# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:56:18 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1-hydroxynonane-1,1-diyl)bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC(O)([P](O)(O)=O)[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
 252  252  '(1-hydroxynonane-1,1-diyl)bis(phosphonic acid)'  ligand  40  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_252
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
 252  CAA   C  CH3   0  -0.663   8.1592  -0.1753  -0.6510
 252  CAI   C  CH2   0  -0.419   7.0003  -0.1399   0.3359
 252  CAJ   C  CH2   0  -0.407   5.6421  -0.0678  -0.3516
 252  CAK   C  CH2   0  -0.413   4.4722  -0.0302   0.6235
 252  CAL   C  CH2   0  -0.415   3.1171   0.0247  -0.0705
 252  CAM   C  CH2   0  -0.412   1.9457   0.0700   0.9021
 252  CAN   C  CH2   0  -0.448   0.5977   0.0740   0.1904
 252  CAO   C  CH2   0  -0.541  -0.5508   0.1488   1.1932
 252  CAP   C  CT    0  -0.272  -1.9978   0.0778   0.6811
 252  P1P   P  P     0   1.388  -2.4171   1.5770  -0.3181
 252  OAE   O  OH1   0  -0.739  -3.9084   1.2034  -0.7667
 252  OAF   O  OH1   0  -0.741  -2.5221   2.7386   0.7839
 252  OAB   O  O     0  -0.689  -1.4943   1.9938  -1.3960
 252  P1R   P  P     0   1.380  -2.4077  -1.4943  -0.2051
 252  OAG   O  OH1   0  -0.742  -1.5021  -2.6403   0.4672
 252  OAH   O  O     0  -0.688  -3.8254  -1.9026  -0.1413
 252  OAC   O  OH1   0  -0.740  -1.7997  -1.1932  -1.6552
 252  OAD   O  OH1   0  -0.665  -2.9047   0.1064   1.7706
 252  HAA1  H  HCH3  0   0.226   9.1221  -0.2187  -0.1407
 252  HAA2  H  HCH3  0   0.216   8.0917  -1.0469  -1.3045
 252  HAA3  H  HCH3  0   0.216   8.1616   0.7126  -1.2860
 252  HAI1  H  HCH2  0   0.210   7.0353  -1.0274   0.9757
 252  HAI2  H  HCH2  0   0.210   7.1126   0.7191   1.0051
 252  HAJ1  H  HCH2  0   0.206   5.6077   0.8191  -0.9946
 252  HAJ2  H  HCH2  0   0.206   5.5294  -0.9287  -1.0205
 252  HAK1  H  HCH2  0   0.208   4.5121  -0.9123   1.2723
 252  HAK2  H  HCH2  0   0.208   4.5784   0.8366   1.2854
 252  HAL1  H  HCH2  0   0.211   3.0771   0.9015  -0.7262
 252  HAL2  H  HCH2  0   0.210   3.0106  -0.8475  -0.7252
 252  HAM1  H  HCH2  0   0.215   2.0006  -0.7900   1.5784
 252  HAM2  H  HCH2  0   0.218   2.0297   0.9604   1.5344
 252  HAN1  H  HCH2  0   0.250   0.5483   0.9154  -0.5003
 252  HAN2  H  HCH2  0   0.213   0.5330  -0.8237  -0.4313
 252  HAO1  H  HCH2  0   0.270  -0.4362  -0.6559   1.9278
 252  HAO2  H  HCH2  0   0.272  -0.4551   1.0801   1.7610
 252  HOAE  H  HOH1  0   0.498  -4.2826   1.7952  -1.4348
 252  HOAF  H  HOH1  0   0.489  -3.0892   2.5315   1.5396
