# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 16:43:13 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC([C@H]1CCCN1[S](=O)(=O)CCCN2C=CC(=O)NC2=O)(c3ccccc3)c4ccccc4
#
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
 MKH  MKH  1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidine-2,4(1H,3H)-dione  ligand  60  33  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MKH
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
 MKH  O1    O  O     0  -0.466   7.8505  -1.2440  -1.8920
 MKH  C2    C  CR6   0   0.567   6.7881  -1.0447  -1.3322
 MKH  N3    N  NR16  0  -0.731   6.6129   0.0736  -0.5304
 MKH  C4    C  CR6   0   0.733   5.4890   0.4523   0.1563
 MKH  N5    N  NR6   0  -0.524   4.4265  -0.4185   0.0453
 MKH  C6    C  CR16  0   0.108   4.5121  -1.5359  -0.7307
 MKH  C7    C  CR16  0  -0.509   5.6183  -1.8846  -1.4086
 MKH  O8    O  O     0  -0.478   5.4380   1.4721   0.8115
 MKH  C9    C  CH2   0  -0.315   3.1728  -0.0901   0.7119
 MKH  C10   C  CH2   0  -0.449   2.2919   0.8152  -0.1390
 MKH  C11   C  CH2   0  -0.615   0.9696   1.0420   0.5756
 MKH  S12   S  S     0   1.375  -0.1418   2.0510  -0.3924
 MKH  N13   N  N     0  -0.622  -1.5653   1.9843   0.4690
 MKH  C14   C  CH2   0  -0.300  -2.0454   3.2112   1.1303
 MKH  C15   C  CH2   0  -0.452  -3.2744   3.5821   0.3220
 MKH  C16   C  CH2   0  -0.455  -3.9072   2.2224   0.0444
 MKH  C17   C  CH1   0  -0.091  -2.7230   1.2386  -0.0753
 MKH  O18   O  OS    0  -0.662   0.3709   3.4164  -0.3722
 MKH  O19   O  OS    0  -0.653  -0.3265   1.4157  -1.6913
 MKH  C20   C  CT    0   0.129  -2.9429  -0.0656   0.7327
 MKH  O21   O  OH1   0  -0.653  -3.0557   0.2684   2.0910
 MKH  C22   C  CR6   0   0.132  -4.2411  -0.7565   0.3340
 MKH  C23   C  CR16  0  -0.296  -4.9559  -1.4894   1.2801
 MKH  C24   C  CR16  0  -0.237  -6.1110  -2.1718   0.9244
 MKH  C25   C  CR16  0  -0.269  -6.5745  -2.1366  -0.3833
 MKH  C26   C  CR16  0  -0.240  -5.8682  -1.4129  -1.3329
 MKH  C27   C  CR16  0  -0.313  -4.7128  -0.7305  -0.9768
 MKH  C28   C  CR6   0   0.075  -1.8036  -1.0674   0.5197
 MKH  C29   C  CR16  0  -0.318  -1.2021  -1.6979   1.6074
 MKH  C30   C  CR16  0  -0.238  -0.1515  -2.5890   1.4241
 MKH  C31   C  CR16  0  -0.276   0.3123  -2.8729   0.1482
 MKH  C32   C  CR16  0  -0.240  -0.3013  -2.2746  -0.9451
 MKH  C33   C  CR16  0  -0.272  -1.3519  -1.3886  -0.7597
 MKH  HN3   H  HNR6  0   0.426   7.4031   0.7011  -0.4435
 MKH  H6    H  HCR6  0   0.310   3.6187  -2.1445  -0.7630
 MKH  H7    H  HCR6  0   0.294   5.6392  -2.7836  -2.0045
 MKH  H9    H  HCH2  0   0.270   2.6603  -1.0302   0.9185
 MKH  H9A   H  HCH2  0   0.287   3.3942   0.3688   1.6733
 MKH  H10   H  HCH2  0   0.269   2.7990   1.7631  -0.3230
 MKH  H10A  H  HCH2  0   0.262   2.1119   0.3391  -1.1051
 MKH  H11   H  HCH2  0   0.305   0.4575   0.0991   0.7651
 MKH  H11A  H  HCH2  0   0.305   1.0984   1.5533   1.5318
