# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:49:01 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: hydrogen [(1R)-2-(3-decyl-1H-imidazol-3-ium-1-yl)-1-hydroxy-1-phosphonoethyl]phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC[n+]1ccn(C[C@](O)([P](O)(O)=O)[P](O)([O-])=O)c1
#
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
 8PH  8PH  'hydrogen [(1R)-2-(3-decyl-1H-imidazol-3-ium-1-yl)-1-hydroxy-1-phosphonoethyl]phosphonate'  ligand  56  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8PH
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
 8PH  OAE  O  OH1    0  -0.748    6.3753  -0.2468  -0.7308
 8PH  PAY  P  P      0   1.383    5.3001   0.9020  -0.3824
 8PH  OAF  O  OH1    0  -0.748    5.4551   1.2044   1.1846
 8PH  OAB  O  O      0  -0.696    5.4826   2.0256  -1.3244
 8PH  CAX  C  CT     0  -0.311    3.6410   0.1229  -0.4105
 8PH  PAZ  P  P      0   1.298    2.2987   1.2065   0.3602
 8PH  OAG  O  OP    -1  -0.768    1.1424   0.9597  -0.5743
 8PH  OAH  O  O      0  -0.766    2.2234   0.9300   1.8315
 8PH  OAC  O  OH1    0  -0.761    2.7962   2.7350   0.0929
 8PH  OAD  O  OH1    0  -0.678    3.3499  -0.0474  -1.7765
 8PH  CAU  C  CH2    0  -0.350    3.6526  -1.2442   0.2956
 8PH  NAW  N  NR5    0  -0.416    2.3836  -1.9265   0.1015
 8PH  CAK  C  CR15   0   0.270    1.3160  -1.8370   0.8845
 8PH  CAJ  C  CR15   0  -0.083    2.0566  -2.6675  -1.0065
 8PH  CAI  C  CR15   0  -0.092    0.7632  -3.0360  -0.8652
 8PH  NAV  N  NR5    1  -0.413    0.3266  -2.5094   0.3246
 8PH  CAT  C  CH2    0  -0.312   -1.0429  -2.5686   0.8213
 8PH  CAS  C  CH2    0  -0.431   -1.9173  -1.5087   0.1686
 8PH  CAR  C  CH2    0  -0.424   -3.3615  -1.6186   0.6384
 8PH  CAQ  C  CH2    0  -0.413   -4.2666  -0.5695   0.0049
 8PH  CAP  C  CH2    0  -0.412   -5.7235  -0.7073   0.4281
 8PH  CAO  C  CH2    0  -0.411   -6.6343   0.3371  -0.2051
 8PH  CAN  C  CH2    0  -0.411   -8.0956   0.1850   0.1985
 8PH  CAM  C  CH2    0  -0.406   -9.0083   1.2225  -0.4431
 8PH  CAL  C  CH2    0  -0.418  -10.4730   1.0635  -0.0534
 8PH  CAA  C  CH3    0  -0.663  -11.3750   2.0997  -0.7096
 8PH  H1   H  HOH1   0   0.492    6.5557  -0.9002  -0.0430
 8PH  H2   H  HOH1   0   0.499    6.2601   1.6855   1.4250
 8PH  H4   H  HOH1   0   0.470    3.2742   3.1159   0.8386
 8PH  H5   H  HOH1   0   0.454    2.4133   0.1999  -1.8781
 8PH  H6   H  HCH2   0   0.297    4.4149  -1.8975  -0.1273
 8PH  H7   H  HCH2   0   0.309    3.8415  -1.1483   1.3621
 8PH  H8   H  HCR5   0   0.359    1.2677  -1.2944   1.8132
 8PH  H9   H  HCR5   0   0.329    2.7690  -2.8869  -1.7813
 8PH  H10  H  HCR5   0   0.330    0.1282  -3.6310  -1.4980
 8PH  H11  H  HCH2   0   0.282   -1.4178  -3.5710   0.6175
 8PH  H12  H  HCH2   0   0.284   -1.0097  -2.4422   1.9026
 8PH  H13  H  HCH2   0   0.241   -1.5150  -0.5179   0.3976
 8PH  H14  H  HCH2   0   0.238   -1.8742  -1.6229  -0.9185
 8PH  H15  H  HCH2   0   0.220   -3.7426  -2.6175   0.4016
