# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:59:01 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 6-(cyclohexylmethoxy)-8-(trifluoromethyl)-9H-purin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]c(nc2c(OCC3CCCCC3)n1)C(F)(F)F
#
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
 JYM  JYM  6-(cyclohexylmethoxy)-8-(trifluoromethyl)-9H-purin-2-amine  ligand  38  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JYM
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
 JYM  FAT   F  F     0  -0.293  -3.2803  -2.7899   0.5527
 JYM  CAS   C  CT    0   1.063  -3.8110  -1.6835   0.0484
 JYM  FAU   F  F     0  -0.310  -4.2422  -1.9637  -1.1876
 JYM  FAV   F  F     0  -0.309  -4.8898  -1.3651   0.7715
 JYM  C8    C  CR5   0   0.170  -2.8180  -0.5719   0.0445
 JYM  N9    N  NR15  0  -0.697  -3.1867   0.7300  -0.1503
 JYM  N7    N  N     0  -0.419  -1.5420  -0.7377   0.1895
 JYM  C5    C  CR56  0  -0.044  -1.0299   0.5263   0.0865
 JYM  C4    C  CR56  0   0.504  -2.0414   1.4601  -0.1246
 JYM  N3    N  N     0  -0.499  -1.9004   2.7694  -0.2640
 JYM  C2    C  CR6   0   0.555  -0.6278   3.1536  -0.1826
 JYM  N2    N  NH2   0  -0.820  -0.3604   4.4600  -0.3234
 JYM  N1    N  N     0  -0.522   0.4448   2.3535   0.0166
 JYM  C6    C  CR6   0   0.512   0.2672   1.0625   0.1485
 JYM  O6    O  O2    0  -0.454   1.2826   0.2495   0.3374
 JYM  CAL   C  CH2   0  -0.146   2.6085   0.7934   0.3662
 JYM  CAM   C  CH1   0  -0.283   3.6009  -0.3478   0.4539
 JYM  CAN   C  CH2   0  -0.424   5.0060   0.2385   0.6082
 JYM  CAO   C  CH2   0  -0.432   6.0726  -0.8482   0.6718
 JYM  CAP   C  CH2   0  -0.429   6.0018  -1.7742  -0.5377
 JYM  CAQ   C  CH2   0  -0.433   4.6050  -2.3645  -0.6942
 JYM  CAR   C  CH2   0  -0.416   3.5365  -1.2782  -0.7582
 JYM  H9    H  HNR5  0   0.434  -4.1192   1.0950  -0.2811
 JYM  H21N  H  HNH2  0   0.401  -1.1107   5.1232  -0.3985
 JYM  H22N  H  HNH2  0   0.402   0.5719   4.8038  -0.1794
 JYM  HAL1  H  HCH2  0   0.227   2.7823   1.3871  -0.5357
 JYM  HAL2  H  HCH2  0   0.240   2.7075   1.4606   1.2268
 JYM  HAM   H  HCH1  0   0.227   3.3794  -0.9308   1.3570
 JYM  HAN1  H  HCH2  0   0.212   5.2118   0.9028  -0.2397
 JYM  HAN2  H  HCH2  0   0.232   5.0522   0.8622   1.5057
 JYM  HAR1  H  HCH2  0   0.234   2.5480  -1.7362  -0.8362
 JYM  HAR2  H  HCH2  0   0.207   3.6758  -0.6817  -1.6682
 JYM  HAO1  H  HCH2  0   0.229   7.0626  -0.3919   0.7447
 JYM  HAO2  H  HCH2  0   0.211   5.9343  -1.4373   1.5850
 JYM  HAP1  H  HCH2  0   0.208   6.2649  -1.2146  -1.4419
 JYM  HAP2  H  HCH2  0   0.227   6.7414  -2.5732  -0.4440
 JYM  HAQ1  H  HCH2  0   0.228   4.5545  -2.9879  -1.5903
 JYM  HAQ2  H  HCH2  0   0.210   4.3991  -3.0283   0.1528

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
 JYM  FAT  CAS   single    1.327  0.020  1.327
 JYM  CAS  FAU   single    1.339  0.020  1.339
 JYM  CAS  FAV   single    1.337  0.020  1.337
 JYM  CAS  C8    single    1.491  0.020  1.491
 JYM  C8   N9    aromatic  1.367  0.020  1.367
 JYM  C8   N7    aromatic  1.295  0.020  1.295
 JYM  N9   C4    aromatic  1.358  0.020  1.358
 JYM  N7   C5    aromatic  1.368  0.020  1.368
 JYM  C5   C4    aromatic  1.393  0.020  1.393
 JYM  C5   C6    aromatic  1.405  0.020  1.405
 JYM  C4   N3    aromatic  1.324  0.020  1.324
