# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:27:51 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 3,3-dimethyl-8-morpholin-4-yl-6-(2-phenylethylsulfanyl)-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)Cc2c(CO1)c(nc(SCCc3ccccc3)c2C#N)N4CCOCC4
#
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
 5QG  5QG  3,3-dimethyl-8-morpholin-4-yl-6-(2-phenylethylsulfanyl)-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile  ligand  56  29  .  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_5QG
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
 5QG  N1   N  NS    0  -0.246  -2.0319  -4.3578   0.0482
 5QG  C1   C  CSP   0  -0.028  -1.8352  -3.2203   0.0356
 5QG  C2   C  CR6   0  -0.075  -1.5939  -1.8241   0.0213
 5QG  C7   C  CR6   0   0.086  -0.2888  -1.3297  -0.0614
 5QG  N6   N  N     0  -0.468  -0.0307  -0.0420  -0.0657
 5QG  C5   C  CR6   0   0.495  -1.0232   0.8410   0.0070
 5QG  N17  N  NT    0  -0.507  -0.6651   2.1664  -0.0319
 5QG  C22  C  CH2   0  -0.314   0.6825   2.4989  -0.4711
 5QG  C21  C  CH2   0  -0.188   0.7066   3.9504  -0.9166
 5QG  O20  O  O2    0  -0.482   0.2812   4.8282   0.1019
 5QG  C19  C  CH2   0  -0.180  -1.0200   4.5069   0.5353
 5QG  C18  C  CH2   0  -0.341  -1.1034   3.0746   1.0235
 5QG  C4   C  CR6   0  -0.158  -2.3814   0.4450   0.0355
 5QG  O8   O  O2    0  -0.486  -4.6867   0.8233  -0.5696
 5QG  C30  C  CT    0   0.195  -5.1104  -0.3127   0.1802
 5QG  C6   C  CH2   0  -0.520  -4.0694  -1.4164  -0.0101
 5QG  C3   C  CR6   0   0.279  -2.6596  -0.9085   0.0443
 5QG  S8   S  S2    0   0.063   1.0456  -2.4630  -0.1544
 5QG  C9   C  CH2   0  -0.537   2.4886  -1.3598  -0.1283
 5QG  C10  C  CH2   0  -0.520   3.7466  -2.2258  -0.1333
 5QG  C11  C  CR6   0   0.126   4.9726  -1.3545  -0.0998
 5QG  C16  C  CR16  0  -0.303   5.4906  -0.9062   1.1134
 5QG  C15  C  CR16  0  -0.240   6.6035  -0.0778   1.1473
 5QG  C14  C  CR16  0  -0.271   7.2148   0.3177  -0.0357
 5QG  C13  C  CR16  0  -0.239   6.7047  -0.1210  -1.2506
 5QG  C12  C  CR16  0  -0.306   5.5910  -0.9493  -1.2800
 5QG  C17  C  CH2   0  -0.235  -3.5174   1.4259  -0.0890
 5QG  C20  C  CH3   0  -0.673  -6.4400  -0.7380  -0.4214
 5QG  C23  C  CH3   0  -0.690  -5.2925   0.0122   1.6625
 5QG  H1   H  HCH2  0   0.231   1.4180   2.3308   0.3258
 5QG  H2   H  HCH2  0   0.262   0.9648   1.8694  -1.3137
 5QG  H3   H  HCH2  0   0.244   1.7251   4.2320  -1.1862
 5QG  H4   H  HCH2  0   0.207   0.0752   4.0628  -1.8092
 5QG  H5   H  HCH2  0   0.245  -1.2725   5.1863   1.3505
 5QG  H6   H  HCH2  0   0.208  -1.7495   4.6607  -0.2725
 5QG  H7   H  HCH2  0   0.263  -2.1218   2.8661   1.3379
