# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:35:24 2021
#   Inital geometry file: a 86 line input string
#   Ligand name: (2R)-({[(3R,6S)-6-carbamoyl-1-formyl-4-methyl-1,2,3,6-tetrahydropyridin-3-yl]amino}oxy)(fluoro)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C[C@H](N(C[C@@H]1NO[C@H](F)C(O)=O)C=O)C(N)=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
 X57  X57  '(2R)-({[(3R,6S)-6-carbamoyl-1-formyl-4-methyl-1,2,3,6-tetrahydropyridin-3-yl]amino}oxy)(fluoro)acetic acid'  ligand  33  19  .  2022-08-11  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_X57
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
 X57  O5   O  O     0  -0.471   7.4840   0.0055  -14.5505
 X57  C9   C  C     0   0.530   7.4189  -0.0964  -13.3386
 X57  N2   N  NH2   0  -0.796   8.3875   0.2814  -12.4980
 X57  C1   C  CH1   0  -0.248   6.1940  -0.7212  -12.6475
 X57  C2   C  C1    0  -0.266   6.5222  -2.1197  -12.2050
 X57  C3   C  C     0   0.127   5.8337  -3.2092  -12.5404
 X57  C8   C  CH3   0  -0.716   6.2326  -4.5753  -12.0781
 X57  C4   C  CH1   0  -0.186   4.6251  -3.0800  -13.4425
 X57  C5   C  CH2   0  -0.322   4.7906  -1.8630  -14.3359
 X57  N    N  NT    0  -0.436   5.0538  -0.6917  -13.5263
 X57  C    C  C1    0   0.263   4.4348   0.4794  -13.7588
 X57  O    O  O     0  -0.482   4.7229   1.5316  -13.2197
 X57  N1   N  NH1   0  -0.357   3.3520  -2.9202  -12.7363
 X57  O2   O  O2    0  -0.387   3.1009  -4.0386  -11.9066
 X57  C6   C  CH1   0   0.356   2.0095  -4.7166  -12.3678
 X57  F    F  F     0  -0.356   2.3066  -5.4175  -13.5103
 X57  C7   C  C     0   0.450   0.8361  -3.7917  -12.6933
 X57  O4   O  OH1   0  -0.586   0.5749  -3.0099  -11.6617
 X57  O3   O  O     0  -0.418   0.2130  -3.8280  -13.7169
 X57  H1   H  HNH2  0   0.407   9.2522   0.6601  -12.8492
 X57  H2   H  HNH2  0   0.413   8.2817   0.2238  -11.4993
 X57  H3   H  HCH1  0   0.310   5.9635  -0.1275  -11.7563
 X57  H4   H  H     0   0.270   7.3830  -2.2054  -11.5510
 X57  H5   H  HCH3  0   0.242   7.1295  -4.5446  -11.4603
 X57  H6   H  HCH3  0   0.248   5.4388  -5.0527  -11.5037
 X57  H7   H  HCH3  0   0.243   6.4342  -5.2242  -12.9337
 X57  H8   H  HCH1  0   0.277   4.5412  -3.9584  -14.0858
 X57  H9   H  HCH2  0   0.277   3.8866  -1.6935  -14.9214
 X57  H10  H  HCH2  0   0.271   5.6106  -2.0385  -15.0355
 X57  H11  H  H     0   0.210   3.6148   0.3886  -14.4863
 X57  H12  H  HNH1  0   0.378   3.4377  -2.1512  -12.0779
 X57  H13  H  HCH1  0   0.266   1.7337  -5.4333  -11.5893
 X57  H14  H  HOH1  0   0.491  -0.1888  -2.4429  -11.8494

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
 X57  C5  N    single  1.448  0.020  1.448
 X57  C5  C4   single  1.519  0.020  1.519
 X57  C   N    single  1.345  0.020  1.345
 X57  C   O    double  1.217  0.020  1.217
 X57  N   C1   single  1.440  0.020  1.440
 X57  C4  N1   single  1.465  0.020  1.465
 X57  C4  C3   single  1.514  0.020  1.514
 X57  O5  C9   double  1.218  0.020  1.218
 X57  F   C6   single  1.373  0.020  1.373
 X57  N1  O2   single  1.415  0.020  1.415
 X57  O2  C6   single  1.365  0.020  1.365
 X57  C9  C1   single  1.539  0.020  1.539
 X57  C9  N2   single  1.337  0.020  1.337
 X57  C1  C2   single  1.503  0.020  1.503
 X57  C6  C7   single  1.529  0.020  1.529
 X57  C3  C2   double  1.332  0.020  1.332
 X57  C3  C8   single  1.496  0.020  1.496
 X57  C7  O3   double  1.199  0.020  1.199
 X57  C7  O4   single  1.320  0.020  1.320
 X57  N2  H1   single  0.860  0.020  1.020
 X57  N2  H2   single  0.860  0.020  1.020
