# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:22:59 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 4-{[6-(cyclohexylmethoxy)-9H-purin-2-yl]amino}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(Nc2nc3[nH]cnc3c(OCC4CCCCC4)n2)cc1
#
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
 N41  N41  4-{[6-(cyclohexylmethoxy)-9H-purin-2-yl]amino}benzamide  ligand  49  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N41
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
 N41  C2    C  CR6   0   0.603  -1.9512   0.0062  -1.4181
 N41  C10   C  CH2   0  -0.152   1.9020   0.4205  -0.3504
 N41  C11   C  CH1   0  -0.281   3.4132   0.4956  -0.2693
 N41  C12   C  CH2   0  -0.424   3.8188   0.7214   1.1892
 N41  C13   C  CH2   0  -0.432   5.3341   0.7870   1.3474
 N41  C14   C  CH2   0  -0.429   6.0022  -0.4657   0.7918
 N41  C15   C  CH2   0  -0.433   5.6067  -0.6959  -0.6627
 N41  C16   C  CH2   0  -0.416   4.0908  -0.7572  -0.8258
 N41  C19   C  CR16  0  -0.273  -1.6075  -0.0978   3.0580
 N41  C20   C  CR6   0  -0.061  -2.7971  -0.2155   3.7714
 N41  C21   C  CR16  0  -0.258  -3.9875  -0.2663   3.0456
 N41  C22   C  CR16  0  -0.348  -3.9819  -0.2270   1.6685
 N41  N25   N  NH2   0  -0.819  -1.7253  -0.5500   5.9065
 N41  N1    N  N     0  -0.534  -0.6646   0.1383  -1.0815
 N41  C6    C  CR6   0   0.548   0.2449   0.2301  -2.0307
 N41  O6    O  O2    0  -0.453   1.5191   0.3607  -1.7297
 N41  C5    C  CR56  0  -0.054  -0.1427   0.1916  -3.3727
 N41  N7    N  N     0  -0.437   0.5293   0.2624  -4.5676
 N41  N9    N  NR15  0  -0.652  -1.6576   0.0437  -4.9302
 N41  C4    C  CR56  0   0.487  -1.5146   0.0551  -3.5807
 N41  N3    N  N     0  -0.499  -2.4506  -0.0416  -2.6475
 N41  N2    N  NH1   0  -0.771  -2.8877  -0.0897  -0.4252
 N41  C17   C  CR6   0   0.371  -2.7800  -0.1176   0.9521
 N41  C18   C  CR16  0  -0.308  -1.5846  -0.0459   1.6742
 N41  C8    C  CR15  0   0.099  -0.4067   0.1705  -5.4638
 N41  O24   O  O     0  -0.488  -3.9130  -0.0244   5.8516
 N41  H101  H  HCH2  0   0.240   1.4441   1.2984   0.1149
 N41  H102  H  HCH2  0   0.227   1.5363  -0.4677   0.1740
 N41  H11   H  HCH1  0   0.228   3.7506   1.3658  -0.8477
 N41  H121  H  HCH2  0   0.232   3.3600   1.6401   1.5654
 N41  H122  H  HCH2  0   0.212   3.4274  -0.0985   1.8036
 N41  H131  H  HCH2  0   0.211   5.7139   1.6667   0.8167
 N41  H132  H  HCH2  0   0.229   5.5917   0.9237   2.4003
 N41  H141  H  HCH2  0   0.227   7.0884  -0.3882   0.8835
 N41  H142  H  HCH2  0   0.208   5.6991  -1.3320   1.3903
 N41  H151  H  HCH2  0   0.210   6.0025   0.1193  -1.2785
 N41  H152  H  HCH2  0   0.228   6.0594  -1.6164  -1.0387
 N41  H161  H  HCH2  0   0.208   3.7036  -1.6341  -0.2922
 N41  H162  H  HCH2  0   0.234   3.8367  -0.8958  -1.8788
 N41  H19   H  HCR6  0   0.253  -0.6571  -0.0198   3.5715
 N41  H21   H  HCR6  0   0.261  -4.9330  -0.3489   3.5650
 N41  H22   H  HCR6  0   0.272  -4.9213  -0.2812   1.1301
 N41  H251  H  HNH2  0   0.403  -1.7302  -0.6150   6.9111
 N41  H252  H  HNH2  0   0.411  -0.9079  -0.8938   5.4350
 N41  H9    H  HNR5  0   0.426  -2.5197  -0.0407  -5.4466
 N41  H2    H  HNH1  0   0.411  -3.8276  -0.1709  -0.7835
 N41  H18   H  HCR6  0   0.308  -0.6441   0.0569   1.1607
