# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:39:42 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2S,3S)-N-[(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-3-methyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](N)C(=O)N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n2cnc3c(N)ncnc23
#
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
 SO8  SO8  (2S,3S)-N-[(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-3-methyl-pentanamide  ligand  52  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SO8
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
 SO8  C     C  C     0   0.548   2.1689   0.0568   0.7954
 SO8  N     N  NH2   0  -0.775   3.0566   2.1151   1.8095
 SO8  O     O  O     0  -0.497   2.5576  -0.7321   1.6468
 SO8  N1    N  N     0  -0.476  -2.8748   3.2832  -0.2624
 SO8  C2    C  CR16  0   0.055  -1.7049   2.8754  -0.7442
 SO8  N3    N  N     0  -0.482  -1.2581   1.6370  -0.8689
 SO8  C4    C  CR56  0   0.502  -2.1527   0.7476  -0.4376
 SO8  C5    C  CR56  0   0.001  -3.4029   1.0170   0.0933
 SO8  C6    C  CR6   0   0.462  -3.7596   2.3769   0.1717
 SO8  N6    N  NH2   0  -0.815  -4.9283   2.7889   0.6609
 SO8  N7    N  N     0  -0.453  -4.0411  -0.1447   0.4410
 SO8  C8    C  CR15  0   0.106  -3.1978  -1.0871   0.1298
 SO8  N9    N  NR5   0  -0.538  -2.0364  -0.6084  -0.4116
 SO8  CA    C  CH1   0  -0.202   2.8724   1.3939   0.5639
 SO8  CB    C  CH1   0  -0.217   4.2208   1.1687  -0.1443
 SO8  NAI   N  NH1   0  -0.661   1.1019  -0.1842   0.0180
 SO8  CAJ   C  CR15  0  -0.137   0.2665  -1.3411   0.1802
 SO8  CAK   C  CR15  0   0.008   0.9102  -2.7066  -0.0655
 SO8  OAL   O  OH1   0  -0.659   1.7547  -2.6030  -1.1774
 SO8  CAM   C  CR15  0  -0.056  -0.3367  -3.5460  -0.3556
 SO8  CAN   C  CH2   0  -0.164  -0.9886  -4.0747   0.9083
 SO8  OAO   O  OH1   0  -0.665  -2.2059  -4.6861   0.5620
 SO8  OAP   O  O     0  -0.490  -1.2146  -2.6718  -1.0684
 SO8  CAQ   C  CR15  0   0.224  -0.8674  -1.3452  -0.8563
 SO8  CG1   C  CH2   0  -0.413   4.8859   2.5107  -0.4643
 SO8  CG2   C  CH3   0  -0.686   4.0508   0.3283  -1.4074
 SO8  HN    H  HNH2  0   0.352   2.1589   2.3433   2.2182
 SO8  HNA   H  HNH2  0   0.342   3.5294   1.5184   2.4781
 SO8  HN6   H  HNH2  0   0.405  -5.1548   3.7682   0.6814
 SO8  HN6A  H  HNH2  0   0.413  -5.6219   2.1323   0.9726
 SO8  H8    H  HCR5  0   0.294  -3.3698  -2.1450   0.2585
 SO8  HA    H  HCH1  0   0.234   2.2540   2.0191  -0.0921
 SO8  HB    H  HCH1  0   0.216   4.8682   0.6198   0.5526
 SO8  HNAI  H  HNH1  0   0.407   0.7606   0.5576  -0.5794
 SO8  HAJ   H  HCR5  0   0.290  -0.1683  -1.3532   1.1863
 SO8  HAK   H  HCR5  0   0.259   1.4386  -3.0696   0.8212
 SO8  HOAL  H  HOH1  0   0.460   2.2258  -3.4356  -1.2823
 SO8  HAM   H  HCR5  0   0.267  -0.1053  -4.3864  -1.0170
 SO8  HAN   H  HCH2  0   0.222  -0.2887  -4.7834   1.3702
 SO8  HANA  H  HCH2  0   0.206  -1.1408  -3.2645   1.6347
 SO8  HOAO  H  HOH1  0   0.461  -2.6378  -4.9721   1.3719
 SO8  HAQ   H  HCR5  0   0.273  -0.5397  -0.8745  -1.7911
 SO8  HD1   H  HCH3  0   0.228   6.7787   3.3707  -1.0788
 SO8  HD1A  H  HCH3  0   0.216   6.9406   1.9472  -0.0569