 5QG  H8   H  HCH2  0   0.249  -0.4637   2.9470   1.9071
 5QG  H9   H  HCH2  0   0.270  -4.2131  -2.1997   0.7385
 5QG  H10  H  HCH2  0   0.281  -4.2140  -1.8961  -0.9844
 5QG  H11  H  HCH2  0   0.287   2.4601  -0.7063  -0.9994
 5QG  H12  H  HCH2  0   0.285   2.4459  -0.7394   0.7663
 5QG  H13  H  HCH2  0   0.264   3.7391  -2.8919   0.7323
 5QG  H14  H  HCH2  0   0.264   3.7607  -2.8562  -1.0251
 5QG  H15  H  HCR6  0   0.249   5.0221  -1.2133   2.0414
 5QG  H16  H  HCR6  0   0.255   6.9972   0.2545   2.0994
 5QG  H17  H  HCR6  0   0.255   8.0849   0.9608  -0.0104
 5QG  H18  H  HCR6  0   0.255   7.1771   0.1770  -2.1778
 5QG  H19  H  HCR6  0   0.249   5.2009  -1.2894  -2.2323
 5QG  H20  H  HCH2  0   0.232  -3.7163   1.9263   0.8673
 5QG  H21  H  HCH2  0   0.267  -3.2435   2.2110  -0.8006
 5QG  H22  H  HCH3  0   0.238  -6.3441  -0.9372  -1.4898
 5QG  H23  H  HCH3  0   0.233  -6.7950  -1.6494   0.0598
 5QG  H24  H  HCH3  0   0.240  -7.1975   0.0338  -0.2790
 5QG  H25  H  HCH3  0   0.244  -5.9613   0.8643   1.7955
 5QG  H26  H  HCH3  0   0.246  -5.7376  -0.8432   2.1713
 5QG  H27  H  HCH3  0   0.239  -4.3525   0.2306   2.1721

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
 5QG  O20  C19  single    1.409  0.020  1.409
 5QG  O20  C21  single    1.410  0.020  1.410
 5QG  C19  C18  single    1.516  0.020  1.516
 5QG  C21  C22  single    1.518  0.020  1.518
 5QG  C13  C14  aromatic  1.389  0.020  1.389
 5QG  C13  C12  aromatic  1.388  0.020  1.388
 5QG  C14  C15  aromatic  1.389  0.020  1.389
 5QG  C18  N17  single    1.460  0.020  1.460
 5QG  C22  N17  single    1.456  0.020  1.456
 5QG  C12  C11  aromatic  1.393  0.020  1.393
 5QG  C15  C16  aromatic  1.388  0.020  1.388
 5QG  N17  C5   single    1.373  0.020  1.373
 5QG  C11  C16  aromatic  1.393  0.020  1.393
 5QG  C11  C10  single    1.504  0.020  1.504
 5QG  C5   N6   aromatic  1.330  0.020  1.330
 5QG  C5   C4   aromatic  1.415  0.020  1.415
 5QG  C17  C4   single    1.506  0.020  1.506
 5QG  C17  O8   single    1.401  0.020  1.401
 5QG  C10  C9   single    1.527  0.020  1.527
 5QG  N6   C7   aromatic  1.313  0.020  1.313
 5QG  C4   C3   aromatic  1.382  0.020  1.382
 5QG  O8   C30  single    1.426  0.020  1.426
 5QG  C9   S8   single    1.817  0.020  1.817
 5QG  C7   S8   single    1.753  0.020  1.753
 5QG  C7   C2   aromatic  1.398  0.020  1.398
 5QG  C3   C2   aromatic  1.405  0.020  1.405
 5QG  C3   C6   single    1.499  0.020  1.499
 5QG  C30  C23  single    1.528  0.020  1.528
 5QG  C30  C20  single    1.520  0.020  1.520
 5QG  C30  C6   single    1.529  0.020  1.529
 5QG  C2   C1   single    1.417  0.020  1.417
 5QG  C1   N1   triple    1.154  0.020  1.154
