# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 14:52:56 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: ~{N}-[3-(diethylamino)propyl]-2-(12-methyl-9-oxidanylidene-5-thia-1,10,11-triazatricyclo[6.4.0.0^{2,6}]dodeca-2(6),3,7,11-tetraen-10-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)CCCNC(=O)CN1N=C(C)n2c3ccsc3cc2C1=O
#
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
 8C3  8C3  ~{N}-[3-(diethylamino)propyl]-2-(12-methyl-9-oxidanylidene-5-thia-1,10,11-triazatricyclo[6.4.0.0^{2,6}]dodeca-2(6),3,7,11-tetraen-10-yl)ethanamide  ligand  51  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8C3
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
 8C3  C1   C  CR56  0   0.234   2.9430  -0.5696  -0.4765
 8C3  C2   C  CR6   0   0.566   1.5711  -0.3703  -0.8784
 8C3  C3   C  CR6   0   0.481   3.1088   1.7804   0.0116
 8C3  O1   O  O     0  -0.466   0.8296  -1.2684  -1.2476
 8C3  O2   O  O     0  -0.468  -0.6973   0.4841   1.1040
 8C3  C11  C  CH3   0  -0.733   3.9184   2.9194   0.5154
 8C3  C12  C  CH2   0  -0.473  -4.8025   0.2191  -0.0801
 8C3  C13  C  CH2   0  -0.216  -3.4557   0.3395   0.6133
 8C3  C14  C  CH2   0  -0.260  -5.8813  -0.2326   0.8958
 8C3  C15  C  CH2   0  -0.279  -8.0343  -1.3184   0.9209
 8C3  C16  C  CH2   0  -0.275  -7.8418   0.9798   0.2036
 8C3  C17  C  CH3   0  -0.642  -7.6749  -2.7405   0.5210
 8C3  C18  C  CH3   0  -0.644  -8.9007   1.0564  -0.8841
 8C3  N1   N  N     0  -0.654   3.6826   0.5254  -0.0472
 8C3  C4   C  CR15  0  -0.371   3.7070  -1.7072  -0.4189
 8C3  N2   N  NR6   0  -0.363   1.1652   0.9332  -0.8279
 8C3  C5   C  CR55  0   0.373   4.9350   0.0855   0.2859
 8C3  N3   N  N     0  -0.278   1.9015   1.9671  -0.3562
 8C3  C6   C  CR55  0  -0.198   4.9622  -1.2861   0.0611
 8C3  C7   C  CH2   0  -0.417  -0.2093   1.2384  -1.1248
 8C3  C8   C  CR15  0  -0.154   6.1587   0.6192   0.7751
 8C3  S1   S  S2    0   0.233   6.5016  -1.9411   0.4528
 8C3  C9   C  C     0   0.558  -1.1280   0.7657  -0.0021
 8C3  C10  C  CR15  0  -0.453   7.0786  -0.3719   0.9081
 8C3  N4   N  NH1   0  -0.641  -2.4219   0.7121  -0.3319
 8C3  N5   N  NT    0  -0.401  -7.1926  -0.3216   0.2751
 8C3  H1   H  HCH3  0   0.281   3.3129   3.8213   0.5110
 8C3  H2   H  HCH3  0   0.255   4.2618   2.7391   1.5348
 8C3  H3   H  HCH3  0   0.255   4.7948   3.0900  -0.1108
 8C3  H4   H  HCH2  0   0.219  -5.0679   1.1824  -0.5263
 8C3  H5   H  HCH2  0   0.233  -4.7389  -0.5058  -0.8960
 8C3  H6   H  HCH2  0   0.229  -3.5147   1.0784   1.4181
 8C3  H7   H  HCH2  0   0.232  -3.1905  -0.6139   1.0775
 8C3  H8   H  HCH2  0   0.223  -5.6002  -1.2176   1.2742
 8C3  H9   H  HCH2  0   0.194  -5.8956   0.4351   1.7741
 8C3  H10  H  HCH2  0   0.220  -9.0702  -1.1373   0.6299
 8C3  H11  H  HCH2  0   0.191  -8.0081  -1.2164   2.0183
 8C3  H12  H  HCH2  0   0.215  -7.0797   1.7319  -0.0086
 8C3  H13  H  HCH2  0   0.191  -8.2794   1.2627   1.1755
 8C3  H14  H  HCH3  0   0.217  -8.3394  -3.4523   1.0121
 8C3  H15  H  HCH3  0   0.220  -7.7752  -2.8719  -0.5567
 8C3  H16  H  HCH3  0   0.211  -6.6542  -3.0062   0.7982
 8C3  H17  H  HCH3  0   0.218  -8.4650   0.8450  -1.8611
