# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 00:40:08 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(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
 6VG  6VG  '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate'  ligand  50  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6VG
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
 6VG  P24  P  P     0   1.455  -5.6029   2.0594  -0.4720
 6VG  O26  O  OH1   0  -0.744  -4.3811   2.7422  -1.2460
 6VG  O23  O  O     0  -0.712  -6.5979   1.5846  -1.4513
 6VG  O27  O  O2    0  -0.588  -4.9824   0.9674   0.5084
 6VG  C28  C  CH2   0  -0.152  -4.3941  -0.2175  -0.0461
 6VG  C29  C  CT    0  -0.163  -3.7888  -1.0408   1.0901
 6VG  C30  C  CH3   0  -0.670  -2.7270  -0.2275   1.8339
 6VG  C31  C  CH3   0  -0.649  -4.8780  -1.4638   2.0799
 6VG  C32  C  CH1   0  -0.036  -3.1593  -2.3379   0.5049
 6VG  O33  O  OH1   0  -0.662  -4.0974  -3.1327  -0.1675
 6VG  C34  C  C     0   0.514  -1.9866  -2.0657  -0.4395
 6VG  O35  O  O     0  -0.498  -2.1956  -1.9215  -1.6395
 6VG  N36  N  NH1   0  -0.631  -0.7775  -2.0049   0.1215
 6VG  C37  C  CH2   0  -0.250   0.4457  -1.7141  -0.5973
 6VG  C38  C  CH2   0  -0.618   1.3313  -0.7986   0.2334
 6VG  C39  C  C     0   0.569   2.6555  -0.5106  -0.4422
 6VG  O40  O  O     0  -0.494   3.1281  -1.2416  -1.3001
 6VG  N41  N  NH1   0  -0.633   3.2731   0.6036  -0.0115
 6VG  C42  C  CH2   0  -0.290   4.5852   1.0038  -0.4578
 6VG  C43  C  CH2   0  -0.560   5.6834   0.2715   0.3093
 6VG  S1   S  S2    0  -0.009   7.2939   0.8636  -0.2794
 6VG  C1   C  C     0   0.261   8.4060  -0.1044   0.6985
 6VG  O1   O  O     0  -0.386   8.0277  -0.8916   1.5274
 6VG  C2   C  CH3   0  -0.751   9.8463   0.1400   0.3522
 6VG  O2   O  OH1   0  -0.732  -6.0936   3.0739   0.6552
 6VG  H1   H  HOH1  0   0.495  -3.7042   3.1526  -0.6916
 6VG  H2   H  HCH2  0   0.245  -5.1651  -0.7908  -0.5675
 6VG  H3   H  HCH2  0   0.246  -3.6250   0.0620  -0.7707
 6VG  H4   H  HCH3  0   0.248  -3.1909   0.5736   2.4082
 6VG  H5   H  HCH3  0   0.233  -2.1835  -0.8549   2.5443
 6VG  H6   H  HCH3  0   0.236  -1.9972   0.2284   1.1635
 6VG  H7   H  HCH3  0   0.240  -5.3456  -0.5955   2.5431
 6VG  H8   H  HCH3  0   0.237  -5.6584  -2.0531   1.5986
 6VG  H9   H  HCH3  0   0.232  -4.4477  -2.0698   2.8803
 6VG  H10  H  HCH1  0   0.257  -2.8009  -2.9167   1.3644
 6VG  H11  H  HOH1  0   0.446  -4.0639  -2.8976  -1.1039
 6VG  H12  H  HNH1  0   0.404  -0.6956  -2.2203   1.1032
 6VG  H13  H  HCH2  0   0.252   0.9695  -2.6419  -0.8331
 6VG  H14  H  HCH2  0   0.258   0.1845  -1.2377  -1.5403
 6VG  H15  H  HCH2  0   0.274   0.8076   0.1344   0.4549
 6VG  H16  H  HCH2  0   0.286   1.5499  -1.2659   1.2000
 6VG  H17  H  HNH1  0   0.407   2.8429   1.1457   0.7202
 6VG  H18  H  HCH2  0   0.259   4.6775   0.8158  -1.5276
 6VG  H19  H  HCH2  0   0.270   4.6718   2.0796  -0.3082
 6VG  H20  H  HCH2  0   0.285   5.5976   0.4687   1.3775
 6VG  H21  H  HCH2  0   0.287   5.6147  -0.8026   0.1426
 6VG  H22  H  HCH3  0   0.286  10.1271  -0.5230  -0.4687
 6VG  H23  H  HCH3  0   0.265  10.0254   1.1634   0.0271
 6VG  H24  H  HCH3  0   0.276  10.4818  -0.0876   1.2058
 6VG  H25  H  HOH1  0   0.504  -6.6244   3.8075   0.3168

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
 6VG  C2   C1   single  1.501  0.020  1.501
