# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:46:24 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (2R)-2,4-dihydroxy-3,3-dimethyl-N-(3-oxo-3-{[(Z)-2-sulfanylethenyl]amino}propyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)N\C=C/S
#
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
 PCO  PCO  (2R)-2,4-dihydroxy-3,3-dimethyl-N-(3-oxo-3-{[(Z)-2-sulfanylethenyl]amino}propyl)butanamide  ligand  38  18  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PCO
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
 PCO  C23   C  C1    0   0.090   0.4821  -0.6893  -4.6706
 PCO  N19   N  NH1   0  -0.664   0.2231  -0.3767  -3.3545
 PCO  C17   C  C     0   0.581   1.1898  -0.2027  -2.4086
 PCO  C16   C  CH2   0  -0.612   0.6597   0.0890  -1.0265
 PCO  C15   C  CH2   0  -0.281   1.6687   0.8441  -0.1673
 PCO  N14   N  NH1   0  -0.626   1.1585   1.1014   1.1609
 PCO  C12   C  C     0   0.512   1.2183   0.2088   2.1534
 PCO  C10   C  CH1   0  -0.031   0.5687   0.6112   3.4787
 PCO  C7    C  CT    0  -0.146  -0.9311   0.2127   3.5795
 PCO  C6    C  CH2   0  -0.130  -1.0883  -1.3021   3.4255
 PCO  O5    O  OH1   0  -0.671  -2.4388  -1.6523   3.6294
 PCO  C8    C  CH3   0  -0.672  -1.7395   0.9380   2.5012
 PCO  C9    C  CH3   0  -0.643  -1.4335   0.6646   4.9547
 PCO  O11   O  OH1   0  -0.663   1.3406   0.0797   4.5218
 PCO  O13   O  O     0  -0.498   1.7748  -0.8788   2.0486
 PCO  O18   O  O     0  -0.467   2.3763  -0.2976  -2.6583
 PCO  C24   C  C1    0  -0.525  -0.4439  -0.8756  -5.6140
 PCO  S25   S  S2    0  -0.218  -2.1764  -0.8541  -5.2646
 PCO  HC23  H  H     0   0.294   1.5292  -0.7850  -4.9232
 PCO  HN19  H  HNH1  0   0.412  -0.7439  -0.2603  -3.0842
 PCO  H161  H  HCH2  0   0.293   0.4161  -0.8697  -0.5567
 PCO  H162  H  HCH2  0   0.273  -0.2763   0.6490  -1.0873
 PCO  H151  H  HCH2  0   0.269   1.9051   1.8060  -0.6199
 PCO  H152  H  HCH2  0   0.257   2.5994   0.2853  -0.0897
 PCO  HN14  H  HNH1  0   0.407   0.6995   1.9825   1.3257
 PCO  HC10  H  HCH1  0   0.250   0.6101   1.7033   3.5734
 PCO  HC61  H  HCH2  0   0.201  -0.7587  -1.6066   2.4242
 PCO  HC62  H  HCH2  0   0.197  -0.4400  -1.8140   4.1492
 PCO  HO5   H  HOH1  0   0.454  -2.5132  -2.6062   3.5394
 PCO  HC81  H  HCH3  0   0.230  -1.4909   0.6030   1.4933
 PCO  HC82  H  HCH3  0   0.246  -2.8058   0.7680   2.6447
 PCO  HC83  H  HCH3  0   0.229  -1.5781   2.0178   2.5462
 PCO  HC91  H  HCH3  0   0.230  -0.9295   0.1425   5.7676
 PCO  HC92  H  HCH3  0   0.222  -1.2672   1.7356   5.0903
 PCO  HC93  H  HCH3  0   0.235  -2.5033   0.4862   5.0538
 PCO  HO11  H  HOH1  0   0.444   1.6916  -0.7683   4.2214
 PCO  HC24  H  H     0   0.286  -0.1302  -1.1174  -6.6196
 PCO  HS25  H  HSH1  0   0.236  -2.5016   0.2565  -5.9401

