# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:56:41 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 9-methyl-4-phenyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nnc2CN=C(c3ccccc3)c4ccsc4n12
#
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
 L5S  L5S  9-methyl-4-phenyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepine  ligand  32  20  .  2022-07-25  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_L5S
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
 L5S  CAS   C  CR5   0   0.046  -0.1397  -0.6876   0.6494
 L5S  CAJ   C  CR15  0  -0.199  -0.6195  -1.9671   1.0614
 L5S  CAP   C  CR15  0  -0.453   0.3430  -2.9215   1.0560
 L5S  CAU   C  CR5   0   0.035   1.1954  -0.7389   0.3387
 L5S  NAV   N  NR5   0  -0.566   1.9611   0.3494  -0.0544
 L5S  CAR   C  CR5   0   0.409   2.9762   0.4627  -0.9662
 L5S  CAA   C  CH3   0  -0.763   3.5273  -0.6508  -1.7710
 L5S  NAM   N  N     0  -0.331   3.3642   1.7027  -1.0052
 L5S  NAN   N  N     0  -0.322   2.6126   2.4241  -0.1299
 L5S  CAT   C  CR5   0   0.395   1.7804   1.6124   0.4388
 L5S  CAK   C  CH2   0  -0.436   0.7222   1.8918   1.4412
 L5S  NAL   N  N     0  -0.354  -0.5953   1.7009   0.8635
 L5S  CAO   C  C     0   0.224  -0.9697   0.5270   0.5406
 L5S  CAQ   C  CR6   0   0.044  -2.3437   0.3623   0.0090
 L5S  CAF   C  CR16  0  -0.282  -3.3649   1.2036   0.4512
 L5S  CAD   C  CR16  0  -0.243  -4.6461   1.0801  -0.0615
 L5S  CAC   C  CR16  0  -0.255  -4.9212   0.1237  -1.0321
 L5S  CAE   C  CR16  0  -0.240  -3.9088  -0.7117  -1.4831
 L5S  CAG   C  CR16  0  -0.288  -2.6281  -0.5980  -0.9607
 L5S  S     S  S2    0   0.281   1.8632  -2.3053   0.5551
 L5S  HAJ   H  HCR5  0   0.285  -1.6417  -2.1576   1.3532
 L5S  HAP   H  HCR5  0   0.313   0.2480  -3.9650   1.3119
 L5S  HAA1  H  HCH3  0   0.272   2.7415  -1.2087  -2.2798
 L5S  HAA2  H  HCH3  0   0.285   4.1985  -0.2428  -2.5228
 L5S  HAA3  H  HCH3  0   0.271   4.0964  -1.3507  -1.1583
 L5S  HAK1  H  HCH2  0   0.278   0.8711   1.2481   2.3177
 L5S  HAK2  H  HCH2  0   0.288   0.8211   2.9246   1.7699
 L5S  HAF   H  HCR6  0   0.257  -3.1539   1.9483   1.2073
 L5S  HAG   H  HCR6  0   0.264  -1.8459  -1.2511  -1.3268
 L5S  HAD   H  HCR6  0   0.261  -5.4325   1.7309   0.2976
 L5S  HAC   H  HCR6  0   0.262  -5.9218   0.0302  -1.4338
 L5S  HAE   H  HCR6  0   0.262  -4.1125  -1.4542  -2.2434

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
 L5S  CAS  CAJ   aromatic  1.427  0.020  1.427
 L5S  CAS  CAU   aromatic  1.372  0.020  1.372
 L5S  CAS  CAO   single    1.475  0.020  1.475
 L5S  CAJ  CAP   aromatic  1.355  0.020  1.355
 L5S  CAP  S     aromatic  1.715  0.020  1.715
 L5S  CAU  NAV   aromatic  1.387  0.020  1.387
 L5S  CAU  S     aromatic  1.717  0.020  1.717
 L5S  NAV  CAR   aromatic  1.369  0.020  1.369
 L5S  NAV  CAT   aromatic  1.368  0.020  1.368
 L5S  CAR  CAA   single    1.480  0.020  1.480
 L5S  CAR  NAM   aromatic  1.300  0.020  1.300
 L5S  NAM  NAN   aromatic  1.361  0.020  1.361
