# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 15:14:22 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (1R,2S,3R,5R)-3-{[5-(1,3-benzothiazol-2-yl)-2-(propylamino)pyrimidin-4-yl]amino}-5-(hydroxymethyl)cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNc1ncc(c(N[C@@H]2C[C@H](CO)[C@@H](O)[C@H]2O)n1)c3sc4ccccc4n3
#
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
 4S1  4S1  (1R,2S,3R,5R)-3-{[5-(1,3-benzothiazol-2-yl)-2-(propylamino)pyrimidin-4-yl]amino}-5-(hydroxymethyl)cyclopentane-1,2-diol  ligand  54  29  .  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_4S1
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
 4S1  C01  C  CR6   0   0.560  -0.6984   0.3546   0.1447
 4S1  N02  N  N     0  -0.522  -2.0226   0.3198   0.2245
 4S1  C03  C  CR6   0   0.610  -2.6927   1.4697   0.2513
 4S1  N04  N  N     0  -0.489  -2.1534   2.7005   0.1956
 4S1  C05  C  CR16  0  -0.053  -0.8397   2.7310   0.1162
 4S1  C06  C  CR6   0  -0.170  -0.0126   1.6156   0.0876
 4S1  N07  N  NH1   0  -0.689  -0.0236  -0.7965   0.1341
 4S1  N08  N  NH1   0  -0.652  -4.0242   1.3845   0.3382
 4S1  C09  C  CR5   0   0.096   1.4200   1.7362  -0.0044
 4S1  C10  C  CH1   0  -0.097  -0.6141  -2.1069   0.1008
 4S1  C11  C  CH1   0   0.031  -0.5018  -2.7987  -1.2536
 4S1  C12  C  CH1   0   0.007  -0.9151  -4.2382  -0.9292
 4S1  C13  C  CH1   0  -0.286  -0.3024  -4.4970   0.4602
 4S1  C14  C  CH2   0  -0.450   0.0789  -3.1095   1.0221
 4S1  O15  O  OH1   0  -0.660  -1.2955  -2.1698  -2.2227
 4S1  O16  O  OH1   0  -0.677  -2.3184  -4.3458  -0.8393
 4S1  C17  C  CH2   0  -0.148   0.8775  -5.4469   0.3825
 4S1  O18  O  OH1   0  -0.671   1.3945  -5.6304   1.6805
 4S1  C19  C  CH2   0  -0.230  -4.9294   2.5110   0.3859
 4S1  C20  C  CH2   0  -0.474  -6.3677   2.0183   0.4271
 4S1  C21  C  CH3   0  -0.664  -7.3637   3.1662   0.4663
 4S1  S22  S  S2    0   0.209   2.1963   3.3155  -0.0997
 4S1  C23  C  CR56  0  -0.264   3.7376   2.5291  -0.1769
 4S1  C24  C  CR56  0   0.414   3.5524   1.1394  -0.1245
 4S1  N25  N  N     0  -0.517   2.2455   0.7363  -0.0284
 4S1  C26  C  CR16  0  -0.281   5.0010   3.0958  -0.2756
 4S1  C27  C  CR16  0  -0.270   6.0918   2.2427  -0.3227
 4S1  C28  C  CR16  0  -0.256   5.9215   0.8560  -0.2710
 4S1  C29  C  CR16  0  -0.320   4.6612   0.2953  -0.1722
 4S1  H1   H  HCR6  0   0.261  -0.4037   3.7265   0.0718
 4S1  H2   H  HNH1  0   0.410   0.9859  -0.7128   0.0569
 4S1  H3   H  HNH1  0   0.395  -4.4085   0.4551   0.3977
 4S1  H4   H  HCH1  0   0.264  -1.6671  -2.0117   0.3657
 4S1  H5   H  HCH1  0   0.212   0.5585  -2.8036  -1.5483
 4S1  H6   H  HCH1  0   0.219  -0.5248  -4.9382  -1.6831
 4S1  H7   H  HCH1  0   0.254  -1.0706  -4.9595   1.0859
 4S1  H8   H  HCH2  0   0.232   1.1628  -2.9633   0.9661
