# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:27:00 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: (2~{S})-2-[[[(3~{R})-3-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](CC[P@@](=O)(C[C@@H](CCC(O)=O)C(O)=O)O[P](O)(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
 S3A  S3A  '(2~{S})-2-[[[(3~{R})-3-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 PERFECT
;

data_comp_S3A
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
 S3A  C1   C  CH1   0  -0.183  11.8553  -18.5778  13.1086
 S3A  C10  C  CH2   0  -0.697  12.1008  -18.9729  10.6229
 S3A  C14  C  CH2   0  -0.711  12.2845  -19.2904   7.7491
 S3A  C15  C  CH1   0  -0.346  12.9393  -19.9422   6.5206
 S3A  C16  C  C     0   0.546  12.9362  -18.9753   5.3585
 S3A  C19  C  CH2   0  -0.475  12.2283  -21.2501   6.1411
 S3A  C20  C  CH2   0  -0.534  12.8865  -21.9585   4.9576
 S3A  C21  C  C     0   0.490  12.2054  -23.2370   4.5550
 S3A  C3   C  C     0   0.522   9.6571  -17.6692  13.6241
 S3A  C5   C  CH3   0  -0.816   8.1729  -17.9104  13.5639
 S3A  C6   C  C     0   0.532  12.3376  -19.0175  14.4854
 S3A  C9   C  CH2   0  -0.465  12.4774  -19.4590  12.0198
 S3A  N2   N  NH1   0  -0.582  10.4229  -18.6135  13.0363
 S3A  O12  O  O2    0  -0.675  14.3870  -19.8953   9.4126
 S3A  O13  O  O     0  -0.691  12.4125  -21.4904   9.4999
 S3A  O17  O  O     0  -0.541  13.9071  -18.6820   4.7080
 S3A  O18  O  OH1   0  -0.441  11.7223  -18.4965   5.1081
 S3A  O22  O  OH1   0  -0.432  11.8655  -23.9905   5.5954
 S3A  O23  O  O     0  -0.618  11.9912  -23.5686   3.4134
 S3A  O25  O  O     0  -0.735  15.1290  -17.8150   8.0421
 S3A  O26  O  OH1   0  -0.656  16.8098  -19.4065   9.2514
 S3A  O27  O  OH1   0  -0.707  15.3253  -17.9876  10.6484
 S3A  O4   O  O     0  -0.491  10.1412  -16.6898  14.1701
 S3A  O7   O  O     0  -0.590  11.6476  -19.5519  15.3124
 S3A  O8   O  OH1   0  -0.422  13.6207  -18.7398  14.6549
 S3A  P11  P  P     0   1.201  12.7445  -20.0524   9.3242
 S3A  P24  P  P     0   1.418  15.4033  -18.6660   9.2136
 S3A  H1   H  HCH1  0   0.277  12.1891  -17.5477  12.9549
 S3A  H2   H  HCH2  0   0.298  12.4430  -17.9484  10.4575
 S3A  H3   H  HCH2  0   0.321  11.0156  -18.9602  10.4910
 S3A  H4   H  HCH2  0   0.311  12.5420  -18.2314   7.8246
 S3A  H5   H  HCH2  0   0.333  11.1944  -19.3412   7.6841
 S3A  H6   H  HCH1  0   0.270  13.9906  -20.1568   6.7226
 S3A  H7   H  HCH2  0   0.307  11.1783  -21.0448   5.9248
 S3A  H8   H  HCH2  0   0.266  12.2509  -21.9013   7.0126
 S3A  H9   H  HCH2  0   0.281  13.9209  -22.2071   5.2080
 S3A  H10  H  HCH2  0   0.277  12.9238  -21.3298   4.0684
 S3A  H11  H  HCH3  0   0.268   7.6665  -16.9980  13.2529
 S3A  H12  H  HCH3  0   0.245   7.8923  -18.7145  12.8866
 S3A  H13  H  HCH3  0   0.278   7.8095  -18.1621  14.5612
 S3A  H14  H  HCH2  0   0.267  12.1526  -20.4935  12.1595
 S3A  H15  H  HCH2  0   0.300  13.5600  -19.4466  12.1393
 S3A  H16  H  HNH1  0   0.413   9.9850  -19.4701  12.7351
 S3A  H17  H  HOH1  0   0.415  11.7512  -17.8947   4.3486
 S3A  H18  H  HOH1  0   0.504  11.4400  -24.8052   5.2872
 S3A  H19  H  HOH1  0   0.503  17.1605  -19.6531   8.3874
 S3A  H20  H  HOH1  0   0.495  15.5788  -17.0546  10.6662
 S3A  H21  H  HOH1  0   0.472  13.9199  -19.0545  15.5201

