# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:08:31 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 3-[[2,4-bis(oxidanylidene)pyrimidin-1-yl]methoxy]-~{N}-[(1~{R})-1-(3-cyclopentyloxyphenyl)ethyl]propane-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N[S](=O)(=O)CCCOCN1C=CC(=O)NC1=O)c2cccc(OC3CCCC3)c2
#
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
 FKM  FKM  3-[[2,4-bis(oxidanylidene)pyrimidin-1-yl]methoxy]-~{N}-[(1~{R})-1-(3-cyclopentyloxyphenyl)ethyl]propane-1-sulfonamide  ligand  60  31  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FKM
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
 FKM  O16  O  OS    0  -0.660   1.2721  -0.4373   1.6791
 FKM  S14  S  S     0   1.365   0.2619  -1.4826   1.6314
 FKM  O15  O  OS    0  -0.671  -0.3987  -1.8991   2.8592
 FKM  C13  C  CH2   0  -0.626  -1.0007  -0.9735   0.4660
 FKM  C12  C  CH2   0  -0.473  -1.6330   0.3504   0.8713
 FKM  C11  C  CH2   0  -0.145  -2.6984   0.7407  -0.1358
 FKM  O10  O  O2    0  -0.464  -3.2456   1.9835   0.2585
 FKM  C9   C  CH2   0  -0.065  -4.0228   2.6045  -0.7040
 FKM  N4   N  NR6   0  -0.543  -5.2955   1.9294  -0.9356
 FKM  C3   C  CR6   0   0.739  -6.2995   2.0785   0.0022
 FKM  O8   O  O     0  -0.473  -6.1784   2.7738   0.9870
 FKM  N2   N  NR16  0  -0.731  -7.4465   1.3822  -0.2736
 FKM  C5   C  CR16  0   0.086  -5.4669   1.1312  -2.0305
 FKM  C6   C  CR16  0  -0.505  -6.5987   0.4540  -2.2801
 FKM  C1   C  CR6   0   0.568  -7.7040   0.5558  -1.3583
 FKM  O7   O  O     0  -0.462  -8.7794  -0.0024  -1.4684
 FKM  N17  N  NC1   0  -0.731   0.9755  -2.8171   0.9912
 FKM  C18  C  CH1   0  -0.182   1.8640  -2.6837  -0.1661
 FKM  C19  C  CH3   0  -0.675   1.9380  -4.0393  -0.8606
 FKM  C20  C  CR6   0   0.217   3.2433  -2.2240   0.2436
 FKM  C25  C  CR16  0  -0.321   3.8796  -2.7703   1.3562
 FKM  C24  C  CR16  0  -0.230   5.1743  -2.3855   1.6547
 FKM  C23  C  CR16  0  -0.392   5.8560  -1.4618   0.8680
 FKM  C22  C  CR6   0   0.405   5.2207  -0.9165  -0.2448
 FKM  C21  C  CR16  0  -0.430   3.9127  -1.3062  -0.5454
 FKM  O26  O  O2    0  -0.488   5.7754  -0.0269  -1.0888
 FKM  C27  C  CH1   0  -0.015   7.0812   0.4874  -0.8246
 FKM  C31  C  CH2   0  -0.456   7.4745   1.3024  -2.0480
 FKM  C30  C  CH2   0  -0.448   6.7554   2.6326  -1.8417
 FKM  C29  C  CH2   0  -0.449   6.9424   2.9030  -0.3438
 FKM  C28  C  CH2   0  -0.474   7.0675   1.5129   0.3209
 FKM  H1   H  HCH2  0   0.295  -0.5245  -0.8989  -0.5141
 FKM  H2   H  HCH2  0   0.301  -1.7338  -1.7814   0.4264
 FKM  H3   H  HCH2  0   0.261  -2.0811   0.2656   1.8635
 FKM  H4   H  HCH2  0   0.261  -0.8700   1.1293   0.9124
 FKM  H5   H  HCH2  0   0.219  -2.2587   0.8176  -1.1397
