# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 22:11:13 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: [4-[3-(difluoro-phosphono-methyl)phenyl]phenyl]methoxyazanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]OCc1ccc(cc1)c2cccc(c2)C(F)(F)[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
 YI1  YI1  '[4-[3-(difluoro-phosphono-methyl)phenyl]phenyl]methoxyazanium'  ligand  37  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_YI1
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
 YI1  FAG   F  F     0  -0.328  -3.9852  -0.6108  -1.6217
 YI1  CAE   C  CT    0   0.551  -2.9613   0.0735  -1.0471
 YI1  FAF   F  F     0  -0.331  -2.4324   0.8770  -2.0107
 YI1  PAB   P  P     0   1.311  -3.7045   1.2158   0.2175
 YI1  OAC   O  O     0  -0.682  -4.6484   2.1978  -0.3496
 YI1  OAA   O  OH1   0  -0.734  -4.2577   0.1292   1.2421
 YI1  OAD   O  OH1   0  -0.733  -2.4477   1.9361   0.8936
 YI1  CAH   C  CR6   0  -0.097  -1.9232  -0.8617  -0.5098
 YI1  CAJ   C  CR16  0  -0.285  -2.2785  -2.1368  -0.0832
 YI1  CAK   C  CR16  0  -0.224  -1.3055  -2.9750   0.4387
 YI1  CAL   C  CR16  0  -0.302   0.0075  -2.5465   0.5487
 YI1  CAM   C  CR6   0   0.117   0.3740  -1.2666   0.1330
 YI1  CAI   C  CR16  0  -0.367  -0.6056  -0.4315  -0.4006
 YI1  CAN   C  CR6   0   0.086   1.7687  -0.7997   0.2565
 YI1  CAQ   C  CR16  0  -0.295   2.8358  -1.6689   0.0264
 YI1  CAR   C  CR16  0  -0.260   4.1440  -1.2322   0.1517
 YI1  CAS   C  CR6   0   0.055   4.4187   0.0834   0.5114
 YI1  CAP   C  CR16  0  -0.263   3.3590   0.9554   0.7374
 YI1  CAO   C  CR16  0  -0.293   2.0503   0.5189   0.6154
 YI1  CAT   C  CH2   0  -0.262   5.8291   0.5602   0.6198
 YI1  OAU   O  OC2   0  -0.360   6.2036   0.9950  -0.7042
 YI1  NAV   N  NT3   1  -0.462   7.5033   1.4589  -0.7117
 YI1  HAA   H  HOH1  0   0.510  -4.8563   0.4666   1.9245
 YI1  HAD   H  HOH1  0   0.501  -1.9498   1.4235   1.5444
 YI1  HAJ   H  HCR6  0   0.273  -3.2995  -2.4857  -0.1525
 YI1  HAI   H  HCR6  0   0.279  -0.3217   0.5493  -0.7600
 YI1  HAK   H  HCR6  0   0.272  -1.5764  -3.9674   0.7723
 YI1  HAL   H  HCR6  0   0.267   0.7479  -3.2077   0.9809
 YI1  HAQ   H  HCR6  0   0.264   2.6468  -2.6928  -0.2698
 YI1  HAO   H  HCR6  0   0.258   1.2442   1.2098   0.8277
 YI1  HAR   H  HCR6  0   0.264   4.9566  -1.9246  -0.0310
 YI1  HAP   H  HCR6  0   0.265   3.5544   1.9808   1.0262
 YI1  HAT1  H  HCH2  0   0.273   5.9177   1.3978   1.3170
 YI1  HAT2  H  HCH2  0   0.272   6.5011  -0.2408   0.9421
 YI1  HAV1  H  HNT3  0   0.500   7.7138   1.7446  -1.6701
 YI1  HAV2  H  HNT3  0   0.479   7.6246   2.2735  -0.1004
 YI1  HAV3  H  HNT3  0   0.480   8.1735   0.7321  -0.4382

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
 YI1  FAG  CAE   single    1.359  0.020  1.359
 YI1  CAE  FAF   single    1.362  0.020  1.362
 YI1  CAE  PAB   single    1.859  0.020  1.859
 YI1  CAE  CAH   single    1.497  0.020  1.497
 YI1  PAB  OAC   double    1.475  0.020  1.475
 YI1  PAB  OAA   single    1.593  0.020  1.593
 YI1  PAB  OAD   single    1.599  0.020  1.599
 YI1  CAH  CAJ   aromatic  1.391  0.020  1.391