 L5S  NAN  CAT   aromatic  1.294  0.020  1.294
 L5S  CAT  CAK   single    1.484  0.020  1.484
 L5S  CAK  NAL   single    1.451  0.020  1.451
 L5S  NAL  CAO   double    1.274  0.020  1.274
 L5S  CAO  CAQ   single    1.482  0.020  1.482
 L5S  CAQ  CAF   aromatic  1.395  0.020  1.395
 L5S  CAQ  CAG   aromatic  1.394  0.020  1.394
 L5S  CAF  CAD   aromatic  1.385  0.020  1.385
 L5S  CAD  CAC   aromatic  1.390  0.020  1.390
 L5S  CAC  CAE   aromatic  1.388  0.020  1.388
 L5S  CAE  CAG   aromatic  1.388  0.020  1.388
 L5S  CAJ  HAJ   single    0.930  0.020  1.080
 L5S  CAP  HAP   single    0.930  0.020  1.080
 L5S  CAA  HAA1  single    0.970  0.020  1.090
 L5S  CAA  HAA2  single    0.970  0.020  1.090
 L5S  CAA  HAA3  single    0.970  0.020  1.090
 L5S  CAK  HAK1  single    0.970  0.020  1.090
 L5S  CAK  HAK2  single    0.970  0.020  1.090
 L5S  CAF  HAF   single    0.930  0.020  1.080
 L5S  CAG  HAG   single    0.930  0.020  1.080
 L5S  CAD  HAD   single    0.930  0.020  1.080
 L5S  CAC  HAC   single    0.930  0.020  1.080
 L5S  CAE  HAE   single    0.930  0.020  1.080

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
 L5S  CAO   CAS  CAU   124.17  3.000
 L5S  CAO   CAS  CAJ   124.77  3.000
 L5S  CAU   CAS  CAJ   111.04  3.000
 L5S  HAJ   CAJ  CAP   123.29  3.000
 L5S  HAJ   CAJ  CAS   123.66  3.000
 L5S  CAP   CAJ  CAS   113.04  3.000
 L5S  HAP   CAP  S     119.66  3.000
 L5S  HAP   CAP  CAJ   128.15  3.000
 L5S  S     CAP  CAJ   112.18  3.000
 L5S  S     CAU  NAV   122.47  3.000
 L5S  S     CAU  CAS   112.59  3.000
 L5S  NAV   CAU  CAS   124.89  3.000
 L5S  CAT   NAV  CAR   105.17  3.000
 L5S  CAT   NAV  CAU   123.31  3.000
 L5S  CAR   NAV  CAU   131.51  3.000
 L5S  NAM   CAR  CAA   126.17  3.000
 L5S  NAM   CAR  NAV   108.67  3.000
 L5S  CAA   CAR  NAV   125.16  3.000
 L5S  HAA3  CAA  HAA2  107.89  3.000
 L5S  HAA3  CAA  HAA1  108.06  3.000
 L5S  HAA2  CAA  HAA1  108.32  3.000
 L5S  HAA3  CAA  CAR   111.82  3.000
 L5S  HAA2  CAA  CAR   108.87  3.000
 L5S  HAA1  CAA  CAR   111.75  3.000
 L5S  NAN   NAM  CAR   108.76  3.000
 L5S  CAT   NAN  NAM   107.78  3.000
 L5S  CAK   CAT  NAN   129.58  3.000
 L5S  CAK   CAT  NAV   120.77  3.000
 L5S  NAN   CAT  NAV   109.62  3.000
 L5S  HAK2  CAK  HAK1  107.64  3.000
 L5S  HAK2  CAK  NAL   109.12  3.000
 L5S  HAK1  CAK  NAL   111.34  3.000
 L5S  HAK2  CAK  CAT   108.54  3.000
 L5S  HAK1  CAK  CAT   109.40  3.000
 L5S  NAL   CAK  CAT   110.71  3.000
 L5S  CAO   NAL  CAK   119.28  3.000
 L5S  CAQ   CAO  NAL   117.76  3.000
 L5S  CAQ   CAO  CAS   117.16  3.000
 L5S  NAL   CAO  CAS   125.08  3.000
 L5S  CAG   CAQ  CAF   119.12  3.000
 L5S  CAG   CAQ  CAO   121.00  3.000
 L5S  CAF   CAQ  CAO   119.85  3.000
 L5S  HAF   CAF  CAD   120.02  3.000
 L5S  HAF   CAF  CAQ   119.59  3.000
 L5S  CAD   CAF  CAQ   120.39  3.000
 L5S  HAD   CAD  CAC   120.11  3.000
 L5S  HAD   CAD  CAF   119.71  3.000
 L5S  CAC   CAD  CAF   120.18  3.000
 L5S  HAC   CAC  CAE   120.12  3.000
 L5S  HAC   CAC  CAD   120.11  3.000
 L5S  CAE   CAC  CAD   119.78  3.000