 N41  H8    H  HCR5  0   0.290  -0.2546   0.1870  -6.5320
 N41  C23   C  C     0   0.486  -2.8656  -0.2557   5.2590

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
 N41  C2   N1    aromatic  1.336  0.020  1.336
 N41  C2   N3    aromatic  1.328  0.020  1.328
 N41  C2   N2    single    1.368  0.020  1.368
 N41  C10  C11   single    1.515  0.020  1.515
 N41  C10  O6    single    1.433  0.020  1.433
 N41  C10  H101  single    0.970  0.020  1.090
 N41  C10  H102  single    0.970  0.020  1.090
 N41  C11  C12   single    1.531  0.020  1.531
 N41  C11  C16   single    1.529  0.020  1.529
 N41  C11  H11   single    0.970  0.020  1.090
 N41  C12  C13   single    1.525  0.020  1.525
 N41  C12  H121  single    0.970  0.020  1.090
 N41  C12  H122  single    0.970  0.020  1.090
 N41  C13  C14   single    1.525  0.020  1.525
 N41  C13  H131  single    0.970  0.020  1.090
 N41  C13  H132  single    0.970  0.020  1.090
 N41  C14  C15   single    1.525  0.020  1.525
 N41  C14  H141  single    0.970  0.020  1.090
 N41  C14  H142  single    0.970  0.020  1.090
 N41  C15  C16   single    1.526  0.020  1.526
 N41  C15  H151  single    0.970  0.020  1.090
 N41  C15  H152  single    0.970  0.020  1.090
 N41  C16  H161  single    0.970  0.020  1.090
 N41  C16  H162  single    0.970  0.020  1.090
 N41  C19  C20   aromatic  1.392  0.020  1.392
 N41  C19  C18   aromatic  1.385  0.020  1.385
 N41  C19  H19   single    0.930  0.020  1.080
 N41  C20  C21   aromatic  1.395  0.020  1.395
 N41  C20  C23   single    1.490  0.020  1.490
 N41  C21  C22   aromatic  1.378  0.020  1.378
 N41  C21  H21   single    0.930  0.020  1.080
 N41  C22  C17   aromatic  1.403  0.020  1.403
 N41  C22  H22   single    0.930  0.020  1.080
 N41  N25  C23   single    1.344  0.020  1.344
 N41  N25  H251  single    0.860  0.020  1.020
 N41  N25  H252  single    0.860  0.020  1.020
 N41  N1   C6    aromatic  1.318  0.020  1.318
 N41  C6   O6    single    1.316  0.020  1.316
 N41  C6   C5    aromatic  1.397  0.020  1.397
 N41  C5   N7    aromatic  1.373  0.020  1.373
 N41  C5   C4    aromatic  1.394  0.020  1.394
 N41  N7   C8    aromatic  1.299  0.020  1.299
 N41  N9   C4    aromatic  1.357  0.020  1.357
 N41  N9   C8    aromatic  1.366  0.020  1.366
 N41  N9   H9    single    0.860  0.020  1.020
 N41  C4   N3    aromatic  1.325  0.020  1.325
 N41  N2   C17   single    1.382  0.020  1.382
 N41  N2   H2    single    0.860  0.020  1.020
 N41  C17  C18   aromatic  1.398  0.020  1.398
 N41  C18  H18   single    0.930  0.020  1.080
 N41  C23  O24   double    1.225  0.020  1.225
 N41  C8   H8    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
 N41  N2    C2   N3    114.33  3.000
 N41  N2    C2   N1    118.89  3.000
 N41  N3    C2   N1    126.78  3.000
 N41  H102  C10  H101  107.91  3.000
 N41  H102  C10  O6    109.76  3.000
 N41  H101  C10  O6    109.34  3.000
 N41  H102  C10  C11   110.36  3.000
 N41  H101  C10  C11   110.79  3.000
 N41  O6    C10  C11   108.67  3.000
 N41  H11   C11  C16   108.75  3.000
 N41  H11   C11  C12   107.67  3.000
 N41  C16   C11  C12   110.50  3.000
 N41  H11   C11  C10   108.51  3.000
 N41  C16   C11  C10   112.45  3.000
 N41  C12   C11  C10   108.82  3.000
 N41  H122  C12  H121  106.59  3.000
