# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:44:45 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl 2,2-dimethylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C(=O)OCC(C)(C)[C@@H](O)C(=O)NCCC(=O)NCCS
#
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
 PN5  PN5  '(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl 2,2-dimethylpropanoate'  ligand  54  24  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PN5
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
 PN5  CP2   C  CH2   0  -0.554   6.8656  -1.5955   0.0432
 PN5  CP3   C  CH2   0  -0.281   6.1108  -0.9131  -1.0922
 PN5  NP4   N  NH1   0  -0.632   4.7336  -0.6540  -0.7493
 PN5  CP5   C  C     0   0.565   4.3383   0.4049  -0.0195
 PN5  OP5   O  O     0  -0.498   5.1113   1.2729   0.3605
 PN5  CP6   C  CH2   0  -0.596   2.8590   0.4333   0.3008
 PN5  CP7   C  CH2   0  -0.276   2.3870   1.8001   0.7815
 PN5  NP8   N  NH1   0  -0.624   0.9695   1.8039   1.0658
 PN5  CP9   C  C     0   0.518   0.0440   2.0289   0.1257
 PN5  OP9   O  O     0  -0.493   0.3255   2.2840  -1.0381
 PN5  CPA   C  CH1   0  -0.027  -1.4175   1.9693   0.5846
 PN5  OPA   O  OH1   0  -0.664  -1.5330   2.1135   1.9819
 PN5  CPB   C  CT    0  -0.218  -2.1689   0.7192   0.0466
 PN5  CPE   C  CH3   0  -0.650  -2.1292   0.6723  -1.4831
 PN5  CPD   C  CH3   0  -0.673  -1.5669  -0.5716   0.6116
 PN5  CPC   C  CH2   0  -0.126  -3.6250   0.8835   0.5028
 PN5  OA6   O  O2    0  -0.456  -4.3742  -0.2320   0.0269
 PN5  CT1   C  C     0   0.647  -5.6750  -0.2741   0.2816
 PN5  OT1   O  O     0  -0.448  -6.2474   0.5836   0.9082
 PN5  CT2   C  CT    0  -0.246  -6.3287  -1.5103  -0.3162
 PN5  CT5   C  CH3   0  -0.642  -5.6604  -2.7692   0.2510
 PN5  CT3   C  CH3   0  -0.632  -7.8140  -1.5205   0.0347
 PN5  CT4   C  CH3   0  -0.642  -6.1588  -1.4752  -1.8417
 PN5  SP1   S  S2    0  -0.259   8.5625  -1.9463  -0.5267
 PN5  HP21  H  HCH2  0   0.274   6.9036  -0.9443   0.9152
 PN5  HP22  H  HCH2  0   0.270   6.3687  -2.5248   0.3201
 PN5  HP31  H  HCH2  0   0.253   6.6021   0.0229  -1.3592
 PN5  HP32  H  HCH2  0   0.263   6.1161  -1.5472  -1.9789
 PN5  HP1   H  HSH1  0   0.228   9.0490  -2.3901   0.6364
 PN5  HP4   H  HNH1  0   0.405   4.0504  -1.3511  -0.9973
 PN5  HP61  H  HCH2  0   0.269   2.2852   0.1250  -0.5765
 PN5  HP62  H  HCH2  0   0.280   2.6645  -0.3171   1.0736
 PN5  HP71  H  HCH2  0   0.259   2.9100   2.0860   1.6920
 PN5  HP72  H  HCH2  0   0.249   2.6008   2.5616   0.0319
 PN5  HP8   H  HNH1  0   0.397   0.6762   1.6580   2.0171
 PN5  HPA   H  HCH1  0   0.267  -1.8929   2.8529   0.1430
 PN5  HA    H  HOH1  0   0.455  -1.5622   1.2498   2.4065
 PN5  HPD1  H  HCH3  0   0.243  -0.5078  -0.6585   0.3641
 PN5  HPD2  H  HCH3  0   0.226  -1.6608  -0.6524   1.6982
 PN5  HPD3  H  HCH3  0   0.259  -2.0668  -1.4439   0.1919
