# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:43:48 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl)phenoxy]ethyl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C1CCN(CCOc2ccc(c(O)c2)c3[nH]ncc3c4ccccc4)CC1
#
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
 GON  GON  1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl)phenoxy]ethyl]piperidine-4-carboxamide  ligand  56  30  .  2022-07-25  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_GON
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
 GON  C13  C  CR16  0  -0.259   2.0031   1.8865   1.0226
 GON  C15  C  CR5   0   0.390   4.2216   1.1209   0.2068
 GON  C20  C  CR6   0   0.045   4.7023  -1.4046   0.0792
 GON  C21  C  CR16  0  -0.323   3.5130  -1.9059   0.6133
 GON  C22  C  CR16  0  -0.238   3.1971  -3.2513   0.4981
 GON  C24  C  CR16  0  -0.238   5.2561  -3.6390  -0.6701
 GON  C26  C  CR6   0   0.345   2.1229   0.7691  -1.0949
 GON  C28  C  CR16  0  -0.443   0.7491   0.8977  -1.2261
 GON  C02  C  C     0   0.533  -7.2539  -1.0475   0.5300
 GON  C04  C  CH1   0  -0.404  -5.9971  -1.3944  -0.2624
 GON  C05  C  CH2   0  -0.427  -4.7393  -1.3751   0.5996
 GON  C06  C  CH2   0  -0.293  -4.2775   0.0367   0.9331
 GON  C08  C  CH2   0  -0.294  -3.5823   2.1597   0.0224
 GON  C09  C  CH2   0  -0.215  -2.1562   2.1849   0.5265
 GON  C11  C  CR6   0   0.406  -0.0024   1.5223  -0.2321
 GON  C12  C  CR16  0  -0.402   0.6303   2.0285   0.9042
 GON  C14  C  CR6   0  -0.135   2.7730   1.2596   0.0493
 GON  C18  C  CR15  0  -0.103   6.3467   0.5552   0.3849
 GON  C19  C  CR5   0  -0.187   5.0576   0.0108   0.2013
 GON  C23  C  CR16  0  -0.270   4.0667  -4.1247  -0.1426
 GON  C25  C  CR16  0  -0.318   5.5687  -2.2918  -0.5633
 GON  C29  C  CH2   0  -0.281  -5.3145   0.9079  -1.0392
 GON  C30  C  CH2   0  -0.446  -5.7732  -0.4747  -1.4690
 GON  N01  N  NH2   0  -0.805  -8.3865  -1.0003  -0.1927
 GON  N07  N  NT    0  -0.413  -4.0859   0.8335  -0.2684
 GON  N16  N  NR15  0  -0.481   5.0290   2.1842   0.3884
 GON  N17  N  N     0  -0.250   6.3103   1.8666   0.5021
 GON  O10  O  O2    0  -0.464  -1.3230   1.5923  -0.4562
 GON  O27  O  OH1   0  -0.614   2.7801   0.1683  -2.1013
 GON  H1   H  HCR6  0   0.268   2.4902   2.2633   1.9131
 GON  H2   H  HCR6  0   0.253   2.8339  -1.2447   1.1362
 GON  H3   H  HCR6  0   0.257   2.2713  -3.6198   0.9205
 GON  H4   H  HCR6  0   0.257   5.9417  -4.3088  -1.1729
 GON  H5   H  HCR6  0   0.270   0.2560   0.5140  -2.1110
 GON  H6   H  HCH1  0   0.283  -6.1520  -2.4132  -0.6367
 GON  H7   H  HCH2  0   0.239  -4.8844  -1.9367   1.5229
 GON  H8   H  HCH2  0   0.231  -3.9444  -1.8805   0.0448
 GON  H9   H  HCH2  0   0.198  -4.9974   0.5170   1.6154
 GON  H10  H  HCH2  0   0.236  -3.3321  -0.0315   1.4748
 GON  H11  H  HCH2  0   0.205  -4.1980   2.6876   0.7710