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
 PCO  C23  N19   single  1.377  0.020  1.377
 PCO  C23  C24   double  1.335  0.020  1.335
 PCO  C23  HC23  single  0.930  0.020  1.080
 PCO  N19  C17   single  1.364  0.020  1.364
 PCO  N19  HN19  single  0.860  0.020  1.020
 PCO  C17  C16   single  1.509  0.020  1.509
 PCO  C17  O18   double  1.216  0.020  1.216
 PCO  C16  C15   single  1.525  0.020  1.525
 PCO  C16  H161  single  0.970  0.020  1.090
 PCO  C16  H162  single  0.970  0.020  1.090
 PCO  C15  N14   single  1.446  0.020  1.446
 PCO  C15  H151  single  0.970  0.020  1.090
 PCO  C15  H152  single  0.970  0.020  1.090
 PCO  N14  C12   single  1.336  0.020  1.336
 PCO  N14  HN14  single  0.860  0.020  1.020
 PCO  C12  C10   single  1.530  0.020  1.530
 PCO  C12  O13   double  1.226  0.020  1.226
 PCO  C10  C7    single  1.555  0.020  1.555
 PCO  C10  O11   single  1.402  0.020  1.402
 PCO  C10  HC10  single  0.970  0.020  1.090
 PCO  C7   C6    single  1.531  0.020  1.531
 PCO  C7   C8    single  1.530  0.020  1.530
 PCO  C7   C9    single  1.532  0.020  1.532
 PCO  C6   O5    single  1.410  0.020  1.410
 PCO  C6   HC61  single  0.970  0.020  1.090
 PCO  C6   HC62  single  0.970  0.020  1.090
 PCO  O5   HO5   single  0.850  0.020  0.980
 PCO  C8   HC81  single  0.970  0.020  1.090
 PCO  C8   HC82  single  0.970  0.020  1.090
 PCO  C8   HC83  single  0.970  0.020  1.090
 PCO  C9   HC91  single  0.970  0.020  1.090
 PCO  C9   HC92  single  0.970  0.020  1.090
 PCO  C9   HC93  single  0.970  0.020  1.090
 PCO  O11  HO11  single  0.850  0.020  0.980
 PCO  C24  S25   single  1.768  0.020  1.768
 PCO  C24  HC24  single  0.930  0.020  1.080
 PCO  S25  HS25  single  1.200  0.020  1.300

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
 PCO  HC23  C23  C24   119.62  3.000
 PCO  HC23  C23  N19   115.17  3.000
 PCO  C24   C23  N19   125.21  3.000
 PCO  HN19  N19  C17   118.56  3.000
 PCO  HN19  N19  C23   117.49  3.000
 PCO  C17   N19  C23   123.95  3.000
 PCO  O18   C17  C16   123.09  3.000
 PCO  O18   C17  N19   122.63  3.000
 PCO  C16   C17  N19   114.27  3.000
 PCO  H162  C16  H161  106.38  3.000
 PCO  H162  C16  C15   110.14  3.000
 PCO  H161  C16  C15   109.81  3.000
 PCO  H162  C16  C17   110.43  3.000
 PCO  H161  C16  C17   107.57  3.000
 PCO  C15   C16  C17   112.29  3.000
 PCO  H152  C15  H151  107.30  3.000
 PCO  H152  C15  N14   109.12  3.000
 PCO  H151  C15  N14   107.53  3.000
 PCO  H152  C15  C16   110.59  3.000
 PCO  H151  C15  C16   110.29  3.000
 PCO  N14   C15  C16   111.85  3.000
 PCO  HN14  N14  C12   118.90  3.000
 PCO  HN14  N14  C15   117.83  3.000
 PCO  C12   N14  C15   123.21  3.000
 PCO  O13   C12  C10   120.01  3.000
 PCO  O13   C12  N14   123.32  3.000
 PCO  C10   C12  N14   116.67  3.000