 N41  H122  C12  C13   109.19  3.000
 N41  H121  C12  C13   110.19  3.000
 N41  H122  C12  C11   109.20  3.000
 N41  H121  C12  C11   109.91  3.000
 N41  C13   C12  C11   111.63  3.000
 N41  H132  C13  H131  106.54  3.000
 N41  H132  C13  C14   110.53  3.000
 N41  H131  C13  C14   109.35  3.000
 N41  H132  C13  C12   109.85  3.000
 N41  H131  C13  C12   109.20  3.000
 N41  C14   C13  C12   111.24  3.000
 N41  H142  C14  H141  106.57  3.000
 N41  H142  C14  C15   109.26  3.000
 N41  H141  C14  C15   110.40  3.000
 N41  H142  C14  C13   109.24  3.000
 N41  H141  C14  C13   110.28  3.000
 N41  C15   C14  C13   110.98  3.000
 N41  H152  C15  H151  106.48  3.000
 N41  H152  C15  C16   109.94  3.000
 N41  H151  C15  C16   109.20  3.000
 N41  H152  C15  C14   110.36  3.000
 N41  H151  C15  C14   109.28  3.000
 N41  C16   C15  C14   111.45  3.000
 N41  H162  C16  H161  106.59  3.000
 N41  H162  C16  C15   109.83  3.000
 N41  H161  C16  C15   109.31  3.000
 N41  H162  C16  C11   110.60  3.000
 N41  H161  C16  C11   108.75  3.000
 N41  C15   C16  C11   111.61  3.000
 N41  H19   C19  C18   117.16  3.000
 N41  H19   C19  C20   120.87  3.000
 N41  C18   C19  C20   121.96  3.000
 N41  C23   C20  C21   118.64  3.000
 N41  C23   C20  C19   123.59  3.000
 N41  C21   C20  C19   117.75  3.000
 N41  H21   C21  C22   119.05  3.000
 N41  H21   C21  C20   119.92  3.000
 N41  C22   C21  C20   121.03  3.000
 N41  H22   C22  C17   119.50  3.000
 N41  H22   C22  C21   119.43  3.000
 N41  C17   C22  C21   121.06  3.000
 N41  H252  N25  H251  116.77  3.000
 N41  H252  N25  C23   122.64  3.000
 N41  H251  N25  C23   119.39  3.000
 N41  C6    N1   C2    119.34  3.000
 N41  C5    C6   O6    119.41  3.000
 N41  C5    C6   N1    119.89  3.000
 N41  O6    C6   N1    120.70  3.000
 N41  C6    O6   C10   118.89  3.000
 N41  C4    C5   N7    110.91  3.000
 N41  C4    C5   C6    114.77  3.000
 N41  N7    C5   C6    134.33  3.000
 N41  C8    N7   C5    104.13  3.000
 N41  H9    N9   C8    126.21  3.000
 N41  H9    N9   C4    126.87  3.000
 N41  C8    N9   C4    106.93  3.000
 N41  N3    C4   N9    128.69  3.000
 N41  N3    C4   C5    126.66  3.000
 N41  N9    C4   C5    104.65  3.000
 N41  C4    N3   C2    112.56  3.000
 N41  H2    N2   C17   115.15  3.000
 N41  H2    N2   C2    112.67  3.000
 N41  C17   N2   C2    132.17  3.000
 N41  C18   C17  N2    125.47  3.000
 N41  C18   C17  C22   118.20  3.000
 N41  N2    C17  C22   116.33  3.000
 N41  H18   C18  C17   120.36  3.000
 N41  H18   C18  C19   119.65  3.000
 N41  C17   C18  C19   119.99  3.000
 N41  H8    C8   N9    121.15  3.000
 N41  H8    C8   N7    125.46  3.000
 N41  N9    C8   N7    113.39  3.000
 N41  O24   C23  N25   122.24  3.000
 N41  O24   C23  C20   121.14  3.000
 N41  N25   C23  C20   116.62  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
 N41  CONST_01  C5    C6   N1   C2      0.00   0.0  0
 N41  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 N41  CONST_03  N9    C4   N3   C2    180.00   0.0  0
 N41  CONST_04  C22   C21  C20  C19     0.00   0.0  0
 N41  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 N41  CONST_06  C17   C18  C19  C20     0.00   0.0  0
 N41  CONST_07  C17   C22  C21  C20     0.00   0.0  0