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
 S3A  O23  C21  double  1.208  0.020  1.208
 S3A  C21  C20  single  1.504  0.020  1.504
 S3A  C21  O22  single  1.329  0.020  1.329
 S3A  O17  C16  double  1.205  0.020  1.205
 S3A  C20  C19  single  1.528  0.020  1.528
 S3A  O18  C16  single  1.329  0.020  1.329
 S3A  C16  C15  single  1.512  0.020  1.512
 S3A  C19  C15  single  1.536  0.020  1.536
 S3A  C15  C14  single  1.537  0.020  1.537
 S3A  C14  P11  single  1.809  0.020  1.809
 S3A  O25  P24  double  1.474  0.020  1.474
 S3A  O26  P24  single  1.590  0.020  1.590
 S3A  P24  O12  single  1.607  0.020  1.607
 S3A  P24  O27  single  1.589  0.020  1.589
 S3A  P11  O12  single  1.652  0.020  1.652
 S3A  P11  O13  double  1.486  0.020  1.486
 S3A  P11  C10  single  1.807  0.020  1.807
 S3A  C10  C9   single  1.526  0.020  1.526
 S3A  C9   C1   single  1.533  0.020  1.533
 S3A  O4   C3   double  1.221  0.020  1.221
 S3A  C3   N2   single  1.350  0.020  1.350
 S3A  C3   C5   single  1.505  0.020  1.505
 S3A  C1   N2   single  1.435  0.020  1.435
 S3A  C1   C6   single  1.524  0.020  1.524
 S3A  C6   O7   double  1.202  0.020  1.202
 S3A  C6   O8   single  1.324  0.020  1.324
 S3A  C1   H1   single  0.970  0.020  1.090
 S3A  C10  H2   single  0.970  0.020  1.090
 S3A  C10  H3   single  0.970  0.020  1.090
 S3A  C14  H4   single  0.970  0.020  1.090
 S3A  C14  H5   single  0.970  0.020  1.090
 S3A  C15  H6   single  0.970  0.020  1.090
 S3A  C19  H7   single  0.970  0.020  1.090
 S3A  C19  H8   single  0.970  0.020  1.090
 S3A  C20  H9   single  0.970  0.020  1.090
 S3A  C20  H10  single  0.970  0.020  1.090
 S3A  C5   H11  single  0.970  0.020  1.090
 S3A  C5   H12  single  0.970  0.020  1.090
 S3A  C5   H13  single  0.970  0.020  1.090
 S3A  C9   H14  single  0.970  0.020  1.090
 S3A  C9   H15  single  0.970  0.020  1.090
 S3A  N2   H16  single  0.860  0.020  1.020
 S3A  O18  H17  single  0.850  0.020  0.980
 S3A  O22  H18  single  0.850  0.020  0.980
 S3A  O26  H19  single  0.850  0.020  0.980
 S3A  O27  H20  single  0.850  0.020  0.980
 S3A  O8   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
 S3A  H1   C1   N2   108.73  3.000
 S3A  H1   C1   C9   108.54  3.000
 S3A  N2   C1   C9   110.80  3.000
 S3A  H1   C1   C6   107.59  3.000
 S3A  N2   C1   C6   110.75  3.000
 S3A  C9   C1   C6   110.33  3.000
 S3A  H3   C10  H2   106.37  3.000
 S3A  H3   C10  P11  105.89  3.000
 S3A  H2   C10  P11  109.86  3.000
 S3A  H3   C10  C9   111.05  3.000
 S3A  H2   C10  C9   111.09  3.000
 S3A  P11  C10  C9   112.30  3.000
 S3A  H5   C14  H4   106.51  3.000
 S3A  H5   C14  P11  106.60  3.000
 S3A  H4   C14  P11  106.75  3.000
 S3A  H5   C14  C15  110.95  3.000
 S3A  H4   C14  C15  111.46  3.000
 S3A  P11  C14  C15  114.14  3.000
 S3A  H6   C15  C19  108.90  3.000
 S3A  H6   C15  C16  105.66  3.000
 S3A  C19  C15  C16  110.72  3.000
 S3A  H6   C15  C14  110.22  3.000
 S3A  C19  C15  C14  111.18  3.000
 S3A  C16  C15  C14  110.02  3.000
 S3A  O18  C16  O17  123.14  3.000
 S3A  O18  C16  C15  112.16  3.000
 S3A  O17  C16  C15  124.69  3.000
 S3A  H8   C19  H7   106.93  3.000
 S3A  H8   C19  C20  109.51  3.000
 S3A  H7   C19  C20  110.37  3.000
