# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 07:29:36 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{[3-hydroxy-6-(naphthalen-1-yl)pyridin-2-yl]carbonyl}glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)c1nc(ccc1O)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
 NKG  NKG  N-{[3-hydroxy-6-(naphthalen-1-yl)pyridin-2-yl]carbonyl}glycine  ligand  38  24  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NKG
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
 NKG  O3   O  O     0  -0.528  -3.6725  -1.6521   0.1345
 NKG  C15  C  C     0   0.610  -2.6085  -1.0420  -0.0311
 NKG  N1   N  NH1   0  -0.652  -2.5364   0.2664  -0.2442
 NKG  C16  C  CH2   0  -0.375  -3.6880   1.1206  -0.2824
 NKG  C17  C  C     0   0.523  -3.2459   2.5622  -0.3244
 NKG  O2   O  OH1   0  -0.584  -4.2845   3.3781  -0.3386
 NKG  O1   O  O     0  -0.428  -2.0958   2.9176  -0.3454
 NKG  C14  C  CR6   0  -0.058  -1.3054  -1.7560   0.0115
 NKG  C    C  CR6   0   0.350  -1.2707  -3.1317   0.2682
 NKG  O    O  OH1   0  -0.622  -2.3618  -3.8650   0.4638
 NKG  N    N  N     0  -0.447  -0.2105  -1.0324  -0.1867
 NKG  C3   C  CR6   0   0.161   0.9830  -1.5931  -0.1368
 NKG  C2   C  CR16  0  -0.299   1.1128  -2.9644   0.1291
 NKG  C1   C  CR16  0  -0.242  -0.0107  -3.7336   0.3257
 NKG  C4   C  CR6   0   0.058   2.1696  -0.7500  -0.4026
 NKG  C13  C  CR16  0  -0.319   3.1185  -1.2190  -1.2800
 NKG  C12  C  CR16  0  -0.246   4.2557  -0.4604  -1.6122
 NKG  C11  C  CR16  0  -0.320   4.4357   0.7761  -1.0612
 NKG  C10  C  CR66  0   0.108   3.4963   1.2950  -0.1402
 NKG  C5   C  CR66  0   0.105   2.3486   0.5295   0.2082
 NKG  C9   C  CR16  0  -0.308   3.6931   2.5671   0.4479
 NKG  C8   C  CR16  0  -0.261   2.8044   3.0636   1.3596
 NKG  C7   C  CR16  0  -0.247   1.6811   2.2979   1.7290
 NKG  C6   C  CR16  0  -0.327   1.4587   1.0680   1.1712
 NKG  H1   H  HNH1  0   0.414  -1.6172   0.6691  -0.3751
 NKG  H2   H  HCH2  0   0.297  -4.3147   0.9204  -1.1574
 NKG  H3   H  HCH2  0   0.298  -4.3219   0.9712   0.5960
 NKG  H4   H  HOH1  0   0.491  -3.9882   4.3007  -0.3663
 NKG  H5   H  HOH1  0   0.479  -3.1349  -3.2567   0.3940
 NKG  H6   H  HCR6  0   0.282   2.0932  -3.4171   0.1943
 NKG  H7   H  HCR6  0   0.288   0.0718  -4.7925   0.5348
 NKG  H8   H  HCR6  0   0.261   2.9786  -2.1838  -1.7517
 NKG  H9   H  HCR6  0   0.261   4.9747  -0.8597  -2.3151
 NKG  H10  H  HCR6  0   0.258   5.3010   1.3739  -1.3213
 NKG  H11  H  HCR6  0   0.256   4.5665   3.1413   0.1625
 NKG  H12  H  HCR6  0   0.259   2.9637   4.0376   1.8032
 NKG  H13  H  HCR6  0   0.258   0.9869   2.6866   2.4628
