# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:32:53 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-{[(5-cyanopyrazin-2-yl)carbamoyl]amino}naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2cc(NC(=O)Nc3cnc(cn3)C#N)ccc2c1
#
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
 H5K  H5K  '6-{[(5-cyanopyrazin-2-yl)carbamoyl]amino}naphthalene-2-carboxylic acid'  ligand  36  25  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H5K
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
 H5K  N5   N  NS    0  -0.238  -9.2276   0.7062   0.5329
 H5K  C13  C  CSP   0   0.064  -8.1203   0.4205   0.3980
 H5K  C11  C  CR6   0   0.133  -6.7407   0.0845   0.2354
 H5K  N3   N  N     0  -0.344  -6.4377  -1.2009   0.0221
 H5K  C10  C  CR16  0  -0.160  -5.1770  -1.4990  -0.1247
 H5K  C12  C  CR16  0  -0.039  -5.7589   1.0575   0.3004
 H5K  N4   N  N     0  -0.380  -4.4767   0.7607   0.1522
 H5K  C9   C  CR6   0   0.518  -4.1694  -0.5048  -0.0625
 H5K  N2   N  NH1   0  -0.772  -2.8758  -0.9134  -0.2303
 H5K  C8   C  C     0   0.735  -1.7255  -0.1376  -0.2259
 H5K  O3   O  O     0  -0.453  -1.7206   1.0667  -0.1269
 H5K  N1   N  NH1   0  -0.790  -0.6042  -0.9095  -0.3577
 H5K  C7   C  CR6   0   0.392   0.7099  -0.4351  -0.3627
 H5K  C6   C  CR16  0  -0.418   1.6919  -1.2345   0.1734
 H5K  C14  C  CR16  0  -0.290   1.0574   0.8053  -0.9562
 H5K  C15  C  CR16  0  -0.304   2.3600   1.2131  -0.9687
 H5K  C16  C  CR66  0   0.129   3.3875   0.4168  -0.4122
 H5K  C5   C  CR66  0   0.145   3.0421  -0.8344   0.1565
 H5K  C4   C  CR16  0  -0.306   4.0694  -1.6393   0.7047
 H5K  C3   C  CR16  0  -0.265   5.3696  -1.2231   0.6897
 H5K  C17  C  CR16  0  -0.322   4.7342   0.8260  -0.4152
 H5K  C2   C  CR6   0  -0.092   5.7155   0.0293   0.1239
 H5K  C1   C  C     0   0.536   7.1135   0.5192   0.0900
 H5K  O2   O  O     0  -0.441   7.4440   1.5903  -0.3621
 H5K  O1   O  OH1   0  -0.595   7.9756  -0.3438   0.6100
 H5K  H7   H  HCR6  0   0.302  -4.9211  -2.5388  -0.2970
 H5K  H8   H  HCR6  0   0.300  -6.0122   2.0960   0.4755
 H5K  H6   H  HNH1  0   0.433  -2.7645  -1.9046  -0.3861
 H5K  H5   H  HNH1  0   0.421  -0.6968  -1.9068  -0.2302
 H5K  H4   H  HCR6  0   0.272   1.4320  -2.1867   0.6217
 H5K  H9   H  HCR6  0   0.278   0.3025   1.4252  -1.4137
 H5K  H10  H  HCR6  0   0.266   2.6189   2.1607  -1.4245
 H5K  H3   H  HCR6  0   0.262   3.8117  -2.5969   1.1400
 H5K  H2   H  HCR6  0   0.266   6.1325  -1.8599   1.1150
 H5K  H11  H  HCR6  0   0.267   4.9883   1.7844  -0.8509
 H5K  H1   H  HOH1  0   0.488   8.8727   0.0199   0.5687

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
 H5K  C4   C3   aromatic  1.365  0.020  1.365
 H5K  C4   C5   aromatic  1.416  0.020  1.416
 H5K  C3   C2   aromatic  1.417  0.020  1.417
 H5K  O2   C1   double    1.209  0.020  1.209
 H5K  O3   C8   double    1.208  0.020  1.208
 H5K  C2   C1   single    1.482  0.020  1.482
 H5K  C2   C17  aromatic  1.374  0.020  1.374
 H5K  C6   C5   aromatic  1.408  0.020  1.408
 H5K  C6   C7   aromatic  1.375  0.020  1.375
 H5K  C5   C16  aromatic  1.417  0.020  1.417
 H5K  C1   O1   single    1.326  0.020  1.326
 H5K  C8   N2   single    1.387  0.020  1.387
 H5K  C8   N1   single    1.368  0.020  1.368
 H5K  N2   C9   single    1.367  0.020  1.367
 H5K  C17  C16  aromatic  1.408  0.020  1.408
 H5K  C7   N1   single    1.397  0.020  1.397
 H5K  C7   C14  aromatic  1.418  0.020  1.418