 S3A  H8   C19  C15  107.58  3.000
 S3A  H7   C19  C15  109.51  3.000
 S3A  C20  C19  C15  112.74  3.000
 S3A  H10  C20  H9   106.61  3.000
 S3A  H10  C20  C21  106.71  3.000
 S3A  H9   C20  C21  107.26  3.000
 S3A  H10  C20  C19  112.29  3.000
 S3A  H9   C20  C19  109.61  3.000
 S3A  C21  C20  C19  113.98  3.000
 S3A  O23  C21  O22  122.60  3.000
 S3A  O22  C21  C20  112.86  3.000
 S3A  O23  C21  C20  124.54  3.000
 S3A  O4   C3   N2   122.04  3.000
 S3A  N2   C3   C5   115.46  3.000
 S3A  O4   C3   C5   122.50  3.000
 S3A  H13  C5   H12  108.22  3.000
 S3A  H13  C5   H11  107.43  3.000
 S3A  H12  C5   H11  108.75  3.000
 S3A  H13  C5   C3   109.21  3.000
 S3A  H12  C5   C3   113.43  3.000
 S3A  H11  C5   C3   109.62  3.000
 S3A  O8   C6   O7   124.16  3.000
 S3A  O8   C6   C1   111.22  3.000
 S3A  O7   C6   C1   124.62  3.000
 S3A  H15  C9   H14  106.98  3.000
 S3A  H15  C9   C10  110.00  3.000
 S3A  H14  C9   C10  110.18  3.000
 S3A  H15  C9   C1   108.60  3.000
 S3A  H14  C9   C1   109.44  3.000
 S3A  C10  C9   C1   111.52  3.000
 S3A  H16  N2   C3   118.55  3.000
 S3A  H16  N2   C1   118.03  3.000
 S3A  C3   N2   C1   121.80  3.000
 S3A  P24  O12  P11  134.00  3.000
 S3A  H17  O18  C16  110.13  3.000
 S3A  H18  O22  C21  109.88  3.000
 S3A  H19  O26  P24  114.80  3.000
 S3A  H20  O27  P24  114.56  3.000
 S3A  H21  O8   C6   110.23  3.000
 S3A  O13  P11  O12  107.92  3.000
 S3A  O13  P11  C14  116.98  3.000
 S3A  O12  P11  C14  105.03  3.000
 S3A  O13  P11  C10  114.42  3.000
 S3A  O12  P11  C10  105.00  3.000
 S3A  C14  P11  C10  106.47  3.000
 S3A  O27  P24  O26  102.76  3.000
 S3A  O27  P24  O25  117.52  3.000
 S3A  O26  P24  O25  116.90  3.000
 S3A  O27  P24  O12  100.58  3.000
 S3A  O26  P24  O12  101.55  3.000
 S3A  O25  P24  O12  114.98  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
 S3A  CONST_01  O4   C3   N2   C1      0.00   0.0  0
 S3A  CONST_02  C5   C3   N2   C1    180.00   0.0  0
 S3A  CONST_03  H16  N2   C3   C5      0.00   0.0  0
 S3A  CONST_04  H21  O8   C6   C1    180.00   0.0  0
 S3A  CONST_05  H17  O18  C16  C15   180.00   0.0  0
 S3A  CONST_06  H18  O22  C21  C20   180.00   0.0  0
 S3A  Var_01    P11  C10  C9   C1   -176.70  30.0  1
 S3A  Var_02    C15  C14  P11  C10   170.60  30.0  1
 S3A  Var_03    C9   C10  P11  C14  -177.13  30.0  3
 S3A  Var_04    C21  C20  C19  C15  -179.51  30.0  1
 S3A  Var_05    O23  C21  C20  C19   137.21  30.0  2
 S3A  Var_06    H11  C5   C3   N2   -133.09  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
 S3A  chir_01  C1   C9   N2   C6   negativ
 S3A  chir_02  C15  C16  C19  C14  positiv
 S3A  chir_03  P11  O12  O13  C10  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
 S3A  plan-1  C1   0.020
 S3A  plan-1  C3   0.020
 S3A  plan-1  C5   0.020
 S3A  plan-1  N2   0.020
 S3A  plan-1  O4   0.020
 S3A  plan-1  H16  0.020
 S3A  plan-2  C15  0.020
 S3A  plan-2  C16  0.020
 S3A  plan-2  O17  0.020
 S3A  plan-2  O18  0.020
 S3A  plan-2  H17  0.020
 S3A  plan-3  C20  0.020
 S3A  plan-3  C21  0.020
 S3A  plan-3  O22  0.020
 S3A  plan-3  O23  0.020
 S3A  plan-3  H18  0.020
 S3A  plan-4  C1   0.020
 S3A  plan-4  C6   0.020
 S3A  plan-4  O7   0.020
 S3A  plan-4  O8   0.020
 S3A  plan-4  H21  0.020

