# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 18:32:32 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-azanyl-7-[[3,4-bis(fluoranyl)phenyl]methyl]-9~{H}-purin-7-ium-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2c([nH]c[n+]2Cc3ccc(F)c(F)c3)n1
#
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
 IPQ  IPQ  "N7-(3,4-difluorobenzyl) guanine"  ligand  30  20  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IPQ
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
 IPQ  C6    C  CR6   0   0.587  37.4774  -0.0123  -0.0961
 IPQ  C10   C  CR6   0   0.394  36.4103  -5.5786  -4.4101
 IPQ  C11   C  CR6   0   0.414  37.7005  -5.7074  -3.9271
 IPQ  C12   C  CR16  0  -0.438  37.9630  -5.5732  -2.5803
 IPQ  C1    C  CR6   0   0.534  38.2372  -2.0972  -0.7049
 IPQ  C8    C  CR56  0   0.110  37.1708  -2.6542   0.0138
 IPQ  C4    C  CR56  0   0.511  36.3505  -1.7493   0.6671
 IPQ  C2    C  CR15  0   0.267  35.6609  -3.7935   1.1005
 IPQ  C7    C  CR6   0   0.105  36.9195  -5.3116  -1.7007
 IPQ  C5    C  CR16  0  -0.272  35.6236  -5.1908  -2.1903
 IPQ  C9    C  CR16  0  -0.391  35.3659  -5.3191  -3.5466
 IPQ  F2    F  F     0  -0.303  38.6960  -5.9538  -4.7827
 IPQ  N1    N  NH2   0  -0.811  37.6592   1.3028  -0.2096
 IPQ  N4    N  N     0  -0.499  38.3610  -0.7978  -0.7513
 IPQ  N3    N  N     0  -0.478  36.4532  -0.4398   0.6495
 IPQ  N9    N  NR15  0  -0.648  35.4231  -2.5054   1.3384
 IPQ  N7    N  NR5   1  -0.465  36.7056  -3.9243   0.3099
 IPQ  O6    O  OH1   0  -0.574  39.1008  -2.8782  -1.3111
 IPQ  H1    H  HCR6  0   0.296  38.9811  -5.6715  -2.2258
 IPQ  HN22  H  HCR5  0   0.376  35.0787  -4.6122   1.4929
 IPQ  H3    H  HCH2  0   0.321  36.7057  -5.9822   0.3341
 IPQ  H4    H  HCH2  0   0.319  38.2662  -5.2579  -0.0168
 IPQ  H5    H  HCR6  0   0.275  34.7956  -4.9969  -1.5197
 IPQ  H6    H  HCR6  0   0.297  34.3602  -5.2227  -3.9339
 IPQ  HN21  H  HNH2  0   0.411  38.4269   1.6691  -0.7443
 IPQ  H2    H  HNH2  0   0.411  37.0477   1.9451   0.2633
 IPQ  HN9   H  HNR5  0   0.459  34.6716  -2.1549   1.9193
 IPQ  H9    H  HOH1  0   0.495  39.7736  -2.3451  -1.7623
 IPQ  C3    C  CH2   0  -0.402  37.2004  -5.1891  -0.2262
 IPQ  F1    F  F     0  -0.301  36.1898  -5.7102  -5.7197

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
 IPQ  F1   C10   single    1.335  0.020  1.335
 IPQ  F2   C11   single    1.336  0.020  1.336
 IPQ  C10  C11   aromatic  1.384  0.020  1.384
 IPQ  C10  C9    aromatic  1.380  0.020  1.380
 IPQ  C11  C12   aromatic  1.379  0.020  1.379
 IPQ  C9   C5    aromatic  1.387  0.020  1.387
 IPQ  C12  C7    aromatic  1.390  0.020  1.390
 IPQ  C5   C7    aromatic  1.391  0.020  1.391
 IPQ  C7   C3    single    1.506  0.020  1.506
 IPQ  O6   C1    single    1.313  0.020  1.313
 IPQ  N4   C1    aromatic  1.306  0.020  1.306
 IPQ  N4   C6    aromatic  1.352  0.020  1.352
 IPQ  C1   C8    aromatic  1.401  0.020  1.401
 IPQ  N1   C6    single    1.332  0.020  1.332
 IPQ  C3   N7    single    1.460  0.020  1.460
 IPQ  C6   N3    aromatic  1.337  0.020  1.337
 IPQ  C8   N7    aromatic  1.385  0.020  1.385
 IPQ  C8   C4    aromatic  1.385  0.020  1.385
 IPQ  N7   C2    aromatic  1.317  0.020  1.317
 IPQ  N3   C4    aromatic  1.314  0.020  1.314
 IPQ  C4   N9    aromatic  1.372  0.020  1.372
 IPQ  C2   N9    aromatic  1.331  0.020  1.331
 IPQ  C12  H1    single    0.930  0.020  1.080
