# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:27:50 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 9-(2-chloroethyl)-8-methyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2c(N)ncnc2n1CCCl
#
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
 JXW  JXW  9-(2-chloroethyl)-8-methyl-purin-6-amine  ligand  24  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JXW
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
 JXW  C    C   CH3   0  -0.767   0.8684   2.9113  -0.2114
 JXW  N    N   N     0  -0.466  -1.3208   1.7821   0.0720
 JXW  C1   C   CR5   0   0.438  -0.0392   1.7390  -0.1649
 JXW  N1   N   NH2   0  -0.819  -4.1035   0.5425   0.4370
 JXW  C2   C   CR56  0   0.003  -1.7339   0.4757   0.0207
 JXW  N2   N   N     0  -0.473  -3.0449  -1.4763   0.0811
 JXW  C3   C   CR6   0   0.442  -2.9844  -0.1434   0.1892
 JXW  N3   N   N     0  -0.459  -0.7092  -1.6896  -0.3657
 JXW  C4   C   CR16  0   0.036  -1.9332  -2.1565  -0.1836
 JXW  N4   N   NR5   0  -0.532   0.4129   0.4577  -0.3793
 JXW  C5   C   CR56  0   0.485  -0.6684  -0.3647  -0.2529
 JXW  C6   C   CH2   0  -0.324   1.7713   0.0315  -0.6248
 JXW  C7   C   CH2   0  -0.456   2.4630  -0.3063   0.6853
 JXW  CL   CL  CL    0  -0.152   4.1491  -0.8133   0.3534
 JXW  H1   H   HCH3  0   0.265   1.6501   2.8459   0.5475
 JXW  H2   H   HCH3  0   0.269   1.3592   2.9981  -1.1820
 JXW  H3   H   HCH3  0   0.277   0.2971   3.8187  -0.0343
 JXW  H4   H   HNH2  0   0.402  -4.9617   0.0553   0.6288
 JXW  H5   H   HNH2  0   0.409  -4.0756   1.5339   0.5971
 JXW  H6   H   HCR6  0   0.250  -2.0513  -3.2323  -0.2583
 JXW  H7   H   HCH2  0   0.290   1.7482  -0.8411  -1.2760
 JXW  H8   H   HCH2  0   0.291   2.3049   0.8230  -1.1490
 JXW  H9   H   HCH2  0   0.293   2.5029   0.5530   1.3514
 JXW  H10  H   HCH2  0   0.297   1.9665  -1.1296   1.1949

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
 JXW  N1  C3   single    1.336  0.020  1.336
 JXW  C3  N2   aromatic  1.339  0.020  1.339
 JXW  C3  C2   aromatic  1.406  0.020  1.406
 JXW  N   C2   aromatic  1.371  0.020  1.371
 JXW  N   C1   aromatic  1.304  0.020  1.304
 JXW  N2  C4   aromatic  1.330  0.020  1.330
 JXW  C2  C5   aromatic  1.384  0.020  1.384
 JXW  C1  C    single    1.483  0.020  1.483
 JXW  C1  N4   aromatic  1.376  0.020  1.376
 JXW  C4  N3   aromatic  1.323  0.020  1.323
 JXW  C5  N4   aromatic  1.364  0.020  1.364
 JXW  C5  N3   aromatic  1.330  0.020  1.330
 JXW  N4  C6   single    1.445  0.020  1.445
 JXW  C7  C6   single    1.520  0.020  1.520
 JXW  C7  CL   single    1.792  0.020  1.792
 JXW  C   H1   single    0.970  0.020  1.090
 JXW  C   H2   single    0.970  0.020  1.090
 JXW  C   H3   single    0.970  0.020  1.090
 JXW  N1  H4   single    0.860  0.020  1.020
 JXW  N1  H5   single    0.860  0.020  1.020
 JXW  C4  H6   single    0.930  0.020  1.080
 JXW  C6  H7   single    0.970  0.020  1.090
 JXW  C6  H8   single    0.970  0.020  1.090
 JXW  C7  H9   single    0.970  0.020  1.090
 JXW  C7  H10  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
 JXW  H3   C   H2  108.36  3.000
 JXW  H3   C   H1  108.25  3.000
 JXW  H2   C   H1  107.53  3.000
 JXW  H3   C   C1  109.45  3.000
 JXW  H2   C   C1  111.47  3.000
 JXW  H1   C   C1  111.66  3.000
