# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:10:51 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: (2S)-3-amino-2-methylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CN)C([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
 BIB  BIB  (2S)-3-amino-2-methylpropanoate  ligand  15  7  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BIB
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
 BIB  O7    O  OC    -1  -0.604   1.9805   0.8511  -0.2813
 BIB  C5    C  C      0   0.414   1.2370  -0.1143  -0.0145
 BIB  O6    O  O      0  -0.625   1.5665  -1.3190  -0.0397
 BIB  C3    C  CH1    0  -0.364  -0.2234   0.1886   0.3970
 BIB  C2    C  CH3    0  -0.654  -0.5569   1.6732   0.3732
 BIB  C4    C  CH2    0  -0.271  -1.1903  -0.6226  -0.4651
 BIB  N1    N  NH2    0  -0.806  -2.5636  -0.5345   0.0177
 BIB  H3    H  HCH1   0   0.208  -0.3468  -0.1741   1.4264
 BIB  H21   H  HCH3   0   0.204  -0.4936   2.0787  -0.6387
 BIB  H22   H  HCH3   0   0.205  -1.5657   1.8636   0.7453
 BIB  H23   H  HCH3   0   0.220   0.1261   2.2464   0.9990
 BIB  H41   H  HCH2   0   0.177  -1.0817  -0.2993  -1.5132
 BIB  H42   H  HCH2   0   0.216  -0.8896  -1.6699  -0.4319
 BIB  HN11  H  HNH2   0   0.338  -2.9493   0.3741  -0.2053
 BIB  HN12  H  HNH2   0   0.343  -3.1365  -1.1988  -0.4872

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
 BIB  O7  C5    deloc   1.247  0.020  1.247
 BIB  C5  O6    deloc   1.249  0.020  1.249
 BIB  C5  C3    single  1.547  0.020  1.547
 BIB  C3  C2    single  1.522  0.020  1.522
 BIB  C3  C4    single  1.528  0.020  1.528
 BIB  C3  H3    single  0.970  0.020  1.090
 BIB  C2  H21   single  0.970  0.020  1.090
 BIB  C2  H22   single  0.970  0.020  1.090
 BIB  C2  H23   single  0.970  0.020  1.090
 BIB  C4  N1    single  1.458  0.020  1.458
 BIB  C4  H41   single  0.970  0.020  1.090
 BIB  C4  H42   single  0.970  0.020  1.090
 BIB  N1  HN11  single  0.890  0.020  1.040
 BIB  N1  HN12  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
 BIB  C3    C5  O6    116.30  3.000
 BIB  C3    C5  O7    117.90  3.000
 BIB  O6    C5  O7    125.79  3.000
 BIB  H3    C3  C4    106.40  3.000
 BIB  H3    C3  C2    108.19  3.000
 BIB  C4    C3  C2    111.74  3.000
 BIB  H3    C3  C5    106.89  3.000
 BIB  C4    C3  C5    110.07  3.000
 BIB  C2    C3  C5    113.19  3.000
 BIB  H23   C2  H22   106.96  3.000
 BIB  H23   C2  H21   107.49  3.000
 BIB  H22   C2  H21   107.73  3.000
 BIB  H23   C2  C3    111.53  3.000
 BIB  H22   C2  C3    111.55  3.000
 BIB  H21   C2  C3    111.35  3.000
 BIB  H42   C4  H41   106.48  3.000
 BIB  H42   C4  N1    107.92  3.000
 BIB  H41   C4  N1    112.95  3.000
 BIB  H42   C4  C3    108.56  3.000
 BIB  H41   C4  C3    108.56  3.000
 BIB  N1    C4  C3    112.14  3.000
 BIB  HN12  N1  HN11  105.28  3.000
 BIB  HN12  N1  C4    109.16  3.000
 BIB  HN11  N1  C4    109.90  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
 BIB  Var_01  HN11  N1  C4  C3  74.05  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
 BIB  chir_01  C3  C5  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
 BIB  plan-1  O7  0.020
 BIB  plan-1  C5  0.020
 BIB  plan-1  O6  0.020
 BIB  plan-1  C3  0.020