 NKG  H14  H  HCR6  0   0.250   0.5894   0.5055   1.4774

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
 NKG  C8   C9   aromatic  1.367  0.020  1.367
 NKG  C8   C7   aromatic  1.409  0.020  1.409
 NKG  C9   C10  aromatic  1.415  0.020  1.415
 NKG  C7   C6   aromatic  1.369  0.020  1.369
 NKG  C10  C11  aromatic  1.414  0.020  1.414
 NKG  C10  C5   aromatic  1.423  0.020  1.423
 NKG  C11  C12  aromatic  1.366  0.020  1.366
 NKG  C6   C5   aromatic  1.417  0.020  1.417
 NKG  C5   C4   aromatic  1.429  0.020  1.429
 NKG  C12  C13  aromatic  1.407  0.020  1.407
 NKG  C4   C13  aromatic  1.375  0.020  1.375
 NKG  C4   C3   single    1.480  0.020  1.480
 NKG  C3   C2   aromatic  1.403  0.020  1.403
 NKG  C3   N    aromatic  1.320  0.020  1.320
 NKG  C2   C1   aromatic  1.376  0.020  1.376
 NKG  N    C14  aromatic  1.327  0.020  1.327
 NKG  C1   C    aromatic  1.398  0.020  1.398
 NKG  C14  C    aromatic  1.400  0.020  1.400
 NKG  C14  C15  single    1.486  0.020  1.486
 NKG  C    O    single    1.329  0.020  1.329
 NKG  O3   C15  double    1.238  0.020  1.238
 NKG  C15  N1   single    1.328  0.020  1.328
 NKG  N1   C16  single    1.434  0.020  1.434
 NKG  C16  C17  single    1.508  0.020  1.508
 NKG  O1   C17  double    1.204  0.020  1.204
 NKG  C17  O2   single    1.321  0.020  1.321
 NKG  N1   H1   single    0.860  0.020  1.020
 NKG  C16  H2   single    0.970  0.020  1.090
 NKG  C16  H3   single    0.970  0.020  1.090
 NKG  O2   H4   single    0.850  0.020  0.980
 NKG  O    H5   single    0.850  0.020  0.980
 NKG  C2   H6   single    0.930  0.020  1.080
 NKG  C1   H7   single    0.930  0.020  1.080
 NKG  C13  H8   single    0.930  0.020  1.080
 NKG  C12  H9   single    0.930  0.020  1.080
 NKG  C11  H10  single    0.930  0.020  1.080
 NKG  C9   H11  single    0.930  0.020  1.080
 NKG  C8   H12  single    0.930  0.020  1.080
 NKG  C7   H13  single    0.930  0.020  1.080
 NKG  C6   H14  single    0.930  0.020  1.080

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
 NKG  C14  C15  N1   115.49  3.000
 NKG  N1   C15  O3   123.64  3.000
 NKG  C14  C15  O3   120.87  3.000
 NKG  H1   N1   C16  119.26  3.000
 NKG  H1   N1   C15  117.53  3.000
 NKG  C16  N1   C15  123.21  3.000
 NKG  H3   C16  H2   106.57  3.000
 NKG  H3   C16  C17  108.84  3.000
 NKG  H2   C16  C17  108.68  3.000
 NKG  H3   C16  N1   111.26  3.000
 NKG  H2   C16  N1   111.84  3.000
 NKG  C17  C16  N1   109.55  3.000
 NKG  O1   C17  O2   124.65  3.000
 NKG  O2   C17  C16  111.11  3.000
 NKG  O1   C17  C16  124.24  3.000
 NKG  H4   O2   C17  110.36  3.000
 NKG  N    C14  C    122.86  3.000
 NKG  C    C14  C15  119.94  3.000
