# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 05:12:25 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: 1-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]-3-[(4~{S})-4-azanyl-5-oxidanylidene-pentyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)NCCC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C=O
#
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
 LTE  LTE  1-[3-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]propyl]-3-[(4~{S})-4-azanyl-5-oxidanylidene-pentyl]guanidine  ligand  60  31  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LTE
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
 LTE  C     C  C1    0   0.198   7.0956  42.5248   1.9196
 LTE  O     O  O     0  -0.390   6.0992  41.8505   1.7926
 LTE  CA    C  CH1   0  -0.178   8.1170  42.3499   3.0073
 LTE  CB    C  CH2   0  -0.432   7.6220  43.2359   4.1627
 LTE  N     N  NH2   0  -0.813   9.3951  42.8090   2.5029
 LTE  CG    C  CH2   0  -0.486   8.5802  43.2895   5.3489
 LTE  CD    C  CH2   0  -0.282   7.9648  43.9899   6.5527
 LTE  NE    N  NH1   0  -0.641   7.5675  45.3329   6.2065
 LTE  CZ    C  C     0   0.553   6.6886  46.0642   6.9545
 LTE  NH1   N  N     0  -0.719   6.1345  45.7091   8.0559
 LTE  NH2   N  NH1   0  -0.636   6.3998  47.3080   6.4227
 LTE  C24   C  CH2   0  -0.302   6.1776  47.4735   4.9954
 LTE  C28   C  CH2   0  -0.446   5.0026  46.6666   4.4511
 LTE  C31   C  CH2   0  -0.478   4.8060  46.8675   2.9535
 LTE  C36   C  CH1   0   0.004   3.5864  46.1246   2.4244
 LTE  C38   C  CH1   0   0.211   3.4800  45.5928   0.1531
 LTE  C39   C  CH1   0  -0.027   4.3247  44.5274   0.8522
 LTE  C40   C  CH1   0  -0.031   3.7840  44.6120   2.2789
 LTE  C49   C  CR15  0   0.111   5.2880  46.8958  -1.0177
 LTE  C50   C  CR56  0  -0.013   4.6070  46.8645  -3.0148
 LTE  C51   C  CR56  0   0.492   3.6674  46.1537  -2.2850
 LTE  C53   C  CR16  0   0.045   2.4401  45.7680  -4.0634
 LTE  C55   C  CR6   0   0.460   4.3630  46.9871  -4.3951
 LTE  N47   N  NR5   0  -0.538   4.1230  46.1765  -0.9978
 LTE  N48   N  N     0  -0.449   5.6119  47.3222  -2.2013
 LTE  N52   N  N     0  -0.457   2.5632  45.5834  -2.7605
 LTE  N54   N  N     0  -0.475   3.2562  46.4190  -4.8879
 LTE  N57   N  NH2   0  -0.816   5.1853  47.6375  -5.2188
 LTE  O37   O  O2    0  -0.496   3.2465  46.5864   1.1095
 LTE  O41   O  OH1   0  -0.673   4.1943  43.3115   0.1948
 LTE  O42   O  OH1   0  -0.666   2.5761  43.9008   2.3209
 LTE  H1    H  H     0   0.205   7.2978  43.3819   1.2508
 LTE  HA    H  HCH1  0   0.247   8.1036  41.3038   3.3427
 LTE  HB3   H  HCH2  0   0.232   7.4395  44.2495   3.7927
 LTE  HB2   H  HCH2  0   0.244   6.6583  42.8452   4.5014
 LTE  H2    H  HNH2  0   0.366  10.0823  42.8177   3.2444
 LTE  H3    H  HNH2  0   0.360   9.7481  42.1585   1.8123
 LTE  HG2   H  HCH2  0   0.250   8.8607  42.2781   5.6530