 PN5  HPE1  H  HCH3  0   0.240  -2.7867  -0.1148  -1.8503
 PN5  HPE2  H  HCH3  0   0.229  -2.4563   1.6162  -1.9234
 PN5  HPE3  H  HCH3  0   0.242  -1.1306   0.4580  -1.8558
 PN5  HPC1  H  HCH2  0   0.239  -3.7047   0.9297   1.5906
 PN5  HPC2  H  HCH2  0   0.242  -4.0391   1.8118   0.0958
 PN5  HT31  H  HCH3  0   0.232  -8.3343  -0.6491  -0.3640
 PN5  HT32  H  HCH3  0   0.231  -8.2813  -2.4104  -0.3897
 PN5  HT33  H  HCH3  0   0.232  -7.9748  -1.5460   1.1128
 PN5  HT41  H  HCH3  0   0.241  -5.1117  -1.5168  -2.1411
 PN5  HT42  H  HCH3  0   0.237  -6.6647  -2.3364  -2.2809
 PN5  HT43  H  HCH3  0   0.235  -6.6005  -0.5756  -2.2744
 PN5  HT51  H  HCH3  0   0.235  -5.7647  -2.8232   1.3362
 PN5  HT52  H  HCH3  0   0.236  -6.1414  -3.6520  -0.1727
 PN5  HT53  H  HCH3  0   0.241  -4.5992  -2.8203   0.0090

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
 PN5  CP2  CP3   single  1.525  0.020  1.525
 PN5  CP2  SP1   single  1.824  0.020  1.824
 PN5  CP3  NP4   single  1.443  0.020  1.443
 PN5  NP4  CP5   single  1.345  0.020  1.345
 PN5  CP5  OP5   double  1.223  0.020  1.223
 PN5  CP5  CP6   single  1.514  0.020  1.514
 PN5  CP6  CP7   single  1.524  0.020  1.524
 PN5  CP7  NP8   single  1.446  0.020  1.446
 PN5  NP8  CP9   single  1.338  0.020  1.338
 PN5  CP9  OP9   double  1.224  0.020  1.224
 PN5  CP9  CPA   single  1.533  0.020  1.533
 PN5  OPA  CPA   single  1.410  0.020  1.410
 PN5  CPB  CPD   single  1.532  0.020  1.532
 PN5  CPB  CPE   single  1.531  0.020  1.531
 PN5  CPB  CPC   single  1.535  0.020  1.535
 PN5  CPB  CPA   single  1.555  0.020  1.555
 PN5  CPC  OA6   single  1.425  0.020  1.425
 PN5  OA6  CT1   single  1.326  0.020  1.326
 PN5  CT1  OT1   double  1.207  0.020  1.207
 PN5  CT1  CT2   single  1.521  0.020  1.521
 PN5  CT2  CT3   single  1.526  0.020  1.526
 PN5  CT2  CT4   single  1.535  0.020  1.535
 PN5  CT2  CT5   single  1.534  0.020  1.534
 PN5  CP2  HP21  single  0.970  0.020  1.090
 PN5  CP2  HP22  single  0.970  0.020  1.090
 PN5  CP3  HP31  single  0.970  0.020  1.090
 PN5  CP3  HP32  single  0.970  0.020  1.090
 PN5  SP1  HP1   single  1.200  0.020  1.300
 PN5  NP4  HP4   single  0.860  0.020  1.020
 PN5  CP6  HP61  single  0.970  0.020  1.090
 PN5  CP6  HP62  single  0.970  0.020  1.090
 PN5  CP7  HP71  single  0.970  0.020  1.090
 PN5  CP7  HP72  single  0.970  0.020  1.090
 PN5  NP8  HP8   single  0.860  0.020  1.020
 PN5  CPA  HPA   single  0.970  0.020  1.090
 PN5  OPA  HA    single  0.850  0.020  0.980
 PN5  CPD  HPD1  single  0.970  0.020  1.090
 PN5  CPD  HPD2  single  0.970  0.020  1.090
 PN5  CPD  HPD3  single  0.970  0.020  1.090
 PN5  CPE  HPE1  single  0.970  0.020  1.090
 PN5  CPE  HPE2  single  0.970  0.020  1.090
 PN5  CPE  HPE3  single  0.970  0.020  1.090
 PN5  CPC  HPC1  single  0.970  0.020  1.090
