# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:01:21 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-[(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[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
 VRT  VRT  N-[(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-pentanamide  ligand  49  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VRT
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
 VRT  C     C  C     0   0.546  -2.2904   0.2078  -0.9862
 VRT  N     N  NH2   0  -0.775  -3.4541   2.1945  -1.9218
 VRT  O     O  O     0  -0.496  -2.6171  -0.5493  -1.8895
 VRT  N1    N  N     0  -0.476   2.8154   3.2548   0.3879
 VRT  C2    C  CR16  0   0.054   1.5994   2.8990   0.7910
 VRT  N3    N  N     0  -0.480   1.0932   1.6814   0.8895
 VRT  C4    C  CR56  0   0.501   1.9768   0.7522   0.5237
 VRT  C5    C  CR56  0   0.001   3.2703   0.9663   0.0780
 VRT  C6    C  CR6   0   0.462   3.6886   2.3094   0.0187
 VRT  N6    N  NH2   0  -0.815   4.9064   2.6683  -0.3853
 VRT  N7    N  N     0  -0.453   3.8816  -0.2227  -0.2228
 VRT  C8    C  CR15  0   0.106   2.9805  -1.1274   0.0332
 VRT  N9    N  NR5   0  -0.539   1.8063  -0.5981   0.4935
 VRT  CA    C  CH1   0  -0.227  -3.0335   1.5151  -0.7159
 VRT  CB    C  CH2   0  -0.407  -4.2389   1.2025   0.1772
 VRT  CD    C  CH3   0  -0.664  -6.1488   2.1158   1.5615
 VRT  CG    C  CH2   0  -0.419  -4.9518   2.4497   0.6824
 VRT  C1'   C  CH1   0   0.225   0.5824  -1.2854   0.8643
 VRT  N10   N  NH1   0  -0.663  -1.2877  -0.0654  -0.1358
 VRT  C2'   C  CH1   0  -0.136  -0.4782  -1.2456  -0.2459
 VRT  C3'   C  CH1   0   0.006  -1.1878  -2.5854  -0.0416
 VRT  O3'   O  OH1   0  -0.665  -2.1072  -2.4357   1.0033
 VRT  C4'   C  CH1   0  -0.057   0.0023  -3.4684   0.3411
 VRT  O4'   O  O2    0  -0.490   0.8619  -2.6224   1.1081
 VRT  C5'   C  CH2   0  -0.164   0.7193  -4.0300  -0.8734
 VRT  O5'   O  OH1   0  -0.665   1.8887  -4.6791  -0.4418
 VRT  HN    H  HNH2  0   0.351  -2.6473   2.4641  -2.4709
 VRT  HNA   H  HNH2  0   0.341  -3.9870   1.5549  -2.4994
 VRT  HN6   H  HNH2  0   0.405   5.1613   3.6396  -0.4315
 VRT  HN6A  H  HNH2  0   0.413   5.5774   1.9833  -0.6854
 VRT  H8    H  HCR5  0   0.294   3.1169  -2.1921  -0.0811
 VRT  HA    H  HCH1  0   0.239  -2.3718   2.1914  -0.1623
 VRT  HB    H  HCH2  0   0.222  -4.9407   0.5730  -0.3813
 VRT  HBA   H  HCH2  0   0.229  -3.9031   0.6038   1.0299
 VRT  HD    H  HCH3  0   0.217  -6.8882   1.5267   1.0157
 VRT  HDA   H  HCH3  0   0.216  -5.8497   1.5366   2.4372
 VRT  HDB   H  HCH3  0   0.228  -6.6449   3.0195   1.9175
 VRT  HG    H  HCH2  0   0.213  -4.2419   3.0644   1.2444
 VRT  HGA   H  HCH2  0   0.222  -5.2733   3.0526  -0.1688
 VRT  H1'   H  HCH1  0   0.273   0.2132  -0.7934   1.7727
 VRT  HN10  H  HNH1  0   0.408  -0.9729   0.6611   0.4938
 VRT  H2'   H  HCH1  0   0.290   0.0210  -1.2715  -1.2214
 VRT  H3'   H  HCH1  0   0.258  -1.6642  -2.9357  -0.9627
