# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:27:13 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 7-methoxy-8-[1-(methylsulfonyl)-1H-pyrazol-4-yl]naphthalene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2ccc(cc2c1c3cnn(c3)[S](C)(=O)=O)C(N)=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
 UI3  UI3  7-methoxy-8-[1-(methylsulfonyl)-1H-pyrazol-4-yl]naphthalene-2-carboximidamide  ligand  40  24  .  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_UI3
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
 UI3  C1    C  CR16  0  -0.381  -1.7897   3.3869   0.2377
 UI3  C2    C  CR16  0  -0.303  -3.0047   2.7690   0.3253
 UI3  C3    C  CR66  0   0.076  -3.1139   1.3655   0.2630
 UI3  C4    C  CR66  0   0.172  -1.9339   0.5919   0.1057
 UI3  C5    C  CR6   0  -0.097  -0.6742   1.2422  -0.0051
 UI3  C6    C  CR6   0   0.351  -0.6113   2.6231   0.0709
 UI3  C9    C  CR16  0  -0.294  -4.3631   0.7139   0.3641
 UI3  C10   C  CR16  0  -0.307  -4.4539  -0.6478   0.3129
 UI3  C11   C  CR6   0   0.055  -3.2838  -1.4316   0.1722
 UI3  C12   C  CR16  0  -0.398  -2.0605  -0.8161   0.0809
 UI3  C16   C  C     0   0.341  -3.3495  -2.9205   0.1365
 UI3  N17   N  N     0  -0.653  -2.3323  -3.5909   0.5215
 UI3  N18   N  NH2   0  -0.824  -4.5447  -3.4369  -0.2737
 UI3  O19   O  O2    0  -0.459   0.6051   3.1813  -0.0335
 UI3  C20   C  CH3   0  -0.442   0.7286   4.5914  -0.0250
 UI3  C24   C  CR5   0  -0.170   0.5524   0.4666  -0.2278
 UI3  C25   C  CR15  0   0.067   1.6557   0.3777   0.5777
 UI3  N26   N  NR5   0  -0.476   2.5162  -0.4615  -0.0564
 UI3  N27   N  N     0  -0.251   2.0499  -0.9057  -1.2291
 UI3  C28   C  CR15  0  -0.037   0.8659  -0.3559  -1.3405
 UI3  S34   S  S     0   1.367   4.0888  -0.9071   0.4299
 UI3  O35   O  OS    0  -0.617   4.2431  -2.3083   0.1158
 UI3  O36   O  OS    0  -0.628   4.1978  -0.4348   1.7941
 UI3  C37   C  CH3   0  -0.787   5.1005   0.0641  -0.6460
 UI3  H1    H  HCR6  0   0.288  -1.7451   4.4655   0.2916
 UI3  H2    H  HCR6  0   0.266  -3.9003   3.3654   0.4476
 UI3  H9    H  HCR6  0   0.259  -5.2557   1.3138   0.4943
 UI3  H10   H  HCR6  0   0.258  -5.4225  -1.1196   0.4128
 UI3  H12   H  HCR6  0   0.254  -1.1791  -1.4361  -0.0067
 UI3  H17   H  H     0   0.324  -2.4874  -4.5896   0.4115
 UI3  H181  H  HNH2  0   0.392  -4.5858  -4.4282  -0.4496
 UI3  H182  H  HNH2  0   0.396  -5.1166  -2.8930  -0.8987
 UI3  H201  H  HCH3  0   0.263   1.7865   4.8029  -0.1567
 UI3  H202  H  HCH3  0   0.232   0.1739   5.0563  -0.8435
 UI3  H203  H  HCH3  0   0.232   0.3996   5.0276   0.9213
 UI3  H25   H  HCR5  0   0.315   1.8784   0.8246   1.5319
 UI3  H28   H  HCR5  0   0.277   0.2545  -0.5487  -2.2099
 UI3  H371  H  HCH3  0   0.309   4.9014   1.1173  -0.4656
