# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:30:49 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 8-[(6-iodo-1,3-benzodioxol-5-yl)sulfanyl]-9-{3-[(1-methylethyl)amino]propyl}-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NCCCn1c(Sc2cc3OCOc3cc2I)nc4c(N)ncnc14
#
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
 H71  H71  8-[(6-iodo-1,3-benzodioxol-5-yl)sulfanyl]-9-{3-[(1-methylethyl)amino]propyl}-9H-purin-6-amine  ligand  49  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H71
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
 H71  C96   C  CH3   0  -0.657   7.5636  -3.3170  -0.9622
 H71  C95   C  CH1   0  -0.089   6.7930  -2.5081   0.0728
 H71  C97   C  CH3   0  -0.668   7.7570  -1.7430   0.9812
 H71  N94   N  NH1   0  -0.592   5.8175  -1.6692  -0.6126
 H71  C93   C  CH2   0  -0.256   4.8864  -0.9784   0.2558
 H71  C92   C  CH2   0  -0.454   3.8187  -0.2643  -0.5594
 H71  C91   C  CH2   0  -0.324   2.8192   0.4388   0.3468
 H71  N9    N  NR5   0  -0.517   1.7535   1.0908  -0.3881
 H71  C4    C  CR56  0   0.485   1.6387   2.4250  -0.6516
 H71  N3    N  N     0  -0.457   2.4759   3.4033  -0.3169
 H71  C2    C  CR16  0   0.039   2.0338   4.5831  -0.7174
 H71  N1    N  N     0  -0.473   0.9133   4.8660  -1.3769
 H71  C6    C  CR6   0   0.447   0.0820   3.8710  -1.7074
 H71  N6    N  NH2   0  -0.818  -1.0450   4.1497  -2.3642
 H71  C5    C  CR56  0   0.002   0.4428   2.5624  -1.3386
 H71  N7    N  N     0  -0.425  -0.1615   1.3469  -1.5177
 H71  C8    C  CR5   0   0.278   0.6439   0.5072  -0.9374
 H71  S     S  S2    0   0.079   0.4188  -1.2270  -0.8197
 H71  C1'   C  CR6   0  -0.125  -1.3441  -1.3104  -0.7687
 H71  C6'   C  CR16  0  -0.304  -1.9856  -1.8396  -1.9009
 H71  C5'   C  CR56  0   0.313  -3.3472  -1.9763  -1.8490
 H71  O3'   O  O     0  -0.478  -4.1848  -2.4470  -2.7944
 H71  C'2   C  CH2   0   0.072  -5.4942  -2.4196  -2.2362
 H71  O1'   O  O     0  -0.475  -5.3829  -1.8232  -0.9460
 H71  C4'   C  CR56  0   0.320  -4.0742  -1.5970  -0.7315
 H71  C3'   C  CR16  0  -0.315  -3.4745  -1.0702   0.3854
 H71  C2'   C  CR6   0  -0.196  -2.0809  -0.9423   0.3525
 H71  I     I  I     0   0.100  -1.1524  -0.1503   2.0588
 H71  H961  H  HCH3  0   0.223   8.2626  -4.0030  -0.4821
 H71  H962  H  HCH3  0   0.228   6.8880  -3.9013  -1.5874
 H71  H963  H  HCH3  0   0.215   8.1439  -2.6595  -1.6144
 H71  H95   H  HCH1  0   0.217   6.2210  -3.2064   0.6941
 H71  H971  H  HCH3  0   0.213   8.3772  -1.0602   0.3944
 H71  H972  H  HCH3  0   0.230   7.2330  -1.1545   1.7357
 H71  H973  H  HCH3  0   0.225   8.4239  -2.4273   1.5078
 H71  HN94  H  HNH1  0   0.332   6.3114  -0.9880  -1.1808
 H71  H931  H  HCH2  0   0.220   4.4064  -1.7220   0.9005
 H71  H932  H  HCH2  0   0.198   5.3659  -0.2538   0.9314
 H71  H921  H  HCH2  0   0.242   4.2842   0.4702  -1.2231
 H71  H922  H  HCH2  0   0.233   3.3096  -0.9921  -1.1980
 H71  H911  H  HCH2  0   0.268   2.3626  -0.2665   1.0446
 H71  H912  H  HCH2  0   0.279   3.3129   1.2057   0.9433
 H71  H2    H  HCR6  0   0.251   2.6619   5.4349  -0.4796
 H71  HN61  H  HNH2  0   0.411  -1.6845   3.4227  -2.6323
 H71  HN62  H  HNH2  0   0.403  -1.2731   5.0989  -2.6036
 H71  H6'   H  HCR6  0   0.299  -1.4175  -2.1225  -2.7763
