# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 16:54:28 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-(1,3-benzothiazol-2-yl)-2-(cyclopropylamino)-6-{[(1R,2S,3R,4R)-2,3-dihydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@@H](NC2=C(C(=O)NC(=N2)NC3CC3)c4sc5ccccc5n4)[C@H](O)[C@@H]1O
#
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
 4S2  4S2  5-(1,3-benzothiazol-2-yl)-2-(cyclopropylamino)-6-{[(1R,2S,3R,4R)-2,3-dihydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyrimidin-4(3H)-one  ligand  53  30  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4S2
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
 4S2  C01  C  CR6   0   0.568  -0.5338   0.8812  -0.0349
 4S2  N02  N  N     0  -0.505  -1.7390   1.4750  -0.0201
 4S2  C03  C  CR6   0   0.765  -1.8015   2.7767   0.0422
 4S2  N04  N  NR16  0  -0.743  -0.6953   3.5594   0.0768
 4S2  C05  C  CR6   0   0.536   0.5923   3.0462   0.0470
 4S2  C06  C  CR6   0  -0.337   0.6808   1.6259  -0.0082
 4S2  N07  N  NH1   0  -0.684  -0.5168  -0.4474  -0.0666
 4S2  N08  N  NH1   0  -0.671  -2.9888   3.3892   0.0800
 4S2  O09  O  O     0  -0.489   1.5451   3.8215   0.0718
 4S2  C10  C  CR5   0   0.121   1.9745   1.0134  -0.0356
 4S2  C11  C  CH1   0  -0.107  -1.6710  -1.3059  -0.1118
 4S2  C12  C  CH1   0   0.026  -1.7720  -2.1111  -1.4018
 4S2  C13  C  CH1   0   0.009  -2.8439  -3.1521  -1.0630
 4S2  C14  C  CH1   0  -0.290  -2.5365  -3.5377   0.3942
 4S2  C15  C  CH2   0  -0.449  -1.6458  -2.4042   0.9529
 4S2  O16  O  OH1   0  -0.661  -2.0854  -1.2906  -2.4948
 4S2  O17  O  OH1   0  -0.676  -4.1293  -2.5772  -1.1254
 4S2  C18  C  CH2   0  -0.147  -1.8741  -4.9011   0.4756
 4S2  O19  O  OH1   0  -0.671  -1.5858  -5.1850   1.8252
 4S2  C20  C  CH1   0  -0.078  -4.2206   2.6746  -0.0082
 4S2  C21  C  CH2   0  -0.513  -5.3553   3.1572   0.8369
 4S2  C22  C  CH2   0  -0.467  -4.6726   1.8645   1.1606
 4S2  S23  S  S2    0   0.220   3.4545   1.9740  -0.0029
 4S2  C24  C  CR56  0  -0.274   4.3751   0.5041  -0.0651
 4S2  C25  C  CR56  0   0.412   3.5068  -0.5957  -0.1046
 4S2  N26  N  N     0  -0.544   2.1765  -0.2743  -0.0857
 4S2  C27  C  CR16  0  -0.289   5.7547   0.3394  -0.0798
 4S2  C28  C  CR16  0  -0.274   6.2603  -0.9495  -0.1355
 4S2  C29  C  CR16  0  -0.260   5.4026  -2.0535  -0.1753
 4S2  C30  C  CR16  0  -0.324   4.0295  -1.8886  -0.1602
 4S2  H1   H  HNR6  0   0.423  -0.7842   4.5656   0.1242
 4S2  H3   H  HNH1  0   0.413  -3.0184   4.3950   0.0170
 4S2  H4   H  HCH1  0   0.285  -2.5597  -0.6834  -0.0082
 4S2  H5   H  HCH1  0   0.213  -0.8175  -2.6357  -1.5599
 4S2  H6   H  HCH1  0   0.220  -2.7773  -4.0191  -1.7375