 GON  H12  H  HCH2  0   0.243  -3.6358   2.7566  -0.8920
 GON  H13  H  HCH2  0   0.242  -1.8692   3.2275   0.7013
 GON  H14  H  HCH2  0   0.230  -2.0551   1.6568   1.4803
 GON  H15  H  HCR6  0   0.280   0.0833   2.5197   1.6958
 GON  H16  H  HCR5  0   0.263   7.2844   0.0242   0.4590
 GON  H17  H  HCR6  0   0.256   3.8203  -5.1750  -0.2281
 GON  H18  H  HCR6  0   0.251   6.4914  -1.9237  -0.9952
 GON  H19  H  HCH2  0   0.241  -5.1330   1.5190  -1.9265
 GON  H20  H  HCH2  0   0.190  -6.1202   1.4111  -0.4738
 GON  H21  H  HCH2  0   0.239  -5.0015  -0.9221  -2.1001
 GON  H22  H  HCH2  0   0.237  -6.6654  -0.3887  -2.0911
 GON  H23  H  HNH2  0   0.404  -8.4132  -1.2503  -1.1656
 GON  H24  H  HNH2  0   0.397  -9.2696  -0.8405   0.2636
 GON  H26  H  HNR5  0   0.421   4.7471   3.1524   0.4117
 GON  H27  H  HOH1  0   0.479   3.7329   0.1706  -1.9443
 GON  O03  O  O     0  -0.486  -7.2485  -0.8500   1.7368

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
 GON  C18  N17  aromatic  1.317  0.020  1.317
 GON  C18  C19  aromatic  1.411  0.020  1.411
 GON  C22  C21  aromatic  1.387  0.020  1.387
 GON  C22  C23  aromatic  1.389  0.020  1.389
 GON  C21  C20  aromatic  1.397  0.020  1.397
 GON  N17  N16  aromatic  1.325  0.020  1.325
 GON  C23  C24  aromatic  1.389  0.020  1.389
 GON  C19  C20  single    1.464  0.020  1.464
 GON  C19  C15  aromatic  1.390  0.020  1.390
 GON  C20  C25  aromatic  1.397  0.020  1.397
 GON  N16  C15  aromatic  1.347  0.020  1.347
 GON  C24  C25  aromatic  1.387  0.020  1.387
 GON  C15  C14  single    1.464  0.020  1.464
 GON  C14  C13  aromatic  1.390  0.020  1.390
 GON  C14  C26  aromatic  1.404  0.020  1.404
 GON  C13  C12  aromatic  1.385  0.020  1.385
 GON  O27  C26  single    1.344  0.020  1.344
 GON  C26  C28  aromatic  1.386  0.020  1.386
 GON  C12  C11  aromatic  1.396  0.020  1.396
 GON  C28  C11  aromatic  1.394  0.020  1.394
 GON  C11  O10  single    1.341  0.020  1.341
 GON  O10  C09  single    1.418  0.020  1.418
 GON  C09  C08  single    1.513  0.020  1.513
 GON  C08  N07  single    1.448  0.020  1.448
 GON  N07  C29  single    1.452  0.020  1.452
 GON  N07  C06  single    1.454  0.020  1.454
 GON  C29  C30  single    1.519  0.020  1.519
 GON  C06  C05  single    1.522  0.020  1.522
 GON  C30  C04  single    1.534  0.020  1.534
 GON  C05  C04  single    1.525  0.020  1.525
 GON  O03  C02  double    1.223  0.020  1.223
 GON  C04  C02  single    1.526  0.020  1.526
 GON  C02  N01  single    1.344  0.020  1.344
 GON  C13  H1   single    0.930  0.020  1.080
 GON  C21  H2   single    0.930  0.020  1.080
 GON  C22  H3   single    0.930  0.020  1.080
 GON  C24  H4   single    0.930  0.020  1.080
 GON  C28  H5   single    0.930  0.020  1.080
 GON  C04  H6   single    0.970  0.020  1.090