 H71  H'21  H  HCH2  0   0.250  -6.1519  -1.8173  -2.8643
 H71  H'22  H  HCH2  0   0.247  -5.8781  -3.4378  -2.1395
 H71  H3'   H  HCR6  0   0.302  -4.0565  -0.7776   1.2480

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
 H71  C96  C95   single    1.523  0.020  1.523
 H71  C96  H961  single    0.970  0.020  1.090
 H71  C96  H962  single    0.970  0.020  1.090
 H71  C96  H963  single    0.970  0.020  1.090
 H71  C95  C97   single    1.530  0.020  1.530
 H71  C95  N94   single    1.458  0.020  1.458
 H71  C95  H95   single    0.970  0.020  1.090
 H71  C97  H971  single    0.970  0.020  1.090
 H71  C97  H972  single    0.970  0.020  1.090
 H71  C97  H973  single    0.970  0.020  1.090
 H71  N94  C93   single    1.449  0.020  1.449
 H71  N94  HN94  single    0.890  0.020  1.040
 H71  C93  C92   single    1.521  0.020  1.521
 H71  C93  H931  single    0.970  0.020  1.090
 H71  C93  H932  single    0.970  0.020  1.090
 H71  C92  C91   single    1.521  0.020  1.521
 H71  C92  H921  single    0.970  0.020  1.090
 H71  C92  H922  single    0.970  0.020  1.090
 H71  C91  N9    single    1.450  0.020  1.450
 H71  C91  H911  single    0.970  0.020  1.090
 H71  C91  H912  single    0.970  0.020  1.090
 H71  N9   C4    aromatic  1.365  0.020  1.365
 H71  N9   C8    aromatic  1.369  0.020  1.369
 H71  C4   N3    aromatic  1.330  0.020  1.330
 H71  C4   C5    aromatic  1.386  0.020  1.386
 H71  N3   C2    aromatic  1.322  0.020  1.322
 H71  C2   N1    aromatic  1.331  0.020  1.331
 H71  C2   H2    single    0.930  0.020  1.080
 H71  N1   C6    aromatic  1.338  0.020  1.338
 H71  C6   N6    single    1.334  0.020  1.334
 H71  C6   C5    aromatic  1.407  0.020  1.407
 H71  N6   HN61  single    0.860  0.020  1.020
 H71  N6   HN62  single    0.860  0.020  1.020
 H71  C5   N7    aromatic  1.369  0.020  1.369
 H71  N7   C8    aromatic  1.300  0.020  1.300
 H71  C8   S     single    1.753  0.020  1.753
 H71  S    C1'   single    1.766  0.020  1.766
 H71  C1'  C6'   aromatic  1.405  0.020  1.405
 H71  C1'  C2'   aromatic  1.391  0.020  1.391
 H71  C6'  C5'   aromatic  1.369  0.020  1.369
 H71  C6'  H6'   single    0.930  0.020  1.080
 H71  C5'  O3'   single    1.348  0.020  1.348
 H71  C5'  C4'   aromatic  1.386  0.020  1.386
 H71  O3'  C'2   single    1.424  0.020  1.424
 H71  C'2  O1'   single    1.426  0.020  1.426
 H71  C'2  H'21  single    0.970  0.020  1.090
 H71  C'2  H'22  single    0.970  0.020  1.090
 H71  O1'  C4'   single    1.345  0.020  1.345
 H71  C4'  C3'   aromatic  1.373  0.020  1.373
 H71  C3'  C2'   aromatic  1.400  0.020  1.400
 H71  C3'  H3'   single    0.930  0.020  1.080
 H71  C2'  I     single    2.098  0.020  2.098

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
 H71  H963  C96  H962  108.01  3.000
 H71  H963  C96  H961  107.51  3.000
 H71  H962  C96  H961  108.21  3.000
 H71  H963  C96  C95   110.77  3.000
 H71  H962  C96  C95   111.15  3.000
 H71  H961  C96  C95   111.05  3.000
 H71  H95   C95  N94   106.50  3.000
 H71  H95   C95  C97   108.12  3.000
 H71  N94   C95  C97   114.40  3.000
 H71  H95   C95  C96   108.12  3.000
 H71  N94   C95  C96   108.94  3.000
 H71  C97   C95  C96   110.51  3.000
 H71  H973  C97  H972  107.35  3.000
 H71  H973  C97  H971  107.70  3.000
