# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:35:24 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 8-(2,5-dimethoxybenzyl)-2-fluoro-9-pent-4-yn-1-yl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(Cc2nc3c(N)nc(F)nc3n2CCCC#C)c1
#
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
 PUZ  PUZ  8-(2,5-dimethoxybenzyl)-2-fluoro-9-pent-4-yn-1-yl-9H-purin-6-amine  ligand  47  27  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PUZ
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
 PUZ  C19   C  CSP1  0  -0.557   5.6366  -0.1345  -0.7385
 PUZ  C18   C  CSP   0   0.287   4.5264  -0.5343  -0.5068
 PUZ  C17   C  CH2   0  -0.587   3.1699  -0.9950  -0.2459
 PUZ  C16   C  CH2   0  -0.446   2.1153  -0.0600  -0.8409
 PUZ  C15   C  CH2   0  -0.317   0.7184  -0.6041  -0.5811
 PUZ  N2    N  NR5   0  -0.542  -0.3272   0.3355  -0.9429
 PUZ  C12   C  CR56  0   0.483  -1.0835   0.2458  -2.0690
 PUZ  N4    N  N     0  -0.494  -1.0494  -0.7035  -3.0088
 PUZ  C11   C  CR56  0  -0.006  -1.9143   1.3511  -2.0533
 PUZ  C13   C  CR6   0   0.459  -2.8034   1.4798  -3.1353
 PUZ  N5    N  NH2   0  -0.811  -3.6636   2.4877  -3.2522
 PUZ  N3    N  N     0  -0.505  -2.7759   0.5339  -4.0858
 PUZ  C14   C  CR6   0   0.566  -1.9228  -0.4528  -3.9434
 PUZ  F1    F  F     0  -0.290  -1.9604  -1.3494  -4.9285
 PUZ  N1    N  N     0  -0.468  -1.6763   2.1115  -0.9415
 PUZ  C10   C  CR5   0   0.498  -0.7291   1.4877  -0.3000
 PUZ  C9    C  CH2   0  -0.614  -0.1132   2.0102   0.9572
 PUZ  C1    C  CR6   0   0.021   0.1158   0.9933   2.0424
 PUZ  C2    C  CR6   0   0.359  -0.9509   0.2275   2.5363
 PUZ  O2    O  O2    0  -0.466  -2.1596   0.4858   1.9947
 PUZ  C7    C  CH3   0  -0.433  -3.2571  -0.3104   2.3860
 PUZ  C3    C  CR16  0  -0.367  -0.7067  -0.7302   3.5077
 PUZ  C4    C  CR16  0  -0.378   0.5807  -0.9335   4.0036
 PUZ  C5    C  CR6   0   0.376   1.6374  -0.1713   3.5296
 PUZ  C6    C  CR16  0  -0.395   1.3856   0.7920   2.5501
 PUZ  O5    O  O2    0  -0.477   2.9207  -0.2895   3.9339
 PUZ  C8    C  CH3   0  -0.434   3.2280  -1.2770   4.8947
 PUZ  H19   H  H     0   0.278   6.6298   0.2050  -0.9237
 PUZ  H171  H  HCH2  0   0.272   3.0226  -1.0770   0.8355
 PUZ  H172  H  HCH2  0   0.278   3.0501  -2.0046  -0.6484
 PUZ  H161  H  HCH2  0   0.260   2.2725   0.0467  -1.9159
 PUZ  H162  H  HCH2  0   0.248   2.2331   0.9342  -0.4063
 PUZ  H151  H  HCH2  0   0.274   0.5962  -0.8910   0.4617
 PUZ  H152  H  HCH2  0   0.282   0.5525  -1.5019  -1.1762
 PUZ  H5N1  H  HNH2  0   0.408  -4.2520   2.5664  -4.0638
 PUZ  H5N2  H  HNH2  0   0.415  -3.6896   3.2268  -2.5717
 PUZ  H9C1  H  HCH2  0   0.292  -0.7672   2.8116   1.3069
 PUZ  H9C2  H  HCH2  0   0.289   0.8418   2.4844   0.7141
 PUZ  H7C1  H  HCH3  0   0.259  -4.1125   0.0375   1.8123
 PUZ  H7C2  H  HCH3  0   0.225  -3.0934  -1.3691   2.1663
 PUZ  H7C3  H  HCH3  0   0.225  -3.4824  -0.2037   3.4507
 PUZ  H3    H  HCR6  0   0.282  -1.5052  -1.3426   3.9040
 PUZ  H4    H  HCR6  0   0.281   0.7211  -1.6942   4.7592
 PUZ  H6    H  HCR6  0   0.263   2.2107   1.3831   2.1671
 PUZ  H8C1  H  HCH3  0   0.258   4.2993  -1.2167   5.0715
