# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:32:46 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (2R,3R)-3-methyl-2,3-dihydro-1H-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C=CN[C@H]1C(O)=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
 BGX  BGX  '(2R,3R)-3-methyl-2,3-dihydro-1H-pyrrole-2-carboxylic acid'  ligand  18  9  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BGX
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
 BGX  C1    C  C     0   0.530  -1.3469  -3.9244   1.2137
 BGX  C2    C  CR15  0  -0.161  -1.6912  -2.6167   0.5441
 BGX  C3    C  CR15  0  -0.275  -2.4114  -1.6360   1.5265
 BGX  C4    C  CR15  0  -0.338  -1.7288  -0.3345   1.1929
 BGX  C5    C  CR15  0  -0.026  -0.6977  -0.5610   0.3817
 BGX  C6    C  CH3   0  -0.658  -3.9238  -1.6155   1.3565
 BGX  O1    O  O     0  -0.434  -0.2401  -4.2790   1.5260
 BGX  N1    N  NR15  0  -0.622  -0.5030  -1.9098   0.0994
 BGX  O2    O  OH1   0  -0.594  -2.4410  -4.6425   1.4449
 BGX  HC2   H  HCR5  0   0.275  -2.3641  -2.8281  -0.2978
 BGX  HC3   H  HCR5  0   0.249  -2.1887  -1.9138   2.5653
 BGX  HC4   H  HCR5  0   0.245  -2.0044   0.6175   1.6214
 BGX  HC5   H  HCR5  0   0.265  -0.0007   0.1616  -0.0201
 BGX  HC61  H  HCH3  0   0.233  -4.3733  -0.8811   2.0259
 BGX  HC62  H  HCH3  0   0.222  -4.1961  -1.3483   0.3343
 BGX  HC63  H  HCH3  0   0.233  -4.3677  -2.5850   1.5851
 BGX  HN1   H  HNR5  0   0.375  -0.2064  -2.1220  -0.8416
 BGX  HO2   H  HOH1  0   0.482  -2.2107  -5.4579   1.9150

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
 BGX  C1  C2    single  1.509  0.020  1.509
 BGX  C1  O1    double  1.203  0.020  1.203
 BGX  C1  O2    single  1.329  0.020  1.329
 BGX  C2  C3    single  1.564  0.020  1.564
 BGX  C2  N1    single  1.452  0.020  1.452
 BGX  C2  HC2   single  0.970  0.020  1.090
 BGX  C3  C4    single  1.507  0.020  1.507
 BGX  C3  C6    single  1.522  0.020  1.522
 BGX  C3  HC3   single  0.970  0.020  1.090
 BGX  C4  C5    double  1.331  0.020  1.331
 BGX  C4  HC4   single  0.930  0.020  1.080
 BGX  C5  N1    single  1.392  0.020  1.392
 BGX  C5  HC5   single  0.930  0.020  1.080
 BGX  C6  HC61  single  0.970  0.020  1.090
 BGX  C6  HC62  single  0.970  0.020  1.090
 BGX  C6  HC63  single  0.970  0.020  1.090
 BGX  N1  HN1   single  0.890  0.020  1.040
 BGX  O2  HO2   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
 BGX  O2    C1  O1    123.56  3.000
 BGX  O2    C1  C2    110.96  3.000
 BGX  O1    C1  C2    125.48  3.000
 BGX  HC2   C2  N1    111.12  3.000
 BGX  HC2   C2  C3    108.67  3.000
 BGX  N1    C2  C3    105.30  3.000
 BGX  HC2   C2  C1    108.25  3.000
 BGX  N1    C2  C1    111.78  3.000
 BGX  C3    C2  C1    111.70  3.000
 BGX  HC3   C3  C6    108.09  3.000
 BGX  HC3   C3  C4    109.63  3.000
 BGX  C6    C3  C4    114.44  3.000
 BGX  HC3   C3  C2    110.01  3.000
 BGX  C6    C3  C2    113.32  3.000
 BGX  C4    C3  C2    101.18  3.000
 BGX  HC4   C4  C5    126.12  3.000
 BGX  HC4   C4  C3    123.91  3.000
 BGX  C5    C4  C3    109.80  3.000
 BGX  HC5   C5  N1    118.82  3.000
 BGX  HC5   C5  C4    127.73  3.000
 BGX  N1    C5  C4    113.38  3.000
 BGX  HC63  C6  HC62  108.21  3.000
 BGX  HC63  C6  HC61  107.59  3.000
 BGX  HC62  C6  HC61  107.89  3.000
 BGX  HC63  C6  C3    111.66  3.000
 BGX  HC62  C6  C3    110.85  3.000
 BGX  HC61  C6  C3    110.49  3.000
 BGX  HN1   N1  C5    115.72  3.000
 BGX  HN1   N1  C2    115.06  3.000
 BGX  C5    N1  C2    107.17  3.000
 BGX  HO2   O2  C1    110.09  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
 BGX  CONST_01  HO2  O2  C1  C2  180.00   0.0  0
 BGX  Var_01    C4   C5  N1  C2   13.01  30.0  1
 BGX  Var_02    N1   C5  C4  C3   -1.92  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
 BGX  chir_01  C2  C1  C3  N1  negativ
 BGX  chir_02  C3  C2  C4  C6  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
 BGX  plan-1  C2   0.020
 BGX  plan-1  C5   0.020
 BGX  plan-1  N1   0.020
 BGX  plan-1  HN1  0.020
 BGX  plan-2  C1   0.020
 BGX  plan-2  C2   0.020
 BGX  plan-2  O1   0.020
 BGX  plan-2  O2   0.020
 BGX  plan-2  HO2  0.020

