# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:49:32 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  28  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.631  -0.0977  -0.1513  -0.7500
 5HR  C20   C  CR6    0   0.080  -2.4636  -0.4260  -0.1015
 5HR  C21   C  CR16   0  -0.300  -3.4913  -1.1615   0.4902
 5HR  C22   C  CR16   0  -0.244  -4.7515  -0.6128   0.6718
 5HR  C24   C  CR16   0  -0.240  -3.9906   1.4372  -0.3113
 5HR  O10   O  O      0  -0.891   1.7899   0.9227   1.2264
 5HR  P4    P  P      0   1.157   2.9630   0.3521   0.3937
 5HR  O8    O  OP    -1  -0.903   3.4475   1.3047  -0.7072
 5HR  O9    O  OP    -1  -0.902   4.0909  -0.2239   1.2628
 5HR  C3    C  CH1    0  -0.372   2.2284  -1.1239  -0.4828
 5HR  N6    N  NH2    0  -0.808   1.8269  -2.1902   0.4501
 5HR  C2    C  CH2    0  -0.280   1.0672  -0.7441  -1.3994
 5HR  C1    C  CH2    0  -0.306  -1.1114  -1.0742  -0.2991
 5HR  C25   C  CR16   0  -0.308  -2.7298   0.8797  -0.4989
 5HR  C23   C  CR16   0  -0.275  -5.0070   0.6946   0.2717
 5HR  H11   H  HNH1   0   0.344   0.2497   0.4062   0.0303
 5HR  H211  H  HCR6   0   0.241  -3.3003  -2.1797   0.8123
 5HR  H221  H  HCR6   0   0.249  -5.5355  -1.2031   1.1295
 5HR  H241  H  HCR6   0   0.247  -4.1779   2.4568  -0.6245
 5HR  H31   H  HCH1   0   0.180   3.0028  -1.5505  -1.1352
 5HR  H62   H  HNH2   0   0.324   2.6445  -2.4129   1.0083
 5HR  H61   H  HNH2   0   0.324   1.1959  -1.7709   1.1254
 5HR  H22   H  HCH2   0   0.194   0.7348  -1.6221  -1.9653
 5HR  H21   H  HCH2   0   0.198   1.4588  -0.0333  -2.1344
 5HR  H12   H  HCH2   0   0.230  -1.2206  -1.8617  -1.0524
 5HR  H13   H  HCH2   0   0.203  -0.8623  -1.6045   0.6323
 5HR  H251  H  HCR6   0   0.241  -1.9408   1.4590  -0.9602
 5HR  H231  H  HCR6   0   0.249  -5.9887   1.1275   0.4166

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  1.391  0.020  1.391
 5HR  C22  C21   aromatic  1.386  0.020  1.386
 5HR  C23  C24   aromatic  1.387  0.020  1.387
 5HR  C21  C20   aromatic  1.395  0.020  1.395
 5HR  C24  C25   aromatic  1.391  0.020  1.391
 5HR  O10  P4    deloc     1.548  0.020  1.548
 5HR  C2   N1    single    1.460  0.020  1.460
 5HR  C2   C3    single    1.527  0.020  1.527
 5HR  C20  C25   aromatic  1.391  0.020  1.391
 5HR  C20  C1    single    1.512  0.020  1.512
 5HR  N1   C1    single    1.443  0.020  1.443
 5HR  N6   C3    single    1.473  0.020  1.473
 5HR  P4   C3    single    1.867  0.020  1.867
 5HR  P4   O8    deloc     1.534  0.020  1.534
 5HR  P4   O9    deloc     1.536  0.020  1.536
 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  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   110.47  3.000
 5HR  H11   N1   C2   106.89  3.000
 5HR  C1    N1   C2   116.10  3.000
 5HR  C25   C20  C1   122.42  3.000
 5HR  C1    C20  C21  119.21  3.000
 5HR  C25   C20  C21  118.37  3.000
 5HR  H211  C21  C22  119.51  3.000
 5HR  H211  C21  C20  119.40  3.000
 5HR  C22   C21  C20  121.09  3.000
 5HR  H221  C22  C23  120.07  3.000
 5HR  H221  C22  C21  119.85  3.000
 5HR  C23   C22  C21  120.09  3.000
 5HR  H241  C24  C23  119.92  3.000
 5HR  H241  C24  C25  119.67  3.000
 5HR  C23   C24  C25  120.41  3.000
 5HR  C3    P4   O9   104.95  3.000
 5HR  O9    P4   O8   114.01  3.000
 5HR  C3    P4   O8   106.15  3.000
 5HR  O9    P4   O10  112.98  3.000
 5HR  O8    P4   O10  113.36  3.000
 5HR  C3    P4   O10  104.23  3.000
 5HR  H31   C3   C2   106.02  3.000
 5HR  H31   C3   N6   106.69  3.000
 5HR  C2    C3   N6   110.67  3.000
 5HR  H31   C3   P4   107.96  3.000
 5HR  N6    C3   P4   112.47  3.000
 5HR  C2    C3   P4   112.60  3.000
 5HR  H61   N6   H62  103.04  3.000
 5HR  H61   N6   C3   106.98  3.000
 5HR  H62   N6   C3   106.72  3.000
 5HR  H21   C2   H22  106.38  3.000
 5HR  H21   C2   C3   107.00  3.000
 5HR  H22   C2   C3   109.95  3.000
 5HR  H21   C2   N1   108.69  3.000
 5HR  H22   C2   N1   108.24  3.000
 5HR  C3    C2   N1   116.15  3.000
 5HR  H13   C1   H12  104.97  3.000
 5HR  H13   C1   C20  107.36  3.000
 5HR  H12   C1   C20  107.99  3.000
 5HR  H13   C1   N1   114.44  3.000
 5HR  H12   C1   N1   108.36  3.000
 5HR  C20   C1   N1   113.25  3.000
 5HR  H251  C25  C24  120.25  3.000
 5HR  H251  C25  C20  119.01  3.000
 5HR  C24   C25  C20  120.74  3.000
 5HR  H231  C23  C24  120.43  3.000
 5HR  H231  C23  C22  120.26  3.000
 5HR  C24   C23  C22  119.30  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   -172.04  30.0  3
 5HR  Var_02    C2    N1   C1   C20  -159.35  30.0  1
 5HR  Var_03    C1    N1   C2   C3    -89.55  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