 4S1  H9   H  HCH2  0   0.255  -0.2053  -2.9795   2.0654
 4S1  H10  H  HOH1  0   0.459  -1.0129  -2.4671  -3.0936
 4S1  H11  H  HOH1  0   0.440  -2.6923  -3.8780  -1.5953
 4S1  H12  H  HCH2  0   0.206   0.5474  -6.3978  -0.0575
 4S1  H13  H  HCH2  0   0.191   1.6366  -5.0295  -0.2948
 4S1  H14  H  HOH1  0   0.454   2.1920  -6.1630   1.6155
 4S1  H15  H  HCH2  0   0.227  -4.7254   3.1301   1.2651
 4S1  H16  H  HCH2  0   0.228  -4.7823   3.1506  -0.4890
 4S1  H17  H  HCH2  0   0.231  -6.5578   1.3925  -0.4492
 4S1  H18  H  HCH2  0   0.231  -6.5044   1.3782   1.3033
 4S1  H19  H  HCH3  0   0.236  -8.3871   2.7928   0.4899
 4S1  H20  H  HCH3  0   0.223  -7.2196   3.7898   1.3499
 4S1  H21  H  HCH3  0   0.223  -7.2657   3.8067  -0.4114
 4S1  H22  H  HCR6  0   0.274   5.1326   4.1687  -0.3158
 4S1  H23  H  HCR6  0   0.264   7.0880   2.6574  -0.4007
 4S1  H24  H  HCR6  0   0.262   6.7891   0.2112  -0.3090
 4S1  H25  H  HCR6  0   0.264   4.5257  -0.7777  -0.1336

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
 4S1  C27  C28  aromatic  1.398  0.020  1.398
 4S1  C27  C26  aromatic  1.386  0.020  1.386
 4S1  C28  C29  aromatic  1.383  0.020  1.383
 4S1  C26  C23  aromatic  1.388  0.020  1.388
 4S1  C29  C24  aromatic  1.394  0.020  1.394
 4S1  C23  C24  aromatic  1.403  0.020  1.403
 4S1  C23  S22  aromatic  1.732  0.020  1.732
 4S1  C24  N25  aromatic  1.371  0.020  1.371
 4S1  S22  C09  aromatic  1.762  0.020  1.762
 4S1  N25  C09  aromatic  1.297  0.020  1.297
 4S1  C09  C06  single    1.441  0.020  1.441
 4S1  O18  C17  single    1.409  0.020  1.409
 4S1  C06  C05  aromatic  1.389  0.020  1.389
 4S1  C06  C01  aromatic  1.437  0.020  1.437
 4S1  C17  C13  single    1.517  0.020  1.517
 4S1  C05  N04  aromatic  1.316  0.020  1.316
 4S1  N07  C01  single    1.334  0.020  1.334
 4S1  N07  C10  single    1.438  0.020  1.438
 4S1  C01  N02  aromatic  1.327  0.020  1.327
 4S1  C14  C13  single    1.545  0.020  1.545
 4S1  C14  C10  single    1.528  0.020  1.528
 4S1  N04  C03  aromatic  1.345  0.020  1.345
 4S1  C13  C12  single    1.540  0.020  1.540
 4S1  C10  C11  single    1.525  0.020  1.525
 4S1  N02  C03  aromatic  1.331  0.020  1.331
 4S1  C03  N08  single    1.337  0.020  1.337
 4S1  C12  C11  single    1.532  0.020  1.532
 4S1  C12  O16  single    1.410  0.020  1.410
 4S1  C11  O15  single    1.402  0.020  1.402
 4S1  N08  C19  single    1.446  0.020  1.446
 4S1  C19  C20  single    1.521  0.020  1.521
 4S1  C20  C21  single    1.520  0.020  1.520
 4S1  C05  H1   single    0.930  0.020  1.080
 4S1  N07  H2   single    0.860  0.020  1.020
 4S1  N08  H3   single    0.860  0.020  1.020
 4S1  C10  H4   single    0.970  0.020  1.090
 4S1  C11  H5   single    0.970  0.020  1.090
