# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:57:36 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: (2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](CCC(O)=O)[P@@](=O)(C[C@@H](CCC(O)=O)C(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
 RZP  RZP  '(2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid'  ligand  48  27  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RZP
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
 RZP  C5   C  CH1   0  -0.360  12.0344  -16.9733  75.8226
 RZP  C21  C  C     0   0.557  11.1229  -12.8942  81.7982
 RZP  C19  C  CH2   0  -0.427  11.5947  -14.8935  80.3458
 RZP  C9   C  CH2   0  -0.456  12.6144  -16.4847  74.4956
 RZP  C14  C  CH2   0  -0.745  12.0895  -16.7827  78.7511
 RZP  C15  C  CH1   0  -0.370  12.5470  -16.0570  80.0272
 RZP  C16  C  C     0   0.556  12.5511  -17.0412  81.1769
 RZP  C10  C  CH2   0  -0.551  12.0925  -17.3293  73.3347
 RZP  C1   C  C     0   0.531   9.7770  -17.8599  76.2597
 RZP  C3   C  CH3   0  -0.775   8.3054  -17.5772  76.1204
 RZP  N4   N  NH1   0  -0.640  10.5965  -16.8629  75.8495
 RZP  O12  O  OH1   0  -0.590  12.6516  -15.6331  71.7971
 RZP  O13  O  O     0  -0.445  13.0272  -17.7349  71.1590
 RZP  O17  O  OH1   0  -0.583  13.6149  -16.9111  81.9552
 RZP  O18  O  O     0  -0.435  11.6686  -17.8369  81.3806
 RZP  O2   O  O     0  -0.484  10.2026  -18.9159  76.6988
 RZP  O22  O  O     0  -0.442  10.2428  -12.5292  81.0596
 RZP  O23  O  OH1   0  -0.596  11.4411  -12.2554  82.9193
 RZP  O7   O  O2    0  -0.705  14.3037  -16.2299  77.2345
 RZP  O8   O  O     0  -0.678  12.4093  -14.5302  77.1019
 RZP  P24  P  P     0   1.462  15.1751  -17.5759  77.4028
 RZP  P6   P  P     0   1.280  12.6721  -15.9871  77.2333
 RZP  H1   H  HCH1  0   0.311  12.3021  -18.0194  75.9817
 RZP  H2   H  HCH2  0   0.284  11.9454  -14.7119  82.4891
 RZP  H3   H  HCH2  0   0.288  13.0297  -13.7622  81.5089
 RZP  H4   H  HCH2  0   0.270  11.5833  -14.2334  79.4793
 RZP  H5   H  HCH2  0   0.249  10.5815  -15.2869  80.4584
 RZP  H6   H  HCH2  0   0.265  13.7031  -16.5537  74.5358
 RZP  H7   H  HCH2  0   0.265  12.3668  -15.4317  74.3525
 RZP  H8   H  HCH2  0   0.311  10.9991  -16.8126  78.7113
 RZP  H9   H  HCH2  0   0.308  12.4166  -17.8251  78.7249
 RZP  H10  H  HCH1  0   0.287  13.5579  -15.6595  79.9101
 RZP  H11  H  HCH2  0   0.285  11.0031  -17.2411  73.2693
 RZP  H12  H  HCH2  0   0.272  12.3130  -18.3841  73.5004
 RZP  H13  H  HCH3  0   0.270   7.7972  -17.8167  77.0533
 RZP  H14  H  HCH3  0   0.254   8.0825  -16.5466  75.8527
 RZP  H15  H  HCH3  0   0.275   7.8926  -18.2270  75.3480
 RZP  H16  H  HNH1  0   0.412  10.1883  -16.0046  75.5119
 RZP  H17  H  HOH1  0   0.483  12.9960  -15.4261  70.9151
 RZP  H18  H  HOH1  0   0.482  13.5591  -17.5264  82.7028
 RZP  H19  H  HOH1  0   0.480  10.8700  -11.4810  83.0313
 RZP  H20  H  HOH1  0   0.508  16.7621  -17.3210  75.9322
 RZP  H21  H  HOH1  0   0.510  15.7039  -18.4093  79.3437
 RZP  C20  C  CH2   0  -0.593  11.9921  -14.1032  81.5818
 RZP  C11  C  C     0   0.540  12.6490  -16.9469  71.9901
 RZP  O25  O  OH1   0  -0.713  16.5993  -17.1286  76.8660
 RZP  O26  O  O     0  -0.689  14.5634  -18.7659  76.7838
 RZP  O27  O  OH1   0  -0.720  15.3718  -17.5778  78.9772