 VRT  HO3'  H  HOH1  0   0.460  -2.5931  -3.2604   1.1032
 VRT  H4'   H  HCH1  0   0.267  -0.3038  -4.2959   0.9887
 VRT  H5'   H  HCH2  0   0.223   0.0271  -4.7180  -1.3763
 VRT  H5'A  H  HCH2  0   0.206   0.9460  -3.2302  -1.5916
 VRT  HO5'  H  HOH1  0   0.461   2.3639  -4.9869  -1.2189
 VRT  H2    H  HCR6  0   0.255   0.9420   3.7144   1.0723

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
 VRT  C    O     double    1.223  0.020  1.223
 VRT  C    CA    single    1.528  0.020  1.528
 VRT  C    N10   single    1.343  0.020  1.343
 VRT  N    CA    single    1.447  0.020  1.447
 VRT  N1   C2    aromatic  1.330  0.020  1.330
 VRT  N1   C6    aromatic  1.339  0.020  1.339
 VRT  C2   N3    aromatic  1.322  0.020  1.322
 VRT  N3   C4    aromatic  1.333  0.020  1.333
 VRT  C4   C5    aromatic  1.385  0.020  1.385
 VRT  C4   N9    aromatic  1.361  0.020  1.361
 VRT  C5   C6    aromatic  1.408  0.020  1.408
 VRT  C5   N7    aromatic  1.370  0.020  1.370
 VRT  C6   N6    single    1.332  0.020  1.332
 VRT  N7   C8    aromatic  1.302  0.020  1.302
 VRT  C8   N9    aromatic  1.368  0.020  1.368
 VRT  N9   C1'   single    1.452  0.020  1.452
 VRT  CA   CB    single    1.532  0.020  1.532
 VRT  CB   CG    single    1.523  0.020  1.523
 VRT  CD   CG    single    1.522  0.020  1.522
 VRT  C1'  C2'   single    1.536  0.020  1.536
 VRT  C1'  O4'   single    1.387  0.020  1.387
 VRT  N10  C2'   single    1.435  0.020  1.435
 VRT  C2'  C3'   single    1.530  0.020  1.530
 VRT  C3'  O3'   single    1.400  0.020  1.400
 VRT  C3'  C4'   single    1.531  0.020  1.531
 VRT  C4'  O4'   single    1.429  0.020  1.429
 VRT  C4'  C5'   single    1.518  0.020  1.518
 VRT  C5'  O5'   single    1.405  0.020  1.405
 VRT  N    HN    single    0.890  0.020  1.040
 VRT  N    HNA   single    0.890  0.020  1.040
 VRT  C2   H2    single    0.930  0.020  1.080
 VRT  N6   HN6   single    0.860  0.020  1.020
 VRT  N6   HN6A  single    0.860  0.020  1.020
 VRT  C8   H8    single    0.930  0.020  1.080
 VRT  CA   HA    single    0.970  0.020  1.090
 VRT  CB   HB    single    0.970  0.020  1.090
 VRT  CB   HBA   single    0.970  0.020  1.090
 VRT  CD   HD    single    0.970  0.020  1.090
 VRT  CD   HDA   single    0.970  0.020  1.090
 VRT  CD   HDB   single    0.970  0.020  1.090
 VRT  CG   HG    single    0.970  0.020  1.090
 VRT  CG   HGA   single    0.970  0.020  1.090
 VRT  C1'  H1'   single    0.970  0.020  1.090
 VRT  N10  HN10  single    0.860  0.020  1.020
 VRT  C2'  H2'   single    0.970  0.020  1.090
 VRT  C3'  H3'   single    0.970  0.020  1.090
 VRT  O3'  HO3'  single    0.850  0.020  0.980
 VRT  C4'  H4'   single    0.970  0.020  1.090
 VRT  C5'  H5'   single    0.970  0.020  1.090
 VRT  C5'  H5'A  single    0.970  0.020  1.090
 VRT  O5'  HO5'  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
 VRT  N10   C    CA   115.16  3.000
