# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:23:06 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1sc(nc1CSc2nc(N)cc(N)n2)c3ccc(OC)c(O)c3
#
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
 2XL  2XL  5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenol  ligand  48  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2XL
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
 2XL  CAB  C  CH3   0  -0.434   8.0838  -1.1410  -0.2345
 2XL  OAP  O  O2    0  -0.482   6.8965  -1.7584   0.2268
 2XL  CAX  C  CR6   0   0.297   5.7359  -1.0863   0.1211
 2XL  CAU  C  CR6   0   0.313   4.6052  -1.7803   0.5929
 2XL  CAI  C  CR16  0  -0.393   3.3629  -1.1838   0.5373
 2XL  OAE  O  OH1   0  -0.630   4.7130  -3.0223   1.1023
 2XL  CAG  C  CR16  0  -0.361   5.5863   0.1902  -0.3967
 2XL  CAF  C  CR16  0  -0.337   4.3308   0.7830  -0.4486
 2XL  CAV  C  CR6   0   0.087   3.2106   0.1066   0.0173
 2XL  CBA  C  CR5   0   0.012   1.8780   0.7027  -0.0155
 2XL  NAO  N  N     0  -0.404   0.7960   0.0900   0.3499
 2XL  SAR  S  S2    0   0.233   1.5996   2.3315  -0.5426
 2XL  CAZ  C  CR5   0  -0.240  -0.0852   2.1418  -0.2440
 2XL  CAK  C  CH2   0  -0.508  -1.0592   3.2528  -0.4451
 2XL  CAJ  C  CH2   0  -0.414  -1.0302   4.2772   0.6920
 2XL  CAA  C  CH3   0  -0.667  -2.0766   5.3663   0.5132
 2XL  CAY  C  CR5   0   0.342  -0.3068   0.8852   0.2381
 2XL  CAL  C  CH2   0  -0.650  -1.6463   0.3434   0.6110
 2XL  SAQ  S  S2    0   0.042  -2.3728  -0.4064  -0.8815
 2XL  C2   C  CR6   0   0.240  -3.9310  -0.9930  -0.3067
 2XL  N3   N  N     0  -0.483  -4.2433  -0.8158   0.9573
 2XL  N1   N  N     0  -0.499  -4.6405  -1.5705  -1.2584
 2XL  C6   C  CR6   0   0.491  -5.8430  -2.0392  -0.8855
 2XL  NAC  N  NH2   0  -0.833  -6.5970  -2.6004  -1.8496
 2XL  C5   C  CR16  0  -0.499  -6.2957  -1.9213   0.4294
 2XL  C4   C  CR6   0   0.503  -5.4476  -1.2875   1.3336
 2XL  NAD  N  NH2   0  -0.831  -5.7936  -1.0851   2.6200
 2XL  H1   H  HCH3  0   0.235   8.2946  -0.2166   0.3085
 2XL  H2   H  HCH3  0   0.266   8.8893  -1.8476  -0.0546
 2XL  H3   H  HCH3  0   0.235   8.0343  -0.9222  -1.3037
 2XL  H4   H  HCR6  0   0.266   2.5005  -1.7242   0.9063
 2XL  H5   H  HOH1  0   0.474   5.6350  -3.3069   1.0981
 2XL  H6   H  HCR6  0   0.290   6.4405   0.7401  -0.7678
 2XL  H7   H  HCR6  0   0.255   4.2519   1.7804  -0.8632
 2XL  H8   H  HCH2  0   0.260  -0.8681   3.7538  -1.3975
 2XL  H9   H  HCH2  0   0.250  -2.0612   2.8237  -0.5290
