# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 12:28:13 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-(5-{[(1S)-2-carboxy-1-formylethyl]carbamoyl}pyridin-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](NC(=O)c1cncc(c1)c2ccc(cc2)C(O)=O)C=O
#
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
 NA4  NA4  '4-(5-{[(1S)-2-carboxy-1-formylethyl]carbamoyl}pyridin-3-yl)benzoic acid'  ligand  39  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NA4
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
 NA4  C7   C  CR16  0  -0.203  -0.2587   0.0974  -0.1050
 NA4  C8   C  CR6   0   0.013  -1.2918   0.8432   0.4486
 NA4  C9   C  CR16  0  -0.084  -0.9335   1.9579   1.2091
 NA4  N2   N  N     0  -0.391   0.3169   2.3413   1.4111
 NA4  C10  C  CR16  0  -0.077   1.2908   1.6154   0.8805
 NA4  C6   C  CR6   0  -0.128   1.0583   0.4706   0.1252
 NA4  C5   C  C     0   0.554   2.1537  -0.3342  -0.4915
 NA4  O4   O  O     0  -0.473   1.9691  -0.9602  -1.5227
 NA4  N1   N  NH1   0  -0.643   3.3342  -0.3039   0.1546
 NA4  C3   C  CH1   0  -0.204   4.4722  -1.0530  -0.2954
 NA4  C2   C  CH2   0  -0.611   5.7730  -0.3479   0.0636
 NA4  C4   C  C1    0   0.195   4.4785  -2.4680   0.2415
 NA4  O3   O  O     0  -0.356   3.6012  -2.9396   0.9122
 NA4  C1   C  C     0   0.571   5.9603   0.9273  -0.7182
 NA4  O2   O  O     0  -0.431   5.3719   1.2013  -1.7322
 NA4  O1   O  OH1   0  -0.590   6.8799   1.7057  -0.1660
 NA4  C15  C  CR16  0  -0.241  -4.4134  -1.2192   0.0295
 NA4  C16  C  CR16  0  -0.296  -3.0872  -0.8652   0.2047
 NA4  C11  C  CR6   0   0.095  -2.7045   0.4753   0.2560
 NA4  C12  C  CR16  0  -0.294  -3.6883   1.4568   0.1250
 NA4  C13  C  CR16  0  -0.240  -5.0148   1.1064  -0.0462
 NA4  C14  C  CR6   0  -0.092  -5.3911  -0.2339  -0.0955
 NA4  C17  C  C     0   0.534  -6.8276  -0.5572  -0.2759
 NA4  O5   O  OH1   0  -0.593  -7.0625  -1.8597  -0.3402
 NA4  O6   O  O     0  -0.437  -7.6972   0.2776  -0.3547
 NA4  H7   H  HCR6  0   0.278  -0.4726  -0.7683  -0.7194
 NA4  H9   H  HCR6  0   0.274  -1.7001   2.5580   1.6876
 NA4  H10  H  HCR6  0   0.273   2.2988   1.9796   1.0479
 NA4  HN1  H  HNH1  0   0.413   3.3636   0.0522   1.0977
 NA4  H3   H  HCH1  0   0.307   4.4243  -1.1531  -1.3846
 NA4  H21  H  HCH2  0   0.315   6.6228  -1.0002  -0.1636
 NA4  H22  H  HCH2  0   0.301   5.8306  -0.1461   1.1358
 NA4  H4   H  H     0   0.209   5.3652  -3.0560  -0.0543
 NA4  HO1  H  HOH1  0   0.484   7.0122   2.4996  -0.7059
 NA4  H16  H  HCR6  0   0.268  -2.3472  -1.6460   0.3234
 NA4  H12  H  HCR6  0   0.266  -3.4184   2.5050   0.1373
 NA4  H13  H  HCR6  0   0.271  -5.7601   1.8832  -0.1489
 NA4  HO5  H  HOH1  0   0.489  -8.0117  -2.0202  -0.4506
 NA4  H15  H  HCR6  0   0.272  -4.6730  -2.2682   0.0005

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
 NA4  C7   C8   aromatic  1.389  0.020  1.389
 NA4  C7   C6   aromatic  1.388  0.020  1.388
 NA4  C7   H7   single    0.930  0.020  1.080
 NA4  C8   C9   aromatic  1.396  0.020  1.396
 NA4  C8   C11  single    1.472  0.020  1.472
 NA4  C9   N2   aromatic  1.323  0.020  1.323
 NA4  C9   H9   single    0.930  0.020  1.080
 NA4  N2   C10  aromatic  1.326  0.020  1.326
 NA4  C10  C6   aromatic  1.391  0.020  1.391
 NA4  C10  H10  single    0.930  0.020  1.080
 NA4  C6   C5   single    1.493  0.020  1.493