 SO8  HD1B  H  HCH3  0   0.218   6.4923   1.7730  -1.7501
 SO8  HG1   H  HCH2  0   0.206   4.3217   2.9981  -1.2675
 SO8  HG1A  H  HCH2  0   0.231   4.8049   3.1618   0.4068
 SO8  HG2   H  HCH3  0   0.234   5.0029   0.2045  -1.9229
 SO8  HG2A  H  HCH3  0   0.245   3.6659  -0.6702  -1.2040
 SO8  HG2B  H  HCH3  0   0.214   3.3608   0.8114  -2.1043
 SO8  CD1   C  CH3   0  -0.670   6.3515   2.3908  -0.8622
 SO8  H2    H  HCR6  0   0.255  -1.0345   3.6613  -1.0741

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
 SO8  C    O     double    1.224  0.020  1.224
 SO8  C    CA    single    1.529  0.020  1.529
 SO8  C    NAI   single    1.342  0.020  1.342
 SO8  N    CA    single    1.451  0.020  1.451
 SO8  N1   C2    aromatic  1.329  0.020  1.329
 SO8  N1   C6    aromatic  1.339  0.020  1.339
 SO8  C2   N3    aromatic  1.322  0.020  1.322
 SO8  N3   C4    aromatic  1.333  0.020  1.333
 SO8  C4   C5    aromatic  1.385  0.020  1.385
 SO8  C4   N9    aromatic  1.361  0.020  1.361
 SO8  C5   C6    aromatic  1.408  0.020  1.408
 SO8  C5   N7    aromatic  1.370  0.020  1.370
 SO8  C6   N6    single    1.332  0.020  1.332
 SO8  N7   C8    aromatic  1.302  0.020  1.302
 SO8  C8   N9    aromatic  1.368  0.020  1.368
 SO8  N9   CAQ   single    1.452  0.020  1.452
 SO8  CA   CB    single    1.540  0.020  1.540
 SO8  CB   CG1   single    1.532  0.020  1.532
 SO8  CB   CG2   single    1.527  0.020  1.527
 SO8  NAI  CAJ   single    1.436  0.020  1.436
 SO8  CAJ  CAK   single    1.529  0.020  1.529
 SO8  CAJ  CAQ   single    1.536  0.020  1.536
 SO8  CAK  OAL   single    1.400  0.020  1.400
 SO8  CAK  CAM   single    1.531  0.020  1.531
 SO8  CAM  CAN   single    1.517  0.020  1.517
 SO8  CAM  OAP   single    1.429  0.020  1.429
 SO8  CAN  OAO   single    1.405  0.020  1.405
 SO8  OAP  CAQ   single    1.388  0.020  1.388
 SO8  CD1  CG1   single    1.523  0.020  1.523
 SO8  N    HN    single    0.890  0.020  1.040
 SO8  N    HNA   single    0.890  0.020  1.040
 SO8  C2   H2    single    0.930  0.020  1.080
 SO8  N6   HN6   single    0.860  0.020  1.020
 SO8  N6   HN6A  single    0.860  0.020  1.020
 SO8  C8   H8    single    0.930  0.020  1.080
 SO8  CA   HA    single    0.970  0.020  1.090
 SO8  CB   HB    single    0.970  0.020  1.090
 SO8  NAI  HNAI  single    0.860  0.020  1.020
 SO8  CAJ  HAJ   single    0.970  0.020  1.090
 SO8  CAK  HAK   single    0.970  0.020  1.090
 SO8  OAL  HOAL  single    0.850  0.020  0.980
 SO8  CAM  HAM   single    0.970  0.020  1.090
 SO8  CAN  HAN   single    0.970  0.020  1.090
 SO8  CAN  HANA  single    0.970  0.020  1.090
 SO8  OAO  HOAO  single    0.850  0.020  0.980
 SO8  CAQ  HAQ   single    0.970  0.020  1.090
 SO8  CD1  HD1   single    0.970  0.020  1.090
 SO8  CD1  HD1A  single    0.970  0.020  1.090
 SO8  CD1  HD1B  single    0.970  0.020  1.090
 SO8  CG1  HG1   single    0.970  0.020  1.090
 SO8  CG1  HG1A  single    0.970  0.020  1.090
 SO8  CG2  HG2   single    0.970  0.020  1.090
 SO8  CG2  HG2A  single    0.970  0.020  1.090
 SO8  CG2  HG2B  single    0.970  0.020  1.090

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
 SO8  NAI   C    CA    115.81  3.000
