# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 23:01:31 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 8-{[(2-cyanopyridin-3-yl)methyl]sulfanyl}-6-hydroxy-3,4-dihydro-1H-pyrano[3,4-c]pyridine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1nc(SCc2cccnc2C#N)c3COCCc3c1C#N
#
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
 07M  07M  8-{[(2-cyanopyridin-3-yl)methyl]sulfanyl}-6-hydroxy-3,4-dihydro-1H-pyrano[3,4-c]pyridine-5-carbonitrile  ligand  35  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_07M
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
 07M  C1   C  CR6   0   0.098   3.3096  -0.3768   0.5716
 07M  C2   C  CH2   0  -0.644   1.8809  -0.8205   0.5854
 07M  C3   C  CH2   0  -0.180  -3.9148   2.6746   0.1256
 07M  O4   O  O2    0  -0.465  -2.7420   3.0178  -0.5794
 07M  C5   C  CH2   0  -0.200  -1.6120   2.3667  -0.0685
 07M  C6   C  CH2   0  -0.519  -4.2850   1.2277  -0.1472
 07M  C7   C  CR6   0   0.279  -3.0920   0.3375   0.0228
 07M  C8   C  CR6   0  -0.067  -1.8220   0.8810   0.0709
 07M  C9   C  CR6   0   0.084  -0.7541  -0.0051   0.2673
 07M  N10  N  N     0  -0.452  -0.8867  -1.3131   0.3822
 07M  C11  C  CR6   0   0.523  -2.0900  -1.8419   0.3135
 07M  C12  C  CR6   0  -0.239  -3.2351  -1.0538   0.1367
 07M  C13  C  CSP   0  -0.002  -4.5129  -1.6634   0.0755
 07M  N14  N  NS    0  -0.260  -5.5410  -2.1850   0.0240
 07M  O15  O  OH1   0  -0.572  -2.1180  -3.1624   0.4321
 07M  S16  S  S2    0   0.114   0.8589   0.6711   0.3753
 07M  C17  C  CR6   0   0.188   3.9990  -0.1367  -0.6160
 07M  N18  N  N     0  -0.366   5.2625   0.2656  -0.6917
 07M  C19  C  CR16  0  -0.047   5.9130   0.4578   0.4433
 07M  C20  C  CR16  0  -0.287   5.3309   0.2577   1.6900
 07M  C21  C  CR16  0  -0.148   4.0148  -0.1613   1.7504
 07M  C22  C  CSP   0   0.022   3.3355  -0.3251  -1.8793
 07M  N23  N  NS    0  -0.169   2.8052  -0.4775  -2.8893
 07M  H1   H  HCH2  0   0.315   1.6609  -1.5220  -0.2184
 07M  H2   H  HCH2  0   0.303   1.6327  -1.2966   1.5321
 07M  H3   H  HCH2  0   0.216  -3.7811   2.8328   1.2036
 07M  H4   H  HCH2  0   0.246  -4.7072   3.3407  -0.2140
 07M  H5   H  HCH2  0   0.253  -0.7920   2.5682  -0.7635
 07M  H6   H  HCH2  0   0.223  -1.3208   2.7883   0.9056
 07M  H7   H  HCH2  0   0.263  -5.0892   0.9185   0.5242
 07M  H8   H  HCH2  0   0.271  -4.6684   1.1177  -1.1660
 07M  H10  H  HCR6  0   0.254   6.9423   0.7848   0.3618
 07M  H11  H  HCR6  0   0.252   5.9028   0.4287   2.5908
 07M  H12  H  HCR6  0   0.250   3.5331  -0.3283   2.7050
 07M  H9   H  HOH1  0   0.465  -3.0124  -3.5249   0.3898

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
 07M  N23  C22  triple    1.151  0.020  1.151
 07M  C22  C17  single    1.439  0.020  1.439
 07M  N18  C17  aromatic  1.328  0.020  1.328
 07M  N18  C19  aromatic  1.322  0.020  1.322
 07M  C17  C1   aromatic  1.394  0.020  1.394
 07M  C19  C20  aromatic  1.390  0.020  1.390
 07M  C1   C2   single    1.496  0.020  1.496
 07M  C1   C21  aromatic  1.390  0.020  1.390