 8C3  H18  H  HCH3  0   0.214  -9.7165   0.3519  -0.7191
 8C3  H19  H  HCH3  0   0.217  -9.3384   2.0547  -0.9176
 8C3  H20  H  HCR5  0   0.254   3.3910  -2.7007  -0.6900
 8C3  H21  H  HCH2  0   0.290  -0.2921   2.3201  -1.2275
 8C3  H22  H  HCH2  0   0.267  -0.5000   0.7965  -2.0781
 8C3  H23  H  HCR5  0   0.254   6.3634   1.6507   1.0131
 8C3  H24  H  HCR5  0   0.268   8.0938  -0.2659   1.2584
 8C3  H25  H  HNH1  0   0.369  -2.7018   0.9792  -1.2626

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
 8C3  C10  S1   aromatic  1.733  0.020  1.733
 8C3  C10  C8   aromatic  1.359  0.020  1.359
 8C3  S1   C6   aromatic  1.718  0.020  1.718
 8C3  C8   C5   aromatic  1.422  0.020  1.422
 8C3  C6   C5   aromatic  1.390  0.020  1.390
 8C3  C6   C4   aromatic  1.408  0.020  1.408
 8C3  C5   N1   aromatic  1.369  0.020  1.369
 8C3  C4   C1   aromatic  1.372  0.020  1.372
 8C3  N1   C1   aromatic  1.389  0.020  1.389
 8C3  N1   C3   single    1.381  0.020  1.381
 8C3  C1   C2   single    1.443  0.020  1.443
 8C3  C11  C3   single    1.485  0.020  1.485
 8C3  C3   N3   double    1.276  0.020  1.276
 8C3  C2   O1   double    1.222  0.020  1.222
 8C3  C2   N2   single    1.366  0.020  1.366
 8C3  N3   N2   single    1.354  0.020  1.354
 8C3  N2   C7   single    1.439  0.020  1.439
 8C3  C7   C9   single    1.526  0.020  1.526
 8C3  O2   C9   double    1.220  0.020  1.220
 8C3  C9   N4   single    1.336  0.020  1.336
 8C3  N4   C13  single    1.449  0.020  1.449
 8C3  C13  C12  single    1.520  0.020  1.520
 8C3  C12  C14  single    1.523  0.020  1.523
 8C3  C14  N5   single    1.453  0.020  1.453
 8C3  N5   C15  single    1.456  0.020  1.456
 8C3  N5   C16  single    1.456  0.020  1.456
 8C3  C17  C15  single    1.520  0.020  1.520
 8C3  C18  C16  single    1.520  0.020  1.520
 8C3  C11  H1   single    0.970  0.020  1.090
 8C3  C11  H2   single    0.970  0.020  1.090
 8C3  C11  H3   single    0.970  0.020  1.090
 8C3  C12  H4   single    0.970  0.020  1.090
 8C3  C12  H5   single    0.970  0.020  1.090
 8C3  C13  H6   single    0.970  0.020  1.090
 8C3  C13  H7   single    0.970  0.020  1.090
 8C3  C14  H8   single    0.970  0.020  1.090
 8C3  C14  H9   single    0.970  0.020  1.090
 8C3  C15  H10  single    0.970  0.020  1.090
 8C3  C15  H11  single    0.970  0.020  1.090
 8C3  C16  H12  single    0.970  0.020  1.090
 8C3  C16  H13  single    0.970  0.020  1.090
 8C3  C17  H14  single    0.970  0.020  1.090
 8C3  C17  H15  single    0.970  0.020  1.090
 8C3  C17  H16  single    0.970  0.020  1.090
 8C3  C18  H17  single    0.970  0.020  1.090
 8C3  C18  H18  single    0.970  0.020  1.090
 8C3  C18  H19  single    0.970  0.020  1.090
 8C3  C4   H20  single    0.930  0.020  1.080
 8C3  C7   H21  single    0.970  0.020  1.090
 8C3  C7   H22  single    0.970  0.020  1.090
 8C3  C8   H23  single    0.930  0.020  1.080
 8C3  C10  H24  single    0.930  0.020  1.080
 8C3  N4   H25  single    0.860  0.020  1.020

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
 8C3  C4   C1   N1   110.13  3.000
 8C3  N1   C1   C2   118.90  3.000
