# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 11:31:00 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5'-deoxy-5'-[(L-valylsulfamoyl)amino]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)N[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(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
 VAA  VAA  5'-deoxy-5'-[(L-valylsulfamoyl)amino]adenosine  ligand  54  30  .  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_VAA
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
 VAA  N     N  NH2   0  -0.784   2.3719  -1.4789   1.5208
 VAA  CA    C  CH1   0  -0.212   1.8745  -1.0003   2.7916
 VAA  CB    C  CH1   0  -0.247   2.9319  -0.5489   3.8339
 VAA  CG1   C  CH3   0  -0.663   3.7520  -1.7537   4.2840
 VAA  CG2   C  CH3   0  -0.662   3.8362   0.5676   3.3237
 VAA  C     C  C     0   0.597   0.9062   0.1330   2.5148
 VAA  O     O  O     0  -0.433   1.0283   0.9179   1.5998
 VAA  S     S  S     0   1.538  -1.3732   1.3566   3.2318
 VAA  O1S   O  OS    0  -0.647  -2.3724   0.9065   4.1733
 VAA  O2S   O  OS    0  -0.630  -0.8082   2.6806   3.3201
 VAA  N3S   N  NC1   0  -0.819  -0.1410   0.2186   3.3953
 VAA  N5'   N  NC1   0  -0.739  -1.9576   1.1845   1.7188
 VAA  C5'   C  CH2   0  -0.298  -2.4406  -0.1236   1.2955
 VAA  C4'   C  CH1   0  -0.023  -3.0025  -0.0091  -0.1130
 VAA  O4'   O  O2    0  -0.496  -2.0227   0.5600  -0.9854
 VAA  C1'   C  CH1   0   0.224  -1.5816  -0.3921  -1.9233
 VAA  N9    N  NR5   0  -0.552  -0.1699  -0.2563  -2.1428
 VAA  C4    C  CR56  0   0.493   0.4042   0.3815  -3.2097
 VAA  N3    N  N     0  -0.459  -0.1968   0.9288  -4.2624
 VAA  C2    C  CR16  0   0.044   0.6764   1.4487  -5.1081
 VAA  N1    N  N     0  -0.474   2.0028   1.4757  -5.0138
 VAA  C6    C  CR6   0   0.459   2.5915   0.9229  -3.9468
 VAA  N6    N  NH2   0  -0.817   3.9207   0.9543  -3.8436
 VAA  C5    C  CR56  0  -0.009   1.7664   0.3352  -2.9708
 VAA  N7    N  N     0  -0.454   2.0318  -0.3040  -1.7860
 VAA  C8    C  CR15  0   0.126   0.8647  -0.6335  -1.3238
 VAA  C2'   C  CH1   0  -0.060  -2.0138  -1.7455  -1.3661
 VAA  O2'   O  OH1   0  -0.651  -2.1090  -2.6747  -2.4007
 VAA  C3'   C  CH1   0  -0.026  -3.3426  -1.3739  -0.6987
 VAA  O3'   O  OH1   0  -0.665  -4.3581  -1.2122  -1.6509
 VAA  HN2   H  HNH2  0   0.362   3.0332  -2.2305   1.6642
 VAA  H     H  HNH2  0   0.357   2.8549  -0.7485   1.0133
 VAA  HA    H  HCH1  0   0.272   1.3097  -1.8184   3.2524
 VAA  HB    H  HCH1  0   0.235   2.3849  -0.1777   4.7078
 VAA  HG11  H  HCH3  0   0.240   4.4703  -1.4646   5.0516
 VAA  HG12  H  HCH3  0   0.233   3.1160  -2.5359   4.7020
 VAA  HG13  H  HCH3  0   0.217   4.3204  -2.1883   3.4590
 VAA  HG21  H  HCH3  0   0.217   4.3611   0.2734   2.4130
 VAA  HG22  H  HCH3  0   0.235   3.2906   1.4877   3.1152
 VAA  HG23  H  HCH3  0   0.238   4.5955   0.8025   4.0701
 VAA  HNS3  H  HNC1  0   0.447  -0.2751  -0.4872   4.1093
 VAA  HN'5  H  HNC1  0   0.420  -1.3546   1.6358   1.0365
 VAA  H5'1  H  HCH2  0   0.242  -1.6487  -0.8824   1.3332
 VAA  H5'2  H  HCH2  0   0.289  -3.2404  -0.4469   1.9612
 VAA  H4'   H  HCH1  0   0.280  -3.8779   0.6458  -0.0978
 VAA  H1'   H  HCH1  0   0.264  -2.0551  -0.2190  -2.8946
 VAA  H2    H  HCR6  0   0.253   0.2623   1.9148  -5.9957
