# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 07:32:28 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 3-(2-hydroxy-2,2-diphosphonoethyl)-1-nonyl-1H-imidazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCn1cc[n+](CC(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
 PVZ  PVZ  3-(2-hydroxy-2,2-diphosphonoethyl)-1-nonyl-1H-imidazol-3-ium  ligand  54  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PVZ
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
 PVZ  C01   C  CH3   0  -0.661  11.0195   1.6834   0.0265
 PVZ  C02   C  CH2   0  -0.419   9.5479   1.8308   0.3884
 PVZ  C03   C  CH2   0  -0.406   8.6918   0.6873  -0.1420
 PVZ  C04   C  CH2   0  -0.412   7.2167   0.8180   0.2165
 PVZ  C05   C  CH2   0  -0.412   6.3651  -0.3192  -0.3334
 PVZ  C06   C  CH2   0  -0.414   4.8913  -0.2030   0.0353
 PVZ  C07   C  CH2   0  -0.425   4.0458  -1.3238  -0.5556
 PVZ  C08   C  CH2   0  -0.434   2.5770  -1.2247  -0.1638
 PVZ  C09   C  CH2   0  -0.314   1.7613  -2.3200  -0.8321
 PVZ  N10   N  NR5   0  -0.416   0.3577  -2.2769  -0.4320
 PVZ  C11   C  CR15  0  -0.084  -0.1724  -2.8695   0.6856
 PVZ  C12   C  CR15  0  -0.083  -1.4871  -2.5545   0.7167
 PVZ  N13   N  NR5   1  -0.426  -1.7321  -1.7695  -0.3840
 PVZ  C14   C  CR15  0   0.270  -0.5980  -1.6150  -1.0595
 PVZ  C15   C  CH2   0  -0.350  -2.9953  -1.1536  -0.7491
 PVZ  C16   C  CT    0  -0.318  -3.0466   0.3226  -0.3170
 PVZ  O17   O  OH1   0  -0.654  -1.9962   1.0355  -0.9146
 PVZ  P18   P  P     0   1.408  -4.5590   1.1661  -0.9749
 PVZ  O19   O  O     0  -0.682  -4.5299   2.6268  -0.7609
 PVZ  O20   O  OH1   0  -0.732  -4.6090   0.8335  -2.5368
 PVZ  O21   O  OH1   0  -0.739  -5.6880   0.3008  -0.2546
 PVZ  P22   P  P     0   1.398  -3.0341   0.4190   1.5431
 PVZ  O23   O  OH1   0  -0.720  -3.7350   1.7759   1.9943
 PVZ  O24   O  O     0  -0.674  -3.6726  -0.7361   2.2043
 PVZ  O25   O  OH1   0  -0.748  -1.4530   0.5967   1.7165
 PVZ  H01   H  HCH3  0   0.215  11.4356   0.7601   0.4342
 PVZ  H01A  H  HCH3  0   0.215  11.1568   1.6552  -1.0562
 PVZ  H01B  H  HCH3  0   0.225  11.6143   2.5123   0.4125
 PVZ  H02   H  HCH2  0   0.210   9.4402   1.8893   1.4761
 PVZ  H02A  H  HCH2  0   0.210   9.1675   2.7789  -0.0043
 PVZ  H03   H  HCH2  0   0.206   8.7974   0.6322  -1.2314
 PVZ  H03A  H  HCH2  0   0.206   9.0769  -0.2622   0.2466
 PVZ  H04   H  HCH2  0   0.207   7.1097   0.8598   1.3062
 PVZ  H04A  H  HCH2  0   0.207   6.8340   1.7722  -0.1623
 PVZ  H05   H  HCH2  0   0.208   6.4647  -0.3500  -1.4241
 PVZ  H05A  H  HCH2  0   0.209   6.7553  -1.2750   0.0332
 PVZ  H06   H  HCH2  0   0.213   4.7866  -0.2016   1.1255
 PVZ  H06A  H  HCH2  0   0.213   4.5041   0.7617  -0.3100
 PVZ  H07   H  HCH2  0   0.223   4.1353  -1.3059  -1.6469
 PVZ  H07A  H  HCH2  0   0.224   4.4429  -2.2911  -0.2310
 PVZ  H08   H  HCH2  0   0.244   2.4750  -1.3007   0.9224
