# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 23:21:51 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](c1ccc(cc1)n2cccn2)[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
 1OT  1OT  '{(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid'  ligand  27  17  .  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_1OT
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
 1OT  O1   O  OP    -1  -0.886  -2.6455   2.0276  -0.1037
 1OT  P    P  P      0   1.160  -3.1991   0.6055  -0.2468
 1OT  O2   O  OP    -1  -0.902  -4.6481   0.4576   0.2412
 1OT  O3   O  O      0  -0.898  -2.9324  -0.0450  -1.6107
 1OT  C1   C  CH1    0  -0.440  -2.2277  -0.4743   0.9602
 1OT  N1   N  NH2    0  -0.809  -2.7162  -1.8581   0.9319
 1OT  C2   C  CR6    0   0.155  -0.7589  -0.4008   0.7037
 1OT  C10  C  CR16   0  -0.279  -0.0472   0.7634   1.0065
 1OT  C9   C  CR16   0  -0.304   1.3087   0.8798   0.7613
 1OT  C5   C  CR6    0   0.348   2.0040  -0.1770   0.1777
 1OT  C4   C  CR16   0  -0.311   1.3189  -1.3424  -0.1368
 1OT  C3   C  CR16   0  -0.329  -0.0404  -1.4459   0.1291
 1OT  N2   N  NR5    0  -0.402   3.3887  -0.0556  -0.0819
 1OT  N3   N  N      0  -0.282   4.0233   1.0890   0.1764
 1OT  C8   C  CR15   0  -0.035   5.2775   0.8867  -0.1706
 1OT  C7   C  CR15   0  -0.514   5.4686  -0.4149  -0.6656
 1OT  C6   C  CR15   0   0.034   4.2255  -0.9895  -0.5914
 1OT  H3   H  HCH1   0   0.207  -2.4108  -0.0833   1.9683
 1OT  H4   H  HNH2   0   0.332  -3.6936  -1.8220   1.1977
 1OT  H5   H  HNH2   0   0.323  -2.7498  -2.1401  -0.0436
 1OT  H7   H  HCR6   0   0.234  -0.5720   1.6012   1.4439
 1OT  H8   H  HCR6   0   0.264   1.8258   1.7921   1.0226
 1OT  H9   H  HCR6   0   0.266   1.8213  -2.1872  -0.5886
 1OT  H10  H  HCR6   0   0.238  -0.5352  -2.3773  -0.1112
 1OT  H11  H  HCR5   0   0.265   6.0054   1.6754  -0.0559
 1OT  H12  H  HCR5   0   0.266   6.3781  -0.8673  -1.0228
 1OT  H13  H  HCR5   0   0.298   3.8987  -1.9782  -0.8631

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
 1OT  O3   P    deloc     1.535  0.020  1.535
 1OT  O1   P    deloc     1.533  0.020  1.533
 1OT  P    O2   deloc     1.536  0.020  1.536
 1OT  P    C1   single    1.888  0.020  1.888
 1OT  N1   C1   single    1.468  0.020  1.468
 1OT  C1   C2   single    1.493  0.020  1.493
 1OT  C2   C10  aromatic  1.398  0.020  1.398
 1OT  C2   C3   aromatic  1.392  0.020  1.392
 1OT  C10  C9   aromatic  1.383  0.020  1.383
 1OT  C3   C4   aromatic  1.389  0.020  1.389
 1OT  C9   C5   aromatic  1.393  0.020  1.393
 1OT  C4   C5   aromatic  1.388  0.020  1.388
 1OT  C5   N2   single    1.414  0.020  1.414
 1OT  N2   C6   aromatic  1.354  0.020  1.354
 1OT  N2   N3   aromatic  1.334  0.020  1.334
 1OT  C6   C7   aromatic  1.372  0.020  1.372
 1OT  N3   C8   aromatic  1.317  0.020  1.317
 1OT  C7   C8   aromatic  1.406  0.020  1.406
 1OT  C1   H3   single    0.970  0.020  1.090
 1OT  N1   H4   single    0.890  0.020  1.040
 1OT  N1   H5   single    0.890  0.020  1.040
 1OT  C10  H7   single    0.930  0.020  1.080
 1OT  C9   H8   single    0.930  0.020  1.080
 1OT  C4   H9   single    0.930  0.020  1.080
 1OT  C3   H10  single    0.930  0.020  1.080
 1OT  C8   H11  single    0.930  0.020  1.080
 1OT  C7   H12  single    0.930  0.020  1.080
 1OT  C6   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
 1OT  C1   P    O3   103.67  3.000
 1OT  C1   P    O2   103.13  3.000
 1OT  O3   P    O2   113.92  3.000
 1OT  C1   P    O1   106.56  3.000
 1OT  O2   P    O1   113.60  3.000
 1OT  O3   P    O1   114.42  3.000