 FKM  H6   H  HCH2  0   0.225  -3.4725  -0.0356  -0.1775
 FKM  H7   H  HCH2  0   0.276  -4.2163   3.6187  -0.3648
 FKM  H8   H  HCH2  0   0.254  -3.5175   2.6480  -1.6743
 FKM  H9   H  HNR6  0   0.427  -8.1919   1.4930   0.4035
 FKM  H10  H  HCR6  0   0.327  -4.6211   1.0823  -2.7023
 FKM  H11  H  HCR6  0   0.295  -6.6898  -0.1623  -3.1608
 FKM  H12  H  HNC1  0   0.420   0.3635  -3.6254   0.9769
 FKM  H13  H  HCH1  0   0.260   1.4569  -1.9669  -0.8893
 FKM  H14  H  HCH3  0   0.242   2.3336  -4.8016  -0.1885
 FKM  H15  H  HCH3  0   0.248   0.9541  -4.3564  -1.2091
 FKM  H16  H  HCH3  0   0.256   2.5968  -3.9756  -1.7251
 FKM  H17  H  HCR6  0   0.244   3.3627  -3.4823   1.9865
 FKM  H18  H  HCR6  0   0.254   5.6743  -2.8037   2.5191
 FKM  H19  H  HCR6  0   0.274   6.8643  -1.1822   1.1399
 FKM  H20  H  HCR6  0   0.249   3.4212  -0.8723  -1.4095
 FKM  H21  H  HCH1  0   0.249   7.7720  -0.3422  -0.6437
 FKM  H22  H  HCH2  0   0.235   8.5567   1.4553  -2.0244
 FKM  H23  H  HCH2  0   0.244   7.2349   0.7982  -2.9857
 FKM  H24  H  HCH2  0   0.234   7.1552   3.4318  -2.4666
 FKM  H25  H  HCH2  0   0.225   5.6963   2.5291  -2.0883
 FKM  H26  H  HCH2  0   0.230   7.8563   3.4778  -0.1836
 FKM  H27  H  HCH2  0   0.234   6.1249   3.4889   0.0767
 FKM  H28  H  HCH2  0   0.249   6.2549   1.3189   1.0230
 FKM  H29  H  HCH2  0   0.243   7.9913   1.4355   0.8965

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
 FKM  O7   C1   double    1.217  0.020  1.217
 FKM  C24  C25  aromatic  1.383  0.020  1.383
 FKM  C24  C23  aromatic  1.392  0.020  1.392
 FKM  C1   C6   single    1.443  0.020  1.443
 FKM  C1   N2   single    1.388  0.020  1.388
 FKM  C25  C20  aromatic  1.393  0.020  1.393
 FKM  C23  C22  aromatic  1.393  0.020  1.393
 FKM  C6   C5   double    1.342  0.020  1.342
 FKM  N2   C3   single    1.370  0.020  1.370
 FKM  C20  C18  single    1.510  0.020  1.510
 FKM  C20  C21  aromatic  1.383  0.020  1.383
 FKM  C22  C21  aromatic  1.398  0.020  1.398
 FKM  C22  O26  single    1.346  0.020  1.346
 FKM  C19  C18  single    1.525  0.020  1.525
 FKM  C18  N17  single    1.465  0.020  1.465
 FKM  O26  C27  single    1.428  0.020  1.428
 FKM  C5   N4   single    1.366  0.020  1.366
 FKM  C3   O8   double    1.212  0.020  1.212
 FKM  C3   N4   single    1.382  0.020  1.382
 FKM  C27  C31  single    1.522  0.020  1.522
 FKM  C27  C28  single    1.538  0.020  1.538
 FKM  C31  C30  single    1.526  0.020  1.526
 FKM  N4   C9   single    1.459  0.020  1.459
 FKM  O15  S14  double    1.455  0.020  1.455
 FKM  N17  S14  single    1.643  0.020  1.643
 FKM  S14  C13  single    1.792  0.020  1.792
 FKM  S14  O16  double    1.454  0.020  1.454
 FKM  C13  C12  single    1.522  0.020  1.522
