# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 23:54:35 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2-{2-[(3,5-dichlorophenyl)amino]-2-oxoethoxy}phenyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)c1ccccc1OCC(=O)Nc2cc(Cl)cc(Cl)c2
#
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
 Y03  Y03  '(2-{2-[(3,5-dichlorophenyl)amino]-2-oxoethoxy}phenyl)phosphonic acid'  ligand  35  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y03
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
 Y03  OAS  O   OH1   0  -0.781   2.4795   1.8130  -0.5006
 Y03  PAR  P   P     0   1.366   3.8278   1.4396   0.2609
 Y03  OAU  O   O     0  -0.710   4.9069   2.3831  -0.1219
 Y03  OAT  O   OH1   0  -0.745   3.4900   1.3733   1.8308
 Y03  CAM  C   CR6   0  -0.371   4.2381  -0.2744  -0.0909
 Y03  CAN  C   CR16  0  -0.266   5.5140  -0.5868  -0.5485
 Y03  CAO  C   CR16  0  -0.257   5.8471  -1.8937  -0.8743
 Y03  CAP  C   CR16  0  -0.241   4.8958  -2.8943  -0.7412
 Y03  CAQ  C   CR16  0  -0.352   3.6173  -2.6061  -0.2817
 Y03  CAL  C   CR6   0   0.414   3.2937  -1.2958   0.0424
 Y03  OAK  O   O2    0  -0.482   2.0886  -0.9205   0.5190
 Y03  CAA  C   CH2   0  -0.305   0.9323  -1.6112   0.1331
 Y03  CAB  C   C     0   0.571  -0.1734  -0.5755   0.0176
 Y03  OAD  O   O     0  -0.477   0.0712   0.6126  -0.1171
 Y03  NAC  N   NH1   0  -0.743  -1.4117  -1.1030   0.0381
 Y03  CAE  C   CR6   0   0.388  -2.6433  -0.4742  -0.1616
 Y03  CAF  C   CR16  0  -0.302  -3.7627  -1.3072  -0.1855
 Y03  CAG  C   CR6   0  -0.028  -5.0145  -0.7573  -0.3790
 Y03  CL1  CL  CL    0  -0.103  -6.3921  -1.7996  -0.4068
 Y03  CAH  C   CR16  0  -0.198  -5.2000   0.6049  -0.5541
 Y03  CAI  C   CR6   0  -0.028  -4.0712   1.4045  -0.5246
 Y03  CL2  CL  CL    0  -0.105  -4.2580   3.1108  -0.7356
 Y03  CAJ  C   CR16  0  -0.266  -2.7947   0.9007  -0.3310
 Y03  H1   H   HOH1  0   0.500   1.6633   1.3013  -0.2887
 Y03  H2   H   HOH1  0   0.491   3.2182   2.2209   2.2101
 Y03  H3   H   HCR6  0   0.273   6.2485   0.1997  -0.6592
 Y03  H4   H   HCR6  0   0.264   6.8404  -2.1286  -1.2310
 Y03  H5   H   HCR6  0   0.273   5.1472  -3.9168  -0.9898
 Y03  H6   H   HCR6  0   0.291   2.8938  -3.4034  -0.1707
 Y03  H7   H   HCH2  0   0.291   1.0424  -2.0888  -0.8478
 Y03  H8   H   HCH2  0   0.282   0.6721  -2.3917   0.8543
 Y03  H9   H   HNH1  0   0.436  -1.4661  -2.1027   0.1766
 Y03  H10  H   HCR6  0   0.304  -3.6509  -2.3761  -0.0577
 Y03  H11  H   HCR6  0   0.304  -6.1842   1.0236  -0.7080
 Y03  H12  H   HCR6  0   0.312  -1.9521   1.5704  -0.3133

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
 Y03  OAU  PAR  double    1.484  0.020  1.484
 Y03  CL1  CAG  single    1.728  0.020  1.728
 Y03  OAK  CAA  single    1.401  0.020  1.401
 Y03  OAK  CAL  single    1.349  0.020  1.349
 Y03  CAA  CAB  single    1.519  0.020  1.519
 Y03  CAQ  CAL  aromatic  1.388  0.020  1.388
 Y03  CAQ  CAP  aromatic  1.389  0.020  1.389
 Y03  CAF  CAG  aromatic  1.381  0.020  1.381
 Y03  CAF  CAE  aromatic  1.396  0.020  1.396