 LTE  HG3   H  HCH2  0   0.239   9.5071  43.8010   5.0740
 LTE  HD2   H  HCH2  0   0.239   8.6742  43.9697   7.3885
 LTE  HD3   H  HCH2  0   0.237   7.0782  43.4362   6.8717
 LTE  HE    H  HNH1  0   0.388   8.2190  45.8515   5.6384
 LTE  HH11  H  H     0   0.328   6.5354  44.8515   8.4167
 LTE  HH21  H  HNH1  0   0.369   5.7027  47.7737   6.9849
 LTE  H30   H  HCH2  0   0.228   7.0872  47.2239   4.4448
 LTE  H29   H  HCH2  0   0.250   6.0106  48.5375   4.8201
 LTE  H32   H  HCH2  0   0.233   4.0905  46.9570   4.9819
 LTE  H33   H  HCH2  0   0.230   5.1700  45.6084   4.6722
 LTE  H35   H  HCH2  0   0.223   5.7104  46.5572   2.4177
 LTE  H34   H  HCH2  0   0.252   4.6754  47.9326   2.7423
 LTE  H61   H  HCH1  0   0.252   2.7364  46.3371   3.0829
 LTE  H62   H  HCH1  0   0.262   2.5451  45.1536  -0.2111
 LTE  H44   H  HCH1  0   0.220   5.3720  44.8682   0.8721
 LTE  H43   H  HCH1  0   0.237   4.5011  44.2297   3.0178
 LTE  H58   H  HCR5  0   0.294   5.8558  47.0845  -0.1187
 LTE  H56   H  HCR6  0   0.252   1.5605  45.3334  -4.5259
 LTE  H59   H  HNH2  0   0.404   4.9608  47.7252  -6.1948
 LTE  H60   H  HNH2  0   0.411   6.0103  48.0967  -4.8757
 LTE  H46   H  HOH1  0   0.461   4.7794  42.6670   0.6232
 LTE  H45   H  HOH1  0   0.457   2.1982  43.9980   3.2006

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
 LTE  N57  C55   single    1.333  0.020  1.333
 LTE  N54  C55   aromatic  1.338  0.020  1.338
 LTE  N54  C53   aromatic  1.330  0.020  1.330
 LTE  C55  C50   aromatic  1.407  0.020  1.407
 LTE  C53  N52   aromatic  1.322  0.020  1.322
 LTE  C50  N48   aromatic  1.372  0.020  1.372
 LTE  C50  C51   aromatic  1.386  0.020  1.386
 LTE  N52  C51   aromatic  1.331  0.020  1.331
 LTE  N48  C49   aromatic  1.299  0.020  1.299
 LTE  C51  N47   aromatic  1.366  0.020  1.366
 LTE  C49  N47   aromatic  1.369  0.020  1.369
 LTE  N47  C38   single    1.442  0.020  1.442
 LTE  O41  C39   single    1.388  0.020  1.388
 LTE  C38  C39   single    1.529  0.020  1.529
 LTE  C38  O37   single    1.399  0.020  1.399
 LTE  C39  C40   single    1.528  0.020  1.528
 LTE  O37  C36   single    1.435  0.020  1.435
 LTE  C40  O42   single    1.402  0.020  1.402
 LTE  C40  C36   single    1.532  0.020  1.532
 LTE  C36  C31   single    1.523  0.020  1.523
 LTE  C31  C28   single    1.524  0.020  1.524
 LTE  C28  C24   single    1.526  0.020  1.526
 LTE  C24  NH2   single    1.454  0.020  1.454
 LTE  N    CA    single    1.449  0.020  1.449
 LTE  C    CA    single    1.502  0.020  1.502
 LTE  C    O     double    1.210  0.020  1.210
 LTE  NH2  CZ    single    1.383  0.020  1.383
 LTE  CA   CB    single    1.538  0.020  1.538
 LTE  CB   CG    single    1.526  0.020  1.526
 LTE  NE   CZ    single    1.366  0.020  1.366
 LTE  NE   CD    single    1.443  0.020  1.443
 LTE  CG   CD    single    1.523  0.020  1.523