 YI1  CAH  CAI   aromatic  1.390  0.020  1.390
 YI1  CAJ  CAK   aromatic  1.386  0.020  1.386
 YI1  CAK  CAL   aromatic  1.386  0.020  1.386
 YI1  CAL  CAM   aromatic  1.395  0.020  1.395
 YI1  CAM  CAI   aromatic  1.393  0.020  1.393
 YI1  CAM  CAN   single    1.476  0.020  1.476
 YI1  CAN  CAQ   aromatic  1.395  0.020  1.395
 YI1  CAN  CAO   aromatic  1.395  0.020  1.395
 YI1  CAQ  CAR   aromatic  1.385  0.020  1.385
 YI1  CAR  CAS   aromatic  1.391  0.020  1.391
 YI1  CAS  CAP   aromatic  1.391  0.020  1.391
 YI1  CAS  CAT   single    1.493  0.020  1.493
 YI1  CAP  CAO   aromatic  1.385  0.020  1.385
 YI1  CAT  OAU   single    1.443  0.020  1.443
 YI1  OAU  NAV   single    1.380  0.020  1.380
 YI1  OAA  HAA   single    0.850  0.020  0.980
 YI1  OAD  HAD   single    0.850  0.020  0.980
 YI1  CAJ  HAJ   single    0.930  0.020  1.080
 YI1  CAI  HAI   single    0.930  0.020  1.080
 YI1  CAK  HAK   single    0.930  0.020  1.080
 YI1  CAL  HAL   single    0.930  0.020  1.080
 YI1  CAQ  HAQ   single    0.930  0.020  1.080
 YI1  CAO  HAO   single    0.930  0.020  1.080
 YI1  CAR  HAR   single    0.930  0.020  1.080
 YI1  CAP  HAP   single    0.930  0.020  1.080
 YI1  CAT  HAT1  single    0.970  0.020  1.090
 YI1  CAT  HAT2  single    0.970  0.020  1.090
 YI1  NAV  HAV1  single    0.890  0.020  1.040
 YI1  NAV  HAV2  single    0.890  0.020  1.040
 YI1  NAV  HAV3  single    0.890  0.020  1.040

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
 YI1  CAH   CAE  PAB   114.64  3.000
 YI1  CAH   CAE  FAF   110.69  3.000
 YI1  PAB   CAE  FAF   105.91  3.000
 YI1  CAH   CAE  FAG   111.08  3.000
 YI1  PAB   CAE  FAG   107.21  3.000
 YI1  FAF   CAE  FAG   106.89  3.000
 YI1  OAD   PAB  OAA   107.96  3.000
 YI1  OAD   PAB  OAC   111.45  3.000
 YI1  OAA   PAB  OAC   118.63  3.000
 YI1  OAD   PAB  CAE   104.49  3.000
 YI1  OAA   PAB  CAE    99.05  3.000
 YI1  OAC   PAB  CAE   113.78  3.000
 YI1  HAA   OAA  PAB   115.49  3.000
 YI1  HAD   OAD  PAB   116.79  3.000
 YI1  CAI   CAH  CAJ   120.11  3.000
 YI1  CAI   CAH  CAE   119.48  3.000
 YI1  CAJ   CAH  CAE   120.38  3.000
 YI1  HAJ   CAJ  CAK   119.46  3.000
 YI1  HAJ   CAJ  CAH   121.16  3.000
 YI1  CAK   CAJ  CAH   119.38  3.000
 YI1  HAK   CAK  CAL   119.78  3.000
 YI1  HAK   CAK  CAJ   119.68  3.000
 YI1  CAL   CAK  CAJ   120.53  3.000
 YI1  HAL   CAL  CAM   119.98  3.000
 YI1  HAL   CAL  CAK   119.40  3.000
 YI1  CAM   CAL  CAK   120.61  3.000
 YI1  CAN   CAM  CAI   120.45  3.000
 YI1  CAN   CAM  CAL   120.91  3.000
 YI1  CAI   CAM  CAL   118.64  3.000
 YI1  HAI   CAI  CAM   119.06  3.000
 YI1  HAI   CAI  CAH   120.19  3.000
 YI1  CAM   CAI  CAH   120.72  3.000
 YI1  CAO   CAN  CAQ   118.47  3.000
 YI1  CAO   CAN  CAM   120.75  3.000
 YI1  CAQ   CAN  CAM   120.78  3.000
 YI1  HAQ   CAQ  CAR   119.21  3.000
 YI1  HAQ   CAQ  CAN   120.05  3.000
 YI1  CAR   CAQ  CAN   120.73  3.000
 YI1  HAR   CAR  CAS   120.00  3.000
 YI1  HAR   CAR  CAQ   119.46  3.000
 YI1  CAS   CAR  CAQ   120.54  3.000
 YI1  CAT   CAS  CAP   120.52  3.000
 YI1  CAT   CAS  CAR   120.49  3.000
 YI1  CAP   CAS  CAR   118.97  3.000
