# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:26:41 2021
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-oxidanyl-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)(=O)C[C@@H](CCC(O)=O)C(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
 RZV  RZV  '(2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-oxidanyl-phosphoryl]methyl]pentanedioic acid'  ligand  43  23  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RZV
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
 RZV  C5   C  CH1   0  -0.354   0.7210  6.8377   6.2539
 RZV  C1   C  C     0   0.505   0.9047  8.4217   4.3111
 RZV  C10  C  CH2   0  -0.556   1.1623  4.6044   5.1822
 RZV  C11  C  C     0   0.543   1.7554  3.2232   5.2584
 RZV  C14  C  CH2   0  -0.747  -0.0649  6.9467   9.1045
 RZV  C15  C  CH1   0  -0.360  -0.2766  7.7802  10.3755
 RZV  C16  C  C     0   0.543   1.0608  8.0977  11.0152
 RZV  C19  C  CH2   0  -0.414  -1.1563  7.0080  11.3639
 RZV  C20  C  CH2   0  -0.596  -1.4629  7.8136  12.6165
 RZV  C21  C  C     0   0.557  -2.3903  7.1032  13.5639
 RZV  C3   C  CH3   0  -0.813  -0.5969  8.4960   4.2214
 RZV  C9   C  CH2   0  -0.452   1.3035  5.4407   6.4511
 RZV  N4   N  NH1   0  -0.616   1.4270  7.5667   5.2251
 RZV  O12  O  OH1   0  -0.589   1.5919  2.6567   6.4477
 RZV  O13  O  O     0  -0.448   2.2974  2.6675   4.3350
 RZV  O17  O  O     0  -0.438   1.7982  7.2581  11.4679
 RZV  O18  O  OH1   0  -0.583   1.3234  9.3954  11.0417
 RZV  O2   O  O     0  -0.486   1.6344  9.0732   3.5802
 RZV  O22  O  OH1   0  -0.595  -2.6011  7.8133  14.6669
 RZV  O23  O  O     0  -0.442  -2.8928  6.0252  13.3676
 RZV  O7   O  OH1   0  -0.752   2.2825  7.8841   8.2531
 RZV  O8   O  O     0  -0.701   0.1547  9.2306   7.5240
 RZV  P6   P  P     0   1.289   0.7362  7.8791   7.7754
 RZV  H1   H  HCH1  0   0.307  -0.3290  6.7355   5.9692
 RZV  H2   H  HCH2  0   0.276   1.6176  5.1100   4.3312
 RZV  H3   H  HCH2  0   0.287   0.0999  4.4842   4.9417
 RZV  H4   H  HCH2  0   0.307  -1.0402  6.6340   8.7212
 RZV  H5   H  HCH2  0   0.297   0.4920  6.0344   9.3297
 RZV  H6   H  HCH1  0   0.284  -0.7796  8.7117  10.1072
 RZV  H7   H  HCH2  0   0.259  -2.0861  6.7525  10.8529
 RZV  H8   H  HCH2  0   0.248  -0.6692  6.0665  11.6249
 RZV  H9   H  HCH2  0   0.284  -0.5515  8.0611  13.1695
 RZV  H10  H  HCH2  0   0.288  -1.9184  8.7741  12.3551
 RZV  H11  H  HCH3  0   0.272  -0.8777  9.2022   3.4447
 RZV  H12  H  HCH3  0   0.266  -1.0258  7.5233   3.9742
 RZV  H13  H  HCH3  0   0.270  -1.0361  8.8200   5.1640
 RZV  H14  H  HCH2  0   0.272   0.7778  4.9573   7.2754
 RZV  H15  H  HCH2  0   0.259   2.3534  5.5138   6.7457
 RZV  H16  H  HNH1  0   0.396   2.4373  7.5380   5.2625
 RZV  H17  H  HOH1  0   0.483   1.9706  1.7646   6.4442
 RZV  H18  H  HOH1  0   0.481   2.1853  9.5525  11.4579
 RZV  H19  H  HOH1  0   0.480  -3.2008  7.3355  15.2592
 RZV  H20  H  HOH1  0   0.491   2.7962  8.6275   7.9093

