# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 13:52:12 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-(carbamoylamino)-1-(7-ethoxynaphthalen-1-yl)-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2cccc(n3cc(NC(N)=O)c(n3)C(N)=O)c2c1
#
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
 1YZ  1YZ  4-(carbamoylamino)-1-(7-ethoxynaphthalen-1-yl)-1H-pyrazole-3-carboxamide  ligand  42  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1YZ
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
 1YZ  N1   N  NR5   0  -0.386   0.6881   0.7471  -0.5150
 1YZ  N2   N  N     0  -0.286   0.7739  -0.3375  -1.2533
 1YZ  C1   C  CR5   0   0.072   1.9285  -0.8989  -0.9275
 1YZ  C2   C  CR5   0   0.129   2.6064  -0.1355   0.0522
 1YZ  C3   C  CR15  0  -0.007   1.7655   0.9284   0.2947
 1YZ  N3   N  NH1   0  -0.761   3.8336  -0.4580   0.5935
 1YZ  C4   C  C     0   0.661   4.4469   0.2401   1.5975
 1YZ  N4   N  NH2   0  -0.850   5.6221  -0.2943   2.0065
 1YZ  O1   O  O     0  -0.519   3.9527   1.2416   2.0972
 1YZ  C5   C  C     0   0.511   2.3900  -2.1562  -1.5437
 1YZ  N5   N  NH2   0  -0.807   1.5559  -2.7153  -2.4247
 1YZ  O2   O  O     0  -0.497   3.4820  -2.6328  -1.2391
 1YZ  C6   C  CR6   0   0.287  -0.4134   1.6304  -0.6321
 1YZ  C7   C  CR16  0  -0.283  -0.1772   2.9190  -1.0237
 1YZ  C8   C  CR16  0  -0.277  -1.2363   3.8411  -1.1257
 1YZ  C9   C  CR16  0  -0.302  -2.5119   3.4437  -0.8406
 1YZ  C10  C  CR66  0   0.139  -1.7227   1.1780  -0.3092
 1YZ  C11  C  CR66  0   0.071  -2.7818   2.1187  -0.4285
 1YZ  C12  C  CR16  0  -0.293  -4.0896   1.7004  -0.1043
 1YZ  C13  C  CR16  0  -0.375  -4.3503   0.4296   0.3272
 1YZ  C14  C  CR6   0   0.422  -3.2918  -0.4999   0.4551
 1YZ  C15  C  CR16  0  -0.434  -2.0043  -0.1260   0.1390
 1YZ  O3   O  O2    0  -0.472  -3.4659  -1.7639   0.8745
 1YZ  C16  C  CH2   0  -0.192  -4.7647  -2.2101   1.2498
 1YZ  C17  C  CH3   0  -0.682  -4.6536  -3.6566   1.6683
 1YZ  H1   H  HCR5  0   0.308   1.8280   1.7661   0.9639
 1YZ  H2   H  HNH1  0   0.412   4.2506  -1.3030   0.2278
 1YZ  H4   H  HNH2  0   0.403   6.1066  -0.9812   1.4541
 1YZ  H3   H  HNH2  0   0.403   6.1937   0.2556   2.6243
 1YZ  H5   H  HNH2  0   0.413   0.6650  -2.3007  -2.6405
 1YZ  H6   H  HNH2  0   0.408   1.7981  -3.5817  -2.8764
 1YZ  H7   H  HCR6  0   0.281   0.8315   3.2288  -1.2651
 1YZ  H8   H  HCR6  0   0.266  -1.0293   4.8557  -1.4368
 1YZ  H9   H  HCR6  0   0.263  -3.3345   4.1436  -0.9200
 1YZ  H10  H  HCR6  0   0.267  -4.9033   2.4090  -0.1951
 1YZ  H11  H  HCR6  0   0.287  -5.3678   0.1558   0.5679
 1YZ  H12  H  HCR6  0   0.255  -1.2143  -0.8579   0.2380
 1YZ  H14  H  HCH2  0   0.228  -5.1492  -1.6018   2.0749
 1YZ  H13  H  HCH2  0   0.228  -5.4590  -2.1093   0.4096
 1YZ  H16  H  HCH3  0   0.239  -5.6353  -4.0226   1.9668
 1YZ  H17  H  HCH3  0   0.236  -4.2986  -4.2815   0.8486