 PUZ  H8C2  H  HCH3  0   0.225   2.7067  -1.1056   5.8407
 PUZ  H8C3  H  HCH3  0   0.225   2.9871  -2.2830   4.5396

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
 PUZ  C19  C18   triple    1.202  0.020  1.202
 PUZ  C19  H19   single    0.913  0.020  1.066
 PUZ  C18  C17   single    1.456  0.020  1.456
 PUZ  C17  C16   single    1.530  0.020  1.530
 PUZ  C17  H171  single    0.939  0.020  1.096
 PUZ  C17  H172  single    0.939  0.020  1.096
 PUZ  C16  C15   single    1.521  0.020  1.521
 PUZ  C16  H161  single    0.939  0.020  1.096
 PUZ  C16  H162  single    0.939  0.020  1.096
 PUZ  C15  N2    single    1.452  0.020  1.452
 PUZ  C15  H151  single    0.939  0.020  1.096
 PUZ  C15  H152  single    0.939  0.020  1.096
 PUZ  N2   C12   aromatic  1.359  0.020  1.359
 PUZ  N2   C10   aromatic  1.379  0.020  1.379
 PUZ  C12  N4    aromatic  1.336  0.020  1.336
 PUZ  C12  C11   aromatic  1.383  0.020  1.383
 PUZ  N4   C14   aromatic  1.304  0.020  1.304
 PUZ  C11  C13   aromatic  1.406  0.020  1.406
 PUZ  C11  N1    aromatic  1.368  0.020  1.368
 PUZ  C13  N5    single    1.330  0.020  1.330
 PUZ  C13  N3    aromatic  1.341  0.020  1.341
 PUZ  N5   H5N1  single    0.868  0.020  1.013
 PUZ  N5   H5N2  single    0.868  0.020  1.013
 PUZ  N3   C14   aromatic  1.312  0.020  1.312
 PUZ  C14  F1    single    1.333  0.020  1.333
 PUZ  N1   C10   aromatic  1.303  0.020  1.303
 PUZ  C10  C9    single    1.494  0.020  1.494
 PUZ  C9   C1    single    1.505  0.020  1.505
 PUZ  C9   H9C1  single    0.939  0.020  1.096
 PUZ  C9   H9C2  single    0.939  0.020  1.096
 PUZ  C1   C2    aromatic  1.403  0.020  1.403
 PUZ  C1   C6    aromatic  1.382  0.020  1.382
 PUZ  C2   O2    single    1.349  0.020  1.349
 PUZ  C2   C3    aromatic  1.386  0.020  1.386
 PUZ  O2   C7    single    1.411  0.020  1.411
 PUZ  C7   H7C1  single    0.939  0.020  1.096
 PUZ  C7   H7C2  single    0.939  0.020  1.096
 PUZ  C7   H7C3  single    0.939  0.020  1.096
 PUZ  C3   C4    aromatic  1.395  0.020  1.395
 PUZ  C3   H3    single    0.929  0.020  1.085
 PUZ  C4   C5    aromatic  1.387  0.020  1.387
 PUZ  C4   H4    single    0.929  0.020  1.085
 PUZ  C5   C6    aromatic  1.397  0.020  1.397
 PUZ  C5   O5    single    1.351  0.020  1.351
 PUZ  C6   H6    single    0.929  0.020  1.085
 PUZ  O5   C8    single    1.412  0.020  1.412
 PUZ  C8   H8C1  single    0.939  0.020  1.096
 PUZ  C8   H8C2  single    0.939  0.020  1.096
 PUZ  C8   H8C3  single    0.939  0.020  1.096

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
 PUZ  H19   C19  C18   180.00  3.000
 PUZ  C17   C18  C19   180.00  3.000
 PUZ  H172  C17  H171  106.24  3.000
 PUZ  H172  C17  C16   110.22  3.000
 PUZ  H171  C17  C16   109.71  3.000
 PUZ  H172  C17  C18   109.16  3.000
 PUZ  H171  C17  C18   109.03  3.000
 PUZ  C16   C17  C18   112.28  3.000
 PUZ  H162  C16  H161  106.71  3.000
 PUZ  H162  C16  C15   110.91  3.000
 PUZ  H161  C16  C15   109.59  3.000
 PUZ  H162  C16  C17   109.11  3.000
 PUZ  H161  C16  C17   110.09  3.000
 PUZ  C15   C16  C17   110.36  3.000
 PUZ  H152  C15  H151  106.80  3.000
