# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:31:52 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: [(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(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
 VDW  VDW  '[(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium'  ligand  36  20  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VDW
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
 VDW  N1    N  NT3    1  -0.807  20.8092   5.1689  -13.3934
 VDW  CA1   C  CH1    0  -0.248  19.6714   5.0033  -12.4387
 VDW  C1    C  C      0   0.455  18.9013   3.7248  -12.8775
 VDW  O11   O  O      0  -0.561  17.8749   3.4725  -12.2406
 VDW  O12   O  OC    -1  -0.585  19.4232   3.0883  -13.8172
 VDW  CB1   C  CH2    0  -0.441  18.8096   6.2532  -12.3357
 VDW  CG1   C  CH2    0  -0.604  18.0142   6.5629  -13.5956
 VDW  CD1   C  C      0   0.576  17.2698   7.8809  -13.5170
 VDW  OE1   O  O      0  -0.482  17.5503   8.7631  -12.7214
 VDW  N2    N  NH1    0  -0.640  16.2914   8.0245  -14.4299
 VDW  CA2   C  CH1    0  -0.174  15.5236   9.2376  -14.5415
 VDW  C2    C  C      0   0.533  14.6132   9.4270  -13.3229
 VDW  O2    O  O      0  -0.488  14.0118   8.4804  -12.8399
 VDW  CB2   C  CH2    0  -0.582  14.6746   9.1425  -15.8092
 VDW  SG2   S  S2     0  -0.236  13.6971  10.6641  -16.0422
 VDW  N3    N  NH1    0  -0.600  14.4723  10.6942  -12.9250
 VDW  CA3   C  CH2    0  -0.438  13.6258  11.0883  -11.8278
 VDW  C3    C  C      0   0.400  14.2498  10.9472  -10.4169
 VDW  O31   O  O      0  -0.593  15.4091  10.5117  -10.3336
 VDW  O32   O  OC    -1  -0.614  13.4935  11.3072   -9.4944
 VDW  HN13  H  HNT3   0   0.462  21.7126   5.2630  -12.9339
 VDW  HN11  H  HNT3   0   0.449  20.7849   4.2966  -13.9585
 VDW  HN12  H  HNT3   0   0.459  20.7104   5.9618  -14.0259
 VDW  HA1   H  HCH1   0   0.310  20.1185   4.8109  -11.4621
 VDW  HB13  H  HCH2   0   0.258  19.4410   7.1010  -12.0645
 VDW  HB12  H  HCH2   0   0.264  18.1270   6.1003  -11.5002
 VDW  HG13  H  HCH2   0   0.273  17.3049   5.7587  -13.8039
 VDW  HG12  H  HCH2   0   0.275  18.6612   6.6248  -14.4779
 VDW  HN2   H  HNH1   0   0.408  16.0475   7.2414  -15.0163
 VDW  HA2   H  HCH1   0   0.278  16.2038  10.0888  -14.6439
 VDW  HB23  H  HCH2   0   0.280  14.0103   8.2795  -15.7473
 VDW  HB22  H  HCH2   0   0.299  15.3331   9.0135  -16.6675
 VDW  HSG   H  HSH1   0   0.229  13.4385  10.4712  -17.3401
 VDW  HN3   H  HNH1   0   0.395  15.1022  11.3853  -13.2982
 VDW  HA31  H  HCH2   0   0.249  13.3435  12.1312  -11.9842
 VDW  HA32  H  HCH2   0   0.242  12.6993  10.5128  -11.8649

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
 VDW  SG2  CB2   single  1.824  0.020  1.824
 VDW  CB2  CA2   single  1.529  0.020  1.529
 VDW  CA2  N2    single  1.440  0.020  1.440
 VDW  CA2  C2    single  1.533  0.020  1.533
 VDW  N2   CD1   single  1.346  0.020  1.346
 VDW  O11  C1    deloc   1.234  0.020  1.234
 VDW  CG1  CD1   single  1.516  0.020  1.516
 VDW  CG1  CB1   single  1.522  0.020  1.522
 VDW  O12  C1    deloc   1.249  0.020  1.249
 VDW  CD1  OE1   double  1.221  0.020  1.221
 VDW  C1   CA1   single  1.556  0.020  1.556
 VDW  N1   CA1   single  1.495  0.020  1.495
 VDW  C2   N3    single  1.336  0.020  1.336
 VDW  C2   O2    double  1.221  0.020  1.221
 VDW  N3   CA3   single  1.441  0.020  1.441
 VDW  CA1  CB1   single  1.522  0.020  1.522
 VDW  CA3  C3    single  1.549  0.020  1.549
 VDW  C3   O31   deloc   1.241  0.020  1.241
 VDW  C3   O32   deloc   1.246  0.020  1.246
 VDW  N1   HN13  single  0.890  0.020  1.040
 VDW  N1   HN11  single  0.890  0.020  1.040
 VDW  N1   HN12  single  0.890  0.020  1.040
 VDW  CA1  HA1   single  0.970  0.020  1.090
 VDW  CB1  HB13  single  0.970  0.020  1.090
 VDW  CB1  HB12  single  0.970  0.020  1.090
 VDW  CG1  HG13  single  0.970  0.020  1.090
 VDW  CG1  HG12  single  0.970  0.020  1.090
 VDW  N2   HN2   single  0.860  0.020  1.020
