# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:44:33 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 3-phosphono-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C[P](O)(O)=O)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
 APO  APO  '3-phosphono-D-alanine    '  D-peptide  15  10  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_APO
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
 APO  C1    C  CH1    0  -0.184   0.1634   0.4747  -1.1071
 APO  N2    N  NH2    0  -0.843   1.6175   0.5835  -1.0633
 APO  C3    C  C      0   0.396  -0.3154   0.0616  -2.5104
 APO  O4    O  O      0  -0.620   0.4588  -0.6362  -3.2018
 APO  O5    O  OC    -1  -0.632  -1.4689   0.4136  -2.8394
 APO  C6    C  CH2    0  -0.732  -0.4082  -0.5085  -0.0710
 APO  P7    P  P      0   1.170  -0.1070  -0.0370   1.7050
 APO  O8    O  OP    -1  -0.910  -0.6962  -1.1920   2.5278
 APO  O9    O  OP    -1  -0.897   1.4253   0.0889   1.8545
 APO  O10   O  O      0  -0.912  -0.8413   1.2973   1.8990
 APO  HC1   H  HCH1   0   0.169  -0.2664   1.4585  -0.8820
 APO  HN21  H  HNH2   0   0.330   1.8923   0.4625  -0.0897
 APO  HN22  H  HNH2   0   0.306   1.9851  -0.2110  -1.5734
 APO  HC61  H  HCH2   0   0.183  -1.4907  -0.5977  -0.2188
 APO  HC62  H  HCH2   0   0.177   0.0069  -1.5054  -0.2712

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
 APO  C1  N2    single  1.459  0.020  1.459
 APO  C1  C3    single  1.539  0.020  1.539
 APO  C1  C6    single  1.538  0.020  1.538
 APO  C1  HC1   single  0.970  0.020  1.090
 APO  N2  HN21  single  0.890  0.020  1.040
 APO  N2  HN22  single  0.890  0.020  1.040
 APO  C3  O4    deloc   1.251  0.020  1.251
 APO  C3  O5    deloc   1.250  0.020  1.250
 APO  C6  P7    single  1.862  0.020  1.862
 APO  C6  HC61  single  0.970  0.020  1.090
 APO  C6  HC62  single  0.970  0.020  1.090
 APO  P7  O8    deloc   1.536  0.020  1.536
 APO  P7  O9    deloc   1.545  0.020  1.545
 APO  P7  O10   deloc   1.535  0.020  1.535

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
 APO  HC1   C1  C6    106.83  3.000
 APO  HC1   C1  C3    107.81  3.000
 APO  C6    C1  C3    109.08  3.000
 APO  HC1   C1  N2    108.51  3.000
 APO  C6    C1  N2    113.44  3.000
 APO  C3    C1  N2    110.94  3.000
 APO  HN22  N2  HN21  106.87  3.000
 APO  HN22  N2  C1    106.74  3.000
 APO  HN21  N2  C1    106.77  3.000
 APO  O5    C3  O4    125.65  3.000
 APO  O5    C3  C1    116.83  3.000
 APO  O4    C3  C1    117.46  3.000
 APO  HC62  C6  HC61  105.95  3.000
 APO  HC62  C6  P7    110.04  3.000
 APO  HC61  C6  P7    107.99  3.000
 APO  HC62  C6  C1    108.47  3.000
 APO  HC61  C6  C1    109.15  3.000
 APO  P7    C6  C1    114.86  3.000
 APO  O10   P7  O9    113.04  3.000
 APO  O10   P7  O8    113.73  3.000
 APO  O9    P7  O8    112.95  3.000
 APO  O10   P7  C6    105.26  3.000
 APO  O9    P7  C6    105.87  3.000
 APO  O8    P7  C6    104.98  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
 APO  Var_01  O8  P7  C6  C1  -177.11  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
 APO  chir_01  C1  N2  C3  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
 APO  plan-1  C1  0.020
 APO  plan-1  C3  0.020
 APO  plan-1  O4  0.020
 APO  plan-1  O5  0.020

