# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:17:16 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2S)-1-(pentanoyloxy)propan-2-yl hexanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)O[C@@H](C)COC(=O)CCCC
#
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
 3PK  3PK  '(2S)-1-(pentanoyloxy)propan-2-yl hexanoate'  ligand  44  18  .  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_3PK
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
 3PK  CA1   C  C     0   0.609   3.1008  -0.5618   0.5516
 3PK  OA1   O  O     0  -0.452   3.6076  -1.0478   1.5315
 3PK  CA2   C  CH2   0  -0.583   3.6992   0.5303  -0.2913
 3PK  CA3   C  CH2   0  -0.412   5.0761   0.9800   0.1689
 3PK  CA4   C  CH2   0  -0.421   5.6328   2.0890  -0.7161
 3PK  CA5   C  CH3   0  -0.662   7.0087   2.5589  -0.2670
 3PK  CB1   C  C     0   0.610  -2.1903  -1.2063   0.0053
 3PK  OB1   O  O     0  -0.452  -2.7628  -2.2583  -0.1316
 3PK  CB2   C  CH2   0  -0.583  -2.8608   0.1364   0.1204
 3PK  CB3   C  CH2   0  -0.417  -4.3655   0.0895  -0.0885
 3PK  CB4   C  CH2   0  -0.410  -5.0066   1.4612   0.0811
 3PK  CB5   C  CH2   0  -0.419  -6.5141   1.4417  -0.1363
 3PK  CB6   C  CH3   0  -0.662  -7.1556   2.8090   0.0541
 3PK  CG1   C  CH2   0  -0.192   1.2156  -1.9701   0.7797
 3PK  OG1   O  O2    0  -0.459   1.9143  -0.9389   0.0848
 3PK  CG2   C  CH1   0  -0.025  -0.0573  -2.2794   0.0256
 3PK  OG2   O  O2    0  -0.469  -0.8672  -1.0930   0.0863
 3PK  CG3   C  CH3   0  -0.684   0.1757  -2.7037  -1.4133
 3PK  H1A2  H  HCH2  0   0.272   3.7341   0.1825  -1.3285
 3PK  H2A2  H  HCH2  0   0.274   3.0023   1.3748  -0.2917
 3PK  H1A3  H  HCH2  0   0.224   5.0259   1.3325   1.2028
 3PK  H2A3  H  HCH2  0   0.224   5.7664   0.1320   0.1650
 3PK  H1A4  H  HCH2  0   0.216   5.6847   1.7365  -1.7508
 3PK  H2A4  H  HCH2  0   0.216   4.9378   2.9342  -0.7194
 3PK  H1A5  H  HCH3  0   0.217   6.9814   2.9387   0.7560
 3PK  H2A5  H  HCH3  0   0.218   7.7331   1.7433  -0.2964
 3PK  H3A5  H  HCH3  0   0.228   7.3857   3.3582  -0.9057
 3PK  H1B2  H  HCH2  0   0.274  -2.6249   0.5431   1.1094
 3PK  H2B2  H  HCH2  0   0.271  -2.3925   0.8201  -0.5941
 3PK  H1B3  H  HCH2  0   0.224  -4.5874  -0.2953  -1.0879
 3PK  H2B3  H  HCH2  0   0.224  -4.8170  -0.6103   0.6195
 3PK  HB4   H  HCH2  0   0.211  -4.7906   1.8432   1.0849
 3PK  HB5   H  HCH2  0   0.212  -6.7282   1.0718  -1.1435
 3PK  H1B6  H  HCH3  0   0.227  -8.2326   2.7738  -0.1133
 3PK  H2B6  H  HCH3  0   0.216  -6.9906   3.1852   1.0657
 3PK  H3B6  H  HCH3  0   0.216  -6.7376   3.5409  -0.6398
 3PK  H1G1  H  HCH2  0   0.248   1.8194  -2.8788   0.8325
 3PK  H2G1  H  HCH2  0   0.257   0.9879  -1.6550   1.8010
 3PK  HG2   H  HCH1  0   0.260  -0.5506  -3.0877   0.5724
 3PK  H1G3  H  HCH3  0   0.241   0.6078  -1.8995  -2.0074
 3PK  H2G3  H  HCH3  0   0.241   0.8601  -3.5523  -1.4408
 3PK  H3G3  H  HCH3  0   0.249  -0.7540  -3.0178  -1.8844
 3PK  H25   H  HCH2  0   0.211  -4.5487   2.1706  -0.6170