 PVZ  H08A  H  HCH2  0   0.239   2.1786  -0.2486  -0.4557
 PVZ  H09   H  HCH2  0   0.289   1.7978  -2.2294  -1.9169
 PVZ  H09A  H  HCH2  0   0.288   2.1371  -3.3086  -0.5714
 PVZ  H11   H  HCR5  0   0.337   0.4209  -3.4686   1.3540
 PVZ  H12   H  HCR5  0   0.341  -2.2584  -2.8219   1.4165
 PVZ  H14   H  HCR5  0   0.372  -0.4806  -1.0692  -1.9806
 PVZ  H15   H  HCH2  0   0.321  -3.0857  -1.2236  -1.8324
 PVZ  H15A  H  HCH2  0   0.327  -3.7997  -1.7373  -0.3089
 PVZ  HO17  H  HOH1  0   0.477  -1.2902   1.2155  -0.2816
 PVZ  HO20  H  HOH1  0   0.503  -4.9456  -0.0338  -2.7990
 PVZ  HO21  H  HOH1  0   0.510  -6.5962   0.6266  -0.3428
 PVZ  HO23  H  HOH1  0   0.497  -3.4397   2.5916   1.5649
 PVZ  HO25  H  HOH1  0   0.514  -1.1218   0.7166   2.6189

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
 PVZ  C02  C01   single    1.523  0.020  1.523
 PVZ  C01  H01   single    0.970  0.020  1.090
 PVZ  C01  H01A  single    0.970  0.020  1.090
 PVZ  C01  H01B  single    0.970  0.020  1.090
 PVZ  C03  C02   single    1.524  0.020  1.524
 PVZ  C02  H02   single    0.970  0.020  1.090
 PVZ  C02  H02A  single    0.970  0.020  1.090
 PVZ  C04  C03   single    1.524  0.020  1.524
 PVZ  C03  H03   single    0.970  0.020  1.090
 PVZ  C03  H03A  single    0.970  0.020  1.090
 PVZ  C04  C05   single    1.523  0.020  1.523
 PVZ  C04  H04   single    0.970  0.020  1.090
 PVZ  C04  H04A  single    0.970  0.020  1.090
 PVZ  C05  C06   single    1.524  0.020  1.524
 PVZ  C05  H05   single    0.970  0.020  1.090
 PVZ  C05  H05A  single    0.970  0.020  1.090
 PVZ  C07  C06   single    1.523  0.020  1.523
 PVZ  C06  H06   single    0.970  0.020  1.090
 PVZ  C06  H06A  single    0.970  0.020  1.090
 PVZ  C07  C08   single    1.523  0.020  1.523
 PVZ  C07  H07   single    0.970  0.020  1.090
 PVZ  C07  H07A  single    0.970  0.020  1.090
 PVZ  C09  C08   single    1.520  0.020  1.520
 PVZ  C08  H08   single    0.970  0.020  1.090
 PVZ  C08  H08A  single    0.970  0.020  1.090
 PVZ  C09  N10   single    1.460  0.020  1.460
 PVZ  C09  H09   single    0.970  0.020  1.090
 PVZ  C09  H09A  single    0.970  0.020  1.090
 PVZ  N10  C14   aromatic  1.321  0.020  1.321
 PVZ  N10  C11   aromatic  1.372  0.020  1.372
 PVZ  C11  C12   aromatic  1.352  0.020  1.352
 PVZ  C11  H11   single    0.930  0.020  1.080
 PVZ  N13  C12   aromatic  1.374  0.020  1.374
 PVZ  C12  H12   single    0.930  0.020  1.080
 PVZ  C14  N13   aromatic  1.329  0.020  1.329
 PVZ  N13  C15   single    1.452  0.020  1.452
 PVZ  C14  H14   single    0.930  0.020  1.080
 PVZ  C16  C15   single    1.539  0.020  1.539
 PVZ  C15  H15   single    0.970  0.020  1.090
 PVZ  C15  H15A  single    0.970  0.020  1.090
 PVZ  P18  C16   single    1.852  0.020  1.852
 PVZ  C16  O17   single    1.403  0.020  1.403
 PVZ  C16  P22   single    1.863  0.020  1.863
 PVZ  O17  HO17  single    0.850  0.020  0.980
 PVZ  O19  P18   double    1.477  0.020  1.477
