# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:05:00 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  36  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 OK
;

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   8.1051   0.0590  -0.7365
 252  CAI   C  CH2    0  -0.419   6.9672   0.0613   0.2751
 252  CAJ   C  CH2    0  -0.405   5.5927   0.0072  -0.3810
 252  CAK   C  CH2    0  -0.409   4.4424   0.0147   0.6181
 252  CAL   C  CH2    0  -0.406   3.0704  -0.0505  -0.0414
 252  CAM   C  CH2    0  -0.409   1.9111  -0.0196   0.9475
 252  CAN   C  CH2    0  -0.417   0.5463  -0.0929   0.2723
 252  CAO   C  CH2    0  -0.390  -0.6018  -0.0250   1.2684
 252  CAP   C  CT     0  -0.292  -2.0419  -0.0042   0.7313
 252  P1P   P  P      0   1.146  -2.4724   1.6868   0.0091
 252  OAE   O  OP    -1  -0.894  -3.5666   1.5575  -1.0519
 252  OAF   O  OP    -1  -0.926  -3.0085   2.3682   1.3142
 252  OAB   O  O      0  -0.892  -1.2068   2.3812  -0.5159
 252  P1R   P  P      0   1.183  -2.3871  -1.4775  -0.3601
 252  OAG   O  OP    -1  -0.942  -1.7542  -2.6788   0.3801
 252  OAH   O  O      0  -0.924  -3.9107  -1.6292  -0.4765
 252  OAC   O  OP    -1  -0.929  -1.6982  -1.1946  -1.7071
 252  OAD   O  OH1    0  -0.767  -2.8962  -0.1058   1.8897
 252  HAA1  H  HCH3   0   0.224   9.0797   0.0928  -0.2480
 252  HAA2  H  HCH3   0   0.215   8.0776  -0.8391  -1.3565
 252  HAA3  H  HCH3   0   0.215   8.0392   0.9207  -1.4032
 252  HAI1  H  HCH2   0   0.209   7.0768  -0.7905   0.9540
 252  HAI2  H  HCH2   0   0.209   7.0339   0.9565   0.9017
 252  HAJ1  H  HCH2   0   0.204   5.4844   0.8572  -1.0645
 252  HAJ2  H  HCH2   0   0.204   5.5254  -0.8908  -1.0060
 252  HAK1  H  HCH2   0   0.202   4.5546  -0.8305   1.3067
 252  HAK2  H  HCH2   0   0.202   4.5060   0.9170   1.2373
 252  HAL1  H  HCH2   0   0.199   2.9652   0.7852  -0.7428
 252  HAL2  H  HCH2   0   0.199   3.0043  -0.9604  -0.6493
 252  HAM1  H  HCH2   0   0.187   2.0203  -0.8493   1.6571
 252  HAM2  H  HCH2   0   0.187   1.9782   0.8958   1.5489
 252  HAN1  H  HCH2   0   0.203   0.4394   0.7280  -0.4360
 252  HAN2  H  HCH2   0   0.189   0.4752  -1.0172  -0.3027
 252  HAO1  H  HCH2   0   0.159  -0.5206  -0.8894   1.9377
 252  HAO2  H  HCH2   0   0.147  -0.4555   0.8612   1.9036
 252  HOAD  H  HOH1   0   0.398  -3.1029   0.8497   2.0381

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  1.524  0.020  1.524
 252  CAK  HAK1  single  0.970  0.020  1.090
 252  CAK  HAK2  single  0.970  0.020  1.090
 252  CAL  CAM   single  1.524  0.020  1.524
 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  1.521  0.020  1.521
 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  1.888  0.020  1.888
 252  CAP  OAD   single  1.443  0.020  1.443
 252  CAP  P1R   single  1.866  0.020  1.866
 252  P1P  OAB   deloc   1.536  0.020  1.536
 252  P1P  OAE   deloc   1.530  0.020  1.530
 252  P1P  OAF   deloc   1.567  0.020  1.567
 252  P1R  OAH   deloc   1.536  0.020  1.536
 252  P1R  OAC   deloc   1.539  0.020  1.539
 252  P1R  OAG   deloc   1.547  0.020  1.547