 3PK  H26   H  HCH2  0   0.212  -6.9691   0.7234   0.5527

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
 3PK  CA1  OA1   double  1.206  0.020  1.206
 3PK  CA1  CA2   single  1.504  0.020  1.504
 3PK  CA2  CA3   single  1.520  0.020  1.520
 3PK  CA2  H1A2  single  0.970  0.020  1.090
 3PK  CA2  H2A2  single  0.970  0.020  1.090
 3PK  CA3  CA4   single  1.524  0.020  1.524
 3PK  CA3  H1A3  single  0.970  0.020  1.090
 3PK  CA3  H2A3  single  0.970  0.020  1.090
 3PK  CA4  CA5   single  1.522  0.020  1.522
 3PK  CA4  H1A4  single  0.970  0.020  1.090
 3PK  CA4  H2A4  single  0.970  0.020  1.090
 3PK  CA5  H1A5  single  0.970  0.020  1.090
 3PK  CA5  H2A5  single  0.970  0.020  1.090
 3PK  CA5  H3A5  single  0.970  0.020  1.090
 3PK  CB1  OB1   double  1.205  0.020  1.205
 3PK  CB1  CB2   single  1.505  0.020  1.505
 3PK  CB2  CB3   single  1.520  0.020  1.520
 3PK  CB2  H1B2  single  0.970  0.020  1.090
 3PK  CB2  H2B2  single  0.970  0.020  1.090
 3PK  CB3  CB4   single  1.524  0.020  1.524
 3PK  CB3  H1B3  single  0.970  0.020  1.090
 3PK  CB3  H2B3  single  0.970  0.020  1.090
 3PK  CB4  CB5   single  1.523  0.020  1.523
 3PK  CB4  HB4   single  0.970  0.020  1.090
 3PK  CB5  CB6   single  1.522  0.020  1.522
 3PK  CB5  HB5   single  0.970  0.020  1.090
 3PK  CB6  H1B6  single  0.970  0.020  1.090
 3PK  CB6  H2B6  single  0.970  0.020  1.090
 3PK  CB6  H3B6  single  0.970  0.020  1.090
 3PK  CG1  OG1   single  1.426  0.020  1.426
 3PK  CG1  H1G1  single  0.970  0.020  1.090
 3PK  CG1  H2G1  single  0.970  0.020  1.090
 3PK  OG1  CA1   single  1.330  0.020  1.330
 3PK  CG2  CG1   single  1.512  0.020  1.512
 3PK  CG2  HG2   single  0.970  0.020  1.090
 3PK  OG2  CG2   single  1.438  0.020  1.438
 3PK  OG2  CB1   single  1.330  0.020  1.330
 3PK  CG3  CG2   single  1.518  0.020  1.518
 3PK  CG3  H1G3  single  0.970  0.020  1.090
 3PK  CG3  H2G3  single  0.970  0.020  1.090
 3PK  CG3  H3G3  single  0.970  0.020  1.090
 3PK  CB4  H25   single  0.970  0.020  1.090
 3PK  CB5  H26   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
 3PK  OG1   CA1  CA2   111.37  3.000
 3PK  OG1   CA1  OA1   123.11  3.000
 3PK  CA2   CA1  OA1   125.53  3.000
 3PK  H2A2  CA2  H1A2  105.37  3.000
 3PK  H2A2  CA2  CA3   110.40  3.000
 3PK  H1A2  CA2  CA3   110.62  3.000
 3PK  H2A2  CA2  CA1   107.88  3.000
 3PK  H1A2  CA2  CA1   108.25  3.000
 3PK  CA3   CA2  CA1   113.93  3.000
 3PK  H2A3  CA3  H1A3  106.40  3.000
 3PK  H2A3  CA3  CA4   109.36  3.000
 3PK  H1A3  CA3  CA4   109.35  3.000
 3PK  H2A3  CA3  CA2   109.96  3.000
 3PK  H1A3  CA3  CA2   109.89  3.000
 3PK  CA4   CA3  CA2   111.74  3.000
 3PK  H2A4  CA4  H1A4  106.03  3.000
 3PK  H2A4  CA4  CA5   109.67  3.000
 3PK  H1A4  CA4  CA5   109.61  3.000
 3PK  H2A4  CA4  CA3   109.37  3.000
 3PK  H1A4  CA4  CA3   109.39  3.000
 3PK  CA5   CA4  CA3   112.56  3.000
 3PK  H3A5  CA5  H2A5  107.61  3.000
 3PK  H3A5  CA5  H1A5  107.61  3.000
 3PK  H2A5  CA5  H1A5  107.56  3.000