 4S2  H7   H  HCH1  0   0.254  -3.4806  -3.5856   0.9436
 4S2  H8   H  HCH2  0   0.233  -0.6181  -2.7558   1.0876
 4S2  H9   H  HCH2  0   0.254  -1.9814  -2.0414   1.9235
 4S2  H10  H  HOH1  0   0.459  -1.8970  -1.7738  -3.3056
 4S2  H11  H  HOH1  0   0.441  -4.1678  -2.0426  -1.9275
 4S2  H12  H  HCH2  0   0.206  -2.5470  -5.6529   0.0418
 4S2  H13  H  HCH2  0   0.191  -0.9621  -4.9014  -0.1386
 4S2  H14  H  HOH1  0   0.454  -1.0884  -6.0068   1.8604
 4S2  H15  H  HCH1  0   0.270  -4.4601   2.2928  -0.9953
 4S2  H16  H  HCH2  0   0.260  -5.1734   4.0017   1.4899
 4S2  H17  H  HCH2  0   0.261  -6.3459   3.1310   0.4030
 4S2  H18  H  HCH2  0   0.255  -5.1841   0.9350   0.9492
 4S2  H19  H  HCH2  0   0.256  -4.0245   1.8353   2.0264
 4S2  H20  H  HCR6  0   0.268   6.4206   1.1919  -0.0494
 4S2  H21  H  HCR6  0   0.257   7.3315  -1.1012  -0.1484
 4S2  H22  H  HCR6  0   0.256   5.8199  -3.0511  -0.2197
 4S2  H23  H  HCR6  0   0.257   3.3619  -2.7401  -0.1917
 4S2  H2   H  HNH1  0   0.412   0.4124  -0.8677  -0.0827

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
 4S2  C28  C29  aromatic  1.398  0.020  1.398
 4S2  C28  C27  aromatic  1.386  0.020  1.386
 4S2  C29  C30  aromatic  1.383  0.020  1.383
 4S2  C27  C24  aromatic  1.390  0.020  1.390
 4S2  C30  C25  aromatic  1.396  0.020  1.396
 4S2  C24  C25  aromatic  1.402  0.020  1.402
 4S2  C24  S23  aromatic  1.736  0.020  1.736
 4S2  C25  N26  aromatic  1.369  0.020  1.369
 4S2  S23  C10  aromatic  1.765  0.020  1.765
 4S2  N26  C10  aromatic  1.304  0.020  1.304
 4S2  C10  C06  single    1.432  0.020  1.432
 4S2  O09  C05  double    1.229  0.020  1.229
 4S2  C06  C05  single    1.424  0.020  1.424
 4S2  C06  C01  double    1.425  0.020  1.425
 4S2  C05  N04  single    1.386  0.020  1.386
 4S2  N07  C01  single    1.329  0.020  1.329
 4S2  N07  C11  single    1.439  0.020  1.439
 4S2  C01  N02  single    1.344  0.020  1.344
 4S2  C15  C11  single    1.530  0.020  1.530
 4S2  C15  C14  single    1.546  0.020  1.546
 4S2  C11  C12  single    1.524  0.020  1.524
 4S2  N04  C03  single    1.355  0.020  1.355
 4S2  O19  C18  single    1.409  0.020  1.409
 4S2  N02  C03  double    1.305  0.020  1.305
 4S2  C14  C18  single    1.518  0.020  1.518
 4S2  C14  C13  single    1.538  0.020  1.538
 4S2  C03  N08  single    1.337  0.020  1.337
 4S2  C12  C13  single    1.532  0.020  1.532
 4S2  C12  O16  single    1.402  0.020  1.402
 4S2  C13  O17  single    1.410  0.020  1.410
 4S2  N08  C20  single    1.427  0.020  1.427
 4S2  C20  C21  single    1.495  0.020  1.495
 4S2  C20  C22  single    1.492  0.020  1.492
 4S2  C21  C22  single    1.497  0.020  1.497
 4S2  N04  H1   single    0.860  0.020  1.020
