# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:19:29 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: 9-[7-(3-carboxyphenyl)-5,6-dideoxy-beta-D-ribo-heptodialdo-1,4-furanosyl]-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CCC(=O)c4cccc(c4)C(O)=O)[C@@H](O)[C@H]3O
#
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
 V47  V47  9-[7-(3-carboxyphenyl)-5,6-dideoxy-beta-D-ribo-heptodialdo-1,4-furanosyl]-9H-purin-6-amine  ligand  49  30  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V47
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
 V47  O4   O  OH1   0  -0.662   9.0532  -23.4419   7.1623
 V47  C4   C  CR15  0   0.100  13.9597  -24.2516   7.4067
 V47  C5   C  CH1   0   0.178  12.4357  -22.2174   7.2155
 V47  C6   C  CH1   0   0.026  10.8727  -22.9860   8.7660
 V47  C3   C  CR56  0  -0.002  14.9691  -24.1742   5.5539
 V47  C2   C  CR56  0   0.486  14.0920  -23.1011   5.5545
 V47  C1   C  CR16  0   0.039  14.7255  -22.4534   3.5552
 V47  N1   N  N     0  -0.474  15.6098  -23.4375   3.4134
 V47  C7   C  CH2   0  -0.466  10.9158  -24.0981   9.7943
 V47  N2   N  N     0  -0.459  13.9288  -22.2067   4.5806
 V47  C8   C  CH2   0  -0.602  11.4823  -23.7002  11.1494
 V47  C9   C  C     0   0.382  10.6063  -22.7830  11.9636
 V47  C10  C  CR6   0   0.015  11.1528  -22.2480  13.2474
 V47  C11  C  CR16  0  -0.284  12.4063  -22.6172  13.7333
 V47  C12  C  CR16  0  -0.222  12.8755  -22.1010  14.9317
 V47  C13  C  CR16  0  -0.255  12.1030  -21.2091  15.6570
 V47  C14  C  CR6   0  -0.063  10.8463  -20.8321  15.1822
 V47  C15  C  C     0   0.541   9.9751  -19.8776  15.9158
 V47  C16  C  CR16  0  -0.281  10.3793  -21.3554  13.9837
 V47  O    O  O2    0  -0.499  12.1849  -22.4430   8.5663
 V47  C17  C  CH1   0  -0.004  10.4346  -23.4432   7.3709
 V47  C18  C  CH1   0  -0.046  11.1110  -22.4070   6.4782
 V47  O5   O  OH1   0  -0.663  10.4486  -21.1717   6.5121
 V47  N4   N  NR5   0  -0.536  13.4449  -23.1661   6.7529
 V47  N3   N  N     0  -0.451  14.8708  -24.8814   6.7226
 V47  C    C  CR6   0   0.458  15.7633  -24.3258   4.4019
 V47  N    N  NH2   0  -0.817  16.6508  -25.3110   4.2608
 V47  H1   H  HOH1  0   0.465   8.6610  -24.1925   7.6185
 V47  H3   H  HCH1  0   0.285  12.8387  -21.2129   7.0592
 V47  H4   H  HCH1  0   0.246  10.2092  -22.1827   9.1026
 V47  H5   H  HOH1  0   0.490   9.9238  -18.8165  17.4793
 V47  H6   H  HCR6  0   0.252  14.6519  -21.7690   2.7171
 V47  H7   H  HCH2  0   0.251   9.9028  -24.4914   9.9118
 V47  H8   H  HCH2  0   0.247  11.5161  -24.9260   9.4057
 V47  H9   H  HCH2  0   0.297  11.6499  -24.6034  11.7460
 V47  H10  H  HCH2  0   0.280  12.4728  -23.2523  11.0341
 V47  H11  H  HCR6  0   0.277  13.0311  -23.3114  13.1881
 V47  H12  H  HCR6  0   0.276  13.8488  -22.3947  15.2995