 3PK  H3A5  CA5  CA4   111.48  3.000
 3PK  H2A5  CA5  CA4   111.19  3.000
 3PK  H1A5  CA5  CA4   111.19  3.000
 3PK  OG2   CB1  CB2   111.25  3.000
 3PK  OG2   CB1  OB1   123.61  3.000
 3PK  CB2   CB1  OB1   125.14  3.000
 3PK  H2B2  CB2  H1B2  105.39  3.000
 3PK  H2B2  CB2  CB3   110.69  3.000
 3PK  H1B2  CB2  CB3   110.42  3.000
 3PK  H2B2  CB2  CB1   108.47  3.000
 3PK  H1B2  CB2  CB1   107.72  3.000
 3PK  CB3   CB2  CB1   113.77  3.000
 3PK  H2B3  CB3  H1B3  106.43  3.000
 3PK  H2B3  CB3  CB4   109.30  3.000
 3PK  H1B3  CB3  CB4   109.45  3.000
 3PK  H2B3  CB3  CB2   109.86  3.000
 3PK  H1B3  CB3  CB2   109.71  3.000
 3PK  CB4   CB3  CB2   111.93  3.000
 3PK  H25   CB4  HB4   106.00  3.000
 3PK  H25   CB4  CB5   109.33  3.000
 3PK  HB4   CB4  CB5   109.29  3.000
 3PK  H25   CB4  CB3   109.65  3.000
 3PK  HB4   CB4  CB3   109.45  3.000
 3PK  CB5   CB4  CB3   112.89  3.000
 3PK  H26   CB5  HB5   106.04  3.000
 3PK  H26   CB5  CB6   109.61  3.000
 3PK  HB5   CB5  CB6   109.65  3.000
 3PK  H26   CB5  CB4   109.27  3.000
 3PK  HB5   CB5  CB4   109.22  3.000
 3PK  CB6   CB5  CB4   112.81  3.000
 3PK  H3B6  CB6  H2B6  107.46  3.000
 3PK  H3B6  CB6  H1B6  107.59  3.000
 3PK  H2B6  CB6  H1B6  107.62  3.000
 3PK  H3B6  CB6  CB5   111.18  3.000
 3PK  H2B6  CB6  CB5   111.20  3.000
 3PK  H1B6  CB6  CB5   111.59  3.000
 3PK  H2G1  CG1  H1G1  108.05  3.000
 3PK  H2G1  CG1  CG2   110.47  3.000
 3PK  H1G1  CG1  CG2   108.63  3.000
 3PK  CG2   CG1  OG1   108.51  3.000
 3PK  H2G1  CG1  OG1   110.42  3.000
 3PK  H1G1  CG1  OG1   110.75  3.000
 3PK  CG1   OG1  CA1   118.11  3.000
 3PK  HG2   CG2  CG3   109.68  3.000
 3PK  CG3   CG2  OG2   110.92  3.000
 3PK  HG2   CG2  OG2   109.56  3.000
 3PK  CG3   CG2  CG1   113.63  3.000
 3PK  OG2   CG2  CG1   106.52  3.000
 3PK  HG2   CG2  CG1   106.36  3.000
 3PK  CG2   OG2  CB1   119.17  3.000
 3PK  H3G3  CG3  H2G3  107.49  3.000
 3PK  H3G3  CG3  H1G3  108.40  3.000
 3PK  H2G3  CG3  H1G3  108.16  3.000
 3PK  H3G3  CG3  CG2   111.09  3.000
 3PK  H2G3  CG3  CG2   109.74  3.000
 3PK  H1G3  CG3  CG2   111.81  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
 3PK  Var_01  CA4   CA3  CA2  CA1  -179.83  30.0  3
 3PK  Var_02  CG2   CG1  OG1  CA1  -176.81  30.0  1
 3PK  Var_03  CA3   CA2  CA1  OA1     1.81  30.0  3
 3PK  Var_04  CA5   CA4  CA3  CA2   179.69  30.0  3
 3PK  Var_05  CB4   CB3  CB2  CB1   178.17  30.0  3
 3PK  Var_06  CB3   CB2  CB1  OB1    -5.73  30.0  3
 3PK  Var_07  CB5   CB4  CB3  CB2   179.48  30.0  3
 3PK  Var_08  CB6   CB5  CB4  CB3   179.14  30.0  3
 3PK  Var_09  H1A5  CA5  CA4  CA3   -59.35  30.0  3
 3PK  Var_10  H1B6  CB6  CB5  CB4   179.57  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
 3PK  chir_01  CG2  CG1  OG2  CG3  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
 3PK  plan-1  CA1  0.020
 3PK  plan-1  OA1  0.020
 3PK  plan-1  CA2  0.020
 3PK  plan-1  OG1  0.020
 3PK  plan-2  CB1  0.020
 3PK  plan-2  OB1  0.020
 3PK  plan-2  CB2  0.020
 3PK  plan-2  OG2  0.020

