# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 22:51:16 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 2'-deoxy-2'-(L-valylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(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
 2VA  2VA  2'-deoxy-2'-(L-valylamino)adenosine  L-peptide  49  26  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2VA
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
 2VA  CG2   C  CH3   0  -0.679  71.8736  31.2310  17.9136
 2VA  CB    C  CH1   0  -0.232  72.1309  30.7878  19.3509
 2VA  CG1   C  CH3   0  -0.672  73.4885  31.3079  19.8159
 2VA  CA    C  CH1   0  -0.172  71.0025  31.2561  20.2851
 2VA  N     N  NH2   0  -0.806  71.2580  30.8470  21.6573
 2VA  C     C  C     0   0.551  69.6778  30.6260  19.8554
 2VA  O     O  O     0  -0.475  69.4465  29.4382  20.0022
 2VA  NAZ   N  NH1   0  -0.639  68.7870  31.4916  19.3280
 2VA  C2'   C  CH1   0  -0.205  67.4684  31.1042  18.9025
 2VA  C3'   C  CH1   0   0.042  67.3398  30.9449  17.3839
 2VA  O3'   O  OH1   0  -0.643  68.4513  30.3107  16.8343
 2VA  C4'   C  CH1   0  -0.021  67.1394  32.3969  16.9427
 2VA  C5'   C  CH2   0  -0.157  66.4244  32.5432  15.6230
 2VA  O5'   O  OH1   0  -0.661  66.3382  33.9058  15.2912
 2VA  O4'   O  O2    0  -0.489  66.3691  32.9852  17.9929
 2VA  C1'   C  CH1   0   0.199  66.4662  32.2382  19.1667
 2VA  N9    N  NR5   0  -0.532  65.1498  31.7328  19.5244
 2VA  C8    C  CR15  0   0.102  64.0694  31.4909  18.7203
 2VA  N7    N  N     0  -0.449  63.0474  31.0060  19.3632
 2VA  C5    C  CR56  0  -0.002  63.4715  30.9185  20.6632
 2VA  C4    C  CR56  0   0.488  64.7776  31.3651  20.7844
 2VA  N3    N  N     0  -0.458  65.5020  31.4164  21.9005
 2VA  C2    C  CR16  0   0.041  64.8154  30.9843  22.9443
 2VA  N1    N  N     0  -0.470  63.5651  30.5318  22.9815
 2VA  C6    C  CR6   0   0.456  62.8536  30.4813  21.8497
 2VA  N6    N  NH2   0  -0.815  61.6054  30.0107  21.8837
 2VA  HG21  H  HCH3  0   0.231  72.6861  30.9036  17.2638
 2VA  HG22  H  HCH3  0   0.241  70.9482  30.8260  17.5051
 2VA  HG23  H  HCH3  0   0.216  71.8181  32.3203  17.8451
 2VA  HB    H  HCH1  0   0.224  72.1526  29.6935  19.3852
 2VA  HG11  H  HCH3  0   0.219  73.4941  32.3993  19.8726
 2VA  HG12  H  HCH3  0   0.230  73.7785  30.9140  20.7900
 2VA  HG13  H  HCH3  0   0.236  74.2664  31.0122  19.1109
 2VA  HA    H  HCH1  0   0.221  70.9259  32.3508  20.1777
 2VA  H     H  HNH2  0   0.355  72.0832  31.3235  21.9969
 2VA  H2    H  HNH2  0   0.350  70.5046  31.1642  22.2557
 2VA  HAZ   H  HNH1  0   0.410  69.0770  32.4513  19.2149
 2VA  H2'   H  HCH1  0   0.303  67.1925  30.1951  19.4353
 2VA  H3'   H  HCH1  0   0.240  66.4187  30.3796  17.1802
 2VA  H1    H  HOH1  0   0.463  68.2290  29.9974  15.9520
 2VA  H4'   H  HCH1  0   0.243  68.1163  32.8968  16.8819
 2VA  H5'1  H  HCH2  0   0.207  65.4351  32.0710  15.6934
 2VA  H5'2  H  HCH2  0   0.207  66.9947  31.9755  14.8748
