# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:53:01 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-(carbamoylamino)-1-(naphthalen-1-yl)-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)Nc1cn(nc1C(N)=O)c2cccc3ccccc23
#
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
 M0Y  M0Y  4-(carbamoylamino)-1-(naphthalen-1-yl)-1H-pyrazole-3-carboxamide  ligand  35  22  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M0Y
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
 M0Y  C1   C  CR16  0  -0.252   4.6000   1.2704   1.4134
 M0Y  C2   C  CR16  0  -0.249   3.2813   1.7141   1.6377
 M0Y  C3   C  CR16  0  -0.296   2.2237   1.1101   1.0139
 M0Y  C4   C  CR66  0   0.102   2.4345   0.0225   0.1328
 M0Y  C5   C  CR66  0   0.093   3.7617  -0.4413  -0.0755
 M0Y  C6   C  CR16  0  -0.309   4.8319   0.2144   0.5774
 M0Y  C7   C  CR16  0  -0.308   3.9930  -1.5592  -0.9107
 M0Y  C8   C  CR16  0  -0.265   2.9538  -2.2017  -1.5217
 M0Y  C9   C  CR16  0  -0.290   1.6364  -1.7405  -1.3430
 M0Y  C10  C  CR6   0   0.305   1.3871  -0.6584  -0.5440
 M0Y  N1   N  NR5   0  -0.387   0.0456  -0.2372  -0.3779
 M0Y  C11  C  CR15  0  -0.006  -0.9853  -1.0139   0.0520
 M0Y  C12  C  CR5   0   0.127  -2.1062  -0.2142   0.0107
 M0Y  C13  C  CR5   0   0.076  -1.6296   1.0302  -0.4656
 M0Y  N2   N  N     0  -0.286  -0.3266   0.9834  -0.6958
 M0Y  C14  C  C     0   0.510  -2.4178   2.2548  -0.6963
 M0Y  O1   O  O     0  -0.496  -3.6292   2.2634  -0.4859
 M0Y  N3   N  NH2   0  -0.807  -1.7332   3.3143  -1.1357
 M0Y  N4   N  NH1   0  -0.760  -3.4167  -0.4794   0.3495
 M0Y  C15  C  C     0   0.659  -3.8834  -1.6963   0.7642
 M0Y  O2   O  O     0  -0.517  -3.1573  -2.6737   0.8796
 M0Y  N5   N  NH2   0  -0.848  -5.2191  -1.7265   0.9960
 M0Y  H1   H  HCR6  0   0.263   5.4244   1.7641   1.9104
 M0Y  H2   H  HCR6  0   0.264   3.1049   2.5426   2.3111
 M0Y  H3   H  HCR6  0   0.254   1.2233   1.4729   1.1994
 M0Y  H4   H  HCR6  0   0.261   5.8410  -0.1409   0.4080
 M0Y  H5   H  HCR6  0   0.264   5.0096  -1.9041  -1.0532
 M0Y  H6   H  HCR6  0   0.269   3.1327  -3.0592  -2.1558
 M0Y  H7   H  HCR6  0   0.283   0.8191  -2.2354  -1.8512
 M0Y  H8   H  HCR5  0   0.309  -0.8315  -2.0327   0.3563
 M0Y  H9   H  HNH2  0   0.413  -0.7394   3.2722  -1.2858
 M0Y  H10  H  HNH2  0   0.409  -2.2037   4.1863  -1.3136
 M0Y  H11  H  HNH1  0   0.412  -4.0524   0.2965   0.2304
 M0Y  H12  H  HNH2  0   0.402  -5.7387  -0.8749   1.1311
 M0Y  H13  H  HNH2  0   0.402  -5.5818  -2.5337   1.4742

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
 M0Y  C8   C7   aromatic  1.366  0.020  1.366
 M0Y  C8   C9   aromatic  1.407  0.020  1.407
 M0Y  C7   C5   aromatic  1.414  0.020  1.414
 M0Y  C9   C10  aromatic  1.368  0.020  1.368
 M0Y  C5   C6   aromatic  1.415  0.020  1.415
 M0Y  C5   C4   aromatic  1.421  0.020  1.421
 M0Y  C6   C1   aromatic  1.367  0.020  1.367
 M0Y  C10  C4   aromatic  1.421  0.020  1.421
 M0Y  C10  N1   single    1.416  0.020  1.416
 M0Y  C4   C3   aromatic  1.415  0.020  1.415
 M0Y  N2   N1   aromatic  1.315  0.020  1.315
 M0Y  N2   C13  aromatic  1.324  0.020  1.324
 M0Y  N1   C11  aromatic  1.360  0.020  1.360
 M0Y  C1   C2   aromatic  1.409  0.020  1.409
 M0Y  N3   C14  single    1.336  0.020  1.336
 M0Y  C3   C2   aromatic  1.368  0.020  1.368
 M0Y  C13  C14  single    1.474  0.020  1.474