 5QG  C22  H1   single    0.970  0.020  1.090
 5QG  C22  H2   single    0.970  0.020  1.090
 5QG  C21  H3   single    0.970  0.020  1.090
 5QG  C21  H4   single    0.970  0.020  1.090
 5QG  C19  H5   single    0.970  0.020  1.090
 5QG  C19  H6   single    0.970  0.020  1.090
 5QG  C18  H7   single    0.970  0.020  1.090
 5QG  C18  H8   single    0.970  0.020  1.090
 5QG  C6   H9   single    0.970  0.020  1.090
 5QG  C6   H10  single    0.970  0.020  1.090
 5QG  C9   H11  single    0.970  0.020  1.090
 5QG  C9   H12  single    0.970  0.020  1.090
 5QG  C10  H13  single    0.970  0.020  1.090
 5QG  C10  H14  single    0.970  0.020  1.090
 5QG  C16  H15  single    0.930  0.020  1.080
 5QG  C15  H16  single    0.930  0.020  1.080
 5QG  C14  H17  single    0.930  0.020  1.080
 5QG  C13  H18  single    0.930  0.020  1.080
 5QG  C12  H19  single    0.930  0.020  1.080
 5QG  C17  H20  single    0.970  0.020  1.090
 5QG  C17  H21  single    0.970  0.020  1.090
 5QG  C20  H22  single    0.970  0.020  1.090
 5QG  C20  H23  single    0.970  0.020  1.090
 5QG  C20  H24  single    0.970  0.020  1.090
 5QG  C23  H25  single    0.970  0.020  1.090
 5QG  C23  H26  single    0.970  0.020  1.090
 5QG  C23  H27  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
 5QG  C2   C1   N1   180.00  3.000
 5QG  C3   C2   C7   118.59  3.000
 5QG  C3   C2   C1   120.85  3.000
 5QG  C7   C2   C1   120.53  3.000
 5QG  S8   C7   N6   118.95  3.000
 5QG  S8   C7   C2   119.02  3.000
 5QG  N6   C7   C2   122.03  3.000
 5QG  C5   N6   C7   120.26  3.000
 5QG  C4   C5   N17  121.39  3.000
 5QG  C4   C5   N6   122.10  3.000
 5QG  N17  C5   N6   116.38  3.000
 5QG  C18  N17  C22  110.73  3.000
 5QG  C22  N17  C5   118.06  3.000
 5QG  C18  N17  C5   120.10  3.000
 5QG  H2   C22  H1   107.43  3.000
 5QG  H2   C22  C21  108.75  3.000
 5QG  H1   C22  C21  110.42  3.000
 5QG  H2   C22  N17  109.96  3.000
 5QG  H1   C22  N17  111.48  3.000
 5QG  C21  C22  N17  108.76  3.000
 5QG  H4   C21  H3   108.02  3.000
 5QG  H4   C21  O20  110.46  3.000
 5QG  H3   C21  O20  107.42  3.000
 5QG  H4   C21  C22  109.08  3.000
 5QG  H3   C21  C22  109.52  3.000
 5QG  O20  C21  C22  112.23  3.000
 5QG  C19  O20  C21  111.03  3.000
 5QG  H6   C19  H5   107.96  3.000
 5QG  H6   C19  C18  109.42  3.000
 5QG  H5   C19  C18  109.58  3.000
 5QG  H6   C19  O20  110.79  3.000
 5QG  H5   C19  O20  107.56  3.000
 5QG  C18  C19  O20  111.44  3.000
 5QG  H8   C18  H7   106.92  3.000
 5QG  H8   C18  C19  109.69  3.000
 5QG  H7   C18  C19  109.04  3.000
 5QG  H8   C18  N17  109.55  3.000
 5QG  H7   C18  N17  111.81  3.000
 5QG  C19  C18  N17  109.79  3.000
