# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 18:56:14 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc2CN=C(c3ccccc3F)c4cc(Cl)ccc4n12
#
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
 08J  08J  8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine  ligand  36  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_08J
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
 08J  CAU   C   CR6   0   0.007   0.0558   0.4537  -0.4578
 08J  CAK   C   CR16  0  -0.256  -0.8689   1.4947  -0.5007
 08J  CAP   C   CR6   0  -0.027  -0.4741   2.7923  -0.2380
 08J  CLAC  CL  CL    0  -0.112  -1.6396   4.0666  -0.3086
 08J  CAH   C   CR16  0  -0.217   0.8436   3.0843   0.0767
 08J  CAI   C   CR16  0  -0.275   1.7686   2.0576   0.1158
 08J  CAV   C   CR6   0   0.316   1.3868   0.7450  -0.1369
 08J  NAW   N   NR5   0  -0.589   2.3433  -0.2840  -0.0890
 08J  CAR   C   CR5   0   0.418   3.3360  -0.4960   0.8292
 08J  CAA   C   CH3   0  -0.761   3.5457   0.3279   2.0484
 08J  NAN   N   N     0  -0.454   4.0487  -1.5387   0.4966
 08J  CAJ   C   CR15  0  -0.254   3.5142  -2.0267  -0.6644
 08J  CAS   C   CR5   0   0.261   2.4548  -1.2693  -1.0505
 08J  CAL   C   CH2   0  -0.441   1.4361  -1.3722  -2.1214
 08J  NAM   N   N     0  -0.326   0.1587  -1.7465  -1.5353
 08J  CAO   C   C     0   0.243  -0.4271  -0.9165  -0.7755
 08J  CAT   C   CR6   0  -0.193  -1.7410  -1.3174  -0.2160
 08J  CAG   C   CR16  0  -0.264  -2.6925  -1.9449  -1.0185
 08J  CAE   C   CR16  0  -0.258  -3.9156  -2.3370  -0.4990
 08J  CAD   C   CR16  0  -0.239  -4.1998  -2.1181   0.8433
 08J  CAF   C   CR16  0  -0.400  -3.2641  -1.5092   1.6670
 08J  CAQ   C   CR6   0   0.546  -2.0567  -1.1210   1.1217
 08J  FAB   F   F     0  -0.300  -1.1422  -0.5552   1.9236
 08J  H1    H   HCR6  0   0.290  -1.9013   1.2853  -0.7482
 08J  H2    H   HCR6  0   0.295   1.1552   4.1005   0.2731
 08J  H3    H   HCR6  0   0.291   2.8019   2.2923   0.3278
 08J  H4    H   HCH3  0   0.260   2.6043   0.6221   2.5125
 08J  H5    H   HCH3  0   0.275   4.1159  -0.2524   2.7702
 08J  H6    H   HCH3  0   0.263   4.1104   1.2375   1.8392
 08J  H7    H   HCR5  0   0.261   3.9112  -2.9011  -1.1569
 08J  H8    H   HCH2  0   0.267   1.3563  -0.4299  -2.6788
 08J  H9    H   HCH2  0   0.278   1.7347  -2.1402  -2.8328
 08J  H10   H   HCR6  0   0.269  -2.4659  -2.1099  -2.0635
 08J  H11   H   HCR6  0   0.267  -4.6470  -2.8110  -1.1392
 08J  H12   H   HCR6  0   0.274  -5.1514  -2.4254   1.2555
 08J  H13   H   HCR6  0   0.284  -3.4627  -1.3449   2.7178

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
 08J  CAJ  NAN   aromatic  1.368  0.020  1.368
 08J  CAJ  CAS   aromatic  1.358  0.020  1.358
 08J  NAN  CAR   aromatic  1.306  0.020  1.306
 08J  CAS  CAL   single    1.482  0.020  1.482
 08J  CAS  NAW   aromatic  1.381  0.020  1.381
 08J  CAR  CAA   single    1.486  0.020  1.486
 08J  CAR  NAW   aromatic  1.369  0.020  1.369
 08J  CAL  NAM   single    1.454  0.020  1.454
 08J  NAW  CAV   aromatic  1.406  0.020  1.406
 08J  NAM  CAO   double    1.269  0.020  1.269
 08J  CAV  CAI   aromatic  1.390  0.020  1.390
 08J  CAV  CAU   aromatic  1.400  0.020  1.400
 08J  FAB  CAQ   single    1.341  0.020  1.341
 08J  CAO  CAU   single    1.487  0.020  1.487
 08J  CAO  CAT   single    1.483  0.020  1.483
 08J  CAI  CAH   aromatic  1.382  0.020  1.382
 08J  CAU  CAK   aromatic  1.393  0.020  1.393
