# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:46:23 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: [(1R)-1-amino-2-(benzylamino)ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CNCc1ccccc1)[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
 5HR  5HR  '[(1R)-1-amino-2-(benzylamino)ethyl]phosphonic acid'  ligand  30  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5HR
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
 5HR  N1    N  NH1   0  -0.595  -0.0725  -1.1229  -0.1396
 5HR  C20   C  CR6   0   0.062  -2.4233  -0.5099  -0.3769
 5HR  C21   C  CR16  0  -0.307  -3.7319  -0.9538  -0.5482
 5HR  C22   C  CR16  0  -0.243  -4.8055  -0.1992  -0.0936
 5HR  C24   C  CR16  0  -0.242  -3.2799   1.4567   0.7338
 5HR  O10   O  O     0  -0.713   1.5735   1.3924   1.1031
 5HR  P4    P  P     0   1.361   2.3392   0.7456   0.0082
 5HR  O8    O  OH1   0  -0.749   1.9264   1.1417  -1.4949
 5HR  O9    O  OH1   0  -0.753   3.8892   1.1842   0.1790
 5HR  C3    C  CH1   0  -0.394   2.3677  -1.0897  -0.0320
 5HR  N6    N  NH2   0  -0.795   2.5219  -1.6205   1.3134
 5HR  C2    C  CH2   0  -0.259   1.1350  -1.6587  -0.7204
 5HR  C1    C  CH2   0  -0.293  -1.2694  -1.3140  -0.9224
 5HR  C25   C  CR16  0  -0.311  -2.2072   0.7031   0.2752
 5HR  C23   C  CR16  0  -0.271  -4.5830   1.0117   0.5486
 5HR  H11   H  HNH1  0   0.345  -0.2157  -1.4907   0.7925
 5HR  H211  H  HCR6  0   0.244  -3.9167  -1.9021  -1.0401
 5HR  H221  H  HCR6  0   0.252  -5.8156  -0.5617  -0.2358
 5HR  H241  H  HCR6  0   0.249  -3.0963   2.3958   1.2408
 5HR  H2    H  HOH1  0   0.490   1.7446   2.0830  -1.6214
 5HR  H3    H  HOH1  0   0.483   4.4884   0.8394  -0.4951
 5HR  H31   H  HCH1  0   0.288   3.2406  -1.3997  -0.6145
 5HR  H62   H  HNH2  0   0.364   3.4477  -1.4288   1.6730
 5HR  H61   H  HNH2  0   0.352   1.8715  -1.1848   1.9559
 5HR  H22   H  HCH2  0   0.220   1.2036  -2.7559  -0.6797
 5HR  H21   H  HCH2  0   0.238   1.1589  -1.3855  -1.7767
 5HR  H12   H  HCH2  0   0.242  -1.0586  -0.9722  -1.9414
 5HR  H13   H  HCH2  0   0.212  -1.5728  -2.3677  -1.0191
 5HR  H251  H  HCR6  0   0.270  -1.1913   1.0462   0.4307
 5HR  H231  H  HCR6  0   0.251  -5.4178   1.6009   0.9063

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
 5HR  C22  C23   aromatic  1.389  0.020  1.389
 5HR  C22  C21   aromatic  1.389  0.020  1.389
 5HR  C23  C24   aromatic  1.389  0.020  1.389
 5HR  C21  C20   aromatic  1.392  0.020  1.392
 5HR  C24  C25   aromatic  1.389  0.020  1.389
 5HR  O10  P4    double    1.484  0.020  1.484
 5HR  C2   N1    single    1.443  0.020  1.443
 5HR  C2   C3    single    1.522  0.020  1.522
 5HR  C20  C25   aromatic  1.394  0.020  1.394
 5HR  C20  C1    single    1.508  0.020  1.508
 5HR  N1   C1    single    1.443  0.020  1.443
 5HR  N6   C3    single    1.455  0.020  1.455
 5HR  P4   C3    single    1.836  0.020  1.836
 5HR  P4   O8    single    1.608  0.020  1.608
 5HR  P4   O9    single    1.620  0.020  1.620
 5HR  N1   H11   single    0.890  0.020  1.040
 5HR  C21  H211  single    0.930  0.020  1.080
 5HR  C22  H221  single    0.930  0.020  1.080
 5HR  C24  H241  single    0.930  0.020  1.080
 5HR  O8   H2    single    0.850  0.020  0.980
 5HR  O9   H3    single    0.850  0.020  0.980
 5HR  C3   H31   single    0.970  0.020  1.090
 5HR  N6   H62   single    0.890  0.020  1.040
 5HR  N6   H61   single    0.890  0.020  1.040
 5HR  C2   H22   single    0.970  0.020  1.090