 H5K  C16  C15  aromatic  1.414  0.020  1.414
 H5K  C9   C10  aromatic  1.417  0.020  1.417
 H5K  C9   N4   aromatic  1.320  0.020  1.320
 H5K  C14  C15  aromatic  1.365  0.020  1.365
 H5K  C10  N3   aromatic  1.304  0.020  1.304
 H5K  N4   C12  aromatic  1.324  0.020  1.324
 H5K  N3   C11  aromatic  1.338  0.020  1.338
 H5K  C12  C11  aromatic  1.384  0.020  1.384
 H5K  C11  C13  single    1.429  0.020  1.429
 H5K  C13  N5   triple    1.152  0.020  1.152
 H5K  C10  H7   single    0.930  0.020  1.080
 H5K  C12  H8   single    0.930  0.020  1.080
 H5K  N2   H6   single    0.860  0.020  1.020
 H5K  N1   H5   single    0.860  0.020  1.020
 H5K  C6   H4   single    0.930  0.020  1.080
 H5K  C14  H9   single    0.930  0.020  1.080
 H5K  C15  H10  single    0.930  0.020  1.080
 H5K  C4   H3   single    0.930  0.020  1.080
 H5K  C3   H2   single    0.930  0.020  1.080
 H5K  C17  H11  single    0.930  0.020  1.080
 H5K  O1   H1   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
 H5K  C11  C13  N5   180.00  3.000
 H5K  C12  C11  N3   121.49  3.000
 H5K  C12  C11  C13  120.95  3.000
 H5K  N3   C11  C13  117.56  3.000
 H5K  C10  N3   C11  117.17  3.000
 H5K  H7   C10  C9   120.79  3.000
 H5K  H7   C10  N3   117.72  3.000
 H5K  C9   C10  N3   121.48  3.000
 H5K  H8   C12  N4   117.34  3.000
 H5K  H8   C12  C11  121.05  3.000
 H5K  N4   C12  C11  121.61  3.000
 H5K  C9   N4   C12  117.29  3.000
 H5K  N2   C9   N4   121.80  3.000
 H5K  N4   C9   C10  120.96  3.000
 H5K  N2   C9   C10  117.24  3.000
 H5K  H6   N2   C8   117.27  3.000
 H5K  H6   N2   C9   114.63  3.000
 H5K  C8   N2   C9   128.10  3.000
 H5K  N1   C8   O3   124.54  3.000
 H5K  N1   C8   N2   111.34  3.000
 H5K  O3   C8   N2   124.12  3.000
 H5K  H5   N1   C7   114.97  3.000
 H5K  H5   N1   C8   118.04  3.000
 H5K  C7   N1   C8   125.44  3.000
 H5K  C14  C7   C6   119.77  3.000
 H5K  C14  C7   N1   121.93  3.000
 H5K  C6   C7   N1   118.23  3.000
 H5K  H4   C6   C5   118.97  3.000
 H5K  H4   C6   C7   120.04  3.000
 H5K  C5   C6   C7   120.99  3.000
 H5K  H9   C14  C15  119.50  3.000
 H5K  H9   C14  C7   120.57  3.000
 H5K  C15  C14  C7   119.93  3.000
 H5K  H10  C15  C16  119.00  3.000
 H5K  H10  C15  C14  119.56  3.000
 H5K  C16  C15  C14  121.44  3.000
 H5K  C17  C16  C5   119.39  3.000
 H5K  C17  C16  C15  122.05  3.000
 H5K  C5   C16  C15  118.56  3.000
 H5K  C4   C5   C16  118.72  3.000
 H5K  C16  C5   C6   119.29  3.000
 H5K  C4   C5   C6   121.98  3.000
 H5K  H3   C4   C3   120.04  3.000
 H5K  H3   C4   C5   119.06  3.000
 H5K  C3   C4   C5   120.90  3.000
 H5K  H2   C3   C2   120.37  3.000
 H5K  H2   C3   C4   119.22  3.000
 H5K  C2   C3   C4   120.41  3.000
 H5K  H11  C17  C2   120.22  3.000
 H5K  H11  C17  C16  118.86  3.000
 H5K  C2   C17  C16  120.92  3.000
 H5K  C1   C2   C17  118.23  3.000
 H5K  C17  C2   C3   119.65  3.000
 H5K  C1   C2   C3   122.11  3.000
 H5K  O1   C1   O2   123.07  3.000
 H5K  O1   C1   C2   112.91  3.000
 H5K  O2   C1   C2   124.02  3.000
 H5K  H1   O1   C1   109.94  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
 H5K  CONST_01  C9   C10  N3   C11     0.00   0.0  0
 H5K  CONST_02  C9   N4   C12  C11     0.00   0.0  0
 H5K  CONST_03  N4   C9   C10  N3      0.00   0.0  0
 H5K  CONST_04  N4   C12  C11  N3      0.00   0.0  0
 H5K  CONST_05  C12  N4   C9   C10     0.00   0.0  0
 H5K  CONST_06  C12  C11  N3   C10     0.00   0.0  0