 N41  CONST_08  C18   C19  C20  C21     0.00   0.0  0
 N41  CONST_09  C18   C17  C22  C21     0.00   0.0  0
 N41  CONST_10  C4    N3   C2   N1      0.00   0.0  0
 N41  CONST_11  N7    C5   C6   N1    180.00   0.0  0
 N41  CONST_12  C4    C5   C6   N1      0.00   0.0  0
 N41  CONST_13  N3    C2   N1   C6      0.00   0.0  0
 N41  CONST_14  C8    N7   C5   C6    180.00   0.0  0
 N41  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 N41  CONST_16  N3    C4   C5   C6      0.00   0.0  0
 N41  CONST_17  N9    C8   N7   C5      0.00   0.0  0
 N41  CONST_18  C8    N9   C4   C5      0.00   0.0  0
 N41  CONST_19  N9    C4   C5   N7      0.00   0.0  0
 N41  CONST_20  N3    C4   C5   N7    180.00   0.0  0
 N41  CONST_21  C4    N9   C8   N7      0.00   0.0  0
 N41  CONST_22  C8    N7   C5   C4      0.00   0.0  0
 N41  CONST_23  C8    N9   C4   N3    180.00   0.0  0
 N41  CONST_24  O6    C6   N1   C2    180.00   0.0  0
 N41  CONST_25  N2    C17  C18  C19   180.00   0.0  0
 N41  CONST_26  N2    C17  C22  C21   180.00   0.0  0
 N41  CONST_27  C23   C20  C21  C22   180.00   0.0  0
 N41  CONST_28  N2    C2   N1   C6    180.00   0.0  0
 N41  CONST_29  N7    C5   C6   O6      0.00   0.0  0
 N41  CONST_30  C4    C5   C6   O6    180.00   0.0  0
 N41  CONST_31  N2    C2   N3   C4    180.00   0.0  0
 N41  CONST_32  C23   C20  C19  C18   180.00   0.0  0
 N41  CONST_33  H21   C21  C20  C19   180.00   0.0  0
 N41  CONST_34  H18   C18  C19  C20   180.00   0.0  0
 N41  CONST_35  H22   C22  C21  C20   180.00   0.0  0
 N41  CONST_36  H19   C19  C20  C21   180.00   0.0  0
 N41  CONST_37  H8    C8   N7   C5    180.00   0.0  0
 N41  CONST_38  H9    N9   C4   C5    180.00   0.0  0
 N41  CONST_39  H251  N25  C23  C20   180.00   0.0  0
 N41  CONST_40  H252  N25  C23  C20     0.00   0.0  0
 N41  Var_01    C14   C13  C12  C11   -55.89  30.0  1
 N41  Var_02    C14   C15  C16  C11    55.46  30.0  1
 N41  Var_03    C15   C14  C13  C12    55.50  30.0  1
 N41  Var_04    C16   C15  C14  C13   -55.34  30.0  1
 N41  Var_05    C22   C17  N2   C2   -179.96  30.0  2
 N41  Var_06    C17   N2   C2   N1     -2.19  30.0  2
 N41  Var_07    N1    C6   O6   C10    -0.87  30.0  1
 N41  Var_08    N25   C23  C20  C19   -18.18  30.0  2
 N41  Var_09    H101  C10  O6   C6    -61.96  30.0  2

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
 N41  chir_01  C11  C10  C12  C16  negativ

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
 N41  plan-1  C19   0.020
 N41  plan-1  C20   0.020
 N41  plan-1  C21   0.020
 N41  plan-1  C22   0.020
 N41  plan-1  N2    0.020
 N41  plan-1  C17   0.020
 N41  plan-1  C18   0.020
 N41  plan-1  H19   0.020
 N41  plan-1  H21   0.020
 N41  plan-1  H22   0.020
 N41  plan-1  H18   0.020
 N41  plan-1  C23   0.020
 N41  plan-2  C2    0.020
 N41  plan-2  N1    0.020
 N41  plan-2  C6    0.020
 N41  plan-2  O6    0.020
 N41  plan-2  C5    0.020
 N41  plan-2  N7    0.020
 N41  plan-2  N9    0.020
 N41  plan-2  C4    0.020
 N41  plan-2  N3    0.020
 N41  plan-2  N2    0.020
 N41  plan-2  C8    0.020
 N41  plan-2  H9    0.020
 N41  plan-2  H8    0.020
 N41  plan-3  C20   0.020
 N41  plan-3  N25   0.020
 N41  plan-3  O24   0.020
 N41  plan-3  H251  0.020
 N41  plan-3  H252  0.020
 N41  plan-3  C23   0.020