 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  107.52  3.000
 252  HAA3  CAA  HAA1  107.65  3.000
 252  HAA2  CAA  HAA1  107.60  3.000
 252  HAA3  CAA  CAI   111.07  3.000
 252  HAA2  CAA  CAI   111.08  3.000
 252  HAA1  CAA  CAI   111.72  3.000
 252  HAI2  CAI  HAI1  105.97  3.000
 252  HAI2  CAI  CAJ   109.29  3.000
 252  HAI1  CAI  CAJ   109.25  3.000
 252  HAI2  CAI  CAA   109.63  3.000
 252  HAI1  CAI  CAA   109.64  3.000
 252  CAJ   CAI  CAA   112.83  3.000
 252  HAJ2  CAJ  HAJ1  105.89  3.000
 252  HAJ2  CAJ  CAK   109.36  3.000
 252  HAJ1  CAJ  CAK   109.30  3.000
 252  HAJ2  CAJ  CAI   109.26  3.000
 252  HAJ1  CAJ  CAI   109.27  3.000
 252  CAK   CAJ  CAI   113.48  3.000
 252  HAK2  CAK  HAK1  105.90  3.000
 252  HAK2  CAK  CAL   109.39  3.000
 252  HAK1  CAK  CAL   109.33  3.000
 252  HAK2  CAK  CAJ   109.31  3.000
 252  HAK1  CAK  CAJ   109.33  3.000
 252  CAL   CAK  CAJ   113.32  3.000
 252  HAL2  CAL  HAL1  105.79  3.000
 252  HAL2  CAL  CAM   109.31  3.000
 252  HAL1  CAL  CAM   109.07  3.000
 252  HAL2  CAL  CAK   109.26  3.000
 252  HAL1  CAL  CAK   109.32  3.000
 252  CAM   CAL  CAK   113.78  3.000
 252  HAM2  CAM  HAM1  105.68  3.000
 252  HAM2  CAM  CAN   109.73  3.000
 252  HAM1  CAM  CAN   109.83  3.000
 252  HAM2  CAM  CAL   109.03  3.000
 252  HAM1  CAM  CAL   109.18  3.000
 252  CAN   CAM  CAL   113.12  3.000
 252  HAN2  CAN  HAN1  106.82  3.000
 252  HAN2  CAN  CAO   109.49  3.000
 252  HAN1  CAN  CAO   108.54  3.000
 252  HAN2  CAN  CAM   109.43  3.000
 252  HAN1  CAN  CAM   109.85  3.000
 252  CAO   CAN  CAM   112.55  3.000
 252  HAO2  CAO  HAO1  105.83  3.000
 252  HAO2  CAO  CAP   108.39  3.000
 252  HAO1  CAO  CAP   107.06  3.000
 252  HAO2  CAO  CAN   108.28  3.000
 252  HAO1  CAO  CAN   107.98  3.000
 252  CAP   CAO  CAN   118.61  3.000
 252  OAD   CAP  P1R   107.73  3.000
 252  P1R   CAP  P1P   116.18  3.000
 252  OAD   CAP  P1P   103.59  3.000
 252  P1R   CAP  CAO   111.53  3.000
 252  OAD   CAP  CAO   105.86  3.000
 252  P1P   CAP  CAO   111.06  3.000
 252  OAB   P1P  OAF   111.72  3.000
 252  OAF   P1P  OAE   111.70  3.000
 252  OAB   P1P  OAE   112.98  3.000
 252  OAF   P1P  CAP    98.56  3.000
 252  OAE   P1P  CAP   110.65  3.000
 252  OAB   P1P  CAP   110.34  3.000
 252  OAC   P1R  OAH   113.32  3.000
 252  OAC   P1R  OAG   112.24  3.000
 252  OAH   P1R  OAG   111.44  3.000
 252  OAG   P1R  CAP   104.93  3.000
 252  OAC   P1R  CAP   106.50  3.000
 252  OAH   P1R  CAP   107.82  3.000
 252  HOAD  OAD  CAP   100.15  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  -179.76  30.0  3
 252  Var_02  CAL   CAK  CAJ  CAI  -179.55  30.0  3
 252  Var_03  CAM   CAL  CAK  CAJ  -179.01  30.0  3
 252  Var_04  CAN   CAM  CAL  CAK  -179.70  30.0  3
 252  Var_05  CAO   CAN  CAM  CAL  -178.52  30.0  3
 252  Var_06  CAP   CAO  CAN  CAM   176.46  30.0  3
 252  Var_07  P1P   CAP  CAO  CAN   -75.12  30.0  3
 252  Var_08  OAB   P1P  CAP  CAO    28.18  30.0  3
 252  Var_09  OAH   P1R  CAP  CAO   162.04  30.0  3
 252  Var_10  HAA1  CAA  CAI  CAJ  -179.70  30.0  3