 4S2  N08  H3   single    0.860  0.020  1.020
 4S2  C11  H4   single    0.970  0.020  1.090
 4S2  C12  H5   single    0.970  0.020  1.090
 4S2  C13  H6   single    0.970  0.020  1.090
 4S2  C14  H7   single    0.970  0.020  1.090
 4S2  C15  H8   single    0.970  0.020  1.090
 4S2  C15  H9   single    0.970  0.020  1.090
 4S2  O16  H10  single    0.850  0.020  0.980
 4S2  O17  H11  single    0.850  0.020  0.980
 4S2  C18  H12  single    0.970  0.020  1.090
 4S2  C18  H13  single    0.970  0.020  1.090
 4S2  O19  H14  single    0.850  0.020  0.980
 4S2  C20  H15  single    0.970  0.020  1.090
 4S2  C21  H16  single    0.970  0.020  1.090
 4S2  C21  H17  single    0.970  0.020  1.090
 4S2  C22  H18  single    0.970  0.020  1.090
 4S2  C22  H19  single    0.970  0.020  1.090
 4S2  C27  H20  single    0.930  0.020  1.080
 4S2  C28  H21  single    0.930  0.020  1.080
 4S2  C29  H22  single    0.930  0.020  1.080
 4S2  C30  H23  single    0.930  0.020  1.080
 4S2  N07  H2   single    0.860  0.020  1.020

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
 4S2  N07  C01  C06  120.80  3.000
 4S2  N07  C01  N02  116.97  3.000
 4S2  C06  C01  N02  122.23  3.000
 4S2  C03  N02  C01  118.97  3.000
 4S2  N08  C03  N04  117.37  3.000
 4S2  N08  C03  N02  120.07  3.000
 4S2  N04  C03  N02  122.56  3.000
 4S2  H1   N04  C05  116.80  3.000
 4S2  H1   N04  C03  120.27  3.000
 4S2  C05  N04  C03  122.93  3.000
 4S2  O09  C05  C06  125.58  3.000
 4S2  C06  C05  N04  115.32  3.000
 4S2  O09  C05  N04  119.09  3.000
 4S2  C10  C06  C05  118.92  3.000
 4S2  C05  C06  C01  117.97  3.000
 4S2  C10  C06  C01  123.11  3.000
 4S2  H2   N07  C11  118.97  3.000
 4S2  H2   N07  C01  115.08  3.000
 4S2  C11  N07  C01  125.93  3.000
 4S2  H3   N08  C20  118.07  3.000
 4S2  H3   N08  C03  118.78  3.000
 4S2  C20  N08  C03  122.39  3.000
 4S2  N26  C10  S23  114.10  3.000
 4S2  N26  C10  C06  124.26  3.000
 4S2  S23  C10  C06  121.64  3.000
 4S2  H4   C11  C15  110.94  3.000
 4S2  H4   C11  C12  109.16  3.000
 4S2  C15  C11  C12  102.17  3.000
 4S2  H4   C11  N07  108.07  3.000
 4S2  C12  C11  N07  113.26  3.000
 4S2  C15  C11  N07  113.15  3.000
 4S2  H5   C12  O16  111.15  3.000
 4S2  H5   C12  C13  108.34  3.000
 4S2  O16  C12  C13  114.43  3.000
 4S2  H5   C12  C11  108.42  3.000
 4S2  O16  C12  C11  111.43  3.000
 4S2  C13  C12  C11  102.60  3.000
 4S2  H6   C13  O17  110.45  3.000
 4S2  H6   C13  C14  111.78  3.000
 4S2  O17  C13  C14  109.05  3.000
 4S2  H6   C13  C12  110.94  3.000
 4S2  O17  C13  C12  110.55  3.000
 4S2  C14  C13  C12  103.89  3.000
 4S2  H7   C14  C18  108.09  3.000
 4S2  H7   C14  C15  110.36  3.000