 4S1  C12  H6   single    0.970  0.020  1.090
 4S1  C13  H7   single    0.970  0.020  1.090
 4S1  C14  H8   single    0.970  0.020  1.090
 4S1  C14  H9   single    0.970  0.020  1.090
 4S1  O15  H10  single    0.850  0.020  0.980
 4S1  O16  H11  single    0.850  0.020  0.980
 4S1  C17  H12  single    0.970  0.020  1.090
 4S1  C17  H13  single    0.970  0.020  1.090
 4S1  O18  H14  single    0.850  0.020  0.980
 4S1  C19  H15  single    0.970  0.020  1.090
 4S1  C19  H16  single    0.970  0.020  1.090
 4S1  C20  H17  single    0.970  0.020  1.090
 4S1  C20  H18  single    0.970  0.020  1.090
 4S1  C21  H19  single    0.970  0.020  1.090
 4S1  C21  H20  single    0.970  0.020  1.090
 4S1  C21  H21  single    0.970  0.020  1.090
 4S1  C26  H22  single    0.930  0.020  1.080
 4S1  C27  H23  single    0.930  0.020  1.080
 4S1  C28  H24  single    0.930  0.020  1.080
 4S1  C29  H25  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
 4S1  N07  C01  C06  121.03  3.000
 4S1  N07  C01  N02  118.84  3.000
 4S1  C06  C01  N02  120.12  3.000
 4S1  C03  N02  C01  118.74  3.000
 4S1  N08  C03  N04  117.41  3.000
 4S1  N08  C03  N02  116.59  3.000
 4S1  N04  C03  N02  126.00  3.000
 4S1  C05  N04  C03  115.08  3.000
 4S1  H1   C05  C06  119.70  3.000
 4S1  H1   C05  N04  115.07  3.000
 4S1  C06  C05  N04  125.23  3.000
 4S1  C09  C06  C05  121.76  3.000
 4S1  C05  C06  C01  114.82  3.000
 4S1  C09  C06  C01  123.42  3.000
 4S1  H2   N07  C10  118.78  3.000
 4S1  H2   N07  C01  115.60  3.000
 4S1  C10  N07  C01  125.36  3.000
 4S1  H3   N08  C19  118.55  3.000
 4S1  H3   N08  C03  116.26  3.000
 4S1  C19  N08  C03  125.17  3.000
 4S1  N25  C09  S22  114.18  3.000
 4S1  N25  C09  C06  124.73  3.000
 4S1  S22  C09  C06  121.09  3.000
 4S1  H4   C10  C14  110.42  3.000
 4S1  H4   C10  C11  109.07  3.000
 4S1  C14  C10  C11  101.80  3.000
 4S1  H4   C10  N07  108.15  3.000
 4S1  C11  C10  N07  113.82  3.000
 4S1  C14  C10  N07  113.44  3.000
 4S1  H5   C11  O15  111.25  3.000
 4S1  H5   C11  C12  108.20  3.000
 4S1  O15  C11  C12  114.53  3.000
 4S1  H5   C11  C10  108.11  3.000
 4S1  O15  C11  C10  111.64  3.000
 4S1  C12  C11  C10  102.61  3.000
 4S1  H6   C12  O16  110.37  3.000
 4S1  H6   C12  C13  111.72  3.000
 4S1  O16  C12  C13  109.00  3.000
 4S1  H6   C12  C11  110.91  3.000
 4S1  O16  C12  C11  110.70  3.000
 4S1  C13  C12  C11  103.98  3.000
 4S1  H7   C13  C17  108.12  3.000
 4S1  H7   C13  C14  110.19  3.000
 4S1  C17  C13  C14  112.90  3.000
 4S1  H7   C13  C12  107.93  3.000
 4S1  C14  C13  C12  105.98  3.000
 4S1  C17  C13  C12  111.62  3.000
 4S1  H9   C14  H8   106.94  3.000
 4S1  H9   C14  C13  113.03  3.000
 4S1  H8   C14  C13  110.22  3.000
 4S1  H9   C14  C10  112.39  3.000