 PUZ  H152  C15  N2    106.70  3.000
 PUZ  H151  C15  N2    109.18  3.000
 PUZ  H152  C15  C16   109.95  3.000
 PUZ  H151  C15  C16   111.16  3.000
 PUZ  N2    C15  C16   112.79  3.000
 PUZ  C10   N2   C12   106.21  3.000
 PUZ  C10   N2   C15   129.38  3.000
 PUZ  C12   N2   C15   124.37  3.000
 PUZ  C11   C12  N4    126.24  3.000
 PUZ  C11   C12  N2    105.79  3.000
 PUZ  N4    C12  N2    127.97  3.000
 PUZ  C14   N4   C12   110.52  3.000
 PUZ  N1    C11  C13   133.19  3.000
 PUZ  N1    C11  C12   110.43  3.000
 PUZ  C13   C11  C12   116.37  3.000
 PUZ  N3    C13  N5    119.04  3.000
 PUZ  N3    C13  C11   117.88  3.000
 PUZ  N5    C13  C11   123.08  3.000
 PUZ  H5N2  N5   H5N1  118.28  3.000
 PUZ  H5N2  N5   C13   120.96  3.000
 PUZ  H5N1  N5   C13   120.57  3.000
 PUZ  C14   N3   C13   117.83  3.000
 PUZ  F1    C14  N3    114.04  3.000
 PUZ  F1    C14  N4    114.80  3.000
 PUZ  N3    C14  N4    131.15  3.000
 PUZ  C10   N1   C11   105.10  3.000
 PUZ  C9    C10  N1    123.12  3.000
 PUZ  C9    C10  N2    124.34  3.000
 PUZ  N1    C10  N2    112.47  3.000
 PUZ  H9C2  C9   H9C1  106.02  3.000
 PUZ  H9C2  C9   C1    108.70  3.000
 PUZ  H9C1  C9   C1    110.86  3.000
 PUZ  H9C2  C9   C10   108.94  3.000
 PUZ  H9C1  C9   C10   106.21  3.000
 PUZ  C1    C9   C10   115.67  3.000
 PUZ  C6    C1   C2    119.32  3.000
 PUZ  C6    C1   C9    120.20  3.000
 PUZ  C2    C1   C9    120.47  3.000
 PUZ  C3    C2   O2    124.85  3.000
 PUZ  C3    C2   C1    119.34  3.000
 PUZ  O2    C2   C1    115.81  3.000
 PUZ  C7    O2   C2    118.51  3.000
 PUZ  H7C3  C7   H7C2  108.72  3.000
 PUZ  H7C3  C7   H7C1  108.69  3.000
 PUZ  H7C2  C7   H7C1  108.76  3.000
 PUZ  H7C3  C7   O2    112.04  3.000
 PUZ  H7C2  C7   O2    111.97  3.000
 PUZ  H7C1  C7   O2    106.56  3.000
 PUZ  H3    C3   C4    117.95  3.000
 PUZ  H3    C3   C2    121.21  3.000
 PUZ  C4    C3   C2    120.84  3.000
 PUZ  H4    C4   C5    121.78  3.000
 PUZ  H4    C4   C3    118.09  3.000
 PUZ  C5    C4   C3    120.12  3.000
 PUZ  O5    C5   C6    116.21  3.000
 PUZ  O5    C5   C4    125.01  3.000
 PUZ  C6    C5   C4    118.78  3.000
 PUZ  H6    C6   C5    119.09  3.000
 PUZ  H6    C6   C1    119.32  3.000
 PUZ  C5    C6   C1    121.58  3.000
 PUZ  C8    O5   C5    118.15  3.000
 PUZ  H8C3  C8   H8C2  108.66  3.000
 PUZ  H8C3  C8   H8C1  108.71  3.000
 PUZ  H8C2  C8   H8C1  108.68  3.000
 PUZ  H8C3  C8   O5    112.00  3.000
 PUZ  H8C2  C8   O5    112.04  3.000
 PUZ  H8C1  C8   O5    106.64  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
 PUZ  CONST_01  C14   N4   C12  N2    180.00   0.0  0
 PUZ  CONST_02  C13   C11  C12  N2    180.00   0.0  0
 PUZ  CONST_03  N1    C11  C12  N2      0.00   0.0  0
 PUZ  CONST_04  C11   N1   C10  N2      0.00   0.0  0
 PUZ  CONST_05  N1    C10  N2   C12     0.00   0.0  0
 PUZ  CONST_06  N3    C14  N4   C12     0.00   0.0  0
 PUZ  CONST_07  N3    C13  C11  C12     0.00   0.0  0
 PUZ  CONST_08  C10   N1   C11  C12     0.00   0.0  0
 PUZ  CONST_09  C10   N2   C12  N4    180.00   0.0  0
 PUZ  CONST_10  C13   C11  C12  N4      0.00   0.0  0