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
 RZP  O13  C11  double  1.206  0.020  1.206
 RZP  O12  C11  single  1.328  0.020  1.328
 RZP  C11  C10  single  1.505  0.020  1.505
 RZP  C10  C9   single  1.528  0.020  1.528
 RZP  C9   C5   single  1.528  0.020  1.528
 RZP  N4   C5   single  1.442  0.020  1.442
 RZP  N4   C1   single  1.354  0.020  1.354
 RZP  C3   C1   single  1.505  0.020  1.505
 RZP  C5   P6   single  1.836  0.020  1.836
 RZP  O26  P24  double  1.474  0.020  1.474
 RZP  C1   O2   double  1.220  0.020  1.220
 RZP  O8   P6   double  1.486  0.020  1.486
 RZP  O7   P6   single  1.650  0.020  1.650
 RZP  O7   P24  single  1.612  0.020  1.612
 RZP  P6   C14  single  1.810  0.020  1.810
 RZP  P24  O25  single  1.586  0.020  1.586
 RZP  P24  O27  single  1.587  0.020  1.587
 RZP  C14  C15  single  1.538  0.020  1.538
 RZP  C15  C19  single  1.537  0.020  1.537
 RZP  C15  C16  single  1.513  0.020  1.513
 RZP  C19  C20  single  1.520  0.020  1.520
 RZP  C16  O18  double  1.206  0.020  1.206
 RZP  C16  O17  single  1.325  0.020  1.325
 RZP  O22  C21  double  1.206  0.020  1.206
 RZP  C20  C21  single  1.505  0.020  1.505
 RZP  C21  O23  single  1.329  0.020  1.329
 RZP  C5   H1   single  0.970  0.020  1.090
 RZP  C20  H2   single  0.970  0.020  1.090
 RZP  C20  H3   single  0.970  0.020  1.090
 RZP  C19  H4   single  0.970  0.020  1.090
 RZP  C19  H5   single  0.970  0.020  1.090
 RZP  C9   H6   single  0.970  0.020  1.090
 RZP  C9   H7   single  0.970  0.020  1.090
 RZP  C14  H8   single  0.970  0.020  1.090
 RZP  C14  H9   single  0.970  0.020  1.090
 RZP  C15  H10  single  0.970  0.020  1.090
 RZP  C10  H11  single  0.970  0.020  1.090
 RZP  C10  H12  single  0.970  0.020  1.090
 RZP  C3   H13  single  0.970  0.020  1.090
 RZP  C3   H14  single  0.970  0.020  1.090
 RZP  C3   H15  single  0.970  0.020  1.090
 RZP  N4   H16  single  0.860  0.020  1.020
 RZP  O12  H17  single  0.850  0.020  0.980
 RZP  O17  H18  single  0.850  0.020  0.980
 RZP  O23  H19  single  0.850  0.020  0.980
 RZP  O25  H20  single  0.850  0.020  0.980
 RZP  O27  H21  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
 RZP  H1   C5   P6   108.52  3.000
 RZP  H1   C5   N4   108.38  3.000
 RZP  P6   C5   N4   106.91  3.000
 RZP  H1   C5   C9   109.87  3.000
 RZP  P6   C5   C9   111.32  3.000
 RZP  N4   C5   C9   111.72  3.000
 RZP  O23  C21  O22  123.10  3.000
 RZP  O23  C21  C20  111.67  3.000
 RZP  O22  C21  C20  125.23  3.000
 RZP  H5   C19  H4   106.88  3.000
 RZP  H5   C19  C15  108.87  3.000
 RZP  H4   C19  C15  107.47  3.000
 RZP  H5   C19  C20  110.24  3.000
 RZP  H4   C19  C20  109.54  3.000
 RZP  C15  C19  C20  113.59  3.000
 RZP  H7   C9   H6   106.98  3.000
 RZP  H7   C9   C10  110.88  3.000
 RZP  H6   C9   C10  109.49  3.000
 RZP  H7   C9   C5   109.65  3.000
 RZP  H6   C9   C5   109.05  3.000
 RZP  C10  C9   C5   110.70  3.000
 RZP  H9   C14  H8   105.78  3.000
 RZP  H9   C14  P6   107.63  3.000
 RZP  H8   C14  P6   107.64  3.000
 RZP  H9   C14  C15  112.40  3.000
 RZP  H8   C14  C15  109.90  3.000
 RZP  P6   C14  C15  113.12  3.000
 RZP  H10  C15  C16  108.39  3.000
 RZP  H10  C15  C14  110.98  3.000
 RZP  C16  C15  C14  108.92  3.000