 6VG  C1   O1   double  1.204  0.020  1.204
 6VG  C1   S1   single  1.769  0.020  1.769
 6VG  S1   C43  single  1.814  0.020  1.814
 6VG  C43  C42  single  1.527  0.020  1.527
 6VG  O40  C39  double  1.222  0.020  1.222
 6VG  C42  N41  single  1.443  0.020  1.443
 6VG  C39  N41  single  1.345  0.020  1.345
 6VG  C39  C38  single  1.514  0.020  1.514
 6VG  C38  C37  single  1.521  0.020  1.521
 6VG  C37  N36  single  1.448  0.020  1.448
 6VG  N36  C34  single  1.334  0.020  1.334
 6VG  O33  C32  single  1.401  0.020  1.401
 6VG  C34  C32  single  1.530  0.020  1.530
 6VG  C34  O35  double  1.227  0.020  1.227
 6VG  C32  C29  single  1.556  0.020  1.556
 6VG  C31  C29  single  1.531  0.020  1.531
 6VG  C29  C30  single  1.530  0.020  1.530
 6VG  C29  C28  single  1.528  0.020  1.528
 6VG  C28  O27  single  1.434  0.020  1.434
 6VG  O27  P24  single  1.593  0.020  1.593
 6VG  O23  P24  double  1.475  0.020  1.475
 6VG  P24  O26  single  1.599  0.020  1.599
 6VG  P24  O2   single  1.594  0.020  1.594
 6VG  O26  H1   single  0.850  0.020  0.980
 6VG  C28  H2   single  0.970  0.020  1.090
 6VG  C28  H3   single  0.970  0.020  1.090
 6VG  C30  H4   single  0.970  0.020  1.090
 6VG  C30  H5   single  0.970  0.020  1.090
 6VG  C30  H6   single  0.970  0.020  1.090
 6VG  C31  H7   single  0.970  0.020  1.090
 6VG  C31  H8   single  0.970  0.020  1.090
 6VG  C31  H9   single  0.970  0.020  1.090
 6VG  C32  H10  single  0.970  0.020  1.090
 6VG  O33  H11  single  0.850  0.020  0.980
 6VG  N36  H12  single  0.860  0.020  1.020
 6VG  C37  H13  single  0.970  0.020  1.090
 6VG  C37  H14  single  0.970  0.020  1.090
 6VG  C38  H15  single  0.970  0.020  1.090
 6VG  C38  H16  single  0.970  0.020  1.090
 6VG  N41  H17  single  0.860  0.020  1.020
 6VG  C42  H18  single  0.970  0.020  1.090
 6VG  C42  H19  single  0.970  0.020  1.090
 6VG  C43  H20  single  0.970  0.020  1.090
 6VG  C43  H21  single  0.970  0.020  1.090
 6VG  C2   H22  single  0.970  0.020  1.090
 6VG  C2   H23  single  0.970  0.020  1.090
 6VG  C2   H24  single  0.970  0.020  1.090
 6VG  O2   H25  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
 6VG  O2   P24  O27   96.95  3.000
 6VG  O2   P24  O23  117.83  3.000
 6VG  O27  P24  O23  116.79  3.000
 6VG  O2   P24  O26  107.80  3.000
 6VG  O23  P24  O26  109.36  3.000
 6VG  O27  P24  O26  107.03  3.000
 6VG  H1   O26  P24  116.02  3.000
 6VG  C28  O27  P24  119.21  3.000
 6VG  H3   C28  H2   108.31  3.000
 6VG  H3   C28  C29  110.61  3.000
 6VG  H2   C28  C29  110.58  3.000
 6VG  H3   C28  O27  109.49  3.000
 6VG  H2   C28  O27  109.17  3.000
 6VG  C29  C28  O27  108.67  3.000
 6VG  C32  C29  C31  107.49  3.000
 6VG  C31  C29  C30  109.04  3.000
 6VG  C32  C29  C30  110.19  3.000
 6VG  C30  C29  C28  110.48  3.000
 6VG  C31  C29  C28  110.35  3.000
 6VG  C32  C29  C28  109.25  3.000
 6VG  H6   C30  H5   107.86  3.000
 6VG  H6   C30  H4   107.55  3.000
 6VG  H5   C30  H4   106.93  3.000
 6VG  H6   C30  C29  112.81  3.000
 6VG  H5   C30  C29  110.86  3.000
 6VG  H4   C30  C29  110.58  3.000
 6VG  H9   C31  H8   107.80  3.000
 6VG  H9   C31  H7   107.44  3.000
 6VG  H8   C31  H7   108.14  3.000
 6VG  H9   C31  C29  110.29  3.000
 6VG  H8   C31  C29  111.91  3.000
 6VG  H7   C31  C29  111.09  3.000
 6VG  H10  C32  C34  109.10  3.000
 6VG  H10  C32  O33  107.19  3.000
 6VG  C34  C32  O33  108.53  3.000