 8PH  H16  H  HCH2   0   0.222   -3.4041  -1.5244   1.7286
 8PH  H17  H  HCH2   0   0.213   -3.9029   0.4298   0.2671
 8PH  H18  H  HCH2   0   0.212   -4.1967  -0.6424  -1.0858
 8PH  H19  H  HCH2   0   0.208   -6.0827  -1.7081   0.1640
 8PH  H20  H  HCH2   0   0.208   -5.7953  -0.6376   1.5192
 8PH  H21  H  HCH2   0   0.207   -6.2837   1.3383   0.0691
 8PH  H22  H  HCH2   0   0.206   -6.5512   0.2756  -1.2960
 8PH  H23  H  HCH2   0   0.206   -8.4428  -0.8184  -0.0722
 8PH  H24  H  HCH2   0   0.206   -8.1814   0.2510   1.2889
 8PH  H25  H  HCH2   0   0.205   -8.6675   2.2268  -0.1671
 8PH  H26  H  HCH2   0   0.205   -8.9158   1.1613  -1.5334
 8PH  H27  H  HCH2   0   0.209  -10.8123   0.0590  -0.3248
 8PH  H28  H  HCH2   0   0.210  -10.5681   1.1312   1.0349
 8PH  H29  H  HCH3   0   0.216  -11.0897   3.1122  -0.4182
 8PH  H30  H  HCH3   0   0.215  -11.3133   2.0421  -1.7981
 8PH  H31  H  HCH3   0   0.226  -12.4199   1.9588  -0.4304

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
 8PH  CAA  CAL  single    1.522  0.020  1.522
 8PH  CAL  CAM  single    1.524  0.020  1.524
 8PH  CAM  CAN  single    1.524  0.020  1.524
 8PH  CAN  CAO  single    1.524  0.020  1.524
 8PH  CAO  CAP  single    1.524  0.020  1.524
 8PH  CAP  CAQ  single    1.523  0.020  1.523
 8PH  CAQ  CAR  single    1.523  0.020  1.523
 8PH  CAR  CAS  single    1.523  0.020  1.523
 8PH  CAS  CAT  single    1.521  0.020  1.521
 8PH  CAT  NAV  single    1.458  0.020  1.458
 8PH  NAV  CAK  aromatic  1.321  0.020  1.321
 8PH  NAV  CAI  aromatic  1.372  0.020  1.372
 8PH  CAK  NAW  aromatic  1.327  0.020  1.327
 8PH  CAI  CAJ  aromatic  1.352  0.020  1.352
 8PH  OAB  PAY  double    1.478  0.020  1.478
 8PH  NAW  CAJ  aromatic  1.372  0.020  1.372
 8PH  NAW  CAU  single    1.454  0.020  1.454
 8PH  OAF  PAY  single    1.603  0.020  1.603
 8PH  PAY  OAE  single    1.612  0.020  1.612
 8PH  PAY  CAX  single    1.833  0.020  1.833
 8PH  CAU  CAX  single    1.539  0.020  1.539
 8PH  CAX  OAD  single    1.407  0.020  1.407
 8PH  CAX  PAZ  single    1.889  0.020  1.889
 8PH  OAH  PAZ  double    1.499  0.020  1.499
 8PH  PAZ  OAG  single    1.507  0.020  1.507
 8PH  PAZ  OAC  single    1.629  0.020  1.629
 8PH  OAE  H1   single    0.850  0.020  0.980
 8PH  OAF  H2   single    0.850  0.020  0.980
 8PH  OAC  H4   single    0.850  0.020  0.980
 8PH  OAD  H5   single    0.850  0.020  0.980
 8PH  CAU  H6   single    0.970  0.020  1.090
 8PH  CAU  H7   single    0.970  0.020  1.090
 8PH  CAK  H8   single    0.930  0.020  1.080
 8PH  CAJ  H9   single    0.930  0.020  1.080
 8PH  CAI  H10  single    0.930  0.020  1.080
 8PH  CAT  H11  single    0.970  0.020  1.090
 8PH  CAT  H12  single    0.970  0.020  1.090
 8PH  CAS  H13  single    0.970  0.020  1.090
 8PH  CAS  H14  single    0.970  0.020  1.090
 8PH  CAR  H15  single    0.970  0.020  1.090
 8PH  CAR  H16  single    0.970  0.020  1.090
 8PH  CAQ  H17  single    0.970  0.020  1.090
 8PH  CAQ  H18  single    0.970  0.020  1.090