 V47  H13  H  HCR6  0   0.278  12.4861  -20.8138  16.5873
 V47  H14  H  HCR6  0   0.271   9.4042  -21.0658  13.6151
 V47  H15  H  HCH1  0   0.230  10.8711  -24.4294   7.1564
 V47  H16  H  HCH1  0   0.263  11.2575  -22.7639   5.4521
 V47  H17  H  HOH1  0   0.458   9.5195  -21.3155   6.3022
 V47  H18  H  HNH2  0   0.404  17.1979  -25.3843   3.4207
 V47  H19  H  HNH2  0   0.411  16.8071  -25.9814   4.9927
 V47  H2   H  HCR5  0   0.297  13.6335  -24.5289   8.3962
 V47  O3   O  O     0  -0.434   8.8835  -19.5359  15.5301
 V47  O2   O  OH1   0  -0.592  10.5216  -19.4394  17.0394
 V47  O1   O  O     0  -0.392   9.4843  -22.4903  11.6108

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
 V47  N    C    single    1.333  0.020  1.333
 V47  C    N1   aromatic  1.338  0.020  1.338
 V47  C    C3   aromatic  1.407  0.020  1.407
 V47  N1   C1   aromatic  1.331  0.020  1.331
 V47  C3   N3   aromatic  1.370  0.020  1.370
 V47  C3   C2   aromatic  1.386  0.020  1.386
 V47  N3   C4   aromatic  1.302  0.020  1.302
 V47  C1   N2   aromatic  1.322  0.020  1.322
 V47  C2   N2   aromatic  1.332  0.020  1.332
 V47  C2   N4   aromatic  1.364  0.020  1.364
 V47  C4   N4   aromatic  1.368  0.020  1.368
 V47  O5   C18  single    1.402  0.020  1.402
 V47  N4   C5   single    1.460  0.020  1.460
 V47  C18  C5   single    1.528  0.020  1.528
 V47  C18  C17  single    1.526  0.020  1.526
 V47  C5   O    single    1.392  0.020  1.392
 V47  O4   C17  single    1.397  0.020  1.397
 V47  C17  C6   single    1.532  0.020  1.532
 V47  O    C6   single    1.434  0.020  1.434
 V47  C6   C7   single    1.515  0.020  1.515
 V47  C7   C8   single    1.522  0.020  1.522
 V47  C8   C9   single    1.507  0.020  1.507
 V47  O1   C9   double    1.212  0.020  1.212
 V47  C9   C10  single    1.494  0.020  1.494
 V47  C10  C11  aromatic  1.394  0.020  1.394
 V47  C10  C16  aromatic  1.392  0.020  1.392
 V47  C11  C12  aromatic  1.387  0.020  1.387
 V47  C16  C14  aromatic  1.389  0.020  1.389
 V47  C12  C13  aromatic  1.385  0.020  1.385
 V47  C14  C13  aromatic  1.395  0.020  1.395
 V47  C14  C15  single    1.486  0.020  1.486
 V47  O3   C15  double    1.207  0.020  1.207
 V47  C15  O2   single    1.324  0.020  1.324
 V47  O4   H1   single    0.850  0.020  0.980
 V47  C4   H2   single    0.930  0.020  1.080
 V47  C5   H3   single    0.970  0.020  1.090
 V47  C6   H4   single    0.970  0.020  1.090
 V47  O2   H5   single    0.850  0.020  0.980
 V47  C1   H6   single    0.930  0.020  1.080
 V47  C7   H7   single    0.970  0.020  1.090
 V47  C7   H8   single    0.970  0.020  1.090
 V47  C8   H9   single    0.970  0.020  1.090
 V47  C8   H10  single    0.970  0.020  1.090
 V47  C11  H11  single    0.930  0.020  1.080
 V47  C12  H12  single    0.930  0.020  1.080