 H71  H972  C97  H971  107.86  3.000
 H71  H973  C97  C95   110.99  3.000
 H71  H972  C97  C95   112.20  3.000
 H71  H971  C97  C95   110.56  3.000
 H71  HN94  N94  C93   109.16  3.000
 H71  HN94  N94  C95   108.89  3.000
 H71  C93   N94  C95   115.00  3.000
 H71  H932  C93  H931  106.06  3.000
 H71  H932  C93  C92   109.01  3.000
 H71  H931  C93  C92   109.07  3.000
 H71  H932  C93  N94   113.69  3.000
 H71  H931  C93  N94   108.11  3.000
 H71  C92   C93  N94   110.72  3.000
 H71  H922  C92  H921  106.89  3.000
 H71  H922  C92  C91   110.46  3.000
 H71  H921  C92  C91   109.31  3.000
 H71  H922  C92  C93   109.10  3.000
 H71  H921  C92  C93   109.97  3.000
 H71  C91   C92  C93   111.03  3.000
 H71  H912  C91  H911  107.11  3.000
 H71  H912  C91  N9    107.10  3.000
 H71  H911  C91  N9    107.88  3.000
 H71  H912  C91  C92   110.71  3.000
 H71  H911  C91  C92   110.90  3.000
 H71  N9    C91  C92   112.89  3.000
 H71  C8    N9   C4    105.74  3.000
 H71  C8    N9   C91   127.43  3.000
 H71  C4    N9   C91   126.83  3.000
 H71  C5    C4   N3    126.50  3.000
 H71  C5    C4   N9    105.37  3.000
 H71  N3    C4   N9    128.12  3.000
 H71  C2    N3   C4    111.69  3.000
 H71  H2    C2   N1    115.42  3.000
 H71  H2    C2   N3    116.15  3.000
 H71  N1    C2   N3    128.43  3.000
 H71  C6    N1   C2    119.18  3.000
 H71  C5    C6   N6    122.69  3.000
 H71  C5    C6   N1    117.89  3.000
 H71  N6    C6   N1    119.42  3.000
 H71  HN62  N6   HN61  118.39  3.000
 H71  HN62  N6   C6    120.41  3.000
 H71  HN61  N6   C6    121.20  3.000
 H71  N7    C5   C6    132.72  3.000
 H71  N7    C5   C4    110.96  3.000
 H71  C6    C5   C4    116.32  3.000
 H71  C8    N7   C5    103.98  3.000
 H71  S     C8   N7    126.12  3.000
 H71  S     C8   N9    119.94  3.000
 H71  N7    C8   N9    113.95  3.000
 H71  C1'   S    C8    100.19  3.000
 H71  C2'   C1'  C6'   120.48  3.000
 H71  C2'   C1'  S     122.66  3.000
 H71  C6'   C1'  S     116.78  3.000
 H71  H6'   C6'  C5'   121.81  3.000
 H71  H6'   C6'  C1'   120.74  3.000
 H71  C5'   C6'  C1'   117.46  3.000
 H71  C4'   C5'  O3'   109.58  3.000
 H71  C4'   C5'  C6'   121.65  3.000
 H71  O3'   C5'  C6'   128.76  3.000
 H71  C'2   O3'  C5'   106.85  3.000
 H71  H'22  C'2  H'21  110.71  3.000
 H71  H'22  C'2  O1'   109.71  3.000
 H71  H'21  C'2  O1'   109.71  3.000
 H71  H'22  C'2  O3'   109.88  3.000
 H71  H'21  C'2  O3'   109.84  3.000
 H71  O1'   C'2  O3'   106.92  3.000
 H71  C4'   O1'  C'2   106.89  3.000
 H71  C3'   C4'  O1'   128.26  3.000
 H71  C3'   C4'  C5'   122.13  3.000
 H71  O1'   C4'  C5'   109.61  3.000
 H71  H3'   C3'  C2'   122.01  3.000
 H71  H3'   C3'  C4'   121.19  3.000
 H71  C2'   C3'  C4'   116.79  3.000
 H71  I     C2'  C3'   117.13  3.000
 H71  I     C2'  C1'   121.40  3.000
 H71  C3'   C2'  C1'   121.47  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