 PVZ  O21  P18   single    1.594  0.020  1.594
 PVZ  O20  P18   single    1.598  0.020  1.598
 PVZ  O20  HO20  single    0.850  0.020  0.980
 PVZ  O21  HO21  single    0.850  0.020  0.980
 PVZ  O24  P22   double    1.476  0.020  1.476
 PVZ  P22  O23   single    1.592  0.020  1.592
 PVZ  P22  O25   single    1.600  0.020  1.600
 PVZ  O23  HO23  single    0.850  0.020  0.980
 PVZ  O25  HO25  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
 PVZ  H01B  C01  H01A  107.58  3.000
 PVZ  H01B  C01  H01   107.62  3.000
 PVZ  H01A  C01  H01   107.49  3.000
 PVZ  H01B  C01  C02   111.68  3.000
 PVZ  H01A  C01  C02   111.09  3.000
 PVZ  H01   C01  C02   111.19  3.000
 PVZ  H02A  C02  H02   106.03  3.000
 PVZ  H02A  C02  C03   109.26  3.000
 PVZ  H02   C02  C03   109.31  3.000
 PVZ  H02A  C02  C01   109.54  3.000
 PVZ  H02   C02  C01   109.66  3.000
 PVZ  C03   C02  C01   112.81  3.000
 PVZ  H03A  C03  H03   105.96  3.000
 PVZ  H03A  C03  C04   109.34  3.000
 PVZ  H03   C03  C04   109.36  3.000
 PVZ  H03A  C03  C02   109.23  3.000
 PVZ  H03   C03  C02   109.25  3.000
 PVZ  C04   C03  C02   113.43  3.000
 PVZ  H04A  C04  H04   106.05  3.000
 PVZ  H04A  C04  C05   109.27  3.000
 PVZ  H04   C04  C05   109.44  3.000
 PVZ  H04A  C04  C03   109.36  3.000
 PVZ  H04   C04  C03   109.38  3.000
 PVZ  C05   C04  C03   113.09  3.000
 PVZ  H05A  C05  H05   106.04  3.000
 PVZ  H05A  C05  C06   109.28  3.000
 PVZ  H05   C05  C06   109.33  3.000
 PVZ  H05A  C05  C04   109.35  3.000
 PVZ  H05   C05  C04   109.24  3.000
 PVZ  C06   C05  C04   113.35  3.000
 PVZ  H06A  C06  H06   106.19  3.000
 PVZ  H06A  C06  C07   109.24  3.000
 PVZ  H06   C06  C07   109.51  3.000
 PVZ  H06A  C06  C05   109.44  3.000
 PVZ  H06   C06  C05   109.48  3.000
 PVZ  C07   C06  C05   112.76  3.000
 PVZ  H07A  C07  H07   106.28  3.000
 PVZ  H07A  C07  C08   109.33  3.000
 PVZ  H07   C07  C08   109.52  3.000
 PVZ  H07A  C07  C06   109.50  3.000
 PVZ  H07   C07  C06   109.21  3.000
 PVZ  C08   C07  C06   112.80  3.000
 PVZ  H08A  C08  H08   107.04  3.000
 PVZ  H08A  C08  C09   109.28  3.000
 PVZ  H08   C08  C09   109.66  3.000
 PVZ  H08A  C08  C07   109.91  3.000
 PVZ  H08   C08  C07   109.93  3.000
 PVZ  C09   C08  C07   110.93  3.000
 PVZ  H09A  C09  H09   107.60  3.000
 PVZ  H09A  C09  N10   107.02  3.000
 PVZ  H09   C09  N10   107.62  3.000
 PVZ  H09A  C09  C08   111.32  3.000
 PVZ  H09   C09  C08   111.09  3.000
 PVZ  N10   C09  C08   111.96  3.000
 PVZ  C14   N10  C11   108.90  3.000
 PVZ  C11   N10  C09   125.60  3.000
 PVZ  C14   N10  C09   125.45  3.000
 PVZ  H11   C11  C12   130.66  3.000
 PVZ  H11   C11  N10   122.25  3.000
 PVZ  C12   C11  N10   107.09  3.000
 PVZ  H12   C12  N13   122.38  3.000
 PVZ  H12   C12  C11   130.87  3.000
 PVZ  N13   C12  C11   106.74  3.000
 PVZ  C15   N13  C14   124.42  3.000
 PVZ  C15   N13  C12   126.79  3.000
