# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:45:11 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: N-tert-butyl-2-{4-[(5,5-dioxido-2-phenyl-7,8-dihydro-6H-thiopyrano[3,2-d]pyrimidin-4-yl)amino]phenyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)Cc1ccc(Nc2nc(nc3CCC[S](=O)(=O)c23)c4ccccc4)cc1
#
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
 NVW  NVW  N-tert-butyl-2-{4-[(5,5-dioxido-2-phenyl-7,8-dihydro-6H-thiopyrano[3,2-d]pyrimidin-4-yl)amino]phenyl}acetamide  ligand  61  33  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NVW
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
 NVW  N1   N  N     0  -0.478  -3.5561   1.8744  -0.1640
 NVW  C1   C  CR6   0   0.600  -2.2005  -0.4657   0.2249
 NVW  N2   N  N     0  -0.479  -1.5606   0.6941   0.2356
 NVW  C2   C  CR6   0   0.413  -2.2510   1.8070   0.0575
 NVW  C3   C  CR6   0  -0.024  -1.4959   3.0760   0.1013
 NVW  N3   N  NH1   0  -0.779  -1.4706  -1.5865   0.3972
 NVW  C4   C  CR16  0  -0.276  -0.1215   3.0707   0.3452
 NVW  C5   C  CR16  0  -0.240   0.5856   4.2616   0.3912
 NVW  C6   C  CR16  0  -0.250  -0.0689   5.4711   0.1933
 NVW  C7   C  CR16  0  -0.240  -1.4365   5.4836  -0.0513
 NVW  C8   C  CR16  0  -0.276  -2.1468   4.2942  -0.0963
 NVW  C9   C  CR6   0   0.354  -4.2378   0.7324  -0.1917
 NVW  C10  C  CR6   0  -0.374  -3.6072  -0.4868   0.0264
 NVW  S1   S  S     0   1.196  -4.4815  -2.0223   0.0082
 NVW  C11  C  CH2   0  -0.597  -6.1856  -1.5209   0.0781
 NVW  C12  C  CH2   0  -0.493  -6.4206  -0.3844  -0.8992
 NVW  C13  C  CH2   0  -0.518  -5.7108   0.8774  -0.4408
 NVW  O1   O  OS    0  -0.669  -4.2227  -2.6781  -1.2742
 NVW  O2   O  OS    0  -0.668  -4.1319  -2.7714   1.2162
 NVW  C14  C  CR6   0   0.315  -0.0699  -1.6405   0.5557
 NVW  C15  C  CR16  0  -0.252   0.6107  -0.8265   1.4575
 NVW  C16  C  CR16  0  -0.305   2.0138  -2.6930  -0.0345
 NVW  C17  C  CR16  0  -0.302   0.6387  -2.5823  -0.1810
 NVW  C18  C  CR6   0   0.158   2.7104  -1.8634   0.8354
 NVW  C19  C  CR16  0  -0.300   1.9855  -0.9366   1.5799
 NVW  C20  C  CH2   0  -0.694   4.2005  -1.9407   0.9518
 NVW  C21  C  C     0   0.567   4.9033  -0.9301   0.0463
 NVW  N4   N  NH1   0  -0.649   6.2422  -1.0025   0.1006
 NVW  O3   O  O     0  -0.486   4.2804  -0.1406  -0.6463
 NVW  C22  C  CT    0   0.100   7.2020  -0.1761  -0.6414
 NVW  C23  C  CH3   0  -0.640   7.0354   1.3023  -0.2871
 NVW  C24  C  CH3   0  -0.680   8.5891  -0.6422  -0.2023
 NVW  C25  C  CH3   0  -0.640   7.0514  -0.3902  -2.1482
 NVW  H1   H  HNH1  0   0.409  -1.9166  -2.4806   0.2695
 NVW  H2   H  HCR6  0   0.264   0.3918   2.1313   0.5008
 NVW  H3   H  HCR6  0   0.261   1.6508   4.2456   0.5807
 NVW  H4   H  HCR6  0   0.263   0.4852   6.4001   0.2312
 NVW  H5   H  HCR6  0   0.261  -1.9518   6.4221  -0.2078
 NVW  H6   H  HCR6  0   0.258  -3.2115   4.3072  -0.2840
 NVW  H7   H  HCH2  0   0.335  -6.7574  -2.4193  -0.1618
 NVW  H8   H  HCH2  0   0.313  -6.3990  -1.2267   1.1068
 NVW  H9   H  HCH2  0   0.271  -6.0996  -0.6721  -1.9025
 NVW  H10  H  HCH2  0   0.292  -7.4921  -0.1959  -0.9566