 H71  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 H71  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 H71  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 H71  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 H71  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 H71  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 H71  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 H71  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 H71  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 H71  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 H71  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 H71  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 H71  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 H71  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 H71  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 H71  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 H71  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 H71  CONST_18  C4'   C5'  C6'  C1'     0.00   0.0  0
 H71  CONST_19  C4'   C3'  C2'  C1'     0.00   0.0  0
 H71  CONST_20  C3'   C2'  C1'  C6'     0.00   0.0  0
 H71  CONST_21  C3'   C4'  C5'  C6'     0.00   0.0  0
 H71  CONST_22  C2'   C1'  C6'  C5'     0.00   0.0  0
 H71  CONST_23  C2'   C3'  C4'  C5'     0.00   0.0  0
 H71  CONST_24  N3    C4   N9   C91     0.00   0.0  0
 H71  CONST_25  C5    C4   N9   C91   180.00   0.0  0
 H71  CONST_26  N7    C8   N9   C91   180.00   0.0  0
 H71  CONST_27  S     C8   N9   C4    180.00   0.0  0
 H71  CONST_28  N6    C6   C5   C4    180.00   0.0  0
 H71  CONST_29  N6    C6   N1   C2    180.00   0.0  0
 H71  CONST_30  N7    C5   C6   N6      0.00   0.0  0
 H71  CONST_31  S     C8   N7   C5    180.00   0.0  0
 H71  CONST_32  C5'   C6'  C1'  S     180.00   0.0  0
 H71  CONST_33  C3'   C2'  C1'  S     180.00   0.0  0
 H71  CONST_34  I     C2'  C1'  C6'   180.00   0.0  0
 H71  CONST_35  I     C2'  C3'  C4'   180.00   0.0  0
 H71  CONST_36  H2    C2   N3   C4    180.00   0.0  0
 H71  CONST_37  H3'   C3'  C2'  C1'   180.00   0.0  0
 H71  CONST_38  H6'   C6'  C5'  O3'     0.00   0.0  0
 H71  CONST_39  HN61  N6   C6   N1    180.00   0.0  0
 H71  CONST_40  HN62  N6   C6   N1      0.00   0.0  0
 H71  Var_01    O1'   C'2  O3'  C5'     3.80  30.0  1
 H71  Var_02    C4'   C5'  O3'  C'2    -2.50  30.0  1
 H71  Var_03    C3'   C4'  O1'  C'2  -178.11  30.0  1
 H71  Var_04    C6'   C1'  S    C8    109.79  30.0  2
 H71  Var_05    C4    N9   C91  C92  -102.45  30.0  2
 H71  Var_06    N9    C91  C92  C93  -177.79  30.0  3
 H71  Var_07    C93   N94  C95  C96   171.95  30.0  3
 H71  Var_08    C92   C93  N94  C95  -173.46  30.0  3
 H71  Var_09    C91   C92  C93  N94   178.77  30.0  3
 H71  Var_10    H971  C97  C95  C96    59.65  30.0  3
 H71  Var_11    H961  C96  C95  C97    56.96  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
 H71  plan-1  C91   0.020
 H71  plan-1  N9    0.020
 H71  plan-1  C4    0.020
 H71  plan-1  N3    0.020
 H71  plan-1  C2    0.020
 H71  plan-1  N1    0.020
 H71  plan-1  C6    0.020
 H71  plan-1  N6    0.020
 H71  plan-1  C5    0.020
 H71  plan-1  N7    0.020
 H71  plan-1  C8    0.020
 H71  plan-1  S     0.020
 H71  plan-1  H2    0.020
 H71  plan-2  S     0.020
 H71  plan-2  C1'   0.020
 H71  plan-2  C6'   0.020
 H71  plan-2  C5'   0.020
 H71  plan-2  O3'   0.020
 H71  plan-2  O1'   0.020
 H71  plan-2  C4'   0.020
 H71  plan-2  C3'   0.020
 H71  plan-2  C2'   0.020
 H71  plan-2  I     0.020
 H71  plan-2  H6'   0.020
 H71  plan-2  H3'   0.020
 H71  plan-3  C6    0.020
 H71  plan-3  N6    0.020
 H71  plan-3  HN61  0.020
 H71  plan-3  HN62  0.020

