# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 16:33:59 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2-{2-[(3-chlorophenyl)amino]-2-oxoethoxy}phenyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)c1ccccc1OCC(=O)Nc2cccc(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
 Y06  Y06  '(2-{2-[(3-chlorophenyl)amino]-2-oxoethoxy}phenyl)phosphonic acid'  ligand  35  22  .  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_Y06
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
 Y06  OAS  O   OH1   0  -0.746   3.2839  -1.6124   1.7060
 Y06  PAR  P   P     0   1.366   3.5320  -1.4114   0.1308
 Y06  OAU  O   O     0  -0.711   4.6569  -2.1908  -0.4432
 Y06  OAT  O   OH1   0  -0.782   2.1736  -1.7757  -0.6158
 Y06  CAM  C   CR6   0  -0.370   3.7919   0.3635   0.0220
 Y06  CAN  C   CR16  0  -0.266   5.0084   0.8453  -0.4501
 Y06  CAO  C   CR16  0  -0.257   5.2141   2.2081  -0.6085
 Y06  CAP  C   CR16  0  -0.241   4.1937   3.0942  -0.2955
 Y06  CAQ  C   CR16  0  -0.351   2.9734   2.6355   0.1833
 Y06  CAL  C   CR6   0   0.412   2.7794   1.2705   0.3439
 Y06  OAK  O   O2    0  -0.481   1.6431   0.7306   0.8309
 Y06  CAA  C   CH2   0  -0.307   0.4103   1.3500   0.5833
 Y06  CAB  C   C     0   0.567  -0.6106   0.2351   0.4290
 Y06  OAD  O   O     0  -0.481  -0.2803  -0.8976   0.1113
 Y06  NAC  N   NH1   0  -0.737  -1.8777   0.6328   0.6324
 Y06  CAE  C   CR6   0   0.376  -3.0678  -0.0794   0.4291
 Y06  CAF  C   CR16  0  -0.302  -4.2337   0.6827   0.3506
 Y06  CAG  C   CR6   0  -0.025  -5.4493   0.0519   0.1661
 Y06  CL1  CL  CL    0  -0.120  -6.8850   1.0155   0.0640
 Y06  CAH  C   CR16  0  -0.228  -5.5442  -1.3261   0.0528
 Y06  CAI  C   CR16  0  -0.252  -4.3770  -2.0684   0.1356
 Y06  CAJ  C   CR16  0  -0.295  -3.1404  -1.4674   0.3242
 Y06  H1   H   HOH1  0   0.490   3.1079  -2.5296   1.9592
 Y06  H2   H   HOH1  0   0.500   1.3296  -1.3892  -0.2773
 Y06  H3   H   HCR6  0   0.272   5.7949   0.1482  -0.7070
 Y06  H4   H   HCR6  0   0.264   6.1615   2.5745  -0.9791
 Y06  H5   H   HCR6  0   0.273   4.3445   4.1587  -0.4177
 Y06  H6   H   HCR6  0   0.290   2.1945   3.3436   0.4363
 Y06  H7   H   HCH2  0   0.279   0.1348   2.0337   1.3916
 Y06  H8   H   HCH2  0   0.289   0.4195   1.9255  -0.3502
 Y06  H9   H   HNH1  0   0.432  -2.0026   1.6027   0.8864
 Y06  H10  H   HCR6  0   0.297  -4.1857   1.7617   0.4279
 Y06  H11  H   HCR6  0   0.283  -6.5016  -1.8025  -0.0960
 Y06  H12  H   HCR6  0   0.275  -4.4290  -3.1459   0.0569
 Y06  H13  H   HCR6  0   0.288  -2.2598  -2.0835   0.3944

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
 Y06  OAU  PAR  double    1.484  0.020  1.484
 Y06  CL1  CAG  single    1.732  0.020  1.732
 Y06  OAK  CAA  single    1.402  0.020  1.402
 Y06  OAK  CAL  single    1.349  0.020  1.349
 Y06  CAA  CAB  single    1.520  0.020  1.520
 Y06  CAF  CAG  aromatic  1.382  0.020  1.382
 Y06  CAF  CAE  aromatic  1.395  0.020  1.395
 Y06  CAQ  CAL  aromatic  1.388  0.020  1.388