 1OT  H3   C1   C2   107.73  3.000
 1OT  H3   C1   N1   107.35  3.000
 1OT  C2   C1   N1   111.75  3.000
 1OT  H3   C1   P    107.32  3.000
 1OT  C2   C1   P    111.61  3.000
 1OT  N1   C1   P    110.83  3.000
 1OT  H5   N1   H4   103.29  3.000
 1OT  H5   N1   C1   106.93  3.000
 1OT  H4   N1   C1   106.40  3.000
 1OT  C3   C2   C10  116.87  3.000
 1OT  C3   C2   C1   122.80  3.000
 1OT  C10  C2   C1   120.31  3.000
 1OT  H7   C10  C9   118.84  3.000
 1OT  H7   C10  C2   119.08  3.000
 1OT  C9   C10  C2   122.07  3.000
 1OT  H8   C9   C5   120.19  3.000
 1OT  H8   C9   C10  119.83  3.000
 1OT  C5   C9   C10  119.98  3.000
 1OT  N2   C5   C4   120.92  3.000
 1OT  N2   C5   C9   120.03  3.000
 1OT  C4   C5   C9   119.05  3.000
 1OT  H9   C4   C3   118.44  3.000
 1OT  H9   C4   C5   121.41  3.000
 1OT  C3   C4   C5   120.15  3.000
 1OT  H10  C3   C4   117.99  3.000
 1OT  H10  C3   C2   120.13  3.000
 1OT  C4   C3   C2   121.88  3.000
 1OT  C6   N2   N3   111.77  3.000
 1OT  N3   N2   C5   120.26  3.000
 1OT  C6   N2   C5   127.97  3.000
 1OT  C8   N3   N2   105.68  3.000
 1OT  H11  C8   C7   128.49  3.000
 1OT  H11  C8   N3   120.13  3.000
 1OT  C7   C8   N3   111.37  3.000
 1OT  H12  C7   C6   127.41  3.000
 1OT  H12  C7   C8   128.37  3.000
 1OT  C6   C7   C8   104.22  3.000
 1OT  H13  C6   C7   130.28  3.000
 1OT  H13  C6   N2   122.77  3.000
 1OT  C7   C6   N2   106.96  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
 1OT  CONST_01  C5   C9   C10  C2     0.00  0.0  0
 1OT  CONST_02  C5   C4   C3   C2     0.00  0.0  0
 1OT  CONST_03  C4   C3   C2   C10    0.00  0.0  0
 1OT  CONST_04  C4   C5   C9   C10    0.00  0.0  0
 1OT  CONST_05  N2   C5   C9   C10  180.00  0.0  0
 1OT  CONST_06  C3   C2   C10  C9     0.00  0.0  0
 1OT  CONST_07  C3   C4   C5   C9     0.00  0.0  0
 1OT  CONST_08  C6   N2   C5   C9   180.00  0.0  0
 1OT  CONST_09  N3   N2   C5   C9     0.00  0.0  0
 1OT  CONST_10  C7   C6   N2   C5   180.00  0.0  0
 1OT  CONST_11  C8   N3   N2   C5   180.00  0.0  0
 1OT  CONST_12  C6   N2   C5   C4     0.00  0.0  0
 1OT  CONST_13  N3   N2   C5   C4   180.00  0.0  0
 1OT  CONST_14  N2   C5   C4   C3   180.00  0.0  0
 1OT  CONST_15  C8   C7   C6   N2     0.00  0.0  0
 1OT  CONST_16  C7   C8   N3   N2     0.00  0.0  0
 1OT  CONST_17  C7   C6   N2   N3     0.00  0.0  0
 1OT  CONST_18  C6   C7   C8   N3     0.00  0.0  0
 1OT  CONST_19  C6   N2   N3   C8     0.00  0.0  0
 1OT  CONST_20  C9   C10  C2   C1   180.00  0.0  0
 1OT  CONST_21  C4   C3   C2   C1   180.00  0.0  0
 1OT  CONST_22  H8   C9   C10  C2   180.00  0.0  0
 1OT  CONST_23  H9   C4   C3   C2   180.00  0.0  0
 1OT  CONST_24  H10  C3   C2   C10  180.00  0.0  0
 1OT  CONST_25  H7   C10  C9   C5   180.00  0.0  0
 1OT  CONST_26  H13  C6   N2   C5     0.00  0.0  0
 1OT  CONST_27  H12  C7   C6   N2   180.00  0.0  0
 1OT  CONST_28  H11  C8   N3   N2   180.00  0.0  0

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
 1OT  chir_01  C1  P  N1  C2  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
 1OT  plan-1  C5   0.020
 1OT  plan-1  N2   0.020
 1OT  plan-1  N3   0.020
 1OT  plan-1  C8   0.020
 1OT  plan-1  C7   0.020
 1OT  plan-1  C6   0.020
 1OT  plan-1  H11  0.020
 1OT  plan-1  H12  0.020
 1OT  plan-1  H13  0.020
 1OT  plan-2  C1   0.020
 1OT  plan-2  C2   0.020
 1OT  plan-2  C10  0.020
 1OT  plan-2  C9   0.020
 1OT  plan-2  C5   0.020
 1OT  plan-2  C4   0.020
 1OT  plan-2  C3   0.020
 1OT  plan-2  N2   0.020
 1OT  plan-2  H7   0.020
 1OT  plan-2  H8   0.020
 1OT  plan-2  H9   0.020
 1OT  plan-2  H10  0.020