 1YZ  H15  H  HCH3  0   0.236  -3.9788  -3.7760   2.5159

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
 1YZ  C8   C9   aromatic  1.366  0.020  1.366
 1YZ  C8   C7   aromatic  1.408  0.020  1.408
 1YZ  C9   C11  aromatic  1.414  0.020  1.414
 1YZ  C7   C6   aromatic  1.367  0.020  1.367
 1YZ  C11  C12  aromatic  1.411  0.020  1.411
 1YZ  C11  C10  aromatic  1.422  0.020  1.422
 1YZ  C12  C13  aromatic  1.367  0.020  1.367
 1YZ  C6   C10  aromatic  1.422  0.020  1.422
 1YZ  C6   N1   single    1.417  0.020  1.417
 1YZ  C10  C15  aromatic  1.407  0.020  1.407
 1YZ  N1   N2   aromatic  1.315  0.020  1.315
 1YZ  N1   C3   aromatic  1.360  0.020  1.360
 1YZ  C13  C14  aromatic  1.414  0.020  1.414
 1YZ  N2   C1   aromatic  1.325  0.020  1.325
 1YZ  C3   C2   aromatic  1.378  0.020  1.378
 1YZ  C15  C14  aromatic  1.377  0.020  1.377
 1YZ  C14  O3   single    1.343  0.020  1.343
 1YZ  C1   C2   aromatic  1.415  0.020  1.415
 1YZ  C1   C5   single    1.474  0.020  1.474
 1YZ  C2   N3   single    1.379  0.020  1.379
 1YZ  N5   C5   single    1.336  0.020  1.336
 1YZ  O1   C4   double    1.223  0.020  1.223
 1YZ  C5   O2   double    1.230  0.020  1.230
 1YZ  O3   C16  single    1.424  0.020  1.424
 1YZ  N3   C4   single    1.368  0.020  1.368
 1YZ  C4   N4   single    1.354  0.020  1.354
 1YZ  C16  C17  single    1.510  0.020  1.510
 1YZ  C3   H1   single    0.930  0.020  1.080
 1YZ  N3   H2   single    0.860  0.020  1.020
 1YZ  N4   H4   single    0.890  0.020  1.040
 1YZ  N4   H3   single    0.890  0.020  1.040
 1YZ  N5   H5   single    0.860  0.020  1.020
 1YZ  N5   H6   single    0.860  0.020  1.020
 1YZ  C7   H7   single    0.930  0.020  1.080
 1YZ  C8   H8   single    0.930  0.020  1.080
 1YZ  C9   H9   single    0.930  0.020  1.080
 1YZ  C12  H10  single    0.930  0.020  1.080
 1YZ  C13  H11  single    0.930  0.020  1.080
 1YZ  C15  H12  single    0.930  0.020  1.080
 1YZ  C16  H14  single    0.970  0.020  1.090
 1YZ  C16  H13  single    0.970  0.020  1.090
 1YZ  C17  H16  single    0.970  0.020  1.090
 1YZ  C17  H17  single    0.970  0.020  1.090
 1YZ  C17  H15  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
 1YZ  C6   N1   C3   125.60  3.000
 1YZ  C3   N1   N2   113.12  3.000
 1YZ  C6   N1   N2   121.24  3.000
 1YZ  C1   N2   N1   105.57  3.000
 1YZ  C5   C1   C2   126.84  3.000
 1YZ  C5   C1   N2   122.11  3.000
 1YZ  C2   C1   N2   111.05  3.000
 1YZ  N3   C2   C3   130.88  3.000
 1YZ  N3   C2   C1   124.88  3.000
 1YZ  C3   C2   C1   104.25  3.000
 1YZ  H1   C3   C2   132.57  3.000
 1YZ  H1   C3   N1   121.41  3.000
 1YZ  C2   C3   N1   106.02  3.000
 1YZ  H2   N3   C4   120.48  3.000
 1YZ  H2   N3   C2   114.86  3.000
 1YZ  C4   N3   C2   124.58  3.000
 1YZ  O1   C4   N4   123.38  3.000
 1YZ  N4   C4   N3   114.17  3.000
 1YZ  O1   C4   N3   122.44  3.000