 NVW  H11  H  HCH2  0   0.284  -6.1634   1.2335   0.4908
 NVW  H12  H  HCH2  0   0.287  -5.8460   1.6774  -1.1689
 NVW  H13  H  HCR6  0   0.266   0.0742  -0.1112   2.0634
 NVW  H14  H  HCR6  0   0.253   2.5473  -3.4334  -0.6186
 NVW  H15  H  HCR6  0   0.268   0.1167  -3.2274  -0.8775
 NVW  H16  H  HCR6  0   0.251   2.5012  -0.2923   2.2822
 NVW  H17  H  HCH2  0   0.290   4.5158  -1.7565   1.9830
 NVW  H18  H  HCH2  0   0.289   4.5556  -2.9440   0.7015
 NVW  H19  H  HNH1  0   0.401   6.6340  -1.7112   0.7013
 NVW  H20  H  HCH3  0   0.225   7.1335   1.4542   0.7889
 NVW  H21  H  HCH3  0   0.224   7.8099   1.8920  -0.7802
 NVW  H22  H  HCH3  0   0.239   6.0678   1.6887  -0.6019
 NVW  H23  H  HCH3  0   0.237   8.7423  -1.6994  -0.4285
 NVW  H24  H  HCH3  0   0.241   9.3591  -0.0750  -0.7244
 NVW  H25  H  HCH3  0   0.238   8.7346  -0.4962   0.8699
 NVW  H26  H  HCH3  0   0.238   6.0756  -0.0665  -2.5063
 NVW  H27  H  HCH3  0   0.224   7.8122   0.1798  -2.6838
 NVW  H28  H  HCH3  0   0.225   7.1795  -1.4431  -2.4045

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
 NVW  C25  C22  single    1.529  0.020  1.529
 NVW  C24  C22  single    1.528  0.020  1.528
 NVW  C23  C22  single    1.529  0.020  1.529
 NVW  C22  N4   single    1.468  0.020  1.468
 NVW  C6   C5   aromatic  1.389  0.020  1.389
 NVW  C6   C7   aromatic  1.389  0.020  1.389
 NVW  N4   C21  single    1.342  0.020  1.342
 NVW  C5   C4   aromatic  1.386  0.020  1.386
 NVW  C7   C8   aromatic  1.386  0.020  1.386
 NVW  O3   C21  double    1.221  0.020  1.221
 NVW  C21  C20  single    1.528  0.020  1.528
 NVW  C4   C3   aromatic  1.396  0.020  1.396
 NVW  C8   C3   aromatic  1.395  0.020  1.395
 NVW  C20  C18  single    1.497  0.020  1.497
 NVW  C3   C2   single    1.477  0.020  1.477
 NVW  C19  C18  aromatic  1.392  0.020  1.392
 NVW  C19  C15  aromatic  1.385  0.020  1.385
 NVW  C18  C16  aromatic  1.389  0.020  1.389
 NVW  C2   N2   aromatic  1.322  0.020  1.322
 NVW  C2   N1   aromatic  1.325  0.020  1.325
 NVW  C15  C14  aromatic  1.393  0.020  1.393
 NVW  C16  C17  aromatic  1.387  0.020  1.387
 NVW  N2   C1   aromatic  1.325  0.020  1.325
 NVW  N1   C9   aromatic  1.330  0.020  1.330
 NVW  C14  C17  aromatic  1.390  0.020  1.390
 NVW  C14  N3   single    1.411  0.020  1.411
 NVW  C1   N3   single    1.349  0.020  1.349
 NVW  C1   C10  aromatic  1.421  0.020  1.421
 NVW  C9   C10  aromatic  1.390  0.020  1.390
 NVW  C9   C13  single    1.501  0.020  1.501
 NVW  C10  S1   single    1.767  0.020  1.767
 NVW  C13  C12  single    1.519  0.020  1.519
 NVW  C12  C11  single    1.517  0.020  1.517
 NVW  S1   O2   double    1.464  0.020  1.464
 NVW  S1   C11  single    1.778  0.020  1.778
 NVW  S1   O1   double    1.463  0.020  1.463
 NVW  N3   H1   single    0.860  0.020  1.020
 NVW  C4   H2   single    0.930  0.020  1.080
 NVW  C5   H3   single    0.930  0.020  1.080
 NVW  C6   H4   single    0.930  0.020  1.080
 NVW  C7   H5   single    0.930  0.020  1.080
 NVW  C8   H6   single    0.930  0.020  1.080