 PCO  HC10  C10  O11   106.99  3.000
 PCO  HC10  C10  C7    106.61  3.000
 PCO  O11   C10  C7    112.68  3.000
 PCO  HC10  C10  C12   108.70  3.000
 PCO  O11   C10  C12   108.12  3.000
 PCO  C7    C10  C12   113.48  3.000
 PCO  C9    C7   C8    108.63  3.000
 PCO  C9    C7   C6    110.40  3.000
 PCO  C8    C7   C6    110.11  3.000
 PCO  C9    C7   C10   107.39  3.000
 PCO  C8    C7   C10   110.01  3.000
 PCO  C6    C7   C10   110.24  3.000
 PCO  HC62  C6   HC61  107.14  3.000
 PCO  HC62  C6   O5    110.76  3.000
 PCO  HC61  C6   O5    110.53  3.000
 PCO  HC62  C6   C7    109.54  3.000
 PCO  HC61  C6   C7    109.61  3.000
 PCO  O5    C6   C7    109.24  3.000
 PCO  HO5   O5   C6    107.88  3.000
 PCO  HC83  C8   HC82  107.06  3.000
 PCO  HC83  C8   HC81  107.93  3.000
 PCO  HC82  C8   HC81  107.27  3.000
 PCO  HC83  C8   C7    111.18  3.000
 PCO  HC82  C8   C7    110.50  3.000
 PCO  HC81  C8   C7    112.65  3.000
 PCO  HC93  C9   HC92  107.39  3.000
 PCO  HC93  C9   HC91  107.94  3.000
 PCO  HC92  C9   HC91  107.86  3.000
 PCO  HC93  C9   C7    110.82  3.000
 PCO  HC92  C9   C7    110.53  3.000
 PCO  HC91  C9   C7    112.13  3.000
 PCO  HO11  O11  C10   107.55  3.000
 PCO  HC24  C24  S25   118.11  3.000
 PCO  HC24  C24  C23   119.17  3.000
 PCO  S25   C24  C23   122.58  3.000
 PCO  HS25  S25  C24    98.53  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
 PCO  CONST_01  C16   C17  N19  C23   180.00   0.0  0
 PCO  CONST_02  O18   C17  N19  C23     0.00   0.0  0
 PCO  CONST_03  C10   C12  N14  C15   180.00   0.0  0
 PCO  CONST_04  O13   C12  N14  C15     0.00   0.0  0
 PCO  CONST_05  HN19  N19  C17  C16     0.00   0.0  0
 PCO  CONST_06  HN14  N14  C12  C10     0.00   0.0  0
 PCO  Var_01    S25   C24  C23  N19    -4.43   0.0  2
 PCO  Var_02    C15   C16  C17  N19  -155.40  30.0  3
 PCO  Var_03    C24   C23  N19  C17   179.44  30.0  1
 PCO  Var_04    N14   C15  C16  C17  -179.16  30.0  3
 PCO  Var_05    C12   N14  C15  C16    83.60  30.0  3
 PCO  Var_06    O5    C6   C7   C10   175.23  30.0  3
 PCO  Var_07    HC81  C8   C7   C10    67.43  30.0  3
 PCO  Var_08    HC91  C9   C7   C10   -64.00  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
 PCO  chir_01  C10  C12  C7  O11  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
 PCO  plan-1  C23   0.020
 PCO  plan-1  N19   0.020
 PCO  plan-1  C17   0.020
 PCO  plan-1  C16   0.020
 PCO  plan-1  O18   0.020
 PCO  plan-1  HN19  0.020
 PCO  plan-2  C15   0.020
 PCO  plan-2  N14   0.020
 PCO  plan-2  C12   0.020
 PCO  plan-2  C10   0.020
 PCO  plan-2  O13   0.020
 PCO  plan-2  HN14  0.020
 PCO  plan-3  C23   0.020
 PCO  plan-3  N19   0.020
 PCO  plan-3  C24   0.020
 PCO  plan-3  S25   0.020
 PCO  plan-3  HC23  0.020
 PCO  plan-3  HC24  0.020