 2VA  H5'   H  HOH1  0   0.457  65.8762  33.9820  14.4513
 2VA  H1'   H  HCH1  0   0.281  66.7935  32.8628  20.0029
 2VA  H8    H  HCR5  0   0.301  64.0857  31.6996  17.6620
 2VA  HC2   H  HCR6  0   0.250  65.3345  30.9973  23.8968
 2VA  HN61  H  HNH2  0   0.410  61.0217  30.0320  21.0658
 2VA  HN62  H  HNH2  0   0.402  61.1791  29.7761  22.7639

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
 2VA  CG2  CB    single    1.526  0.020  1.526
 2VA  CG2  HG21  single    0.970  0.020  1.090
 2VA  CG2  HG22  single    0.970  0.020  1.090
 2VA  CG2  HG23  single    0.970  0.020  1.090
 2VA  CB   CG1   single    1.526  0.020  1.526
 2VA  CB   CA    single    1.540  0.027  1.540
 2VA  CB   HB    single    0.970  0.020  1.090
 2VA  CG1  HG11  single    0.970  0.020  1.090
 2VA  CG1  HG12  single    0.970  0.020  1.090
 2VA  CG1  HG13  single    0.970  0.020  1.090
 2VA  CA   N     single    1.458  0.019  1.458
 2VA  CA   C     single    1.525  0.021  1.525
 2VA  CA   HA    single    0.970  0.020  0.970
 2VA  N    H     single    0.860  0.020  0.860
 2VA  N    H2    single    0.890  0.020  1.040
 2VA  C    O     double    1.231  0.020  1.231
 2VA  C    NAZ   single    1.349  0.020  1.349
 2VA  NAZ  C2'   single    1.439  0.020  1.439
 2VA  NAZ  HAZ   single    0.860  0.020  1.020
 2VA  C2'  C3'   single    1.532  0.020  1.532
 2VA  C2'  C1'   single    1.536  0.020  1.536
 2VA  C2'  H2'   single    0.970  0.020  1.090
 2VA  C3'  O3'   single    1.393  0.020  1.393
 2VA  C3'  C4'   single    1.531  0.020  1.531
 2VA  C3'  H3'   single    0.970  0.020  1.090
 2VA  O3'  H1    single    0.850  0.020  0.980
 2VA  C4'  C5'   single    1.508  0.020  1.508
 2VA  C4'  O4'   single    1.429  0.020  1.429
 2VA  C4'  H4'   single    0.970  0.020  1.090
 2VA  C5'  O5'   single    1.405  0.020  1.405
 2VA  C5'  H5'1  single    0.970  0.020  1.090
 2VA  C5'  H5'2  single    0.970  0.020  1.090
 2VA  O5'  H5'   single    0.850  0.020  0.980
 2VA  O4'  C1'   single    1.395  0.020  1.395
 2VA  C1'  N9    single    1.455  0.020  1.455
 2VA  C1'  H1'   single    0.970  0.020  1.090
 2VA  N9   C8    aromatic  1.368  0.020  1.368
 2VA  N9   C4    aromatic  1.364  0.020  1.364
 2VA  C8   N7    aromatic  1.301  0.020  1.301
 2VA  C8   H8    single    0.930  0.020  1.080
 2VA  N7   C5    aromatic  1.370  0.020  1.370
 2VA  C5   C4    aromatic  1.386  0.020  1.386
 2VA  C5   C6    aromatic  1.407  0.020  1.407
 2VA  C4   N3    aromatic  1.332  0.020  1.332
 2VA  N3   C2    aromatic  1.322  0.020  1.322
 2VA  C2   N1    aromatic  1.330  0.020  1.330
 2VA  C2   HC2   single    0.930  0.020  1.080
 2VA  N1   C6    aromatic  1.338  0.020  1.338
 2VA  C6   N6    single    1.334  0.020  1.334
 2VA  N6   HN61  single    0.860  0.020  1.020
 2VA  N6   HN62  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
 2VA  HG23  CG2  HG22  107.68  3.000
 2VA  HG23  CG2  HG21  107.44  3.000
 2VA  HG22  CG2  HG21  107.32  3.000