 NVW  C11  H7   single    0.970  0.020  1.090
 NVW  C11  H8   single    0.970  0.020  1.090
 NVW  C12  H9   single    0.970  0.020  1.090
 NVW  C12  H10  single    0.970  0.020  1.090
 NVW  C13  H11  single    0.970  0.020  1.090
 NVW  C13  H12  single    0.970  0.020  1.090
 NVW  C15  H13  single    0.930  0.020  1.080
 NVW  C16  H14  single    0.930  0.020  1.080
 NVW  C17  H15  single    0.930  0.020  1.080
 NVW  C19  H16  single    0.930  0.020  1.080
 NVW  C20  H17  single    0.970  0.020  1.090
 NVW  C20  H18  single    0.970  0.020  1.090
 NVW  N4   H19  single    0.860  0.020  1.020
 NVW  C23  H20  single    0.970  0.020  1.090
 NVW  C23  H21  single    0.970  0.020  1.090
 NVW  C23  H22  single    0.970  0.020  1.090
 NVW  C24  H23  single    0.970  0.020  1.090
 NVW  C24  H24  single    0.970  0.020  1.090
 NVW  C24  H25  single    0.970  0.020  1.090
 NVW  C25  H26  single    0.970  0.020  1.090
 NVW  C25  H27  single    0.970  0.020  1.090
 NVW  C25  H28  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
 NVW  C9   N1   C2   117.67  3.000
 NVW  C10  C1   N3   122.78  3.000
 NVW  C10  C1   N2   119.50  3.000
 NVW  N3   C1   N2   117.72  3.000
 NVW  C2   N2   C1   118.93  3.000
 NVW  C3   C2   N2   116.89  3.000
 NVW  N2   C2   N1   125.43  3.000
 NVW  C3   C2   N1   117.68  3.000
 NVW  C8   C3   C4   119.16  3.000
 NVW  C8   C3   C2   120.49  3.000
 NVW  C4   C3   C2   120.35  3.000
 NVW  H1   N3   C14  114.82  3.000
 NVW  H1   N3   C1   118.81  3.000
 NVW  C14  N3   C1   125.70  3.000
 NVW  H2   C4   C5   119.95  3.000
 NVW  H2   C4   C3   119.71  3.000
 NVW  C5   C4   C3   120.33  3.000
 NVW  H3   C5   C6   120.10  3.000
 NVW  H3   C5   C4   119.70  3.000
 NVW  C6   C5   C4   120.20  3.000
 NVW  H4   C6   C7   120.16  3.000
 NVW  H4   C6   C5   120.07  3.000
 NVW  C7   C6   C5   119.77  3.000
 NVW  H5   C7   C8   119.71  3.000
 NVW  H5   C7   C6   120.13  3.000
 NVW  C8   C7   C6   120.16  3.000
 NVW  H6   C8   C7   119.99  3.000
 NVW  H6   C8   C3   119.63  3.000
 NVW  C7   C8   C3   120.37  3.000
 NVW  C13  C9   C10  123.79  3.000
 NVW  C13  C9   N1   115.05  3.000
 NVW  C10  C9   N1   121.15  3.000
 NVW  S1   C10  C9   122.42  3.000
 NVW  S1   C10  C1   120.28  3.000
 NVW  C9   C10  C1   117.27  3.000
 NVW  O2   S1   O1   116.85  3.000
 NVW  O1   S1   C11  109.29  3.000
 NVW  O2   S1   C11  109.93  3.000
 NVW  O1   S1   C10  108.11  3.000
 NVW  C11  S1   C10  103.23  3.000
 NVW  O2   S1   C10  108.54  3.000
 NVW  H8   C11  H7   109.07  3.000
 NVW  H8   C11  C12  112.03  3.000
 NVW  H7   C11  C12  113.19  3.000
 NVW  H8   C11  S1   107.49  3.000
 NVW  H7   C11  S1   105.15  3.000
 NVW  C12  C11  S1   109.54  3.000
 NVW  H10  C12  H9   106.64  3.000
 NVW  H10  C12  C13  109.38  3.000
 NVW  H9   C12  C13  111.03  3.000
 NVW  H10  C12  C11  108.41  3.000
 NVW  H9   C12  C11  110.42  3.000
 NVW  C13  C12  C11  110.83  3.000
 NVW  H12  C13  H11  106.16  3.000
 NVW  H12  C13  C12  110.50  3.000
 NVW  H11  C13  C12  109.50  3.000
 NVW  H12  C13  C9   107.66  3.000
 NVW  H11  C13  C9   107.21  3.000