 5QG  C17  C4   C3   119.12  3.000
 5QG  C3   C4   C5   117.87  3.000
 5QG  C17  C4   C5   122.69  3.000
 5QG  C17  O8   C30  114.24  3.000
 5QG  C23  C30  C20  109.82  3.000
 5QG  C20  C30  C6   110.14  3.000
 5QG  C23  C30  C6   110.81  3.000
 5QG  C6   C30  O8   107.90  3.000
 5QG  C20  C30  O8   105.95  3.000
 5QG  C23  C30  O8   112.09  3.000
 5QG  H10  C6   H9   106.14  3.000
 5QG  H10  C6   C3   107.74  3.000
 5QG  H9   C6   C3   109.97  3.000
 5QG  H10  C6   C30  109.68  3.000
 5QG  H9   C6   C30  110.03  3.000
 5QG  C3   C6   C30  113.02  3.000
 5QG  C6   C3   C4   121.39  3.000
 5QG  C6   C3   C2   119.45  3.000
 5QG  C4   C3   C2   119.04  3.000
 5QG  C9   S8   C7   102.20  3.000
 5QG  H12  C9   H11  108.30  3.000
 5QG  H12  C9   C10  110.97  3.000
 5QG  H11  C9   C10  111.04  3.000
 5QG  H12  C9   S8   109.06  3.000
 5QG  H11  C9   S8   109.39  3.000
 5QG  C10  C9   S8   108.06  3.000
 5QG  H14  C10  H13  107.17  3.000
 5QG  H14  C10  C11  110.00  3.000
 5QG  H13  C10  C11  109.95  3.000
 5QG  H14  C10  C9   109.91  3.000
 5QG  H13  C10  C9   109.72  3.000
 5QG  C11  C10  C9   110.05  3.000
 5QG  C12  C11  C16  118.63  3.000
 5QG  C16  C11  C10  120.58  3.000
 5QG  C12  C11  C10  120.77  3.000
 5QG  H15  C16  C15  119.66  3.000
 5QG  H15  C16  C11  119.58  3.000
 5QG  C15  C16  C11  120.76  3.000
 5QG  H16  C15  C14  120.11  3.000
 5QG  H16  C15  C16  119.76  3.000
 5QG  C14  C15  C16  120.13  3.000
 5QG  H17  C14  C13  120.23  3.000
 5QG  H17  C14  C15  120.20  3.000
 5QG  C13  C14  C15  119.57  3.000
 5QG  H18  C13  C12  119.75  3.000
 5QG  H18  C13  C14  120.14  3.000
 5QG  C12  C13  C14  120.11  3.000
 5QG  H19  C12  C13  119.64  3.000
 5QG  H19  C12  C11  119.57  3.000
 5QG  C13  C12  C11  120.79  3.000
 5QG  H21  C17  H20  106.55  3.000
 5QG  H21  C17  O8   107.13  3.000
 5QG  H20  C17  O8   110.11  3.000
 5QG  H21  C17  C4   109.40  3.000
 5QG  H20  C17  C4   111.20  3.000
 5QG  O8   C17  C4   112.21  3.000
 5QG  H24  C20  H23  107.93  3.000
 5QG  H24  C20  H22  108.55  3.000
 5QG  H23  C20  H22  107.96  3.000
 5QG  H24  C20  C30  110.97  3.000
 5QG  H23  C20  C30  110.12  3.000
 5QG  H22  C20  C30  111.20  3.000
 5QG  H27  C23  H26  106.90  3.000
 5QG  H27  C23  H25  108.34  3.000
 5QG  H26  C23  H25  107.80  3.000
 5QG  H27  C23  C30  113.12  3.000
 5QG  H26  C23  C30  109.54  3.000
 5QG  H25  C23  C30  110.92  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
 5QG  CONST_01  C5   N6   C7   C2      0.00   0.0  0
 5QG  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 5QG  CONST_03  C4   C5   N6   C7      0.00   0.0  0
 5QG  CONST_04  C4   C3   C2   C7      0.00   0.0  0