 VAA  H61   H  HNH2  0   0.404   4.4789   1.3412  -4.5849
 VAA  H62   H  HNH2  0   0.411   4.3913   0.5147  -3.0724
 VAA  H8    H  HCR5  0   0.286   0.7147  -1.1580  -0.3920
 VAA  H2'   H  HCH1  0   0.250  -1.3178  -2.0778  -0.5853
 VAA  HO'2  H  HOH1  0   0.472  -2.0961  -3.5616  -2.0267
 VAA  H3'   H  HCH1  0   0.260  -3.6216  -2.0941   0.0815
 VAA  HT'3  H  HOH1  0   0.452  -4.3539  -1.9859  -2.2267

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
 VAA  N    CA    single    1.446  0.020  1.446
 VAA  N    HN2   single    0.890  0.020  1.040
 VAA  N    H     single    0.860  0.020  1.020
 VAA  CA   CB    single    1.552  0.020  1.552
 VAA  CA   C     single    1.516  0.020  1.516
 VAA  CA   HA    single    0.970  0.020  1.090
 VAA  CB   CG1   single    1.525  0.020  1.525
 VAA  CB   CG2   single    1.525  0.020  1.525
 VAA  CB   HB    single    0.970  0.020  1.090
 VAA  CG1  HG11  single    0.970  0.020  1.090
 VAA  CG1  HG12  single    0.970  0.020  1.090
 VAA  CG1  HG13  single    0.970  0.020  1.090
 VAA  CG2  HG21  single    0.970  0.020  1.090
 VAA  CG2  HG22  single    0.970  0.020  1.090
 VAA  CG2  HG23  single    0.970  0.020  1.090
 VAA  C    O     double    1.212  0.020  1.212
 VAA  C    N3S   single    1.371  0.020  1.371
 VAA  S    O1S   double    1.445  0.020  1.445
 VAA  S    O2S   double    1.442  0.020  1.442
 VAA  S    N3S   single    1.685  0.020  1.685
 VAA  S    N5'   single    1.631  0.020  1.631
 VAA  N3S  HNS3  single    0.860  0.020  1.020
 VAA  N5'  C5'   single    1.457  0.020  1.457
 VAA  N5'  HN'5  single    0.890  0.020  1.040
 VAA  C5'  C4'   single    1.521  0.020  1.521
 VAA  C5'  H5'1  single    0.970  0.020  1.090
 VAA  C5'  H5'2  single    0.970  0.020  1.090
 VAA  C4'  O4'   single    1.430  0.020  1.430
 VAA  C4'  C3'   single    1.524  0.020  1.524
 VAA  C4'  H4'   single    0.970  0.020  1.090
 VAA  O4'  C1'   single    1.407  0.020  1.407
 VAA  C1'  N9    single    1.435  0.020  1.435
 VAA  C1'  C2'   single    1.526  0.020  1.526
 VAA  C1'  H1'   single    0.970  0.020  1.090
 VAA  N9   C4    aromatic  1.369  0.020  1.369
 VAA  N9   C8    aromatic  1.372  0.020  1.372
 VAA  C4   N3    aromatic  1.330  0.020  1.330
 VAA  C4   C5    aromatic  1.384  0.020  1.384
 VAA  N3   C2    aromatic  1.322  0.020  1.322
 VAA  C2   N1    aromatic  1.330  0.020  1.330
 VAA  C2   H2    single    0.930  0.020  1.080
 VAA  N1   C6    aromatic  1.338  0.020  1.338
 VAA  C6   N6    single    1.334  0.020  1.334
 VAA  C6   C5    aromatic  1.407  0.020  1.407
 VAA  N6   H61   single    0.860  0.020  1.020
 VAA  N6   H62   single    0.860  0.020  1.020
 VAA  C5   N7    aromatic  1.372  0.020  1.372
 VAA  N7   C8    aromatic  1.298  0.020  1.298
 VAA  C8   H8    single    0.930  0.020  1.080
 VAA  C2'  O2'   single    1.394  0.020  1.394
 VAA  C2'  C3'   single    1.533  0.020  1.533
 VAA  C2'  H2'   single    0.970  0.020  1.090
 VAA  O2'  HO'2  single    0.850  0.020  0.980
 VAA  C3'  O3'   single    1.402  0.020  1.402
 VAA  C3'  H3'   single    0.970  0.020  1.090
 VAA  O3'  HT'3  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
 VAA  H     N    HN2   107.18  3.000
 VAA  H     N    CA    111.46  3.000
 VAA  HN2   N    CA    110.26  3.000
 VAA  HA    CA   C     107.80  3.000