 5HR  C2   H21   single    0.970  0.020  1.090
 5HR  C1   H12   single    0.970  0.020  1.090
 5HR  C1   H13   single    0.970  0.020  1.090
 5HR  C25  H251  single    0.930  0.020  1.080
 5HR  C23  H231  single    0.930  0.020  1.080

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
 5HR  H11   N1   C1   109.51  3.000
 5HR  H11   N1   C2   110.74  3.000
 5HR  C1    N1   C2   115.25  3.000
 5HR  C25   C20  C1   120.96  3.000
 5HR  C1    C20  C21  120.30  3.000
 5HR  C25   C20  C21  118.73  3.000
 5HR  H211  C21  C22  119.47  3.000
 5HR  H211  C21  C20  119.66  3.000
 5HR  C22   C21  C20  120.87  3.000
 5HR  H221  C22  C23  120.15  3.000
 5HR  H221  C22  C21  119.76  3.000
 5HR  C23   C22  C21  120.09  3.000
 5HR  H241  C24  C23  119.95  3.000
 5HR  H241  C24  C25  119.62  3.000
 5HR  C23   C24  C25  120.43  3.000
 5HR  C3    P4   O9   104.96  3.000
 5HR  O9    P4   O8   106.11  3.000
 5HR  C3    P4   O8   103.28  3.000
 5HR  O9    P4   O10  107.33  3.000
 5HR  O8    P4   O10  116.72  3.000
 5HR  C3    P4   O10  117.37  3.000
 5HR  H2    O8   P4   114.22  3.000
 5HR  H3    O9   P4   115.06  3.000
 5HR  H31   C3   C2   107.42  3.000
 5HR  H31   C3   N6   107.73  3.000
 5HR  C2    C3   N6   111.57  3.000
 5HR  H31   C3   P4   107.89  3.000
 5HR  N6    C3   P4   110.26  3.000
 5HR  C2    C3   P4   111.78  3.000
 5HR  H61   N6   H62  106.30  3.000
 5HR  H61   N6   C3   111.20  3.000
 5HR  H62   N6   C3   110.90  3.000
 5HR  H21   C2   H22  106.50  3.000
 5HR  H21   C2   C3   109.05  3.000
 5HR  H22   C2   C3   107.79  3.000
 5HR  H21   C2   N1   108.35  3.000
 5HR  H22   C2   N1   114.06  3.000
 5HR  C3    C2   N1   110.90  3.000
 5HR  H13   C1   H12  105.67  3.000
 5HR  H13   C1   C20  109.34  3.000
 5HR  H12   C1   C20  108.50  3.000
 5HR  H13   C1   N1   113.77  3.000
 5HR  H12   C1   N1   107.68  3.000
 5HR  C20   C1   N1   111.58  3.000
 5HR  H251  C25  C24  120.33  3.000
 5HR  H251  C25  C20  119.21  3.000
 5HR  C24   C25  C20  120.46  3.000
 5HR  H231  C23  C24  120.32  3.000
 5HR  H231  C23  C22  120.25  3.000
 5HR  C24   C23  C22  119.42  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
 5HR  CONST_01  C23   C22  C21  C20     0.00   0.0  0
 5HR  CONST_02  C23   C24  C25  C20     0.00   0.0  0
 5HR  CONST_03  C24   C23  C22  C21     0.00   0.0  0
 5HR  CONST_04  C24   C25  C20  C21     0.00   0.0  0
 5HR  CONST_05  C25   C24  C23  C22     0.00   0.0  0
 5HR  CONST_06  C25   C20  C21  C22     0.00   0.0  0
 5HR  CONST_07  C1    C20  C21  C22   180.00   0.0  0
 5HR  CONST_08  C1    C20  C25  C24   180.00   0.0  0
 5HR  CONST_09  H221  C22  C21  C20   180.00   0.0  0
 5HR  CONST_10  H241  C24  C25  C20   180.00   0.0  0
 5HR  CONST_11  H231  C23  C22  C21   180.00   0.0  0
 5HR  CONST_12  H251  C25  C20  C21   180.00   0.0  0
 5HR  CONST_13  H211  C21  C20  C25   180.00   0.0  0
 5HR  Var_01    C21   C20  C1   N1   -151.12  30.0  2
 5HR  Var_02    C2    N1   C1   C20  -169.37  30.0  2
 5HR  Var_03    C1    N1   C2   C3    164.56  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
 5HR  chir_01  C3  C2  N6  P4  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
 5HR  plan-1  C20   0.020
 5HR  plan-1  C21   0.020
 5HR  plan-1  C22   0.020
 5HR  plan-1  C24   0.020
 5HR  plan-1  C1    0.020
 5HR  plan-1  C25   0.020
 5HR  plan-1  C23   0.020
 5HR  plan-1  H211  0.020
 5HR  plan-1  H221  0.020
 5HR  plan-1  H241  0.020
 5HR  plan-1  H251  0.020
 5HR  plan-1  H231  0.020

