# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 09:44:59 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  17  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.414  -1.1014  -3.8424   1.2395
 BGX  C2    C  CR15   0  -0.233  -1.9331  -2.7378   0.5386
 BGX  C3    C  CR15   0  -0.256  -2.5960  -1.7532   1.5301
 BGX  C4    C  CR15   0  -0.344  -1.6212  -0.6040   1.4917
 BGX  C5    C  CR15   0  -0.039  -0.8343  -0.7425   0.4233
 BGX  C6    C  CH3    0  -0.653  -3.9955  -1.3212   1.0925
 BGX  O1    O  O      0  -0.606   0.0522  -4.0471   0.8134
 BGX  N1    N  NR15   0  -0.608  -1.1182  -1.8829  -0.3260
 BGX  O2    O  OC    -1  -0.609  -1.6836  -4.4667   2.1471
 BGX  HC2   H  HCR5   0   0.230  -2.6998  -3.2530  -0.0539
 BGX  HC3   H  HCR5   0   0.226  -2.6732  -2.2100   2.5195
 BGX  HC4   H  HCR5   0   0.227  -1.6424   0.2452   2.1592
 BGX  HC5   H  HCR5   0   0.247  -0.0633  -0.0647   0.0790
 BGX  HC61  H  HCH3   0   0.221  -4.3969  -0.5547   1.7581
 BGX  HC62  H  HCH3   0   0.215  -3.9794  -0.9080   0.0820
 BGX  HC63  H  HCH3   0   0.219  -4.6903  -2.1640   1.1008
 BGX  HN1   H  HNR5   0   0.351  -0.2912  -2.3724  -0.6449

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  1.550  0.020  1.550
 BGX  C1  O1    deloc   1.247  0.020  1.247
 BGX  C1  O2    deloc   1.246  0.020  1.246
 BGX  C2  C3    single  1.547  0.020  1.547
 BGX  C2  N1    single  1.464  0.020  1.464
 BGX  C2  HC2   single  0.970  0.020  1.090
 BGX  C3  C4    single  1.507  0.020  1.507
 BGX  C3  C6    single  1.529  0.020  1.529
 BGX  C3  HC3   single  0.970  0.020  1.090
 BGX  C4  C5    double  1.334  0.020  1.334
 BGX  C4  HC4   single  0.930  0.020  1.080
 BGX  C5  N1    single  1.394  0.020  1.394
 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

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    126.80  3.000
 BGX  O2    C1  C2    115.83  3.000
 BGX  O1    C1  C2    117.32  3.000
 BGX  HC2   C2  N1    110.14  3.000
 BGX  HC2   C2  C3    110.21  3.000
 BGX  N1    C2  C3    104.21  3.000
 BGX  HC2   C2  C1    106.53  3.000
 BGX  N1    C2  C1    112.61  3.000
 BGX  C3    C2  C1    113.19  3.000
 BGX  HC3   C3  C6    108.23  3.000
 BGX  HC3   C3  C4    112.80  3.000
 BGX  C6    C3  C4    111.67  3.000
 BGX  HC3   C3  C2    110.16  3.000
 BGX  C6    C3  C2    112.88  3.000
 BGX  C4    C3  C2    101.06  3.000
 BGX  HC4   C4  C5    126.01  3.000
 BGX  HC4   C4  C3    124.81  3.000
 BGX  C5    C4  C3    108.83  3.000
 BGX  HC5   C5  N1    119.10  3.000
 BGX  HC5   C5  C4    127.56  3.000
 BGX  N1    C5  C4    113.29  3.000
 BGX  HC63  C6  HC62  107.96  3.000
 BGX  HC63  C6  HC61  107.65  3.000
 BGX  HC62  C6  HC61  107.70  3.000
 BGX  HC63  C6  C3    111.23  3.000
 BGX  HC62  C6  C3    111.01  3.000
 BGX  HC61  C6  C3    111.13  3.000
 BGX  HN1   N1  C5    113.49  3.000
 BGX  HN1   N1  C2    111.00  3.000
 BGX  C5    N1  C2    105.89  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  Var_01  C4  C5  N1  C2  -16.05  30.0  1
 BGX  Var_02  N1  C5  C4  C3   -0.58  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