 LTE  CZ   NH1   double    1.283  0.020  1.283
 LTE  C    H1    single    0.930  0.020  1.080
 LTE  CA   HA    single    0.970  0.020  1.090
 LTE  CB   HB3   single    0.970  0.020  1.090
 LTE  CB   HB2   single    0.970  0.020  1.090
 LTE  N    H2    single    0.890  0.020  1.040
 LTE  N    H3    single    0.890  0.020  1.040
 LTE  CG   HG2   single    0.970  0.020  1.090
 LTE  CG   HG3   single    0.970  0.020  1.090
 LTE  CD   HD2   single    0.970  0.020  1.090
 LTE  CD   HD3   single    0.970  0.020  1.090
 LTE  NE   HE    single    0.890  0.020  1.040
 LTE  NH1  HH11  single    0.890  0.020  1.040
 LTE  NH2  HH21  single    0.890  0.020  1.040
 LTE  C24  H30   single    0.970  0.020  1.090
 LTE  C24  H29   single    0.970  0.020  1.090
 LTE  C28  H32   single    0.970  0.020  1.090
 LTE  C28  H33   single    0.970  0.020  1.090
 LTE  C31  H35   single    0.970  0.020  1.090
 LTE  C31  H34   single    0.970  0.020  1.090
 LTE  C36  H61   single    0.970  0.020  1.090
 LTE  C38  H62   single    0.970  0.020  1.090
 LTE  C39  H44   single    0.970  0.020  1.090
 LTE  C40  H43   single    0.970  0.020  1.090
 LTE  C49  H58   single    0.930  0.020  1.080
 LTE  C53  H56   single    0.930  0.020  1.080
 LTE  N57  H59   single    0.860  0.020  1.020
 LTE  N57  H60   single    0.860  0.020  1.020
 LTE  O41  H46   single    0.850  0.020  0.980
 LTE  O42  H45   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
 LTE  H1    C    CA   113.81  3.000
 LTE  H1    C    O    121.28  3.000
 LTE  CA    C    O    124.82  3.000
 LTE  HA    CA   N    114.76  3.000
 LTE  HA    CA   CB   108.37  3.000
 LTE  N     CA   CB   111.28  3.000
 LTE  HA    CA   C    108.88  3.000
 LTE  CB    CA   C    104.95  3.000
 LTE  N     CA   C    108.11  3.000
 LTE  HB2   CB   HB3  106.77  3.000
 LTE  HB2   CB   CG   108.98  3.000
 LTE  HB3   CB   CG   109.58  3.000
 LTE  HB2   CB   CA   108.09  3.000
 LTE  HB3   CB   CA   109.46  3.000
 LTE  CG    CB   CA   113.72  3.000
 LTE  H3    N    H2   105.60  3.000
 LTE  H3    N    CA   109.97  3.000
 LTE  H2    N    CA   110.31  3.000
 LTE  HG3   CG   HG2  106.57  3.000
 LTE  HG3   CG   CD   109.04  3.000
 LTE  HG2   CG   CD   108.03  3.000
 LTE  HG3   CG   CB   110.68  3.000
 LTE  HG2   CG   CB   110.18  3.000
 LTE  CD    CG   CB   112.15  3.000
 LTE  HD3   CD   HD2  107.04  3.000
 LTE  HD3   CD   NE   108.56  3.000
 LTE  HD2   CD   NE   112.23  3.000
 LTE  HD3   CD   CG   109.00  3.000
 LTE  HD2   CD   CG   109.43  3.000
 LTE  NE    CD   CG   110.47  3.000
 LTE  HE    NE   CZ   116.67  3.000
 LTE  HE    NE   CD   115.86  3.000
 LTE  CZ    NE   CD   122.96  3.000
 LTE  NH2   CZ   NH1  119.26  3.000
 LTE  NH1   CZ   NE   126.84  3.000
 LTE  NH2   CZ   NE   113.90  3.000
 LTE  HH11  NH1  CZ   111.66  3.000
 LTE  HH21  NH2  C24  112.87  3.000
 LTE  HH21  NH2  CZ   110.18  3.000
