# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:59:06 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (3S)-3-{[(5-bromopyridin-3-yl)carbonyl]amino}-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](NC(=O)c1cncc(Br)c1)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
 NA3  NA3  '(3S)-3-{[(5-bromopyridin-3-yl)carbonyl]amino}-4-oxobutanoic acid'  ligand  25  17  .  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_NA3
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
 NA3  C7   C   CR16   0  -0.122  -1.4430  -0.0222  -0.3785
 NA3  C8   C   CR6    0  -0.180  -2.5616   0.5620   0.1840
 NA3  C9   C   CR16   0  -0.030  -2.5167   1.0039   1.5017
 NA3  N2   N   N      0  -0.389  -1.4289   0.8843   2.2451
 NA3  C10  C   CR16   0  -0.067  -0.3446   0.3423   1.7080
 NA3  C6   C   CR6    0  -0.133  -0.2931  -0.1174   0.3968
 NA3  BR1  BR  BR     0  -0.008  -4.1424   0.7592  -0.8119
 NA3  C5   C   C      0   0.550   0.9181  -0.7637  -0.1979
 NA3  O4   O   O      0  -0.483   0.8041  -1.6275  -1.0549
 NA3  N1   N   NH1    0  -0.641   2.0984  -0.3235   0.2542
 NA3  C3   C   CH1    0  -0.175   3.3490  -0.8869  -0.1779
 NA3  C2   C   CH2    0  -0.632   4.4983   0.0781   0.0832
 NA3  C4   C   C1     0   0.186   3.6231  -2.2153   0.4790
 NA3  O3   O   O      0  -0.371   2.9191  -2.7415   1.3005
 NA3  C1   C   C      0   0.432   4.4708   1.3356  -0.8187
 NA3  O2   O   OC    -1  -0.611   5.0818   2.3269  -0.3789
 NA3  O1   O   O      0  -0.594   3.8740   1.2365  -1.9058
 NA3  H7   H   HCR6   0   0.298  -1.4476  -0.3883  -1.3968
 NA3  H9   H   HCR6   0   0.291  -3.3830   1.4607   1.9665
 NA3  H10  H   HCR6   0   0.278   0.5131   0.2512   2.3656
 NA3  HN1  H   HNH1   0   0.412   2.1305   0.4382   0.9124
 NA3  H3   H   HCH1   0   0.280   3.3176  -1.0738  -1.2568
 NA3  H21  H   HCH2   0   0.265   5.4431  -0.4424  -0.1068
 NA3  H22  H   HCH2   0   0.245   4.5227   0.3635   1.1385
 NA3  H4   H   H      0   0.200   4.5544  -2.6960   0.1261

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
 NA3  C7   C8   aromatic  1.382  0.020  1.382
 NA3  C7   C6   aromatic  1.390  0.020  1.390
 NA3  C7   H7   single    0.930  0.020  1.080
 NA3  C8   C9   aromatic  1.390  0.020  1.390
 NA3  C8   BR1  single    1.879  0.020  1.879
 NA3  C9   N2   aromatic  1.323  0.020  1.323
 NA3  C9   H9   single    0.930  0.020  1.080
 NA3  N2   C10  aromatic  1.326  0.020  1.326
 NA3  C10  C6   aromatic  1.390  0.020  1.390
 NA3  C10  H10  single    0.930  0.020  1.080
 NA3  C6   C5   single    1.496  0.020  1.496
 NA3  C5   O4   double    1.222  0.020  1.222
 NA3  C5   N1   single    1.338  0.020  1.338
 NA3  N1   C3   single    1.438  0.020  1.438
 NA3  N1   HN1  single    0.860  0.020  1.020
 NA3  C3   C2   single    1.523  0.020  1.523
 NA3  C3   C4   single    1.507  0.020  1.507
 NA3  C3   H3   single    0.970  0.020  1.090
 NA3  C2   C1   single    1.548  0.020  1.548
 NA3  C2   H21  single    0.970  0.020  1.090
 NA3  C2   H22  single    0.970  0.020  1.090
 NA3  C4   O3   double    1.203  0.020  1.203
 NA3  C4   H4   single    0.930  0.020  1.080
 NA3  C1   O2   deloc     1.245  0.020  1.245
 NA3  C1   O1   deloc     1.244  0.020  1.244