 Y06  CAQ  CAP  aromatic  1.389  0.020  1.389
 Y06  CAL  CAM  aromatic  1.397  0.020  1.397
 Y06  OAD  CAB  double    1.222  0.020  1.222
 Y06  CAB  NAC  single    1.343  0.020  1.343
 Y06  CAP  CAO  aromatic  1.387  0.020  1.387
 Y06  CAG  CAH  aromatic  1.386  0.020  1.386
 Y06  CAM  PAR  single    1.797  0.020  1.797
 Y06  CAM  CAN  aromatic  1.391  0.020  1.391
 Y06  PAR  OAS  single    1.607  0.020  1.607
 Y06  PAR  OAT  single    1.592  0.020  1.592
 Y06  NAC  CAE  single    1.402  0.020  1.402
 Y06  CAO  CAN  aromatic  1.387  0.020  1.387
 Y06  CAE  CAJ  aromatic  1.394  0.020  1.394
 Y06  CAH  CAI  aromatic  1.386  0.020  1.386
 Y06  CAJ  CAI  aromatic  1.388  0.020  1.388
 Y06  OAS  H1   single    0.850  0.020  0.980
 Y06  OAT  H2   single    0.850  0.020  0.980
 Y06  CAN  H3   single    0.930  0.020  1.080
 Y06  CAO  H4   single    0.930  0.020  1.080
 Y06  CAP  H5   single    0.930  0.020  1.080
 Y06  CAQ  H6   single    0.930  0.020  1.080
 Y06  CAA  H7   single    0.970  0.020  1.090
 Y06  CAA  H8   single    0.970  0.020  1.090
 Y06  NAC  H9   single    0.860  0.020  1.020
 Y06  CAF  H10  single    0.930  0.020  1.080
 Y06  CAH  H11  single    0.930  0.020  1.080
 Y06  CAI  H12  single    0.930  0.020  1.080
 Y06  CAJ  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
 Y06  H1   OAS  PAR  113.77  3.000
 Y06  CAM  PAR  OAT  108.72  3.000
 Y06  OAT  PAR  OAU  110.19  3.000
 Y06  CAM  PAR  OAU  112.68  3.000
 Y06  OAT  PAR  OAS  107.41  3.000
 Y06  CAM  PAR  OAS  101.84  3.000
 Y06  OAU  PAR  OAS  115.50  3.000
 Y06  H2   OAT  PAR  118.59  3.000
 Y06  CAL  CAM  CAN  119.15  3.000
 Y06  CAN  CAM  PAR  119.28  3.000
 Y06  CAL  CAM  PAR  121.50  3.000
 Y06  H3   CAN  CAO  119.87  3.000
 Y06  H3   CAN  CAM  119.55  3.000
 Y06  CAO  CAN  CAM  120.58  3.000
 Y06  H4   CAO  CAP  120.36  3.000
 Y06  H4   CAO  CAN  120.12  3.000
 Y06  CAP  CAO  CAN  119.51  3.000
 Y06  H5   CAP  CAQ  119.10  3.000
 Y06  H5   CAP  CAO  120.02  3.000
 Y06  CAQ  CAP  CAO  120.88  3.000
 Y06  H6   CAQ  CAL  121.04  3.000
 Y06  H6   CAQ  CAP  119.78  3.000
 Y06  CAL  CAQ  CAP  119.17  3.000
 Y06  OAK  CAL  CAQ  123.58  3.000
 Y06  CAQ  CAL  CAM  120.70  3.000
 Y06  OAK  CAL  CAM  115.71  3.000
 Y06  CAA  OAK  CAL  120.01  3.000
 Y06  H8   CAA  H7   107.65  3.000
 Y06  H8   CAA  CAB  107.71  3.000
 Y06  H7   CAA  CAB  111.36  3.000
 Y06  H8   CAA  OAK  112.02  3.000
 Y06  H7   CAA  OAK  111.54  3.000
 Y06  CAB  CAA  OAK  106.53  3.000
 Y06  NAC  CAB  OAD  124.66  3.000
 Y06  NAC  CAB  CAA  113.64  3.000
 Y06  OAD  CAB  CAA  121.66  3.000
 Y06  H9   NAC  CAE  114.79  3.000
 Y06  H9   NAC  CAB  116.03  3.000
 Y06  CAE  NAC  CAB  128.93  3.000
 Y06  CAJ  CAE  CAF  119.75  3.000
 Y06  CAJ  CAE  NAC  124.13  3.000
 Y06  CAF  CAE  NAC  116.11  3.000
 Y06  H10  CAF  CAG  120.22  3.000
 Y06  H10  CAF  CAE  120.22  3.000
 Y06  CAG  CAF  CAE  119.56  3.000
 Y06  CAH  CAG  CL1  119.45  3.000
 Y06  CAH  CAG  CAF  121.67  3.000