 IPQ  C2   HN22  single    0.930  0.020  1.080
 IPQ  C3   H3    single    0.970  0.020  1.090
 IPQ  C3   H4    single    0.970  0.020  1.090
 IPQ  C5   H5    single    0.930  0.020  1.080
 IPQ  C9   H6    single    0.930  0.020  1.080
 IPQ  N1   HN21  single    0.860  0.020  1.020
 IPQ  N1   H2    single    0.860  0.020  1.020
 IPQ  N9   HN9   single    0.860  0.020  1.020
 IPQ  O6   H9    single    0.850  0.020  0.980

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
 IPQ  N3    C6   N4    125.82  3.000
 IPQ  N3    C6   N1    117.88  3.000
 IPQ  N4    C6   N1    116.30  3.000
 IPQ  F1    C10  C9    120.51  3.000
 IPQ  C9    C10  C11   120.32  3.000
 IPQ  F1    C10  C11   119.17  3.000
 IPQ  F2    C11  C12   120.12  3.000
 IPQ  C12   C11  C10   120.63  3.000
 IPQ  F2    C11  C10   119.25  3.000
 IPQ  H1    C12  C7    121.06  3.000
 IPQ  H1    C12  C11   119.35  3.000
 IPQ  C7    C12  C11   119.59  3.000
 IPQ  O6    C1   N4    120.87  3.000
 IPQ  N4    C1   C8    119.06  3.000
 IPQ  O6    C1   C8    120.07  3.000
 IPQ  N7    C8   C4    107.42  3.000
 IPQ  C4    C8   C1    115.65  3.000
 IPQ  N7    C8   C1    136.88  3.000
 IPQ  N9    C4   N3    127.50  3.000
 IPQ  N9    C4   C8    105.73  3.000
 IPQ  N3    C4   C8    126.77  3.000
 IPQ  HN22  C2   N7    124.85  3.000
 IPQ  HN22  C2   N9    124.96  3.000
 IPQ  N7    C2   N9    110.19  3.000
 IPQ  C5    C7   C3    120.76  3.000
 IPQ  C3    C7   C12   119.67  3.000
 IPQ  C5    C7   C12   119.56  3.000
 IPQ  H5    C5   C9    118.70  3.000
 IPQ  H5    C5   C7    120.66  3.000
 IPQ  C9    C5   C7    120.64  3.000
 IPQ  H6    C9   C5    120.98  3.000
 IPQ  H6    C9   C10   119.75  3.000
 IPQ  C5    C9   C10   119.27  3.000
 IPQ  H2    N1   HN21  118.84  3.000
 IPQ  H2    N1   C6    120.51  3.000
 IPQ  HN21  N1   C6    120.62  3.000
 IPQ  C1    N4   C6    119.93  3.000
 IPQ  C4    N3   C6    112.71  3.000
 IPQ  HN9   N9   C2    124.75  3.000
 IPQ  HN9   N9   C4    126.28  3.000
 IPQ  C2    N9   C4    108.97  3.000
 IPQ  C3    N7   C2    125.13  3.000
 IPQ  C2    N7   C8    107.69  3.000
 IPQ  C3    N7   C8    127.03  3.000
 IPQ  H9    O6   C1    110.14  3.000
 IPQ  H4    C3   H3    107.43  3.000
 IPQ  H4    C3   N7    108.42  3.000
 IPQ  H3    C3   N7    106.73  3.000
 IPQ  H4    C3   C7    111.46  3.000
 IPQ  H3    C3   C7    111.07  3.000
 IPQ  N7    C3   C7    111.52  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
 IPQ  CONST_01  C8    C1   N4   C6      0.00   0.0  0
 IPQ  CONST_02  C8    C4   N3   C6      0.00   0.0  0
 IPQ  CONST_03  N9    C4   N3   C6    180.00   0.0  0
 IPQ  CONST_04  C7    C12  C11  C10     0.00   0.0  0
 IPQ  CONST_05  C7    C5   C9   C10     0.00   0.0  0
 IPQ  CONST_06  C5    C9   C10  C11     0.00   0.0  0
 IPQ  CONST_07  C5    C7   C12  C11     0.00   0.0  0
 IPQ  CONST_08  C9    C10  C11  C12     0.00   0.0  0
 IPQ  CONST_09  C9    C5   C7   C12     0.00   0.0  0
 IPQ  CONST_10  N3    C6   N4   C1      0.00   0.0  0
 IPQ  CONST_11  C2    N7   C8   C1    180.00   0.0  0
 IPQ  CONST_12  N3    C4   C8   C1      0.00   0.0  0
 IPQ  CONST_13  N9    C4   C8   C1    180.00   0.0  0
 IPQ  CONST_14  N9    C2   N7   C8      0.00   0.0  0
 IPQ  CONST_15  C2    N9   C4   C8      0.00   0.0  0
 IPQ  CONST_16  N4    C1   C8   C4      0.00   0.0  0
 IPQ  CONST_17  C2    N7   C8   C4      0.00   0.0  0