 FKM  C28  C29  single    1.546  0.020  1.546
 FKM  C30  C29  single    1.534  0.020  1.534
 FKM  C9   O10  single    1.384  0.020  1.384
 FKM  C11  O10  single    1.414  0.020  1.414
 FKM  C11  C12  single    1.517  0.020  1.517
 FKM  C13  H1   single    0.970  0.020  1.090
 FKM  C13  H2   single    0.970  0.020  1.090
 FKM  C12  H3   single    0.970  0.020  1.090
 FKM  C12  H4   single    0.970  0.020  1.090
 FKM  C11  H5   single    0.970  0.020  1.090
 FKM  C11  H6   single    0.970  0.020  1.090
 FKM  C9   H7   single    0.970  0.020  1.090
 FKM  C9   H8   single    0.970  0.020  1.090
 FKM  N2   H9   single    0.860  0.020  1.020
 FKM  C5   H10  single    0.930  0.020  1.080
 FKM  C6   H11  single    0.930  0.020  1.080
 FKM  N17  H12  single    0.890  0.020  1.040
 FKM  C18  H13  single    0.970  0.020  1.090
 FKM  C19  H14  single    0.970  0.020  1.090
 FKM  C19  H15  single    0.970  0.020  1.090
 FKM  C19  H16  single    0.970  0.020  1.090
 FKM  C25  H17  single    0.930  0.020  1.080
 FKM  C24  H18  single    0.930  0.020  1.080
 FKM  C23  H19  single    0.930  0.020  1.080
 FKM  C21  H20  single    0.930  0.020  1.080
 FKM  C27  H21  single    0.970  0.020  1.090
 FKM  C31  H22  single    0.970  0.020  1.090
 FKM  C31  H23  single    0.970  0.020  1.090
 FKM  C30  H24  single    0.970  0.020  1.090
 FKM  C30  H25  single    0.970  0.020  1.090
 FKM  C29  H26  single    0.970  0.020  1.090
 FKM  C29  H27  single    0.970  0.020  1.090
 FKM  C28  H28  single    0.970  0.020  1.090
 FKM  C28  H29  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
 FKM  N17  S14  C13  106.46  3.000
 FKM  C13  S14  O15  108.07  3.000
 FKM  N17  S14  O15  107.06  3.000
 FKM  C13  S14  O16  107.85  3.000
 FKM  N17  S14  O16  107.15  3.000
 FKM  O15  S14  O16  119.56  3.000
 FKM  H2   C13  H1   108.11  3.000
 FKM  H2   C13  C12  111.98  3.000
 FKM  H1   C13  C12  111.14  3.000
 FKM  H2   C13  S14  106.65  3.000
 FKM  H1   C13  S14  107.20  3.000
 FKM  C12  C13  S14  111.51  3.000
 FKM  H4   C12  H3   107.95  3.000
 FKM  H4   C12  C11  109.42  3.000
 FKM  H3   C12  C11  109.57  3.000
 FKM  H4   C12  C13  109.90  3.000
 FKM  H3   C12  C13  110.17  3.000
 FKM  C11  C12  C13  109.80  3.000
 FKM  H6   C11  H5   107.29  3.000
 FKM  H6   C11  O10  111.07  3.000
 FKM  H5   C11  O10  110.37  3.000
 FKM  H6   C11  C12  109.80  3.000
 FKM  H5   C11  C12  110.10  3.000
 FKM  O10  C11  C12  108.22  3.000
 FKM  C9   O10  C11  114.69  3.000
 FKM  H8   C9   H7   108.77  3.000
 FKM  H8   C9   N4   106.28  3.000
 FKM  H7   C9   N4   109.02  3.000
 FKM  H8   C9   O10  112.02  3.000
 FKM  H7   C9   O10  107.55  3.000
 FKM  N4   C9   O10  113.11  3.000
