# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:56:31 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: [(R)-amino(4-carbamimidoylphenyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](c1ccc(cc1)C(N)=N)[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
 1OS  1OS  '[(R)-amino(4-carbamimidoylphenyl)methyl]phosphonic acid'  ligand  27  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1OS
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
 1OS  O1   O  O     0  -0.708   2.4027   0.6062  -1.6876
 1OS  P    P  P     0   1.354   2.5788  -0.2078  -0.4612
 1OS  O2   O  OH1   0  -0.742   2.1419  -1.7281  -0.7520
 1OS  O3   O  OH1   0  -0.746   4.0668  -0.2603   0.1449
 1OS  C6   C  CH1   0  -0.461   1.6283   0.3897   0.9895
 1OS  N3   N  NH2   0  -0.782   2.0080   1.7385   1.3686
 1OS  C5   C  CR6   0   0.137   0.1617   0.2697   0.6598
 1OS  C7   C  CR16  0  -0.281  -0.5121   1.2811  -0.0206
 1OS  C8   C  CR16  0  -0.261  -1.8505   1.1433  -0.3456
 1OS  C2   C  CR6   0   0.036  -2.5554  -0.0072   0.0005
 1OS  C1   C  C     0   0.334  -3.9901  -0.1310  -0.3788
 1OS  N1   N  NH2   0  -0.823  -4.7184  -1.0123   0.3680
 1OS  N2   N  N     0  -0.651  -4.4151   0.5373  -1.3814
 1OS  C3   C  CR16  0  -0.277  -1.8816  -1.0208   0.6775
 1OS  C4   C  CR16  0  -0.284  -0.5394  -0.8823   0.9972
 1OS  H1   H  HOH1  0   0.491   2.3053  -2.3579  -0.0379
 1OS  H2   H  HOH1  0   0.496   4.7658  -0.3375  -0.5195
 1OS  H3   H  HCH1  0   0.309   1.8493  -0.2745   1.8298
 1OS  H4   H  HNH2  0   0.369   2.9443   1.7421   1.7515
 1OS  H5   H  HNH2  0   0.359   2.0258   2.3565   0.5670
 1OS  H7   H  HCR6  0   0.251  -0.0038   2.1939  -0.3014
 1OS  H8   H  HCR6  0   0.257  -2.3603   1.9381  -0.8728
 1OS  H9   H  HNH2  0   0.395  -4.4476  -1.1681   1.3251
 1OS  H10  H  HNH2  0   0.391  -5.7160  -1.0233   0.2257
 1OS  H11  H  H     0   0.324  -5.4110   0.3916  -1.5244
 1OS  H12  H  HCR6  0   0.259  -2.3877  -1.9383   0.9480
 1OS  H13  H  HCR6  0   0.255  -0.0365  -1.6865   1.5209

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
 1OS  O1  P    double    1.483  0.020  1.483
 1OS  O2  P    single    1.608  0.020  1.608
 1OS  O3  P    single    1.608  0.020  1.608
 1OS  P   C6   single    1.834  0.020  1.834
 1OS  N3  C6   single    1.452  0.020  1.452
 1OS  C6  C5   single    1.508  0.020  1.508
 1OS  C5  C4   aromatic  1.390  0.020  1.390
 1OS  C5  C7   aromatic  1.393  0.020  1.393
 1OS  C4  C3   aromatic  1.387  0.020  1.387
 1OS  C7  C8   aromatic  1.384  0.020  1.384
 1OS  C3  C2   aromatic  1.393  0.020  1.393
 1OS  C8  C2   aromatic  1.393  0.020  1.393
 1OS  C2  C1   single    1.489  0.020  1.489
 1OS  C1  N2   double    1.278  0.020  1.278
 1OS  C1  N1   single    1.366  0.020  1.366
 1OS  O2  H1   single    0.850  0.020  0.980
 1OS  O3  H2   single    0.850  0.020  0.980
 1OS  C6  H3   single    0.970  0.020  1.090
 1OS  N3  H4   single    0.890  0.020  1.040
 1OS  N3  H5   single    0.890  0.020  1.040
 1OS  C7  H7   single    0.930  0.020  1.080
 1OS  C8  H8   single    0.930  0.020  1.080
 1OS  N1  H9   single    0.890  0.020  1.040