 JYM  N3   C2    aromatic  1.332  0.020  1.332
 JYM  C2   N2    single    1.341  0.020  1.341
 JYM  C2   N1    aromatic  1.353  0.020  1.353
 JYM  N1   C6    aromatic  1.310  0.020  1.310
 JYM  C6   O6    single    1.314  0.020  1.314
 JYM  O6   CAL   single    1.433  0.020  1.433
 JYM  CAL  CAM   single    1.515  0.020  1.515
 JYM  CAM  CAN   single    1.530  0.020  1.530
 JYM  CAM  CAR   single    1.529  0.020  1.529
 JYM  CAN  CAO   single    1.524  0.020  1.524
 JYM  CAO  CAP   single    1.525  0.020  1.525
 JYM  CAP  CAQ   single    1.524  0.020  1.524
 JYM  CAQ  CAR   single    1.525  0.020  1.525
 JYM  N9   H9    single    0.860  0.020  1.020
 JYM  N2   H21N  single    0.860  0.020  1.020
 JYM  N2   H22N  single    0.860  0.020  1.020
 JYM  CAL  HAL1  single    0.970  0.020  1.090
 JYM  CAL  HAL2  single    0.970  0.020  1.090
 JYM  CAM  HAM   single    0.970  0.020  1.090
 JYM  CAN  HAN1  single    0.970  0.020  1.090
 JYM  CAN  HAN2  single    0.970  0.020  1.090
 JYM  CAR  HAR1  single    0.970  0.020  1.090
 JYM  CAR  HAR2  single    0.970  0.020  1.090
 JYM  CAO  HAO1  single    0.970  0.020  1.090
 JYM  CAO  HAO2  single    0.970  0.020  1.090
 JYM  CAP  HAP1  single    0.970  0.020  1.090
 JYM  CAP  HAP2  single    0.970  0.020  1.090
 JYM  CAQ  HAQ1  single    0.970  0.020  1.090
 JYM  CAQ  HAQ2  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
 JYM  C8    CAS  FAV   111.18  3.000
 JYM  C8    CAS  FAU   111.61  3.000
 JYM  FAV   CAS  FAU   106.81  3.000
 JYM  C8    CAS  FAT   110.88  3.000
 JYM  FAV   CAS  FAT   108.41  3.000
 JYM  FAU   CAS  FAT   107.78  3.000
 JYM  N7    C8   N9    113.80  3.000
 JYM  N7    C8   CAS   124.11  3.000
 JYM  N9    C8   CAS   122.07  3.000
 JYM  H9    N9   C4    125.93  3.000
 JYM  H9    N9   C8    127.71  3.000
 JYM  C4    N9   C8    106.36  3.000
 JYM  C5    N7   C8    104.02  3.000
 JYM  C6    C5   C4    114.92  3.000
 JYM  C6    C5   N7    134.03  3.000
 JYM  C4    C5   N7    111.05  3.000
 JYM  N3    C4   C5    126.98  3.000
 JYM  N3    C4   N9    128.25  3.000
 JYM  C5    C4   N9    104.77  3.000
 JYM  C2    N3   C4    112.37  3.000
 JYM  N1    C2   N2    115.69  3.000
 JYM  N1    C2   N3    126.58  3.000
 JYM  N2    C2   N3    117.72  3.000
 JYM  H22N  N2   H21N  118.58  3.000
 JYM  H22N  N2   C2    120.25  3.000
 JYM  H21N  N2   C2    120.15  3.000
 JYM  C6    N1   C2    119.36  3.000
 JYM  O6    C6   N1    121.29  3.000
 JYM  O6    C6   C5    118.91  3.000
 JYM  N1    C6   C5    119.79  3.000
 JYM  CAL   O6   C6    118.86  3.000
 JYM  HAL2  CAL  HAL1  107.66  3.000
 JYM  HAL2  CAL  CAM   110.78  3.000
 JYM  HAL1  CAL  CAM   110.64  3.000
 JYM  HAL2  CAL  O6    109.34  3.000
 JYM  HAL1  CAL  O6    109.66  3.000
 JYM  CAM   CAL  O6    108.74  3.000
 JYM  HAM   CAM  CAR   108.69  3.000
 JYM  HAM   CAM  CAN   107.81  3.000
 JYM  CAR   CAM  CAN   110.59  3.000
 JYM  HAM   CAM  CAL   108.39  3.000
 JYM  CAR   CAM  CAL   112.63  3.000
 JYM  CAN   CAM  CAL   108.59  3.000
 JYM  HAN2  CAN  HAN1  106.32  3.000
 JYM  HAN2  CAN  CAO   110.05  3.000
 JYM  HAN1  CAN  CAO   109.45  3.000
 JYM  HAN2  CAN  CAM   109.87  3.000
 JYM  HAN1  CAN  CAM   109.05  3.000
 JYM  CAO   CAN  CAM   111.94  3.000
 JYM  HAO2  CAO  HAO1  106.46  3.000
 JYM  HAO2  CAO  CAP   109.19  3.000