 H5K  CONST_07  C4   C5   C6   C7    180.00   0.0  0
 H5K  CONST_08  C16  C5   C6   C7      0.00   0.0  0
 H5K  CONST_09  C16  C15  C14  C7      0.00   0.0  0
 H5K  CONST_10  C3   C4   C5   C6    180.00   0.0  0
 H5K  CONST_11  C17  C16  C5   C6    180.00   0.0  0
 H5K  CONST_12  C15  C16  C5   C6      0.00   0.0  0
 H5K  CONST_13  C15  C14  C7   C6      0.00   0.0  0
 H5K  CONST_14  C5   C6   C7   C14     0.00   0.0  0
 H5K  CONST_15  C5   C16  C15  C14     0.00   0.0  0
 H5K  CONST_16  C17  C16  C15  C14   180.00   0.0  0
 H5K  CONST_17  C4   C5   C16  C15   180.00   0.0  0
 H5K  CONST_18  C2   C17  C16  C15   180.00   0.0  0
 H5K  CONST_19  C3   C4   C5   C16     0.00   0.0  0
 H5K  CONST_20  C3   C2   C17  C16     0.00   0.0  0
 H5K  CONST_21  C2   C3   C4   C5      0.00   0.0  0
 H5K  CONST_22  C2   C17  C16  C5      0.00   0.0  0
 H5K  CONST_23  C17  C2   C3   C4      0.00   0.0  0
 H5K  CONST_24  C17  C16  C5   C4      0.00   0.0  0
 H5K  CONST_25  C10  N3   C11  C13   180.00   0.0  0
 H5K  CONST_26  N4   C12  C11  C13   180.00   0.0  0
 H5K  CONST_27  N2   C9   C10  N3    180.00   0.0  0
 H5K  CONST_28  N2   C9   N4   C12   180.00   0.0  0
 H5K  CONST_29  C5   C6   C7   N1    180.00   0.0  0
 H5K  CONST_30  C15  C14  C7   N1    180.00   0.0  0
 H5K  CONST_31  C1   C2   C17  C16   180.00   0.0  0
 H5K  CONST_32  C1   C2   C3   C4    180.00   0.0  0
 H5K  CONST_33  H7   C10  N3   C11   180.00   0.0  0
 H5K  CONST_34  H8   C12  C11  N3    180.00   0.0  0
 H5K  CONST_35  H10  C15  C14  C7    180.00   0.0  0
 H5K  CONST_36  H3   C4   C5   C6      0.00   0.0  0
 H5K  CONST_37  H9   C14  C7   C6    180.00   0.0  0
 H5K  CONST_38  H4   C6   C7   C14   180.00   0.0  0
 H5K  CONST_39  H11  C17  C16  C15     0.00   0.0  0
 H5K  CONST_40  H2   C3   C4   C5    180.00   0.0  0
 H5K  CONST_41  C8   N2   C9   C10   180.00   0.0  0
 H5K  CONST_42  C8   N2   C9   N4      0.00   0.0  0
 H5K  CONST_45  H6   N2   C9   C10     0.00   0.0  0
 H5K  CONST_47  O3   C8   N2   C9      0.00   0.0  0
 H5K  CONST_48  C7   N1   C8   O3      0.00   0.0  0
 H5K  CONST_49  N1   C8   N2   C9    180.00   0.0  0
 H5K  CONST_50  C7   N1   C8   N2    180.00   0.0  0
 H5K  CONST_51  H1   O1   C1   C2    180.00   0.0  0
 H5K  Var_01    O2   C1   C2   C3   -178.64  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
 H5K  plan-1  N5   0.020
 H5K  plan-1  C13  0.020
 H5K  plan-1  C11  0.020
 H5K  plan-1  N3   0.020
 H5K  plan-1  C10  0.020
 H5K  plan-1  C12  0.020
 H5K  plan-1  N4   0.020
 H5K  plan-1  C9   0.020
 H5K  plan-1  N2   0.020
 H5K  plan-1  H7   0.020
 H5K  plan-1  H8   0.020
 H5K  plan-2  C2   0.020
 H5K  plan-2  C1   0.020
 H5K  plan-2  O2   0.020
 H5K  plan-2  O1   0.020
 H5K  plan-2  H1   0.020
 H5K  plan-3  N1   0.020
 H5K  plan-3  C7   0.020
 H5K  plan-3  C6   0.020
 H5K  plan-3  C14  0.020
 H5K  plan-3  C15  0.020
 H5K  plan-3  C16  0.020
 H5K  plan-3  C5   0.020
 H5K  plan-3  C4   0.020
 H5K  plan-3  C3   0.020
 H5K  plan-3  C17  0.020
 H5K  plan-3  C2   0.020
 H5K  plan-3  C1   0.020
 H5K  plan-3  H4   0.020
 H5K  plan-3  H9   0.020
 H5K  plan-3  H10  0.020
 H5K  plan-3  H3   0.020
 H5K  plan-3  H2   0.020
 H5K  plan-3  H11  0.020
 H5K  plan-4  C9   0.020
 H5K  plan-4  N2   0.020
 H5K  plan-4  C8   0.020
 H5K  plan-4  O3   0.020
 H5K  plan-4  N1   0.020
 H5K  plan-4  C7   0.020
 H5K  plan-4  H6   0.020
 H5K  plan-4  H5   0.020