 RZP  H10  C15  C19  108.68  3.000
 RZP  C16  C15  C19  109.66  3.000
 RZP  C14  C15  C19  110.18  3.000
 RZP  O18  C16  O17  123.61  3.000
 RZP  O17  C16  C15  112.62  3.000
 RZP  O18  C16  C15  123.75  3.000
 RZP  H12  C10  H11  106.74  3.000
 RZP  H12  C10  C11  107.87  3.000
 RZP  H11  C10  C11  107.10  3.000
 RZP  H12  C10  C9   110.51  3.000
 RZP  H11  C10  C9   109.93  3.000
 RZP  C11  C10  C9   114.35  3.000
 RZP  O2   C1   N4   122.35  3.000
 RZP  O2   C1   C3   122.47  3.000
 RZP  N4   C1   C3   115.18  3.000
 RZP  H15  C3   H14  108.22  3.000
 RZP  H15  C3   H13  107.40  3.000
 RZP  H14  C3   H13  108.87  3.000
 RZP  H15  C3   C1   108.89  3.000
 RZP  H14  C3   C1   113.65  3.000
 RZP  H13  C3   C1   109.61  3.000
 RZP  H16  N4   C1   118.88  3.000
 RZP  H16  N4   C5   117.54  3.000
 RZP  C1   N4   C5   123.54  3.000
 RZP  H17  O12  C11  110.14  3.000
 RZP  H18  O17  C16  110.15  3.000
 RZP  H19  O23  C21  109.92  3.000
 RZP  P6   O7   P24  131.11  3.000
 RZP  O7   P24  O27   99.88  3.000
 RZP  O27  P24  O26  117.85  3.000
 RZP  O7   P24  O26  113.94  3.000
 RZP  O27  P24  O25  102.99  3.000
 RZP  O7   P24  O25  102.38  3.000
 RZP  O26  P24  O25  117.26  3.000
 RZP  O8   P6   O7   108.62  3.000
 RZP  O7   P6   C14  104.66  3.000
 RZP  O8   P6   C14  116.62  3.000
 RZP  C14  P6   C5   107.24  3.000
 RZP  O7   P6   C5   105.37  3.000
 RZP  O8   P6   C5   113.41  3.000
 RZP  H3   C20  H2   105.61  3.000
 RZP  H3   C20  C19  110.83  3.000
 RZP  H2   C20  C19  111.96  3.000
 RZP  H3   C20  C21  107.87  3.000
 RZP  H2   C20  C21  107.65  3.000
 RZP  C19  C20  C21  112.57  3.000
 RZP  O13  C11  O12  123.07  3.000
 RZP  O12  C11  C10  112.46  3.000
 RZP  O13  C11  C10  124.45  3.000
 RZP  H20  O25  P24  114.94  3.000
 RZP  H21  O27  P24  114.80  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
 RZP  CONST_01  C3   C1   N4   C5    180.00   0.0  0
 RZP  CONST_02  O2   C1   N4   C5      0.00   0.0  0
 RZP  CONST_03  H16  N4   C1   C3      0.00   0.0  0
 RZP  CONST_04  H19  O23  C21  C20   180.00   0.0  0
 RZP  CONST_05  H18  O17  C16  C15   180.00   0.0  0
 RZP  CONST_06  H17  O12  C11  C10   180.00   0.0  0
 RZP  Var_01    C11  C10  C9   C5   -178.07  30.0  1
 RZP  Var_02    C15  C14  P6   C5   -179.81  30.0  3
 RZP  Var_03    C15  C19  C20  C21   174.56  30.0  1
 RZP  Var_04    O22  C21  C20  C19    -3.34  30.0  3
 RZP  Var_05    O13  C11  C10  C9    136.46  30.0  2
 RZP  Var_06    H13  C3   C1   N4   -131.15  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
 RZP  chir_01  C5   C9   N4   P6   positiv
 RZP  chir_02  C15  C16  C19  C14  positiv
 RZP  chir_03  P6   O8   O7   C14  both

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
 RZP  plan-1  C5   0.020
 RZP  plan-1  C1   0.020
 RZP  plan-1  C3   0.020
 RZP  plan-1  N4   0.020
 RZP  plan-1  O2   0.020
 RZP  plan-1  H16  0.020
 RZP  plan-2  C21  0.020
 RZP  plan-2  O22  0.020
 RZP  plan-2  O23  0.020
 RZP  plan-2  H19  0.020
 RZP  plan-2  C20  0.020
 RZP  plan-3  C15  0.020
 RZP  plan-3  C16  0.020
 RZP  plan-3  O17  0.020
 RZP  plan-3  O18  0.020
 RZP  plan-3  H18  0.020
 RZP  plan-4  C10  0.020
 RZP  plan-4  O12  0.020
 RZP  plan-4  O13  0.020
 RZP  plan-4  H17  0.020
 RZP  plan-4  C11  0.020

