# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:01:15 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: ethyl 4-(2-cyanoethylsulfanyl)-6-methoxy-quinoline-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1cnc2ccc(OC)cc2c1SCCC#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
 U53  U53  'ethyl 4-(2-cyanoethylsulfanyl)-6-methoxy-quinoline-3-carboxylate'  ligand  38  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U53
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
 U53  O2   O  O     0  -0.421   3.0640  -0.5538   0.4438
 U53  C12  C  C     0   0.539   2.6587   0.5632   0.2519
 U53  O1   O  O2    0  -0.450   3.4245   1.5982  -0.0395
 U53  C13  C  CH2   0  -0.181   4.8494   1.3958  -0.0870
 U53  C14  C  CH3   0  -0.689   5.4929   2.7299  -0.3715
 U53  C10  C  CR6   0  -0.102   1.2288   0.9730   0.3594
 U53  C11  C  CR16  0  -0.086   0.9271   2.1718   1.0564
 U53  N1   N  N     0  -0.418  -0.2818   2.5947   1.2784
 U53  C4   C  CR66  0   0.188  -1.3178   1.8680   0.8044
 U53  C3   C  CR16  0  -0.271  -2.6268   2.3325   1.0427
 U53  C2   C  CR16  0  -0.374  -3.7160   1.6466   0.5827
 U53  C6   C  CR6   0  -0.086   0.1939   0.2177  -0.1390
 U53  S    S  S2    0   0.033   0.4904  -1.2308  -1.1177
 U53  C7   C  CH2   0  -0.542   0.3879  -2.5010   0.1829
 U53  C8   C  CH2   0  -0.536   0.6293  -3.8583  -0.4752
 U53  C9   C  CSP   0   0.130   0.5647  -4.9253   0.5102
 U53  N    N  NS    0  -0.267   0.5055  -5.7630   1.2962
 U53  C5   C  CR66  0   0.160  -1.1424   0.6651   0.0698
 U53  C15  C  CR16  0  -0.438  -2.2724  -0.0237  -0.4030
 U53  C1   C  CR6   0   0.423  -3.5414   0.4495  -0.1516
 U53  O    O  O2    0  -0.467  -4.5619  -0.2730  -0.6368
 U53  C    C  CH3   0  -0.442  -5.8907   0.1561  -0.3991
 U53  H1   H  HCH2  0   0.241   5.1906   0.9901   0.8672
 U53  H2   H  HCH2  0   0.241   5.0848   0.6698  -0.8672
 U53  H3   H  HCH3  0   0.238   5.1601   3.1432  -1.3236
 U53  H4   H  HCH3  0   0.238   5.2833   3.4528   0.4166
 U53  H5   H  HCH3  0   0.242   6.5731   2.5978  -0.4246
 U53  H6   H  HCR6  0   0.276   1.7352   2.7776   1.4506
 U53  H7   H  HCR6  0   0.276  -2.7547   3.2507   1.6008
 U53  H8   H  HCR6  0   0.294  -4.7034   2.0367   0.7863
 U53  H9   H  HCH2  0   0.301   1.1482  -2.2983   0.9335
 U53  H10  H  HCH2  0   0.296  -0.5969  -2.4723   0.6478
 U53  H11  H  HCH2  0   0.322  -0.1176  -4.0608  -1.2451
 U53  H12  H  HCH2  0   0.322   1.6106  -3.8922  -0.9520
 U53  H13  H  HCR6  0   0.275  -2.1468  -0.9325  -0.9774
 U53  H14  H  HCH3  0   0.234  -6.0942   1.1283  -0.8543
 U53  H15  H  HCH3  0   0.265  -6.5372  -0.5867  -0.8588
 U53  H16  H  HCH3  0   0.234  -6.1191   0.2071   0.6680

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
 U53  O2   C12  double    1.204  0.020  1.204
 U53  S    C7   single    1.821  0.020  1.821
 U53  S    C6   single    1.773  0.020  1.773
 U53  C13  C14  single    1.508  0.020  1.508
 U53  C13  O1   single    1.440  0.020  1.440
 U53  C7   C8   single    1.528  0.020  1.528
 U53  C12  O1   single    1.320  0.020  1.320
 U53  C12  C10  single    1.491  0.020  1.491
 U53  C    O    single    1.416  0.020  1.416