 8C3  C4   C1   C2   130.97  3.000
 8C3  N2   C2   O1   122.15  3.000
 8C3  N2   C2   C1   113.82  3.000
 8C3  O1   C2   C1   124.02  3.000
 8C3  N3   C3   N1   120.92  3.000
 8C3  N3   C3   C11  120.09  3.000
 8C3  N1   C3   C11  118.99  3.000
 8C3  H3   C11  H2   108.03  3.000
 8C3  H3   C11  H1   108.40  3.000
 8C3  H2   C11  H1   108.45  3.000
 8C3  H3   C11  C3   111.30  3.000
 8C3  H2   C11  C3   111.22  3.000
 8C3  H1   C11  C3   109.36  3.000
 8C3  H5   C12  H4   107.06  3.000
 8C3  H5   C12  C14  108.83  3.000
 8C3  H4   C12  C14  110.52  3.000
 8C3  H5   C12  C13  109.97  3.000
 8C3  H4   C12  C13  109.35  3.000
 8C3  C14  C12  C13  111.03  3.000
 8C3  H7   C13  H6   106.84  3.000
 8C3  H7   C13  N4   109.15  3.000
 8C3  H6   C13  N4   110.15  3.000
 8C3  H7   C13  C12  109.86  3.000
 8C3  H6   C13  C12  109.96  3.000
 8C3  N4   C13  C12  110.79  3.000
 8C3  H9   C14  H8   105.86  3.000
 8C3  H9   C14  N5   111.43  3.000
 8C3  H8   C14  N5   108.97  3.000
 8C3  H9   C14  C12  109.86  3.000
 8C3  H8   C14  C12  107.88  3.000
 8C3  N5   C14  C12  112.55  3.000
 8C3  H11  C15  H10  105.83  3.000
 8C3  H11  C15  N5   111.38  3.000
 8C3  H10  C15  N5   108.48  3.000
 8C3  H11  C15  C17  110.04  3.000
 8C3  H10  C15  C17  108.03  3.000
 8C3  N5   C15  C17  112.77  3.000
 8C3  H13  C16  H12  105.76  3.000
 8C3  H13  C16  N5   111.28  3.000
 8C3  H12  C16  N5   108.31  3.000
 8C3  H13  C16  C18  109.95  3.000
 8C3  H12  C16  C18  108.21  3.000
 8C3  N5   C16  C18  113.00  3.000
 8C3  H16  C17  H15  107.94  3.000
 8C3  H16  C17  H14  107.26  3.000
 8C3  H15  C17  H14  108.09  3.000
 8C3  H16  C17  C15  112.47  3.000
 8C3  H15  C17  C15  110.55  3.000
 8C3  H14  C17  C15  110.36  3.000
 8C3  H19  C18  H18  107.20  3.000
 8C3  H19  C18  H17  108.08  3.000
 8C3  H18  C18  H17  108.01  3.000
 8C3  H19  C18  C16  110.35  3.000
 8C3  H18  C18  C16  112.36  3.000
 8C3  H17  C18  C16  110.68  3.000
 8C3  C5   N1   C3   131.45  3.000
 8C3  C3   N1   C1   120.54  3.000
 8C3  C5   N1   C1   108.00  3.000
 8C3  H20  C4   C6   128.53  3.000
 8C3  H20  C4   C1   126.23  3.000
 8C3  C6   C4   C1   105.24  3.000
 8C3  C7   N2   N3   115.42  3.000
 8C3  C7   N2   C2   118.59  3.000
 8C3  N3   N2   C2   125.44  3.000
 8C3  C8   C5   C6   114.16  3.000
 8C3  C6   C5   N1   107.20  3.000
 8C3  C8   C5   N1   138.65  3.000
 8C3  N2   N3   C3   120.21  3.000
 8C3  S1   C6   C5   110.90  3.000
 8C3  C5   C6   C4   109.43  3.000
 8C3  S1   C6   C4   139.67  3.000
 8C3  H22  C7   H21  107.44  3.000
 8C3  H22  C7   C9   110.93  3.000
 8C3  H21  C7   C9   109.34  3.000
 8C3  H22  C7   N2   110.44  3.000
 8C3  H21  C7   N2   107.61  3.000
 8C3  C9   C7   N2   110.95  3.000
 8C3  H23  C8   C10  123.21  3.000
 8C3  H23  C8   C5   126.76  3.000
 8C3  C10  C8   C5   110.03  3.000
 8C3  C10  S1   C6    90.75  3.000
 8C3  N4   C9   C7   114.45  3.000
 8C3  N4   C9   O2   123.80  3.000
 8C3  C7   C9   O2   121.74  3.000
 8C3  H24  C10  S1   119.17  3.000
 8C3  H24  C10  C8   126.66  3.000
 8C3  S1   C10  C8   114.17  3.000
 8C3  H25  N4   C9   119.09  3.000
 8C3  H25  N4   C13  118.18  3.000