 GON  C05  H7   single    0.970  0.020  1.090
 GON  C05  H8   single    0.970  0.020  1.090
 GON  C06  H9   single    0.970  0.020  1.090
 GON  C06  H10  single    0.970  0.020  1.090
 GON  C08  H11  single    0.970  0.020  1.090
 GON  C08  H12  single    0.970  0.020  1.090
 GON  C09  H13  single    0.970  0.020  1.090
 GON  C09  H14  single    0.970  0.020  1.090
 GON  C12  H15  single    0.930  0.020  1.080
 GON  C18  H16  single    0.930  0.020  1.080
 GON  C23  H17  single    0.930  0.020  1.080
 GON  C25  H18  single    0.930  0.020  1.080
 GON  C29  H19  single    0.970  0.020  1.090
 GON  C29  H20  single    0.970  0.020  1.090
 GON  C30  H21  single    0.970  0.020  1.090
 GON  C30  H22  single    0.970  0.020  1.090
 GON  N01  H23  single    0.860  0.020  1.020
 GON  N01  H24  single    0.860  0.020  1.020
 GON  N16  H26  single    0.860  0.020  1.020
 GON  O27  H27  single    0.850  0.020  0.980

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
 GON  H1   C13  C14  118.91  3.000
 GON  H1   C13  C12  118.72  3.000
 GON  C14  C13  C12  122.35  3.000
 GON  N16  C15  C19  105.69  3.000
 GON  N16  C15  C14  122.19  3.000
 GON  C19  C15  C14  132.11  3.000
 GON  C25  C20  C19  120.12  3.000
 GON  C25  C20  C21  118.43  3.000
 GON  C19  C20  C21  121.44  3.000
 GON  H2   C21  C22  119.33  3.000
 GON  H2   C21  C20  119.98  3.000
 GON  C22  C21  C20  120.69  3.000
 GON  H3   C22  C23  120.09  3.000
 GON  H3   C22  C21  119.52  3.000
 GON  C23  C22  C21  120.38  3.000
 GON  H4   C24  C25  119.61  3.000
 GON  H4   C24  C23  120.16  3.000
 GON  C25  C24  C23  120.23  3.000
 GON  O27  C26  C14  122.68  3.000
 GON  O27  C26  C28  117.09  3.000
 GON  C14  C26  C28  120.23  3.000
 GON  H5   C28  C11  119.72  3.000
 GON  H5   C28  C26  119.71  3.000
 GON  C11  C28  C26  120.57  3.000
 GON  O03  C02  N01  121.91  3.000
 GON  N01  C02  C04  115.01  3.000
 GON  O03  C02  C04  123.07  3.000
 GON  H6   C04  C30  108.02  3.000
 GON  H6   C04  C05  108.74  3.000
 GON  C30  C04  C05  108.46  3.000
 GON  H6   C04  C02  105.80  3.000
 GON  C05  C04  C02  112.52  3.000
 GON  C30  C04  C02  113.11  3.000
 GON  H8   C05  H7   106.76  3.000
 GON  H8   C05  C06  108.63  3.000
 GON  H7   C05  C06  109.42  3.000
 GON  H8   C05  C04  107.88  3.000
 GON  H7   C05  C04  111.24  3.000
 GON  C06  C05  C04  112.69  3.000
 GON  H10  C06  H9   106.61  3.000
 GON  H10  C06  N07  109.27  3.000
 GON  H9   C06  N07  111.02  3.000
 GON  H10  C06  C05  108.26  3.000
 GON  H9   C06  C05  109.98  3.000
 GON  N07  C06  C05  111.53  3.000
 GON  H12  C08  H11  106.19  3.000
 GON  H12  C08  N07  108.36  3.000
 GON  H11  C08  N07  112.35  3.000
 GON  H12  C08  C09  108.41  3.000
 GON  H11  C08  C09  106.97  3.000
 GON  N07  C08  C09  114.21  3.000
 GON  H14  C09  H13  107.22  3.000