 NKG  N    C14  C15  117.19  3.000
 NKG  C1   C    O    119.76  3.000
 NKG  O    C    C14  123.29  3.000
 NKG  C1   C    C14  116.95  3.000
 NKG  H5   O    C    107.02  3.000
 NKG  C3   N    C14  120.58  3.000
 NKG  C4   C3   C2   121.12  3.000
 NKG  C2   C3   N    120.41  3.000
 NKG  C4   C3   N    118.45  3.000
 NKG  H6   C2   C1   119.84  3.000
 NKG  H6   C2   C3   120.28  3.000
 NKG  C1   C2   C3   119.87  3.000
 NKG  H7   C1   C2   120.82  3.000
 NKG  H7   C1   C    119.86  3.000
 NKG  C2   C1   C    119.31  3.000
 NKG  C5   C4   C13  119.46  3.000
 NKG  C13  C4   C3   118.28  3.000
 NKG  C5   C4   C3   122.26  3.000
 NKG  H8   C13  C12  118.82  3.000
 NKG  H8   C13  C4   119.52  3.000
 NKG  C12  C13  C4   121.64  3.000
 NKG  H9   C12  C11  120.58  3.000
 NKG  H9   C12  C13  119.44  3.000
 NKG  C11  C12  C13  119.97  3.000
 NKG  H10  C11  C10  118.98  3.000
 NKG  H10  C11  C12  120.53  3.000
 NKG  C10  C11  C12  120.50  3.000
 NKG  C9   C10  C5   119.61  3.000
 NKG  C5   C10  C11  119.86  3.000
 NKG  C9   C10  C11  120.54  3.000
 NKG  C6   C5   C10  117.93  3.000
 NKG  C6   C5   C4   123.49  3.000
 NKG  C10  C5   C4   118.56  3.000
 NKG  H11  C9   C8   120.49  3.000
 NKG  H11  C9   C10  118.62  3.000
 NKG  C8   C9   C10  120.89  3.000
 NKG  H12  C8   C7   119.95  3.000
 NKG  H12  C8   C9   120.31  3.000
 NKG  C7   C8   C9   119.74  3.000
 NKG  H13  C7   C6   119.65  3.000
 NKG  H13  C7   C8   119.61  3.000
 NKG  C6   C7   C8   120.74  3.000
 NKG  H14  C6   C7   118.91  3.000
 NKG  H14  C6   C5   120.02  3.000
 NKG  C7   C6   C5   121.08  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
 NKG  CONST_01  C4   C3   N    C14  180.00   0.0  0
 NKG  CONST_02  C2   C3   N    C14    0.00   0.0  0
 NKG  CONST_03  C2   C1   C    C14    0.00   0.0  0
 NKG  CONST_04  C3   C2   C1   C      0.00   0.0  0
 NKG  CONST_05  C3   N    C14  C      0.00   0.0  0
 NKG  CONST_08  C1   C2   C3   N      0.00   0.0  0
 NKG  CONST_09  C1   C    C14  N      0.00   0.0  0
 NKG  CONST_10  C10  C5   C4   C3   180.00   0.0  0
 NKG  CONST_11  C6   C5   C4   C3     0.00   0.0  0
 NKG  CONST_12  C12  C13  C4   C3   180.00   0.0  0
 NKG  CONST_15  C4   C3   C2   C1   180.00   0.0  0
 NKG  CONST_16  C9   C10  C5   C4   180.00   0.0  0
 NKG  CONST_17  C11  C10  C5   C4     0.00   0.0  0
 NKG  CONST_18  C7   C6   C5   C4   180.00   0.0  0
 NKG  CONST_19  C11  C12  C13  C4     0.00   0.0  0
 NKG  CONST_20  C10  C11  C12  C13    0.00   0.0  0
 NKG  CONST_21  C10  C5   C4   C13    0.00   0.0  0
 NKG  CONST_22  C6   C5   C4   C13  180.00   0.0  0
 NKG  CONST_23  C9   C10  C11  C12  180.00   0.0  0