 2XL  H10  H  HCH2  0   0.229  -1.1911   3.7595   1.6411
 2XL  H11  H  HCH2  0   0.226  -0.0342   4.7242   0.7513
 2XL  H12  H  HCH3  0   0.222  -3.0821   4.9434   0.4751
 2XL  H13  H  HCH3  0   0.234  -2.0473   6.0772   1.3388
 2XL  H14  H  HCH3  0   0.222  -1.9182   5.9244  -0.4110
 2XL  H15  H  HCH2  0   0.302  -1.5480  -0.4132   1.3872
 2XL  H16  H  HCH2  0   0.289  -2.3071   1.1269   0.9768
 2XL  H17  H  HNH2  0   0.392  -6.1632  -2.8302  -2.7272
 2XL  H18  H  HNH2  0   0.400  -7.4198  -3.1223  -1.6035
 2XL  H19  H  HCR6  0   0.269  -7.2608  -2.3051   0.7310
 2XL  H20  H  HNH2  0   0.399  -6.5809  -1.5772   3.0050
 2XL  H21  H  HNH2  0   0.392  -5.0745  -0.8159   3.2699

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
 2XL  CAK  CAJ  single    1.531  0.020  1.531
 2XL  CAK  CAZ  single    1.491  0.020  1.491
 2XL  CAJ  CAA  single    1.521  0.020  1.521
 2XL  SAR  CAZ  aromatic  1.722  0.020  1.722
 2XL  SAR  CBA  aromatic  1.734  0.020  1.734
 2XL  CAZ  CAY  aromatic  1.364  0.020  1.364
 2XL  CAF  CAG  aromatic  1.389  0.020  1.389
 2XL  CAF  CAV  aromatic  1.389  0.020  1.389
 2XL  NAD  C4   single    1.347  0.020  1.347
 2XL  CAB  OAP  single    1.416  0.020  1.416
 2XL  CAG  CAX  aromatic  1.386  0.020  1.386
 2XL  C4   C5   aromatic  1.392  0.020  1.392
 2XL  C4   N3   aromatic  1.347  0.020  1.347
 2XL  C5   C6   aromatic  1.396  0.020  1.396
 2XL  CBA  CAV  single    1.460  0.020  1.460
 2XL  CBA  NAO  aromatic  1.296  0.020  1.296
 2XL  CAV  CAI  aromatic  1.400  0.020  1.400
 2XL  N3   C2   aromatic  1.314  0.020  1.314
 2XL  C6   NAC  single    1.346  0.020  1.346
 2XL  C6   N1   aromatic  1.343  0.020  1.343
 2XL  CAX  OAP  single    1.345  0.020  1.345
 2XL  CAX  CAU  aromatic  1.408  0.020  1.408
 2XL  C2   N1   aromatic  1.320  0.020  1.320
 2XL  C2   SAQ  single    1.761  0.020  1.761
 2XL  CAY  NAO  aromatic  1.364  0.020  1.364
 2XL  CAY  CAL  single    1.492  0.020  1.492
 2XL  SAQ  CAL  single    1.821  0.020  1.821
 2XL  CAI  CAU  aromatic  1.379  0.020  1.379
 2XL  CAU  OAE  single    1.347  0.020  1.347
 2XL  CAB  H1   single    0.970  0.020  1.090
 2XL  CAB  H2   single    0.970  0.020  1.090
 2XL  CAB  H3   single    0.970  0.020  1.090
 2XL  CAI  H4   single    0.930  0.020  1.080
 2XL  OAE  H5   single    0.850  0.020  0.980
 2XL  CAG  H6   single    0.930  0.020  1.080
 2XL  CAF  H7   single    0.930  0.020  1.080
 2XL  CAK  H8   single    0.970  0.020  1.090