 07M  C2   S16  single    1.820  0.020  1.820
 07M  S16  C9   single    1.752  0.020  1.752
 07M  C20  C21  aromatic  1.383  0.020  1.383
 07M  C5   O4   single    1.401  0.020  1.401
 07M  C5   C8   single    1.507  0.020  1.507
 07M  C9   C8   aromatic  1.401  0.020  1.401
 07M  C9   N10  aromatic  1.320  0.020  1.320
 07M  O4   C3   single    1.411  0.020  1.411
 07M  C8   C7   aromatic  1.382  0.020  1.382
 07M  N10  C11  aromatic  1.316  0.020  1.316
 07M  C3   C6   single    1.518  0.020  1.518
 07M  C7   C6   single    1.498  0.020  1.498
 07M  C7   C12  aromatic  1.403  0.020  1.403
 07M  C11  O15  single    1.326  0.020  1.326
 07M  C11  C12  aromatic  1.401  0.020  1.401
 07M  C12  C13  single    1.417  0.020  1.417
 07M  C13  N14  triple    1.154  0.020  1.154
 07M  C2   H1   single    0.970  0.020  1.090
 07M  C2   H2   single    0.970  0.020  1.090
 07M  C3   H3   single    0.970  0.020  1.090
 07M  C3   H4   single    0.970  0.020  1.090
 07M  C5   H5   single    0.970  0.020  1.090
 07M  C5   H6   single    0.970  0.020  1.090
 07M  C6   H7   single    0.970  0.020  1.090
 07M  C6   H8   single    0.970  0.020  1.090
 07M  C19  H10  single    0.930  0.020  1.080
 07M  C20  H11  single    0.930  0.020  1.080
 07M  C21  H12  single    0.930  0.020  1.080
 07M  O15  H9   single    0.850  0.020  0.980

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
 07M  C21  C1   C17  116.41  3.000
 07M  C21  C1   C2   121.49  3.000
 07M  C17  C1   C2   122.09  3.000
 07M  H2   C2   H1   108.30  3.000
 07M  H2   C2   S16  109.32  3.000
 07M  H1   C2   S16  109.21  3.000
 07M  H2   C2   C1   110.83  3.000
 07M  H1   C2   C1   112.15  3.000
 07M  S16  C2   C1   106.99  3.000
 07M  H4   C3   H3   107.86  3.000
 07M  H4   C3   C6   110.45  3.000
 07M  H3   C3   C6   110.09  3.000
 07M  H4   C3   O4   107.46  3.000
 07M  H3   C3   O4   110.76  3.000
 07M  C6   C3   O4   110.17  3.000
 07M  C5   O4   C3   112.04  3.000
 07M  H6   C5   H5   107.07  3.000
 07M  H6   C5   C8   109.43  3.000
 07M  H5   C5   C8   110.18  3.000
 07M  H6   C5   O4   110.99  3.000
 07M  H5   C5   O4   106.71  3.000
 07M  C8   C5   O4   112.31  3.000
 07M  H8   C6   H7   106.61  3.000
 07M  H8   C6   C7   108.96  3.000
 07M  H7   C6   C7   110.38  3.000
 07M  H8   C6   C3   110.40  3.000
 07M  H7   C6   C3   109.81  3.000
 07M  C7   C6   C3   110.59  3.000
 07M  C12  C7   C8   118.73  3.000
 07M  C12  C7   C6   121.14  3.000
 07M  C8   C7   C6   120.13  3.000
 07M  C9   C8   C7   117.16  3.000
 07M  C7   C8   C5   120.83  3.000
 07M  C9   C8   C5   122.01  3.000
 07M  S16  C9   N10  118.01  3.000
 07M  N10  C9   C8   124.21  3.000
 07M  S16  C9   C8   117.78  3.000
 07M  C11  N10  C9   119.05  3.000
 07M  O15  C11  C12  123.65  3.000
 07M  C12  C11  N10  121.85  3.000
 07M  O15  C11  N10  114.50  3.000
 07M  C13  C12  C11  120.02  3.000
 07M  C13  C12  C7   121.00  3.000
 07M  C11  C12  C7   118.98  3.000
 07M  N14  C13  C12  180.00  3.000
 07M  H9   O15  C11  112.91  3.000
