# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:35:28 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 3,3',3''-phosphoryltripropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[P](=O)(CCC(O)=O)CCC(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
 Z3P  Z3P  '3,3',3''-phosphoryltripropanoic acid'  ligand  29  17  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z3P
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
 Z3P  O01   O  O      0  -0.604   3.9796   1.6731   1.5252
 Z3P  C02   C  C      0   0.419   4.1073   1.2153   0.3744
 Z3P  O03   O  OC    -1  -0.630   5.1802   1.0102  -0.2305
 Z3P  C04   C  CH2    0  -0.587   2.8281   0.8723  -0.4156
 Z3P  C05   C  CH2    0  -0.663   1.5262   1.0266   0.3573
 Z3P  P06   P  P      0   1.053   0.0648   0.6854  -0.6756
 Z3P  O07   O  O      0  -0.766   0.0855   1.4378  -1.9877
 Z3P  C08   C  CH2    0  -0.691   0.0158  -1.1200  -0.9229
 Z3P  C09   C  CH2    0  -0.597  -0.1822  -1.9455   0.3397
 Z3P  C10   C  C      0   0.422  -0.1803  -3.4750   0.1312
 Z3P  O11   O  O      0  -0.603   0.0015  -3.9070  -1.0219
 Z3P  O12   O  OC    -1  -0.628  -0.3634  -4.1548   1.1620
 Z3P  C13   C  CH2    0  -0.660  -1.3683   1.1196   0.3586
 Z3P  C14   C  CH2    0  -0.590  -2.6942   0.8037  -0.3184
 Z3P  C15   C  C      0   0.420  -3.9483   1.2979   0.4320
 Z3P  O16   O  O      0  -0.604  -3.7815   1.9573   1.4749
 Z3P  O17   O  OC    -1  -0.629  -5.0408   0.9896  -0.0874
 Z3P  H041  H  HCH2   0   0.235   2.8036   1.5095  -1.3051
 Z3P  H042  H  HCH2   0   0.228   2.9304  -0.1489  -0.7969
 Z3P  H051  H  HCH2   0   0.251   1.5065   0.3673   1.2287
 Z3P  H052  H  HCH2   0   0.257   1.4252   2.0458   0.7387
 Z3P  H081  H  HCH2   0   0.258  -0.7835  -1.3155  -1.6425
 Z3P  H082  H  HCH2   0   0.261   0.9453  -1.3998  -1.4246
 Z3P  H091  H  HCH2   0   0.235   0.5933  -1.7129   1.0767
 Z3P  H092  H  HCH2   0   0.236  -1.1269  -1.6769   0.8223
 Z3P  H131  H  HCH2   0   0.250  -1.2852   0.6103   1.3214
 Z3P  H132  H  HCH2   0   0.260  -1.2869   2.1893   0.5679
 Z3P  H141  H  HCH2   0   0.235  -2.7097   1.2318  -1.3258
 Z3P  H142  H  HCH2   0   0.231  -2.7981  -0.2766  -0.4650

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
 Z3P  O01  C02   deloc   1.245  0.020  1.245
 Z3P  C02  O03   deloc   1.249  0.020  1.249
 Z3P  C02  C04   single  1.542  0.020  1.542
 Z3P  C04  C05   single  1.522  0.020  1.522
 Z3P  C05  P06   single  1.822  0.020  1.822
 Z3P  P06  O07   double  1.513  0.020  1.513
 Z3P  P06  C08   single  1.823  0.020  1.823
 Z3P  P06  C13   single  1.820  0.020  1.820
 Z3P  C08  C09   single  1.522  0.020  1.522
 Z3P  C09  C10   single  1.544  0.020  1.544
 Z3P  C10  O11   deloc   1.245  0.020  1.245
 Z3P  C10  O12   deloc   1.248  0.020  1.248
 Z3P  C13  C14   single  1.522  0.020  1.522
 Z3P  C14  C15   single  1.543  0.020  1.543
 Z3P  C15  O16   deloc   1.245  0.020  1.245
 Z3P  C15  O17   deloc   1.248  0.020  1.248
 Z3P  C04  H041  single  0.970  0.020  1.090
 Z3P  C04  H042  single  0.970  0.020  1.090
 Z3P  C05  H051  single  0.970  0.020  1.090
 Z3P  C05  H052  single  0.970  0.020  1.090