 LTE  C24   NH2  CZ   120.77  3.000
 LTE  H29   C24  H30  105.62  3.000
 LTE  H29   C24  C28  109.91  3.000
 LTE  H30   C24  C28  109.92  3.000
 LTE  H29   C24  NH2  106.98  3.000
 LTE  H30   C24  NH2  109.98  3.000
 LTE  C28   C24  NH2  114.06  3.000
 LTE  H33   C28  H32  106.63  3.000
 LTE  H33   C28  C31  110.24  3.000
 LTE  H32   C28  C31  109.52  3.000
 LTE  H33   C28  C24  108.76  3.000
 LTE  H32   C28  C24  109.17  3.000
 LTE  C31   C28  C24  112.35  3.000
 LTE  H34   C31  H35  106.25  3.000
 LTE  H34   C31  C36  108.20  3.000
 LTE  H35   C31  C36  110.66  3.000
 LTE  H34   C31  C28  109.49  3.000
 LTE  H35   C31  C28  109.68  3.000
 LTE  C36   C31  C28  112.36  3.000
 LTE  H61   C36  O37  107.73  3.000
 LTE  H61   C36  C40  110.39  3.000
 LTE  O37   C36  C40  105.15  3.000
 LTE  H61   C36  C31  108.53  3.000
 LTE  C40   C36  C31  114.28  3.000
 LTE  O37   C36  C31  110.56  3.000
 LTE  H62   C38  O37  111.70  3.000
 LTE  H62   C38  N47  106.11  3.000
 LTE  O37   C38  N47  109.43  3.000
 LTE  H62   C38  C39  110.13  3.000
 LTE  O37   C38  C39  105.94  3.000
 LTE  N47   C38  C39  113.62  3.000
 LTE  H44   C39  O41  111.65  3.000
 LTE  H44   C39  C40  107.60  3.000
 LTE  O41   C39  C40  117.22  3.000
 LTE  H44   C39  C38  108.53  3.000
 LTE  C40   C39  C38  101.12  3.000
 LTE  O41   C39  C38  109.99  3.000
 LTE  H43   C40  O42  111.45  3.000
 LTE  H43   C40  C39  112.20  3.000
 LTE  O42   C40  C39  107.74  3.000
 LTE  H43   C40  C36  111.34  3.000
 LTE  O42   C40  C36  112.75  3.000
 LTE  C39   C40  C36  100.89  3.000
 LTE  H58   C49  N48  124.76  3.000
 LTE  H58   C49  N47  121.80  3.000
 LTE  N48   C49  N47  113.44  3.000
 LTE  N48   C50  C55  132.83  3.000
 LTE  N48   C50  C51  110.82  3.000
 LTE  C55   C50  C51  116.34  3.000
 LTE  N52   C51  N47  128.37  3.000
 LTE  N47   C51  C50  105.17  3.000
 LTE  N52   C51  C50  126.46  3.000
 LTE  H56   C53  N54  115.42  3.000
 LTE  H56   C53  N52  116.10  3.000
 LTE  N54   C53  N52  128.48  3.000
 LTE  N57   C55  N54  119.32  3.000
 LTE  N54   C55  C50  117.89  3.000
 LTE  N57   C55  C50  122.79  3.000
 LTE  C51   N47  C49  106.20  3.000
 LTE  C49   N47  C38  127.13  3.000
 LTE  C51   N47  C38  126.65  3.000
 LTE  C50   N48  C49  104.37  3.000
 LTE  C53   N52  C51  111.70  3.000
 LTE  C55   N54  C53  119.14  3.000
 LTE  H60   N57  H59  118.36  3.000
 LTE  H60   N57  C55  121.23  3.000
 LTE  H59   N57  C55  120.31  3.000
 LTE  C38   O37  C36  111.01  3.000
 LTE  H46   O41  C39  108.42  3.000
 LTE  H45   O42  C40  108.32  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
 LTE  CONST_01  C55   C50  N48  C49   180.00   0.0  0
 LTE  CONST_02  C51   C50  N48  C49     0.00   0.0  0
 LTE  CONST_03  C50   C51  N47  C49     0.00   0.0  0
 LTE  CONST_04  N52   C51  N47  C49   180.00   0.0  0
 LTE  CONST_05  C53   N54  C55  C50     0.00   0.0  0