 GON  H14  C09  O10  110.35  3.000
 GON  H13  C09  O10  110.75  3.000
 GON  H14  C09  C08  111.67  3.000
 GON  H13  C09  C08  108.42  3.000
 GON  O10  C09  C08  108.42  3.000
 GON  O10  C11  C12  124.30  3.000
 GON  O10  C11  C28  115.79  3.000
 GON  C12  C11  C28  119.91  3.000
 GON  H15  C12  C11  122.13  3.000
 GON  H15  C12  C13  119.06  3.000
 GON  C11  C12  C13  118.80  3.000
 GON  C26  C14  C15  120.84  3.000
 GON  C26  C14  C13  118.13  3.000
 GON  C15  C14  C13  121.03  3.000
 GON  H16  C18  N17  120.49  3.000
 GON  H16  C18  C19  127.75  3.000
 GON  N17  C18  C19  111.74  3.000
 GON  C18  C19  C20  127.25  3.000
 GON  C20  C19  C15  128.79  3.000
 GON  C18  C19  C15  103.93  3.000
 GON  H17  C23  C24  120.29  3.000
 GON  H17  C23  C22  120.28  3.000
 GON  C24  C23  C22  119.43  3.000
 GON  H18  C25  C24  119.42  3.000
 GON  H18  C25  C20  119.74  3.000
 GON  C24  C25  C20  120.83  3.000
 GON  H20  C29  H19  106.37  3.000
 GON  H20  C29  N07  111.62  3.000
 GON  H19  C29  N07  108.61  3.000
 GON  H20  C29  C30  109.82  3.000
 GON  H19  C29  C30  109.24  3.000
 GON  N07  C29  C30  111.05  3.000
 GON  H22  C30  H21  106.29  3.000
 GON  H22  C30  C29  109.67  3.000
 GON  H21  C30  C29  108.84  3.000
 GON  H22  C30  C04  112.11  3.000
 GON  H21  C30  C04  108.17  3.000
 GON  C29  C30  C04  111.56  3.000
 GON  H24  N01  H23  117.06  3.000
 GON  H24  N01  C02  120.06  3.000
 GON  H23  N01  C02  122.29  3.000
 GON  C29  N07  C08  110.73  3.000
 GON  C29  N07  C06  110.80  3.000
 GON  C08  N07  C06  112.44  3.000
 GON  H26  N16  N17  119.89  3.000
 GON  H26  N16  C15  126.38  3.000
 GON  N17  N16  C15  113.69  3.000
 GON  N16  N17  C18  104.94  3.000
 GON  C11  O10  C09  118.98  3.000
 GON  H27  O27  C26  111.08  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
 GON  CONST_03  C28  C26  C14  C13    0.00   0.0  0
 GON  CONST_04  C28  C11  C12  C13    0.00   0.0  0
 GON  CONST_05  N17  C18  C19  C15    0.00   0.0  0
 GON  CONST_08  C18  N17  N16  C15    0.00   0.0  0
 GON  CONST_09  C12  C13  C14  C15  180.00   0.0  0
 GON  CONST_10  C28  C26  C14  C15  180.00   0.0  0
 GON  CONST_11  C23  C22  C21  C20    0.00   0.0  0
 GON  CONST_12  N17  C18  C19  C20  180.00   0.0  0
 GON  CONST_13  N16  C15  C19  C20  180.00   0.0  0
 GON  CONST_14  C14  C15  C19  C20    0.00   0.0  0
 GON  CONST_15  C23  C24  C25  C20    0.00   0.0  0
 GON  CONST_16  C24  C23  C22  C21    0.00   0.0  0
 GON  CONST_18  C24  C25  C20  C21    0.00   0.0  0
 GON  CONST_19  C19  C20  C21  C22  180.00   0.0  0
 GON  CONST_20  C25  C20  C21  C22    0.00   0.0  0
 GON  CONST_21  C25  C24  C23  C22    0.00   0.0  0
 GON  CONST_22  C19  C20  C25  C24  180.00   0.0  0
 GON  CONST_25  C12  C13  C14  C26    0.00   0.0  0
 GON  CONST_26  C12  C11  C28  C26    0.00   0.0  0