 PVZ  C14   N13  C12   108.75  3.000
 PVZ  H14   C14  N13   125.91  3.000
 PVZ  H14   C14  N10   125.54  3.000
 PVZ  N13   C14  N10   108.52  3.000
 PVZ  H15A  C15  H15   107.86  3.000
 PVZ  H15A  C15  C16   112.13  3.000
 PVZ  H15   C15  C16   109.76  3.000
 PVZ  H15A  C15  N13   108.31  3.000
 PVZ  H15   C15  N13   107.16  3.000
 PVZ  C16   C15  N13   111.42  3.000
 PVZ  P22   C16  P18   109.67  3.000
 PVZ  P22   C16  O17   113.20  3.000
 PVZ  P18   C16  O17   103.21  3.000
 PVZ  P22   C16  C15   109.26  3.000
 PVZ  O17   C16  C15   110.05  3.000
 PVZ  P18   C16  C15   111.36  3.000
 PVZ  HO17  O17  C16   111.29  3.000
 PVZ  O21   P18  O20   107.85  3.000
 PVZ  O20   P18  O19   110.38  3.000
 PVZ  O21   P18  O19   119.03  3.000
 PVZ  O20   P18  C16   106.14  3.000
 PVZ  O21   P18  C16    99.82  3.000
 PVZ  O19   P18  C16   112.52  3.000
 PVZ  HO20  O20  P18   117.57  3.000
 PVZ  HO21  O21  P18   116.11  3.000
 PVZ  O25   P22  O24   117.75  3.000
 PVZ  O25   P22  O23   108.03  3.000
 PVZ  O24   P22  O23   110.45  3.000
 PVZ  O25   P22  C16    96.93  3.000
 PVZ  O23   P22  C16   108.91  3.000
 PVZ  O24   P22  C16   113.82  3.000
 PVZ  HO23  O23  P22   117.27  3.000
 PVZ  HO25  O25  P22   116.90  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
 PVZ  CONST_01  C12  N13  C14  N10     0.00   0.0  0
 PVZ  CONST_02  N13  C12  C11  N10     0.00   0.0  0
 PVZ  CONST_03  N13  C14  N10  C11     0.00   0.0  0
 PVZ  CONST_04  C14  N13  C12  C11     0.00   0.0  0
 PVZ  CONST_05  C14  N10  C11  C12     0.00   0.0  0
 PVZ  CONST_06  N13  C14  N10  C09   180.00   0.0  0
 PVZ  CONST_07  C12  C11  N10  C09   180.00   0.0  0
 PVZ  CONST_08  C15  N13  C14  N10   180.00   0.0  0
 PVZ  CONST_09  C15  N13  C12  C11   180.00   0.0  0
 PVZ  CONST_10  H12  C12  C11  N10   180.00   0.0  0
 PVZ  CONST_11  H14  C14  N10  C11   180.00   0.0  0
 PVZ  CONST_12  H11  C11  C12  N13   180.00   0.0  0
 PVZ  Var_01    C14  N10  C09  C08    91.44  30.0  2
 PVZ  Var_02    C16  C15  N13  C12    98.51  30.0  2
 PVZ  Var_03    N10  C09  C08  C07   177.83  30.0  2
 PVZ  Var_04    P18  C16  C15  N13   172.56  30.0  2
 PVZ  Var_05    C04  C03  C02  C01   179.79  30.0  2
 PVZ  Var_06    C05  C04  C03  C02   179.22  30.0  1
 PVZ  Var_07    C06  C05  C04  C03   179.33  30.0  3
 PVZ  Var_08    C07  C06  C05  C04   178.30  30.0  3
 PVZ  Var_09    C08  C07  C06  C05   178.81  30.0  2
 PVZ  Var_10    C09  C08  C07  C06   177.11  30.0  3
 PVZ  Var_11    O19  P18  C16  C15  -170.88  30.0  1
 PVZ  Var_12    O24  P22  C16  C15   -30.57  30.0  3
 PVZ  Var_13    H01  C01  C02  C03   -59.92  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
 PVZ  plan-1  C09  0.020
 PVZ  plan-1  N10  0.020
 PVZ  plan-1  C11  0.020
 PVZ  plan-1  C12  0.020
 PVZ  plan-1  N13  0.020
 PVZ  plan-1  C14  0.020
 PVZ  plan-1  C15  0.020
 PVZ  plan-1  H11  0.020
 PVZ  plan-1  H12  0.020
 PVZ  plan-1  H14  0.020