 MKH  H14   H  HCH2  0   0.249  -2.3114   2.9773   2.1629
 MKH  H14A  H  HCH2  0   0.276  -1.2803   3.9807   1.1570
 MKH  H15   H  HCH2  0   0.251  -3.9428   4.2530   0.8611
 MKH  H15A  H  HCH2  0   0.238  -2.9745   4.0740  -0.6059
 MKH  H16   H  HCH2  0   0.249  -4.5590   1.9439   0.8735
 MKH  H16A  H  HCH2  0   0.257  -4.5124   2.2182  -0.8604
 MKH  H17   H  HCH1  0   0.282  -2.5432   1.0068  -1.1233
 MKH  HO21  H  HOH1  0   0.458  -2.2161   0.6488   2.3771
 MKH  H23   H  HCR6  0   0.255  -4.6139  -1.5394   2.3044
 MKH  H24   H  HCR6  0   0.256  -6.6494  -2.7354   1.6755
 MKH  H25   H  HCR6  0   0.256  -7.4770  -2.6664  -0.6591
 MKH  H26   H  HCR6  0   0.257  -6.2154  -1.3728  -2.3571
 MKH  H27   H  HCR6  0   0.256  -4.1958  -0.1707  -1.7451
 MKH  H29   H  HCR6  0   0.256  -1.5421  -1.4987   2.6145
 MKH  H30   H  HCR6  0   0.260   0.3071  -3.0567   2.2857
 MKH  H31   H  HCR6  0   0.261   1.1337  -3.5636   0.0070
 MKH  H32   H  HCR6  0   0.260   0.0392  -2.4954  -1.9482
 MKH  H33   H  HCR6  0   0.249  -1.8091  -0.9480  -1.6346

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
 MKH  O1   C2    double    1.217  0.020  1.217
 MKH  C2   N3    single    1.387  0.020  1.387
 MKH  C2   C7    single    1.442  0.020  1.442
 MKH  N3   C4    single    1.370  0.020  1.370
 MKH  C4   N5    single    1.378  0.020  1.378
 MKH  C4   O8    double    1.213  0.020  1.213
 MKH  N5   C6    single    1.363  0.020  1.363
 MKH  N5   C9    single    1.457  0.020  1.457
 MKH  C6   C7    double    1.343  0.020  1.343
 MKH  C9   C10   single    1.523  0.020  1.523
 MKH  C10  C11   single    1.520  0.020  1.520
 MKH  C11  S12   single    1.786  0.020  1.786
 MKH  S12  N13   single    1.665  0.020  1.665
 MKH  S12  O18   double    1.459  0.020  1.459
 MKH  S12  O19   double    1.458  0.020  1.458
 MKH  N13  C14   single    1.474  0.020  1.474
 MKH  N13  C17   single    1.481  0.020  1.481
 MKH  C14  C15   single    1.517  0.020  1.517
 MKH  C15  C16   single    1.525  0.020  1.525
 MKH  C16  C17   single    1.544  0.020  1.544
 MKH  C17  C20   single    1.550  0.020  1.550
 MKH  C20  O21   single    1.403  0.020  1.403
 MKH  C20  C22   single    1.524  0.020  1.524
 MKH  C20  C28   single    1.532  0.020  1.532
 MKH  C22  C23   aromatic  1.394  0.020  1.394
 MKH  C22  C27   aromatic  1.393  0.020  1.393
 MKH  C23  C24   aromatic  1.388  0.020  1.388
 MKH  C24  C25   aromatic  1.388  0.020  1.388
 MKH  C25  C26   aromatic  1.387  0.020  1.387
 MKH  C26  C27   aromatic  1.388  0.020  1.388
 MKH  C28  C29   aromatic  1.394  0.020  1.394
 MKH  C28  C33   aromatic  1.394  0.020  1.394
 MKH  C29  C30   aromatic  1.390  0.020  1.390
 MKH  C30  C31   aromatic  1.387  0.020  1.387
 MKH  C31  C32   aromatic  1.389  0.020  1.389
 MKH  C32  C33   aromatic  1.387  0.020  1.387
 MKH  N3   HN3   single    0.860  0.020  1.020
 MKH  C6   H6    single    0.930  0.020  1.080
 MKH  C7   H7    single    0.930  0.020  1.080
