# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:47:37 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (2S)-3-[bis(oxidanylidene)-$l^{5}-sulfanyl]-2-[[2-(hydroxymethyl)-3-oxidanyl-propyl]amino]-3-methyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)([C@@H](NCC(CO)CO)C(O)=O)[S](=O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 3GE  3GE  '(2S)-3-[bis(oxidanylidene)-$l^{5}-sulfanyl]-2-[[2-(hydroxymethyl)-3-oxidanyl-propyl]amino]-3-methyl-butanoic acid'  ligand  34  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3GE
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
 3GE  OAC  O  OH1    0  -0.675   9.7941  33.9095  5.5376
 3GE  CAI  C  CH2    0  -0.137   8.4890  33.6897  5.0454
 3GE  CAN  C  CH1    0  -0.312   8.0811  34.8605  4.1622
 3GE  CAK  C  CH2    0  -0.188   6.7398  34.5880  3.4971
 3GE  OAG  O  OH1    0  -0.673   5.7148  34.5936  4.4688
 3GE  CAJ  C  CH2    0  -0.251   8.1044  36.1736  4.9500
 3GE  N    N  NH1    0  -0.620   7.5593  37.2783  4.1849
 3GE  CA   C  CH1    0  -0.083   7.7689  38.5625  4.8137
 3GE  C    C  C      0   0.403   9.2991  38.9345  4.8289
 3GE  O    O  O      0  -0.576   9.9425  38.6980  3.7958
 3GE  OXT  O  OC    -1  -0.589   9.7111  39.4382  5.8876
 3GE  CB   C  CT     0  -0.332   7.0214  39.6834  4.0824
 3GE  CG1  C  CH3    0  -0.631   7.1222  39.6442  2.5713
 3GE  CG2  C  CH3    0  -0.645   7.3173  41.0696  4.6322
 3GE  SAP  S  S3     0   1.100   5.1427  39.4521  4.4729
 3GE  OAE  O  OS     0  -0.630   4.9609  39.5296  5.9340
 3GE  OAF  O  OS     0  -0.627   4.6475  38.2404  3.7851
 3GE  H1   H  HCH2   0   0.194   7.7680  33.5839  5.8658
 3GE  H2   H  HCH1   0   0.233   8.8057  34.9391  3.3428
 3GE  H3   H  HCH2   0   0.209   6.5645  35.3488  2.7276
 3GE  H4   H  HCH2   0   0.210   6.7889  33.6237  2.9722
 3GE  H5   H  HOH1   0   0.454   4.8690  34.5573  4.0140
 3GE  H6   H  HCH2   0   0.234   9.1416  36.3981  5.2004
 3GE  H7   H  HCH1   0   0.213   7.4465  38.5756  5.8660
 3GE  H9   H  HCH3   0   0.265   8.1629  39.8181  2.3006
 3GE  H10  H  HCH3   0   0.253   6.8328  38.6842  2.1513
 3GE  H11  H  HCH3   0   0.241   6.5185  40.4296  2.1156
 3GE  H12  H  HCH3   0   0.257   7.2603  41.1123  5.7179
 3GE  H13  H  HCH3   0   0.266   8.3243  41.3626  4.3372
 3GE  H14  H  HCH3   0   0.250   6.6356  41.8103  4.2132
 3GE  H17  H  HOH1   0   0.453  10.0024  33.2038  6.1559
 3GE  H18  H  HCH2   0   0.197   8.4403  32.7641  4.4554
 3GE  H19  H  HCH2   0   0.188   7.5830  36.0338  5.9106
 3GE  H20  H  HNH1   0   0.347   6.5662  37.1180  4.0689

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
 3GE  OAF  SAP  double  1.479  0.020  1.479
 3GE  O    C    deloc   1.240  0.020  1.240
 3GE  CG1  CB   single  1.515  0.020  1.515
 3GE  C    OXT  deloc   1.243  0.020  1.243
 3GE  C    CA   single  1.575  0.020  1.575
 3GE  SAP  CB   single  1.933  0.020  1.933
 3GE  SAP  OAE  double  1.474  0.020  1.474
 3GE  CAK  CAN  single  1.522  0.020  1.522
 3GE  CAK  OAG  single  1.412  0.020  1.412
 3GE  CB   CA   single  1.533  0.020  1.533
 3GE  CB   CG2  single  1.520  0.020  1.520
 3GE  N    CA   single  1.445  0.020  1.445
 3GE  N    CAJ  single  1.450  0.020  1.450
 3GE  CAN  CAJ  single  1.531  0.020  1.531
 3GE  CAN  CAI  single  1.522  0.020  1.522
 3GE  CAI  OAC  single  1.412  0.020  1.412
 3GE  CAI  H1   single  0.970  0.020  1.090
 3GE  CAN  H2   single  0.970  0.020  1.090
 3GE  CAK  H3   single  0.970  0.020  1.090