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
 NA3  H7   C7   C6   120.34  3.000
 NA3  H7   C7   C8   121.52  3.000
 NA3  C6   C7   C8   118.14  3.000
 NA3  BR1  C8   C9   119.74  3.000
 NA3  BR1  C8   C7   120.65  3.000
 NA3  C9   C8   C7   119.61  3.000
 NA3  H9   C9   N2   117.01  3.000
 NA3  H9   C9   C8   120.96  3.000
 NA3  N2   C9   C8   122.03  3.000
 NA3  C10  N2   C9   118.79  3.000
 NA3  H10  C10  C6   120.98  3.000
 NA3  H10  C10  N2   115.81  3.000
 NA3  C6   C10  N2   123.20  3.000
 NA3  C5   C6   C10  123.21  3.000
 NA3  C5   C6   C7   118.53  3.000
 NA3  C10  C6   C7   118.21  3.000
 NA3  N1   C5   O4   123.47  3.000
 NA3  N1   C5   C6   115.95  3.000
 NA3  O4   C5   C6   120.57  3.000
 NA3  HN1  N1   C3   117.70  3.000
 NA3  HN1  N1   C5   119.84  3.000
 NA3  C3   N1   C5   122.45  3.000
 NA3  H3   C3   C4   106.51  3.000
 NA3  H3   C3   C2   107.37  3.000
 NA3  C4   C3   C2   110.27  3.000
 NA3  H3   C3   N1   109.74  3.000
 NA3  C4   C3   N1   111.87  3.000
 NA3  C2   C3   N1   110.88  3.000
 NA3  H22  C2   H21  105.80  3.000
 NA3  H22  C2   C1   110.53  3.000
 NA3  H21  C2   C1   107.47  3.000
 NA3  H22  C2   C3   110.34  3.000
 NA3  H21  C2   C3   108.67  3.000
 NA3  C1   C2   C3   113.67  3.000
 NA3  H4   C4   O3   121.37  3.000
 NA3  H4   C4   C3   113.40  3.000
 NA3  O3   C4   C3   125.22  3.000
 NA3  O1   C1   O2   127.42  3.000
 NA3  O1   C1   C2   116.93  3.000
 NA3  O2   C1   C2   115.62  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
 NA3  CONST_01  N2   C9   C8   C7    0.00   0.0  0
 NA3  CONST_02  N2   C10  C6   C7    0.00   0.0  0
 NA3  CONST_03  C10  C6   C7   C8    0.00   0.0  0
 NA3  CONST_04  C10  N2   C9   C8    0.00   0.0  0
 NA3  CONST_05  C6   C7   C8   C9    0.00   0.0  0
 NA3  CONST_06  C6   C10  N2   C9    0.00   0.0  0
 NA3  CONST_07  C5   C6   C7   C8  180.00   0.0  0
 NA3  CONST_08  BR1  C8   C9   N2  180.00   0.0  0
 NA3  CONST_09  C5   C6   C10  N2  180.00   0.0  0
 NA3  CONST_10  BR1  C8   C7   C6  180.00   0.0  0
 NA3  CONST_11  H9   C9   C8   C7  180.00   0.0  0
 NA3  CONST_12  H10  C10  C6   C7  180.00   0.0  0
 NA3  CONST_13  H7   C7   C8   C9  180.00   0.0  0
 NA3  CONST_14  C3   N1   C5   C6  180.00   0.0  0
 NA3  CONST_15  HN1  N1   C5   C6    0.00   0.0  0
 NA3  CONST_16  C3   N1   C5   O4    0.00   0.0  0
 NA3  Var_01    O4   C5   C6   C7  -28.83  30.0  2
 NA3  Var_02    O2   C1   C2   C3  157.30  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
 NA3  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
 NA3  plan-1  C7   0.020
 NA3  plan-1  C8   0.020
 NA3  plan-1  C9   0.020
 NA3  plan-1  N2   0.020
 NA3  plan-1  C10  0.020
 NA3  plan-1  C6   0.020
 NA3  plan-1  BR1  0.020
 NA3  plan-1  C5   0.020
 NA3  plan-1  H7   0.020
 NA3  plan-1  H9   0.020
 NA3  plan-1  H10  0.020
 NA3  plan-2  C6   0.020
 NA3  plan-2  C5   0.020
 NA3  plan-2  O4   0.020
 NA3  plan-2  N1   0.020
 NA3  plan-2  C3   0.020
 NA3  plan-2  HN1  0.020
 NA3  plan-3  C2   0.020
 NA3  plan-3  C1   0.020
 NA3  plan-3  O2   0.020
 NA3  plan-3  O1   0.020
 NA3  plan-4  C3   0.020
 NA3  plan-4  C4   0.020
 NA3  plan-4  O3   0.020
 NA3  plan-4  H4   0.020