 2XL  CAK  H9   single    0.970  0.020  1.090
 2XL  CAJ  H10  single    0.970  0.020  1.090
 2XL  CAJ  H11  single    0.970  0.020  1.090
 2XL  CAA  H12  single    0.970  0.020  1.090
 2XL  CAA  H13  single    0.970  0.020  1.090
 2XL  CAA  H14  single    0.970  0.020  1.090
 2XL  CAL  H15  single    0.970  0.020  1.090
 2XL  CAL  H16  single    0.970  0.020  1.090
 2XL  NAC  H17  single    0.890  0.020  1.040
 2XL  NAC  H18  single    0.890  0.020  1.040
 2XL  C5   H19  single    0.930  0.020  1.080
 2XL  NAD  H20  single    0.890  0.020  1.040
 2XL  NAD  H21  single    0.890  0.020  1.040

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
 2XL  H3   CAB  H2   109.02  3.000
 2XL  H3   CAB  H1   109.01  3.000
 2XL  H2   CAB  H1   108.96  3.000
 2XL  H3   CAB  OAP  111.61  3.000
 2XL  H2   CAB  OAP  106.51  3.000
 2XL  H1   CAB  OAP  111.65  3.000
 2XL  CAX  OAP  CAB  118.69  3.000
 2XL  CAG  CAX  CAU  119.51  3.000
 2XL  CAU  CAX  OAP  114.85  3.000
 2XL  CAG  CAX  OAP  125.64  3.000
 2XL  OAE  CAU  CAI  119.09  3.000
 2XL  OAE  CAU  CAX  121.13  3.000
 2XL  CAI  CAU  CAX  119.78  3.000
 2XL  H4   CAI  CAV  120.02  3.000
 2XL  H4   CAI  CAU  119.20  3.000
 2XL  CAV  CAI  CAU  120.78  3.000
 2XL  H5   OAE  CAU  110.30  3.000
 2XL  H6   CAG  CAF  118.94  3.000
 2XL  H6   CAG  CAX  120.76  3.000
 2XL  CAF  CAG  CAX  120.30  3.000
 2XL  H7   CAF  CAV  121.21  3.000
 2XL  H7   CAF  CAG  118.24  3.000
 2XL  CAV  CAF  CAG  120.56  3.000
 2XL  CBA  CAV  CAF  121.98  3.000
 2XL  CBA  CAV  CAI  118.95  3.000
 2XL  CAF  CAV  CAI  119.07  3.000
 2XL  SAR  CBA  NAO  113.31  3.000
 2XL  NAO  CBA  CAV  124.23  3.000
 2XL  SAR  CBA  CAV  122.46  3.000
 2XL  CAY  NAO  CBA  112.10  3.000
 2XL  CAZ  SAR  CBA   90.05  3.000
 2XL  CAY  CAZ  CAK  128.90  3.000
 2XL  CAY  CAZ  SAR  108.77  3.000
 2XL  CAK  CAZ  SAR  122.26  3.000
 2XL  H9   CAK  H8   105.87  3.000
 2XL  H9   CAK  CAJ  109.70  3.000
 2XL  H8   CAK  CAJ  109.71  3.000
 2XL  H9   CAK  CAZ  108.45  3.000
 2XL  H8   CAK  CAZ  110.17  3.000
 2XL  CAJ  CAK  CAZ  112.71  3.000
 2XL  H11  CAJ  H10  106.30  3.000
 2XL  H11  CAJ  CAA  109.90  3.000
 2XL  H10  CAJ  CAA  109.87  3.000
 2XL  H11  CAJ  CAK  109.34  3.000
 2XL  H10  CAJ  CAK  108.98  3.000
 2XL  CAA  CAJ  CAK  112.26  3.000
 2XL  H14  CAA  H13  107.71  3.000
 2XL  H14  CAA  H12  107.60  3.000
 2XL  H13  CAA  H12  107.70  3.000
 2XL  H14  CAA  CAJ  111.46  3.000
 2XL  H13  CAA  CAJ  111.07  3.000
 2XL  H12  CAA  CAJ  111.13  3.000
