# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 22:07:18 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  32  17  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.439   3.9893   1.6127   1.5969
 Z3P  C02   C  C     0   0.559   4.0181   1.2421   0.4509
 Z3P  O03   O  OH1   0  -0.594   5.1424   1.0907  -0.2397
 Z3P  C04   C  CH2   0  -0.581   2.8112   0.8953  -0.3801
 Z3P  C05   C  CH2   0  -0.690   1.5084   1.0348   0.3913
 Z3P  P06   P  P     0   1.068   0.0674   0.6928  -0.6691
 Z3P  O07   O  O     0  -0.735   0.1026   1.4336  -1.9790
 Z3P  C08   C  CH2   0  -0.720   0.0245  -1.1153  -0.9117
 Z3P  C09   C  CH2   0  -0.592  -0.1890  -1.9261   0.3559
 Z3P  C10   C  C     0   0.565  -0.1529  -3.4131   0.1138
 Z3P  O11   O  O     0  -0.437   0.0182  -3.9384  -0.9564
 Z3P  O12   O  OH1   0  -0.593  -0.3372  -4.0896   1.2411
 Z3P  C13   C  CH2   0  -0.693  -1.3689   1.1171   0.3646
 Z3P  C14   C  CH2   0  -0.584  -2.6793   0.8629  -0.3634
 Z3P  C15   C  C     0   0.561  -3.8824   1.2899   0.4358
 Z3P  O16   O  O     0  -0.439  -3.8453   1.7886   1.5318
 Z3P  O17   O  OH1   0  -0.594  -5.0113   1.0474  -0.2197
 Z3P  H1    H  HOH1  0   0.481   5.9046   1.3165   0.3141
 Z3P  H041  H  HCH2  0   0.296   2.8083   1.5405  -1.2627
 Z3P  H042  H  HCH2  0   0.287   2.9477  -0.1223  -0.7578
 Z3P  H051  H  HCH2  0   0.281   1.4895   0.3698   1.2578
 Z3P  H052  H  HCH2  0   0.294   1.3932   2.0520   0.7725
 Z3P  H081  H  HCH2  0   0.292  -0.7648  -1.3156  -1.6403
 Z3P  H082  H  HCH2  0   0.293   0.9633  -1.3923  -1.3970
 Z3P  H091  H  HCH2  0   0.293   0.5660  -1.6970   1.1132
 Z3P  H092  H  HCH2  0   0.292  -1.1511  -1.6912   0.8191
 Z3P  H3    H  HOH1  0   0.483  -0.3111  -5.0422   1.0668
 Z3P  H131  H  HCH2  0   0.282  -1.3205   0.5611   1.3033
 Z3P  H132  H  HCH2  0   0.298  -1.2659   2.1746   0.6195
 Z3P  H141  H  HCH2  0   0.297  -2.6982   1.3925  -1.3197
 Z3P  H142  H  HCH2  0   0.287  -2.8048  -0.1961  -0.6087
 Z3P  H4    H  HOH1  0   0.482  -5.7713   1.3208   0.3154

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   double  1.205  0.020  1.205
 Z3P  C02  O03   single  1.328  0.020  1.328
 Z3P  C02  C04   single  1.506  0.020  1.506
 Z3P  C04  C05   single  1.520  0.020  1.520
 Z3P  C05  P06   single  1.821  0.020  1.821
 Z3P  P06  O07   double  1.505  0.020  1.505
 Z3P  P06  C08   single  1.825  0.020  1.825
 Z3P  P06  C13   single  1.820  0.020  1.820
 Z3P  C08  C09   single  1.520  0.020  1.520
 Z3P  C09  C10   single  1.507  0.020  1.507
 Z3P  C10  O11   double  1.204  0.020  1.204
 Z3P  C10  O12   single  1.328  0.020  1.328
 Z3P  C13  C14   single  1.520  0.020  1.520
 Z3P  C14  C15   single  1.506  0.020  1.506
 Z3P  C15  O16   double  1.205  0.020  1.205
 Z3P  C15  O17   single  1.328  0.020  1.328
 Z3P  O03  H1    single  0.850  0.020  0.980
 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  O12  H3    single  0.850  0.020  0.980
 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
