# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 19:52:48 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-2-{[(S)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[P](O)(=O)C[C@@H](CC(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
 B88  B88  '(2S)-2-{[(S)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid'  ligand  26  15  .  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_B88
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
 B88  O4    O  O      0  -0.821   1.7636  -1.8102   0.0418
 B88  P2    P  P      0   1.182   1.7382  -0.3097   0.2636
 B88  O5    O  OP    -1  -0.836   1.6970   0.2103   1.6936
 B88  C9    C  CH1    0  -0.329   3.2539   0.4126  -0.5278
 B88  N1    N  NH2    0  -0.794   3.2762   1.8521  -0.2892
 B88  C12   C  CH3    0  -0.673   4.5016  -0.3132  -0.0264
 B88  C6    C  CH2    0  -0.684   0.3701   0.4589  -0.6895
 B88  C7    C  CH1    0  -0.324  -1.0064   0.2381  -0.0634
 B88  C8    C  C      0   0.421  -1.4325  -1.2405  -0.1197
 B88  O1    O  OC    -1  -0.634  -1.7473  -1.7957   0.9538
 B88  O6    O  O      0  -0.630  -1.4717  -1.7677  -1.2517
 B88  C13   C  CH2    0  -0.514  -2.0677   1.0961  -0.7647
 B88  C14   C  C      0   0.388  -3.4405   0.9905  -0.0861
 B88  O3    O  OC    -1  -0.626  -4.3707   0.4583  -0.7277
 B88  O2    O  O      0  -0.631  -3.5217   1.4467   1.0758
 B88  H9    H  HCH1   0   0.212   3.1681   0.2505  -1.6090
 B88  HN1   H  HNH2   0   0.326   3.2315   2.0103   0.7108
 B88  HN1A  H  HNH2   0   0.332   4.1640   2.2356  -0.5945
 B88  H12   H  HCH3   0   0.217   4.4752  -1.3769  -0.2629
 B88  H12A  H  HCH3   0   0.217   5.4040   0.1087  -0.4761
 B88  H12B  H  HCH3   0   0.209   4.5947  -0.2148   1.0579
 B88  H6    H  HCH2   0   0.218   0.5788   1.5318  -0.7549
 B88  H6A   H  HCH2   0   0.211   0.3742   0.0764  -1.7137
 B88  H7    H  HCH1   0   0.184  -0.9602   0.5534   0.9816
 B88  H13   H  HCH2   0   0.197  -1.7389   2.1419  -0.7451
 B88  H13A  H  HCH2   0   0.183  -2.1278   0.7991  -1.8144

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
 B88  P2   O4    deloc   1.517  0.020  1.517
 B88  C6   P2    single  1.836  0.020  1.836
 B88  P2   C9    single  1.856  0.020  1.856
 B88  P2   O5    deloc   1.522  0.020  1.522
 B88  C12  C9    single  1.528  0.020  1.528
 B88  C9   N1    single  1.459  0.020  1.459
 B88  C9   H9    single  0.970  0.020  1.090
 B88  N1   HN1   single  0.890  0.020  1.040
 B88  N1   HN1A  single  0.890  0.020  1.040
 B88  C12  H12   single  0.970  0.020  1.090
 B88  C12  H12A  single  0.970  0.020  1.090
 B88  C12  H12B  single  0.970  0.020  1.090
 B88  C7   C6    single  1.528  0.020  1.528
 B88  C6   H6    single  0.970  0.020  1.090
 B88  C6   H6A   single  0.970  0.020  1.090
 B88  C13  C7    single  1.534  0.020  1.534
 B88  C7   C8    single  1.540  0.020  1.540
 B88  C7   H7    single  0.970  0.020  1.090
 B88  C8   O6    deloc   1.249  0.020  1.249
 B88  C8   O1    deloc   1.249  0.020  1.249
 B88  C14  C13   single  1.535  0.020  1.535
 B88  C13  H13   single  0.970  0.020  1.090
 B88  C13  H13A  single  0.970  0.020  1.090
 B88  O2   C14   deloc   1.251  0.020  1.251
 B88  C14  O3    deloc   1.249  0.020  1.249

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
 B88  C6    P2   C9    102.96  3.000
 B88  C9    P2   O5    106.84  3.000
 B88  C6    P2   O5    108.94  3.000
 B88  O5    P2   O4    118.41  3.000
 B88  C9    P2   O4    107.99  3.000
 B88  C6    P2   O4    110.53  3.000
 B88  H9    C9   C12   108.49  3.000
 B88  H9    C9   N1    107.95  3.000
 B88  C12   C9   N1    113.73  3.000
 B88  H9    C9   P2    107.39  3.000
 B88  N1    C9   P2    109.07  3.000
 B88  C12   C9   P2    110.00  3.000
 B88  HN1A  N1   HN1   106.06  3.000
 B88  HN1A  N1   C9    109.70  3.000
 B88  HN1   N1   C9    108.34  3.000
 B88  H12B  C12  H12A  107.65  3.000
 B88  H12B  C12  H12   107.78  3.000
 B88  H12A  C12  H12   107.91  3.000
 B88  H12B  C12  C9    110.63  3.000
 B88  H12A  C12  C9    110.84  3.000
 B88  H12   C12  C9    111.87  3.000
 B88  H6A   C6   H6    106.63  3.000
 B88  H6A   C6   C7    109.67  3.000
 B88  H6    C6   C7    109.74  3.000
 B88  H6A   C6   P2    109.69  3.000
 B88  H6    C6   P2    107.41  3.000
 B88  C7    C6   P2    113.45  3.000
 B88  H7    C7   C13   107.76  3.000
 B88  H7    C7   C8    108.89  3.000
 B88  C13   C7   C8    109.20  3.000
 B88  H7    C7   C6    108.18  3.000
 B88  C8    C7   C6    111.90  3.000
 B88  C13   C7   C6    110.79  3.000
 B88  O6    C8   O1    125.69  3.000
 B88  O1    C8   C7    117.72  3.000
 B88  O6    C8   C7    116.55  3.000
 B88  H13A  C13  H13   107.03  3.000
 B88  H13A  C13  C14   110.90  3.000
 B88  H13   C13  C14   109.02  3.000
 B88  H13A  C13  C7    108.98  3.000
 B88  H13   C13  C7    108.53  3.000
 B88  C14   C13  C7    112.22  3.000
 B88  O2    C14  O3    125.75  3.000
 B88  O3    C14  C13   117.92  3.000
 B88  O2    C14  C13   116.33  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
 B88  Var_01  C7  C6   P2   O4  76.02  30.0  1
 B88  Var_02  O2  C14  C13  C7  65.55  30.0  2

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
 B88  chir_02  C9  P2  C12  N1  positiv
 B88  chir_03  C7  C6  C13  C8  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
 B88  plan-1  C7   0.020
 B88  plan-1  C8   0.020
 B88  plan-1  O1   0.020
 B88  plan-1  O6   0.020
 B88  plan-2  C13  0.020
 B88  plan-2  C14  0.020
 B88  plan-2  O3   0.020
 B88  plan-2  O2   0.020