 8C3  C9   N4   C13  122.68  3.000
 8C3  C16  N5   C15  112.08  3.000
 8C3  C16  N5   C14  111.62  3.000
 8C3  C15  N5   C14  111.97  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
 8C3  CONST_01  S1   C6   C4   C1    180.00   0.0  0
 8C3  CONST_02  C5   C6   C4   C1      0.00   0.0  0
 8C3  CONST_03  C8   C5   N1   C1    180.00   0.0  0
 8C3  CONST_04  C6   C5   N1   C1      0.00   0.0  0
 8C3  CONST_05  C10  C8   C5   N1    180.00   0.0  0
 8C3  CONST_06  S1   C6   C5   N1    180.00   0.0  0
 8C3  CONST_07  C4   C6   C5   N1      0.00   0.0  0
 8C3  CONST_08  C6   C4   C1   N1      0.00   0.0  0
 8C3  CONST_09  C10  S1   C6   C4    180.00   0.0  0
 8C3  CONST_10  C8   C5   C6   C4    180.00   0.0  0
 8C3  CONST_11  C5   N1   C1   C4      0.00   0.0  0
 8C3  CONST_12  S1   C10  C8   C5      0.00   0.0  0
 8C3  CONST_13  C10  S1   C6   C5      0.00   0.0  0
 8C3  CONST_14  C8   C10  S1   C6      0.00   0.0  0
 8C3  CONST_15  C10  C8   C5   C6      0.00   0.0  0
 8C3  CONST_16  S1   C6   C5   C8      0.00   0.0  0
 8C3  CONST_17  N3   C3   N1   C1      0.00   0.0  0
 8C3  CONST_18  N3   N2   C2   C1      0.00   0.0  0
 8C3  CONST_19  N2   N3   C3   N1      0.00   0.0  0
 8C3  CONST_20  N3   C3   N1   C5    180.00   0.0  0
 8C3  CONST_21  C11  C3   N1   C1    180.00   0.0  0
 8C3  CONST_22  C7   N2   C2   C1    180.00   0.0  0
 8C3  CONST_23  N3   N2   C2   O1    180.00   0.0  0
 8C3  CONST_24  C5   N1   C3   C11     0.00   0.0  0
 8C3  CONST_25  N2   N3   C3   C11   180.00   0.0  0
 8C3  CONST_26  H20  C4   C1   C2      0.00   0.0  0
 8C3  CONST_27  H23  C8   C5   N1      0.00   0.0  0
 8C3  CONST_28  H24  C10  C8   C5    180.00   0.0  0
 8C3  CONST_29  C7   N2   C2   O1      0.00   0.0  0
 8C3  CONST_30  C13  N4   C9   O2      0.00   0.0  0
 8C3  CONST_31  C7   C9   N4   C13   180.00   0.0  0
 8C3  CONST_32  H25  N4   C9   O2    180.00   0.0  0
 8C3  Var_01    C9   C7   N2   C2     71.47  30.0  3
 8C3  Var_02    H1   C11  C3   N1   -179.03  30.0  3
 8C3  Var_03    N2   C7   C9   O2     16.51  30.0  1
 8C3  Var_04    C9   N4   C13  C12  -173.79  30.0  1
 8C3  Var_05    C15  N5   C14  C12   151.59  30.0  3
 8C3  Var_06    N5   C14  C12  C13   178.33  30.0  3
 8C3  Var_07    N4   C13  C12  C14   177.48  30.0  1
 8C3  Var_08    C17  C15  N5   C14   -77.27  30.0  3
 8C3  Var_09    C18  C16  N5   C14   156.89  30.0  3
 8C3  Var_10    H14  C17  C15  N5   -178.99  30.0  3
 8C3  Var_11    H17  C18  C16  N5    -58.86  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
 8C3  plan-1  C1   0.020
 8C3  plan-1  C2   0.020
 8C3  plan-1  C3   0.020
 8C3  plan-1  O1   0.020
 8C3  plan-1  C11  0.020
 8C3  plan-1  N1   0.020
 8C3  plan-1  C4   0.020
 8C3  plan-1  N2   0.020
 8C3  plan-1  C5   0.020
 8C3  plan-1  N3   0.020
 8C3  plan-1  C6   0.020
 8C3  plan-1  C7   0.020
 8C3  plan-1  C8   0.020
 8C3  plan-1  S1   0.020
 8C3  plan-1  C10  0.020
 8C3  plan-1  H20  0.020
 8C3  plan-1  H23  0.020
 8C3  plan-1  H24  0.020
 8C3  plan-2  O2   0.020
 8C3  plan-2  C13  0.020
 8C3  plan-2  C7   0.020
 8C3  plan-2  C9   0.020
 8C3  plan-2  N4   0.020
 8C3  plan-2  H25  0.020