 252  HOAG  H  HOH1  0   0.493  -0.5514  -2.6030   0.3024
 252  HOAC  H  HOH1  0   0.501  -2.0367  -1.8374  -2.3382
 252  HOAD  H  HOH1  0   0.476  -2.4095   0.0600   2.5971

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
 252  CAA  CAI   single  1.523  0.020  1.523
 252  CAA  HAA1  single  0.970  0.020  1.090
 252  CAA  HAA2  single  0.970  0.020  1.090
 252  CAA  HAA3  single  0.970  0.020  1.090
 252  CAI  CAJ   single  1.524  0.020  1.524
 252  CAI  HAI1  single  0.970  0.020  1.090
 252  CAI  HAI2  single  0.970  0.020  1.090
 252  CAJ  CAK   single  1.524  0.020  1.524
 252  CAJ  HAJ1  single  0.970  0.020  1.090
 252  CAJ  HAJ2  single  0.970  0.020  1.090
 252  CAK  CAL   single  1.523  0.020  1.523
 252  CAK  HAK1  single  0.970  0.020  1.090
 252  CAK  HAK2  single  0.970  0.020  1.090
 252  CAL  CAM   single  1.523  0.020  1.523
 252  CAL  HAL1  single  0.970  0.020  1.090
 252  CAL  HAL2  single  0.970  0.020  1.090
 252  CAM  CAN   single  1.524  0.020  1.524
 252  CAM  HAM1  single  0.970  0.020  1.090
 252  CAM  HAM2  single  0.970  0.020  1.090
 252  CAN  CAO   single  1.526  0.020  1.526
 252  CAN  HAN1  single  0.970  0.020  1.090
 252  CAN  HAN2  single  0.970  0.020  1.090
 252  CAO  CAP   single  1.537  0.020  1.537
 252  CAO  HAO1  single  0.970  0.020  1.090
 252  CAO  HAO2  single  0.970  0.020  1.090
 252  CAP  P1P   single  1.850  0.020  1.850
 252  CAP  OAD   single  1.418  0.020  1.418
 252  CAP  P1R   single  1.851  0.020  1.851
 252  P1P  OAB   double  1.479  0.020  1.479
 252  P1P  OAE   single  1.601  0.020  1.601
 252  P1P  OAF   single  1.605  0.020  1.605
 252  OAE  HOAE  single  0.850  0.020  0.980
 252  OAF  HOAF  single  0.850  0.020  0.980
 252  P1R  OAH   double  1.477  0.020  1.477
 252  P1R  OAC   single  1.601  0.020  1.601
 252  P1R  OAG   single  1.608  0.020  1.608
 252  OAG  HOAG  single  0.850  0.020  0.980
 252  OAC  HOAC  single  0.850  0.020  0.980
 252  OAD  HOAD  single  0.850  0.020  0.980

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
 252  HAA3  CAA  HAA2  107.54  3.000
 252  HAA3  CAA  HAA1  107.62  3.000
 252  HAA2  CAA  HAA1  107.63  3.000
 252  HAA3  CAA  CAI   111.09  3.000
 252  HAA2  CAA  CAI   111.07  3.000
 252  HAA1  CAA  CAI   111.70  3.000
 252  HAI2  CAI  HAI1  106.00  3.000
 252  HAI2  CAI  CAJ   109.28  3.000
 252  HAI1  CAI  CAJ   109.30  3.000
 252  HAI2  CAI  CAA   109.66  3.000
 252  HAI1  CAI  CAA   109.61  3.000
 252  CAJ   CAI  CAA   112.77  3.000
 252  HAJ2  CAJ  HAJ1  105.93  3.000
 252  HAJ2  CAJ  CAK   109.33  3.000
 252  HAJ1  CAJ  CAK   109.35  3.000
 252  HAJ2  CAJ  CAI   109.26  3.000
