# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:24:39 2022
#   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  39  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.329   0.7720  6.7909   6.2662
 RZV  C1   C  C      0   0.479   0.8528  8.3164   4.2687
 RZV  C10  C  CH2    0  -0.573   1.0510  4.4743   5.2531
 RZV  C11  C  C      0   0.408   1.6227  3.0447   5.3431
 RZV  C14  C  CH2    0  -0.710   0.1058  7.0108   9.0858
 RZV  C15  C  CH1    0  -0.311  -0.1388  7.8552  10.3411
 RZV  C16  C  C      0   0.404   1.1859  8.1871  11.0637
 RZV  C19  C  CH2    0  -0.383  -1.1088  7.1367  11.2852
 RZV  C20  C  CH2    0  -0.582  -1.4882  7.9590  12.5074
 RZV  C21  C  C      0   0.404  -2.5449  7.3531  13.4539
 RZV  C3   C  CH3    0  -0.803  -0.6546  8.3506   4.2160
 RZV  C9   C  CH2    0  -0.419   1.3411  5.3865   6.4350
 RZV  N4   N  NH1    0  -0.594   1.4123  7.4607   5.1442
 RZV  O12  O  OC    -1  -0.605   2.2595  2.7353   6.3701
 RZV  O13  O  O      0  -0.626   1.3923  2.3102   4.3591
 RZV  O17  O  O      0  -0.619   1.8545  7.2129  11.4722
 RZV  O18  O  OC    -1  -0.621   1.4814  9.3929  11.2013
 RZV  O2   O  O      0  -0.507   1.5387  9.0125   3.5266
 RZV  O22  O  OC    -1  -0.628  -2.9949  8.1271  14.3266
 RZV  O23  O  O      0  -0.607  -2.8549  6.1541  13.2988
 RZV  O7   O  OP    -1  -0.812   2.4804  7.9879   8.0283
 RZV  O8   O  O      0  -0.808   0.2345  9.1896   7.4367
 RZV  P6   P  P      0   1.193   0.9907  7.9084   7.7459
 RZV  H1   H  HCH1   0   0.244  -0.2971  6.7095   6.0570
 RZV  H2   H  HCH2   0   0.216   1.4224  4.9291   4.3289
 RZV  H3   H  HCH2   0   0.211  -0.0341  4.3986   5.1118
 RZV  H4   H  HCH2   0   0.217  -0.8574  6.6801   8.6787
 RZV  H5   H  HCH2   0   0.220   0.6516  6.1044   9.3595
 RZV  H6   H  HCH1   0   0.178  -0.6098  8.7947  10.0336
 RZV  H7   H  HCH2   0   0.190  -2.0151  6.8832  10.7251
 RZV  H8   H  HCH2   0   0.187  -0.6701  6.1832  11.5916
 RZV  H9   H  HCH2   0   0.216  -0.5946  8.1620  13.1100
 RZV  H10  H  HCH2   0   0.200  -1.8387  8.9472  12.1889
 RZV  H11  H  HCH3   0   0.254  -0.9767  9.0007   3.4064
 RZV  H12  H  HCH3   0   0.253  -1.0741  7.3564   4.0553
 RZV  H13  H  HCH3   0   0.262  -1.0566  8.7285   5.1554
 RZV  H14  H  HCH2   0   0.223   0.9222  4.9465   7.3431
 RZV  H15  H  HCH2   0   0.205   2.4187  5.4562   6.6084
 RZV  H16  H  HNH1   0   0.370   2.4200  7.5202   5.2063

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  1.509  0.020  1.509
 RZV  O2   C1   double  1.227  0.020  1.227
 RZV  C1   N4   single  1.346  0.020  1.346
 RZV  O13  C11  deloc   1.249  0.020  1.249
 RZV  N4   C5   single  1.455  0.020  1.455
 RZV  C11  C10  single  1.542  0.020  1.542
 RZV  C11  O12  deloc   1.247  0.020  1.247
 RZV  C10  C9   single  1.521  0.020  1.521
 RZV  C5   C9   single  1.525  0.020  1.525
 RZV  C5   P6   single  1.867  0.020  1.867
 RZV  O8   P6   deloc   1.520  0.020  1.520
 RZV  P6   O7   deloc   1.518  0.020  1.518
 RZV  P6   C14  single  1.840  0.020  1.840
 RZV  C14  C15  single  1.532  0.020  1.532
 RZV  O17  C16  deloc   1.250  0.020  1.250
 RZV  C15  C16  single  1.545  0.020  1.545
 RZV  C15  C19  single  1.532  0.020  1.532
 RZV  C16  O18  deloc   1.249  0.020  1.249
 RZV  C19  C20  single  1.521  0.020  1.521
 RZV  O23  C21  deloc   1.248  0.020  1.248
 RZV  C20  C21  single  1.543  0.020  1.543
 RZV  C21  O22  deloc   1.250  0.020  1.250
 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  0.890  0.020  1.040