 MKH  C9   H9    single    0.970  0.020  1.090
 MKH  C9   H9A   single    0.970  0.020  1.090
 MKH  C10  H10   single    0.970  0.020  1.090
 MKH  C10  H10A  single    0.970  0.020  1.090
 MKH  C11  H11   single    0.970  0.020  1.090
 MKH  C11  H11A  single    0.970  0.020  1.090
 MKH  C14  H14   single    0.970  0.020  1.090
 MKH  C14  H14A  single    0.970  0.020  1.090
 MKH  C15  H15   single    0.970  0.020  1.090
 MKH  C15  H15A  single    0.970  0.020  1.090
 MKH  C16  H16   single    0.970  0.020  1.090
 MKH  C16  H16A  single    0.970  0.020  1.090
 MKH  C17  H17   single    0.970  0.020  1.090
 MKH  O21  HO21  single    0.850  0.020  0.980
 MKH  C23  H23   single    0.930  0.020  1.080
 MKH  C24  H24   single    0.930  0.020  1.080
 MKH  C25  H25   single    0.930  0.020  1.080
 MKH  C26  H26   single    0.930  0.020  1.080
 MKH  C27  H27   single    0.930  0.020  1.080
 MKH  C29  H29   single    0.930  0.020  1.080
 MKH  C30  H30   single    0.930  0.020  1.080
 MKH  C31  H31   single    0.930  0.020  1.080
 MKH  C32  H32   single    0.930  0.020  1.080
 MKH  C33  H33   single    0.930  0.020  1.080

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
 MKH  C7    C2   N3   113.43  3.000
 MKH  C7    C2   O1   126.04  3.000
 MKH  N3    C2   O1   120.53  3.000
 MKH  HN3   N3   C4   115.20  3.000
 MKH  HN3   N3   C2   116.78  3.000
 MKH  C4    N3   C2   128.02  3.000
 MKH  O8    C4   N5   122.83  3.000
 MKH  O8    C4   N3   122.50  3.000
 MKH  N5    C4   N3   114.67  3.000
 MKH  C9    N5   C6   119.95  3.000
 MKH  C9    N5   C4   118.95  3.000
 MKH  C6    N5   C4   121.02  3.000
 MKH  H6    C6   C7   121.27  3.000
 MKH  H6    C6   N5   115.24  3.000
 MKH  C7    C6   N5   123.49  3.000
 MKH  H7    C7   C6   120.73  3.000
 MKH  H7    C7   C2   119.93  3.000
 MKH  C6    C7   C2   119.34  3.000
 MKH  H9A   C9   H9   106.97  3.000
 MKH  H9A   C9   C10  111.14  3.000
 MKH  H9    C9   C10  110.27  3.000
 MKH  H9A   C9   N5   108.91  3.000
 MKH  H9    C9   N5   107.26  3.000
 MKH  C10   C9   N5   112.09  3.000
 MKH  H10A  C10  H10  107.83  3.000
 MKH  H10A  C10  C11  109.73  3.000
 MKH  H10   C10  C11  110.74  3.000
 MKH  H10A  C10  C9   109.30  3.000
 MKH  H10   C10  C9   109.99  3.000
 MKH  C11   C10  C9   109.22  3.000
 MKH  H11A  C11  H11  107.96  3.000
 MKH  H11A  C11  S12  106.47  3.000
 MKH  H11   C11  S12  106.90  3.000
 MKH  H11A  C11  C10  112.27  3.000
 MKH  H11   C11  C10  111.19  3.000
 MKH  S12   C11  C10  111.77  3.000
 MKH  O19   S12  O18  117.70  3.000
 MKH  O19   S12  N13  109.58  3.000
 MKH  O18   S12  N13  109.32  3.000
 MKH  O19   S12  C11  108.40  3.000
 MKH  O18   S12  C11  107.61  3.000
 MKH  N13   S12  C11  103.23  3.000
 MKH  C17   N13  C14  109.23  3.000
 MKH  C17   N13  S12  119.89  3.000
 MKH  C14   N13  S12  118.50  3.000
 MKH  H14A  C14  H14  107.48  3.000
 MKH  H14A  C14  C15  114.26  3.000