 VAA  HA    CA   CB    106.61  3.000
 VAA  C     CA   CB    109.90  3.000
 VAA  HA    CA   N     107.44  3.000
 VAA  C     CA   N     107.86  3.000
 VAA  CB    CA   N     116.88  3.000
 VAA  HB    CB   CG2   108.35  3.000
 VAA  HB    CB   CG1   107.50  3.000
 VAA  CG2   CB   CG1   110.99  3.000
 VAA  HB    CB   CA    107.10  3.000
 VAA  CG2   CB   CA    113.10  3.000
 VAA  CG1   CB   CA    109.56  3.000
 VAA  HG13  CG1  HG12  107.91  3.000
 VAA  HG13  CG1  HG11  107.13  3.000
 VAA  HG12  CG1  HG11  107.72  3.000
 VAA  HG13  CG1  CB    111.80  3.000
 VAA  HG12  CG1  CB    111.46  3.000
 VAA  HG11  CG1  CB    110.64  3.000
 VAA  HG23  CG2  HG22  107.32  3.000
 VAA  HG23  CG2  HG21  107.11  3.000
 VAA  HG22  CG2  HG21  107.98  3.000
 VAA  HG23  CG2  CB    109.98  3.000
 VAA  HG22  CG2  CB    112.67  3.000
 VAA  HG21  CG2  CB    111.54  3.000
 VAA  N3S   C    O     121.44  3.000
 VAA  N3S   C    CA    114.66  3.000
 VAA  O     C    CA    123.90  3.000
 VAA  N5'   S    N3S   106.31  3.000
 VAA  N5'   S    O2S   107.10  3.000
 VAA  N3S   S    O2S   109.12  3.000
 VAA  N5'   S    O1S   108.89  3.000
 VAA  N3S   S    O1S   103.42  3.000
 VAA  O2S   S    O1S   121.13  3.000
 VAA  HNS3  N3S  S     116.24  3.000
 VAA  HNS3  N3S  C     120.69  3.000
 VAA  S     N3S  C     122.57  3.000
 VAA  HN'5  N5'  C5'   113.59  3.000
 VAA  HN'5  N5'  S     111.30  3.000
 VAA  C5'   N5'  S     118.87  3.000
 VAA  H5'2  C5'  H5'1  107.67  3.000
 VAA  H5'2  C5'  C4'   108.48  3.000
 VAA  H5'1  C5'  C4'   110.52  3.000
 VAA  H5'2  C5'  N5'   109.40  3.000
 VAA  H5'1  C5'  N5'   111.81  3.000
 VAA  C4'   C5'  N5'   108.90  3.000
 VAA  H4'   C4'  C3'   111.30  3.000
 VAA  H4'   C4'  O4'   108.59  3.000
 VAA  C3'   C4'  O4'   105.95  3.000
 VAA  H4'   C4'  C5'   109.15  3.000
 VAA  C3'   C4'  C5'   111.78  3.000
 VAA  O4'   C4'  C5'   109.99  3.000
 VAA  C1'   O4'  C4'   110.62  3.000
 VAA  H1'   C1'  C2'   109.99  3.000
 VAA  H1'   C1'  N9    105.95  3.000
 VAA  C2'   C1'  N9    114.73  3.000
 VAA  H1'   C1'  O4'   110.41  3.000
 VAA  C2'   C1'  O4'   105.54  3.000
 VAA  N9    C1'  O4'   110.26  3.000
 VAA  C8    N9   C4    106.08  3.000
 VAA  C8    N9   C1'   128.63  3.000
 VAA  C4    N9   C1'   125.15  3.000
 VAA  C5    C4   N3    126.53  3.000
 VAA  C5    C4   N9    105.22  3.000
 VAA  N3    C4   N9    128.24  3.000
 VAA  C2    N3   C4    111.70  3.000
 VAA  H2    C2   N1    115.47  3.000
 VAA  H2    C2   N3    116.12  3.000
 VAA  N1    C2   N3    128.41  3.000
 VAA  C6    N1   C2    119.14  3.000
 VAA  C5    C6   N6    122.73  3.000
 VAA  C5    C6   N1    117.89  3.000
 VAA  N6    C6   N1    119.37  3.000
 VAA  H62   N6   H61   118.31  3.000
 VAA  H62   N6   C6    121.07  3.000
 VAA  H61   N6   C6    120.35  3.000
 VAA  N7    C5   C6    132.87  3.000
 VAA  N7    C5   C4    110.80  3.000
 VAA  C6    C5   C4    116.33  3.000
 VAA  C8    N7   C5    104.59  3.000
 VAA  H8    C8   N7    123.75  3.000
 VAA  H8    C8   N9    122.94  3.000
 VAA  N7    C8   N9    113.30  3.000
 VAA  H2'   C2'  C3'   108.26  3.000
 VAA  H2'   C2'  O2'   111.69  3.000
 VAA  C3'   C2'  O2'   115.19  3.000
 VAA  H2'   C2'  C1'   110.41  3.000
 VAA  C3'   C2'  C1'   100.92  3.000
 VAA  O2'   C2'  C1'   109.85  3.000
 VAA  HO'2  O2'  C2'   108.96  3.000