 4S2  C18  C14  C15  112.81  3.000
 4S2  H7   C14  C13  108.32  3.000
 4S2  C18  C14  C13  111.30  3.000
 4S2  C15  C14  C13  105.88  3.000
 4S2  H9   C15  H8   106.65  3.000
 4S2  H9   C15  C14  112.88  3.000
 4S2  H8   C15  C14  110.48  3.000
 4S2  H9   C15  C11  112.08  3.000
 4S2  H8   C15  C11  109.38  3.000
 4S2  C14  C15  C11  105.39  3.000
 4S2  H10  O16  C12  108.61  3.000
 4S2  H11  O17  C13  107.41  3.000
 4S2  H13  C18  H12  106.70  3.000
 4S2  H13  C18  O19  111.42  3.000
 4S2  H12  C18  O19  111.46  3.000
 4S2  H13  C18  C14  109.40  3.000
 4S2  H12  C18  C14  109.04  3.000
 4S2  O19  C18  C14  108.76  3.000
 4S2  H14  O19  C18  108.26  3.000
 4S2  H15  C20  C22  117.04  3.000
 4S2  H15  C20  C21  117.41  3.000
 4S2  C22  C20  C21   60.16  3.000
 4S2  H15  C20  N08  115.03  3.000
 4S2  C22  C20  N08  119.01  3.000
 4S2  C21  C20  N08  117.30  3.000
 4S2  H17  C21  H16  114.49  3.000
 4S2  H17  C21  C22  118.90  3.000
 4S2  H16  C21  C22  117.80  3.000
 4S2  H17  C21  C20  117.41  3.000
 4S2  H16  C21  C20  117.72  3.000
 4S2  C22  C21  C20   59.83  3.000
 4S2  H19  C22  H18  114.61  3.000
 4S2  H19  C22  C21  118.00  3.000
 4S2  H18  C22  C21  118.94  3.000
 4S2  H19  C22  C20  117.39  3.000
 4S2  H18  C22  C20  117.17  3.000
 4S2  C21  C22  C20   60.01  3.000
 4S2  C24  S23  C10   89.03  3.000
 4S2  C27  C24  C25  121.45  3.000
 4S2  C25  C24  S23  109.69  3.000
 4S2  C27  C24  S23  128.86  3.000
 4S2  C30  C25  N26  125.60  3.000
 4S2  N26  C25  C24  114.67  3.000
 4S2  C30  C25  C24  119.73  3.000
 4S2  C25  N26  C10  112.51  3.000
 4S2  H20  C27  C28  120.62  3.000
 4S2  H20  C27  C24  121.16  3.000
 4S2  C28  C27  C24  118.22  3.000
 4S2  H21  C28  C29  119.75  3.000
 4S2  H21  C28  C27  119.48  3.000
 4S2  C29  C28  C27  120.78  3.000
 4S2  H22  C29  C30  119.54  3.000
 4S2  H22  C29  C28  119.50  3.000
 4S2  C30  C29  C28  120.96  3.000
 4S2  H23  C30  C29  121.21  3.000
 4S2  H23  C30  C25  119.93  3.000
 4S2  C29  C30  C25  118.86  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
 4S2  CONST_01  C27  C24  S23  C10   180.00   0.0  0
 4S2  CONST_02  C25  C24  S23  C10     0.00   0.0  0
 4S2  CONST_03  C30  C25  N26  C10   180.00   0.0  0
 4S2  CONST_04  C24  C25  N26  C10     0.00   0.0  0
 4S2  CONST_05  C28  C27  C24  S23   180.00   0.0  0
 4S2  CONST_06  C30  C25  C24  S23   180.00   0.0  0
 4S2  CONST_07  N26  C25  C24  S23     0.00   0.0  0
 4S2  CONST_08  C25  N26  C10  S23     0.00   0.0  0
 4S2  CONST_09  C29  C28  C27  C24     0.00   0.0  0
 4S2  CONST_10  C29  C30  C25  C24     0.00   0.0  0
 4S2  CONST_11  N26  C10  S23  C24     0.00   0.0  0
