# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 06:07:43 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 9-[(2~{S})-oxan-2-yl]purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3CCCCO3
#
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
 KF5  KF5  9-[(2~{S})-oxan-2-yl]purin-6-amine  ligand  29  16  .  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_KF5
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
 KF5  C2   C  CR16  0   0.045   2.3760   1.6636  -1.1203
 KF5  C4   C  CR56  0   0.485   0.9309   0.3191  -0.1594
 KF5  C5   C  CR56  0  -0.009   1.9236  -0.5632   0.2348
 KF5  C6   C  CR6   0   0.458   3.2408  -0.2203  -0.1222
 KF5  C8   C  CR15  0   0.113   0.1116  -1.3842   0.9389
 KF5  CAK  C  CH1   0   0.212  -1.5614   0.2983   0.0949
 KF5  CAM  C  CH2   0  -0.192  -3.4599  -0.0785  -1.2304
 KF5  CAN  C  CH2   0  -0.456  -4.3969   0.0055  -0.0390
 KF5  CAO  C  CH2   0  -0.457  -3.7796   0.8807   1.0461
 KF5  CAP  C  CH2   0  -0.478  -2.3728   0.3920   1.3786
 KF5  N1   N  N     0  -0.474   3.4292   0.9133  -0.8073
 KF5  N3   N  N     0  -0.458   1.1022   1.4493  -0.8410
 KF5  N6   N  NH2   0  -0.817   4.2929  -0.9804   0.1858
 KF5  N7   N  N     0  -0.451   1.3886  -1.6247   0.9194
 KF5  N9   N  NR5   0  -0.545  -0.2337  -0.2179   0.3113
 KF5  OAL  O  O2    0  -0.483  -2.1710  -0.5391  -0.8514
 KF5  H1   H  HCR6  0   0.252   2.5974   2.5682  -1.6767
 KF5  H2   H  HCR5  0   0.296  -0.6289  -2.0228   1.3964
 KF5  H3   H  HCH1  0   0.242  -1.4323   1.3090  -0.3163
 KF5  H4   H  HCH2  0   0.246  -3.8275  -0.7778  -1.9817
 KF5  H5   H  HCH2  0   0.208  -3.3764   0.9090  -1.7060
 KF5  H6   H  HCH2  0   0.243  -5.3559   0.4119  -0.3666
 KF5  H7   H  HCH2  0   0.230  -4.5903  -0.9975   0.3518
 KF5  H8   H  HCH2  0   0.229  -3.7300   1.9165   0.6953
 KF5  H9   H  HCH2  0   0.249  -4.3984   0.8829   1.9443
 KF5  H10  H  HCH2  0   0.240  -2.4280  -0.5865   1.8646
 KF5  H11  H  HCH2  0   0.257  -1.8724   1.0729   2.0697
 KF5  H12  H  HNH2  0   0.403   5.2234  -0.6690  -0.0330
 KF5  H13  H  HNH2  0   0.411   4.1878  -1.8061   0.7486

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
 KF5  N6   C6   single    1.334  0.020  1.334
 KF5  C6   N1   aromatic  1.338  0.020  1.338
 KF5  C6   C5   aromatic  1.407  0.020  1.407
 KF5  N1   C2   aromatic  1.330  0.020  1.330
 KF5  N7   C5   aromatic  1.372  0.020  1.372
 KF5  N7   C8   aromatic  1.300  0.020  1.300
 KF5  C5   C4   aromatic  1.385  0.020  1.385
 KF5  C2   N3   aromatic  1.322  0.020  1.322
 KF5  CAP  CAO  single    1.526  0.020  1.526
 KF5  CAP  CAK  single    1.522  0.020  1.522
 KF5  C8   N9   aromatic  1.369  0.020  1.369
 KF5  C4   N3   aromatic  1.331  0.020  1.331
 KF5  C4   N9   aromatic  1.366  0.020  1.366
 KF5  N9   CAK  single    1.441  0.020  1.441
 KF5  CAO  CAN  single    1.525  0.020  1.525
 KF5  CAK  OAL  single    1.403  0.020  1.403
 KF5  CAN  CAM  single    1.518  0.020  1.518
 KF5  OAL  CAM  single    1.420  0.020  1.420
 KF5  C2   H1   single    0.930  0.020  1.080
 KF5  C8   H2   single    0.930  0.020  1.080
 KF5  CAK  H3   single    0.970  0.020  1.090
 KF5  CAM  H4   single    0.970  0.020  1.090
 KF5  CAM  H5   single    0.970  0.020  1.090
 KF5  CAN  H6   single    0.970  0.020  1.090
 KF5  CAN  H7   single    0.970  0.020  1.090
 KF5  CAO  H8   single    0.970  0.020  1.090
 KF5  CAO  H9   single    0.970  0.020  1.090
 KF5  CAP  H10  single    0.970  0.020  1.090
 KF5  CAP  H11  single    0.970  0.020  1.090
 KF5  N6   H12  single    0.860  0.020  1.020
 KF5  N6   H13  single    0.860  0.020  1.020