 M0Y  C13  C12  aromatic  1.415  0.020  1.415
 M0Y  C11  C12  aromatic  1.378  0.020  1.378
 M0Y  C14  O1   double    1.230  0.020  1.230
 M0Y  C12  N4   single    1.379  0.020  1.379
 M0Y  N4   C15  single    1.368  0.020  1.368
 M0Y  O2   C15  double    1.223  0.020  1.223
 M0Y  C15  N5   single    1.356  0.020  1.356
 M0Y  C1   H1   single    0.930  0.020  1.080
 M0Y  C2   H2   single    0.930  0.020  1.080
 M0Y  C3   H3   single    0.930  0.020  1.080
 M0Y  C6   H4   single    0.930  0.020  1.080
 M0Y  C7   H5   single    0.930  0.020  1.080
 M0Y  C8   H6   single    0.930  0.020  1.080
 M0Y  C9   H7   single    0.930  0.020  1.080
 M0Y  C11  H8   single    0.930  0.020  1.080
 M0Y  N3   H9   single    0.860  0.020  1.020
 M0Y  N3   H10  single    0.860  0.020  1.020
 M0Y  N4   H11  single    0.860  0.020  1.020
 M0Y  N5   H12  single    0.890  0.020  1.040
 M0Y  N5   H13  single    0.890  0.020  1.040

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
 M0Y  H1   C1   C6   120.28  3.000
 M0Y  H1   C1   C2   119.75  3.000
 M0Y  C6   C1   C2   119.97  3.000
 M0Y  H2   C2   C3   119.72  3.000
 M0Y  H2   C2   C1   119.51  3.000
 M0Y  C3   C2   C1   120.77  3.000
 M0Y  H3   C3   C4   120.19  3.000
 M0Y  H3   C3   C2   119.29  3.000
 M0Y  C4   C3   C2   120.52  3.000
 M0Y  C10  C4   C5   117.53  3.000
 M0Y  C10  C4   C3   123.71  3.000
 M0Y  C5   C4   C3   118.76  3.000
 M0Y  C7   C5   C6   121.00  3.000
 M0Y  C6   C5   C4   119.18  3.000
 M0Y  C7   C5   C4   119.81  3.000
 M0Y  H4   C6   C5   118.72  3.000
 M0Y  H4   C6   C1   120.48  3.000
 M0Y  C5   C6   C1   120.80  3.000
 M0Y  H5   C7   C8   120.36  3.000
 M0Y  H5   C7   C5   118.88  3.000
 M0Y  C8   C7   C5   120.76  3.000
 M0Y  H6   C8   C9   119.29  3.000
 M0Y  H6   C8   C7   120.63  3.000
 M0Y  C9   C8   C7   120.08  3.000
 M0Y  H7   C9   C10  119.89  3.000
 M0Y  H7   C9   C8   119.83  3.000
 M0Y  C10  C9   C8   120.27  3.000
 M0Y  N1   C10  C9   118.46  3.000
 M0Y  N1   C10  C4   120.00  3.000
 M0Y  C9   C10  C4   121.53  3.000
 M0Y  N2   N1   C11  113.07  3.000
 M0Y  C11  N1   C10  125.82  3.000
 M0Y  N2   N1   C10  121.05  3.000
 M0Y  H8   C11  C12  132.50  3.000
 M0Y  H8   C11  N1   121.49  3.000
 M0Y  C12  C11  N1   106.00  3.000
 M0Y  N4   C12  C13  124.88  3.000
 M0Y  N4   C12  C11  130.85  3.000
 M0Y  C13  C12  C11  104.27  3.000
 M0Y  C14  C13  N2   121.89  3.000
 M0Y  C14  C13  C12  127.08  3.000
 M0Y  N2   C13  C12  111.03  3.000
 M0Y  C13  N2   N1   105.62  3.000
 M0Y  N3   C14  O1   123.76  3.000
 M0Y  O1   C14  C13  120.38  3.000
 M0Y  N3   C14  C13  115.86  3.000
 M0Y  H10  N3   H9   118.13  3.000
 M0Y  H10  N3   C14  120.38  3.000
 M0Y  H9   N3   C14  121.48  3.000
 M0Y  H11  N4   C15  120.30  3.000
 M0Y  H11  N4   C12  114.91  3.000
 M0Y  C15  N4   C12  124.74  3.000
 M0Y  N5   C15  O2   123.43  3.000
 M0Y  N5   C15  N4   114.06  3.000
 M0Y  O2   C15  N4   122.48  3.000
 M0Y  H13  N5   H12  115.40  3.000
 M0Y  H13  N5   C15  117.02  3.000
 M0Y  H12  N5   C15  120.83  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
 M0Y  CONST_01  C7   C5   C6   C1   180.00   0.0  0
 M0Y  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 M0Y  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 M0Y  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 M0Y  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 M0Y  CONST_06  C10  C4   C3   C2   180.00   0.0  0