 X57  C1  H3   single  0.970  0.020  1.090
 X57  C2  H4   single  0.930  0.020  1.080
 X57  C8  H5   single  0.970  0.020  1.090
 X57  C8  H6   single  0.970  0.020  1.090
 X57  C8  H7   single  0.970  0.020  1.090
 X57  C4  H8   single  0.970  0.020  1.090
 X57  C5  H9   single  0.970  0.020  1.090
 X57  C5  H10  single  0.970  0.020  1.090
 X57  C   H11  single  0.930  0.020  1.080
 X57  N1  H12  single  0.890  0.020  1.040
 X57  C6  H13  single  0.970  0.020  1.090
 X57  O4  H14  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
 X57  C1   C9  N2  114.14  3.000
 X57  N2   C9  O5  124.28  3.000
 X57  C1   C9  O5  121.56  3.000
 X57  H2   N2  H1  117.26  3.000
 X57  H2   N2  C9  122.12  3.000
 X57  H1   N2  C9  120.59  3.000
 X57  H3   C1  N   108.59  3.000
 X57  H3   C1  C2  108.10  3.000
 X57  N    C1  C2  111.81  3.000
 X57  H3   C1  C9  108.23  3.000
 X57  C2   C1  C9  109.64  3.000
 X57  N    C1  C9  110.36  3.000
 X57  H4   C2  C3  119.84  3.000
 X57  H4   C2  C1  115.11  3.000
 X57  C3   C2  C1  125.04  3.000
 X57  C4   C3  C8  118.35  3.000
 X57  C8   C3  C2  122.09  3.000
 X57  C4   C3  C2  119.54  3.000
 X57  H7   C8  H6  106.67  3.000
 X57  H7   C8  H5  107.99  3.000
 X57  H6   C8  H5  108.24  3.000
 X57  H7   C8  C3  110.46  3.000
 X57  H6   C8  C3  111.62  3.000
 X57  H5   C8  C3  111.65  3.000
 X57  H8   C4  N1  107.76  3.000
 X57  H8   C4  C5  107.84  3.000
 X57  N1   C4  C5  106.92  3.000
 X57  H8   C4  C3  110.11  3.000
 X57  N1   C4  C3  114.58  3.000
 X57  C5   C4  C3  109.39  3.000
 X57  H10  C5  H9  107.67  3.000
 X57  H10  C5  N   110.59  3.000
 X57  H9   C5  N   108.98  3.000
 X57  H10  C5  C4  109.26  3.000
 X57  H9   C5  C4  110.50  3.000
 X57  N    C5  C4  109.82  3.000
 X57  C    N   C5  121.61  3.000
 X57  C    N   C1  119.19  3.000
 X57  C5   N   C1  117.95  3.000
 X57  H11  C   O   122.75  3.000
 X57  H11  C   N   112.67  3.000
 X57  O    C   N   124.57  3.000
 X57  H12  N1  O2  103.49  3.000
 X57  H12  N1  C4  108.77  3.000
 X57  O2   N1  C4  110.53  3.000
 X57  C6   O2  N1  109.65  3.000
 X57  H13  C6  C7  110.76  3.000
 X57  H13  C6  F   108.21  3.000
 X57  C7   C6  F   107.32  3.000
 X57  H13  C6  O2  106.66  3.000
 X57  C7   C6  O2  112.64  3.000
 X57  F    C6  O2  111.20  3.000
 X57  O3   C7  O4  125.60  3.000
 X57  O4   C7  C6  110.10  3.000
 X57  O3   C7  C6  124.21  3.000
 X57  H14  O4  C7  110.54  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
 X57  CONST_01  O    C   N   C1    0.00   0.0  0
 X57  CONST_02  O    C   N   C5  180.00   0.0  0
 X57  CONST_03  H1   N2  C9  C1  180.00   0.0  0
 X57  CONST_04  H2   N2  C9  C1    0.00   0.0  0
 X57  CONST_05  H14  O4  C7  C6  180.00   0.0  0
 X57  Var_01    C4   C5  N   C1   57.38  30.0  1
 X57  Var_02    C4   C3  C2  C1    0.44  30.0  1
 X57  Var_03    H5   C8  C3  C2   -0.24  30.0  3
 X57  Var_04    H12  N1  O2  C6  129.61  30.0  1

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
 X57  chir_01  C1  N   C9  C2  positiv
 X57  chir_02  C4  N1  C5  C3  negativ
 X57  chir_03  C6  F   O2  C7  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
 X57  plan-1  O5   0.020
 X57  plan-1  C9   0.020
 X57  plan-1  N2   0.020
 X57  plan-1  C1   0.020
 X57  plan-1  H1   0.020
 X57  plan-1  H2   0.020
 X57  plan-2  C1   0.020
 X57  plan-2  C5   0.020
 X57  plan-2  N    0.020
 X57  plan-2  C    0.020
 X57  plan-2  O    0.020
 X57  plan-2  H11  0.020
 X57  plan-3  C6   0.020
 X57  plan-3  C7   0.020
 X57  plan-3  O4   0.020
 X57  plan-3  O3   0.020
 X57  plan-3  H14  0.020