 NA4  C5   O4   double    1.220  0.020  1.220
 NA4  C5   N1   single    1.346  0.020  1.346
 NA4  N1   C3   single    1.435  0.020  1.435
 NA4  N1   HN1  single    0.860  0.020  1.020
 NA4  C3   C2   single    1.522  0.020  1.522
 NA4  C3   C4   single    1.513  0.020  1.513
 NA4  C3   H3   single    0.970  0.020  1.090
 NA4  C2   C1   single    1.507  0.020  1.507
 NA4  C2   H21  single    0.970  0.020  1.090
 NA4  C2   H22  single    0.970  0.020  1.090
 NA4  C4   O3   double    1.201  0.020  1.201
 NA4  C4   H4   single    0.930  0.020  1.080
 NA4  C1   O2   double    1.204  0.020  1.204
 NA4  C1   O1   single    1.325  0.020  1.325
 NA4  O1   HO1  single    0.850  0.020  0.980
 NA4  C15  C16  aromatic  1.384  0.020  1.384
 NA4  C15  C14  aromatic  1.394  0.020  1.394
 NA4  C15  H15  single    0.930  0.020  1.080
 NA4  C16  C11  aromatic  1.395  0.020  1.395
 NA4  C16  H16  single    0.930  0.020  1.080
 NA4  C11  C12  aromatic  1.396  0.020  1.396
 NA4  C12  C13  aromatic  1.383  0.020  1.383
 NA4  C12  H12  single    0.930  0.020  1.080
 NA4  C13  C14  aromatic  1.393  0.020  1.393
 NA4  C13  H13  single    0.930  0.020  1.080
 NA4  C14  C17  single    1.483  0.020  1.483
 NA4  C17  O5   single    1.325  0.020  1.325
 NA4  C17  O6   double    1.208  0.020  1.208
 NA4  O5   HO5  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
 NA4  H7   C7   C6   119.77  3.000
 NA4  H7   C7   C8   120.55  3.000
 NA4  C6   C7   C8   119.68  3.000
 NA4  C11  C8   C9   121.13  3.000
 NA4  C11  C8   C7   121.82  3.000
 NA4  C9   C8   C7   117.05  3.000
 NA4  H9   C9   N2   116.11  3.000
 NA4  H9   C9   C8   120.04  3.000
 NA4  N2   C9   C8   123.84  3.000
 NA4  C10  N2   C9   118.32  3.000
 NA4  H10  C10  C6   121.02  3.000
 NA4  H10  C10  N2   115.92  3.000
 NA4  C6   C10  N2   123.04  3.000
 NA4  C5   C6   C10  123.05  3.000
 NA4  C5   C6   C7   118.87  3.000
 NA4  C10  C6   C7   118.03  3.000
 NA4  N1   C5   O4   123.34  3.000
 NA4  N1   C5   C6   115.67  3.000
 NA4  O4   C5   C6   120.98  3.000
 NA4  HN1  N1   C3   117.04  3.000
 NA4  HN1  N1   C5   118.83  3.000
 NA4  C3   N1   C5   122.23  3.000
 NA4  H3   C3   C4   105.52  3.000
 NA4  H3   C3   C2   108.32  3.000
 NA4  C4   C3   C2   110.23  3.000
 NA4  H3   C3   N1   108.97  3.000
 NA4  C4   C3   N1   112.35  3.000
 NA4  C2   C3   N1   111.22  3.000
 NA4  H22  C2   H21  105.83  3.000
 NA4  H22  C2   C1   110.25  3.000
 NA4  H21  C2   C1   107.45  3.000
 NA4  H22  C2   C3   111.22  3.000
 NA4  H21  C2   C3   109.77  3.000
 NA4  C1   C2   C3   112.06  3.000
 NA4  H4   C4   O3   121.81  3.000
 NA4  H4   C4   C3   113.96  3.000
 NA4  O3   C4   C3   124.22  3.000
 NA4  O1   C1   O2   123.80  3.000
 NA4  O1   C1   C2   111.53  3.000
 NA4  O2   C1   C2   124.66  3.000
 NA4  HO1  O1   C1   110.10  3.000
 NA4  H15  C15  C14  121.01  3.000
 NA4  H15  C15  C16  118.80  3.000
 NA4  C14  C15  C16  120.19  3.000
 NA4  H16  C16  C11  120.11  3.000
 NA4  H16  C16  C15  118.99  3.000
 NA4  C11  C16  C15  120.89  3.000
 NA4  C12  C11  C16  118.62  3.000
 NA4  C12  C11  C8   120.85  3.000
 NA4  C16  C11  C8   120.54  3.000
 NA4  H12  C12  C13  119.08  3.000
 NA4  H12  C12  C11  120.28  3.000
 NA4  C13  C12  C11  120.63  3.000
 NA4  H13  C13  C14  120.11  3.000
 NA4  H13  C13  C12  119.40  3.000
 NA4  C14  C13  C12  120.49  3.000