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   108.12  3.000
 RZV  H1   C5   N4   108.50  3.000
 RZV  P6   C5   N4   106.50  3.000
 RZV  H1   C5   C9   108.53  3.000
 RZV  P6   C5   C9   114.83  3.000
 RZV  N4   C5   C9   110.19  3.000
 RZV  O2   C1   N4   121.44  3.000
 RZV  N4   C1   C3   116.90  3.000
 RZV  O2   C1   C3   121.64  3.000
 RZV  H3   C10  H2   104.80  3.000
 RZV  H3   C10  C9   109.28  3.000
 RZV  H2   C10  C9   110.01  3.000
 RZV  H3   C10  C11  108.07  3.000
 RZV  H2   C10  C11  107.97  3.000
 RZV  C9   C10  C11  116.10  3.000
 RZV  O13  C11  O12  126.64  3.000
 RZV  O12  C11  C10  117.85  3.000
 RZV  O13  C11  C10  115.51  3.000
 RZV  H5   C14  H4   106.35  3.000
 RZV  H5   C14  P6   110.29  3.000
 RZV  H4   C14  P6   107.41  3.000
 RZV  H5   C14  C15  109.36  3.000
 RZV  H4   C14  C15  109.27  3.000
 RZV  P6   C14  C15  113.86  3.000
 RZV  H6   C15  C19  107.64  3.000
 RZV  H6   C15  C16  108.41  3.000
 RZV  C19  C15  C16  110.81  3.000
 RZV  H6   C15  C14  108.14  3.000
 RZV  C19  C15  C14  110.32  3.000
 RZV  C16  C15  C14  111.38  3.000
 RZV  O18  C16  O17  126.13  3.000
 RZV  O18  C16  C15  117.50  3.000
 RZV  O17  C16  C15  116.36  3.000
 RZV  H8   C19  H7   105.88  3.000
 RZV  H8   C19  C20  110.26  3.000
 RZV  H7   C19  C20  109.25  3.000
 RZV  H8   C19  C15  109.12  3.000
 RZV  H7   C19  C15  108.50  3.000
 RZV  C20  C19  C15  113.54  3.000
 RZV  H10  C20  H9   104.68  3.000
 RZV  H10  C20  C21  108.26  3.000
 RZV  H9   C20  C21  107.08  3.000
 RZV  H10  C20  C19  109.49  3.000
 RZV  H9   C20  C19  109.78  3.000
 RZV  C21  C20  C19  116.84  3.000
 RZV  O23  C21  O22  126.30  3.000
 RZV  O22  C21  C20  115.58  3.000
 RZV  O23  C21  C20  118.11  3.000
 RZV  H13  C3   H12  107.53  3.000
 RZV  H13  C3   H11  108.99  3.000
 RZV  H12  C3   H11  108.74  3.000
 RZV  H13  C3   C1   110.27  3.000
 RZV  H12  C3   C1   111.63  3.000
 RZV  H11  C3   C1   109.61  3.000
 RZV  H15  C9   H14  105.77  3.000
 RZV  H15  C9   C10  110.44  3.000
 RZV  H14  C9   C10  109.35  3.000
 RZV  H15  C9   C5   109.06  3.000
 RZV  H14  C9   C5   108.65  3.000
 RZV  C10  C9   C5   113.28  3.000
 RZV  H16  N4   C1   114.63  3.000
 RZV  H16  N4   C5   114.72  3.000
 RZV  C1   N4   C5   127.68  3.000
 RZV  O8   P6   O7   118.81  3.000
 RZV  O7   P6   C14  111.23  3.000
 RZV  O8   P6   C14  108.68  3.000
 RZV  C14  P6   C5   103.23  3.000
 RZV  O7   P6   C5   107.08  3.000
 RZV  O8   P6   C5   106.56  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_02  O2   C1   N4   C5    180.00   0.0  0
 RZV  CONST_03  H16  N4   C1   C3    180.00   0.0  0
 RZV  Var_01    C11  C10  C9   C5    178.79  30.0  1
 RZV  Var_02    C15  C14  P6   C5   -167.06  30.0  3
 RZV  Var_03    C21  C20  C19  C15   175.43  30.0  3
 RZV  Var_04    O23  C21  C20  C19    11.95  30.0  3
 RZV  Var_05    O13  C11  C10  C9   -179.14  30.0  2
 RZV  Var_06    H11  C3   C1   N4   -174.27  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

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-3  C15  0.020
 RZV  plan-3  C16  0.020
 RZV  plan-3  O17  0.020
 RZV  plan-3  O18  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