 1OS  N1  H10  single    0.890  0.020  1.040
 1OS  N2  H11  single    0.890  0.020  1.040
 1OS  C3  H12  single    0.930  0.020  1.080
 1OS  C4  H13  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
 1OS  C6   P   O3  101.08  3.000
 1OS  C6   P   O2  108.07  3.000
 1OS  O3   P   O2  106.78  3.000
 1OS  C6   P   O1  114.45  3.000
 1OS  O3   P   O1  116.09  3.000
 1OS  O2   P   O1  109.70  3.000
 1OS  H1   O2  P   115.88  3.000
 1OS  H2   O3  P   114.36  3.000
 1OS  H3   C6  C5  108.43  3.000
 1OS  H3   C6  N3  108.11  3.000
 1OS  C5   C6  N3  112.68  3.000
 1OS  H3   C6  P   107.76  3.000
 1OS  C5   C6  P   107.76  3.000
 1OS  N3   C6  P   111.94  3.000
 1OS  H5   N3  H4  106.34  3.000
 1OS  H5   N3  C6  111.41  3.000
 1OS  H4   N3  C6  110.14  3.000
 1OS  C4   C5  C7  118.45  3.000
 1OS  C7   C5  C6  121.30  3.000
 1OS  C4   C5  C6  120.22  3.000
 1OS  H7   C7  C8  118.52  3.000
 1OS  H7   C7  C5  120.81  3.000
 1OS  C8   C7  C5  120.68  3.000
 1OS  H8   C8  C2  119.31  3.000
 1OS  H8   C8  C7  119.81  3.000
 1OS  C2   C8  C7  120.88  3.000
 1OS  C3   C2  C1  121.97  3.000
 1OS  C1   C2  C8  119.53  3.000
 1OS  C3   C2  C8  118.49  3.000
 1OS  N2   C1  N1  126.11  3.000
 1OS  N1   C1  C2  115.35  3.000
 1OS  N2   C1  C2  118.48  3.000
 1OS  H10  N1  H9  113.51  3.000
 1OS  H10  N1  C1  117.24  3.000
 1OS  H9   N1  C1  118.44  3.000
 1OS  H11  N2  C1  111.18  3.000
 1OS  H12  C3  C4  118.66  3.000
 1OS  H12  C3  C2  120.82  3.000
 1OS  C4   C3  C2  120.51  3.000
 1OS  H13  C4  C3  119.12  3.000
 1OS  H13  C4  C5  119.89  3.000
 1OS  C3   C4  C5  120.99  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
 1OS  CONST_01  C2   C3  C4  C5    0.00   0.0  0
 1OS  CONST_02  C2   C8  C7  C5    0.00   0.0  0
 1OS  CONST_03  C3   C4  C5  C7    0.00   0.0  0
 1OS  CONST_04  C3   C2  C8  C7    0.00   0.0  0
 1OS  CONST_05  C4   C5  C7  C8    0.00   0.0  0
 1OS  CONST_06  C4   C3  C2  C8    0.00   0.0  0
 1OS  CONST_07  C3   C4  C5  C6  180.00   0.0  0
 1OS  CONST_08  C8   C7  C5  C6  180.00   0.0  0
 1OS  CONST_09  C1   C2  C8  C7  180.00   0.0  0
 1OS  CONST_10  C4   C3  C2  C1  180.00   0.0  0
 1OS  CONST_11  H12  C3  C4  C5  180.00   0.0  0
 1OS  CONST_12  H8   C8  C7  C5  180.00   0.0  0
 1OS  CONST_13  H13  C4  C5  C7  180.00   0.0  0
 1OS  CONST_14  H7   C7  C8  C2  180.00   0.0  0
 1OS  CONST_15  H11  N2  C1  C2  180.00   0.0  0
 1OS  CONST_17  H10  N1  C1  C2  180.00   0.0  0
 1OS  Var_01    N2   C1  C2  C8   24.90  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
 1OS  chir_01  C6  P  N3  C5  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
 1OS  plan-1  C6   0.020
 1OS  plan-1  C5   0.020
 1OS  plan-1  C7   0.020
 1OS  plan-1  C8   0.020
 1OS  plan-1  C2   0.020
 1OS  plan-1  C1   0.020
 1OS  plan-1  C3   0.020
 1OS  plan-1  C4   0.020
 1OS  plan-1  H7   0.020
 1OS  plan-1  H8   0.020
 1OS  plan-1  H12  0.020
 1OS  plan-1  H13  0.020
 1OS  plan-2  C2   0.020
 1OS  plan-2  C1   0.020
 1OS  plan-2  N1   0.020
 1OS  plan-2  N2   0.020
 1OS  plan-2  H9   0.020
 1OS  plan-2  H10  0.020
 1OS  plan-2  H11  0.020