 Y03  CAL  CAM  aromatic  1.397  0.020  1.397
 Y03  CAB  OAD  double    1.220  0.020  1.220
 Y03  CAB  NAC  single    1.346  0.020  1.346
 Y03  CAP  CAO  aromatic  1.387  0.020  1.387
 Y03  CAM  PAR  single    1.797  0.020  1.797
 Y03  CAM  CAN  aromatic  1.391  0.020  1.391
 Y03  PAR  OAS  single    1.593  0.020  1.593
 Y03  PAR  OAT  single    1.607  0.020  1.607
 Y03  CAG  CAH  aromatic  1.386  0.020  1.386
 Y03  NAC  CAE  single    1.397  0.020  1.397
 Y03  CAO  CAN  aromatic  1.387  0.020  1.387
 Y03  CAE  CAJ  aromatic  1.394  0.020  1.394
 Y03  CAH  CAI  aromatic  1.384  0.020  1.384
 Y03  CAJ  CAI  aromatic  1.386  0.020  1.386
 Y03  CAI  CL2  single    1.729  0.020  1.729
 Y03  OAS  H1   single    0.850  0.020  0.980
 Y03  OAT  H2   single    0.850  0.020  0.980
 Y03  CAN  H3   single    0.930  0.020  1.080
 Y03  CAO  H4   single    0.930  0.020  1.080
 Y03  CAP  H5   single    0.930  0.020  1.080
 Y03  CAQ  H6   single    0.930  0.020  1.080
 Y03  CAA  H7   single    0.970  0.020  1.090
 Y03  CAA  H8   single    0.970  0.020  1.090
 Y03  NAC  H9   single    0.860  0.020  1.020
 Y03  CAF  H10  single    0.930  0.020  1.080
 Y03  CAH  H11  single    0.930  0.020  1.080
 Y03  CAJ  H12  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
 Y03  H1   OAS  PAR  118.43  3.000
 Y03  CAM  PAR  OAT  101.53  3.000
 Y03  OAT  PAR  OAU  115.54  3.000
 Y03  CAM  PAR  OAU  112.95  3.000
 Y03  OAT  PAR  OAS  107.38  3.000
 Y03  CAM  PAR  OAS  108.86  3.000
 Y03  OAU  PAR  OAS  110.07  3.000
 Y03  H2   OAT  PAR  113.95  3.000
 Y03  CAL  CAM  CAN  119.15  3.000
 Y03  CAN  CAM  PAR  119.21  3.000
 Y03  CAL  CAM  PAR  121.61  3.000
 Y03  H3   CAN  CAO  119.85  3.000
 Y03  H3   CAN  CAM  119.54  3.000
 Y03  CAO  CAN  CAM  120.60  3.000
 Y03  H4   CAO  CAP  120.34  3.000
 Y03  H4   CAO  CAN  120.17  3.000
 Y03  CAP  CAO  CAN  119.49  3.000
 Y03  H5   CAP  CAQ  119.08  3.000
 Y03  H5   CAP  CAO  120.03  3.000
 Y03  CAQ  CAP  CAO  120.90  3.000
 Y03  H6   CAQ  CAL  121.03  3.000
 Y03  H6   CAQ  CAP  119.77  3.000
 Y03  CAL  CAQ  CAP  119.19  3.000
 Y03  OAK  CAL  CAQ  123.60  3.000
 Y03  CAQ  CAL  CAM  120.67  3.000
 Y03  OAK  CAL  CAM  115.72  3.000
 Y03  CAA  OAK  CAL  120.18  3.000
 Y03  H8   CAA  H7   107.63  3.000
 Y03  H8   CAA  CAB  111.31  3.000
 Y03  H7   CAA  CAB  107.58  3.000
 Y03  H8   CAA  OAK  111.49  3.000
 Y03  H7   CAA  OAK  112.22  3.000
 Y03  CAB  CAA  OAK  106.58  3.000
 Y03  NAC  CAB  OAD  124.58  3.000
 Y03  NAC  CAB  CAA  113.65  3.000
 Y03  OAD  CAB  CAA  121.74  3.000
 Y03  H9   NAC  CAE  114.66  3.000
 Y03  H9   NAC  CAB  116.06  3.000
 Y03  CAE  NAC  CAB  129.22  3.000
 Y03  CAJ  CAE  CAF  119.98  3.000
 Y03  CAJ  CAE  NAC  123.86  3.000
 Y03  CAF  CAE  NAC  116.16  3.000
 Y03  H10  CAF  CAG  120.23  3.000
 Y03  H10  CAF  CAE  120.31  3.000
 Y03  CAG  CAF  CAE  119.46  3.000
 Y03  CAH  CAG  CL1  118.96  3.000
 Y03  CAH  CAG  CAF  122.04  3.000
 Y03  CL1  CAG  CAF  119.00  3.000
 Y03  H11  CAH  CAI  121.48  3.000
 Y03  H11  CAH  CAG  121.39  3.000
 Y03  CAI  CAH  CAG  117.13  3.000