 M0Y  CONST_07  C7   C5   C4   C3   180.00   0.0  0
 M0Y  CONST_08  C6   C5   C4   C3     0.00   0.0  0
 M0Y  CONST_09  C9   C10  C4   C3   180.00   0.0  0
 M0Y  CONST_10  N1   C10  C4   C3     0.00   0.0  0
 M0Y  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 M0Y  CONST_12  C8   C7   C5   C4     0.00   0.0  0
 M0Y  CONST_13  C8   C9   C10  C4     0.00   0.0  0
 M0Y  CONST_16  C9   C8   C7   C5     0.00   0.0  0
 M0Y  CONST_17  C9   C10  C4   C5     0.00   0.0  0
 M0Y  CONST_18  N1   C10  C4   C5   180.00   0.0  0
 M0Y  CONST_19  C8   C7   C5   C6   180.00   0.0  0
 M0Y  CONST_20  C10  C4   C5   C6   180.00   0.0  0
 M0Y  CONST_21  C10  C9   C8   C7     0.00   0.0  0
 M0Y  CONST_22  C10  C4   C5   C7     0.00   0.0  0
 M0Y  CONST_23  N1   C10  C9   C8   180.00   0.0  0
 M0Y  CONST_26  C13  N2   N1   C10  180.00   0.0  0
 M0Y  CONST_27  C12  C11  N1   C10  180.00   0.0  0
 M0Y  CONST_28  C12  C13  N2   N1     0.00   0.0  0
 M0Y  CONST_29  C13  C12  C11  N1     0.00   0.0  0
 M0Y  CONST_30  C13  N2   N1   C11    0.00   0.0  0
 M0Y  CONST_31  N2   C13  C12  C11    0.00   0.0  0
 M0Y  CONST_32  N2   N1   C11  C12    0.00   0.0  0
 M0Y  CONST_33  C14  C13  N2   N1   180.00   0.0  0
 M0Y  CONST_34  N4   C12  C11  N1   180.00   0.0  0
 M0Y  CONST_35  C14  C13  C12  C11  180.00   0.0  0
 M0Y  CONST_36  N4   C12  C13  N2   180.00   0.0  0
 M0Y  CONST_37  H3   C3   C2   C1   180.00   0.0  0
 M0Y  CONST_38  H4   C6   C1   C2   180.00   0.0  0
 M0Y  CONST_39  H1   C1   C2   C3   180.00   0.0  0
 M0Y  CONST_40  H5   C7   C5   C4   180.00   0.0  0
 M0Y  CONST_41  H7   C9   C10  C4   180.00   0.0  0
 M0Y  CONST_42  H2   C2   C3   C4   180.00   0.0  0
 M0Y  CONST_43  H6   C8   C7   C5   180.00   0.0  0
 M0Y  CONST_44  H8   C11  N1   C10    0.00   0.0  0
 M0Y  CONST_45  C15  N4   C12  C11    0.00   0.0  0
 M0Y  CONST_46  C15  N4   C12  C13  180.00   0.0  0
 M0Y  CONST_47  H11  N4   C12  C11  180.00   0.0  0
 M0Y  CONST_48  O2   C15  N4   C12    0.00   0.0  0
 M0Y  CONST_49  N5   C15  N4   C12  180.00   0.0  0
 M0Y  CONST_50  H9   N3   C14  C13    0.00   0.0  0
 M0Y  CONST_51  H10  N3   C14  C13  180.00   0.0  0
 M0Y  CONST_53  H13  N5   C15  O2     0.00   0.0  0
 M0Y  Var_01    N3   C14  C13  C12  179.15  30.0  2

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
 M0Y  plan-1  C10  0.020
 M0Y  plan-1  N1   0.020
 M0Y  plan-1  C11  0.020
 M0Y  plan-1  C12  0.020
 M0Y  plan-1  C13  0.020
 M0Y  plan-1  N2   0.020
 M0Y  plan-1  C14  0.020
 M0Y  plan-1  N4   0.020
 M0Y  plan-1  H8   0.020
 M0Y  plan-2  C1   0.020
 M0Y  plan-2  C2   0.020
 M0Y  plan-2  C3   0.020
 M0Y  plan-2  C4   0.020
 M0Y  plan-2  C5   0.020
 M0Y  plan-2  C6   0.020
 M0Y  plan-2  C7   0.020
 M0Y  plan-2  C8   0.020
 M0Y  plan-2  C9   0.020
 M0Y  plan-2  C10  0.020
 M0Y  plan-2  N1   0.020
 M0Y  plan-2  H1   0.020
 M0Y  plan-2  H2   0.020
 M0Y  plan-2  H3   0.020
 M0Y  plan-2  H4   0.020
 M0Y  plan-2  H5   0.020
 M0Y  plan-2  H6   0.020
 M0Y  plan-2  H7   0.020
 M0Y  plan-3  C13  0.020
 M0Y  plan-3  C14  0.020
 M0Y  plan-3  O1   0.020
 M0Y  plan-3  N3   0.020
 M0Y  plan-3  H9   0.020
 M0Y  plan-3  H10  0.020
 M0Y  plan-4  C12  0.020
 M0Y  plan-4  N4   0.020
 M0Y  plan-4  C15  0.020
 M0Y  plan-4  O2   0.020
 M0Y  plan-4  N5   0.020
 M0Y  plan-4  H11  0.020
 M0Y  plan-4  H12  0.020
 M0Y  plan-4  H13  0.020