 PN5  CPC  HPC2  single  0.970  0.020  1.090
 PN5  CT3  HT31  single  0.970  0.020  1.090
 PN5  CT3  HT32  single  0.970  0.020  1.090
 PN5  CT3  HT33  single  0.970  0.020  1.090
 PN5  CT4  HT41  single  0.970  0.020  1.090
 PN5  CT4  HT42  single  0.970  0.020  1.090
 PN5  CT4  HT43  single  0.970  0.020  1.090
 PN5  CT5  HT51  single  0.970  0.020  1.090
 PN5  CT5  HT52  single  0.970  0.020  1.090
 PN5  CT5  HT53  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
 PN5  HP22  CP2  HP21  108.81  3.000
 PN5  HP22  CP2  SP1   109.85  3.000
 PN5  HP21  CP2  SP1   109.44  3.000
 PN5  HP22  CP2  CP3   110.19  3.000
 PN5  HP21  CP2  CP3   110.24  3.000
 PN5  SP1   CP2  CP3   108.30  3.000
 PN5  HP32  CP3  HP31  107.34  3.000
 PN5  HP32  CP3  NP4   107.61  3.000
 PN5  HP31  CP3  NP4   109.53  3.000
 PN5  HP32  CP3  CP2   110.05  3.000
 PN5  HP31  CP3  CP2   110.09  3.000
 PN5  NP4   CP3  CP2   112.09  3.000
 PN5  HP4   NP4  CP5   118.62  3.000
 PN5  HP4   NP4  CP3   117.69  3.000
 PN5  CP5   NP4  CP3   123.42  3.000
 PN5  CP6   CP5  OP5   122.60  3.000
 PN5  CP6   CP5  NP4   114.62  3.000
 PN5  OP5   CP5  NP4   122.78  3.000
 PN5  HP62  CP6  HP61  106.27  3.000
 PN5  HP62  CP6  CP7   109.70  3.000
 PN5  HP61  CP6  CP7   110.10  3.000
 PN5  HP62  CP6  CP5   108.07  3.000
 PN5  HP61  CP6  CP5   109.75  3.000
 PN5  CP7   CP6  CP5   112.72  3.000
 PN5  HP72  CP7  HP71  107.32  3.000
 PN5  HP72  CP7  NP8   109.02  3.000
 PN5  HP71  CP7  NP8   107.82  3.000
 PN5  HP72  CP7  CP6   110.43  3.000
 PN5  HP71  CP7  CP6   110.53  3.000
 PN5  NP8   CP7  CP6   111.60  3.000
 PN5  HP8   NP8  CP9   119.14  3.000
 PN5  HP8   NP8  CP7   118.13  3.000
 PN5  CP9   NP8  CP7   122.71  3.000
 PN5  CPA   CP9  OP9   120.79  3.000
 PN5  CPA   CP9  NP8   116.26  3.000
 PN5  OP9   CP9  NP8   122.94  3.000
 PN5  HPA   CPA  CPB   107.41  3.000
 PN5  HPA   CPA  OPA   106.34  3.000
 PN5  CPB   CPA  OPA   112.69  3.000
 PN5  HPA   CPA  CP9   105.16  3.000
 PN5  CPB   CPA  CP9   112.86  3.000
 PN5  OPA   CPA  CP9   111.77  3.000
 PN5  HA    OPA  CPA   110.35  3.000
 PN5  CPC   CPB  CPD   110.69  3.000
 PN5  CPC   CPB  CPE   108.96  3.000
 PN5  CPD   CPB  CPE   109.42  3.000
 PN5  CPC   CPB  CPA   105.64  3.000
 PN5  CPE   CPB  CPA   110.97  3.000
 PN5  CPD   CPB  CPA   111.09  3.000
 PN5  HPE3  CPE  HPE2  107.90  3.000
 PN5  HPE3  CPE  HPE1  107.24  3.000
 PN5  HPE2  CPE  HPE1  107.93  3.000
 PN5  HPE3  CPE  CPB   111.87  3.000
 PN5  HPE2  CPE  CPB   111.64  3.000
 PN5  HPE1  CPE  CPB   110.08  3.000
 PN5  HPD3  CPD  HPD2  106.51  3.000
 PN5  HPD3  CPD  HPD1  107.11  3.000
 PN5  HPD2  CPD  HPD1  107.63  3.000
 PN5  HPD3  CPD  CPB   110.61  3.000
 PN5  HPD2  CPD  CPB   113.26  3.000
 PN5  HPD1  CPD  CPB   111.39  3.000
 PN5  HPC2  CPC  HPC1  107.87  3.000
 PN5  HPC2  CPC  OA6   109.91  3.000
 PN5  HPC1  CPC  OA6   109.11  3.000