 VDW  CA2  HA2   single  0.970  0.020  1.090
 VDW  CB2  HB23  single  0.970  0.020  1.090
 VDW  CB2  HB22  single  0.970  0.020  1.090
 VDW  SG2  HSG   single  1.200  0.020  1.300
 VDW  N3   HN3   single  0.860  0.020  1.020
 VDW  CA3  HA31  single  0.970  0.020  1.090
 VDW  CA3  HA32  single  0.970  0.020  1.090

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
 VDW  HN12  N1   HN11  108.25  3.000
 VDW  HN12  N1   HN13  107.12  3.000
 VDW  HN11  N1   HN13  110.11  3.000
 VDW  HN12  N1   CA1   114.13  3.000
 VDW  HN11  N1   CA1   103.68  3.000
 VDW  HN13  N1   CA1   113.42  3.000
 VDW  HA1   CA1  CB1   108.44  3.000
 VDW  HA1   CA1  C1    108.09  3.000
 VDW  CB1   CA1  C1    114.44  3.000
 VDW  HA1   CA1  N1    106.22  3.000
 VDW  CB1   CA1  N1    112.54  3.000
 VDW  C1    CA1  N1    106.72  3.000
 VDW  O12   C1   O11   129.16  3.000
 VDW  O12   C1   CA1   115.10  3.000
 VDW  O11   C1   CA1   115.73  3.000
 VDW  HB12  CB1  HB13  106.32  3.000
 VDW  HB12  CB1  CG1   109.63  3.000
 VDW  HB13  CB1  CG1   110.49  3.000
 VDW  HB12  CB1  CA1   106.94  3.000
 VDW  HB13  CB1  CA1   109.10  3.000
 VDW  CG1   CB1  CA1   114.02  3.000
 VDW  HG12  CG1  HG13  105.75  3.000
 VDW  HG12  CG1  CD1   106.42  3.000
 VDW  HG13  CG1  CD1   109.34  3.000
 VDW  HG12  CG1  CB1   111.68  3.000
 VDW  HG13  CG1  CB1   110.33  3.000
 VDW  CD1   CG1  CB1   113.00  3.000
 VDW  N2    CD1  OE1   122.15  3.000
 VDW  OE1   CD1  CG1   123.32  3.000
 VDW  N2    CD1  CG1   114.50  3.000
 VDW  HN2   N2   CA2   118.70  3.000
 VDW  HN2   N2   CD1   119.17  3.000
 VDW  CA2   N2   CD1   122.01  3.000
 VDW  HA2   CA2  CB2   108.42  3.000
 VDW  HA2   CA2  C2    110.33  3.000
 VDW  CB2   CA2  C2    109.70  3.000
 VDW  HA2   CA2  N2    109.34  3.000
 VDW  C2    CA2  N2    111.05  3.000
 VDW  CB2   CA2  N2    107.94  3.000
 VDW  N3    C2   O2    124.45  3.000
 VDW  O2    C2   CA2   120.74  3.000
 VDW  N3    C2   CA2   114.63  3.000
 VDW  HB22  CB2  HB23  108.61  3.000
 VDW  HB22  CB2  SG2   108.79  3.000
 VDW  HB23  CB2  SG2   109.93  3.000
 VDW  HB22  CB2  CA2   108.96  3.000
 VDW  HB23  CB2  CA2   109.90  3.000
 VDW  SG2   CB2  CA2   110.60  3.000
 VDW  HSG   SG2  CB2    96.16  3.000
 VDW  HN3   N3   CA3   117.52  3.000
 VDW  HN3   N3   C2    118.35  3.000
 VDW  CA3   N3   C2    123.26  3.000
 VDW  HA32  CA3  HA31  106.23  3.000
 VDW  HA32  CA3  C3    108.96  3.000
 VDW  HA31  CA3  C3    108.76  3.000
 VDW  HA32  CA3  N3    109.19  3.000
 VDW  HA31  CA3  N3    107.71  3.000
 VDW  C3    CA3  N3    115.60  3.000
 VDW  O32   C3   O31   128.21  3.000
 VDW  O32   C3   CA3   113.80  3.000
 VDW  O31   C3   CA3   117.99  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
 VDW  CONST_01  CA2  N2   CD1  CG1   180.00   0.0  0
 VDW  CONST_02  CA2  N2   CD1  OE1     0.00   0.0  0
 VDW  CONST_03  CA3  N3   C2   CA2   180.00   0.0  0
 VDW  CONST_04  CA3  N3   C2   O2      0.00   0.0  0
 VDW  CONST_05  HN2  N2   CD1  CG1     0.00   0.0  0
 VDW  CONST_06  HN3  N3   C2   CA2     0.00   0.0  0
 VDW  Var_01    CD1  CG1  CB1  CA1  -174.44  30.0  1
 VDW  Var_02    N2   CD1  CG1  CB1  -163.05  30.0  3
 VDW  Var_03    C3   CA3  N3   C2     82.80  30.0  3
 VDW  Var_04    O31  C3   CA3  N3     -0.12  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
 VDW  chir_01  CA1  C1  N1   CB1  negativ
 VDW  chir_02  CA2  N2  CB2  C2   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
 VDW  plan-1  CG1  0.020
 VDW  plan-1  CD1  0.020
 VDW  plan-1  OE1  0.020
 VDW  plan-1  N2   0.020
 VDW  plan-1  CA2  0.020
 VDW  plan-1  HN2  0.020
 VDW  plan-2  CA2  0.020
 VDW  plan-2  C2   0.020
 VDW  plan-2  O2   0.020
 VDW  plan-2  N3   0.020
 VDW  plan-2  CA3  0.020
 VDW  plan-2  HN3  0.020
 VDW  plan-3  CA1  0.020
 VDW  plan-3  C1   0.020
 VDW  plan-3  O11  0.020
 VDW  plan-3  O12  0.020
 VDW  plan-4  CA3  0.020
 VDW  plan-4  C3   0.020
 VDW  plan-4  O31  0.020
 VDW  plan-4  O32  0.020