 3GE  CAK  H4   single  0.970  0.020  1.090
 3GE  OAG  H5   single  0.850  0.020  0.980
 3GE  CAJ  H6   single  0.970  0.020  1.090
 3GE  CA   H7   single  0.970  0.020  1.090
 3GE  CG1  H9   single  0.970  0.020  1.090
 3GE  CG1  H10  single  0.970  0.020  1.090
 3GE  CG1  H11  single  0.970  0.020  1.090
 3GE  CG2  H12  single  0.970  0.020  1.090
 3GE  CG2  H13  single  0.970  0.020  1.090
 3GE  CG2  H14  single  0.970  0.020  1.090
 3GE  OAC  H17  single  0.850  0.020  0.980
 3GE  CAI  H18  single  0.970  0.020  1.090
 3GE  CAJ  H19  single  0.970  0.020  1.090
 3GE  N    H20  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
 3GE  H17  OAC  CAI  108.07  3.000
 3GE  H18  CAI  H1   106.93  3.000
 3GE  H18  CAI  CAN  108.93  3.000
 3GE  H1   CAI  CAN  109.38  3.000
 3GE  H18  CAI  OAC  111.05  3.000
 3GE  H1   CAI  OAC  111.21  3.000
 3GE  CAN  CAI  OAC  109.28  3.000
 3GE  H2   CAN  CAJ  108.24  3.000
 3GE  H2   CAN  CAK  105.59  3.000
 3GE  CAJ  CAN  CAK  113.07  3.000
 3GE  H2   CAN  CAI  108.15  3.000
 3GE  CAJ  CAN  CAI  110.91  3.000
 3GE  CAK  CAN  CAI  110.61  3.000
 3GE  H4   CAK  H3   106.31  3.000
 3GE  H4   CAK  OAG  111.38  3.000
 3GE  H3   CAK  OAG  111.36  3.000
 3GE  H4   CAK  CAN  109.06  3.000
 3GE  H3   CAK  CAN  108.87  3.000
 3GE  OAG  CAK  CAN  109.77  3.000
 3GE  H5   OAG  CAK  108.24  3.000
 3GE  H19  CAJ  H6   106.02  3.000
 3GE  H19  CAJ  N    112.25  3.000
 3GE  H6   CAJ  N    108.78  3.000
 3GE  H19  CAJ  CAN  109.42  3.000
 3GE  H6   CAJ  CAN  108.01  3.000
 3GE  N    CAJ  CAN  112.09  3.000
 3GE  H20  N    CA   109.44  3.000
 3GE  H20  N    CAJ  107.97  3.000
 3GE  CA   N    CAJ  113.13  3.000
 3GE  H7   CA   CB   107.73  3.000
 3GE  H7   CA   C    105.82  3.000
 3GE  CB   CA   C    107.80  3.000
 3GE  H7   CA   N    112.59  3.000
 3GE  CB   CA   N    111.81  3.000
 3GE  C    CA   N    110.80  3.000
 3GE  OXT  C    O    127.97  3.000
 3GE  OXT  C    CA   115.22  3.000
 3GE  O    C    CA   116.82  3.000
 3GE  SAP  CB   CG2  103.02  3.000
 3GE  CG2  CB   CG1  111.80  3.000
 3GE  SAP  CB   CG1  105.25  3.000
 3GE  CG2  CB   CA   113.53  3.000
 3GE  SAP  CB   CA   106.86  3.000
 3GE  CG1  CB   CA   115.11  3.000
 3GE  H11  CG1  H10  109.10  3.000
 3GE  H11  CG1  H9   108.06  3.000
 3GE  H10  CG1  H9   107.42  3.000
 3GE  H11  CG1  CB   111.19  3.000
 3GE  H10  CG1  CB   112.99  3.000
 3GE  H9   CG1  CB   107.90  3.000
 3GE  H14  CG2  H13  106.93  3.000
 3GE  H14  CG2  H12  108.90  3.000
 3GE  H13  CG2  H12  107.94  3.000
 3GE  H14  CG2  CB   111.02  3.000
 3GE  H13  CG2  CB   109.10  3.000
 3GE  H12  CG2  CB   112.73  3.000
 3GE  OAF  SAP  OAE  117.56  3.000
 3GE  OAE  SAP  CB   108.29  3.000
 3GE  OAF  SAP  CB   109.24  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
 3GE  Var_01  CAK  CAN  CAI  OAC   174.00  30.0  2
 3GE  Var_02  OAG  CAK  CAN  CAI    68.65  30.0  2
 3GE  Var_03  N    CAJ  CAN  CAI  -172.69  30.0  3
 3GE  Var_04  CA   N    CAJ  CAN  -170.41  30.0  2
 3GE  Var_05  OAF  SAP  CB   CA    -69.96  30.0  2
 3GE  Var_06  H9   CG1  CB   CA    -65.23  30.0  3
 3GE  Var_07  H12  CG2  CB   CA    -47.06  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
 3GE  chir_01  CA  C  CB  N  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
 3GE  plan-1  CA   0.020
 3GE  plan-1  C    0.020
 3GE  plan-1  O    0.020
 3GE  plan-1  OXT  0.020
 3GE  plan-2  CB   0.020
 3GE  plan-2  SAP  0.020
 3GE  plan-2  OAE  0.020
 3GE  plan-2  OAF  0.020