 FKM  C5   N4   C3   121.06  3.000
 FKM  C3   N4   C9   118.43  3.000
 FKM  C5   N4   C9   120.47  3.000
 FKM  N2   C3   O8   122.62  3.000
 FKM  O8   C3   N4   122.75  3.000
 FKM  N2   C3   N4   114.64  3.000
 FKM  H9   N2   C1   116.81  3.000
 FKM  H9   N2   C3   115.21  3.000
 FKM  C1   N2   C3   127.98  3.000
 FKM  H10  C5   C6   121.42  3.000
 FKM  H10  C5   N4   115.23  3.000
 FKM  C6   C5   N4   123.35  3.000
 FKM  H11  C6   C1   119.81  3.000
 FKM  H11  C6   C5   120.75  3.000
 FKM  C1   C6   C5   119.44  3.000
 FKM  O7   C1   C6   125.94  3.000
 FKM  C6   C1   N2   113.53  3.000
 FKM  O7   C1   N2   120.53  3.000
 FKM  H12  N17  C18  115.31  3.000
 FKM  H12  N17  S14  113.01  3.000
 FKM  C18  N17  S14  119.81  3.000
 FKM  H13  C18  C20  108.60  3.000
 FKM  H13  C18  C19  107.38  3.000
 FKM  C20  C18  C19  110.47  3.000
 FKM  H13  C18  N17  110.81  3.000
 FKM  C19  C18  N17  107.95  3.000
 FKM  C20  C18  N17  111.55  3.000
 FKM  H16  C19  H15  108.01  3.000
 FKM  H16  C19  H14  108.10  3.000
 FKM  H15  C19  H14  108.71  3.000
 FKM  H16  C19  C18  109.82  3.000
 FKM  H15  C19  C18  111.11  3.000
 FKM  H14  C19  C18  110.99  3.000
 FKM  C21  C20  C25  119.65  3.000
 FKM  C21  C20  C18  119.29  3.000
 FKM  C25  C20  C18  120.95  3.000
 FKM  H17  C25  C24  120.29  3.000
 FKM  H17  C25  C20  120.32  3.000
 FKM  C24  C25  C20  119.38  3.000
 FKM  H18  C24  C23  118.78  3.000
 FKM  H18  C24  C25  119.81  3.000
 FKM  C23  C24  C25  121.41  3.000
 FKM  H19  C23  C22  121.68  3.000
 FKM  H19  C23  C24  119.11  3.000
 FKM  C22  C23  C24  119.22  3.000
 FKM  O26  C22  C21  115.79  3.000
 FKM  O26  C22  C23  124.89  3.000
 FKM  C21  C22  C23  119.32  3.000
 FKM  H20  C21  C22  118.94  3.000
 FKM  H20  C21  C20  120.04  3.000
 FKM  C22  C21  C20  121.02  3.000
 FKM  C27  O26  C22  119.92  3.000
 FKM  H21  C27  C28  112.83  3.000
 FKM  H21  C27  C31  112.07  3.000
 FKM  C28  C27  C31  104.13  3.000
 FKM  H21  C27  O26  109.56  3.000
 FKM  C28  C27  O26  111.71  3.000
 FKM  C31  C27  O26  106.28  3.000
 FKM  H23  C31  H22  107.49  3.000
 FKM  H23  C31  C30  114.55  3.000
 FKM  H22  C31  C30  109.98  3.000
 FKM  H23  C31  C27  112.75  3.000
 FKM  H22  C31  C27  108.26  3.000
 FKM  C30  C31  C27  103.67  3.000
 FKM  H25  C30  H24  107.19  3.000
 FKM  H25  C30  C29  110.82  3.000
 FKM  H24  C30  C29  112.69  3.000
 FKM  H25  C30  C31  110.11  3.000
 FKM  H24  C30  C31  112.87  3.000
 FKM  C29  C30  C31  103.20  3.000
 FKM  H27  C29  H26  106.75  3.000
 FKM  H27  C29  C28  112.22  3.000
 FKM  H26  C29  C28  110.04  3.000
 FKM  H27  C29  C30  112.34  3.000
 FKM  H26  C29  C30  109.78  3.000
 FKM  C28  C29  C30  105.74  3.000
 FKM  H29  C28  H28  106.17  3.000