 8PH  CAP  H19  single    0.970  0.020  1.090
 8PH  CAP  H20  single    0.970  0.020  1.090
 8PH  CAO  H21  single    0.970  0.020  1.090
 8PH  CAO  H22  single    0.970  0.020  1.090
 8PH  CAN  H23  single    0.970  0.020  1.090
 8PH  CAN  H24  single    0.970  0.020  1.090
 8PH  CAM  H25  single    0.970  0.020  1.090
 8PH  CAM  H26  single    0.970  0.020  1.090
 8PH  CAL  H27  single    0.970  0.020  1.090
 8PH  CAL  H28  single    0.970  0.020  1.090
 8PH  CAA  H29  single    0.970  0.020  1.090
 8PH  CAA  H30  single    0.970  0.020  1.090
 8PH  CAA  H31  single    0.970  0.020  1.090

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
 8PH  H1   OAE  PAY  116.93  3.000
 8PH  CAX  PAY  OAB  115.16  3.000
 8PH  CAX  PAY  OAF  100.53  3.000
 8PH  OAB  PAY  OAF  117.89  3.000
 8PH  CAX  PAY  OAE  107.31  3.000
 8PH  OAF  PAY  OAE  106.33  3.000
 8PH  OAB  PAY  OAE  108.77  3.000
 8PH  H2   OAF  PAY  114.63  3.000
 8PH  CAU  CAX  OAD  109.85  3.000
 8PH  OAD  CAX  PAZ  108.57  3.000
 8PH  CAU  CAX  PAZ  109.13  3.000
 8PH  PAZ  CAX  PAY  113.14  3.000
 8PH  OAD  CAX  PAY  104.69  3.000
 8PH  CAU  CAX  PAY  111.33  3.000
 8PH  OAC  PAZ  OAH  110.45  3.000
 8PH  OAC  PAZ  OAG  106.63  3.000
 8PH  OAH  PAZ  OAG  122.68  3.000
 8PH  OAC  PAZ  CAX  104.72  3.000
 8PH  OAG  PAZ  CAX  101.43  3.000
 8PH  OAH  PAZ  CAX  109.28  3.000
 8PH  H4   OAC  PAZ  113.27  3.000
 8PH  H5   OAD  CAX  105.63  3.000
 8PH  H7   CAU  H6   108.19  3.000
 8PH  H7   CAU  NAW  108.90  3.000
 8PH  H6   CAU  NAW  106.11  3.000
 8PH  H7   CAU  CAX  111.91  3.000
 8PH  H6   CAU  CAX  111.10  3.000
 8PH  NAW  CAU  CAX  110.43  3.000
 8PH  CAJ  NAW  CAK  108.73  3.000
 8PH  CAJ  NAW  CAU  124.69  3.000
 8PH  CAK  NAW  CAU  126.29  3.000
 8PH  H8   CAK  NAV  126.06  3.000
 8PH  H8   CAK  NAW  125.38  3.000
 8PH  NAV  CAK  NAW  108.56  3.000
 8PH  H9   CAJ  CAI  130.80  3.000
 8PH  H9   CAJ  NAW  122.28  3.000
 8PH  CAI  CAJ  NAW  106.90  3.000
 8PH  H10  CAI  NAV  122.30  3.000
 8PH  H10  CAI  CAJ  130.82  3.000
 8PH  NAV  CAI  CAJ  106.88  3.000
 8PH  CAT  NAV  CAI  125.35  3.000
 8PH  CAI  NAV  CAK  108.93  3.000
 8PH  CAT  NAV  CAK  125.45  3.000
 8PH  H12  CAT  H11  107.64  3.000
 8PH  H12  CAT  CAS  111.26  3.000
 8PH  H11  CAT  CAS  111.29  3.000
 8PH  H12  CAT  NAV  107.75  3.000
 8PH  H11  CAT  NAV  107.27  3.000
 8PH  CAS  CAT  NAV  111.43  3.000
 8PH  H14  CAS  H13  106.75  3.000
 8PH  H14  CAS  CAR  109.66  3.000
 8PH  H13  CAS  CAR  110.46  3.000
 8PH  H14  CAS  CAT  109.34  3.000
 8PH  H13  CAS  CAT  109.27  3.000
 8PH  CAR  CAS  CAT  111.26  3.000
 8PH  H16  CAR  H15  106.27  3.000
 8PH  H16  CAR  CAQ  109.37  3.000
 8PH  H15  CAR  CAQ  109.36  3.000
 8PH  H16  CAR  CAS  109.75  3.000
 8PH  H15  CAR  CAS  109.22  3.000
 8PH  CAQ  CAR  CAS  112.68  3.000
 8PH  H18  CAQ  H17  106.13  3.000
 8PH  H18  CAQ  CAP  109.37  3.000
 8PH  H17  CAQ  CAP  109.49  3.000
 8PH  H18  CAQ  CAR  109.29  3.000
 8PH  H17  CAQ  CAR  109.35  3.000