 VRT  N10   C    O    122.77  3.000
 VRT  CA    C    O    122.03  3.000
 VRT  HNA   N    HN   106.15  3.000
 VRT  HNA   N    CA   109.37  3.000
 VRT  HN    N    CA   110.21  3.000
 VRT  C6    N1   C2   119.42  3.000
 VRT  H2    C2   N3   116.16  3.000
 VRT  H2    C2   N1   115.59  3.000
 VRT  N3    C2   N1   128.25  3.000
 VRT  C4    N3   C2   111.56  3.000
 VRT  N9    C4   C5   105.26  3.000
 VRT  N9    C4   N3   127.89  3.000
 VRT  C5    C4   N3   126.84  3.000
 VRT  N7    C5   C6   133.31  3.000
 VRT  N7    C5   C4   110.68  3.000
 VRT  C6    C5   C4   116.01  3.000
 VRT  N6    C6   C5   122.77  3.000
 VRT  N6    C6   N1   119.31  3.000
 VRT  C5    C6   N1   117.92  3.000
 VRT  HN6A  N6   HN6  118.40  3.000
 VRT  HN6A  N6   C6   121.15  3.000
 VRT  HN6   N6   C6   120.40  3.000
 VRT  C8    N7   C5   104.54  3.000
 VRT  H8    C8   N9   121.73  3.000
 VRT  H8    C8   N7   125.24  3.000
 VRT  N9    C8   N7   113.03  3.000
 VRT  C1'   N9   C8   128.78  3.000
 VRT  C1'   N9   C4   124.72  3.000
 VRT  C8    N9   C4   106.49  3.000
 VRT  HA    CA   CB   107.84  3.000
 VRT  HA    CA   N    107.86  3.000
 VRT  CB    CA   N    110.67  3.000
 VRT  HA    CA   C    108.88  3.000
 VRT  CB    CA   C    108.13  3.000
 VRT  N     CA   C    113.32  3.000
 VRT  HBA   CB   HB   106.22  3.000
 VRT  HBA   CB   CG   109.46  3.000
 VRT  HB    CB   CG   109.86  3.000
 VRT  HBA   CB   CA   108.92  3.000
 VRT  HB    CB   CA   108.90  3.000
 VRT  CG    CB   CA   113.24  3.000
 VRT  HDB   CD   HDA  107.61  3.000
 VRT  HDB   CD   HD   107.59  3.000
 VRT  HDA   CD   HD   107.47  3.000
 VRT  HDB   CD   CG   111.38  3.000
 VRT  HDA   CD   CG   111.36  3.000
 VRT  HD    CD   CG   111.23  3.000
 VRT  HGA   CG   HG   106.33  3.000
 VRT  HGA   CG   CD   109.88  3.000
 VRT  HG    CG   CD   109.68  3.000
 VRT  HGA   CG   CB   109.36  3.000
 VRT  HG    CG   CB   109.07  3.000
 VRT  CD    CG   CB   112.34  3.000
 VRT  H1'   C1'  O4'  110.76  3.000
 VRT  H1'   C1'  C2'  110.76  3.000
 VRT  O4'   C1'  C2'  106.93  3.000
 VRT  H1'   C1'  N9   106.43  3.000
 VRT  O4'   C1'  N9   109.34  3.000
 VRT  C2'   C1'  N9   112.65  3.000
 VRT  HN10  N10  C2'  117.56  3.000
 VRT  HN10  N10  C    118.72  3.000
 VRT  C2'   N10  C    122.67  3.000
 VRT  H2'   C2'  C3'  108.02  3.000
 VRT  H2'   C2'  N10  110.16  3.000
 VRT  C3'   C2'  N10  116.63  3.000
 VRT  H2'   C2'  C1'  109.16  3.000
 VRT  C3'   C2'  C1'  101.60  3.000
 VRT  N10   C2'  C1'  110.81  3.000
 VRT  H3'   C3'  C4'  111.35  3.000
 VRT  H3'   C3'  O3'  112.12  3.000
 VRT  C4'   C3'  O3'  112.69  3.000
 VRT  H3'   C3'  C2'  111.71  3.000
 VRT  C4'   C3'  C2'  100.25  3.000
 VRT  O3'   C3'  C2'  108.10  3.000
 VRT  HO3'  O3'  C3'  108.51  3.000
 VRT  H4'   C4'  C5'  109.01  3.000
 VRT  H4'   C4'  O4'  107.35  3.000
 VRT  C5'   C4'  O4'  111.36  3.000
 VRT  H4'   C4'  C3'  111.52  3.000
 VRT  C5'   C4'  C3'  112.37  3.000
 VRT  O4'   C4'  C3'  105.09  3.000