 FKM  H29  C28  C29  111.04  3.000
 FKM  H28  C28  C29  112.10  3.000
 FKM  H29  C28  C27  109.76  3.000
 FKM  H28  C28  C27  111.55  3.000
 FKM  C29  C28  C27  106.27  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
 FKM  CONST_01  C23  C24  C25  C20     0.00   0.0  0
 FKM  CONST_02  C23  C22  C21  C20     0.00   0.0  0
 FKM  CONST_03  C22  C23  C24  C25     0.00   0.0  0
 FKM  CONST_04  C22  C21  C20  C25     0.00   0.0  0
 FKM  CONST_05  C21  C20  C25  C24     0.00   0.0  0
 FKM  CONST_06  C21  C22  C23  C24     0.00   0.0  0
 FKM  CONST_07  C1   N2   C3   N4      0.00   0.0  0
 FKM  CONST_08  C6   C1   N2   C3      0.00   0.0  0
 FKM  CONST_09  C5   N4   C3   N2      0.00   0.0  0
 FKM  CONST_10  C24  C25  C20  C18   180.00   0.0  0
 FKM  CONST_11  C22  C21  C20  C18   180.00   0.0  0
 FKM  CONST_12  O26  C22  C21  C20   180.00   0.0  0
 FKM  CONST_13  O26  C22  C23  C24   180.00   0.0  0
 FKM  CONST_14  N2   C3   N4   C9    180.00   0.0  0
 FKM  CONST_15  O7   C1   N2   C3    180.00   0.0  0
 FKM  CONST_16  C1   N2   C3   O8    180.00   0.0  0
 FKM  CONST_17  C5   N4   C3   O8    180.00   0.0  0
 FKM  CONST_18  H18  C24  C25  C20   180.00   0.0  0
 FKM  CONST_19  H19  C23  C24  C25   180.00   0.0  0
 FKM  CONST_20  H20  C21  C20  C25   180.00   0.0  0
 FKM  CONST_21  H17  C25  C24  C23   180.00   0.0  0
 FKM  CONST_22  H9   N2   C3   N4    180.00   0.0  0
 FKM  CONST_23  O8   C3   N4   C9      0.00   0.0  0
 FKM  Var_01    C29  C30  C31  C27    41.06  30.0  1
 FKM  Var_02    C30  C29  C28  C27     5.16  30.0  1
 FKM  Var_03    C28  C29  C30  C31   -28.22  30.0  1
 FKM  Var_04    C5   N4   C9   O10  -102.14  30.0  2
 FKM  Var_05    N4   C9   O10  C11    70.62  30.0  1
 FKM  Var_06    C18  N17  S14  O16   -42.90  30.0  1
 FKM  Var_07    C12  C13  S14  O16   -58.88  30.0  3
 FKM  Var_08    C11  C12  C13  S14  -179.73  30.0  3
 FKM  Var_09    O10  C11  C12  C13  -178.96  30.0  1

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
 FKM  chir_01  C18  C20  C19  N17  negativ
 FKM  chir_02  C27  O26  C31  C28  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
 FKM  plan-1  C9   0.020
 FKM  plan-1  N4   0.020
 FKM  plan-1  C3   0.020
 FKM  plan-1  O8   0.020
 FKM  plan-1  N2   0.020
 FKM  plan-1  C5   0.020
 FKM  plan-1  C6   0.020
 FKM  plan-1  C1   0.020
 FKM  plan-1  O7   0.020
 FKM  plan-1  H9   0.020
 FKM  plan-1  H10  0.020
 FKM  plan-1  H11  0.020
 FKM  plan-2  C18  0.020
 FKM  plan-2  C20  0.020
 FKM  plan-2  C25  0.020
 FKM  plan-2  C24  0.020
 FKM  plan-2  C23  0.020
 FKM  plan-2  C22  0.020
 FKM  plan-2  C21  0.020
 FKM  plan-2  O26  0.020
 FKM  plan-2  H17  0.020
 FKM  plan-2  H18  0.020
 FKM  plan-2  H19  0.020
 FKM  plan-2  H20  0.020