 YI1  HAP   CAP  CAO   119.49  3.000
 YI1  HAP   CAP  CAS   119.97  3.000
 YI1  CAO   CAP  CAS   120.53  3.000
 YI1  HAO   CAO  CAP   119.02  3.000
 YI1  HAO   CAO  CAN   120.21  3.000
 YI1  CAP   CAO  CAN   120.75  3.000
 YI1  HAT2  CAT  HAT1  108.86  3.000
 YI1  HAT2  CAT  OAU   109.36  3.000
 YI1  HAT1  CAT  OAU   109.46  3.000
 YI1  HAT2  CAT  CAS   111.59  3.000
 YI1  HAT1  CAT  CAS   111.56  3.000
 YI1  OAU   CAT  CAS   105.95  3.000
 YI1  NAV   OAU  CAT   110.54  3.000
 YI1  HAV3  NAV  HAV2  109.05  3.000
 YI1  HAV3  NAV  HAV1  108.27  3.000
 YI1  HAV2  NAV  HAV1  108.22  3.000
 YI1  HAV3  NAV  OAU   112.07  3.000
 YI1  HAV2  NAV  OAU   112.03  3.000
 YI1  HAV1  NAV  OAU   107.05  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
 YI1  CONST_01  CAL   CAK  CAJ  CAH    0.00   0.0  0
 YI1  CONST_02  CAL   CAM  CAI  CAH    0.00   0.0  0
 YI1  CONST_03  CAN   CAM  CAI  CAH  180.00   0.0  0
 YI1  CONST_04  CAM   CAI  CAH  CAJ    0.00   0.0  0
 YI1  CONST_05  CAM   CAL  CAK  CAJ    0.00   0.0  0
 YI1  CONST_06  CAI   CAH  CAJ  CAK    0.00   0.0  0
 YI1  CONST_07  CAI   CAM  CAL  CAK    0.00   0.0  0
 YI1  CONST_08  CAN   CAM  CAL  CAK  180.00   0.0  0
 YI1  CONST_11  CAR   CAQ  CAN  CAM  180.00   0.0  0
 YI1  CONST_12  CAP   CAO  CAN  CAM  180.00   0.0  0
 YI1  CONST_15  CAS   CAR  CAQ  CAN    0.00   0.0  0
 YI1  CONST_16  CAS   CAP  CAO  CAN    0.00   0.0  0
 YI1  CONST_17  CAP   CAO  CAN  CAQ    0.00   0.0  0
 YI1  CONST_18  CAP   CAS  CAR  CAQ    0.00   0.0  0
 YI1  CONST_19  CAO   CAN  CAQ  CAR    0.00   0.0  0
 YI1  CONST_20  CAO   CAP  CAS  CAR    0.00   0.0  0
 YI1  CONST_21  CAK   CAJ  CAH  CAE  180.00   0.0  0
 YI1  CONST_22  CAM   CAI  CAH  CAE  180.00   0.0  0
 YI1  CONST_23  CAT   CAS  CAR  CAQ  180.00   0.0  0
 YI1  CONST_24  CAT   CAS  CAP  CAO  180.00   0.0  0
 YI1  CONST_25  HAK   CAK  CAJ  CAH  180.00   0.0  0
 YI1  CONST_26  HAI   CAI  CAH  CAJ  180.00   0.0  0
 YI1  CONST_27  HAL   CAL  CAK  CAJ  180.00   0.0  0
 YI1  CONST_28  HAJ   CAJ  CAK  CAL  180.00   0.0  0
 YI1  CONST_29  HAQ   CAQ  CAN  CAM    0.00   0.0  0
 YI1  CONST_30  HAO   CAO  CAN  CAM    0.00   0.0  0
 YI1  CONST_31  HAR   CAR  CAQ  CAN  180.00   0.0  0
 YI1  CONST_32  HAP   CAP  CAO  CAN  180.00   0.0  0
 YI1  Var_01    CAJ   CAH  CAE  FAG  -28.66  30.0  2
 YI1  Var_02    OAU   CAT  CAS  CAR   87.20  30.0  2
 YI1  Var_03    CAH   CAE  PAB  OAC  175.57  30.0  2
 YI1  Var_04    HAV1  NAV  OAU  CAT  179.59  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
 YI1  plan-1  CAE  0.020
 YI1  plan-1  CAH  0.020
 YI1  plan-1  CAJ  0.020
 YI1  plan-1  CAK  0.020
 YI1  plan-1  CAL  0.020
 YI1  plan-1  CAM  0.020
 YI1  plan-1  CAI  0.020
 YI1  plan-1  CAN  0.020
 YI1  plan-1  HAJ  0.020
 YI1  plan-1  HAI  0.020
 YI1  plan-1  HAK  0.020
 YI1  plan-1  HAL  0.020
 YI1  plan-2  CAM  0.020
 YI1  plan-2  CAN  0.020
 YI1  plan-2  CAQ  0.020
 YI1  plan-2  CAR  0.020
 YI1  plan-2  CAS  0.020
 YI1  plan-2  CAP  0.020
 YI1  plan-2  CAO  0.020
 YI1  plan-2  CAT  0.020
 YI1  plan-2  HAQ  0.020
 YI1  plan-2  HAO  0.020
 YI1  plan-2  HAR  0.020
 YI1  plan-2  HAP  0.020