 07M  C9   S16  C2   101.99  3.000
 07M  C22  C17  N18  115.35  3.000
 07M  N18  C17  C1   124.83  3.000
 07M  C22  C17  C1   119.82  3.000
 07M  C19  N18  C17  117.59  3.000
 07M  H10  C19  C20  120.59  3.000
 07M  H10  C19  N18  116.54  3.000
 07M  C20  C19  N18  122.87  3.000
 07M  H11  C20  C21  121.02  3.000
 07M  H11  C20  C19  120.20  3.000
 07M  C21  C20  C19  118.78  3.000
 07M  H12  C21  C20  120.60  3.000
 07M  H12  C21  C1   119.88  3.000
 07M  C20  C21  C1   119.52  3.000
 07M  N23  C22  C17  180.00  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
 07M  CONST_01  C19  N18  C17  C1      0.00   0.0  0
 07M  CONST_02  C19  C20  C21  C1      0.00   0.0  0
 07M  CONST_03  N10  C9   C8   C7      0.00   0.0  0
 07M  CONST_04  N10  C11  C12  C7      0.00   0.0  0
 07M  CONST_05  C11  N10  C9   C8      0.00   0.0  0
 07M  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 07M  CONST_07  C12  C7   C8   C9      0.00   0.0  0
 07M  CONST_08  C12  C11  N10  C9      0.00   0.0  0
 07M  CONST_09  C20  C19  N18  C17     0.00   0.0  0
 07M  CONST_10  C20  C21  C1   C17     0.00   0.0  0
 07M  CONST_11  C21  C1   C17  N18     0.00   0.0  0
 07M  CONST_12  C21  C20  C19  N18     0.00   0.0  0
 07M  CONST_13  N18  C17  C1   C2    180.00   0.0  0
 07M  CONST_14  C20  C21  C1   C2    180.00   0.0  0
 07M  CONST_15  S16  C9   C8   C5      0.00   0.0  0
 07M  CONST_16  C13  C12  C7   C6      0.00   0.0  0
 07M  CONST_17  S16  C9   C8   C7    180.00   0.0  0
 07M  CONST_18  O15  C11  C12  C7    180.00   0.0  0
 07M  CONST_19  C13  C12  C7   C8    180.00   0.0  0
 07M  CONST_20  O15  C11  N10  C9    180.00   0.0  0
 07M  CONST_21  C13  C12  C11  N10   180.00   0.0  0
 07M  CONST_22  S16  C9   N10  C11   180.00   0.0  0
 07M  CONST_23  C22  C17  N18  C19   180.00   0.0  0
 07M  CONST_24  C22  C17  C1   C21   180.00   0.0  0
 07M  CONST_25  H11  C20  C21  C1    180.00   0.0  0
 07M  CONST_26  H10  C19  N18  C17   180.00   0.0  0
 07M  CONST_27  H12  C21  C1   C17   180.00   0.0  0
 07M  Var_01    C8   C5   O4   C3     50.59  30.0  1
 07M  Var_02    C8   C7   C6   C3    -15.13  30.0  1
 07M  Var_03    C9   C8   C5   O4    165.22  30.0  1
 07M  Var_04    C7   C6   C3   O4     48.53  30.0  1
 07M  Var_05    C6   C3   O4   C5    -69.12  30.0  1
 07M  Var_06    C8   C9   S16  C2   -178.79  30.0  2
 07M  Var_07    C17  C1   C2   S16   -81.70  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
 07M  plan-1  C1   0.020
 07M  plan-1  C2   0.020
 07M  plan-1  C17  0.020
 07M  plan-1  N18  0.020
 07M  plan-1  C19  0.020
 07M  plan-1  C20  0.020
 07M  plan-1  C21  0.020
 07M  plan-1  C22  0.020
 07M  plan-1  N23  0.020
 07M  plan-1  H10  0.020
 07M  plan-1  H11  0.020
 07M  plan-1  H12  0.020
 07M  plan-2  C5   0.020
 07M  plan-2  C6   0.020
 07M  plan-2  C7   0.020
 07M  plan-2  C8   0.020
 07M  plan-2  C9   0.020
 07M  plan-2  N10  0.020
 07M  plan-2  C11  0.020
 07M  plan-2  C12  0.020
 07M  plan-2  C13  0.020
 07M  plan-2  N14  0.020
 07M  plan-2  O15  0.020
 07M  plan-2  S16  0.020