 VAA  H3'   C3'  O3'   111.99  3.000
 VAA  H3'   C3'  C2'   111.76  3.000
 VAA  O3'   C3'  C2'   111.12  3.000
 VAA  H3'   C3'  C4'   111.79  3.000
 VAA  O3'   C3'  C4'   108.63  3.000
 VAA  C2'   C3'  C4'   101.02  3.000
 VAA  HT'3  O3'  C3'   108.05  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
 VAA  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 VAA  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 VAA  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 VAA  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 VAA  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 VAA  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 VAA  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 VAA  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 VAA  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 VAA  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 VAA  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 VAA  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 VAA  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 VAA  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 VAA  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 VAA  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 VAA  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 VAA  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 VAA  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 VAA  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 VAA  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 VAA  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 VAA  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 VAA  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 VAA  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 VAA  CONST_26  H61   N6   C6   N1      0.00   0.0  0
 VAA  CONST_27  H62   N6   C6   N1    180.00   0.0  0
 VAA  CONST_28  S     N3S  C    CA    180.00   0.0  0
 VAA  CONST_29  S     N3S  C    O       0.00   0.0  0
 VAA  CONST_30  HNS3  N3S  C    CA      0.00   0.0  0
 VAA  Var_01    C4'   C5'  N5'  S     176.81  30.0  3
 VAA  Var_02    O1S   S    N3S  C     168.24  30.0  1
 VAA  Var_03    C5'   N5'  S    O1S   -54.94  30.0  3
 VAA  Var_04    HG11  CG1  CB   CA   -177.37  30.0  3
 VAA  Var_05    HG21  CG2  CB   CA    -57.86  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
 VAA  chir_01  CA   N    CB   C    negativ
 VAA  chir_02  C4'  C5'  O4'  C3'  negativ
 VAA  chir_03  C1'  O4'  N9   C2'  negativ
 VAA  chir_04  C2'  O2'  C1'  C3'  negativ
 VAA  chir_05  C3'  O3'  C4'  C2'  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
 VAA  plan-1  C1'   0.020
 VAA  plan-1  N9    0.020
 VAA  plan-1  C4    0.020
 VAA  plan-1  N3    0.020
 VAA  plan-1  C2    0.020
 VAA  plan-1  N1    0.020
 VAA  plan-1  C6    0.020
 VAA  plan-1  N6    0.020
 VAA  plan-1  C5    0.020
 VAA  plan-1  N7    0.020
 VAA  plan-1  C8    0.020
 VAA  plan-1  H2    0.020
 VAA  plan-1  H8    0.020
 VAA  plan-2  C6    0.020
 VAA  plan-2  N6    0.020
 VAA  plan-2  H61   0.020
 VAA  plan-2  H62   0.020
 VAA  plan-3  CA    0.020
 VAA  plan-3  C     0.020
 VAA  plan-3  O     0.020
 VAA  plan-3  S     0.020
 VAA  plan-3  N3S   0.020
 VAA  plan-3  HNS3  0.020