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
 KF5  H1   C2   N3   116.12  3.000
 KF5  H1   C2   N1   115.43  3.000
 KF5  N3   C2   N1   128.45  3.000
 KF5  N9   C4   N3   128.32  3.000
 KF5  N9   C4   C5   105.22  3.000
 KF5  N3   C4   C5   126.46  3.000
 KF5  N7   C5   C6   132.87  3.000
 KF5  N7   C5   C4   110.81  3.000
 KF5  C6   C5   C4   116.32  3.000
 KF5  N6   C6   N1   119.34  3.000
 KF5  N1   C6   C5   117.91  3.000
 KF5  N6   C6   C5   122.74  3.000
 KF5  H2   C8   N9   121.69  3.000
 KF5  H2   C8   N7   124.81  3.000
 KF5  N9   C8   N7   113.49  3.000
 KF5  H3   CAK  OAL  110.35  3.000
 KF5  H3   CAK  N9   106.11  3.000
 KF5  OAL  CAK  N9   106.73  3.000
 KF5  H3   CAK  CAP  108.77  3.000
 KF5  OAL  CAK  CAP  111.97  3.000
 KF5  N9   CAK  CAP  112.75  3.000
 KF5  H5   CAM  H4   107.67  3.000
 KF5  H5   CAM  OAL  109.75  3.000
 KF5  H4   CAM  OAL  106.37  3.000
 KF5  H5   CAM  CAN  109.67  3.000
 KF5  H4   CAM  CAN  111.60  3.000
 KF5  OAL  CAM  CAN  111.64  3.000
 KF5  H7   CAN  H6   107.06  3.000
 KF5  H7   CAN  CAO  110.10  3.000
 KF5  H6   CAN  CAO  110.82  3.000
 KF5  H7   CAN  CAM  109.81  3.000
 KF5  H6   CAN  CAM  109.11  3.000
 KF5  CAO  CAN  CAM  109.90  3.000
 KF5  H9   CAO  H8   106.72  3.000
 KF5  H9   CAO  CAP  110.14  3.000
 KF5  H8   CAO  CAP  109.34  3.000
 KF5  H9   CAO  CAN  110.95  3.000
 KF5  H8   CAO  CAN  109.47  3.000
 KF5  CAP  CAO  CAN  110.15  3.000
 KF5  H11  CAP  H10  107.45  3.000
 KF5  H11  CAP  CAO  111.14  3.000
 KF5  H10  CAP  CAO  109.68  3.000
 KF5  H11  CAP  CAK  109.15  3.000
 KF5  H10  CAP  CAK  110.29  3.000
 KF5  CAO  CAP  CAK  109.12  3.000
 KF5  C6   N1   C2   119.14  3.000
 KF5  C4   N3   C2   111.72  3.000
 KF5  H13  N6   H12  118.25  3.000
 KF5  H13  N6   C6   121.00  3.000
 KF5  H12  N6   C6   120.22  3.000
 KF5  C8   N7   C5   104.33  3.000
 KF5  CAK  N9   C8   127.34  3.000
 KF5  CAK  N9   C4   126.37  3.000
 KF5  C8   N9   C4   106.14  3.000
 KF5  CAM  OAL  CAK  112.38  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
 KF5  CONST_01  C5   C6   N1   C2     0.00   0.0  0
 KF5  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 KF5  CONST_03  N9   C4   N3   C2   180.00   0.0  0
 KF5  CONST_04  N1   C6   C5   C4     0.00   0.0  0
 KF5  CONST_05  C8   N7   C5   C4     0.00   0.0  0
 KF5  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 KF5  CONST_07  N7   C8   N9   C4     0.00   0.0  0
 KF5  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 KF5  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 KF5  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 KF5  CONST_11  C8   N7   C5   C6   180.00   0.0  0
 KF5  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 KF5  CONST_13  N9   C4   C5   C6   180.00   0.0  0
 KF5  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 KF5  CONST_15  N7   C5   C6   N1   180.00   0.0  0
 KF5  CONST_16  N7   C5   C4   N3   180.00   0.0  0
 KF5  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 KF5  CONST_18  CAK  N9   C4   C5   180.00   0.0  0
 KF5  CONST_19  N7   C8   N9   CAK  180.00   0.0  0
 KF5  CONST_20  N3   C4   N9   CAK    0.00   0.0  0
 KF5  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 KF5  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 KF5  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 KF5  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 KF5  CONST_25  H2   C8   N9   C4   180.00   0.0  0
 KF5  CONST_26  H12  N6   C6   C5   180.00   0.0  0
 KF5  CONST_27  H13  N6   C6   C5     0.00   0.0  0
 KF5  Var_01    CAN  CAO  CAP  CAK   53.09  30.0  1
 KF5  Var_02    CAN  CAM  OAL  CAK  -59.63  30.0  1
 KF5  Var_03    CAP  CAO  CAN  CAM  -52.85  30.0  1
 KF5  Var_04    OAL  CAM  CAN  CAO   55.37  30.0  1

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
 KF5  chir_01  CAK  CAP  N9  OAL  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
 KF5  plan-1  C2   0.020
 KF5  plan-1  C4   0.020
 KF5  plan-1  C5   0.020
 KF5  plan-1  C6   0.020
 KF5  plan-1  C8   0.020
 KF5  plan-1  CAK  0.020
 KF5  plan-1  N1   0.020
 KF5  plan-1  N3   0.020
 KF5  plan-1  N6   0.020
 KF5  plan-1  N7   0.020
 KF5  plan-1  N9   0.020
 KF5  plan-1  H1   0.020
 KF5  plan-1  H2   0.020
 KF5  plan-2  C6   0.020
 KF5  plan-2  N6   0.020
 KF5  plan-2  H12  0.020
 KF5  plan-2  H13  0.020

