# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 16:42:33 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-[(2,5-dichlorobenzyl)sulfanyl]-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(O)n2nc(SCc3cc(Cl)ccc3Cl)nc2n1
#
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
 AVQ  AVQ  2-[(2,5-dichlorobenzyl)sulfanyl]-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-ol  ligand  31  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AVQ
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
 AVQ  CLD   CL  CL    0  -0.111   2.2368  -2.8128   0.3607
 AVQ  CAQ   C   CR6   0  -0.093   3.1569  -1.3736   0.0889
 AVQ  CAF   C   CR16  0  -0.195   4.5202  -1.4016   0.3378
 AVQ  CAE   C   CR16  0  -0.230   5.2840  -0.2640   0.1367
 AVQ  CAO   C   CR6   0  -0.016   4.6647   0.8907  -0.3135
 AVQ  CLC   CL  CL    0  -0.116   5.6031   2.3216  -0.5658
 AVQ  CAH   C   CR16  0  -0.257   3.3041   0.9186  -0.5657
 AVQ  CAR   C   CR6   0   0.177   2.5276  -0.2203  -0.3752
 AVQ  CAI   C   CH2   0  -0.622   1.0562  -0.1601  -0.6451
 AVQ  SAM   S   S2    0   0.073   0.2266   0.1222   0.9541
 AVQ  CAS   C   CR5   0   0.220  -1.4417   0.1309   0.4549
 AVQ  NAK   N   N     0  -0.503  -1.8465  -0.0005  -0.8169
 AVQ  NAL   N   N     0  -0.300  -2.3852   0.2836   1.3644
 AVQ  NAU   N   N     0  -0.404  -3.4918   0.2484   0.6017
 AVQ  CAT   C   CR56  0   0.616  -3.1647   0.0755  -0.7221
 AVQ  NAJ   N   N     0  -0.479  -4.0772   0.0113  -1.6839
 AVQ  CAN   C   CR6   0   0.268  -5.3384   0.1236  -1.3117
 AVQ  CAA   C   CH3   0  -0.736  -6.3890   0.0584  -2.3717
 AVQ  CAG   C   CR16  0  -0.490  -5.7325   0.3010   0.0287
 AVQ  CAP   C   CR6   0   0.658  -4.7735   0.3650   1.0080
 AVQ  OAB   O   OH1   0  -0.561  -4.9386   0.5282   2.2974
 AVQ  HAF   H   HCR6  0   0.294   4.9914  -2.3085   0.6905
 AVQ  HAE   H   HCR6  0   0.294   6.3474  -0.2861   0.3300
 AVQ  HAH   H   HCR6  0   0.290   2.8345   1.8271  -0.9196
 AVQ  HAI1  H   HCH2  0   0.312   0.8251   0.6627  -1.3182
 AVQ  HAI2  H   HCH2  0   0.306   0.6840  -1.0834  -1.0856
 AVQ  HAB   H   HOH1  0   0.510  -5.8756   0.6194   2.5183
 AVQ  HAA1  H   HCH3  0   0.261  -5.9404  -0.0347  -3.3574
 AVQ  HAA2  H   HCH3  0   0.265  -7.0490  -0.7942  -2.2052
 AVQ  HAA3  H   HCH3  0   0.264  -7.0111   0.9538  -2.3511
 AVQ  HAG   H   HCR6  0   0.306  -6.7780   0.3906   0.2884

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
 AVQ  CLD  CAQ   single    1.730  0.020  1.730
 AVQ  CAQ  CAF   aromatic  1.386  0.020  1.386
 AVQ  CAQ  CAR   aromatic  1.393  0.020  1.393
 AVQ  CAF  CAE   aromatic  1.385  0.020  1.385
 AVQ  CAE  CAO   aromatic  1.386  0.020  1.386
 AVQ  CAO  CLC   single    1.730  0.020  1.730
 AVQ  CAO  CAH   aromatic  1.384  0.020  1.384
 AVQ  CAH  CAR   aromatic  1.391  0.020  1.391
 AVQ  CAR  CAI   single    1.497  0.020  1.497
 AVQ  CAI  SAM   single    1.824  0.020  1.824
 AVQ  SAM  CAS   single    1.741  0.020  1.741
 AVQ  CAS  NAK   aromatic  1.341  0.020  1.341
