# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:33:13 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  29  15  .  2021-08-07  2021-08-07  
;
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  -0.716   1.6269  -1.8070   0.0719
 B88  P2    P  P     0   1.270   1.6965  -0.3187   0.1544
 B88  O5    O  OH1   0  -0.763   1.6874   0.1617   1.7029
 B88  C9    C  CH1   0  -0.342   3.1928   0.4517  -0.5676
 B88  N1    N  NH2   0  -0.814   3.2230   1.8302  -0.0921
 B88  C12   C  CH3   0  -0.676   4.4470  -0.3629  -0.2743
 B88  C6    C  CH2   0  -0.727   0.2999   0.5342  -0.6370
 B88  C7    C  CH1   0  -0.360  -1.0699   0.3021   0.0163
 B88  C8    C  C     0   0.555  -1.4006  -1.1770   0.0285
 B88  O1    O  OH1   0  -0.583  -1.3039  -1.7162   1.2318
 B88  O6    O  O     0  -0.447  -1.6973  -1.7983  -0.9622
 B88  C13   C  CH2   0  -0.568  -2.1187   1.0754  -0.7752
 B88  C14   C  C     0   0.557  -3.5101   0.9071  -0.2333
 B88  O3    O  OH1   0  -0.592  -4.3820   1.6869  -0.8569
 B88  O2    O  O     0  -0.437  -3.8097   0.1501   0.6567
 B88  HO5   H  HOH1  0   0.480   1.7908   1.1188   1.8003
 B88  H9    H  HCH1  0   0.281   3.0229   0.4647  -1.6481
 B88  HN1   H  HNH2  0   0.360   3.8235   1.9061   0.7196
 B88  HN1A  H  HNH2  0   0.371   3.6184   2.4377  -0.7967
 B88  H12   H  HCH3  0   0.241   4.3611  -1.3831  -0.6461
 B88  H12A  H  HCH3  0   0.249   5.3086   0.1012  -0.7549
 B88  H12B  H  HCH3  0   0.231   4.6448  -0.4103   0.7982
 B88  H6    H  HCH2  0   0.297   0.5159   1.6054  -0.6402
 B88  H6A   H  HCH2  0   0.288   0.2789   0.2139  -1.6824
 B88  H7    H  HCH1  0   0.288  -1.0425   0.6740   1.0414
 B88  HO1   H  HOH1  0   0.477  -1.4725  -2.6690   1.1808
 B88  H13   H  HCH2  0   0.303  -1.8661   2.1386  -0.7781
 B88  H13A  H  HCH2  0   0.295  -2.1159   0.7658  -1.8242
 B88  HO3   H  HOH1  0   0.483  -5.2715   1.5492  -0.4978

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    double  1.492  0.020  1.492
 B88  C6   P2    single  1.818  0.020  1.818
 B88  P2   C9    single  1.831  0.020  1.831
 B88  P2   O5    single  1.621  0.020  1.621
 B88  O5   HO5   single  0.850  0.020  0.980
 B88  C12  C9    single  1.524  0.020  1.524
 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  1.535  0.020  1.535
 B88  C6   H6    single  0.970  0.020  1.090
 B88  C6   H6A   single  0.970  0.020  1.090
 B88  C13  C7    single  1.525  0.020  1.525
 B88  C7   C8    single  1.516  0.020  1.516
 B88  C7   H7    single  0.970  0.020  1.090
 B88  C8   O6    double  1.206  0.020  1.206
 B88  C8   O1    single  1.322  0.020  1.322
 B88  O1   HO1   single  0.850  0.020  0.980
 B88  C14  C13   single  1.503  0.020  1.503
 B88  C13  H13   single  0.970  0.020  1.090
 B88  C13  H13A  single  0.970  0.020  1.090
 B88  O2   C14   double  1.206  0.020  1.206
 B88  C14  O3    single  1.326  0.020  1.326
 B88  O3   HO3   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
 B88  C6    P2   C9    105.00  3.000
 B88  C9    P2   O5    104.86  3.000
 B88  C6    P2   O5    105.81  3.000
 B88  O5    P2   O4    110.37  3.000
 B88  C9    P2   O4    115.84  3.000
 B88  C6    P2   O4    114.09  3.000
 B88  HO5   O5   P2    112.87  3.000
 B88  H9    C9   C12   108.93  3.000
 B88  H9    C9   N1    108.30  3.000
 B88  C12   C9   N1    115.18  3.000
 B88  H9    C9   P2    105.51  3.000
 B88  N1    C9   P2    106.62  3.000
 B88  C12   C9   P2    111.82  3.000
 B88  HN1A  N1   HN1   106.37  3.000
 B88  HN1A  N1   C9    110.42  3.000
 B88  HN1   N1   C9    110.14  3.000
 B88  H12B  C12  H12A  107.96  3.000
 B88  H12B  C12  H12   108.00  3.000
 B88  H12A  C12  H12   108.09  3.000
 B88  H12B  C12  C9    111.19  3.000
 B88  H12A  C12  C9    109.75  3.000
 B88  H12   C12  C9    111.72  3.000
 B88  H6A   C6   H6    106.75  3.000
 B88  H6A   C6   C7    110.20  3.000
 B88  H6    C6   C7    109.01  3.000
 B88  H6A   C6   P2    107.07  3.000
 B88  H6    C6   P2    108.03  3.000
 B88  C7    C6   P2    115.42  3.000
 B88  H7    C7   C13   109.40  3.000
 B88  H7    C7   C8    109.30  3.000
 B88  C13   C7   C8    110.43  3.000
 B88  H7    C7   C6    109.02  3.000
 B88  C8    C7   C6    110.22  3.000
 B88  C13   C7   C6    108.43  3.000
 B88  O6    C8   O1    123.74  3.000
 B88  O1    C8   C7    112.91  3.000
 B88  O6    C8   C7    123.34  3.000
 B88  HO1   O1   C8    109.90  3.000
 B88  H13A  C13  H13   105.80  3.000
 B88  H13A  C13  C14   108.45  3.000
 B88  H13   C13  C14   108.90  3.000
 B88  H13A  C13  C7    110.65  3.000
 B88  H13   C13  C7    109.63  3.000
 B88  C14   C13  C7    113.14  3.000
 B88  O2    C14  O3    123.57  3.000
 B88  O3    C14  C13   111.93  3.000
 B88  O2    C14  C13   124.50  3.000
 B88  HO3   O3   C14   110.23  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  CONST_01  HO1  O1   C8   C7   180.00   0.0  0
 B88  CONST_02  HO3  O3   C14  C13  180.00   0.0  0
 B88  Var_01    C7   C6   P2   O4    65.33  30.0  1
 B88  Var_02    O2   C14  C13  C7    -6.44  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
 B88  chir_04  P2  C6  C9   O5  both

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-1  HO1  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
 B88  plan-2  HO3  0.020

