020
 V9H  plan-2  C17  0.020
 V9H  plan-2  C12  0.020
 V9H  plan-2  C14  0.020
 V9H  plan-2  C19  0.020
 V9H  plan-2  C18  0.020
 V9H  plan-2  C16  0.020
 V9H  plan-2  H12  0.020
 V9H  plan-2  H13  0.020
 V9H  plan-2  H24  0.020
 V9H  plan-2  H25  0.020
 V9H  plan-2  H26  0.020
 V9H  plan-3  C2   0.020
 V9H  plan-3  C1   0.020
 V9H  plan-3  O    0.020
 V9H  plan-3  N    0.020
 V9H  plan-3  C    0.020
 V9H  plan-3  H19  0.020
 V9H  plan-4  N1   0.020
 V9H  plan-4  C4   0.020
 V9H  plan-4  C5   0.020
 V9H  plan-4  C6   0.020
 V9H  plan-4  O1   0.020
 V9H  plan-4  H1   0.020