 UI3  H372  H  HCH3  0   0.321   6.1376  -0.1704  -0.4103
 UI3  H373  H  HCH3  0   0.310   4.8811  -0.2021  -1.6770

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
 UI3  C1   C2    aromatic  1.366  0.020  1.366
 UI3  C1   C6    aromatic  1.414  0.020  1.414
 UI3  C1   H1    single    0.930  0.020  1.080
 UI3  C2   C3    aromatic  1.409  0.020  1.409
 UI3  C2   H2    single    0.930  0.020  1.080
 UI3  C3   C4    aromatic  1.420  0.020  1.420
 UI3  C3   C9    aromatic  1.412  0.020  1.412
 UI3  C4   C5    aromatic  1.422  0.020  1.422
 UI3  C4   C12   aromatic  1.414  0.020  1.414
 UI3  C5   C6    aromatic  1.384  0.020  1.384
 UI3  C5   C24   single    1.468  0.020  1.468
 UI3  C6   O19   single    1.342  0.020  1.342
 UI3  C9   C10   aromatic  1.366  0.020  1.366
 UI3  C9   H9    single    0.930  0.020  1.080
 UI3  C10  C11   aromatic  1.415  0.020  1.415
 UI3  C10  H10   single    0.930  0.020  1.080
 UI3  C11  C12   aromatic  1.372  0.020  1.372
 UI3  C11  C16   single    1.491  0.020  1.491
 UI3  C12  H12   single    0.930  0.020  1.080
 UI3  C16  N17   double    1.278  0.020  1.278
 UI3  C16  N18   single    1.365  0.020  1.365
 UI3  N17  H17   single    0.890  0.020  1.040
 UI3  N18  H181  single    0.890  0.020  1.040
 UI3  N18  H182  single    0.890  0.020  1.040
 UI3  O19  C20   single    1.416  0.020  1.416
 UI3  C20  H201  single    0.970  0.020  1.090
 UI3  C20  H202  single    0.970  0.020  1.090
 UI3  C20  H203  single    0.970  0.020  1.090
 UI3  C24  C25   aromatic  1.369  0.020  1.369
 UI3  C24  C28   aromatic  1.419  0.020  1.419
 UI3  C25  N26   aromatic  1.359  0.020  1.359
 UI3  C25  H25   single    0.930  0.020  1.080
 UI3  N26  N27   aromatic  1.338  0.020  1.338
 UI3  N26  S34   single    1.705  0.020  1.705
 UI3  N27  C28   aromatic  1.310  0.020  1.310
 UI3  C28  H28   single    0.930  0.020  1.080
 UI3  S34  O35   double    1.444  0.020  1.444
 UI3  S34  O36   double    1.448  0.020  1.448
 UI3  S34  C37   single    1.768  0.020  1.768
 UI3  C37  H371  single    0.970  0.020  1.090
 UI3  C37  H372  single    0.970  0.020  1.090
 UI3  C37  H373  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
 UI3  H1    C1   C6    120.70  3.000
 UI3  H1    C1   C2    119.00  3.000
 UI3  C6    C1   C2    120.30  3.000
 UI3  H2    C2   C3    119.30  3.000
 UI3  H2    C2   C1    119.59  3.000
 UI3  C3    C2   C1    121.11  3.000
 UI3  C9    C3   C4    119.45  3.000
 UI3  C9    C3   C2    121.66  3.000
 UI3  C4    C3   C2    118.89  3.000
 UI3  C12   C4   C5    122.23  3.000
 UI3  C12   C4   C3    118.04  3.000
 UI3  C5    C4   C3    119.72  3.000
 UI3  C24   C5   C6    119.82  3.000
 UI3  C24   C5   C4    120.69  3.000
 UI3  C6    C5   C4    119.48  3.000
 UI3  O19   C6   C5    116.85  3.000
 UI3  O19   C6   C1    122.66  3.000