 IPQ  CONST_18  N4    C6   N3   C4      0.00   0.0  0
 IPQ  CONST_19  N7    C2   N9   C4      0.00   0.0  0
 IPQ  CONST_20  N3    C4   N9   C2    180.00   0.0  0
 IPQ  CONST_21  N7    C8   C1   N4    180.00   0.0  0
 IPQ  CONST_22  N7    C8   C4   N3    180.00   0.0  0
 IPQ  CONST_23  N7    C8   C4   N9      0.00   0.0  0
 IPQ  CONST_24  O6    C1   N4   C6    180.00   0.0  0
 IPQ  CONST_25  C3    C7   C12  C11   180.00   0.0  0
 IPQ  CONST_26  F1    C10  C11  C12   180.00   0.0  0
 IPQ  CONST_27  N1    C6   N4   C1    180.00   0.0  0
 IPQ  CONST_28  C3    N7   C8   C1      0.00   0.0  0
 IPQ  CONST_29  O6    C1   C8   C4    180.00   0.0  0
 IPQ  CONST_30  C3    N7   C8   C4    180.00   0.0  0
 IPQ  CONST_31  N1    C6   N3   C4    180.00   0.0  0
 IPQ  CONST_32  C9    C5   C7   C3    180.00   0.0  0
 IPQ  CONST_33  N9    C2   N7   C3    180.00   0.0  0
 IPQ  CONST_34  F2    C11  C12  C7    180.00   0.0  0
 IPQ  CONST_35  F1    C10  C9   C5    180.00   0.0  0
 IPQ  CONST_36  F2    C11  C10  C9    180.00   0.0  0
 IPQ  CONST_37  O6    C1   C8   N7      0.00   0.0  0
 IPQ  CONST_38  H1    C12  C11  C10   180.00   0.0  0
 IPQ  CONST_39  H5    C5   C9   C10   180.00   0.0  0
 IPQ  CONST_40  H6    C9   C10  C11   180.00   0.0  0
 IPQ  CONST_41  H5    C5   C7   C12   180.00   0.0  0
 IPQ  CONST_42  HN22  C2   N7   C8    180.00   0.0  0
 IPQ  CONST_43  HN9   N9   C4   C8    180.00   0.0  0
 IPQ  CONST_44  HN22  C2   N9   C4    180.00   0.0  0
 IPQ  CONST_45  H6    C9   C5   C7    180.00   0.0  0
 IPQ  CONST_46  H1    C12  C7   C5    180.00   0.0  0
 IPQ  CONST_47  HN9   N9   C4   N3      0.00   0.0  0
 IPQ  CONST_48  HN9   N9   C2   N7    180.00   0.0  0
 IPQ  CONST_49  HN21  N1   C6   N4      0.00   0.0  0
 IPQ  CONST_50  H2    N1   C6   N4    180.00   0.0  0
 IPQ  CONST_51  HN21  N1   C6   N3    180.00   0.0  0
 IPQ  CONST_52  H2    N1   C6   N3      0.00   0.0  0
 IPQ  Var_01    N7    C3   C7   C12   125.41  30.0  2
 IPQ  Var_02    C7    C3   N7   C8    -66.77  30.0  1
 IPQ  Var_03    C7    C3   N7   C2    108.14  30.0  1
 IPQ  Var_04    N7    C3   C7   C5    -55.80  30.0  2
 IPQ  Var_05    H3    C3   C7   C12  -115.68  30.0  2
 IPQ  Var_06    H4    C3   C7   C12     4.09  30.0  2
 IPQ  Var_07    H3    C3   N7   C8    171.76  30.0  1
 IPQ  Var_08    H4    C3   N7   C8     56.31  30.0  1
 IPQ  Var_09    H3    C3   N7   C2    -13.33  30.0  1
 IPQ  Var_10    H4    C3   N7   C2   -128.78  30.0  1
 IPQ  Var_11    H3    C3   C7   C5     63.11  30.0  2
 IPQ  Var_12    H4    C3   C7   C5   -177.12  30.0  2

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
 IPQ  plan-1  C10   0.020
 IPQ  plan-1  C11   0.020
 IPQ  plan-1  C12   0.020
 IPQ  plan-1  C7    0.020
 IPQ  plan-1  C5    0.020
 IPQ  plan-1  C9    0.020
 IPQ  plan-1  F2    0.020
 IPQ  plan-1  H1    0.020
 IPQ  plan-1  H5    0.020
 IPQ  plan-1  H6    0.020
 IPQ  plan-1  C3    0.020
 IPQ  plan-1  F1    0.020
 IPQ  plan-2  C6    0.020
 IPQ  plan-2  C1    0.020
 IPQ  plan-2  C8    0.020
 IPQ  plan-2  C4    0.020
 IPQ  plan-2  C2    0.020
 IPQ  plan-2  N1    0.020
 IPQ  plan-2  N4    0.020
 IPQ  plan-2  N3    0.020
 IPQ  plan-2  N9    0.020
 IPQ  plan-2  N7    0.020
 IPQ  plan-2  O6    0.020
 IPQ  plan-2  HN22  0.020
 IPQ  plan-2  HN9   0.020
 IPQ  plan-2  C3    0.020
 IPQ  plan-3  C6    0.020
 IPQ  plan-3  N1    0.020
 IPQ  plan-3  HN21  0.020
 IPQ  plan-3  H2    0.020

