# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:09:38 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  37  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  -0.211  -0.2666   0.1067  -0.1585
 NA4  C8   C  CR6    0   0.015  -1.3037   0.8599   0.3792
 NA4  C9   C  CR16   0  -0.092  -0.9473   2.0214   1.0682
 NA4  N2   N  N      0  -0.392   0.2998   2.4385   1.2204
 NA4  C10  C  CR16   0  -0.085   1.2763   1.7001   0.7117
 NA4  C6   C  CR6    0  -0.123   1.0483   0.5129   0.0238
 NA4  C5   C  C      0   0.543   2.1480  -0.3062  -0.5675
 NA4  O4   O  O      0  -0.484   1.9690  -0.9589  -1.5855
 NA4  N1   N  NH1    0  -0.639   3.3212  -0.2656   0.0824
 NA4  C3   C  CH1    0  -0.183   4.4644  -1.0208  -0.3542
 NA4  C2   C  CH2    0  -0.621   5.7396  -0.4977   0.2961
 NA4  C4   C  C1     0   0.186   4.3193  -2.4927  -0.0642
 NA4  O3   O  O      0  -0.374   3.4109  -2.9938   0.5460
 NA4  C1   C  C      0   0.431   6.1391   0.9185  -0.1792
 NA4  O2   O  O      0  -0.597   5.8201   1.2316  -1.3402
 NA4  O1   O  OC    -1  -0.610   6.7823   1.6032   0.6374
 NA4  C15  C  CR16   0  -0.273  -4.3972  -1.2790   0.1602
 NA4  C16  C  CR16   0  -0.301  -3.0707  -0.8956   0.2731
 NA4  C11  C  CR6    0   0.079  -2.7131   0.4530   0.2467
 NA4  C12  C  CR16   0  -0.298  -3.7257   1.4023   0.1006
 NA4  C13  C  CR16   0  -0.275  -5.0510   1.0119  -0.0074
 NA4  C14  C  CR6    0  -0.106  -5.4097  -0.3332   0.0218
 NA4  C17  C  C      0   0.397  -6.8688  -0.7583  -0.0904
 NA4  O5   O  OC    -1  -0.591  -7.0932  -1.9836  -0.0877
 NA4  O6   O  O      0  -0.592  -7.7104   0.1564  -0.1723
 NA4  H7   H  HCR6   0   0.273  -0.4783  -0.7940  -0.7213
 NA4  H9   H  HCR6   0   0.269  -1.7151   2.6345   1.5285
 NA4  H10  H  HCR6   0   0.269   2.2820   2.0864   0.8406
 NA4  HN1  H  HNH1   0   0.408   3.3627   0.1592   0.9956
 NA4  H3   H  HCH1   0   0.279   4.5800  -0.9188  -1.4380
 NA4  H21  H  HCH2   0   0.263   6.5631  -1.1748   0.0430
 NA4  H22  H  HCH2   0   0.240   5.6503  -0.5310   1.3855
 NA4  H4   H  H      0   0.201   5.1512  -3.1027  -0.4616
 NA4  H12  H  HCR6   0   0.250  -3.4789   2.4561   0.0521
 NA4  H13  H  HCR6   0   0.247  -5.8193   1.7648  -0.1211
 NA4  H15  H  HCR6   0   0.246  -4.6504  -2.3304   0.1898
 NA4  H16  H  HCR6   0   0.252  -2.3094  -1.6547   0.4053

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  1.390  0.020  1.390
 NA4  C7   C6   aromatic  1.388  0.020  1.388
 NA4  C7   H7   single    0.930  0.020  1.080
 NA4  C8   C9   aromatic  1.397  0.020  1.397
 NA4  C8   C11  single    1.473  0.020  1.473
 NA4  C9   N2   aromatic  1.324  0.020  1.324
 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    1.222  0.020  1.222
 NA4  C5   N1   single    1.342  0.020  1.342
 NA4  N1   C3   single    1.438  0.020  1.438
 NA4  N1   HN1  single    0.860  0.020  1.020
 NA4  C3   C2   single    1.524  0.020  1.524
 NA4  C3   C4   single    1.507  0.020  1.507
 NA4  C3   H3   single    0.970  0.020  1.090
 NA4  C2   C1   single    1.546  0.020  1.546
 NA4  C2   H21  single    0.970  0.020  1.090
 NA4  C2   H22  single    0.970  0.020  1.090
 NA4  C4   O3   double    1.204  0.020  1.204
 NA4  C4   H4   single    0.930  0.020  1.080
 NA4  C1   O2   deloc     1.244  0.020  1.244