 2XL  CAL  CAY  CAZ  124.65  3.000
 2XL  CAL  CAY  NAO  119.57  3.000
 2XL  CAZ  CAY  NAO  115.76  3.000
 2XL  H16  CAL  H15  108.39  3.000
 2XL  H16  CAL  SAQ  109.25  3.000
 2XL  H15  CAL  SAQ  109.53  3.000
 2XL  H16  CAL  CAY  111.57  3.000
 2XL  H15  CAL  CAY  110.46  3.000
 2XL  SAQ  CAL  CAY  107.62  3.000
 2XL  C2   SAQ  CAL  102.86  3.000
 2XL  N1   C2   N3   128.66  3.000
 2XL  N1   C2   SAQ  112.70  3.000
 2XL  N3   C2   SAQ  118.64  3.000
 2XL  C4   N3   C2   115.72  3.000
 2XL  C6   N1   C2   115.70  3.000
 2XL  C5   C6   NAC  121.88  3.000
 2XL  NAC  C6   N1   116.61  3.000
 2XL  C5   C6   N1   121.49  3.000
 2XL  H18  NAC  H17  116.62  3.000
 2XL  H18  NAC  C6   119.97  3.000
 2XL  H17  NAC  C6   118.60  3.000
 2XL  H19  C5   C4   121.60  3.000
 2XL  H19  C5   C6   121.48  3.000
 2XL  C4   C5   C6   116.92  3.000
 2XL  NAD  C4   C5   122.14  3.000
 2XL  C5   C4   N3   121.51  3.000
 2XL  NAD  C4   N3   116.33  3.000
 2XL  H21  NAD  H20  116.33  3.000
 2XL  H21  NAD  C4   118.26  3.000
 2XL  H20  NAD  C4   119.55  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
 2XL  CONST_01  CAV  CAF  CAG  CAX     0.00   0.0  0
 2XL  CONST_02  CAV  CAI  CAU  CAX     0.00   0.0  0
 2XL  CONST_03  CAF  CAG  CAX  CAU     0.00   0.0  0
 2XL  CONST_04  CAF  CAV  CAI  CAU     0.00   0.0  0
 2XL  CONST_05  CBA  CAV  CAI  CAU   180.00   0.0  0
 2XL  CONST_06  CAG  CAF  CAV  CAI     0.00   0.0  0
 2XL  CONST_07  SAR  CBA  CAV  CAI   180.00   0.0  0
 2XL  CONST_08  NAO  CBA  CAV  CAI     0.00   0.0  0
 2XL  CONST_09  CAG  CAX  CAU  CAI     0.00   0.0  0
 2XL  CONST_10  CBA  CAV  CAF  CAG   180.00   0.0  0
 2XL  CONST_11  SAR  CBA  CAV  CAF     0.00   0.0  0
 2XL  CONST_12  NAO  CBA  CAV  CAF   180.00   0.0  0
 2XL  CONST_13  CAZ  SAR  CBA  CAV   180.00   0.0  0
 2XL  CONST_14  CAY  NAO  CBA  CAV   180.00   0.0  0
 2XL  CONST_15  CAY  CAZ  SAR  CBA     0.00   0.0  0
 2XL  CONST_16  CAZ  CAY  NAO  CBA     0.00   0.0  0
 2XL  CONST_17  CAZ  SAR  CBA  NAO     0.00   0.0  0
 2XL  CONST_18  SAR  CAZ  CAY  NAO     0.00   0.0  0
 2XL  CONST_19  CAY  NAO  CBA  SAR     0.00   0.0  0
 2XL  CONST_20  C5   C4   N3   C2      0.00   0.0  0
 2XL  CONST_21  C5   C6   N1   C2      0.00   0.0  0
 2XL  CONST_22  C6   C5   C4   N3      0.00   0.0  0
 2XL  CONST_23  C6   N1   C2   N3      0.00   0.0  0
 2XL  CONST_24  C4   C5   C6   N1      0.00   0.0  0
 2XL  CONST_25  C4   N3   C2   N1      0.00   0.0  0
 2XL  CONST_26  CAF  CAG  CAX  OAP   180.00   0.0  0