 1YZ  H3   N4   H4   115.92  3.000
 1YZ  H3   N4   C4   117.59  3.000
 1YZ  H4   N4   C4   121.44  3.000
 1YZ  O2   C5   N5   123.75  3.000
 1YZ  O2   C5   C1   120.33  3.000
 1YZ  N5   C5   C1   115.92  3.000
 1YZ  H6   N5   H5   118.13  3.000
 1YZ  H6   N5   C5   120.39  3.000
 1YZ  H5   N5   C5   121.46  3.000
 1YZ  C10  C6   C7   121.59  3.000
 1YZ  C10  C6   N1   119.91  3.000
 1YZ  C7   C6   N1   118.48  3.000
 1YZ  H7   C7   C8   119.82  3.000
 1YZ  H7   C7   C6   119.64  3.000
 1YZ  C8   C7   C6   120.53  3.000
 1YZ  H8   C8   C9   120.78  3.000
 1YZ  H8   C8   C7   119.43  3.000
 1YZ  C9   C8   C7   119.78  3.000
 1YZ  H9   C9   C11  118.83  3.000
 1YZ  H9   C9   C8   120.39  3.000
 1YZ  C11  C9   C8   120.78  3.000
 1YZ  C15  C10  C11  119.40  3.000
 1YZ  C15  C10  C6   123.45  3.000
 1YZ  C11  C10  C6   117.14  3.000
 1YZ  C12  C11  C10  118.36  3.000
 1YZ  C10  C11  C9   120.17  3.000
 1YZ  C12  C11  C9   121.46  3.000
 1YZ  H10  C12  C13  119.43  3.000
 1YZ  H10  C12  C11  118.90  3.000
 1YZ  C13  C12  C11  121.67  3.000
 1YZ  H11  C13  C14  121.20  3.000
 1YZ  H11  C13  C12  119.03  3.000
 1YZ  C14  C13  C12  119.77  3.000
 1YZ  O3   C14  C15  116.63  3.000
 1YZ  O3   C14  C13  123.34  3.000
 1YZ  C15  C14  C13  120.03  3.000
 1YZ  H12  C15  C14  118.56  3.000
 1YZ  H12  C15  C10  120.67  3.000
 1YZ  C14  C15  C10  120.77  3.000
 1YZ  C16  O3   C14  119.71  3.000
 1YZ  H13  C16  H14  107.73  3.000
 1YZ  H13  C16  C17  110.34  3.000
 1YZ  H14  C16  C17  110.44  3.000
 1YZ  H13  C16  O3   110.33  3.000
 1YZ  H14  C16  O3   110.18  3.000
 1YZ  C17  C16  O3   107.83  3.000
 1YZ  H15  C17  H17  108.68  3.000
 1YZ  H15  C17  H16  107.94  3.000
 1YZ  H17  C17  H16  107.87  3.000
 1YZ  H15  C17  C16  111.47  3.000
 1YZ  H17  C17  C16  111.39  3.000
 1YZ  H16  C17  C16  109.36  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
 1YZ  CONST_01  C8   C7   C6   N1   180.00   0.0  0
 1YZ  CONST_02  C11  C10  C6   N1   180.00   0.0  0
 1YZ  CONST_03  C15  C10  C6   N1     0.00   0.0  0
 1YZ  CONST_04  C2   C1   N2   N1     0.00   0.0  0
 1YZ  CONST_05  C1   C2   C3   N1     0.00   0.0  0
 1YZ  CONST_08  C2   C3   N1   N2     0.00   0.0  0
 1YZ  CONST_09  C3   C2   C1   N2     0.00   0.0  0
 1YZ  CONST_10  C6   N1   N2   C1   180.00   0.0  0
 1YZ  CONST_11  C3   N1   N2   C1     0.00   0.0  0
 1YZ  CONST_12  C6   N1   C3   C2   180.00   0.0  0
 1YZ  CONST_15  C9   C8   C7   C6     0.00   0.0  0
 1YZ  CONST_16  C9   C11  C10  C6     0.00   0.0  0
 1YZ  CONST_17  C12  C11  C10  C6   180.00   0.0  0
 1YZ  CONST_18  C14  C15  C10  C6   180.00   0.0  0
 1YZ  CONST_19  C11  C9   C8   C7     0.00   0.0  0
 1YZ  CONST_20  C11  C10  C6   C7     0.00   0.0  0
 1YZ  CONST_21  C15  C10  C6   C7   180.00   0.0  0
 1YZ  CONST_22  C12  C11  C9   C8   180.00   0.0  0