 UI3  C5    C6   C1    120.49  3.000
 UI3  H9    C9   C10   120.13  3.000
 UI3  H9    C9   C3    118.80  3.000
 UI3  C10   C9   C3    121.07  3.000
 UI3  H10   C10  C11   120.52  3.000
 UI3  H10   C10  C9    119.39  3.000
 UI3  C11   C10  C9    120.06  3.000
 UI3  C16   C11  C12   119.05  3.000
 UI3  C16   C11  C10   121.26  3.000
 UI3  C12   C11  C10   119.68  3.000
 UI3  H12   C12  C11   118.35  3.000
 UI3  H12   C12  C4    119.97  3.000
 UI3  C11   C12  C4    121.68  3.000
 UI3  N18   C16  N17   126.09  3.000
 UI3  N18   C16  C11   115.07  3.000
 UI3  N17   C16  C11   118.80  3.000
 UI3  H17   N17  C16   111.18  3.000
 UI3  H182  N18  H181  113.57  3.000
 UI3  H182  N18  C16   118.66  3.000
 UI3  H181  N18  C16   117.41  3.000
 UI3  C20   O19  C6    119.52  3.000
 UI3  H203  C20  H202  109.03  3.000
 UI3  H203  C20  H201  108.68  3.000
 UI3  H202  C20  H201  108.70  3.000
 UI3  H203  C20  O19   112.13  3.000
 UI3  H202  C20  O19   112.03  3.000
 UI3  H201  C20  O19   106.14  3.000
 UI3  C28   C24  C25   104.22  3.000
 UI3  C28   C24  C5    127.57  3.000
 UI3  C25   C24  C5    128.20  3.000
 UI3  H25   C25  N26   122.60  3.000
 UI3  H25   C25  C24   131.37  3.000
 UI3  N26   C25  C24   106.02  3.000
 UI3  S34   N26  N27   118.99  3.000
 UI3  S34   N26  C25   127.75  3.000
 UI3  N27   N26  C25   113.16  3.000
 UI3  C28   N27  N26   104.49  3.000
 UI3  H28   C28  N27   120.33  3.000
 UI3  H28   C28  C24   127.56  3.000
 UI3  N27   C28  C24   112.10  3.000
 UI3  C37   S34  O36   110.57  3.000
 UI3  C37   S34  O35   109.85  3.000
 UI3  O36   S34  O35   120.89  3.000
 UI3  C37   S34  N26   102.16  3.000
 UI3  O36   S34  N26   104.65  3.000
 UI3  O35   S34  N26   106.86  3.000
 UI3  H373  C37  H372  110.17  3.000
 UI3  H373  C37  H371  110.96  3.000
 UI3  H372  C37  H371  110.31  3.000
 UI3  H373  C37  S34   109.10  3.000
 UI3  H372  C37  S34   107.16  3.000
 UI3  H371  C37  S34   109.06  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
 UI3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 UI3  CONST_02  C9    C3   C2   C1    180.00   0.0  0
 UI3  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 UI3  CONST_04  C24   C5   C6   C1    180.00   0.0  0
 UI3  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 UI3  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 UI3  CONST_07  C12   C4   C3   C2    180.00   0.0  0
 UI3  CONST_08  C10   C9   C3   C2    180.00   0.0  0
 UI3  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 UI3  CONST_10  C6    C5   C4   C3      0.00   0.0  0
 UI3  CONST_11  C24   C5   C4   C3    180.00   0.0  0
 UI3  CONST_12  C11   C12  C4   C3      0.00   0.0  0
 UI3  CONST_13  C11   C10  C9   C3      0.00   0.0  0
 UI3  CONST_14  C10   C9   C3   C4      0.00   0.0  0
