# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:23:31 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(Cc2cccc(Br)c2)c3c(N)ncnc13
#
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
 DXR  DXR  3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  40  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DXR
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
 DXR  N1    N   N     0  -0.466   3.9355  -0.0880  -1.0998
 DXR  C2    C   CR16  0   0.052   4.0636   1.1452  -1.5397
 DXR  N3    N   N     0  -0.481   3.3035   2.2064  -1.2754
 DXR  C4    C   CR6   0   0.434   2.2576   2.0588  -0.4582
 DXR  C5    C   CR56  0  -0.251   2.0065   0.7842   0.1007
 DXR  C6    C   CR56  0   0.593   2.8911  -0.2321  -0.2740
 DXR  NAG   N   NH2   0  -0.821   1.5083   3.1339  -0.2101
 DXR  CAH   C   CR5   0   0.295   1.0889   0.1531   0.9813
 DXR  NAI   N   N     0  -0.271   1.3971  -1.1135   1.1017
 DXR  NAJ   N   NR5   0  -0.380   2.4858  -1.3559   0.3526
 DXR  CAK   C   CT    0   0.061   3.0691  -2.7095   0.2567
 DXR  CAL   C   CH3   0  -0.648   4.5206  -2.6652   0.7342
 DXR  CAM   C   CH3   0  -0.646   2.2726  -3.6624   1.1406
 DXR  CAN   C   CH3   0  -0.648   2.9879  -3.1756  -1.1974
 DXR  CAO   C   CH2   0  -0.602  -0.0840   0.7246   1.7053
 DXR  CAP   C   CR6   0   0.077  -1.1374   1.2923   0.7841
 DXR  CAQ   C   CR16  0  -0.247  -1.5078   0.6012  -0.3674
 DXR  CAR   C   CR6   0  -0.092  -2.4831   1.1276  -1.1983
 DXR  CAS   C   CR16  0  -0.242  -3.1072   2.3345  -0.9149
 DXR  CAT   C   CR16  0  -0.237  -2.7362   3.0157   0.2344
 DXR  CAU   C   CR16  0  -0.318  -1.7606   2.5013   1.0777
 DXR  BRAV  BR  BR    0  -0.045  -2.9771   0.1762  -2.7544
 DXR  H2    H   HCR6  0   0.252   4.8987   1.3294  -2.2080
 DXR  HNAG  H   HNH2  0   0.405   1.7098   3.9962  -0.6877
 DXR  HNAA  H   HNH2  0   0.416   0.6572   3.0865   0.3210
 DXR  HAL   H   HCH3  0   0.235   4.5795  -2.3446   1.7754
 DXR  HALA  H   HCH3  0   0.234   4.9541  -3.6635   0.6658
 DXR  HALB  H   HCH3  0   0.247   5.1258  -1.9933   0.1279
 DXR  HAM   H   HCH3  0   0.238   1.2333  -3.7434   0.8241
 DXR  HAMA  H   HCH3  0   0.237   2.7255  -4.6511   1.0694
 DXR  HAMB  H   HCH3  0   0.238   2.2897  -3.3601   2.1870
 DXR  HAN   H   HCH3  0   0.246   3.5777  -2.5418  -1.8579
 DXR  HANA  H   HCH3  0   0.234   3.3674  -4.1943  -1.2823
 DXR  HANB  H   HCH3  0   0.235   1.9541  -3.1722  -1.5467
 DXR  HAO   H   HCH2  0   0.291  -0.5256  -0.0661   2.3169
 DXR  HAOA  H   HCH2  0   0.275   0.2456   1.5015   2.3997
 DXR  HAQ   H   HCR6  0   0.276  -1.0332  -0.3428  -0.6058
 DXR  HAS   H   HCR6  0   0.281  -3.8635   2.7439  -1.5708
 DXR  HAT   H   HCR6  0   0.272  -3.2102   3.9595   0.4689
 DXR  HAU   H   HCR6  0   0.273  -1.4800   3.0464   1.9712