 GON  CONST_27  C14  C13  C12  C11    0.00   0.0  0
 GON  CONST_28  C14  C26  C28  C11    0.00   0.0  0
 GON  CONST_29  C18  C19  C15  C14  180.00   0.0  0
 GON  CONST_30  N17  N16  C15  C14  180.00   0.0  0
 GON  CONST_32  N16  C15  C19  C18    0.00   0.0  0
 GON  CONST_33  N16  N17  C18  C19    0.00   0.0  0
 GON  CONST_34  N17  N16  C15  C19    0.00   0.0  0
 GON  CONST_35  O27  C26  C14  C13  180.00   0.0  0
 GON  CONST_36  O10  C11  C12  C13  180.00   0.0  0
 GON  CONST_37  O27  C26  C14  C15    0.00   0.0  0
 GON  CONST_38  O10  C11  C28  C26  180.00   0.0  0
 GON  CONST_39  O27  C26  C28  C11  180.00   0.0  0
 GON  CONST_40  H16  C18  C19  C15  180.00   0.0  0
 GON  CONST_41  H1   C13  C14  C15    0.00   0.0  0
 GON  CONST_42  H3   C22  C21  C20  180.00   0.0  0
 GON  CONST_43  H4   C24  C25  C20  180.00   0.0  0
 GON  CONST_44  H17  C23  C22  C21  180.00   0.0  0
 GON  CONST_45  H18  C25  C20  C21  180.00   0.0  0
 GON  CONST_46  H15  C12  C11  C28  180.00   0.0  0
 GON  CONST_47  H5   C28  C11  C12  180.00   0.0  0
 GON  CONST_48  H26  N16  C15  C14    0.00   0.0  0
 GON  CONST_49  H2   C21  C20  C19    0.00   0.0  0
 GON  CONST_50  H23  N01  C02  C04    0.00   0.0  0
 GON  CONST_51  H24  N01  C02  C04  180.00   0.0  0
 GON  Var_01    N07  C29  C30  C04   58.26  30.0  1
 GON  Var_02    N07  C06  C05  C04  -54.94  30.0  1
 GON  Var_03    C29  N07  C06  C05   58.39  30.0  1
 GON  Var_04    C30  C29  N07  C06  -60.30  30.0  1
 GON  Var_05    C09  C08  N07  C06   69.27  30.0  2
 GON  Var_06    C12  C11  O10  C09   -1.67  30.0  2
 GON  Var_07    O10  C09  C08  N07   58.89  30.0  2
 GON  Var_08    H13  C09  O10  C11   60.19  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
 GON  chir_01  C04  C30  C05  C02  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
 GON  plan-1  C15  0.020
 GON  plan-1  C20  0.020
 GON  plan-1  C14  0.020
 GON  plan-1  C18  0.020
 GON  plan-1  C19  0.020
 GON  plan-1  N16  0.020
 GON  plan-1  N17  0.020
 GON  plan-1  H16  0.020
 GON  plan-1  H26  0.020
 GON  plan-2  C20  0.020
 GON  plan-2  C21  0.020
 GON  plan-2  C22  0.020
 GON  plan-2  C24  0.020
 GON  plan-2  C19  0.020
 GON  plan-2  C23  0.020
 GON  plan-2  C25  0.020
 GON  plan-2  H2   0.020
 GON  plan-2  H3   0.020
 GON  plan-2  H4   0.020
 GON  plan-2  H17  0.020
 GON  plan-2  H18  0.020
 GON  plan-3  C13  0.020
 GON  plan-3  C15  0.020
 GON  plan-3  C26  0.020
 GON  plan-3  C28  0.020
 GON  plan-3  C11  0.020
 GON  plan-3  C12  0.020
 GON  plan-3  C14  0.020
 GON  plan-3  O10  0.020
 GON  plan-3  O27  0.020
 GON  plan-3  H1   0.020
 GON  plan-3  H5   0.020
 GON  plan-3  H15  0.020
 GON  plan-4  C02  0.020
 GON  plan-4  C04  0.020
 GON  plan-4  N01  0.020
 GON  plan-4  H23  0.020
 GON  plan-4  H24  0.020
 GON  plan-4  O03  0.020