 UI3  CONST_17  C10   C11  C12  C4      0.00   0.0  0
 UI3  CONST_18  C9    C3   C4   C5    180.00   0.0  0
 UI3  CONST_19  C11   C12  C4   C5    180.00   0.0  0
 UI3  CONST_20  N26   C25  C24  C5    180.00   0.0  0
 UI3  CONST_21  N27   C28  C24  C5    180.00   0.0  0
 UI3  CONST_22  C12   C4   C5   C6    180.00   0.0  0
 UI3  CONST_25  C12   C4   C3   C9      0.00   0.0  0
 UI3  CONST_26  C12   C11  C10  C9      0.00   0.0  0
 UI3  CONST_27  C24   C5   C4   C12     0.00   0.0  0
 UI3  CONST_28  N27   N26  C25  C24     0.00   0.0  0
 UI3  CONST_29  N26   N27  C28  C24     0.00   0.0  0
 UI3  CONST_30  N27   C28  C24  C25     0.00   0.0  0
 UI3  CONST_31  C28   N27  N26  C25     0.00   0.0  0
 UI3  CONST_32  C28   C24  C25  N26     0.00   0.0  0
 UI3  CONST_33  O19   C6   C1   C2    180.00   0.0  0
 UI3  CONST_34  O19   C6   C5   C4    180.00   0.0  0
 UI3  CONST_35  C16   C11  C12  C4    180.00   0.0  0
 UI3  CONST_36  C16   C11  C10  C9    180.00   0.0  0
 UI3  CONST_37  C24   C5   C6   O19     0.00   0.0  0
 UI3  CONST_38  S34   N26  C25  C24   180.00   0.0  0
 UI3  CONST_39  S34   N26  N27  C28   180.00   0.0  0
 UI3  CONST_40  H9    C9   C3   C2      0.00   0.0  0
 UI3  CONST_41  H1    C1   C2   C3    180.00   0.0  0
 UI3  CONST_42  H12   C12  C4   C3    180.00   0.0  0
 UI3  CONST_43  H10   C10  C9   C3    180.00   0.0  0
 UI3  CONST_44  H2    C2   C3   C4    180.00   0.0  0
 UI3  CONST_45  H25   C25  C24  C5      0.00   0.0  0
 UI3  CONST_46  H28   C28  C24  C5      0.00   0.0  0
 UI3  CONST_47  H17   N17  C16  C11   180.00   0.0  0
 UI3  CONST_48  H181  N18  C16  C11   180.00   0.0  0
 UI3  Var_01    N17   C16  C11  C10  -153.23  30.0  2
 UI3  Var_02    O35   S34  N26  C25   141.31  30.0  2
 UI3  Var_03    H201  C20  O19  C6   -177.98  30.0  3
 UI3  Var_04    H371  C37  S34  N26    61.31  30.0  3

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
 UI3  plan-1  C5    0.020
 UI3  plan-1  C24   0.020
 UI3  plan-1  C25   0.020
 UI3  plan-1  N26   0.020
 UI3  plan-1  N27   0.020
 UI3  plan-1  C28   0.020
 UI3  plan-1  S34   0.020
 UI3  plan-1  H25   0.020
 UI3  plan-1  H28   0.020
 UI3  plan-2  C1    0.020
 UI3  plan-2  C2    0.020
 UI3  plan-2  C3    0.020
 UI3  plan-2  C4    0.020
 UI3  plan-2  C5    0.020
 UI3  plan-2  C6    0.020
 UI3  plan-2  C9    0.020
 UI3  plan-2  C10   0.020
 UI3  plan-2  C11   0.020
 UI3  plan-2  C12   0.020
 UI3  plan-2  C16   0.020
 UI3  plan-2  O19   0.020
 UI3  plan-2  C24   0.020
 UI3  plan-2  H1    0.020
 UI3  plan-2  H2    0.020
 UI3  plan-2  H9    0.020
 UI3  plan-2  H10   0.020
 UI3  plan-2  H12   0.020
 UI3  plan-3  C11   0.020
 UI3  plan-3  C16   0.020
 UI3  plan-3  N17   0.020
 UI3  plan-3  N18   0.020
 UI3  plan-3  H17   0.020
 UI3  plan-3  H181  0.020
 UI3  plan-3  H182  0.020