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
 DXR  C2   N1    aromatic  1.316  0.020  1.316
 DXR  N1   C6    aromatic  1.339  0.020  1.339
 DXR  N3   C2    aromatic  1.332  0.020  1.332
 DXR  C2   H2    single    0.930  0.020  1.080
 DXR  N3   C4    aromatic  1.336  0.020  1.336
 DXR  NAG  C4    single    1.334  0.020  1.334
 DXR  C4   C5    aromatic  1.414  0.020  1.414
 DXR  C5   C6    aromatic  1.398  0.020  1.398
 DXR  C5   CAH   aromatic  1.420  0.020  1.420
 DXR  C6   NAJ   aromatic  1.349  0.020  1.349
 DXR  NAG  HNAG  single    0.860  0.020  1.020
 DXR  NAG  HNAA  single    0.860  0.020  1.020
 DXR  CAO  CAH   single    1.492  0.020  1.492
 DXR  CAH  NAI   aromatic  1.309  0.020  1.309
 DXR  NAJ  NAI   aromatic  1.344  0.020  1.344
 DXR  NAJ  CAK   single    1.477  0.020  1.477
 DXR  CAM  CAK   single    1.524  0.020  1.524
 DXR  CAK  CAL   single    1.529  0.020  1.529
 DXR  CAK  CAN   single    1.529  0.020  1.529
 DXR  CAL  HAL   single    0.970  0.020  1.090
 DXR  CAL  HALA  single    0.970  0.020  1.090
 DXR  CAL  HALB  single    0.970  0.020  1.090
 DXR  CAM  HAM   single    0.970  0.020  1.090
 DXR  CAM  HAMA  single    0.970  0.020  1.090
 DXR  CAM  HAMB  single    0.970  0.020  1.090
 DXR  CAN  HAN   single    0.970  0.020  1.090
 DXR  CAN  HANA  single    0.970  0.020  1.090
 DXR  CAN  HANB  single    0.970  0.020  1.090
 DXR  CAP  CAO   single    1.510  0.020  1.510
 DXR  CAO  HAO   single    0.970  0.020  1.090
 DXR  CAO  HAOA  single    0.970  0.020  1.090
 DXR  CAU  CAP   aromatic  1.391  0.020  1.391
 DXR  CAP  CAQ   aromatic  1.393  0.020  1.393
 DXR  CAR  CAQ   aromatic  1.385  0.020  1.385
 DXR  CAQ  HAQ   single    0.930  0.020  1.080
 DXR  CAS  CAR   aromatic  1.388  0.020  1.388
 DXR  CAR  BRAV  single    1.890  0.020  1.890
 DXR  CAT  CAS   aromatic  1.387  0.020  1.387
 DXR  CAS  HAS   single    0.930  0.020  1.080
 DXR  CAT  CAU   aromatic  1.388  0.020  1.388
 DXR  CAT  HAT   single    0.930  0.020  1.080
 DXR  CAU  HAU   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
 DXR  C6    N1   C2    112.52  3.000
 DXR  H2    C2   N3    115.22  3.000
 DXR  H2    C2   N1    116.10  3.000
 DXR  N3    C2   N1    128.68  3.000
 DXR  C4    N3   C2    118.70  3.000
 DXR  NAG   C4   C5    123.59  3.000
 DXR  C5    C4   N3    118.72  3.000
 DXR  NAG   C4   N3    117.69  3.000
 DXR  CAH   C5   C6    104.59  3.000
 DXR  CAH   C5   C4    139.51  3.000
 DXR  C6    C5   C4    115.90  3.000
 DXR  NAJ   C6   C5    106.91  3.000
 DXR  NAJ   C6   N1    127.61  3.000
 DXR  C5    C6   N1    125.47  3.000
 DXR  HNAA  NAG  HNAG  117.47  3.000
 DXR  HNAA  NAG  C4    122.44  3.000
 DXR  HNAG  NAG  C4    119.34  3.000
 DXR  CAO   CAH  NAI   120.73  3.000
 DXR  NAI   CAH  C5    109.58  3.000