 U53  C6   C10  aromatic  1.375  0.020  1.375
 U53  C6   C5   aromatic  1.425  0.020  1.425
 U53  N    C9   triple    1.150  0.020  1.150
 U53  C10  C11  aromatic  1.419  0.020  1.419
 U53  C15  C5   aromatic  1.405  0.020  1.405
 U53  C15  C1   aromatic  1.377  0.020  1.377
 U53  C9   C8   single    1.454  0.020  1.454
 U53  C5   C4   aromatic  1.420  0.020  1.420
 U53  O    C1   single    1.341  0.020  1.341
 U53  C1   C2   aromatic  1.415  0.020  1.415
 U53  C11  N1   aromatic  1.300  0.020  1.300
 U53  C4   N1   aromatic  1.351  0.020  1.351
 U53  C4   C3   aromatic  1.409  0.020  1.409
 U53  C2   C3   aromatic  1.367  0.020  1.367
 U53  C13  H1   single    0.970  0.020  1.090
 U53  C13  H2   single    0.970  0.020  1.090
 U53  C14  H3   single    0.970  0.020  1.090
 U53  C14  H4   single    0.970  0.020  1.090
 U53  C14  H5   single    0.970  0.020  1.090
 U53  C11  H6   single    0.930  0.020  1.080
 U53  C3   H7   single    0.930  0.020  1.080
 U53  C2   H8   single    0.930  0.020  1.080
 U53  C7   H9   single    0.970  0.020  1.090
 U53  C7   H10  single    0.970  0.020  1.090
 U53  C8   H11  single    0.970  0.020  1.090
 U53  C8   H12  single    0.970  0.020  1.090
 U53  C15  H13  single    0.930  0.020  1.080
 U53  C    H14  single    0.970  0.020  1.090
 U53  C    H15  single    0.970  0.020  1.090
 U53  C    H16  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
 U53  C10  C12  O1   110.90  3.000
 U53  C10  C12  O2   124.50  3.000
 U53  O1   C12  O2   124.57  3.000
 U53  C13  O1   C12  118.11  3.000
 U53  H2   C13  H1   108.07  3.000
 U53  H2   C13  C14  111.19  3.000
 U53  H1   C13  C14  111.12  3.000
 U53  H2   C13  O1   109.30  3.000
 U53  H1   C13  O1   109.43  3.000
 U53  C14  C13  O1   107.70  3.000
 U53  H5   C14  H4   107.84  3.000
 U53  H5   C14  H3   107.83  3.000
 U53  H4   C14  H3   108.75  3.000
 U53  H5   C14  C13  108.96  3.000
 U53  H4   C14  C13  111.61  3.000
 U53  H3   C14  C13  111.71  3.000
 U53  C6   C10  C11  118.82  3.000
 U53  C11  C10  C12  118.12  3.000
 U53  C6   C10  C12  123.01  3.000
 U53  H6   C11  N1   116.70  3.000
 U53  H6   C11  C10  119.48  3.000
 U53  N1   C11  C10  123.81  3.000
 U53  C4   N1   C11  118.56  3.000
 U53  C5   C4   C3   118.77  3.000
 U53  C3   C4   N1   118.40  3.000
 U53  C5   C4   N1   122.83  3.000
 U53  H7   C3   C2   120.34  3.000
 U53  H7   C3   C4   118.47  3.000
 U53  C2   C3   C4   121.19  3.000
 U53  H8   C2   C1   121.04  3.000
 U53  H8   C2   C3   118.91  3.000
 U53  C1   C2   C3   120.05  3.000
 U53  C5   C6   S    119.62  3.000
 U53  C5   C6   C10  118.72  3.000
 U53  S    C6   C10  121.54  3.000
 U53  C7   S    C6    99.57  3.000
 U53  H10  C7   H9   109.42  3.000
 U53  H10  C7   C8   110.50  3.000
 U53  H9   C7   C8   110.64  3.000
 U53  H10  C7   S    109.72  3.000
 U53  H9   C7   S    108.88  3.000
 U53  C8   C7   S    107.65  3.000
 U53  H12  C8   H11  107.53  3.000
 U53  H12  C8   C9   108.25  3.000
 U53  H11  C8   C9   108.16  3.000
 U53  H12  C8   C7   110.97  3.000
 U53  H11  C8   C7   111.13  3.000
 U53  C9   C8   C7   110.67  3.000
 U53  N    C9   C8   180.00  3.000