 5QG  CONST_05  C3   C4   C5   N6      0.00   0.0  0
 5QG  CONST_06  C3   C2   C7   N6      0.00   0.0  0
 5QG  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 5QG  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 5QG  CONST_09  C13  C14  C15  C16     0.00   0.0  0
 5QG  CONST_10  C13  C12  C11  C16     0.00   0.0  0
 5QG  CONST_11  C12  C13  C14  C15     0.00   0.0  0
 5QG  CONST_12  C12  C11  C16  C15     0.00   0.0  0
 5QG  CONST_13  N17  C5   N6   C7    180.00   0.0  0
 5QG  CONST_14  C17  C4   C5   N17     0.00   0.0  0
 5QG  CONST_15  C3   C4   C5   N17   180.00   0.0  0
 5QG  CONST_16  N6   C7   C2   C1    180.00   0.0  0
 5QG  CONST_17  C4   C3   C2   C1    180.00   0.0  0
 5QG  CONST_18  C6   C3   C2   C1      0.00   0.0  0
 5QG  CONST_19  S8   C7   N6   C5    180.00   0.0  0
 5QG  CONST_20  S8   C7   C2   C3    180.00   0.0  0
 5QG  CONST_21  C13  C12  C11  C10   180.00   0.0  0
 5QG  CONST_22  C15  C16  C11  C10   180.00   0.0  0
 5QG  CONST_23  H18  C13  C12  C11   180.00   0.0  0
 5QG  CONST_24  H16  C15  C16  C11   180.00   0.0  0
 5QG  CONST_25  H17  C14  C15  C16   180.00   0.0  0
 5QG  CONST_26  H19  C12  C11  C16   180.00   0.0  0
 5QG  CONST_27  H15  C16  C15  C14   180.00   0.0  0
 5QG  Var_01    C30  C6   C3   C2    173.58  30.0  1
 5QG  Var_02    C18  N17  C5   N6   -125.82  30.0  3
 5QG  Var_03    C19  C18  N17  C5   -160.15  30.0  1
 5QG  Var_04    C21  C22  N17  C5    159.68  30.0  1
 5QG  Var_05    O8   C17  C4   C5    155.81  30.0  1
 5QG  Var_06    O20  C19  C18  N17   -56.64  30.0  1
 5QG  Var_07    O20  C21  C22  N17    57.07  30.0  1
 5QG  Var_08    C18  C19  O20  C21    57.24  30.0  1
 5QG  Var_09    C3   C6   C30  O8     42.04  30.0  1
 5QG  Var_10    C12  C11  C10  C9    -92.01  30.0  2
 5QG  Var_11    H25  C23  C30  O8     53.86  30.0  3
 5QG  Var_12    H22  C20  C30  O8     56.48  30.0  3
 5QG  Var_13    C10  C9   S8   C7    177.17  30.0  1
 5QG  Var_14    C11  C10  C9   S8   -179.50  30.0  2

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
 5QG  plan-1  C10  0.020
 5QG  plan-1  C11  0.020
 5QG  plan-1  C16  0.020
 5QG  plan-1  C15  0.020
 5QG  plan-1  C14  0.020
 5QG  plan-1  C13  0.020
 5QG  plan-1  C12  0.020
 5QG  plan-1  H15  0.020
 5QG  plan-1  H16  0.020
 5QG  plan-1  H17  0.020
 5QG  plan-1  H18  0.020
 5QG  plan-1  H19  0.020
 5QG  plan-2  N1   0.020
 5QG  plan-2  C1   0.020
 5QG  plan-2  C2   0.020
 5QG  plan-2  C7   0.020
 5QG  plan-2  N6   0.020
 5QG  plan-2  C5   0.020
 5QG  plan-2  N17  0.020
 5QG  plan-2  C4   0.020
 5QG  plan-2  C6   0.020
 5QG  plan-2  C3   0.020
 5QG  plan-2  S8   0.020
 5QG  plan-2  C17  0.020