 DXR  CAO   CAH  C5    129.69  3.000
 DXR  NAJ   NAI  CAH   108.30  3.000
 DXR  CAK   NAJ  NAI   121.44  3.000
 DXR  CAK   NAJ  C6    127.93  3.000
 DXR  NAI   NAJ  C6    110.61  3.000
 DXR  CAN   CAK  CAM   109.46  3.000
 DXR  CAN   CAK  CAL   110.87  3.000
 DXR  CAM   CAK  CAL   109.46  3.000
 DXR  CAN   CAK  NAJ   108.67  3.000
 DXR  CAL   CAK  NAJ   109.15  3.000
 DXR  CAM   CAK  NAJ   109.20  3.000
 DXR  HALB  CAL  HALA  108.00  3.000
 DXR  HALB  CAL  HAL   108.67  3.000
 DXR  HALA  CAL  HAL   107.91  3.000
 DXR  HALB  CAL  CAK   111.82  3.000
 DXR  HALA  CAL  CAK   109.35  3.000
 DXR  HAL   CAL  CAK   110.97  3.000
 DXR  HAMB  CAM  HAMA  107.94  3.000
 DXR  HAMB  CAM  HAM   108.35  3.000
 DXR  HAMA  CAM  HAM   108.06  3.000
 DXR  HAMB  CAM  CAK   112.05  3.000
 DXR  HAMA  CAM  CAK   108.18  3.000
 DXR  HAM   CAM  CAK   112.11  3.000
 DXR  HANB  CAN  HANA  107.92  3.000
 DXR  HANB  CAN  HAN   108.49  3.000
 DXR  HANA  CAN  HAN   107.94  3.000
 DXR  HANB  CAN  CAK   110.72  3.000
 DXR  HANA  CAN  CAK   109.89  3.000
 DXR  HAN   CAN  CAK   111.76  3.000
 DXR  HAOA  CAO  HAO   106.30  3.000
 DXR  HAOA  CAO  CAP   109.31  3.000
 DXR  HAO   CAO  CAP   109.36  3.000
 DXR  HAOA  CAO  CAH   110.09  3.000
 DXR  HAO   CAO  CAH   108.19  3.000
 DXR  CAP   CAO  CAH   113.35  3.000
 DXR  CAU   CAP  CAQ   119.10  3.000
 DXR  CAQ   CAP  CAO   120.21  3.000
 DXR  CAU   CAP  CAO   120.69  3.000
 DXR  HAQ   CAQ  CAR   120.51  3.000
 DXR  HAQ   CAQ  CAP   119.85  3.000
 DXR  CAR   CAQ  CAP   119.64  3.000
 DXR  BRAV  CAR  CAS   119.23  3.000
 DXR  BRAV  CAR  CAQ   119.13  3.000
 DXR  CAS   CAR  CAQ   121.64  3.000
 DXR  HAS   CAS  CAT   120.25  3.000
 DXR  HAS   CAS  CAR   121.32  3.000
 DXR  CAT   CAS  CAR   118.43  3.000
 DXR  HAT   CAT  CAU   119.97  3.000
 DXR  HAT   CAT  CAS   119.41  3.000
 DXR  CAU   CAT  CAS   120.62  3.000
 DXR  HAU   CAU  CAT   119.76  3.000
 DXR  HAU   CAU  CAP   119.67  3.000
 DXR  CAT   CAU  CAP   120.57  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
 DXR  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 DXR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 DXR  CONST_03  CAH   C5   C6   N1    180.00   0.0  0
 DXR  CONST_04  NAI   NAJ  C6   N1    180.00   0.0  0
 DXR  CONST_05  C5    C6   N1   C2      0.00   0.0  0
 DXR  CONST_06  NAJ   C6   N1   C2    180.00   0.0  0
 DXR  CONST_07  C5    C4   N3   C2      0.00   0.0  0
 DXR  CONST_08  C6    N1   C2   N3      0.00   0.0  0
 DXR  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 DXR  CONST_10  CAH   C5   C4   N3    180.00   0.0  0
 DXR  CONST_11  NAJ   C6   C5   C4    180.00   0.0  0
 DXR  CONST_12  NAI   CAH  C5   C4    180.00   0.0  0
 DXR  CONST_13  NAI   NAJ  C6   C5      0.00   0.0  0