 08J  CAQ  CAT   aromatic  1.388  0.020  1.388
 08J  CAQ  CAF   aromatic  1.381  0.020  1.381
 08J  CAT  CAG   aromatic  1.394  0.020  1.394
 08J  CAF  CAD   aromatic  1.387  0.020  1.387
 08J  CAG  CAE   aromatic  1.385  0.020  1.385
 08J  CAH  CAP   aromatic  1.386  0.020  1.386
 08J  CAK  CAP   aromatic  1.382  0.020  1.382
 08J  CAD  CAE   aromatic  1.389  0.020  1.389
 08J  CAP  CLAC  single    1.728  0.020  1.728
 08J  CAK  H1    single    0.930  0.020  1.080
 08J  CAH  H2    single    0.930  0.020  1.080
 08J  CAI  H3    single    0.930  0.020  1.080
 08J  CAA  H4    single    0.970  0.020  1.090
 08J  CAA  H5    single    0.970  0.020  1.090
 08J  CAA  H6    single    0.970  0.020  1.090
 08J  CAJ  H7    single    0.930  0.020  1.080
 08J  CAL  H8    single    0.970  0.020  1.090
 08J  CAL  H9    single    0.970  0.020  1.090
 08J  CAG  H10   single    0.930  0.020  1.080
 08J  CAE  H11   single    0.930  0.020  1.080
 08J  CAD  H12   single    0.930  0.020  1.080
 08J  CAF  H13   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
 08J  CAO   CAU  CAV   123.33  3.000
 08J  CAO   CAU  CAK   117.80  3.000
 08J  CAV   CAU  CAK   118.87  3.000
 08J  H1    CAK  CAP   119.86  3.000
 08J  H1    CAK  CAU   119.72  3.000
 08J  CAP   CAK  CAU   120.42  3.000
 08J  CAH   CAP  CLAC  119.67  3.000
 08J  CLAC  CAP  CAK   119.48  3.000
 08J  CAH   CAP  CAK   120.85  3.000
 08J  H2    CAH  CAI   120.01  3.000
 08J  H2    CAH  CAP   120.90  3.000
 08J  CAI   CAH  CAP   119.09  3.000
 08J  H3    CAI  CAV   120.22  3.000
 08J  H3    CAI  CAH   118.95  3.000
 08J  CAV   CAI  CAH   120.82  3.000
 08J  NAW   CAV  CAI   119.87  3.000
 08J  CAI   CAV  CAU   119.95  3.000
 08J  NAW   CAV  CAU   120.17  3.000
 08J  CAS   NAW  CAR   107.34  3.000
 08J  CAR   NAW  CAV   129.03  3.000
 08J  CAS   NAW  CAV   123.60  3.000
 08J  NAN   CAR  CAA   125.06  3.000
 08J  CAA   CAR  NAW   124.52  3.000
 08J  NAN   CAR  NAW   110.40  3.000
 08J  H6    CAA  H5    107.50  3.000
 08J  H6    CAA  H4    107.67  3.000
 08J  H5    CAA  H4    108.31  3.000
 08J  H6    CAA  CAR   112.21  3.000
 08J  H5    CAA  CAR   108.82  3.000
 08J  H4    CAA  CAR   112.16  3.000
 08J  CAJ   NAN  CAR   106.72  3.000
 08J  H7    CAJ  CAS   127.51  3.000
 08J  H7    CAJ  NAN   122.18  3.000
 08J  CAS   CAJ  NAN   110.30  3.000
 08J  CAL   CAS  CAJ   134.67  3.000
 08J  CAL   CAS  NAW   119.82  3.000
 08J  CAJ   CAS  NAW   105.24  3.000
 08J  H9    CAL  H8    107.08  3.000
 08J  H9    CAL  NAM   108.82  3.000
 08J  H8    CAL  NAM   111.20  3.000
 08J  H9    CAL  CAS   109.44  3.000
 08J  H8    CAL  CAS   110.94  3.000
 08J  NAM   CAL  CAS   109.30  3.000
 08J  CAO   NAM  CAL   118.59  3.000
 08J  CAT   CAO  NAM   117.27  3.000
 08J  CAT   CAO  CAU   117.13  3.000
 08J  NAM   CAO  CAU   125.51  3.000
 08J  CAQ   CAT  CAG   117.59  3.000
 08J  CAG   CAT  CAO   120.61  3.000
 08J  CAQ   CAT  CAO   121.78  3.000
 08J  H10   CAG  CAE   120.26  3.000
 08J  H10   CAG  CAT   118.79  3.000
 08J  CAE   CAG  CAT   120.94  3.000
 08J  H11   CAE  CAD   120.18  3.000
 08J  H11   CAE  CAG   119.94  3.000
 08J  CAD   CAE  CAG   119.89  3.000
 08J  H12   CAD  CAF   119.46  3.000
 08J  H12   CAD  CAE   120.22  3.000
 08J  CAF   CAD  CAE   120.31  3.000
 08J  H13   CAF  CAQ   120.10  3.000
 08J  H13   CAF  CAD   121.29  3.000
 08J  CAQ   CAF  CAD   118.61  3.000