 NA4  C17  C14  C13  118.40  3.000
 NA4  C17  C14  C15  122.42  3.000
 NA4  C13  C14  C15  119.18  3.000
 NA4  O6   C17  O5   123.26  3.000
 NA4  O6   C17  C14  123.67  3.000
 NA4  O5   C17  C14  113.07  3.000
 NA4  HO5  O5   C17  110.00  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
 NA4  CONST_01  N2   C9   C8   C7     0.00   0.0  0
 NA4  CONST_04  N2   C10  C6   C7     0.00   0.0  0
 NA4  CONST_05  C10  C6   C7   C8     0.00   0.0  0
 NA4  CONST_06  C10  N2   C9   C8     0.00   0.0  0
 NA4  CONST_07  C15  C16  C11  C8   180.00   0.0  0
 NA4  CONST_08  C13  C12  C11  C8   180.00   0.0  0
 NA4  CONST_09  C6   C7   C8   C9     0.00   0.0  0
 NA4  CONST_12  C6   C10  N2   C9     0.00   0.0  0
 NA4  CONST_13  C11  C8   C9   N2   180.00   0.0  0
 NA4  CONST_14  C11  C8   C7   C6   180.00   0.0  0
 NA4  CONST_15  C12  C11  C16  C15    0.00   0.0  0
 NA4  CONST_16  C12  C13  C14  C15    0.00   0.0  0
 NA4  CONST_17  C13  C14  C15  C16    0.00   0.0  0
 NA4  CONST_18  C13  C12  C11  C16    0.00   0.0  0
 NA4  CONST_19  C14  C15  C16  C11    0.00   0.0  0
 NA4  CONST_20  C14  C13  C12  C11    0.00   0.0  0
 NA4  CONST_21  C5   C6   C7   C8   180.00   0.0  0
 NA4  CONST_22  C5   C6   C10  N2   180.00   0.0  0
 NA4  CONST_23  C17  C14  C15  C16  180.00   0.0  0
 NA4  CONST_24  C17  C14  C13  C12  180.00   0.0  0
 NA4  CONST_25  H9   C9   C8   C7   180.00   0.0  0
 NA4  CONST_26  H10  C10  C6   C7   180.00   0.0  0
 NA4  CONST_27  H16  C16  C11  C8     0.00   0.0  0
 NA4  CONST_28  H12  C12  C11  C8     0.00   0.0  0
 NA4  CONST_29  H7   C7   C8   C9   180.00   0.0  0
 NA4  CONST_30  H13  C13  C14  C15  180.00   0.0  0
 NA4  CONST_31  H15  C15  C16  C11  180.00   0.0  0
 NA4  CONST_32  C3   N1   C5   C6   180.00   0.0  0
 NA4  CONST_33  HN1  N1   C5   C6     0.00   0.0  0
 NA4  CONST_34  HO5  O5   C17  C14  180.00   0.0  0
 NA4  CONST_35  C3   N1   C5   O4     0.00   0.0  0
 NA4  CONST_36  HO1  O1   C1   C2   180.00   0.0  0
 NA4  Var_01    O4   C5   C6   C7    26.82  30.0  2
 NA4  Var_02    O5   C17  C14  C15   -1.74  30.0  2
 NA4  Var_03    O2   C1   C2   C3   -18.19  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NA4  chir_01  C3  N1  C2  C4  negativ

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
 NA4  plan-1  C7   0.020
 NA4  plan-1  C8   0.020
 NA4  plan-1  C9   0.020
 NA4  plan-1  N2   0.020
 NA4  plan-1  C10  0.020
 NA4  plan-1  C6   0.020
 NA4  plan-1  C5   0.020
 NA4  plan-1  C11  0.020
 NA4  plan-1  H7   0.020
 NA4  plan-1  H9   0.020
 NA4  plan-1  H10  0.020
 NA4  plan-2  C8   0.020
 NA4  plan-2  C15  0.020
 NA4  plan-2  C16  0.020
 NA4  plan-2  C11  0.020
 NA4  plan-2  C12  0.020
 NA4  plan-2  C13  0.020
 NA4  plan-2  C14  0.020
 NA4  plan-2  C17  0.020
 NA4  plan-2  H16  0.020
 NA4  plan-2  H12  0.020
 NA4  plan-2  H13  0.020
 NA4  plan-2  H15  0.020
 NA4  plan-3  C6   0.020
 NA4  plan-3  C5   0.020
 NA4  plan-3  O4   0.020
 NA4  plan-3  N1   0.020
 NA4  plan-3  C3   0.020
 NA4  plan-3  HN1  0.020
 NA4  plan-4  C2   0.020
 NA4  plan-4  C1   0.020
 NA4  plan-4  O2   0.020
 NA4  plan-4  O1   0.020
 NA4  plan-4  HO1  0.020
 NA4  plan-5  C14  0.020
 NA4  plan-5  C17  0.020
 NA4  plan-5  O5   0.020
 NA4  plan-5  O6   0.020
 NA4  plan-5  HO5  0.020
 NA4  plan-6  C3   0.020
 NA4  plan-6  C4   0.020
 NA4  plan-6  O3   0.020
 NA4  plan-6  H4   0.020