 V47  C13  H13  single    0.930  0.020  1.080
 V47  C16  H14  single    0.930  0.020  1.080
 V47  C17  H15  single    0.970  0.020  1.090
 V47  C18  H16  single    0.970  0.020  1.090
 V47  O5   H17  single    0.850  0.020  0.980
 V47  N    H18  single    0.860  0.020  1.020
 V47  N    H19  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
 V47  H1   O4   C17  109.37  3.000
 V47  H2   C4   N3   124.72  3.000
 V47  H2   C4   N4   121.94  3.000
 V47  N3   C4   N4   113.34  3.000
 V47  H3   C5   N4   107.26  3.000
 V47  H3   C5   C18  111.37  3.000
 V47  N4   C5   C18  111.45  3.000
 V47  H3   C5   O    110.72  3.000
 V47  C18  C5   O    106.97  3.000
 V47  N4   C5   O    109.06  3.000
 V47  H4   C6   C17  109.00  3.000
 V47  H4   C6   O    108.63  3.000
 V47  C17  C6   O    104.35  3.000
 V47  H4   C6   C7   110.31  3.000
 V47  O    C6   C7   110.26  3.000
 V47  C17  C6   C7   114.02  3.000
 V47  C    C3   N3   133.10  3.000
 V47  N3   C3   C2   110.73  3.000
 V47  C    C3   C2   116.16  3.000
 V47  N4   C2   N2   128.05  3.000
 V47  N4   C2   C3   105.30  3.000
 V47  N2   C2   C3   126.65  3.000
 V47  H6   C1   N2   116.15  3.000
 V47  H6   C1   N1   115.43  3.000
 V47  N2   C1   N1   128.42  3.000
 V47  C    N1   C1   119.25  3.000
 V47  H8   C7   H7   105.93  3.000
 V47  H8   C7   C8   108.06  3.000
 V47  H7   C7   C8   110.08  3.000
 V47  H8   C7   C6   109.27  3.000
 V47  H7   C7   C6   108.10  3.000
 V47  C8   C7   C6   115.03  3.000
 V47  C1   N2   C2   111.59  3.000
 V47  H10  C8   H9   104.87  3.000
 V47  H10  C8   C9   109.53  3.000
 V47  H9   C8   C9   107.25  3.000
 V47  H10  C8   C7   110.52  3.000
 V47  H9   C8   C7   109.05  3.000
 V47  C9   C8   C7   115.08  3.000
 V47  C10  C9   C8   118.00  3.000
 V47  C10  C9   O1   120.14  3.000
 V47  C8   C9   O1   121.85  3.000
 V47  C16  C10  C11  119.02  3.000
 V47  C16  C10  C9   118.74  3.000
 V47  C11  C10  C9   122.24  3.000
 V47  H11  C11  C12  118.63  3.000
 V47  H11  C11  C10  120.91  3.000
 V47  C12  C11  C10  120.46  3.000
 V47  H12  C12  C13  119.93  3.000
 V47  H12  C12  C11  119.83  3.000
 V47  C13  C12  C11  120.24  3.000
 V47  H13  C13  C14  120.88  3.000
 V47  H13  C13  C12  119.24  3.000
 V47  C14  C13  C12  119.88  3.000
 V47  C16  C14  C15  118.10  3.000
 V47  C15  C14  C13  122.25  3.000
 V47  C16  C14  C13  119.66  3.000
 V47  C14  C15  O2   112.93  3.000
 V47  O2   C15  O3   123.41  3.000
 V47  C14  C15  O3   123.66  3.000
 V47  H14  C16  C14  119.76  3.000
 V47  H14  C16  C10  119.50  3.000
 V47  C14  C16  C10  120.75  3.000
 V47  C6   O    C5   111.18  3.000
 V47  H15  C17  C18  108.60  3.000
 V47  H15  C17  C6   109.38  3.000
 V47  C18  C17  C6   101.74  3.000
 V47  H15  C17  O4   111.36  3.000
 V47  C6   C17  O4   114.74  3.000
 V47  C18  C17  O4   110.50  3.000