 2XL  CONST_27  CAI  CAU  CAX  OAP   180.00   0.0  0
 2XL  CONST_28  CAG  CAX  CAU  OAE   180.00   0.0  0
 2XL  CONST_29  CAV  CAI  CAU  OAE   180.00   0.0  0
 2XL  CONST_30  CAK  CAZ  SAR  CBA   180.00   0.0  0
 2XL  CONST_31  CAL  CAY  NAO  CBA   180.00   0.0  0
 2XL  CONST_32  CAK  CAZ  CAY  NAO   180.00   0.0  0
 2XL  CONST_33  CAL  CAY  CAZ  SAR   180.00   0.0  0
 2XL  CONST_34  C4   N3   C2   SAQ   180.00   0.0  0
 2XL  CONST_35  C6   N1   C2   SAQ   180.00   0.0  0
 2XL  CONST_36  NAD  C4   N3   C2    180.00   0.0  0
 2XL  CONST_37  NAC  C6   N1   C2    180.00   0.0  0
 2XL  CONST_38  NAD  C4   C5   C6    180.00   0.0  0
 2XL  CONST_39  C4   C5   C6   NAC   180.00   0.0  0
 2XL  CONST_40  H7   CAF  CAG  CAX   180.00   0.0  0
 2XL  CONST_41  H4   CAI  CAU  CAX   180.00   0.0  0
 2XL  CONST_42  H6   CAG  CAX  CAU   180.00   0.0  0
 2XL  CONST_43  H19  C5   C4   N3    180.00   0.0  0
 2XL  CONST_44  H20  NAD  C4   N3    180.00   0.0  0
 2XL  CONST_46  H17  NAC  C6   N1      0.00   0.0  0
 2XL  CONST_47  H18  NAC  C6   N1    180.00   0.0  0
 2XL  Var_01    CAG  CAX  OAP  CAB    -0.69  30.0  2
 2XL  Var_02    SAQ  CAL  CAY  NAO   -90.02  30.0  2
 2XL  Var_03    CAJ  CAK  CAZ  SAR   -77.45  30.0  1
 2XL  Var_04    N3   C2   SAQ  CAL    -0.70  30.0  3
 2XL  Var_05    CAA  CAJ  CAK  CAZ  -177.03  30.0  3
 2XL  Var_06    H1   CAB  OAP  CAX    61.08  30.0  3
 2XL  Var_07    H12  CAA  CAJ  CAK    59.41  30.0  3

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
 2XL  plan-1  CAV  0.020
 2XL  plan-1  CBA  0.020
 2XL  plan-1  NAO  0.020
 2XL  plan-1  SAR  0.020
 2XL  plan-1  CAZ  0.020
 2XL  plan-1  CAK  0.020
 2XL  plan-1  CAY  0.020
 2XL  plan-1  CAL  0.020
 2XL  plan-2  OAP  0.020
 2XL  plan-2  CAX  0.020
 2XL  plan-2  CAU  0.020
 2XL  plan-2  CAI  0.020
 2XL  plan-2  OAE  0.020
 2XL  plan-2  CAG  0.020
 2XL  plan-2  CAF  0.020
 2XL  plan-2  CAV  0.020
 2XL  plan-2  CBA  0.020
 2XL  plan-2  H4   0.020
 2XL  plan-2  H6   0.020
 2XL  plan-2  H7   0.020
 2XL  plan-3  SAQ  0.020
 2XL  plan-3  C2   0.020
 2XL  plan-3  N3   0.020
 2XL  plan-3  N1   0.020
 2XL  plan-3  C6   0.020
 2XL  plan-3  NAC  0.020
 2XL  plan-3  C5   0.020
 2XL  plan-3  C4   0.020
 2XL  plan-3  NAD  0.020
 2XL  plan-3  H19  0.020
 2XL  plan-4  C6   0.020
 2XL  plan-4  NAC  0.020
 2XL  plan-4  H17  0.020
 2XL  plan-4  H18  0.020
 2XL  plan-5  C4   0.020
 2XL  plan-5  NAD  0.020
 2XL  plan-5  H20  0.020
 2XL  plan-5  H21  0.020

