# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 12:58:14 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: [(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON1CCC[C@@H](C1=O)[P](O)(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
 6BM  6BM  '[(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic acid'  ligand  20  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6BM
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
 6BM  N01  N  NT     0  -0.200   2.0276  -0.3252   0.2687
 6BM  C02  C  CH2    0  -0.260   2.6268   0.9798   0.4318
 6BM  C03  C  CH2    0  -0.480   1.8197   2.0116  -0.3323
 6BM  C04  C  CH2    0  -0.429   0.3394   1.7849  -0.0745
 6BM  C05  C  CH1    0  -0.635  -0.1166   0.4238  -0.5936
 6BM  C06  C  C      0   0.537   0.8920  -0.6513  -0.3804
 6BM  O07  O  OH1    0  -0.579   2.9053  -1.3631   0.5057
 6BM  O08  O  O      0  -0.551   0.7441  -1.8301  -0.7248
 6BM  P09  P  P      0   1.200  -1.7587  -0.0798   0.2259
 6BM  O10  O  O      0  -0.900  -1.3372  -0.4850   1.6412
 6BM  O11  O  OP    -1  -0.895  -2.5854   1.2086   0.1595
 6BM  O12  O  OP    -1  -0.891  -2.3322  -1.2170  -0.6172
 6BM  H1   H  HCH2   0   0.235   2.6724   1.2386   1.4944
 6BM  H2   H  HCH2   0   0.249   3.6538   0.9331   0.0619
 6BM  H3   H  HCH2   0   0.242   2.1369   3.0064  -0.0146
 6BM  H4   H  HCH2   0   0.228   2.0311   1.9312  -1.4027
 6BM  H5   H  HCH2   0   0.212   0.1535   1.8510   1.0019
 6BM  H6   H  HCH2   0   0.230  -0.2612   2.5663  -0.5383
 6BM  H7   H  HCH1   0   0.231  -0.2856   0.4828  -1.6752
 6BM  H8   H  HOH1   0   0.456   2.4765  -2.0972   0.0245

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
 6BM  O08  C06  double  1.237  0.020  1.237
 6BM  C05  C06  single  1.489  0.020  1.489
 6BM  C05  C04  single  1.526  0.020  1.526
 6BM  C05  P09  single  1.903  0.020  1.903
 6BM  O10  P09  deloc   1.531  0.020  1.531
 6BM  C06  N01  single  1.348  0.020  1.348
 6BM  C04  C03  single  1.520  0.020  1.520
 6BM  O11  P09  deloc   1.532  0.020  1.532
 6BM  P09  O12  deloc   1.527  0.020  1.527
 6BM  N01  O07  single  1.380  0.020  1.380
 6BM  N01  C02  single  1.445  0.020  1.445
 6BM  C03  C02  single  1.517  0.020  1.517
 6BM  C02  H1   single  0.970  0.020  1.090
 6BM  C02  H2   single  0.970  0.020  1.090
 6BM  C03  H3   single  0.970  0.020  1.090
 6BM  C03  H4   single  0.970  0.020  1.090
 6BM  C04  H5   single  0.970  0.020  1.090
 6BM  C04  H6   single  0.970  0.020  1.090
 6BM  C05  H7   single  0.970  0.020  1.090
 6BM  O07  H8   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
 6BM  O07  N01  C06  115.89  3.000
 6BM  O07  N01  C02  113.33  3.000
 6BM  C06  N01  C02  128.47  3.000
 6BM  H2   C02  H1   107.43  3.000
 6BM  H2   C02  C03  111.02  3.000
 6BM  H1   C02  C03  110.51  3.000
 6BM  H2   C02  N01  108.24  3.000
 6BM  H1   C02  N01  109.89  3.000
 6BM  C03  C02  N01  109.69  3.000
 6BM  H4   C03  H3   107.20  3.000
 6BM  H4   C03  C04  110.07  3.000
 6BM  H3   C03  C04  111.69  3.000
 6BM  H4   C03  C02  109.89  3.000
 6BM  H3   C03  C02  108.59  3.000
 6BM  C04  C03  C02  109.36  3.000
 6BM  H6   C04  H5   106.37  3.000
 6BM  H6   C04  C05  109.28  3.000
 6BM  H5   C04  C05  109.73  3.000
 6BM  H6   C04  C03  110.97  3.000
 6BM  H5   C04  C03  108.86  3.000
 6BM  C05  C04  C03  111.49  3.000
 6BM  H7   C05  P09  107.82  3.000
 6BM  H7   C05  C06  106.53  3.000
 6BM  P09  C05  C06  109.36  3.000
 6BM  H7   C05  C04  109.49  3.000
 6BM  P09  C05  C04  110.32  3.000
 6BM  C06  C05  C04  113.13  3.000
 6BM  O08  C06  C05  124.55  3.000
 6BM  C05  C06  N01  117.69  3.000
 6BM  O08  C06  N01  117.73  3.000
 6BM  H8   O07  N01  101.62  3.000
 6BM  O12  P09  O11  113.55  3.000
 6BM  O12  P09  O10  114.61  3.000
 6BM  O11  P09  O10  114.27  3.000
 6BM  O12  P09  C05  106.46  3.000
 6BM  O11  P09  C05  102.97  3.000
 6BM  O10  P09  C05  103.32  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
 6BM  CONST_03  O07  N01  C06  C05  180.00   0.0  0
 6BM  CONST_04  O08  C06  N01  O07    0.00   0.0  0
 6BM  Var_01    C04  C03  C02  N01   44.73  30.0  1
 6BM  Var_02    C05  C04  C03  C02  -63.06  30.0  1
 6BM  Var_03    C06  N01  C02  C03   -3.48  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
 6BM  chir_01  C05  C06  C04  P09  positiv

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
 6BM  plan-1  N01  0.020
 6BM  plan-1  C02  0.020
 6BM  plan-1  C05  0.020
 6BM  plan-1  C06  0.020
 6BM  plan-1  O07  0.020
 6BM  plan-1  O08  0.020