 Y03  CAJ  CAI  CL2  118.37  3.000
 Y03  CL2  CAI  CAH  118.64  3.000
 Y03  CAJ  CAI  CAH  122.99  3.000
 Y03  H12  CAJ  CAI  119.81  3.000
 Y03  H12  CAJ  CAE  121.79  3.000
 Y03  CAI  CAJ  CAE  118.40  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
 Y03  CONST_01  CAP  CAQ  CAL  CAM     0.00   0.0  0
 Y03  CONST_02  CAP  CAO  CAN  CAM     0.00   0.0  0
 Y03  CONST_03  CAQ  CAL  CAM  CAN     0.00   0.0  0
 Y03  CONST_04  CAQ  CAP  CAO  CAN     0.00   0.0  0
 Y03  CONST_05  CAL  CAQ  CAP  CAO     0.00   0.0  0
 Y03  CONST_06  CAL  CAM  CAN  CAO     0.00   0.0  0
 Y03  CONST_07  CAH  CAG  CAF  CAE     0.00   0.0  0
 Y03  CONST_08  CAH  CAI  CAJ  CAE     0.00   0.0  0
 Y03  CONST_09  CAI  CAH  CAG  CAF     0.00   0.0  0
 Y03  CONST_10  CAI  CAJ  CAE  CAF     0.00   0.0  0
 Y03  CONST_11  CAJ  CAE  CAF  CAG     0.00   0.0  0
 Y03  CONST_12  CAJ  CAI  CAH  CAG     0.00   0.0  0
 Y03  CONST_13  CAQ  CAL  CAM  PAR   180.00   0.0  0
 Y03  CONST_14  CAO  CAN  CAM  PAR   180.00   0.0  0
 Y03  CONST_15  OAK  CAL  CAM  CAN   180.00   0.0  0
 Y03  CONST_16  OAK  CAL  CAQ  CAP   180.00   0.0  0
 Y03  CONST_17  CAG  CAF  CAE  NAC   180.00   0.0  0
 Y03  CONST_18  CAI  CAJ  CAE  NAC   180.00   0.0  0
 Y03  CONST_19  CL1  CAG  CAF  CAE   180.00   0.0  0
 Y03  CONST_20  CL2  CAI  CAJ  CAE   180.00   0.0  0
 Y03  CONST_21  CL2  CAI  CAH  CAG   180.00   0.0  0
 Y03  CONST_22  CAI  CAH  CAG  CL1   180.00   0.0  0
 Y03  CONST_23  H6   CAQ  CAL  CAM   180.00   0.0  0
 Y03  CONST_24  H4   CAO  CAN  CAM   180.00   0.0  0
 Y03  CONST_25  H5   CAP  CAO  CAN   180.00   0.0  0
 Y03  CONST_26  H3   CAN  CAO  CAP   180.00   0.0  0
 Y03  CONST_27  H11  CAH  CAG  CAF   180.00   0.0  0
 Y03  CONST_28  H12  CAJ  CAE  CAF   180.00   0.0  0
 Y03  CONST_29  H10  CAF  CAG  CAH   180.00   0.0  0
 Y03  CONST_30  CAF  CAE  NAC  CAB   180.00   0.0  0
 Y03  CONST_31  CAJ  CAE  NAC  CAB     0.00   0.0  0
 Y03  CONST_32  H9   NAC  CAE  CAF     0.00   0.0  0
 Y03  CONST_33  CAE  NAC  CAB  CAA   180.00   0.0  0
 Y03  CONST_34  CAE  NAC  CAB  OAD     0.00   0.0  0
 Y03  Var_01    CAL  CAM  PAR  OAS   -49.40  30.0  2
 Y03  Var_02    CAB  CAA  OAK  CAL  -143.89  30.0  3
 Y03  Var_03    OAD  CAB  CAA  OAK    20.15  30.0  3

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
 Y03  plan-1  PAR  0.020
 Y03  plan-1  CAM  0.020
 Y03  plan-1  CAN  0.020
 Y03  plan-1  CAO  0.020
 Y03  plan-1  CAP  0.020
 Y03  plan-1  CAQ  0.020
 Y03  plan-1  CAL  0.020
 Y03  plan-1  OAK  0.020
 Y03  plan-1  H3   0.020
 Y03  plan-1  H4   0.020
 Y03  plan-1  H5   0.020
 Y03  plan-1  H6   0.020
 Y03  plan-2  NAC  0.020
 Y03  plan-2  CAE  0.020
 Y03  plan-2  CAF  0.020
 Y03  plan-2  CAG  0.020
 Y03  plan-2  CL1  0.020
 Y03  plan-2  CAH  0.020
 Y03  plan-2  CAI  0.020
 Y03  plan-2  CL2  0.020
 Y03  plan-2  CAJ  0.020
 Y03  plan-2  H10  0.020
 Y03  plan-2  H11  0.020
 Y03  plan-2  H12  0.020
 Y03  plan-3  CAA  0.020
 Y03  plan-3  CAB  0.020
 Y03  plan-3  OAD  0.020
 Y03  plan-3  NAC  0.020
 Y03  plan-3  CAE  0.020
 Y03  plan-3  H9   0.020