 DXR  CONST_14  NAJ   NAI  CAH  C5      0.00   0.0  0
 DXR  CONST_15  NAI   CAH  C5   C6      0.00   0.0  0
 DXR  CONST_16  CAH   NAI  NAJ  C6      0.00   0.0  0
 DXR  CONST_17  NAJ   C6   C5   CAH     0.00   0.0  0
 DXR  CONST_18  CAS   CAT  CAU  CAP     0.00   0.0  0
 DXR  CONST_19  CAS   CAR  CAQ  CAP     0.00   0.0  0
 DXR  CONST_20  CAT   CAU  CAP  CAQ     0.00   0.0  0
 DXR  CONST_21  CAT   CAS  CAR  CAQ     0.00   0.0  0
 DXR  CONST_22  CAU   CAP  CAQ  CAR     0.00   0.0  0
 DXR  CONST_23  CAU   CAT  CAS  CAR     0.00   0.0  0
 DXR  CONST_24  CAK   NAJ  C6   N1      0.00   0.0  0
 DXR  CONST_25  NAG   C4   N3   C2    180.00   0.0  0
 DXR  CONST_26  CAO   CAH  C5   C4      0.00   0.0  0
 DXR  CONST_27  CAK   NAJ  C6   C5    180.00   0.0  0
 DXR  CONST_28  NAG   C4   C5   C6    180.00   0.0  0
 DXR  CONST_29  CAO   CAH  C5   C6    180.00   0.0  0
 DXR  CONST_30  CAH   C5   C4   NAG     0.00   0.0  0
 DXR  CONST_31  CAK   NAJ  NAI  CAH   180.00   0.0  0
 DXR  CONST_32  CAO   CAH  NAI  NAJ   180.00   0.0  0
 DXR  CONST_33  CAT   CAU  CAP  CAO   180.00   0.0  0
 DXR  CONST_34  CAR   CAQ  CAP  CAO   180.00   0.0  0
 DXR  CONST_35  BRAV  CAR  CAQ  CAP   180.00   0.0  0
 DXR  CONST_36  BRAV  CAR  CAS  CAT   180.00   0.0  0
 DXR  CONST_37  H2    C2   N3   C4    180.00   0.0  0
 DXR  CONST_38  HAT   CAT  CAU  CAP   180.00   0.0  0
 DXR  CONST_39  HAU   CAU  CAP  CAQ   180.00   0.0  0
 DXR  CONST_40  HAS   CAS  CAR  CAQ   180.00   0.0  0
 DXR  CONST_41  HAQ   CAQ  CAR  CAS   180.00   0.0  0
 DXR  CONST_42  HNAG  NAG  C4   N3      0.00   0.0  0
 DXR  CONST_43  HNAA  NAG  C4   N3    180.00   0.0  0
 DXR  Var_01    CAP   CAO  CAH  C5     60.51  30.0  2
 DXR  Var_02    CAU   CAP  CAO  CAH  -137.80  30.0  2
 DXR  Var_03    CAM   CAK  NAJ  C6   -179.79  30.0  2
 DXR  Var_04    HAM   CAM  CAK  NAJ    61.80  30.0  3
 DXR  Var_05    HAL   CAL  CAK  NAJ    61.01  30.0  3
 DXR  Var_06    HAN   CAN  CAK  NAJ    63.05  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
 DXR  plan-1  CAO   0.020
 DXR  plan-1  CAP   0.020
 DXR  plan-1  CAQ   0.020
 DXR  plan-1  CAR   0.020
 DXR  plan-1  CAS   0.020
 DXR  plan-1  CAT   0.020
 DXR  plan-1  CAU   0.020
 DXR  plan-1  BRAV  0.020
 DXR  plan-1  HAQ   0.020
 DXR  plan-1  HAS   0.020
 DXR  plan-1  HAT   0.020
 DXR  plan-1  HAU   0.020
 DXR  plan-2  N1    0.020
 DXR  plan-2  C2    0.020
 DXR  plan-2  N3    0.020
 DXR  plan-2  C4    0.020
 DXR  plan-2  C5    0.020
 DXR  plan-2  C6    0.020
 DXR  plan-2  NAG   0.020
 DXR  plan-2  CAH   0.020
 DXR  plan-2  NAI   0.020
 DXR  plan-2  NAJ   0.020
 DXR  plan-2  CAK   0.020
 DXR  plan-2  CAO   0.020
 DXR  plan-2  H2    0.020
 DXR  plan-3  C4    0.020
 DXR  plan-3  NAG   0.020
 DXR  plan-3  HNAG  0.020
 DXR  plan-3  HNAA  0.020