 08J  FAB   CAQ  CAF   118.60  3.000
 08J  CAF   CAQ  CAT   122.66  3.000
 08J  FAB   CAQ  CAT   118.72  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
 08J  CONST_03  CAH   CAI  CAV  CAU     0.00   0.0  0
 08J  CONST_04  CAH   CAP  CAK  CAU     0.00   0.0  0
 08J  CONST_05  NAW   CAV  CAU  CAK   180.00   0.0  0
 08J  CONST_06  CAI   CAV  CAU  CAK     0.00   0.0  0
 08J  CONST_07  CAI   CAH  CAP  CAK     0.00   0.0  0
 08J  CONST_08  CAV   CAI  CAH  CAP     0.00   0.0  0
 08J  CONST_09  CAV   CAU  CAK  CAP     0.00   0.0  0
 08J  CONST_10  NAW   CAV  CAI  CAH   180.00   0.0  0
 08J  CONST_13  CAJ   CAS  NAW  CAV   180.00   0.0  0
 08J  CONST_14  NAN   CAR  NAW  CAV   180.00   0.0  0
 08J  CONST_15  NAN   CAJ  CAS  NAW     0.00   0.0  0
 08J  CONST_16  CAJ   NAN  CAR  NAW     0.00   0.0  0
 08J  CONST_17  CAS   CAJ  NAN  CAR     0.00   0.0  0
 08J  CONST_18  CAJ   CAS  NAW  CAR     0.00   0.0  0
 08J  CONST_19  CAS   NAW  CAR  NAN     0.00   0.0  0
 08J  CONST_20  CAD   CAF  CAQ  CAT     0.00   0.0  0
 08J  CONST_21  CAD   CAE  CAG  CAT     0.00   0.0  0
 08J  CONST_22  CAF   CAQ  CAT  CAG     0.00   0.0  0
 08J  CONST_23  CAF   CAD  CAE  CAG     0.00   0.0  0
 08J  CONST_24  CAQ   CAT  CAG  CAE     0.00   0.0  0
 08J  CONST_25  CAQ   CAF  CAD  CAE     0.00   0.0  0
 08J  CONST_26  CAF   CAQ  CAT  CAO   180.00   0.0  0
 08J  CONST_27  CAE   CAG  CAT  CAO   180.00   0.0  0
 08J  CONST_28  CLAC  CAP  CAK  CAU   180.00   0.0  0
 08J  CONST_29  CAI   CAH  CAP  CLAC  180.00   0.0  0
 08J  CONST_30  CAA   CAR  NAW  CAV     0.00   0.0  0
 08J  CONST_31  CAJ   NAN  CAR  CAA   180.00   0.0  0
 08J  CONST_32  CAS   NAW  CAR  CAA   180.00   0.0  0
 08J  CONST_33  FAB   CAQ  CAT  CAO     0.00   0.0  0
 08J  CONST_34  FAB   CAQ  CAT  CAG   180.00   0.0  0
 08J  CONST_35  FAB   CAQ  CAF  CAD   180.00   0.0  0
 08J  CONST_36  H3    CAI  CAV  CAU   180.00   0.0  0
 08J  CONST_37  H2    CAH  CAP  CAK   180.00   0.0  0
 08J  CONST_38  H1    CAK  CAP  CAH   180.00   0.0  0
 08J  CONST_39  H7    CAJ  CAS  NAW   180.00   0.0  0
 08J  CONST_40  H10   CAG  CAT  CAO     0.00   0.0  0
 08J  CONST_41  H13   CAF  CAQ  CAT   180.00   0.0  0
 08J  CONST_42  H11   CAE  CAG  CAT   180.00   0.0  0
 08J  CONST_43  H12   CAD  CAE  CAG   180.00   0.0  0
 08J  Var_01    CAQ   CAT  CAO  CAU   -48.38  30.0  2
 08J  Var_02    NAM   CAO  CAU  CAK   134.65  30.0  1
 08J  Var_03    NAM   CAL  CAS  NAW   -66.07  30.0  1
 08J  Var_04    H4    CAA  CAR  NAW    38.62  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
 08J  plan-1  CAO   0.020
 08J  plan-1  CAT   0.020
 08J  plan-1  CAG   0.020
 08J  plan-1  CAE   0.020
 08J  plan-1  CAD   0.020
 08J  plan-1  CAF   0.020
 08J  plan-1  CAQ   0.020
 08J  plan-1  FAB   0.020
 08J  plan-1  H10   0.020
 08J  plan-1  H11   0.020
 08J  plan-1  H12   0.020
 08J  plan-1  H13   0.020
 08J  plan-2  CAV   0.020
 08J  plan-2  NAW   0.020
 08J  plan-2  CAR   0.020
 08J  plan-2  CAA   0.020
 08J  plan-2  NAN   0.020
 08J  plan-2  CAJ   0.020
 08J  plan-2  CAS   0.020
 08J  plan-2  CAL   0.020
 08J  plan-2  H7    0.020
 08J  plan-3  CAU   0.020
 08J  plan-3  CAK   0.020
 08J  plan-3  CAP   0.020
 08J  plan-3  CLAC  0.020
 08J  plan-3  CAH   0.020
 08J  plan-3  CAI   0.020
 08J  plan-3  CAV   0.020
 08J  plan-3  NAW   0.020
 08J  plan-3  CAO   0.020
 08J  plan-3  H1    0.020
 08J  plan-3  H2    0.020
 08J  plan-3  H3    0.020