 U53  C15  C5   C6   123.44  3.000
 U53  C15  C5   C4   119.33  3.000
 U53  C6   C5   C4   117.23  3.000
 U53  H13  C15  C1   119.49  3.000
 U53  H13  C15  C5   119.78  3.000
 U53  C1   C15  C5   120.73  3.000
 U53  O    C1   C15  116.73  3.000
 U53  O    C1   C2   123.34  3.000
 U53  C15  C1   C2   119.93  3.000
 U53  C    O    C1   119.33  3.000
 U53  H16  C    H15  108.71  3.000
 U53  H16  C    H14  109.05  3.000
 U53  H15  C    H14  108.73  3.000
 U53  H16  C    O    111.97  3.000
 U53  H15  C    O    106.26  3.000
 U53  H14  C    O    111.99  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
 U53  CONST_01  C15  C5   C6   C10   180.00   0.0  0
 U53  CONST_02  C4   C5   C6   C10     0.00   0.0  0
 U53  CONST_03  C4   N1   C11  C10     0.00   0.0  0
 U53  CONST_04  C5   C6   C10  C11     0.00   0.0  0
 U53  CONST_05  C5   C4   N1   C11     0.00   0.0  0
 U53  CONST_06  C3   C4   N1   C11   180.00   0.0  0
 U53  CONST_07  C6   C10  C11  N1      0.00   0.0  0
 U53  CONST_08  C6   C5   C4   N1      0.00   0.0  0
 U53  CONST_09  C15  C5   C4   N1    180.00   0.0  0
 U53  CONST_10  C2   C3   C4   N1    180.00   0.0  0
 U53  CONST_11  C1   C15  C5   C4      0.00   0.0  0
 U53  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 U53  CONST_13  C6   C5   C4   C3    180.00   0.0  0
 U53  CONST_14  C15  C5   C4   C3      0.00   0.0  0
 U53  CONST_15  C15  C1   C2   C3      0.00   0.0  0
 U53  CONST_16  C5   C15  C1   C2      0.00   0.0  0
 U53  CONST_17  C5   C4   C3   C2      0.00   0.0  0
 U53  CONST_18  C1   C15  C5   C6    180.00   0.0  0
 U53  CONST_19  C5   C6   C10  C12   180.00   0.0  0
 U53  CONST_20  N1   C11  C10  C12   180.00   0.0  0
 U53  CONST_21  S    C6   C10  C11   180.00   0.0  0
 U53  CONST_22  S    C6   C5   C4    180.00   0.0  0
 U53  CONST_23  O    C1   C2   C3    180.00   0.0  0
 U53  CONST_24  C15  C5   C6   S       0.00   0.0  0
 U53  CONST_25  O    C1   C15  C5    180.00   0.0  0
 U53  CONST_26  H7   C3   C4   N1      0.00   0.0  0
 U53  CONST_27  H13  C15  C5   C4    180.00   0.0  0
 U53  CONST_28  H6   C11  N1   C4    180.00   0.0  0
 U53  CONST_29  H8   C2   C3   C4    180.00   0.0  0
 U53  Var_01    C6   C10  C12  O2    -42.81  30.0  2
 U53  Var_02    C5   C6   S    C7    -88.62  30.0  2
 U53  Var_03    C10  C12  O1   C13   175.68  30.0  1
 U53  Var_04    C8   C7   S    C6   -179.73  30.0  3
 U53  Var_05    H14  C    O    C1     62.73  30.0  3
 U53  Var_06    C14  C13  O1   C12  -177.35  30.0  1
 U53  Var_07    C9   C8   C7   S     179.86  30.0  3
 U53  Var_08    H3   C14  C13  O1    -60.25  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
 U53  plan-1  C12  0.020
 U53  plan-1  C10  0.020
 U53  plan-1  C11  0.020
 U53  plan-1  N1   0.020
 U53  plan-1  C4   0.020
 U53  plan-1  C3   0.020
 U53  plan-1  C2   0.020
 U53  plan-1  C6   0.020
 U53  plan-1  S    0.020
 U53  plan-1  C5   0.020
 U53  plan-1  C15  0.020
 U53  plan-1  C1   0.020
 U53  plan-1  O    0.020
 U53  plan-1  H6   0.020
 U53  plan-1  H7   0.020
 U53  plan-1  H8   0.020
 U53  plan-1  H13  0.020
 U53  plan-2  O2   0.020
 U53  plan-2  C12  0.020
 U53  plan-2  O1   0.020
 U53  plan-2  C10  0.020