 Y06  CL1  CAG  CAF  118.89  3.000
 Y06  H11  CAH  CAI  121.25  3.000
 Y06  H11  CAH  CAG  120.71  3.000
 Y06  CAI  CAH  CAG  118.04  3.000
 Y06  H12  CAI  CAJ  118.96  3.000
 Y06  H12  CAI  CAH  119.26  3.000
 Y06  CAJ  CAI  CAH  121.78  3.000
 Y06  H13  CAJ  CAI  119.32  3.000
 Y06  H13  CAJ  CAE  121.48  3.000
 Y06  CAI  CAJ  CAE  119.20  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
 Y06  CONST_01  CAP  CAQ  CAL  CAM    0.00   0.0  0
 Y06  CONST_02  CAP  CAO  CAN  CAM    0.00   0.0  0
 Y06  CONST_03  CAQ  CAL  CAM  CAN    0.00   0.0  0
 Y06  CONST_04  CAQ  CAP  CAO  CAN    0.00   0.0  0
 Y06  CONST_05  CAL  CAQ  CAP  CAO    0.00   0.0  0
 Y06  CONST_06  CAL  CAM  CAN  CAO    0.00   0.0  0
 Y06  CONST_07  CAH  CAG  CAF  CAE    0.00   0.0  0
 Y06  CONST_08  CAH  CAI  CAJ  CAE    0.00   0.0  0
 Y06  CONST_09  CAI  CAH  CAG  CAF    0.00   0.0  0
 Y06  CONST_10  CAI  CAJ  CAE  CAF    0.00   0.0  0
 Y06  CONST_11  CAJ  CAE  CAF  CAG    0.00   0.0  0
 Y06  CONST_12  CAJ  CAI  CAH  CAG    0.00   0.0  0
 Y06  CONST_13  CAQ  CAL  CAM  PAR  180.00   0.0  0
 Y06  CONST_14  CAO  CAN  CAM  PAR  180.00   0.0  0
 Y06  CONST_15  OAK  CAL  CAM  CAN  180.00   0.0  0
 Y06  CONST_16  OAK  CAL  CAQ  CAP  180.00   0.0  0
 Y06  CONST_17  CAG  CAF  CAE  NAC  180.00   0.0  0
 Y06  CONST_18  CAI  CAJ  CAE  NAC  180.00   0.0  0
 Y06  CONST_19  CL1  CAG  CAF  CAE  180.00   0.0  0
 Y06  CONST_20  CAI  CAH  CAG  CL1  180.00   0.0  0
 Y06  CONST_21  H6   CAQ  CAL  CAM  180.00   0.0  0
 Y06  CONST_22  H4   CAO  CAN  CAM  180.00   0.0  0
 Y06  CONST_23  H5   CAP  CAO  CAN  180.00   0.0  0
 Y06  CONST_24  H3   CAN  CAO  CAP  180.00   0.0  0
 Y06  CONST_25  H12  CAI  CAJ  CAE  180.00   0.0  0
 Y06  CONST_26  H11  CAH  CAG  CAF  180.00   0.0  0
 Y06  CONST_27  H13  CAJ  CAE  CAF  180.00   0.0  0
 Y06  CONST_28  H10  CAF  CAG  CAH  180.00   0.0  0
 Y06  CONST_31  H9   NAC  CAE  CAF    0.00   0.0  0
 Y06  CONST_32  CAE  NAC  CAB  CAA  180.00   0.0  0
 Y06  CONST_33  CAE  NAC  CAB  OAD    0.00   0.0  0
 Y06  Var_01    CAL  CAM  PAR  OAS  -64.16  30.0  3
 Y06  Var_02    CAB  CAA  OAK  CAL  145.07  30.0  3
 Y06  Var_03    OAD  CAB  CAA  OAK  -23.04  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
 Y06  plan-1  PAR  0.020
 Y06  plan-1  CAM  0.020
 Y06  plan-1  CAN  0.020
 Y06  plan-1  CAO  0.020
 Y06  plan-1  CAP  0.020
 Y06  plan-1  CAQ  0.020
 Y06  plan-1  CAL  0.020
 Y06  plan-1  OAK  0.020
 Y06  plan-1  H3   0.020
 Y06  plan-1  H4   0.020
 Y06  plan-1  H5   0.020
 Y06  plan-1  H6   0.020
 Y06  plan-2  NAC  0.020
 Y06  plan-2  CAE  0.020
 Y06  plan-2  CAF  0.020
 Y06  plan-2  CAG  0.020
 Y06  plan-2  CL1  0.020
 Y06  plan-2  CAH  0.020
 Y06  plan-2  CAI  0.020
 Y06  plan-2  CAJ  0.020
 Y06  plan-2  H10  0.020
 Y06  plan-2  H11  0.020
 Y06  plan-2  H12  0.020
 Y06  plan-2  H13  0.020
 Y06  plan-3  CAA  0.020
 Y06  plan-3  CAB  0.020
 Y06  plan-3  OAD  0.020
 Y06  plan-3  NAC  0.020
 Y06  plan-3  CAE  0.020
 Y06  plan-3  H9   0.020