 NKG  CONST_24  C5   C10  C11  C12    0.00   0.0  0
 NKG  CONST_25  C5   C4   C13  C12    0.00   0.0  0
 NKG  CONST_26  C8   C9   C10  C11  180.00   0.0  0
 NKG  CONST_27  C6   C5   C10  C11  180.00   0.0  0
 NKG  CONST_28  C7   C8   C9   C10    0.00   0.0  0
 NKG  CONST_29  C7   C6   C5   C10    0.00   0.0  0
 NKG  CONST_30  C8   C9   C10  C5     0.00   0.0  0
 NKG  CONST_31  C8   C7   C6   C5     0.00   0.0  0
 NKG  CONST_32  C6   C7   C8   C9     0.00   0.0  0
 NKG  CONST_33  C6   C5   C10  C9     0.00   0.0  0
 NKG  CONST_34  C3   N    C14  C15  180.00   0.0  0
 NKG  CONST_35  C1   C    C14  C15  180.00   0.0  0
 NKG  CONST_36  C2   C1   C    O    180.00   0.0  0
 NKG  CONST_37  N    C14  C    O    180.00   0.0  0
 NKG  CONST_38  H7   C1   C    C14  180.00   0.0  0
 NKG  CONST_39  H6   C2   C1   C    180.00   0.0  0
 NKG  CONST_40  H8   C13  C4   C3     0.00   0.0  0
 NKG  CONST_41  H14  C6   C5   C4     0.00   0.0  0
 NKG  CONST_42  H9   C12  C13  C4   180.00   0.0  0
 NKG  CONST_43  H10  C11  C12  C13  180.00   0.0  0
 NKG  CONST_44  H11  C9   C10  C11    0.00   0.0  0
 NKG  CONST_45  H12  C8   C9   C10  180.00   0.0  0
 NKG  CONST_46  H13  C7   C6   C5   180.00   0.0  0
 NKG  CONST_47  C14  C15  N1   C16  180.00   0.0  0
 NKG  CONST_48  H1   N1   C15  C14    0.00   0.0  0
 NKG  CONST_49  C16  N1   C15  O3     0.00   0.0  0
 NKG  CONST_50  H4   O2   C17  C16  180.00   0.0  0
 NKG  Var_01    N    C14  C15  O3   179.44  30.0  2
 NKG  Var_02    C17  C16  N1   C15  171.11  30.0  3
 NKG  Var_03    O1   C17  C16  N1     1.18  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
 NKG  plan-1  C15  0.020
 NKG  plan-1  C14  0.020
 NKG  plan-1  C    0.020
 NKG  plan-1  O    0.020
 NKG  plan-1  N    0.020
 NKG  plan-1  C3   0.020
 NKG  plan-1  C2   0.020
 NKG  plan-1  C1   0.020
 NKG  plan-1  C4   0.020
 NKG  plan-1  H6   0.020
 NKG  plan-1  H7   0.020
 NKG  plan-2  C3   0.020
 NKG  plan-2  C4   0.020
 NKG  plan-2  C13  0.020
 NKG  plan-2  C12  0.020
 NKG  plan-2  C11  0.020
 NKG  plan-2  C10  0.020
 NKG  plan-2  C5   0.020
 NKG  plan-2  C9   0.020
 NKG  plan-2  C8   0.020
 NKG  plan-2  C7   0.020
 NKG  plan-2  C6   0.020
 NKG  plan-2  H8   0.020
 NKG  plan-2  H9   0.020
 NKG  plan-2  H10  0.020
 NKG  plan-2  H11  0.020
 NKG  plan-2  H12  0.020
 NKG  plan-2  H13  0.020
 NKG  plan-2  H14  0.020
 NKG  plan-3  O3   0.020
 NKG  plan-3  C15  0.020
 NKG  plan-3  N1   0.020
 NKG  plan-3  C16  0.020
 NKG  plan-3  C14  0.020
 NKG  plan-3  H1   0.020
 NKG  plan-4  C16  0.020
 NKG  plan-4  C17  0.020
 NKG  plan-4  O2   0.020
 NKG  plan-4  O1   0.020
 NKG  plan-4  H4   0.020