 2VA  HG23  CG2  CB    110.92  3.000
 2VA  HG22  CG2  CB    112.86  3.000
 2VA  HG21  CG2  CB    110.39  3.000
 2VA  HB    CB   CA    107.45  3.000
 2VA  HB    CB   CG1   108.26  3.000
 2VA  CA    CB   CG1   111.33  3.000
 2VA  HB    CB   CG2   108.85  3.000
 2VA  CA    CB   CG2   111.10  3.000
 2VA  CG1   CB   CG2   109.75  3.000
 2VA  HG13  CG1  HG12  106.85  3.000
 2VA  HG13  CG1  HG11  107.50  3.000
 2VA  HG12  CG1  HG11  108.25  3.000
 2VA  HG13  CG1  CB    110.18  3.000
 2VA  HG12  CG1  CB    112.69  3.000
 2VA  HG11  CG1  CB    111.14  3.000
 2VA  HA    CA   C     109.00  3.000
 2VA  HA    CA   N     110.00  3.000
 2VA  C     CA   N     111.00  2.800
 2VA  HA    CA   CB    109.00  3.000
 2VA  C     CA   CB    111.40  1.900
 2VA  N     CA   CB    111.50  1.700
 2VA  H2    N    H     105.13  3.000
 2VA  H2    N    CA    109.79  3.000
 2VA  H     N    CA    114.00  3.000
 2VA  NAZ   C    O     123.14  3.000
 2VA  NAZ   C    CA    114.68  3.000
 2VA  O     C    CA    120.80  1.700
 2VA  HAZ   NAZ  C2'   119.11  3.000
 2VA  HAZ   NAZ  C     117.66  3.000
 2VA  C2'   NAZ  C     123.23  3.000
 2VA  H2'   C2'  C1'   111.51  3.000
 2VA  H2'   C2'  C3'   112.13  3.000
 2VA  C1'   C2'  C3'   101.10  3.000
 2VA  H2'   C2'  NAZ   108.19  3.000
 2VA  C1'   C2'  NAZ   110.38  3.000
 2VA  C3'   C2'  NAZ   113.45  3.000
 2VA  H3'   C3'  C4'   108.94  3.000
 2VA  H3'   C3'  O3'   111.18  3.000
 2VA  C4'   C3'  O3'   115.01  3.000
 2VA  H3'   C3'  C2'   107.89  3.000
 2VA  C4'   C3'  C2'   101.42  3.000
 2VA  O3'   C3'  C2'   111.80  3.000
 2VA  H1    O3'  C3'   109.00  3.000
 2VA  H4'   C4'  O4'   109.43  3.000
 2VA  H4'   C4'  C5'   109.20  3.000
 2VA  O4'   C4'  C5'   110.34  3.000
 2VA  H4'   C4'  C3'   109.33  3.000
 2VA  O4'   C4'  C3'   104.43  3.000
 2VA  C5'   C4'  C3'   113.97  3.000
 2VA  H5'2  C5'  H5'1  106.80  3.000
 2VA  H5'2  C5'  O5'   111.85  3.000
 2VA  H5'1  C5'  O5'   112.13  3.000
 2VA  H5'2  C5'  C4'   107.44  3.000
 2VA  H5'1  C5'  C4'   109.22  3.000
 2VA  O5'   C5'  C4'   109.25  3.000
 2VA  H5'   O5'  C5'   108.21  3.000
 2VA  C1'   O4'  C4'   111.13  3.000
 2VA  H1'   C1'  N9    106.33  3.000
 2VA  H1'   C1'  O4'   111.00  3.000
 2VA  N9    C1'  O4'   109.27  3.000
 2VA  H1'   C1'  C2'   110.96  3.000
 2VA  N9    C1'  C2'   112.10  3.000
 2VA  O4'   C1'  C2'   107.22  3.000
 2VA  C4    N9   C8    106.24  3.000
 2VA  C4    N9   C1'   124.59  3.000
 2VA  C8    N9   C1'   129.15  3.000
 2VA  H8    C8   N7    124.66  3.000
 2VA  H8    C8   N9    122.03  3.000
 2VA  N7    C8   N9    113.31  3.000
 2VA  C5    N7   C8    104.45  3.000
 2VA  C6    C5   C4    116.12  3.000
 2VA  C6    C5   N7    133.14  3.000
 2VA  C4    C5   N7    110.74  3.000
 2VA  N3    C4   C5    126.76  3.000
 2VA  N3    C4   N9    127.97  3.000
 2VA  C5    C4   N9    105.26  3.000
 2VA  C2    N3   C4    111.51  3.000
 2VA  HC2   C2   N1    115.42  3.000
 2VA  HC2   C2   N3    116.16  3.000