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
 RZV  C3   C1   single  1.506  0.020  1.506
 RZV  O2   C1   double  1.221  0.020  1.221
 RZV  C1   N4   single  1.356  0.020  1.356
 RZV  O13  C11  double  1.206  0.020  1.206
 RZV  N4   C5   single  1.445  0.020  1.445
 RZV  C11  C10  single  1.505  0.020  1.505
 RZV  C11  O12  single  1.328  0.020  1.328
 RZV  C10  C9   single  1.526  0.020  1.526
 RZV  C5   C9   single  1.526  0.020  1.526
 RZV  C5   P6   single  1.844  0.020  1.844
 RZV  O8   P6   double  1.493  0.020  1.493
 RZV  P6   O7   single  1.618  0.020  1.618
 RZV  P6   C14  single  1.810  0.020  1.810
 RZV  C14  C15  single  1.535  0.020  1.535
 RZV  O17  C16  double  1.206  0.020  1.206
 RZV  C15  C16  single  1.516  0.020  1.516
 RZV  C15  C19  single  1.532  0.020  1.532
 RZV  C16  O18  single  1.324  0.020  1.324
 RZV  C19  C20  single  1.521  0.020  1.521
 RZV  O23  C21  double  1.205  0.020  1.205
 RZV  C20  C21  single  1.504  0.020  1.504
 RZV  C21  O22  single  1.329  0.020  1.329
 RZV  C5   H1   single  0.970  0.020  1.090
 RZV  C10  H2   single  0.970  0.020  1.090
 RZV  C10  H3   single  0.970  0.020  1.090
 RZV  C14  H4   single  0.970  0.020  1.090
 RZV  C14  H5   single  0.970  0.020  1.090
 RZV  C15  H6   single  0.970  0.020  1.090
 RZV  C19  H7   single  0.970  0.020  1.090
 RZV  C19  H8   single  0.970  0.020  1.090
 RZV  C20  H9   single  0.970  0.020  1.090
 RZV  C20  H10  single  0.970  0.020  1.090
 RZV  C3   H11  single  0.970  0.020  1.090
 RZV  C3   H12  single  0.970  0.020  1.090
 RZV  C3   H13  single  0.970  0.020  1.090
 RZV  C9   H14  single  0.970  0.020  1.090
 RZV  C9   H15  single  0.970  0.020  1.090
 RZV  N4   H16  single  0.860  0.020  1.020
 RZV  O12  H17  single  0.850  0.020  0.980
 RZV  O18  H18  single  0.850  0.020  0.980
 RZV  O22  H19  single  0.850  0.020  0.980
 RZV  O7   H20  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
 RZV  H1   C5   P6   106.01  3.000
 RZV  H1   C5   N4   109.34  3.000
 RZV  P6   C5   N4   107.37  3.000
 RZV  H1   C5   C9   108.34  3.000
 RZV  P6   C5   C9   114.02  3.000
 RZV  N4   C5   C9   111.55  3.000
 RZV  O2   C1   N4   120.64  3.000
 RZV  N4   C1   C3   117.08  3.000
 RZV  O2   C1   C3   122.26  3.000
 RZV  H3   C10  H2   106.53  3.000
 RZV  H3   C10  C9   109.41  3.000
 RZV  H2   C10  C9   110.88  3.000
 RZV  H3   C10  C11  107.01  3.000
 RZV  H2   C10  C11  107.50  3.000
 RZV  C9   C10  C11  115.10  3.000
 RZV  O13  C11  O12  122.99  3.000
 RZV  O12  C11  C10  112.86  3.000
 RZV  O13  C11  C10  124.13  3.000
 RZV  H5   C14  H4   106.75  3.000
 RZV  H5   C14  P6   110.85  3.000
 RZV  H4   C14  P6   106.53  3.000
 RZV  H5   C14  C15  110.69  3.000
 RZV  H4   C14  C15  108.82  3.000
 RZV  P6   C14  C15  112.92  3.000
 RZV  H6   C15  C19  108.90  3.000
 RZV  H6   C15  C16  109.35  3.000
 RZV  C19  C15  C16  109.87  3.000
 RZV  H6   C15  C14  108.87  3.000
 RZV  C19  C15  C14  109.87  3.000