 PUZ  CONST_11  N1    C11  C12  N4    180.00   0.0  0
 PUZ  CONST_12  C13   N3   C14  N4      0.00   0.0  0
 PUZ  CONST_13  C10   N2   C12  C11     0.00   0.0  0
 PUZ  CONST_14  C14   N4   C12  C11     0.00   0.0  0
 PUZ  CONST_15  C14   N3   C13  C11     0.00   0.0  0
 PUZ  CONST_16  C10   N1   C11  C13   180.00   0.0  0
 PUZ  CONST_17  N1    C11  C13  N3    180.00   0.0  0
 PUZ  CONST_18  C4    C3   C2   C1      0.00   0.0  0
 PUZ  CONST_19  C4    C5   C6   C1      0.00   0.0  0
 PUZ  CONST_20  C5    C6   C1   C2      0.00   0.0  0
 PUZ  CONST_21  C5    C4   C3   C2      0.00   0.0  0
 PUZ  CONST_22  C6    C1   C2   C3      0.00   0.0  0
 PUZ  CONST_23  C6    C5   C4   C3      0.00   0.0  0
 PUZ  CONST_24  N4    C12  N2   C15     0.00   0.0  0
 PUZ  CONST_25  C11   C12  N2   C15   180.00   0.0  0
 PUZ  CONST_26  N1    C10  N2   C15   180.00   0.0  0
 PUZ  CONST_27  C9    C10  N2   C12   180.00   0.0  0
 PUZ  CONST_28  F1    C14  N4   C12   180.00   0.0  0
 PUZ  CONST_29  N5    C13  C11  C12   180.00   0.0  0
 PUZ  CONST_30  C9    C10  N1   C11   180.00   0.0  0
 PUZ  CONST_31  F1    C14  N3   C13   180.00   0.0  0
 PUZ  CONST_32  N1    C11  C13  N5      0.00   0.0  0
 PUZ  CONST_33  C14   N3   C13  N5    180.00   0.0  0
 PUZ  CONST_34  C3    C2   C1   C9    180.00   0.0  0
 PUZ  CONST_35  C5    C6   C1   C9    180.00   0.0  0
 PUZ  CONST_36  O5    C5   C6   C1    180.00   0.0  0
 PUZ  CONST_37  C6    C1   C2   O2    180.00   0.0  0
 PUZ  CONST_38  C4    C3   C2   O2    180.00   0.0  0
 PUZ  CONST_39  O5    C5   C4   C3    180.00   0.0  0
 PUZ  CONST_40  H3    C3   C2   C1    180.00   0.0  0
 PUZ  CONST_41  H6    C6   C1   C2    180.00   0.0  0
 PUZ  CONST_42  H4    C4   C3   C2    180.00   0.0  0
 PUZ  CONST_43  H5N1  N5   C13  C11   180.00   0.0  0
 PUZ  CONST_44  H5N2  N5   C13  C11     0.00   0.0  0
 PUZ  Var_01    C1    C9   C10  N2    -45.99  30.0  2
 PUZ  Var_02    C2    C1   C9   C10   -56.59  30.0  2
 PUZ  Var_03    C12   N2   C15  C16   103.24  30.0  2
 PUZ  Var_04    C3    C2   O2   C7     -3.23  30.0  2
 PUZ  Var_05    N2    C15  C16  C17   171.28  30.0  3
 PUZ  Var_06    H7C1  C7   O2   C2   -177.99  30.0  3
 PUZ  Var_07    H8C1  C8   O5   C5    179.29  30.0  3
 PUZ  Var_08    C16   C17  C18  C19    -7.47  30.0  3
 PUZ  Var_09    C15   C16  C17  C18   178.23  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
 PUZ  plan-1  C9    0.020
 PUZ  plan-1  C1    0.020
 PUZ  plan-1  C2    0.020
 PUZ  plan-1  O2    0.020
 PUZ  plan-1  C3    0.020
 PUZ  plan-1  C4    0.020
 PUZ  plan-1  C5    0.020
 PUZ  plan-1  C6    0.020
 PUZ  plan-1  O5    0.020
 PUZ  plan-1  H3    0.020
 PUZ  plan-1  H4    0.020
 PUZ  plan-1  H6    0.020
 PUZ  plan-2  C15   0.020
 PUZ  plan-2  N2    0.020
 PUZ  plan-2  C12   0.020
 PUZ  plan-2  N4    0.020
 PUZ  plan-2  C11   0.020
 PUZ  plan-2  C13   0.020
 PUZ  plan-2  N5    0.020
 PUZ  plan-2  N3    0.020
 PUZ  plan-2  C14   0.020
 PUZ  plan-2  F1    0.020
 PUZ  plan-2  N1    0.020
 PUZ  plan-2  C10   0.020
 PUZ  plan-2  C9    0.020
 PUZ  plan-3  C13   0.020
 PUZ  plan-3  N5    0.020
 PUZ  plan-3  H5N1  0.020
 PUZ  plan-3  H5N2  0.020