 SO8  NAI   C    O     122.66  3.000
 SO8  CA    C    O     121.53  3.000
 SO8  HNA   N    HN    106.27  3.000
 SO8  HNA   N    CA    109.45  3.000
 SO8  HN    N    CA    110.25  3.000
 SO8  C6    N1   C2    119.44  3.000
 SO8  H2    C2   N3    116.18  3.000
 SO8  H2    C2   N1    115.59  3.000
 SO8  N3    C2   N1    128.23  3.000
 SO8  C4    N3   C2    111.56  3.000
 SO8  N9    C4   C5    105.29  3.000
 SO8  N9    C4   N3    127.84  3.000
 SO8  C5    C4   N3    126.87  3.000
 SO8  N7    C5   C6    133.36  3.000
 SO8  N7    C5   C4    110.66  3.000
 SO8  C6    C5   C4    115.98  3.000
 SO8  N6    C6   C5    122.78  3.000
 SO8  N6    C6   N1    119.30  3.000
 SO8  C5    C6   N1    117.92  3.000
 SO8  HN6A  N6   HN6   118.34  3.000
 SO8  HN6A  N6   C6    121.16  3.000
 SO8  HN6   N6   C6    120.43  3.000
 SO8  C8    N7   C5    104.55  3.000
 SO8  H8    C8   N9    121.70  3.000
 SO8  H8    C8   N7    125.27  3.000
 SO8  N9    C8   N7    113.02  3.000
 SO8  CAQ   N9   C8    128.86  3.000
 SO8  CAQ   N9   C4    124.65  3.000
 SO8  C8    N9   C4    106.48  3.000
 SO8  HA    CA   CB    107.58  3.000
 SO8  HA    CA   N     107.56  3.000
 SO8  CB    CA   N     110.88  3.000
 SO8  HA    CA   C     109.24  3.000
 SO8  CB    CA   C     110.17  3.000
 SO8  N     CA   C     111.30  3.000
 SO8  HB    CB   CG2   108.39  3.000
 SO8  HB    CB   CG1   108.34  3.000
 SO8  CG2   CB   CG1   110.97  3.000
 SO8  HB    CB   CA    107.31  3.000
 SO8  CG2   CB   CA    111.32  3.000
 SO8  CG1   CB   CA    110.38  3.000
 SO8  HNAI  NAI  CAJ   117.46  3.000
 SO8  HNAI  NAI  C     118.59  3.000
 SO8  CAJ   NAI  C     122.80  3.000
 SO8  HAJ   CAJ  CAQ   109.06  3.000
 SO8  HAJ   CAJ  CAK   107.73  3.000
 SO8  CAQ   CAJ  CAK   101.53  3.000
 SO8  HAJ   CAJ  NAI   110.07  3.000
 SO8  CAQ   CAJ  NAI   110.81  3.000
 SO8  CAK   CAJ  NAI   117.14  3.000
 SO8  HAK   CAK  CAM   111.41  3.000
 SO8  HAK   CAK  OAL   112.14  3.000
 SO8  CAM   CAK  OAL   112.42  3.000
 SO8  HAK   CAK  CAJ   111.67  3.000
 SO8  CAM   CAK  CAJ   100.20  3.000
 SO8  OAL   CAK  CAJ   108.39  3.000
 SO8  HOAL  OAL  CAK   108.54  3.000
 SO8  HAM   CAM  OAP   107.35  3.000
 SO8  HAM   CAM  CAN   109.07  3.000
 SO8  OAP   CAM  CAN   111.39  3.000
 SO8  HAM   CAM  CAK   111.31  3.000
 SO8  OAP   CAM  CAK   105.03  3.000
 SO8  CAN   CAM  CAK   112.53  3.000
 SO8  HANA  CAN  HAN   106.63  3.000
 SO8  HANA  CAN  OAO   111.32  3.000
 SO8  HAN   CAN  OAO   112.02  3.000
 SO8  HANA  CAN  CAM   110.69  3.000
 SO8  HAN   CAN  CAM   107.55  3.000
 SO8  OAO   CAN  CAM   108.57  3.000
 SO8  HOAO  OAO  CAN   108.12  3.000
 SO8  CAQ   OAP  CAM   110.78  3.000
 SO8  HAQ   CAQ  OAP   110.78  3.000
 SO8  HAQ   CAQ  CAJ   110.70  3.000
 SO8  OAP   CAQ  CAJ   106.88  3.000
 SO8  HAQ   CAQ  N9    106.49  3.000
 SO8  OAP   CAQ  N9    109.30  3.000
 SO8  CAJ   CAQ  N9    112.73  3.000
 SO8  HG1A  CG1  HG1   106.35  3.000
 SO8  HG1A  CG1  CD1   109.09  3.000
 SO8  HG1   CG1  CD1   109.80  3.000
 SO8  HG1A  CG1  CB    108.91  3.000
 SO8  HG1   CG1  CB    108.62  3.000
 SO8  CD1   CG1  CB    113.79  3.000
 SO8  HG2B  CG2  HG2A  107.52  3.000
 SO8  HG2B  CG2  HG2   107.46  3.000