 NA4  C1   O1   deloc     1.245  0.020  1.245
 NA4  C15  C16  aromatic  1.385  0.020  1.385
 NA4  C15  C14  aromatic  1.392  0.020  1.392
 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  1.386  0.020  1.386
 NA4  C12  H12  single    0.930  0.020  1.080
 NA4  C13  C14  aromatic  1.392  0.020  1.392
 NA4  C13  H13  single    0.930  0.020  1.080
 NA4  C14  C17  single    1.524  0.020  1.524
 NA4  C17  O5   deloc     1.246  0.020  1.246
 NA4  C17  O6   deloc     1.246  0.020  1.246

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   119.78  3.000
 NA4  H7   C7   C8   120.39  3.000
 NA4  C6   C7   C8   119.82  3.000
 NA4  C11  C8   C9   121.21  3.000
 NA4  C11  C8   C7   121.97  3.000
 NA4  C9   C8   C7   116.82  3.000
 NA4  H9   C9   N2   116.09  3.000
 NA4  H9   C9   C8   119.91  3.000
 NA4  N2   C9   C8   123.99  3.000
 NA4  C10  N2   C9   118.32  3.000
 NA4  H10  C10  C6   120.98  3.000
 NA4  H10  C10  N2   116.03  3.000
 NA4  C6   C10  N2   122.98  3.000
 NA4  C5   C6   C10  122.90  3.000
 NA4  C5   C6   C7   119.02  3.000
 NA4  C10  C6   C7   118.03  3.000
 NA4  N1   C5   O4   123.20  3.000
 NA4  N1   C5   C6   115.82  3.000
 NA4  O4   C5   C6   120.98  3.000
 NA4  HN1  N1   C3   117.63  3.000
 NA4  HN1  N1   C5   119.18  3.000
 NA4  C3   N1   C5   122.14  3.000
 NA4  H3   C3   C4   106.96  3.000
 NA4  H3   C3   C2   107.58  3.000
 NA4  C4   C3   C2   109.49  3.000
 NA4  H3   C3   N1   109.61  3.000
 NA4  C4   C3   N1   112.21  3.000
 NA4  C2   C3   N1   110.81  3.000
 NA4  H22  C2   H21  105.82  3.000
 NA4  H22  C2   C1   110.81  3.000
 NA4  H21  C2   C1   107.51  3.000
 NA4  H22  C2   C3   110.26  3.000
 NA4  H21  C2   C3   108.55  3.000
 NA4  C1   C2   C3   113.54  3.000
 NA4  H4   C4   O3   121.36  3.000
 NA4  H4   C4   C3   113.41  3.000
 NA4  O3   C4   C3   125.22  3.000
 NA4  O1   C1   O2   127.33  3.000
 NA4  O1   C1   C2   115.82  3.000
 NA4  O2   C1   C2   116.81  3.000
 NA4  H15  C15  C14  119.51  3.000
 NA4  H15  C15  C16  119.40  3.000
 NA4  C14  C15  C16  121.09  3.000
 NA4  H16  C16  C11  119.96  3.000
 NA4  H16  C16  C15  119.27  3.000
 NA4  C11  C16  C15  120.75  3.000
 NA4  C12  C11  C16  118.25  3.000
 NA4  C12  C11  C8   121.05  3.000
 NA4  C16  C11  C8   120.69  3.000
 NA4  H12  C12  C13  119.23  3.000
 NA4  H12  C12  C11  120.06  3.000
 NA4  C13  C12  C11  120.69  3.000
 NA4  H13  C13  C14  119.44  3.000
 NA4  H13  C13  C12  119.44  3.000
 NA4  C14  C13  C12  121.12  3.000
 NA4  C17  C14  C13  120.97  3.000
 NA4  C17  C14  C15  120.93  3.000
 NA4  C13  C14  C15  118.09  3.000
 NA4  O6   C17  O5   126.92  3.000
 NA4  O6   C17  C14  116.54  3.000
 NA4  O5   C17  C14  116.54  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  C3   N1   C5   O4     0.00   0.0  0
 NA4  Var_01    O4   C5   C6   C7    29.28  30.0  2
 NA4  Var_02    O5   C17  C14  C15   -1.87  30.0  2
 NA4  Var_03    O2   C1   C2   C3   -30.30  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  H12  0.020
 NA4  plan-2  H13  0.020
 NA4  plan-2  H15  0.020
 NA4  plan-2  H16  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-5  C14  0.020
 NA4  plan-5  C17  0.020
 NA4  plan-5  O5   0.020
 NA4  plan-5  O6   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