 1YZ  CONST_23  C10  C11  C9   C8     0.00   0.0  0
 1YZ  CONST_24  C10  C6   C7   C8     0.00   0.0  0
 1YZ  CONST_25  C13  C12  C11  C9   180.00   0.0  0
 1YZ  CONST_26  C15  C10  C11  C9   180.00   0.0  0
 1YZ  CONST_27  C13  C12  C11  C10    0.00   0.0  0
 1YZ  CONST_28  C13  C14  C15  C10    0.00   0.0  0
 1YZ  CONST_29  C14  C13  C12  C11    0.00   0.0  0
 1YZ  CONST_30  C14  C15  C10  C11    0.00   0.0  0
 1YZ  CONST_31  C15  C10  C11  C12    0.00   0.0  0
 1YZ  CONST_32  C15  C14  C13  C12    0.00   0.0  0
 1YZ  CONST_33  C5   C1   N2   N1   180.00   0.0  0
 1YZ  CONST_34  N3   C2   C3   N1   180.00   0.0  0
 1YZ  CONST_35  N3   C2   C1   N2   180.00   0.0  0
 1YZ  CONST_36  C5   C1   C2   C3   180.00   0.0  0
 1YZ  CONST_37  O3   C14  C15  C10  180.00   0.0  0
 1YZ  CONST_38  O3   C14  C13  C12  180.00   0.0  0
 1YZ  CONST_39  H7   C7   C6   N1     0.00   0.0  0
 1YZ  CONST_40  H1   C3   N1   N2   180.00   0.0  0
 1YZ  CONST_41  H8   C8   C7   C6   180.00   0.0  0
 1YZ  CONST_42  H12  C15  C10  C6     0.00   0.0  0
 1YZ  CONST_43  H9   C9   C8   C7   180.00   0.0  0
 1YZ  CONST_44  H10  C12  C11  C9     0.00   0.0  0
 1YZ  CONST_45  H11  C13  C12  C11  180.00   0.0  0
 1YZ  CONST_46  N5   C5   C1   C2   180.00   0.0  0
 1YZ  CONST_47  C4   N3   C2   C1   180.00   0.0  0
 1YZ  CONST_48  C4   N3   C2   C3     0.00   0.0  0
 1YZ  CONST_49  H2   N3   C2   C1     0.00   0.0  0
 1YZ  CONST_50  O1   C4   N3   C2     0.00   0.0  0
 1YZ  CONST_51  N4   C4   N3   C2   180.00   0.0  0
 1YZ  CONST_52  H5   N5   C5   C1     0.00   0.0  0
 1YZ  CONST_53  H6   N5   C5   C1   180.00   0.0  0
 1YZ  CONST_54  H4   N4   C4   O1   180.00   0.0  0
 1YZ  CONST_55  H3   N4   C4   O1     0.00   0.0  0
 1YZ  Var_01    C17  C16  O3   C14  179.83  30.0  3
 1YZ  Var_02    H16  C17  C16  O3   179.68  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
 1YZ  plan-1  N1   0.020
 1YZ  plan-1  N2   0.020
 1YZ  plan-1  C1   0.020
 1YZ  plan-1  C2   0.020
 1YZ  plan-1  C3   0.020
 1YZ  plan-1  N3   0.020
 1YZ  plan-1  C5   0.020
 1YZ  plan-1  N5   0.020
 1YZ  plan-1  O2   0.020
 1YZ  plan-1  C6   0.020
 1YZ  plan-1  H1   0.020
 1YZ  plan-1  H5   0.020
 1YZ  plan-1  H6   0.020
 1YZ  plan-2  N1   0.020
 1YZ  plan-2  C6   0.020
 1YZ  plan-2  C7   0.020
 1YZ  plan-2  C8   0.020
 1YZ  plan-2  C9   0.020
 1YZ  plan-2  C10  0.020
 1YZ  plan-2  C11  0.020
 1YZ  plan-2  C12  0.020
 1YZ  plan-2  C13  0.020
 1YZ  plan-2  C14  0.020
 1YZ  plan-2  C15  0.020
 1YZ  plan-2  O3   0.020
 1YZ  plan-2  H7   0.020
 1YZ  plan-2  H8   0.020
 1YZ  plan-2  H9   0.020
 1YZ  plan-2  H10  0.020
 1YZ  plan-2  H11  0.020
 1YZ  plan-2  H12  0.020
 1YZ  plan-3  C2   0.020
 1YZ  plan-3  N3   0.020
 1YZ  plan-3  C4   0.020
 1YZ  plan-3  N4   0.020
 1YZ  plan-3  O1   0.020
 1YZ  plan-3  H2   0.020
 1YZ  plan-3  H4   0.020
 1YZ  plan-3  H3   0.020