 LTE  CONST_06  N47   C49  N48  C50     0.00   0.0  0
 LTE  CONST_07  C53   N52  C51  C50     0.00   0.0  0
 LTE  CONST_08  N54   C55  C50  C51     0.00   0.0  0
 LTE  CONST_09  N54   C53  N52  C51     0.00   0.0  0
 LTE  CONST_10  N48   C49  N47  C51     0.00   0.0  0
 LTE  CONST_11  N47   C51  N52  C53   180.00   0.0  0
 LTE  CONST_12  N52   C53  N54  C55     0.00   0.0  0
 LTE  CONST_13  N52   C51  C50  C55     0.00   0.0  0
 LTE  CONST_14  N47   C51  C50  C55   180.00   0.0  0
 LTE  CONST_15  N48   C50  C51  N47     0.00   0.0  0
 LTE  CONST_16  N54   C55  C50  N48   180.00   0.0  0
 LTE  CONST_17  N52   C51  C50  N48   180.00   0.0  0
 LTE  CONST_18  C50   C51  N47  C38   180.00   0.0  0
 LTE  CONST_19  N52   C51  N47  C38     0.00   0.0  0
 LTE  CONST_20  N48   C49  N47  C38   180.00   0.0  0
 LTE  CONST_21  N57   C55  C50  C51   180.00   0.0  0
 LTE  CONST_22  N57   C55  N54  C53   180.00   0.0  0
 LTE  CONST_23  N57   C55  C50  N48     0.00   0.0  0
 LTE  CONST_24  H58   C49  N47  C38     0.00   0.0  0
 LTE  CONST_25  H56   C53  N52  C51   180.00   0.0  0
 LTE  CONST_26  H59   N57  C55  C50   180.00   0.0  0
 LTE  CONST_27  H60   N57  C55  C50     0.00   0.0  0
 LTE  CONST_28  NH2   CZ   NE   CD    180.00   0.0  0
 LTE  CONST_29  NH1   CZ   NE   CD      0.00   0.0  0
 LTE  CONST_32  HH21  NH2  CZ   NE    180.00   0.0  0
 LTE  CONST_33  HH11  NH1  CZ   NE      0.00   0.0  0
 LTE  Var_01    C36   C31  C28  C24  -176.77  30.0  1
 LTE  Var_02    CD    CG   CB   CA   -170.96  30.0  3
 LTE  Var_03    NE    CD   CG   CB    -58.09  30.0  3
 LTE  Var_04    CZ    NE   CD   CG    162.27  30.0  1
 LTE  Var_05    C28   C24  NH2  CZ     60.51  30.0  1
 LTE  Var_06    C31   C28  C24  NH2  -179.94  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
 LTE  chir_01  CA   N    C    CB   positiv
 LTE  chir_02  C36  O37  C40  C31  negativ
 LTE  chir_03  C38  O37  N47  C39  negativ
 LTE  chir_04  C39  O41  C38  C40  negativ
 LTE  chir_05  C40  O42  C39  C36  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
 LTE  plan-1  C38   0.020
 LTE  plan-1  C49   0.020
 LTE  plan-1  C50   0.020
 LTE  plan-1  C51   0.020
 LTE  plan-1  C53   0.020
 LTE  plan-1  C55   0.020
 LTE  plan-1  N47   0.020
 LTE  plan-1  N48   0.020
 LTE  plan-1  N52   0.020
 LTE  plan-1  N54   0.020
 LTE  plan-1  N57   0.020
 LTE  plan-1  H58   0.020
 LTE  plan-1  H56   0.020
 LTE  plan-2  C55   0.020
 LTE  plan-2  N57   0.020
 LTE  plan-2  H59   0.020
 LTE  plan-2  H60   0.020
 LTE  plan-3  CD    0.020
 LTE  plan-3  NE    0.020
 LTE  plan-3  CZ    0.020
 LTE  plan-3  NH1   0.020
 LTE  plan-3  NH2   0.020
 LTE  plan-3  C24   0.020
 LTE  plan-3  HE    0.020
 LTE  plan-3  HH11  0.020
 LTE  plan-3  HH21  0.020
 LTE  plan-4  C     0.020
 LTE  plan-4  O     0.020
 LTE  plan-4  CA    0.020
 LTE  plan-4  H1    0.020