 AVQ  CAS  NAL   aromatic  1.319  0.020  1.319
 AVQ  NAK  CAT   aromatic  1.324  0.020  1.324
 AVQ  NAL  NAU   aromatic  1.344  0.020  1.344
 AVQ  NAU  CAT   aromatic  1.375  0.020  1.375
 AVQ  NAU  CAP   aromatic  1.350  0.020  1.350
 AVQ  CAT  NAJ   aromatic  1.327  0.020  1.327
 AVQ  NAJ  CAN   aromatic  1.320  0.020  1.320
 AVQ  CAN  CAA   single    1.494  0.020  1.494
 AVQ  CAN  CAG   aromatic  1.408  0.020  1.408
 AVQ  CAG  CAP   aromatic  1.372  0.020  1.372
 AVQ  CAP  OAB   single    1.310  0.020  1.310
 AVQ  CAF  HAF   single    0.930  0.020  1.080
 AVQ  CAE  HAE   single    0.930  0.020  1.080
 AVQ  CAH  HAH   single    0.930  0.020  1.080
 AVQ  CAI  HAI1  single    0.970  0.020  1.090
 AVQ  CAI  HAI2  single    0.970  0.020  1.090
 AVQ  OAB  HAB   single    0.850  0.020  0.980
 AVQ  CAA  HAA1  single    0.970  0.020  1.090
 AVQ  CAA  HAA2  single    0.970  0.020  1.090
 AVQ  CAA  HAA3  single    0.970  0.020  1.090
 AVQ  CAG  HAG   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
 AVQ  CAR   CAQ  CAF   121.38  3.000
 AVQ  CAR   CAQ  CLD   120.06  3.000
 AVQ  CAF   CAQ  CLD   118.57  3.000
 AVQ  HAF   CAF  CAE   119.74  3.000
 AVQ  HAF   CAF  CAQ   120.28  3.000
 AVQ  CAE   CAF  CAQ   119.98  3.000
 AVQ  HAE   CAE  CAO   120.98  3.000
 AVQ  HAE   CAE  CAF   119.98  3.000
 AVQ  CAO   CAE  CAF   119.03  3.000
 AVQ  CAH   CAO  CLC   119.35  3.000
 AVQ  CAH   CAO  CAE   121.02  3.000
 AVQ  CLC   CAO  CAE   119.63  3.000
 AVQ  HAH   CAH  CAR   119.32  3.000
 AVQ  HAH   CAH  CAO   120.20  3.000
 AVQ  CAR   CAH  CAO   120.47  3.000
 AVQ  CAI   CAR  CAH   119.40  3.000
 AVQ  CAI   CAR  CAQ   122.49  3.000
 AVQ  CAH   CAR  CAQ   118.10  3.000
 AVQ  HAI2  CAI  HAI1  108.57  3.000
 AVQ  HAI2  CAI  SAM   109.30  3.000
 AVQ  HAI1  CAI  SAM   109.20  3.000
 AVQ  HAI2  CAI  CAR   112.02  3.000
 AVQ  HAI1  CAI  CAR   110.53  3.000
 AVQ  SAM   CAI  CAR   107.17  3.000
 AVQ  CAS   SAM  CAI   100.68  3.000
 AVQ  NAL   CAS  NAK   116.70  3.000
 AVQ  NAL   CAS  SAM   119.22  3.000
 AVQ  NAK   CAS  SAM   124.09  3.000
 AVQ  CAT   NAK  CAS   103.12  3.000
 AVQ  NAU   NAL  CAS   101.22  3.000
 AVQ  CAP   NAU  CAT   121.79  3.000
 AVQ  CAP   NAU  NAL   127.49  3.000
 AVQ  CAT   NAU  NAL   110.72  3.000
 AVQ  NAJ   CAT  NAU   122.71  3.000
 AVQ  NAJ   CAT  NAK   129.04  3.000
 AVQ  NAU   CAT  NAK   108.25  3.000
 AVQ  CAN   NAJ  CAT   116.65  3.000
 AVQ  CAG   CAN  CAA   118.95  3.000
 AVQ  CAG   CAN  NAJ   123.13  3.000
 AVQ  CAA   CAN  NAJ   117.92  3.000
 AVQ  HAA3  CAA  HAA2  107.08  3.000
 AVQ  HAA3  CAA  HAA1  108.84  3.000
 AVQ  HAA2  CAA  HAA1  108.73  3.000
 AVQ  HAA3  CAA  CAN   110.60  3.000
 AVQ  HAA2  CAA  CAN   110.56  3.000
 AVQ  HAA1  CAA  CAN   110.91  3.000
 AVQ  HAG   CAG  CAP   120.04  3.000
 AVQ  HAG   CAG  CAN   120.64  3.000
 AVQ  CAP   CAG  CAN   119.31  3.000
 AVQ  OAB   CAP  CAG   128.33  3.000
 AVQ  OAB   CAP  NAU   115.26  3.000
 AVQ  CAG   CAP  NAU   116.41  3.000
 AVQ  HAB   OAB  CAP   111.02  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