 SO8  HG2A  CG2  HG2   107.04  3.000
 SO8  HG2B  CG2  CB    110.76  3.000
 SO8  HG2A  CG2  CB    112.92  3.000
 SO8  HG2   CG2  CB    110.89  3.000
 SO8  HD1B  CD1  HD1A  107.50  3.000
 SO8  HD1B  CD1  HD1   107.26  3.000
 SO8  HD1A  CD1  HD1   107.47  3.000
 SO8  HD1B  CD1  CG1   112.42  3.000
 SO8  HD1A  CD1  CG1   110.99  3.000
 SO8  HD1   CD1  CG1   110.98  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
 SO8  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 SO8  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 SO8  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 SO8  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 SO8  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 SO8  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 SO8  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 SO8  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 SO8  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 SO8  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 SO8  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 SO8  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 SO8  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 SO8  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 SO8  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 SO8  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 SO8  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 SO8  CONST_18  CAQ   N9   C4   N3     0.00   0.0  0
 SO8  CONST_19  CAQ   N9   C4   C5   180.00   0.0  0
 SO8  CONST_20  CAQ   N9   C8   N7   180.00   0.0  0
 SO8  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 SO8  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 SO8  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 SO8  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 SO8  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 SO8  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 SO8  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 SO8  CONST_28  CAJ   NAI  C    O      0.00   0.0  0
 SO8  CONST_29  CAJ   NAI  C    CA   180.00   0.0  0
 SO8  CONST_30  HNAI  NAI  C    O    180.00   0.0  0
 SO8  Var_01    HD1   CD1  CG1  CB  -179.96  30.0  3

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
 SO8  chir_01  CA   C    N    CB   negativ
 SO8  chir_02  CB   CA   CG1  CG2  positiv
 SO8  chir_03  CAJ  NAI  CAK  CAQ  positiv
 SO8  chir_04  CAK  OAL  CAM  CAJ  positiv
 SO8  chir_05  CAM  OAP  CAK  CAN  negativ
 SO8  chir_06  CAQ  OAP  N9   CAJ  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
 SO8  plan-1  N1    0.020
 SO8  plan-1  C2    0.020
 SO8  plan-1  N3    0.020
 SO8  plan-1  C4    0.020
 SO8  plan-1  C5    0.020
 SO8  plan-1  C6    0.020
 SO8  plan-1  N6    0.020
 SO8  plan-1  N7    0.020
 SO8  plan-1  C8    0.020
 SO8  plan-1  N9    0.020
 SO8  plan-1  CAQ   0.020
 SO8  plan-1  H8    0.020
 SO8  plan-1  H2    0.020
 SO8  plan-2  C6    0.020
 SO8  plan-2  N6    0.020
 SO8  plan-2  HN6   0.020
 SO8  plan-2  HN6A  0.020
 SO8  plan-3  C     0.020
 SO8  plan-3  O     0.020
 SO8  plan-3  CA    0.020
 SO8  plan-3  NAI   0.020
 SO8  plan-3  CAJ   0.020
 SO8  plan-3  HNAI  0.020