 2VA  N1    C2   N3    128.42  3.000
 2VA  C6    N1   C2    119.27  3.000
 2VA  N6    C6   N1    119.28  3.000
 2VA  N6    C6   C5    122.80  3.000
 2VA  N1    C6   C5    117.91  3.000
 2VA  HN62  N6   HN61  118.10  3.000
 2VA  HN62  N6   C6    120.07  3.000
 2VA  HN61  N6   C6    120.99  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
 2VA  CONST_01  C5    N7   C8  N9     0.00   0.0  0
 2VA  CONST_02  N7    C5   C4  N9     0.00   0.0  0
 2VA  CONST_03  C6    C5   C4  N9   180.00   0.0  0
 2VA  CONST_04  C2    N3   C4  N9   180.00   0.0  0
 2VA  CONST_05  C5    C4   N9  C8     0.00   0.0  0
 2VA  CONST_06  N3    C4   N9  C8   180.00   0.0  0
 2VA  CONST_07  C4    C5   N7  C8     0.00   0.0  0
 2VA  CONST_08  C6    C5   N7  C8   180.00   0.0  0
 2VA  CONST_09  C4    N9   C8  N7     0.00   0.0  0
 2VA  CONST_10  N3    C4   C5  N7   180.00   0.0  0
 2VA  CONST_11  N1    C6   C5  N7   180.00   0.0  0
 2VA  CONST_12  C2    N3   C4  C5     0.00   0.0  0
 2VA  CONST_13  C2    N1   C6  C5     0.00   0.0  0
 2VA  CONST_14  N1    C6   C5  C4     0.00   0.0  0
 2VA  CONST_15  N1    C2   N3  C4     0.00   0.0  0
 2VA  CONST_16  C6    C5   C4  N3     0.00   0.0  0
 2VA  CONST_17  C6    N1   C2  N3     0.00   0.0  0
 2VA  CONST_18  N7    C8   N9  C1'  180.00   0.0  0
 2VA  CONST_19  C5    C4   N9  C1'  180.00   0.0  0
 2VA  CONST_20  N3    C4   N9  C1'    0.00   0.0  0
 2VA  CONST_21  N6    C6   C5  N7     0.00   0.0  0
 2VA  CONST_22  N6    C6   C5  C4   180.00   0.0  0
 2VA  CONST_23  N6    C6   N1  C2   180.00   0.0  0
 2VA  CONST_24  H8    C8   N9  C1'    0.00   0.0  0
 2VA  CONST_25  HC2   C2   N3  C4   180.00   0.0  0
 2VA  CONST_26  HN61  N6   C6  C5     0.00   0.0  0
 2VA  CONST_27  HN62  N6   C6  C5   180.00   0.0  0
 2VA  CONST_28  C2'   NAZ  C   CA   180.00   0.0  0
 2VA  CONST_29  C2'   NAZ  C   O      0.00   0.0  0
 2VA  CONST_30  HAZ   NAZ  C   CA     0.00   0.0  0
 2VA  Var_01    HG11  CG1  CB  CG2   65.63  30.0  3
 2VA  Var_02    HG21  CG2  CB  CG1   55.75  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
 2VA  chir_01  CA   CB   N    C    positiv
 2VA  chir_02  C2'  NAZ  C3'  C1'  positiv
 2VA  chir_03  C3'  O3'  C4'  C2'  positiv
 2VA  chir_04  C4'  O4'  C3'  C5'  negativ
 2VA  chir_05  C1'  O4'  N9   C2'  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
 2VA  plan-1  C1'   0.020
 2VA  plan-1  N9    0.020
 2VA  plan-1  C8    0.020
 2VA  plan-1  N7    0.020
 2VA  plan-1  C5    0.020
 2VA  plan-1  C4    0.020
 2VA  plan-1  N3    0.020
 2VA  plan-1  C2    0.020
 2VA  plan-1  N1    0.020
 2VA  plan-1  C6    0.020
 2VA  plan-1  N6    0.020
 2VA  plan-1  H8    0.020
 2VA  plan-1  HC2   0.020
 2VA  plan-2  C6    0.020
 2VA  plan-2  N6    0.020
 2VA  plan-2  HN61  0.020
 2VA  plan-2  HN62  0.020
 2VA  plan-3  CA    0.020
 2VA  plan-3  C     0.020
 2VA  plan-3  O     0.020
 2VA  plan-3  NAZ   0.020
 2VA  plan-3  C2'   0.020
 2VA  plan-3  HAZ   0.020