 Z3P  O17  H4    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
 Z3P  C04   C02  O03   111.43  3.000
 Z3P  C04   C02  O01   125.21  3.000
 Z3P  O03   C02  O01   123.36  3.000
 Z3P  H1    O03  C02   110.01  3.000
 Z3P  H042  C04  H041  105.69  3.000
 Z3P  H042  C04  C05   111.56  3.000
 Z3P  H041  C04  C05   110.69  3.000
 Z3P  H042  C04  C02   107.74  3.000
 Z3P  H041  C04  C02   108.16  3.000
 Z3P  C05   C04  C02   112.69  3.000
 Z3P  H052  C05  H051  106.75  3.000
 Z3P  H052  C05  P06   107.13  3.000
 Z3P  H051  C05  P06   109.50  3.000
 Z3P  H052  C05  C04   110.66  3.000
 Z3P  H051  C05  C04   111.19  3.000
 Z3P  P06   C05  C04   111.43  3.000
 Z3P  C13   P06  C08   106.74  3.000
 Z3P  C13   P06  O07   113.45  3.000
 Z3P  C08   P06  O07   111.87  3.000
 Z3P  C13   P06  C05   104.47  3.000
 Z3P  C08   P06  C05   106.38  3.000
 Z3P  O07   P06  C05   113.31  3.000
 Z3P  H082  C08  H081  106.15  3.000
 Z3P  H082  C08  C09   110.85  3.000
 Z3P  H081  C08  C09   110.91  3.000
 Z3P  H082  C08  P06   106.86  3.000
 Z3P  H081  C08  P06   106.69  3.000
 Z3P  C09   C08  P06   114.90  3.000
 Z3P  H092  C09  H091  105.61  3.000
 Z3P  H092  C09  C10   107.53  3.000
 Z3P  H091  C09  C10   107.54  3.000
 Z3P  H092  C09  C08   111.25  3.000
 Z3P  H091  C09  C08   111.65  3.000
 Z3P  C10   C09  C08   112.89  3.000
 Z3P  O12   C10  O11   123.51  3.000
 Z3P  O12   C10  C09   111.29  3.000
 Z3P  O11   C10  C09   125.21  3.000
 Z3P  H3    O12  C10   110.15  3.000
 Z3P  H132  C13  H131  106.74  3.000
 Z3P  H132  C13  C14   110.78  3.000
 Z3P  H131  C13  C14   111.39  3.000
 Z3P  H132  C13  P06   106.48  3.000
 Z3P  H131  C13  P06   109.55  3.000
 Z3P  C14   C13  P06   111.67  3.000
 Z3P  H142  C14  H141  105.71  3.000
 Z3P  H142  C14  C15   107.55  3.000
 Z3P  H141  C14  C15   108.24  3.000
 Z3P  H142  C14  C13   111.59  3.000
 Z3P  H141  C14  C13   110.66  3.000
 Z3P  C15   C14  C13   112.76  3.000
 Z3P  O17   C15  O16   123.43  3.000
 Z3P  O17   C15  C14   111.43  3.000
 Z3P  O16   C15  C14   125.14  3.000
 Z3P  H4    O17  C15   110.04  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  CONST_01  H1   O03  C02  O01     0.00   0.0  0
 Z3P  CONST_02  H3   O12  C10  C09   180.00   0.0  0
 Z3P  CONST_03  H4   O17  C15  C14   180.00   0.0  0
 Z3P  Var_01    C05  C04  C02  O01    -1.10  30.0  3
 Z3P  Var_02    P06  C05  C04  C02   177.00  30.0  3
 Z3P  Var_03    O07  P06  C05  C04   -49.00  30.0  3
 Z3P  Var_04    C09  C08  P06  C05    63.15  30.0  3
 Z3P  Var_05    C14  C13  P06  C05  -178.87  30.0  3
 Z3P  Var_06    C10  C09  C08  P06  -177.33  30.0  3
 Z3P  Var_07    C15  C14  C13  P06  -176.26  30.0  3
 Z3P  Var_08    O11  C10  C09  C08    -0.33  30.0  3
 Z3P  Var_09    O16  C15  C14  C13     0.40  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-1  H1   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-2  H3   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
 Z3P  plan-3  H4   0.020