 4S1  H8   C14  C10  109.30  3.000
 4S1  C13  C14  C10  104.96  3.000
 4S1  H10  O15  C11  108.71  3.000
 4S1  H11  O16  C12  107.39  3.000
 4S1  H13  C17  H12  106.82  3.000
 4S1  H13  C17  O18  111.32  3.000
 4S1  H12  C17  O18  111.50  3.000
 4S1  H13  C17  C13  109.32  3.000
 4S1  H12  C17  C13  109.20  3.000
 4S1  O18  C17  C13  108.65  3.000
 4S1  H14  O18  C17  108.31  3.000
 4S1  H16  C19  H15  106.67  3.000
 4S1  H16  C19  C20  109.78  3.000
 4S1  H15  C19  C20  109.74  3.000
 4S1  H16  C19  N08  110.18  3.000
 4S1  H15  C19  N08  110.51  3.000
 4S1  C20  C19  N08  109.91  3.000
 4S1  H18  C20  H17  106.58  3.000
 4S1  H18  C20  C21  109.84  3.000
 4S1  H17  C20  C21  109.81  3.000
 4S1  H18  C20  C19  109.24  3.000
 4S1  H17  C20  C19  109.16  3.000
 4S1  C21  C20  C19  112.07  3.000
 4S1  H21  C21  H20  107.70  3.000
 4S1  H21  C21  H19  107.64  3.000
 4S1  H20  C21  H19  107.60  3.000
 4S1  H21  C21  C20  111.33  3.000
 4S1  H20  C21  C20  111.46  3.000
 4S1  H19  C21  C20  110.92  3.000
 4S1  C23  S22  C09   89.28  3.000
 4S1  C26  C23  C24  121.81  3.000
 4S1  C24  C23  S22  109.31  3.000
 4S1  C26  C23  S22  128.88  3.000
 4S1  C29  C24  N25  125.62  3.000
 4S1  N25  C24  C23  114.81  3.000
 4S1  C29  C24  C23  119.56  3.000
 4S1  C24  N25  C09  112.42  3.000
 4S1  H22  C26  C27  120.91  3.000
 4S1  H22  C26  C23  121.22  3.000
 4S1  C27  C26  C23  117.87  3.000
 4S1  H23  C27  C28  119.67  3.000
 4S1  H23  C27  C26  119.43  3.000
 4S1  C28  C27  C26  120.90  3.000
 4S1  H24  C28  C29  119.46  3.000
 4S1  H24  C28  C27  119.49  3.000
 4S1  C29  C28  C27  121.05  3.000
 4S1  H25  C29  C28  121.24  3.000
 4S1  H25  C29  C24  119.96  3.000
 4S1  C28  C29  C24  118.80  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
 4S1  CONST_01  S22  C09  C06  C01   180.00   0.0  0
 4S1  CONST_02  N25  C09  C06  C01     0.00   0.0  0
 4S1  CONST_03  N04  C05  C06  C01     0.00   0.0  0
 4S1  CONST_04  N04  C03  N02  C01     0.00   0.0  0
 4S1  CONST_05  C09  C06  C01  N02   180.00   0.0  0
 4S1  CONST_06  C05  C06  C01  N02     0.00   0.0  0
 4S1  CONST_07  C05  N04  C03  N02     0.00   0.0  0
 4S1  CONST_08  C06  C05  N04  C03     0.00   0.0  0
 4S1  CONST_09  C06  C01  N02  C03     0.00   0.0  0
 4S1  CONST_10  C09  C06  C05  N04   180.00   0.0  0
 4S1  CONST_11  S22  C09  C06  C05     0.00   0.0  0
 4S1  CONST_12  N25  C09  C06  C05   180.00   0.0  0
 4S1  CONST_13  C23  S22  C09  C06   180.00   0.0  0
 4S1  CONST_14  C24  N25  C09  C06   180.00   0.0  0
 4S1  CONST_15  C26  C23  S22  C09   180.00   0.0  0
 4S1  CONST_16  C24  C23  S22  C09     0.00   0.0  0
 4S1  CONST_17  C29  C24  N25  C09   180.00   0.0  0
 4S1  CONST_18  C23  C24  N25  C09     0.00   0.0  0