 6VG  H10  C32  C29  106.11  3.000
 6VG  C34  C32  C29  113.20  3.000
 6VG  O33  C32  C29  112.48  3.000
 6VG  H11  O33  C32  107.69  3.000
 6VG  N36  C34  O35  124.09  3.000
 6VG  O35  C34  C32  119.61  3.000
 6VG  N36  C34  C32  116.30  3.000
 6VG  H12  N36  C37  117.23  3.000
 6VG  H12  N36  C34  118.24  3.000
 6VG  C37  N36  C34  124.46  3.000
 6VG  H14  C37  H13  107.46  3.000
 6VG  H14  C37  C38  110.46  3.000
 6VG  H13  C37  C38  110.51  3.000
 6VG  H14  C37  N36  108.37  3.000
 6VG  H13  C37  N36  109.99  3.000
 6VG  C38  C37  N36  109.98  3.000
 6VG  H16  C38  H15  106.32  3.000
 6VG  H16  C38  C39  107.47  3.000
 6VG  H15  C38  C39  110.32  3.000
 6VG  H16  C38  C37  109.96  3.000
 6VG  H15  C38  C37  110.22  3.000
 6VG  C39  C38  C37  112.34  3.000
 6VG  N41  C39  O40  122.87  3.000
 6VG  N41  C39  C38  114.60  3.000
 6VG  O40  C39  C38  122.52  3.000
 6VG  H17  N41  C42  117.64  3.000
 6VG  H17  N41  C39  118.85  3.000
 6VG  C42  N41  C39  123.27  3.000
 6VG  H19  C42  H18  107.36  3.000
 6VG  H19  C42  C43  110.33  3.000
 6VG  H18  C42  C43  110.46  3.000
 6VG  H19  C42  N41  107.68  3.000
 6VG  H18  C42  N41  109.43  3.000
 6VG  C43  C42  N41  111.45  3.000
 6VG  H21  C43  H20  108.88  3.000
 6VG  H21  C43  S1   109.16  3.000
 6VG  H20  C43  S1   109.21  3.000
 6VG  H21  C43  C42  110.53  3.000
 6VG  H20  C43  C42  110.44  3.000
 6VG  S1   C43  C42  108.60  3.000
 6VG  C1   S1   C43  101.54  3.000
 6VG  C2   C1   O1   124.51  3.000
 6VG  O1   C1   S1   122.74  3.000
 6VG  C2   C1   S1   112.73  3.000
 6VG  H24  C2   H23  109.56  3.000
 6VG  H24  C2   H22  108.22  3.000
 6VG  H23  C2   H22  107.70  3.000
 6VG  H24  C2   C1   110.19  3.000
 6VG  H23  C2   C1   112.31  3.000
 6VG  H22  C2   C1   108.74  3.000
 6VG  H25  O2   P24  113.86  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
 6VG  CONST_01  C37  N36  C34  C32   180.00   0.0  0
 6VG  CONST_02  C37  N36  C34  O35     0.00   0.0  0
 6VG  CONST_03  C42  N41  C39  C38   180.00   0.0  0
 6VG  CONST_04  C42  N41  C39  O40     0.00   0.0  0
 6VG  CONST_05  H12  N36  C34  C32     0.00   0.0  0
 6VG  CONST_06  H17  N41  C39  C38     0.00   0.0  0
 6VG  Var_01    C29  C28  O27  P24   175.91  30.0  1
 6VG  Var_02    C32  C29  C28  O27   179.41  30.0  2
 6VG  Var_03    O2   P24  O27  C28   179.32  30.0  3
 6VG  Var_04    C38  C37  N36  C34   139.76  30.0  2
 6VG  Var_05    C39  C38  C37  N36   177.37  30.0  1
 6VG  Var_06    O40  C39  C38  C37   -22.09  30.0  2
 6VG  Var_07    C43  C42  N41  C39   -82.11  30.0  2
 6VG  Var_08    S1   C43  C42  N41  -178.48  30.0  1
 6VG  Var_09    C2   C1   S1   C43   176.89  30.0  1
 6VG  Var_10    H7   C31  C29  C28   -62.17  30.0  3
 6VG  Var_11    H4   C30  C29  C28    70.29  30.0  3
 6VG  Var_12    H22  C2   C1   S1    -86.99  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
 6VG  chir_01  C32  O33  C34  C29  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
 6VG  plan-1  C32  0.020
 6VG  plan-1  C34  0.020
 6VG  plan-1  O35  0.020
 6VG  plan-1  N36  0.020
 6VG  plan-1  C37  0.020
 6VG  plan-1  H12  0.020
 6VG  plan-2  C38  0.020
 6VG  plan-2  C39  0.020
 6VG  plan-2  O40  0.020
 6VG  plan-2  N41  0.020
 6VG  plan-2  C42  0.020
 6VG  plan-2  H17  0.020
 6VG  plan-3  S1   0.020
 6VG  plan-3  C1   0.020
 6VG  plan-3  O1   0.020
 6VG  plan-3  C2   0.020

