# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 23:29:21 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  25  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 PERFECT
;

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  -0.896   2.4255   0.3171  -1.5559
 1OS  P    P  P      0   1.162   2.6873  -0.4503  -0.2542
 1OS  O2   O  OP    -1  -0.886   2.2079  -1.9052  -0.2660
 1OS  O3   O  OP    -1  -0.901   4.1111  -0.2749   0.2950
 1OS  C6   C  CH1    0  -0.443   1.6222   0.4566   1.0188
 1OS  N3   N  NH2    0  -0.809   2.0454   1.8560   1.1501
 1OS  C5   C  CR6    0   0.164   0.1720   0.3417   0.6913
 1OS  C7   C  CR16   0  -0.321  -0.5685   1.4045   0.1712
 1OS  C8   C  CR16   0  -0.265  -1.9051   1.2571  -0.1663
 1OS  C2   C  CR6    0   0.021  -2.5623   0.0433   0.0146
 1OS  C1   C  C      0   0.323  -3.9944  -0.0878  -0.3569
 1OS  N1   N  NH2    0  -0.824  -4.6635  -1.1206   0.2422
 1OS  N2   N  N      0  -0.659  -4.4896   0.7141  -1.2223
 1OS  C3   C  CR16   0  -0.291  -1.8289  -1.0243   0.5375
 1OS  C4   C  CR16   0  -0.277  -0.4913  -0.8774   0.8588
 1OS  H3   H  HCH1   0   0.208   1.7900  -0.0278   1.9881
 1OS  H4   H  HNH2   0   0.332   3.0103   1.8335   1.4595
 1OS  H5   H  HNH2   0   0.324   2.1130   2.2346   0.2098
 1OS  H7   H  HCR6   0   0.230  -0.1054   2.3737   0.0412
 1OS  H8   H  HCR6   0   0.240  -2.4532   2.1004  -0.5662
 1OS  H9   H  HNH2   0   0.391  -4.3587  -1.4170   1.1546
 1OS  H10  H  HNH2   0   0.387  -5.6644  -1.1464   0.1279
 1OS  H11  H  H      0   0.318  -5.4809   0.5351  -1.3595
 1OS  H12  H  HCR6   0   0.242  -2.2917  -1.9940   0.6768
 1OS  H13  H  HCR6   0   0.230   0.0576  -1.7264   1.2420

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    deloc     1.534  0.020  1.534
 1OS  O2  P    deloc     1.532  0.020  1.532
 1OS  O3  P    deloc     1.536  0.020  1.536
 1OS  P   C6   single    1.891  0.020  1.891
 1OS  N3  C6   single    1.468  0.020  1.468
 1OS  C6  C5   single    1.491  0.020  1.491
 1OS  C5  C4   aromatic  1.398  0.020  1.398
 1OS  C5  C7   aromatic  1.396  0.020  1.396
 1OS  C4  C3   aromatic  1.383  0.020  1.383
 1OS  C7  C8   aromatic  1.386  0.020  1.386
 1OS  C3  C2   aromatic  1.397  0.020  1.397
 1OS  C8  C2   aromatic  1.392  0.020  1.392
 1OS  C2  C1   single    1.485  0.020  1.485
 1OS  C1  N2   double    1.280  0.020  1.280
 1OS  C1  N1   single    1.369  0.020  1.369
 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  103.09  3.000
 1OS  C6   P   O2  106.52  3.000
 1OS  O3   P   O2  113.66  3.000
 1OS  C6   P   O1  103.61  3.000
 1OS  O3   P   O1  113.86  3.000
 1OS  O2   P   O1  114.54  3.000
 1OS  H3   C6  C5  107.99  3.000
 1OS  H3   C6  N3  107.34  3.000
 1OS  C5   C6  N3  111.93  3.000
 1OS  H3   C6  P   107.28  3.000
 1OS  C5   C6  P   111.27  3.000
 1OS  N3   C6  P   110.79  3.000
 1OS  H5   N3  H4  103.15  3.000
 1OS  H5   N3  C6  106.96  3.000
 1OS  H4   N3  C6  106.30  3.000
 1OS  C4   C5  C7  117.19  3.000
 1OS  C7   C5  C6  122.62  3.000
 1OS  C4   C5  C6  120.15  3.000
 1OS  H7   C7  C8  118.59  3.000
 1OS  H7   C7  C5  119.98  3.000
 1OS  C8   C7  C5  121.41  3.000
 1OS  H8   C8  C2  119.23  3.000
 1OS  H8   C8  C7  119.69  3.000
 1OS  C2   C8  C7  121.07  3.000
 1OS  C3   C2  C1  122.17  3.000
 1OS  C1   C2  C8  119.97  3.000
 1OS  C3   C2  C8  117.85  3.000
 1OS  N2   C1  N1  125.43  3.000
 1OS  N1   C1  C2  115.37  3.000
 1OS  N2   C1  C2  119.15  3.000
 1OS  H10  N1  H9  113.32  3.000
 1OS  H10  N1  C1  117.08  3.000
 1OS  H9   N1  C1  118.10  3.000
 1OS  H11  N2  C1  111.00  3.000
 1OS  H12  C3  C4  118.56  3.000
 1OS  H12  C3  C2  120.53  3.000
 1OS  C4   C3  C2  120.89  3.000
 1OS  H13  C4  C3  119.33  3.000
 1OS  H13  C4  C5  119.11  3.000
 1OS  C3   C4  C5  121.57  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   23.28  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