 NVW  C12  C13  C9   115.38  3.000
 NVW  C17  C14  C15  119.35  3.000
 NVW  C17  C14  N3   118.21  3.000
 NVW  C15  C14  N3   122.39  3.000
 NVW  H13  C15  C19  119.76  3.000
 NVW  H13  C15  C14  120.51  3.000
 NVW  C19  C15  C14  119.74  3.000
 NVW  H14  C16  C18  119.91  3.000
 NVW  H14  C16  C17  119.06  3.000
 NVW  C18  C16  C17  121.02  3.000
 NVW  H15  C17  C16  119.86  3.000
 NVW  H15  C17  C14  119.91  3.000
 NVW  C16  C17  C14  120.23  3.000
 NVW  C20  C18  C19  120.74  3.000
 NVW  C19  C18  C16  118.12  3.000
 NVW  C20  C18  C16  121.13  3.000
 NVW  H16  C19  C18  119.64  3.000
 NVW  H16  C19  C15  118.84  3.000
 NVW  C18  C19  C15  121.51  3.000
 NVW  H18  C20  H17  106.07  3.000
 NVW  H18  C20  C21  108.77  3.000
 NVW  H17  C20  C21  108.34  3.000
 NVW  H18  C20  C18  110.67  3.000
 NVW  H17  C20  C18  110.59  3.000
 NVW  C21  C20  C18  112.19  3.000
 NVW  O3   C21  N4   124.53  3.000
 NVW  O3   C21  C20  121.94  3.000
 NVW  N4   C21  C20  113.53  3.000
 NVW  H19  N4   C22  116.28  3.000
 NVW  H19  N4   C21  116.73  3.000
 NVW  C22  N4   C21  126.98  3.000
 NVW  C25  C22  C24  109.26  3.000
 NVW  C24  C22  C23  109.10  3.000
 NVW  C25  C22  C23  110.66  3.000
 NVW  C23  C22  N4   110.85  3.000
 NVW  C24  C22  N4   106.06  3.000
 NVW  C25  C22  N4   110.78  3.000
 NVW  H22  C23  H21  107.96  3.000
 NVW  H22  C23  H20  108.40  3.000
 NVW  H21  C23  H20  107.85  3.000
 NVW  H22  C23  C22  111.90  3.000
 NVW  H21  C23  C22  109.91  3.000
 NVW  H20  C23  C22  110.68  3.000
 NVW  H25  C24  H24  107.87  3.000
 NVW  H25  C24  H23  108.32  3.000
 NVW  H24  C24  H23  107.79  3.000
 NVW  H25  C24  C22  111.25  3.000
 NVW  H24  C24  C22  110.18  3.000
 NVW  H23  C24  C22  111.30  3.000
 NVW  H28  C25  H27  107.87  3.000
 NVW  H28  C25  H26  108.35  3.000
 NVW  H27  C25  H26  107.95  3.000
 NVW  H28  C25  C22  110.79  3.000
 NVW  H27  C25  C22  109.99  3.000
 NVW  H26  C25  C22  111.76  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
 NVW  CONST_01  C4   C3   C2   N1    180.00   0.0  0
 NVW  CONST_02  C8   C3   C2   N1      0.00   0.0  0
 NVW  CONST_03  C1   N2   C2   N1      0.00   0.0  0
 NVW  CONST_04  C1   C10  C9   N1      0.00   0.0  0
 NVW  CONST_05  C3   C2   N2   C1    180.00   0.0  0
 NVW  CONST_06  C4   C3   C2   N2      0.00   0.0  0
 NVW  CONST_07  C8   C3   C2   N2    180.00   0.0  0
 NVW  CONST_08  C9   N1   C2   N2      0.00   0.0  0
 NVW  CONST_09  C9   C10  C1   N2      0.00   0.0  0
 NVW  CONST_10  C5   C4   C3   C2    180.00   0.0  0
 NVW  CONST_11  C7   C8   C3   C2    180.00   0.0  0
 NVW  CONST_12  C10  C1   N2   C2      0.00   0.0  0
 NVW  CONST_13  C10  C9   N1   C2      0.00   0.0  0
 NVW  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 NVW  CONST_15  C6   C7   C8   C3      0.00   0.0  0
 NVW  CONST_16  C9   N1   C2   C3    180.00   0.0  0
 NVW  CONST_17  C7   C6   C5   C4      0.00   0.0  0
 NVW  CONST_18  C7   C8   C3   C4      0.00   0.0  0
 NVW  CONST_19  C8   C7   C6   C5      0.00   0.0  0
 NVW  CONST_20  C8   C3   C4   C5      0.00   0.0  0