 Z3P  C08  H081  single  0.970  0.020  1.090
 Z3P  C08  H082  single  0.970  0.020  1.090
 Z3P  C09  H091  single  0.970  0.020  1.090
 Z3P  C09  H092  single  0.970  0.020  1.090
 Z3P  C13  H131  single  0.970  0.020  1.090
 Z3P  C13  H132  single  0.970  0.020  1.090
 Z3P  C14  H141  single  0.970  0.020  1.090
 Z3P  C14  H142  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
 Z3P  C04   C02  O03   115.34  3.000
 Z3P  C04   C02  O01   118.05  3.000
 Z3P  O03   C02  O01   126.61  3.000
 Z3P  H042  C04  H041  105.19  3.000
 Z3P  H042  C04  C05   110.57  3.000
 Z3P  H041  C04  C05   109.55  3.000
 Z3P  H042  C04  C02   107.96  3.000
 Z3P  H041  C04  C02   107.79  3.000
 Z3P  C05   C04  C02   115.27  3.000
 Z3P  H052  C05  H051  106.41  3.000
 Z3P  H052  C05  P06   107.36  3.000
 Z3P  H051  C05  P06   108.94  3.000
 Z3P  H052  C05  C04   110.54  3.000
 Z3P  H051  C05  C04   111.05  3.000
 Z3P  P06   C05  C04   112.29  3.000
 Z3P  C13   P06  C08   106.99  3.000
 Z3P  C13   P06  O07   112.65  3.000
 Z3P  C08   P06  O07   112.04  3.000
 Z3P  C13   P06  C05   105.36  3.000
 Z3P  C08   P06  C05   106.50  3.000
 Z3P  O07   P06  C05   112.81  3.000
 Z3P  H082  C08  H081  105.90  3.000
 Z3P  H082  C08  C09   110.66  3.000
 Z3P  H081  C08  C09   110.74  3.000
 Z3P  H082  C08  P06   107.04  3.000
 Z3P  H081  C08  P06   106.63  3.000
 Z3P  C09   C08  P06   115.36  3.000
 Z3P  H092  C09  H091  105.22  3.000
 Z3P  H092  C09  C10   107.69  3.000
 Z3P  H091  C09  C10   107.49  3.000
 Z3P  H092  C09  C08   110.19  3.000
 Z3P  H091  C09  C08   110.56  3.000
 Z3P  C10   C09  C08   115.17  3.000
 Z3P  O12   C10  O11   126.68  3.000
 Z3P  O12   C10  C09   115.33  3.000
 Z3P  O11   C10  C09   117.98  3.000
 Z3P  H132  C13  H131  106.37  3.000
 Z3P  H132  C13  C14   110.68  3.000
 Z3P  H131  C13  C14   111.20  3.000
 Z3P  H132  C13  P06   106.48  3.000
 Z3P  H131  C13  P06   109.25  3.000
 Z3P  C14   C13  P06   112.56  3.000
 Z3P  H142  C14  H141  105.14  3.000
 Z3P  H142  C14  C15   107.70  3.000
 Z3P  H141  C14  C15   108.11  3.000
 Z3P  H142  C14  C13   110.30  3.000
 Z3P  H141  C14  C13   109.91  3.000
 Z3P  C15   C14  C13   115.18  3.000
 Z3P  O17   C15  O16   126.63  3.000
 Z3P  O17   C15  C14   115.46  3.000
 Z3P  O16   C15  C14   117.91  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
 Z3P  Var_01  C05  C04  C02  O01    -4.94  30.0  3
 Z3P  Var_02  P06  C05  C04  C02   177.02  30.0  3
 Z3P  Var_03  O07  P06  C05  C04   -49.95  30.0  3
 Z3P  Var_04  C09  C08  P06  C05    63.54  30.0  3
 Z3P  Var_05  C14  C13  P06  C05  -176.03  30.0  3
 Z3P  Var_06  C10  C09  C08  P06  -178.23  30.0  3
 Z3P  Var_07  C15  C14  C13  P06  -173.14  30.0  3
 Z3P  Var_08  O11  C10  C09  C08     1.18  30.0  3
 Z3P  Var_09  O16  C15  C14  C13     3.33  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
 Z3P  plan-1  O01  0.020
 Z3P  plan-1  C02  0.020
 Z3P  plan-1  O03  0.020
 Z3P  plan-1  C04  0.020
 Z3P  plan-2  C09  0.020
 Z3P  plan-2  C10  0.020
 Z3P  plan-2  O11  0.020
 Z3P  plan-2  O12  0.020
 Z3P  plan-3  C14  0.020
 Z3P  plan-3  C15  0.020
 Z3P  plan-3  O16  0.020
 Z3P  plan-3  O17  0.020