 MKH  H14   C14  C15  111.04  3.000
 MKH  H14A  C14  N13  111.81  3.000
 MKH  H14   C14  N13  108.98  3.000
 MKH  C15   C14  N13  103.20  3.000
 MKH  H15A  C15  H15  108.15  3.000
 MKH  H15A  C15  C16  111.15  3.000
 MKH  H15   C15  C16  112.61  3.000
 MKH  H15A  C15  C14  109.89  3.000
 MKH  H15   C15  C14  112.58  3.000
 MKH  C16   C15  C14  102.43  3.000
 MKH  H16A  C16  H16  107.37  3.000
 MKH  H16A  C16  C17  111.07  3.000
 MKH  H16   C16  C17  110.76  3.000
 MKH  H16A  C16  C15  112.67  3.000
 MKH  H16   C16  C15  109.70  3.000
 MKH  C17   C16  C15  105.30  3.000
 MKH  H17   C17  C20  110.25  3.000
 MKH  H17   C17  C16  109.70  3.000
 MKH  C20   C17  C16  112.76  3.000
 MKH  H17   C17  N13  109.40  3.000
 MKH  C20   C17  N13  110.06  3.000
 MKH  C16   C17  N13  104.49  3.000
 MKH  C28   C20  C22  107.50  3.000
 MKH  C28   C20  O21  110.49  3.000
 MKH  C22   C20  O21  107.02  3.000
 MKH  C28   C20  C17  111.86  3.000
 MKH  C22   C20  C17  111.47  3.000
 MKH  O21   C20  C17  108.40  3.000
 MKH  HO21  O21  C20  108.10  3.000
 MKH  C27   C22  C23  118.34  3.000
 MKH  C27   C22  C20  121.75  3.000
 MKH  C23   C22  C20  119.85  3.000
 MKH  H23   C23  C24  118.91  3.000
 MKH  H23   C23  C22  120.34  3.000
 MKH  C24   C23  C22  120.75  3.000
 MKH  H24   C24  C25  120.06  3.000
 MKH  H24   C24  C23  119.48  3.000
 MKH  C25   C24  C23  120.46  3.000
 MKH  H25   C25  C26  120.37  3.000
 MKH  H25   C25  C24  120.41  3.000
 MKH  C26   C25  C24  119.22  3.000
 MKH  H26   C26  C27  119.43  3.000
 MKH  H26   C26  C25  120.26  3.000
 MKH  C27   C26  C25  120.31  3.000
 MKH  H27   C27  C26  118.02  3.000
 MKH  H27   C27  C22  121.05  3.000
 MKH  C26   C27  C22  120.92  3.000
 MKH  C33   C28  C29  118.17  3.000
 MKH  C33   C28  C20  121.27  3.000
 MKH  C29   C28  C20  120.55  3.000
 MKH  H29   C29  C30  118.60  3.000
 MKH  H29   C29  C28  120.51  3.000
 MKH  C30   C29  C28  120.89  3.000
 MKH  H30   C30  C31  120.15  3.000
 MKH  H30   C30  C29  119.50  3.000
 MKH  C31   C30  C29  120.36  3.000
 MKH  H31   C31  C32  120.49  3.000
 MKH  H31   C31  C30  120.29  3.000
 MKH  C32   C31  C30  119.22  3.000
 MKH  H32   C32  C33  119.51  3.000
 MKH  H32   C32  C31  120.18  3.000
 MKH  C33   C32  C31  120.31  3.000
 MKH  H33   C33  C32  118.21  3.000
 MKH  H33   C33  C28  120.78  3.000
 MKH  C32   C33  C28  121.01  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
 MKH  CONST_01  C25  C24  C23  C22     0.00   0.0  0
 MKH  CONST_02  C25  C26  C27  C22     0.00   0.0  0
 MKH  CONST_03  C26  C27  C22  C23     0.00   0.0  0
 MKH  CONST_04  C26  C25  C24  C23     0.00   0.0  0
 MKH  CONST_05  C27  C22  C23  C24     0.00   0.0  0
 MKH  CONST_06  C27  C26  C25  C24     0.00   0.0  0
 MKH  CONST_07  C31  C30  C29  C28     0.00   0.0  0
 MKH  CONST_08  C31  C32  C33  C28     0.00   0.0  0
 MKH  CONST_09  C32  C33  C28  C29     0.00   0.0  0
 MKH  CONST_10  C32  C31  C30  C29     0.00   0.0  0