 252  HAJ1  CAJ  CAI   109.32  3.000
 252  CAK   CAJ  CAI   113.38  3.000
 252  HAK2  CAK  HAK1  106.00  3.000
 252  HAK2  CAK  CAL   109.44  3.000
 252  HAK1  CAK  CAL   109.34  3.000
 252  HAK2  CAK  CAJ   109.37  3.000
 252  HAK1  CAK  CAJ   109.34  3.000
 252  CAL   CAK  CAJ   113.10  3.000
 252  HAL2  CAL  HAL1  106.02  3.000
 252  HAL2  CAL  CAM   109.29  3.000
 252  HAL1  CAL  CAM   109.28  3.000
 252  HAL2  CAL  CAK   109.27  3.000
 252  HAL1  CAL  CAK   109.51  3.000
 252  CAM   CAL  CAK   113.22  3.000
 252  HAM2  CAM  HAM1  106.14  3.000
 252  HAM2  CAM  CAN   109.59  3.000
 252  HAM1  CAM  CAN   109.54  3.000
 252  HAM2  CAM  CAL   109.51  3.000
 252  HAM1  CAM  CAL   109.41  3.000
 252  CAN   CAM  CAL   112.46  3.000
 252  HAN2  CAN  HAN1  105.71  3.000
 252  HAN2  CAN  CAO   111.66  3.000
 252  HAN1  CAN  CAO   110.15  3.000
 252  HAN2  CAN  CAM   108.40  3.000
 252  HAN1  CAN  CAM   109.75  3.000
 252  CAO   CAN  CAM   111.02  3.000
 252  HAO2  CAO  HAO1  105.54  3.000
 252  HAO2  CAO  CAP   107.13  3.000
 252  HAO1  CAO  CAP   106.74  3.000
 252  HAO2  CAO  CAN   108.46  3.000
 252  HAO1  CAO  CAN   109.01  3.000
 252  CAP   CAO  CAN   119.16  3.000
 252  OAD   CAP  P1R   104.09  3.000
 252  P1R   CAP  P1P   112.31  3.000
 252  OAD   CAP  P1P   104.70  3.000
 252  P1R   CAP  CAO   114.05  3.000
 252  OAD   CAP  CAO   110.20  3.000
 252  P1P   CAP  CAO   110.86  3.000
 252  OAB   P1P  OAF   109.72  3.000
 252  OAF   P1P  OAE   107.48  3.000
 252  OAB   P1P  OAE   116.27  3.000
 252  OAF   P1P  CAP   103.33  3.000
 252  OAE   P1P  CAP    99.98  3.000
 252  OAB   P1P  CAP   118.73  3.000
 252  HOAE  OAE  P1P   114.25  3.000
 252  HOAF  OAF  P1P   114.83  3.000
 252  OAC   P1R  OAH   117.11  3.000
 252  OAC   P1R  OAG   107.39  3.000
 252  OAH   P1R  OAG   109.00  3.000
 252  OAG   P1R  CAP   106.29  3.000
 252  OAC   P1R  CAP   100.94  3.000
 252  OAH   P1R  CAP   115.27  3.000
 252  HOAG  OAG  P1R   117.11  3.000
 252  HOAC  OAC  P1R   114.88  3.000
 252  HOAD  OAD  CAP   109.21  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
 252  Var_01  CAK   CAJ  CAI  CAA  -179.94  30.0  3
 252  Var_02  CAL   CAK  CAJ  CAI  -179.30  30.0  3
 252  Var_03  CAM   CAL  CAK  CAJ  -179.69  30.0  3
 252  Var_04  CAN   CAM  CAL  CAK  -177.94  30.0  3
 252  Var_05  CAO   CAN  CAM  CAL  -178.83  30.0  3
 252  Var_06  CAP   CAO  CAN  CAM  -176.31  30.0  3
 252  Var_07  P1P   CAP  CAO  CAN   -67.06  30.0  3
 252  Var_08  OAB   P1P  CAP  CAO    49.81  30.0  3
 252  Var_09  OAH   P1R  CAP  CAO   151.90  30.0  3
 252  Var_10  HAA1  CAA  CAI  CAJ   179.54  30.0  3