 JXW  C2   N   C1  104.94  3.000
 JXW  N4   C1  N   112.47  3.000
 JXW  N4   C1  C   122.02  3.000
 JXW  N    C1  C   125.52  3.000
 JXW  H5   N1  H4  118.14  3.000
 JXW  H5   N1  C3  120.86  3.000
 JXW  H4   N1  C3  120.11  3.000
 JXW  C5   C2  C3  116.17  3.000
 JXW  C5   C2  N   110.73  3.000
 JXW  C3   C2  N   133.10  3.000
 JXW  C4   N2  C3  119.18  3.000
 JXW  N2   C3  C2  117.98  3.000
 JXW  C2   C3  N1  122.78  3.000
 JXW  N2   C3  N1  119.24  3.000
 JXW  C5   N3  C4  111.61  3.000
 JXW  H6   C4  N3  116.19  3.000
 JXW  H6   C4  N2  115.46  3.000
 JXW  N3   C4  N2  128.35  3.000
 JXW  C6   N4  C5  125.67  3.000
 JXW  C6   N4  C1  127.62  3.000
 JXW  C5   N4  C1  106.65  3.000
 JXW  N4   C5  N3  128.08  3.000
 JXW  N3   C5  C2  126.71  3.000
 JXW  N4   C5  C2  105.21  3.000
 JXW  H8   C6  H7  107.75  3.000
 JXW  H8   C6  C7  110.70  3.000
 JXW  H7   C6  C7  110.31  3.000
 JXW  H8   C6  N4  109.15  3.000
 JXW  H7   C6  N4  108.55  3.000
 JXW  C7   C6  N4  110.31  3.000
 JXW  H10  C7  H9  109.13  3.000
 JXW  H10  C7  CL  107.58  3.000
 JXW  H9   C7  CL  107.60  3.000
 JXW  H10  C7  C6  111.36  3.000
 JXW  H9   C7  C6  111.65  3.000
 JXW  CL   C7  C6  109.36  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
 JXW  CONST_01  N2  C3  C2  N    180.00   0.0  0
 JXW  CONST_02  N4  C5  C2  N      0.00   0.0  0
 JXW  CONST_03  N3  C5  C2  N    180.00   0.0  0
 JXW  CONST_04  C5  N4  C1  N      0.00   0.0  0
 JXW  CONST_05  C3  C2  N   C1   180.00   0.0  0
 JXW  CONST_06  C5  C2  N   C1     0.00   0.0  0
 JXW  CONST_07  C2  C5  N4  C1     0.00   0.0  0
 JXW  CONST_08  N3  C5  N4  C1   180.00   0.0  0
 JXW  CONST_09  C4  N2  C3  C2     0.00   0.0  0
 JXW  CONST_10  N4  C1  N   C2     0.00   0.0  0
 JXW  CONST_11  C4  N3  C5  C2     0.00   0.0  0
 JXW  CONST_12  C5  C2  C3  N2     0.00   0.0  0
 JXW  CONST_13  C5  N3  C4  N2     0.00   0.0  0
 JXW  CONST_14  N3  C4  N2  C3     0.00   0.0  0
 JXW  CONST_15  N4  C5  C2  C3   180.00   0.0  0
 JXW  CONST_16  N3  C5  C2  C3     0.00   0.0  0
 JXW  CONST_17  N4  C5  N3  C4   180.00   0.0  0
 JXW  CONST_18  C2  N   C1  C    180.00   0.0  0
 JXW  CONST_19  C5  N4  C1  C    180.00   0.0  0
 JXW  CONST_20  N1  C3  C2  N      0.00   0.0  0
 JXW  CONST_21  C6  N4  C1  N    180.00   0.0  0
 JXW  CONST_22  C4  N2  C3  N1   180.00   0.0  0
 JXW  CONST_23  C5  C2  C3  N1   180.00   0.0  0
 JXW  CONST_24  C6  N4  C5  C2   180.00   0.0  0
 JXW  CONST_25  C6  N4  C5  N3     0.00   0.0  0
 JXW  CONST_26  H6  C4  N2  C3   180.00   0.0  0
 JXW  CONST_27  H4  N1  C3  C2   180.00   0.0  0
 JXW  CONST_28  H5  N1  C3  C2     0.00   0.0  0
 JXW  Var_01    C7  C6  N4  C1    90.80  30.0  2
 JXW  Var_02    H1  C   C1  N    118.86  30.0  2
 JXW  Var_03    CL  C7  C6  N4  -179.36  30.0  1

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
 JXW  plan-1  C   0.020
 JXW  plan-1  N   0.020
 JXW  plan-1  C1  0.020
 JXW  plan-1  N1  0.020
 JXW  plan-1  C2  0.020
 JXW  plan-1  N2  0.020
 JXW  plan-1  C3  0.020
 JXW  plan-1  N3  0.020
 JXW  plan-1  C4  0.020
 JXW  plan-1  N4  0.020
 JXW  plan-1  C5  0.020
 JXW  plan-1  C6  0.020
 JXW  plan-1  H6  0.020
 JXW  plan-2  N1  0.020
 JXW  plan-2  C3  0.020
 JXW  plan-2  H4  0.020
 JXW  plan-2  H5  0.020