 MKH  CONST_11  C33  C28  C29  C30     0.00   0.0  0
 MKH  CONST_12  C33  C32  C31  C30     0.00   0.0  0
 MKH  CONST_13  N5   C4   N3   C2      0.00   0.0  0
 MKH  CONST_14  C6   N5   C4   N3      0.00   0.0  0
 MKH  CONST_15  C7   C2   N3   C4      0.00   0.0  0
 MKH  CONST_16  C24  C23  C22  C20   180.00   0.0  0
 MKH  CONST_17  C26  C27  C22  C20   180.00   0.0  0
 MKH  CONST_18  C30  C29  C28  C20   180.00   0.0  0
 MKH  CONST_19  C32  C33  C28  C20   180.00   0.0  0
 MKH  CONST_20  C4   N3   C2   O1    180.00   0.0  0
 MKH  CONST_21  O8   C4   N3   C2    180.00   0.0  0
 MKH  CONST_22  C9   N5   C4   N3    180.00   0.0  0
 MKH  CONST_23  O8   C4   N5   C6    180.00   0.0  0
 MKH  CONST_24  H24  C24  C23  C22   180.00   0.0  0
 MKH  CONST_25  H26  C26  C27  C22   180.00   0.0  0
 MKH  CONST_26  H27  C27  C22  C23   180.00   0.0  0
 MKH  CONST_27  H25  C25  C24  C23   180.00   0.0  0
 MKH  CONST_28  H23  C23  C24  C25   180.00   0.0  0
 MKH  CONST_29  H30  C30  C29  C28   180.00   0.0  0
 MKH  CONST_30  H32  C32  C33  C28   180.00   0.0  0
 MKH  CONST_31  H33  C33  C28  C29   180.00   0.0  0
 MKH  CONST_32  H31  C31  C30  C29   180.00   0.0  0
 MKH  CONST_33  H29  C29  C30  C31   180.00   0.0  0
 MKH  CONST_34  HN3  N3   C4   N5    180.00   0.0  0
 MKH  CONST_35  C9   N5   C4   O8      0.00   0.0  0
 MKH  Var_01    C16  C15  C14  N13    39.12  30.0  1
 MKH  Var_02    C17  C16  C15  C14   -32.72  30.0  1
 MKH  Var_03    C17  N13  C14  C15   -31.79  30.0  1
 MKH  Var_04    C23  C22  C20  C17  -148.31  30.0  2
 MKH  Var_05    C29  C28  C20  C17   132.22  30.0  2
 MKH  Var_06    C10  C9   N5   C4     85.29  30.0  3
 MKH  Var_07    C14  N13  S12  C11   112.00  30.0  3
 MKH  Var_08    C11  C10  C9   N5    176.35  30.0  3
 MKH  Var_09    N13  S12  C11  C10   172.34  30.0  3
 MKH  Var_10    S12  C11  C10  C9   -177.97  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
 MKH  chir_01  C17  N13  C16  C20  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
 MKH  plan-1  O1   0.020
 MKH  plan-1  C2   0.020
 MKH  plan-1  N3   0.020
 MKH  plan-1  C4   0.020
 MKH  plan-1  N5   0.020
 MKH  plan-1  C6   0.020
 MKH  plan-1  C7   0.020
 MKH  plan-1  O8   0.020
 MKH  plan-1  C9   0.020
 MKH  plan-1  HN3  0.020
 MKH  plan-1  H6   0.020
 MKH  plan-1  H7   0.020
 MKH  plan-2  C20  0.020
 MKH  plan-2  C22  0.020
 MKH  plan-2  C23  0.020
 MKH  plan-2  C24  0.020
 MKH  plan-2  C25  0.020
 MKH  plan-2  C26  0.020
 MKH  plan-2  C27  0.020
 MKH  plan-2  H23  0.020
 MKH  plan-2  H24  0.020
 MKH  plan-2  H25  0.020
 MKH  plan-2  H26  0.020
 MKH  plan-2  H27  0.020
 MKH  plan-3  C20  0.020
 MKH  plan-3  C28  0.020
 MKH  plan-3  C29  0.020
 MKH  plan-3  C30  0.020
 MKH  plan-3  C31  0.020
 MKH  plan-3  C32  0.020
 MKH  plan-3  C33  0.020
 MKH  plan-3  H29  0.020
 MKH  plan-3  H30  0.020
 MKH  plan-3  H31  0.020
 MKH  plan-3  H32  0.020
 MKH  plan-3  H33  0.020