 L5S  HAE   CAE  CAG   119.63  3.000
 L5S  HAE   CAE  CAC   120.27  3.000
 L5S  CAG   CAE  CAC   120.10  3.000
 L5S  HAG   CAG  CAE   119.34  3.000
 L5S  HAG   CAG  CAQ   120.22  3.000
 L5S  CAE   CAG  CAQ   120.43  3.000
 L5S  CAU   S    CAP    91.14  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
 L5S  CONST_01  S     CAP  CAJ  CAS    0.00   0.0  0
 L5S  CONST_04  CAP   S    CAU  CAS    0.00   0.0  0
 L5S  CONST_05  NAV   CAU  CAS  CAJ  180.00   0.0  0
 L5S  CONST_06  S     CAU  CAS  CAJ    0.00   0.0  0
 L5S  CONST_07  CAU   S    CAP  CAJ    0.00   0.0  0
 L5S  CONST_08  CAU   CAS  CAJ  CAP    0.00   0.0  0
 L5S  CONST_09  NAV   CAU  S    CAP  180.00   0.0  0
 L5S  CONST_10  NAM   CAR  NAV  CAU  180.00   0.0  0
 L5S  CONST_11  NAN   CAT  NAV  CAU  180.00   0.0  0
 L5S  CONST_12  NAN   NAM  CAR  NAV    0.00   0.0  0
 L5S  CONST_13  NAM   NAN  CAT  NAV    0.00   0.0  0
 L5S  CONST_15  NAN   CAT  NAV  CAR    0.00   0.0  0
 L5S  CONST_16  CAT   NAN  NAM  CAR    0.00   0.0  0
 L5S  CONST_17  CAT   NAV  CAR  NAM    0.00   0.0  0
 L5S  CONST_19  CAC   CAD  CAF  CAQ    0.00   0.0  0
 L5S  CONST_20  CAC   CAE  CAG  CAQ    0.00   0.0  0
 L5S  CONST_21  CAE   CAG  CAQ  CAF    0.00   0.0  0
 L5S  CONST_22  CAE   CAC  CAD  CAF    0.00   0.0  0
 L5S  CONST_23  CAG   CAQ  CAF  CAD    0.00   0.0  0
 L5S  CONST_24  CAG   CAE  CAC  CAD    0.00   0.0  0
 L5S  CONST_25  CAD   CAF  CAQ  CAO  180.00   0.0  0
 L5S  CONST_26  CAE   CAG  CAQ  CAO  180.00   0.0  0
 L5S  CONST_27  CAA   CAR  NAV  CAU    0.00   0.0  0
 L5S  CONST_28  CAT   NAV  CAR  CAA  180.00   0.0  0
 L5S  CONST_29  NAN   NAM  CAR  CAA  180.00   0.0  0
 L5S  CONST_30  HAP   CAP  CAJ  CAS  180.00   0.0  0
 L5S  CONST_31  HAJ   CAJ  CAS  CAU  180.00   0.0  0
 L5S  CONST_32  HAF   CAF  CAQ  CAO    0.00   0.0  0
 L5S  CONST_33  HAG   CAG  CAQ  CAO    0.00   0.0  0
 L5S  CONST_34  HAD   CAD  CAF  CAQ  180.00   0.0  0
 L5S  CONST_35  HAE   CAE  CAG  CAQ  180.00   0.0  0
 L5S  CONST_36  HAC   CAC  CAD  CAF  180.00   0.0  0
 L5S  Var_01    CAF   CAQ  CAO  CAS  148.48  30.0  2
 L5S  Var_02    NAL   CAO  CAS  CAJ  141.22  30.0  1
 L5S  Var_03    NAL   CAK  CAT  NAV  -66.07  30.0  1
 L5S  Var_04    HAA1  CAA  CAR  NAV   50.87  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
 L5S  plan-1  CAO  0.020
 L5S  plan-1  CAQ  0.020
 L5S  plan-1  CAF  0.020
 L5S  plan-1  CAD  0.020
 L5S  plan-1  CAC  0.020
 L5S  plan-1  CAE  0.020
 L5S  plan-1  CAG  0.020
 L5S  plan-1  HAF  0.020
 L5S  plan-1  HAG  0.020
 L5S  plan-1  HAD  0.020
 L5S  plan-1  HAC  0.020
 L5S  plan-1  HAE  0.020
 L5S  plan-2  CAS  0.020
 L5S  plan-2  CAJ  0.020
 L5S  plan-2  CAP  0.020
 L5S  plan-2  CAU  0.020
 L5S  plan-2  NAV  0.020
 L5S  plan-2  CAO  0.020
 L5S  plan-2  S    0.020
 L5S  plan-2  HAJ  0.020
 L5S  plan-2  HAP  0.020
 L5S  plan-3  CAU  0.020
 L5S  plan-3  NAV  0.020
 L5S  plan-3  CAR  0.020
 L5S  plan-3  CAA  0.020
 L5S  plan-3  NAM  0.020
 L5S  plan-3  NAN  0.020
 L5S  plan-3  CAT  0.020
 L5S  plan-3  CAK  0.020