 NVW  CONST_21  C18  C19  C15  C14     0.00   0.0  0
 NVW  CONST_22  C18  C16  C17  C14     0.00   0.0  0
 NVW  CONST_23  C16  C18  C19  C15     0.00   0.0  0
 NVW  CONST_24  C16  C17  C14  C15     0.00   0.0  0
 NVW  CONST_25  C19  C18  C16  C17     0.00   0.0  0
 NVW  CONST_26  C19  C15  C14  C17     0.00   0.0  0
 NVW  CONST_27  N3   C1   N2   C2    180.00   0.0  0
 NVW  CONST_28  C19  C15  C14  N3    180.00   0.0  0
 NVW  CONST_29  C16  C17  C14  N3    180.00   0.0  0
 NVW  CONST_30  C9   C10  C1   N3    180.00   0.0  0
 NVW  CONST_31  S1   C10  C1   N3      0.00   0.0  0
 NVW  CONST_32  C20  C18  C19  C15   180.00   0.0  0
 NVW  CONST_33  C20  C18  C16  C17   180.00   0.0  0
 NVW  CONST_34  H2   C4   C3   C2      0.00   0.0  0
 NVW  CONST_35  H6   C8   C3   C2      0.00   0.0  0
 NVW  CONST_36  H3   C5   C4   C3    180.00   0.0  0
 NVW  CONST_37  H5   C7   C8   C3    180.00   0.0  0
 NVW  CONST_38  H4   C6   C5   C4    180.00   0.0  0
 NVW  CONST_39  H16  C19  C15  C14   180.00   0.0  0
 NVW  CONST_40  H14  C16  C17  C14   180.00   0.0  0
 NVW  CONST_41  H15  C17  C14  C15   180.00   0.0  0
 NVW  CONST_42  H13  C15  C14  C17   180.00   0.0  0
 NVW  CONST_43  C22  N4   C21  C20   180.00   0.0  0
 NVW  CONST_44  C22  N4   C21  O3      0.00   0.0  0
 NVW  CONST_45  H19  N4   C21  C20     0.00   0.0  0
 NVW  Var_01    C12  C13  C9   N1    161.82  30.0  1
 NVW  Var_02    C11  S1   C10  C1    168.58  30.0  1
 NVW  Var_03    C11  C12  C13  C9     55.06  30.0  1
 NVW  Var_04    C12  C11  S1   C10    45.40  30.0  1
 NVW  Var_05    C13  C12  C11  S1    -68.65  30.0  1
 NVW  Var_06    C15  C14  N3   C1     48.85  30.0  1
 NVW  Var_07    C14  N3   C1   N2     -1.72  30.0  2
 NVW  Var_08    C21  C20  C18  C16    94.29  30.0  1
 NVW  Var_09    N4   C21  C20  C18  -178.18  30.0  2
 NVW  Var_10    C25  C22  N4   C21   -62.57  30.0  3
 NVW  Var_11    H26  C25  C22  N4     63.75  30.0  3
 NVW  Var_12    H23  C24  C22  N4     59.90  30.0  3
 NVW  Var_13    H20  C23  C22  N4     56.15  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
 NVW  plan-1  C2   0.020
 NVW  plan-1  C3   0.020
 NVW  plan-1  C4   0.020
 NVW  plan-1  C5   0.020
 NVW  plan-1  C6   0.020
 NVW  plan-1  C7   0.020
 NVW  plan-1  C8   0.020
 NVW  plan-1  H2   0.020
 NVW  plan-1  H3   0.020
 NVW  plan-1  H4   0.020
 NVW  plan-1  H5   0.020
 NVW  plan-1  H6   0.020
 NVW  plan-2  N3   0.020
 NVW  plan-2  C14  0.020
 NVW  plan-2  C15  0.020
 NVW  plan-2  C16  0.020
 NVW  plan-2  C17  0.020
 NVW  plan-2  C18  0.020
 NVW  plan-2  C19  0.020
 NVW  plan-2  C20  0.020
 NVW  plan-2  H13  0.020
 NVW  plan-2  H14  0.020
 NVW  plan-2  H15  0.020
 NVW  plan-2  H16  0.020
 NVW  plan-3  N1   0.020
 NVW  plan-3  C1   0.020
 NVW  plan-3  N2   0.020
 NVW  plan-3  C2   0.020
 NVW  plan-3  C3   0.020
 NVW  plan-3  N3   0.020
 NVW  plan-3  C9   0.020
 NVW  plan-3  C10  0.020
 NVW  plan-3  S1   0.020
 NVW  plan-3  C13  0.020
 NVW  plan-4  C20  0.020
 NVW  plan-4  C21  0.020
 NVW  plan-4  N4   0.020
 NVW  plan-4  O3   0.020
 NVW  plan-4  C22  0.020
 NVW  plan-4  H19  0.020