 4S2  CONST_12  C28  C29  C30  C25     0.00   0.0  0
 4S2  CONST_13  C28  C27  C24  C25     0.00   0.0  0
 4S2  CONST_14  C29  C30  C25  N26   180.00   0.0  0
 4S2  CONST_15  C27  C24  C25  N26   180.00   0.0  0
 4S2  CONST_16  C30  C29  C28  C27     0.00   0.0  0
 4S2  CONST_17  C30  C25  C24  C27     0.00   0.0  0
 4S2  CONST_18  C24  S23  C10  C06   180.00   0.0  0
 4S2  CONST_19  C25  N26  C10  C06   180.00   0.0  0
 4S2  CONST_20  N04  C03  N02  C01     0.00   0.0  0
 4S2  CONST_21  C05  N04  C03  N02     0.00   0.0  0
 4S2  CONST_22  C06  C05  N04  C03     0.00   0.0  0
 4S2  CONST_23  C06  C01  N02  C03     0.00   0.0  0
 4S2  CONST_24  N08  C03  N02  C01   180.00   0.0  0
 4S2  CONST_25  C11  N07  C01  N02     0.00   0.0  0
 4S2  CONST_26  C20  N08  C03  N02     0.00   0.0  0
 4S2  CONST_27  O09  C05  N04  C03   180.00   0.0  0
 4S2  CONST_28  N07  C01  N02  C03   180.00   0.0  0
 4S2  CONST_29  C20  N08  C03  N04   180.00   0.0  0
 4S2  CONST_30  N08  C03  N04  C05   180.00   0.0  0
 4S2  CONST_31  C11  N07  C01  C06   180.00   0.0  0
 4S2  CONST_32  H20  C27  C24  S23     0.00   0.0  0
 4S2  CONST_33  H21  C28  C27  C24   180.00   0.0  0
 4S2  CONST_34  H23  C30  C25  C24   180.00   0.0  0
 4S2  CONST_35  H22  C29  C30  C25   180.00   0.0  0
 4S2  CONST_36  H1   N04  C03  N02   180.00   0.0  0
 4S2  CONST_37  H2   N07  C01  N02   180.00   0.0  0
 4S2  CONST_38  H3   N08  C03  N02   180.00   0.0  0
 4S2  Var_01    S23  C10  C06  C01   179.93  30.0  2
 4S2  Var_02    C21  C20  N08  C03   142.15  30.0  3
 4S2  Var_03    C22  C21  C20  N08  -109.45  30.0  1
 4S2  Var_04    H18  C22  C21  C20  -106.46  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
 4S2  chir_01  C11  N07  C15  C12  positiv
 4S2  chir_02  C12  O16  C11  C13  negativ
 4S2  chir_03  C13  O17  C12  C14  negativ
 4S2  chir_04  C14  C13  C18  C15  negativ
 4S2  chir_05  C20  N08  C21  C22  both

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
 4S2  plan-1  C01  0.020
 4S2  plan-1  N02  0.020
 4S2  plan-1  C03  0.020
 4S2  plan-1  N04  0.020
 4S2  plan-1  C05  0.020
 4S2  plan-1  C06  0.020
 4S2  plan-1  N07  0.020
 4S2  plan-1  N08  0.020
 4S2  plan-1  O09  0.020
 4S2  plan-1  C10  0.020
 4S2  plan-1  C11  0.020
 4S2  plan-1  C20  0.020
 4S2  plan-1  H1   0.020
 4S2  plan-1  H3   0.020
 4S2  plan-1  H2   0.020
 4S2  plan-2  C06  0.020
 4S2  plan-2  C10  0.020
 4S2  plan-2  S23  0.020
 4S2  plan-2  C24  0.020
 4S2  plan-2  C25  0.020
 4S2  plan-2  N26  0.020
 4S2  plan-2  C27  0.020
 4S2  plan-2  C28  0.020
 4S2  plan-2  C29  0.020
 4S2  plan-2  C30  0.020
 4S2  plan-2  H20  0.020
 4S2  plan-2  H21  0.020
 4S2  plan-2  H22  0.020
 4S2  plan-2  H23  0.020