 PN5  HPC2  CPC  CPB   109.82  3.000
 PN5  HPC1  CPC  CPB   111.72  3.000
 PN5  OA6   CPC  CPB   108.40  3.000
 PN5  CT1   OA6  CPC   118.44  3.000
 PN5  CT2   CT1  OT1   125.31  3.000
 PN5  CT2   CT1  OA6   111.84  3.000
 PN5  OT1   CT1  OA6   122.85  3.000
 PN5  CT4   CT2  CT3   109.65  3.000
 PN5  CT4   CT2  CT5   109.75  3.000
 PN5  CT3   CT2  CT5   109.48  3.000
 PN5  CT5   CT2  CT1   109.54  3.000
 PN5  CT4   CT2  CT1   108.93  3.000
 PN5  CT3   CT2  CT1   109.48  3.000
 PN5  HT53  CT5  HT52  107.77  3.000
 PN5  HT53  CT5  HT51  108.16  3.000
 PN5  HT52  CT5  HT51  107.70  3.000
 PN5  HT53  CT5  CT2   112.37  3.000
 PN5  HT52  CT5  CT2   109.17  3.000
 PN5  HT51  CT5  CT2   111.50  3.000
 PN5  HT33  CT3  HT32  107.60  3.000
 PN5  HT33  CT3  HT31  108.05  3.000
 PN5  HT32  CT3  HT31  107.77  3.000
 PN5  HT33  CT3  CT2   111.78  3.000
 PN5  HT32  CT3  CT2   109.44  3.000
 PN5  HT31  CT3  CT2   112.02  3.000
 PN5  HT43  CT4  HT42  107.65  3.000
 PN5  HT43  CT4  HT41  108.14  3.000
 PN5  HT42  CT4  HT41  107.74  3.000
 PN5  HT43  CT4  CT2   111.59  3.000
 PN5  HT42  CT4  CT2   109.31  3.000
 PN5  HT41  CT4  CT2   112.24  3.000
 PN5  HP1   SP1  CP2    97.50  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
 PN5  CONST_01  OP5   CP5  NP4  CP3     0.00   0.0  0
 PN5  CONST_02  CP6   CP5  NP4  CP3   180.00   0.0  0
 PN5  CONST_03  OP9   CP9  NP8  CP7     0.00   0.0  0
 PN5  CONST_04  CPA   CP9  NP8  CP7   180.00   0.0  0
 PN5  CONST_05  HP4   NP4  CP5  OP5   180.00   0.0  0
 PN5  CONST_06  HP8   NP8  CP9  OP9   180.00   0.0  0
 PN5  Var_01    CP5   NP4  CP3  CP2    81.58  30.0  3
 PN5  Var_02    SP1   CP2  CP3  NP4   177.28  30.0  2
 PN5  Var_03    CP7   CP6  CP5  NP4  -164.28  30.0  3
 PN5  Var_04    NP8   CP7  CP6  CP5   179.35  30.0  3
 PN5  Var_05    CP9   NP8  CP7  CP6   -85.93  30.0  3
 PN5  Var_06    OA6   CPC  CPB  CPA   179.45  30.0  3
 PN5  Var_07    OT1   CT1  OA6  CPC    -0.70  30.0  3
 PN5  Var_08    CT3   CT2  CT1  OA6   178.74  30.0  3
 PN5  Var_09    HPD1  CPD  CPB  CPA   -58.19  30.0  3
 PN5  Var_10    HPE1  CPE  CPB  CPA  -171.13  30.0  3
 PN5  Var_11    HT31  CT3  CT2  CT1    60.85  30.0  3
 PN5  Var_12    HT41  CT4  CT2  CT1    63.06  30.0  3
 PN5  Var_13    HT51  CT5  CT2  CT1    60.47  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
 PN5  chir_01  CPA  CP9  OPA  CPB  positiv

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
 PN5  plan-1  CP3  0.020
 PN5  plan-1  NP4  0.020
 PN5  plan-1  CP5  0.020
 PN5  plan-1  OP5  0.020
 PN5  plan-1  CP6  0.020
 PN5  plan-1  HP4  0.020
 PN5  plan-2  CP7  0.020
 PN5  plan-2  NP8  0.020
 PN5  plan-2  CP9  0.020
 PN5  plan-2  OP9  0.020
 PN5  plan-2  CPA  0.020
 PN5  plan-2  HP8  0.020
 PN5  plan-3  OA6  0.020
 PN5  plan-3  CT1  0.020
 PN5  plan-3  OT1  0.020
 PN5  plan-3  CT2  0.020