 VRT  C4'   O4'  C1'  110.79  3.000
 VRT  H5'A  C5'  H5'  106.67  3.000
 VRT  H5'A  C5'  O5'  111.42  3.000
 VRT  H5'   C5'  O5'  112.08  3.000
 VRT  H5'A  C5'  C4'  110.56  3.000
 VRT  H5'   C5'  C4'  107.49  3.000
 VRT  O5'   C5'  C4'  108.55  3.000
 VRT  HO5'  O5'  C5'  108.11  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
 VRT  CONST_01  C4    N3   C2  N1    0.00   0.0  0
 VRT  CONST_02  C4    C5   C6  N1    0.00   0.0  0
 VRT  CONST_03  N7    C5   C6  N1  180.00   0.0  0
 VRT  CONST_04  C5    C6   N1  C2    0.00   0.0  0
 VRT  CONST_05  C5    C4   N3  C2    0.00   0.0  0
 VRT  CONST_06  N9    C4   N3  C2  180.00   0.0  0
 VRT  CONST_07  C6    N1   C2  N3    0.00   0.0  0
 VRT  CONST_08  C6    C5   C4  N3    0.00   0.0  0
 VRT  CONST_09  N7    C5   C4  N3  180.00   0.0  0
 VRT  CONST_10  C8    N9   C4  N3  180.00   0.0  0
 VRT  CONST_11  C8    N7   C5  C4    0.00   0.0  0
 VRT  CONST_12  N7    C8   N9  C4    0.00   0.0  0
 VRT  CONST_13  C8    N9   C4  C5    0.00   0.0  0
 VRT  CONST_14  N9    C8   N7  C5    0.00   0.0  0
 VRT  CONST_15  N9    C4   C5  C6  180.00   0.0  0
 VRT  CONST_16  C8    N7   C5  C6  180.00   0.0  0
 VRT  CONST_17  N9    C4   C5  N7    0.00   0.0  0
 VRT  CONST_18  C1'   N9   C4  N3    0.00   0.0  0
 VRT  CONST_19  C1'   N9   C4  C5  180.00   0.0  0
 VRT  CONST_20  C1'   N9   C8  N7  180.00   0.0  0
 VRT  CONST_21  N6    C6   N1  C2  180.00   0.0  0
 VRT  CONST_22  N6    C6   C5  C4  180.00   0.0  0
 VRT  CONST_23  N7    C5   C6  N6    0.00   0.0  0
 VRT  CONST_24  H2    C2   N3  C4  180.00   0.0  0
 VRT  CONST_25  H8    C8   N9  C4  180.00   0.0  0
 VRT  CONST_26  HN6   N6   C6  N1    0.00   0.0  0
 VRT  CONST_27  HN6A  N6   C6  N1  180.00   0.0  0
 VRT  CONST_28  C2'   N10  C   O     0.00   0.0  0
 VRT  CONST_29  C2'   N10  C   CA  180.00   0.0  0
 VRT  CONST_30  HN10  N10  C   O   180.00   0.0  0
 VRT  Var_01    CD    CG   CB  CA  179.74  30.0  3
 VRT  Var_02    HD    CD   CG  CB  -60.20  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
 VRT  chir_01  CA   C    N    CB   negativ
 VRT  chir_02  C1'  O4'  N9   C2'  negativ
 VRT  chir_03  C2'  N10  C3'  C1'  positiv
 VRT  chir_04  C3'  O3'  C4'  C2'  positiv
 VRT  chir_05  C4'  O4'  C5'  C3'  positiv

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
 VRT  plan-1  N1    0.020
 VRT  plan-1  C2    0.020
 VRT  plan-1  N3    0.020
 VRT  plan-1  C4    0.020
 VRT  plan-1  C5    0.020
 VRT  plan-1  C6    0.020
 VRT  plan-1  N6    0.020
 VRT  plan-1  N7    0.020
 VRT  plan-1  C8    0.020
 VRT  plan-1  N9    0.020
 VRT  plan-1  C1'   0.020
 VRT  plan-1  H8    0.020
 VRT  plan-1  H2    0.020
 VRT  plan-2  C6    0.020
 VRT  plan-2  N6    0.020
 VRT  plan-2  HN6   0.020
 VRT  plan-2  HN6A  0.020
 VRT  plan-3  C     0.020
 VRT  plan-3  O     0.020
 VRT  plan-3  CA    0.020
 VRT  plan-3  N10   0.020
 VRT  plan-3  C2'   0.020
 VRT  plan-3  HN10  0.020