 AVQ  CONST_01  CAO   CAE  CAF  CAQ    0.00   0.0  0
 AVQ  CONST_02  CAO   CAH  CAR  CAQ    0.00   0.0  0
 AVQ  CONST_03  CAH   CAR  CAQ  CAF    0.00   0.0  0
 AVQ  CONST_04  CAH   CAO  CAE  CAF    0.00   0.0  0
 AVQ  CONST_05  CAR   CAQ  CAF  CAE    0.00   0.0  0
 AVQ  CONST_06  CAR   CAH  CAO  CAE    0.00   0.0  0
 AVQ  CONST_07  NAU   CAT  NAK  CAS    0.00   0.0  0
 AVQ  CONST_08  NAJ   CAT  NAK  CAS  180.00   0.0  0
 AVQ  CONST_09  CAT   NAU  NAL  CAS    0.00   0.0  0
 AVQ  CONST_10  CAP   NAU  NAL  CAS  180.00   0.0  0
 AVQ  CONST_11  NAU   NAL  CAS  NAK    0.00   0.0  0
 AVQ  CONST_12  NAL   NAU  CAT  NAK    0.00   0.0  0
 AVQ  CONST_13  CAP   NAU  CAT  NAK  180.00   0.0  0
 AVQ  CONST_14  CAN   NAJ  CAT  NAK  180.00   0.0  0
 AVQ  CONST_15  CAT   NAK  CAS  NAL    0.00   0.0  0
 AVQ  CONST_16  NAJ   CAT  NAU  NAL  180.00   0.0  0
 AVQ  CONST_17  CAG   CAP  NAU  NAL  180.00   0.0  0
 AVQ  CONST_18  CAN   NAJ  CAT  NAU    0.00   0.0  0
 AVQ  CONST_19  CAN   CAG  CAP  NAU    0.00   0.0  0
 AVQ  CONST_20  CAG   CAP  NAU  CAT    0.00   0.0  0
 AVQ  CONST_21  CAG   CAN  NAJ  CAT    0.00   0.0  0
 AVQ  CONST_22  CAP   NAU  CAT  NAJ    0.00   0.0  0
 AVQ  CONST_23  CAP   CAG  CAN  NAJ    0.00   0.0  0
 AVQ  CONST_24  CAE   CAF  CAQ  CLD  180.00   0.0  0
 AVQ  CONST_25  CAH   CAR  CAQ  CLD  180.00   0.0  0
 AVQ  CONST_26  CAI   CAR  CAQ  CAF  180.00   0.0  0
 AVQ  CONST_27  CLC   CAO  CAE  CAF  180.00   0.0  0
 AVQ  CONST_28  CAI   CAR  CAH  CAO  180.00   0.0  0
 AVQ  CONST_29  CAR   CAH  CAO  CLC  180.00   0.0  0
 AVQ  CONST_30  CAT   NAK  CAS  SAM  180.00   0.0  0
 AVQ  CONST_31  NAU   NAL  CAS  SAM  180.00   0.0  0
 AVQ  CONST_32  OAB   CAP  NAU  NAL    0.00   0.0  0
 AVQ  CONST_33  OAB   CAP  NAU  CAT  180.00   0.0  0
 AVQ  CONST_34  CAA   CAN  NAJ  CAT  180.00   0.0  0
 AVQ  CONST_35  OAB   CAP  CAG  CAN  180.00   0.0  0
 AVQ  CONST_36  CAP   CAG  CAN  CAA  180.00   0.0  0
 AVQ  CONST_37  HAE   CAE  CAF  CAQ  180.00   0.0  0
 AVQ  CONST_38  HAH   CAH  CAR  CAQ  180.00   0.0  0
 AVQ  CONST_39  HAF   CAF  CAE  CAO  180.00   0.0  0
 AVQ  CONST_40  HAG   CAG  CAP  NAU  180.00   0.0  0
 AVQ  Var_01    SAM   CAI  CAR  CAQ   81.65  30.0  2
 AVQ  Var_02    NAK   CAS  SAM  CAI   -2.02  30.0  2
 AVQ  Var_03    HAA1  CAA  CAN  NAJ   -2.55  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
 AVQ  plan-1  CLD  0.020
 AVQ  plan-1  CAQ  0.020
 AVQ  plan-1  CAF  0.020
 AVQ  plan-1  CAE  0.020
 AVQ  plan-1  CAO  0.020
 AVQ  plan-1  CLC  0.020
 AVQ  plan-1  CAH  0.020
 AVQ  plan-1  CAR  0.020
 AVQ  plan-1  CAI  0.020
 AVQ  plan-1  HAF  0.020
 AVQ  plan-1  HAE  0.020
 AVQ  plan-1  HAH  0.020
 AVQ  plan-2  SAM  0.020
 AVQ  plan-2  CAS  0.020
 AVQ  plan-2  NAK  0.020
 AVQ  plan-2  NAL  0.020
 AVQ  plan-2  NAU  0.020
 AVQ  plan-2  CAT  0.020
 AVQ  plan-2  NAJ  0.020
 AVQ  plan-2  CAN  0.020
 AVQ  plan-2  CAA  0.020
 AVQ  plan-2  CAG  0.020
 AVQ  plan-2  CAP  0.020
 AVQ  plan-2  OAB  0.020
 AVQ  plan-2  HAG  0.020