 8PH  CAP  CAQ  CAR  112.98  3.000
 8PH  H20  CAP  H19  106.06  3.000
 8PH  H20  CAP  CAO  109.33  3.000
 8PH  H19  CAP  CAO  109.27  3.000
 8PH  H20  CAP  CAQ  109.49  3.000
 8PH  H19  CAP  CAQ  109.22  3.000
 8PH  CAO  CAP  CAQ  113.22  3.000
 8PH  H22  CAO  H21  106.03  3.000
 8PH  H22  CAO  CAN  109.32  3.000
 8PH  H21  CAO  CAN  109.38  3.000
 8PH  H22  CAO  CAP  109.27  3.000
 8PH  H21  CAO  CAP  109.34  3.000
 8PH  CAN  CAO  CAP  113.25  3.000
 8PH  H24  CAN  H23  106.03  3.000
 8PH  H24  CAN  CAM  109.34  3.000
 8PH  H23  CAN  CAM  109.25  3.000
 8PH  H24  CAN  CAO  109.43  3.000
 8PH  H23  CAN  CAO  109.26  3.000
 8PH  CAM  CAN  CAO  113.27  3.000
 8PH  H26  CAM  H25  105.99  3.000
 8PH  H26  CAM  CAL  109.25  3.000
 8PH  H25  CAM  CAL  109.28  3.000
 8PH  H26  CAM  CAN  109.29  3.000
 8PH  H25  CAM  CAN  109.37  3.000
 8PH  CAL  CAM  CAN  113.39  3.000
 8PH  H28  CAL  H27  106.04  3.000
 8PH  H28  CAL  CAA  109.58  3.000
 8PH  H27  CAL  CAA  109.52  3.000
 8PH  H28  CAL  CAM  109.35  3.000
 8PH  H27  CAL  CAM  109.29  3.000
 8PH  CAA  CAL  CAM  112.84  3.000
 8PH  H31  CAA  H30  107.61  3.000
 8PH  H31  CAA  H29  107.57  3.000
 8PH  H30  CAA  H29  107.48  3.000
 8PH  H31  CAA  CAL  111.67  3.000
 8PH  H30  CAA  CAL  111.12  3.000
 8PH  H29  CAA  CAL  111.19  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
 8PH  CONST_01  CAI  NAV  CAK  NAW     0.00   0.0  0
 8PH  CONST_02  NAV  CAI  CAJ  NAW     0.00   0.0  0
 8PH  CONST_03  CAJ  CAI  NAV  CAK     0.00   0.0  0
 8PH  CONST_04  CAI  CAJ  NAW  CAK     0.00   0.0  0
 8PH  CONST_05  NAV  CAK  NAW  CAJ     0.00   0.0  0
 8PH  CONST_06  NAV  CAK  NAW  CAU   180.00   0.0  0
 8PH  CONST_07  CAI  CAJ  NAW  CAU   180.00   0.0  0
 8PH  CONST_08  CAT  NAV  CAK  NAW   180.00   0.0  0
 8PH  CONST_09  CAT  NAV  CAI  CAJ   180.00   0.0  0
 8PH  CONST_10  H10  CAI  CAJ  NAW   180.00   0.0  0
 8PH  CONST_11  H9   CAJ  NAW  CAK   180.00   0.0  0
 8PH  CONST_12  H8   CAK  NAW  CAJ   180.00   0.0  0
 8PH  Var_01    CAK  NAW  CAU  CAX   -89.87  30.0  1
 8PH  Var_02    CAS  CAT  NAV  CAK    93.47  30.0  1
 8PH  Var_03    CAR  CAS  CAT  NAV   177.18  30.0  2
 8PH  Var_04    CAQ  CAR  CAS  CAT   179.93  30.0  2
 8PH  Var_05    CAP  CAQ  CAR  CAS   177.75  30.0  1
 8PH  Var_06    CAO  CAP  CAQ  CAR  -179.85  30.0  2
 8PH  Var_07    CAN  CAO  CAP  CAQ   178.99  30.0  1
 8PH  Var_08    CAM  CAN  CAO  CAP  -179.55  30.0  2
 8PH  Var_09    CAL  CAM  CAN  CAO   179.37  30.0  1
 8PH  Var_10    CAA  CAL  CAM  CAN  -179.57  30.0  2
 8PH  Var_11    H29  CAA  CAL  CAM   -60.74  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8PH  chir_01  CAX  CAU  OAD  PAZ  negativ

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
 8PH  plan-1  CAU  0.020
 8PH  plan-1  NAW  0.020
 8PH  plan-1  CAK  0.020
 8PH  plan-1  CAJ  0.020
 8PH  plan-1  CAI  0.020
 8PH  plan-1  NAV  0.020
 8PH  plan-1  CAT  0.020
 8PH  plan-1  H8   0.020
 8PH  plan-1  H9   0.020
 8PH  plan-1  H10  0.020