 JYM  HAO1  CAO  CAP   110.40  3.000
 JYM  HAO2  CAO  CAN   109.26  3.000
 JYM  HAO1  CAO  CAN   109.83  3.000
 JYM  CAP   CAO  CAN   111.56  3.000
 JYM  HAP2  CAP  HAP1  106.36  3.000
 JYM  HAP2  CAP  CAQ   110.23  3.000
 JYM  HAP1  CAP  CAQ   109.46  3.000
 JYM  HAP2  CAP  CAO   110.16  3.000
 JYM  HAP1  CAP  CAO   109.47  3.000
 JYM  CAQ   CAP  CAO   111.05  3.000
 JYM  HAQ2  CAQ  HAQ1  106.24  3.000
 JYM  HAQ2  CAQ  CAR   109.41  3.000
 JYM  HAQ1  CAQ  CAR   109.85  3.000
 JYM  HAQ2  CAQ  CAP   109.11  3.000
 JYM  HAQ1  CAQ  CAP   110.33  3.000
 JYM  CAR   CAQ  CAP   111.74  3.000
 JYM  HAR2  CAR  HAR1  106.48  3.000
 JYM  HAR2  CAR  CAQ   109.46  3.000
 JYM  HAR1  CAR  CAQ   109.78  3.000
 JYM  HAR2  CAR  CAM   108.74  3.000
 JYM  HAR1  CAR  CAM   110.47  3.000
 JYM  CAQ   CAR  CAM   111.75  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
 JYM  CONST_01  C5    C4   N9   C8      0.00   0.0  0
 JYM  CONST_02  N3    C4   N9   C8    180.00   0.0  0
 JYM  CONST_03  C4    C5   N7   C8      0.00   0.0  0
 JYM  CONST_04  C6    C5   N7   C8    180.00   0.0  0
 JYM  CONST_05  C5    N7   C8   N9      0.00   0.0  0
 JYM  CONST_06  N7    C5   C4   N9      0.00   0.0  0
 JYM  CONST_07  C6    C5   C4   N9    180.00   0.0  0
 JYM  CONST_08  C2    N3   C4   N9    180.00   0.0  0
 JYM  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 JYM  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 JYM  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 JYM  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 JYM  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 JYM  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 JYM  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 JYM  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 JYM  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 JYM  CONST_18  C4    N9   C8   CAS   180.00   0.0  0
 JYM  CONST_19  C5    N7   C8   CAS   180.00   0.0  0
 JYM  CONST_20  O6    C6   C5   N7      0.00   0.0  0
 JYM  CONST_21  O6    C6   C5   C4    180.00   0.0  0
 JYM  CONST_22  N2    C2   N3   C4    180.00   0.0  0
 JYM  CONST_23  O6    C6   N1   C2    180.00   0.0  0
 JYM  CONST_24  C6    N1   C2   N2    180.00   0.0  0
 JYM  CONST_25  H9    N9   C8   N7    180.00   0.0  0
 JYM  CONST_26  H21N  N2   C2   N3      0.00   0.0  0
 JYM  CONST_27  H22N  N2   C2   N3    180.00   0.0  0
 JYM  Var_01    CAP   CAO  CAN  CAM    55.18  30.0  1
 JYM  Var_02    CAP   CAQ  CAR  CAM   -55.16  30.0  1
 JYM  Var_03    CAQ   CAP  CAO  CAN   -54.72  30.0  1
 JYM  Var_04    CAR   CAQ  CAP  CAO    54.79  30.0  1
 JYM  Var_05    N9    C8   CAS  FAT  -165.64  30.0  2
 JYM  Var_06    CAM   CAL  O6   C6   -174.31  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JYM  chir_01  CAM  CAL  CAN  CAR  positiv

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
 JYM  plan-1  CAS   0.020
 JYM  plan-1  C8    0.020
 JYM  plan-1  N9    0.020
 JYM  plan-1  N7    0.020
 JYM  plan-1  C5    0.020
 JYM  plan-1  C4    0.020
 JYM  plan-1  N3    0.020
 JYM  plan-1  C2    0.020
 JYM  plan-1  N2    0.020
 JYM  plan-1  N1    0.020
 JYM  plan-1  C6    0.020
 JYM  plan-1  O6    0.020
 JYM  plan-1  H9    0.020
 JYM  plan-2  C2    0.020
 JYM  plan-2  N2    0.020
 JYM  plan-2  H21N  0.020
 JYM  plan-2  H22N  0.020