 4S1  CONST_19  C27  C26  C23  S22   180.00   0.0  0
 4S1  CONST_20  C29  C24  C23  S22   180.00   0.0  0
 4S1  CONST_21  N25  C24  C23  S22     0.00   0.0  0
 4S1  CONST_22  C24  N25  C09  S22     0.00   0.0  0
 4S1  CONST_23  C28  C27  C26  C23     0.00   0.0  0
 4S1  CONST_24  C28  C29  C24  C23     0.00   0.0  0
 4S1  CONST_25  N25  C09  S22  C23     0.00   0.0  0
 4S1  CONST_26  C27  C28  C29  C24     0.00   0.0  0
 4S1  CONST_27  C27  C26  C23  C24     0.00   0.0  0
 4S1  CONST_28  C28  C29  C24  N25   180.00   0.0  0
 4S1  CONST_29  C26  C23  C24  N25   180.00   0.0  0
 4S1  CONST_30  C29  C28  C27  C26     0.00   0.0  0
 4S1  CONST_31  C29  C24  C23  C26     0.00   0.0  0
 4S1  CONST_32  N08  C03  N02  C01   180.00   0.0  0
 4S1  CONST_33  N07  C01  N02  C03   180.00   0.0  0
 4S1  CONST_34  N07  C01  C06  C05   180.00   0.0  0
 4S1  CONST_35  N08  C03  N04  C05   180.00   0.0  0
 4S1  CONST_36  C09  C06  C01  N07     0.00   0.0  0
 4S1  CONST_37  C10  N07  C01  N02     0.00   0.0  0
 4S1  CONST_38  C10  N07  C01  C06   180.00   0.0  0
 4S1  CONST_39  H1   C05  C06  C01   180.00   0.0  0
 4S1  CONST_40  H22  C26  C23  S22     0.00   0.0  0
 4S1  CONST_41  H23  C27  C26  C23   180.00   0.0  0
 4S1  CONST_42  H25  C29  C24  C23   180.00   0.0  0
 4S1  CONST_43  H24  C28  C29  C24   180.00   0.0  0
 4S1  CONST_44  C19  N08  C03  N02   180.00   0.0  0
 4S1  CONST_45  C19  N08  C03  N04     0.00   0.0  0
 4S1  CONST_46  H2   N07  C01  N02   180.00   0.0  0
 4S1  CONST_47  H3   N08  C03  N02     0.00   0.0  0
 4S1  Var_01    C20  C19  N08  C03   177.74  30.0  3
 4S1  Var_02    C21  C20  C19  N08  -179.52  30.0  3
 4S1  Var_03    H19  C21  C20  C19   179.69  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
 4S1  chir_01  C10  N07  C14  C11  positiv
 4S1  chir_02  C11  O15  C10  C12  negativ
 4S1  chir_03  C12  O16  C11  C13  negativ
 4S1  chir_04  C13  C12  C14  C17  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
 4S1  plan-1  C01  0.020
 4S1  plan-1  N02  0.020
 4S1  plan-1  C03  0.020
 4S1  plan-1  N04  0.020
 4S1  plan-1  C05  0.020
 4S1  plan-1  C06  0.020
 4S1  plan-1  N07  0.020
 4S1  plan-1  N08  0.020
 4S1  plan-1  C09  0.020
 4S1  plan-1  H1   0.020
 4S1  plan-2  C06  0.020
 4S1  plan-2  C09  0.020
 4S1  plan-2  S22  0.020
 4S1  plan-2  C23  0.020
 4S1  plan-2  C24  0.020
 4S1  plan-2  N25  0.020
 4S1  plan-2  C26  0.020
 4S1  plan-2  C27  0.020
 4S1  plan-2  C28  0.020
 4S1  plan-2  C29  0.020
 4S1  plan-2  H22  0.020
 4S1  plan-2  H23  0.020
 4S1  plan-2  H24  0.020
 4S1  plan-2  H25  0.020
 4S1  plan-3  C01  0.020
 4S1  plan-3  N07  0.020
 4S1  plan-3  C10  0.020
 4S1  plan-3  H2   0.020
 4S1  plan-4  C03  0.020
 4S1  plan-4  N08  0.020
 4S1  plan-4  C19  0.020
 4S1  plan-4  H3   0.020