 RZV  C16  C15  C14  109.97  3.000
 RZV  O18  C16  O17  123.62  3.000
 RZV  O18  C16  C15  112.87  3.000
 RZV  O17  C16  C15  123.51  3.000
 RZV  H8   C19  H7   106.87  3.000
 RZV  H8   C19  C20  110.48  3.000
 RZV  H7   C19  C20  109.75  3.000
 RZV  H8   C19  C15  109.44  3.000
 RZV  H7   C19  C15  107.77  3.000
 RZV  C20  C19  C15  112.35  3.000
 RZV  H10  C20  H9   105.59  3.000
 RZV  H10  C20  C21  107.96  3.000
 RZV  H9   C20  C21  107.58  3.000
 RZV  H10  C20  C19  110.61  3.000
 RZV  H9   C20  C19  111.60  3.000
 RZV  C21  C20  C19  113.14  3.000
 RZV  O23  C21  O22  123.16  3.000
 RZV  O22  C21  C20  111.61  3.000
 RZV  O23  C21  C20  125.23  3.000
 RZV  H13  C3   H12  107.62  3.000
 RZV  H13  C3   H11  108.73  3.000
 RZV  H12  C3   H11  108.40  3.000
 RZV  H13  C3   C1   111.42  3.000
 RZV  H12  C3   C1   111.18  3.000
 RZV  H11  C3   C1   109.41  3.000
 RZV  H15  C9   H14  106.80  3.000
 RZV  H15  C9   C10  110.47  3.000
 RZV  H14  C9   C10  109.94  3.000
 RZV  H15  C9   C5   109.89  3.000
 RZV  H14  C9   C5   108.63  3.000
 RZV  C10  C9   C5   111.02  3.000
 RZV  H16  N4   C1   115.31  3.000
 RZV  H16  N4   C5   116.58  3.000
 RZV  C1   N4   C5   127.56  3.000
 RZV  H17  O12  C11  109.97  3.000
 RZV  H18  O18  C16  110.10  3.000
 RZV  H19  O22  C21  110.01  3.000
 RZV  H20  O7   P6   113.90  3.000
 RZV  O8   P6   O7   114.78  3.000
 RZV  O7   P6   C14  101.98  3.000
 RZV  O8   P6   C14  114.68  3.000
 RZV  C14  P6   C5   108.14  3.000
 RZV  O7   P6   C5   104.67  3.000
 RZV  O8   P6   C5   111.67  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
 RZV  CONST_01  C3   C1   N4   C5      0.00   0.0  0
 RZV  CONST_02  O2   C1   N4   C5    180.00   0.0  0
 RZV  CONST_03  H16  N4   C1   C3    180.00   0.0  0
 RZV  CONST_04  H17  O12  C11  C10   180.00   0.0  0
 RZV  CONST_05  H18  O18  C16  C15   180.00   0.0  0
 RZV  CONST_06  H19  O22  C21  C20   180.00   0.0  0
 RZV  Var_01    C11  C10  C9   C5    177.78  30.0  1
 RZV  Var_02    C15  C14  P6   C5   -172.51  30.0  3
 RZV  Var_03    C21  C20  C19  C15   176.68  30.0  3
 RZV  Var_04    O23  C21  C20  C19    -2.24  30.0  3
 RZV  Var_05    O13  C11  C10  C9   -144.36  30.0  3
 RZV  Var_06    H11  C3   C1   N4   -179.12  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
 RZV  chir_01  C5   N4   C9   P6   negativ
 RZV  chir_02  C15  C19  C16  C14  negativ
 RZV  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
 RZV  plan-1  C5   0.020
 RZV  plan-1  C1   0.020
 RZV  plan-1  C3   0.020
 RZV  plan-1  N4   0.020
 RZV  plan-1  O2   0.020
 RZV  plan-1  H16  0.020
 RZV  plan-2  C10  0.020
 RZV  plan-2  C11  0.020
 RZV  plan-2  O12  0.020
 RZV  plan-2  O13  0.020
 RZV  plan-2  H17  0.020
 RZV  plan-3  C15  0.020
 RZV  plan-3  C16  0.020
 RZV  plan-3  O17  0.020
 RZV  plan-3  O18  0.020
 RZV  plan-3  H18  0.020
 RZV  plan-4  C20  0.020
 RZV  plan-4  C21  0.020
 RZV  plan-4  O22  0.020
 RZV  plan-4  O23  0.020
 RZV  plan-4  H19  0.020