 V47  H16  C18  O5   111.88  3.000
 V47  H16  C18  C17  112.69  3.000
 V47  O5   C18  C17  112.01  3.000
 V47  H16  C18  C5   112.09  3.000
 V47  C17  C18  C5   100.73  3.000
 V47  O5   C18  C5   106.78  3.000
 V47  H17  O5   C18  108.59  3.000
 V47  C2   N4   C5   125.13  3.000
 V47  C5   N4   C4   128.63  3.000
 V47  C2   N4   C4   106.22  3.000
 V47  C3   N3   C4   104.41  3.000
 V47  N    C    N1   119.26  3.000
 V47  N1   C    C3   117.94  3.000
 V47  N    C    C3   122.80  3.000
 V47  H19  N    H18  118.39  3.000
 V47  H19  N    C    121.30  3.000
 V47  H18  N    C    120.30  3.000
 V47  H5   O2   C15  110.08  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
 V47  CONST_01  C    C3   N3   C4    180.00   0.0  0
 V47  CONST_02  C2   C3   N3   C4      0.00   0.0  0
 V47  CONST_03  C3   C2   N4   C4      0.00   0.0  0
 V47  CONST_04  N2   C2   N4   C4    180.00   0.0  0
 V47  CONST_05  C1   N1   C    C3      0.00   0.0  0
 V47  CONST_06  N4   C4   N3   C3      0.00   0.0  0
 V47  CONST_07  C1   N2   C2   C3      0.00   0.0  0
 V47  CONST_08  N1   C    C3   C2      0.00   0.0  0
 V47  CONST_09  N1   C1   N2   C2      0.00   0.0  0
 V47  CONST_10  N3   C4   N4   C2      0.00   0.0  0
 V47  CONST_11  N4   C2   N2   C1    180.00   0.0  0
 V47  CONST_12  N3   C3   C    N1    180.00   0.0  0
 V47  CONST_13  C    N1   C1   N2      0.00   0.0  0
 V47  CONST_14  C    C3   C2   N2      0.00   0.0  0
 V47  CONST_15  N3   C3   C2   N2    180.00   0.0  0
 V47  CONST_16  C13  C12  C11  C10     0.00   0.0  0
 V47  CONST_17  C13  C14  C16  C10     0.00   0.0  0
 V47  CONST_18  C14  C16  C10  C11     0.00   0.0  0
 V47  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 V47  CONST_20  C16  C10  C11  C12     0.00   0.0  0
 V47  CONST_21  C16  C14  C13  C12     0.00   0.0  0
 V47  CONST_22  C    C3   C2   N4    180.00   0.0  0
 V47  CONST_23  N3   C3   C2   N4      0.00   0.0  0
 V47  CONST_24  C3   C2   N4   C5    180.00   0.0  0
 V47  CONST_25  N2   C2   N4   C5      0.00   0.0  0
 V47  CONST_26  N3   C4   N4   C5    180.00   0.0  0
 V47  CONST_27  N    C    C3   C2    180.00   0.0  0
 V47  CONST_28  N    C    N1   C1    180.00   0.0  0
 V47  CONST_29  C12  C11  C10  C9    180.00   0.0  0
 V47  CONST_30  C14  C16  C10  C9    180.00   0.0  0
 V47  CONST_31  C15  C14  C16  C10   180.00   0.0  0
 V47  CONST_32  C15  C14  C13  C12   180.00   0.0  0
 V47  CONST_33  N    C    C3   N3      0.00   0.0  0
 V47  CONST_34  H2   C4   N4   C5      0.00   0.0  0
 V47  CONST_35  H6   C1   N2   C2    180.00   0.0  0
 V47  CONST_36  H12  C12  C11  C10   180.00   0.0  0
 V47  CONST_37  H14  C16  C10  C11   180.00   0.0  0
 V47  CONST_38  H13  C13  C12  C11   180.00   0.0  0
 V47  CONST_39  H11  C11  C12  C13   180.00   0.0  0
 V47  CONST_40  H18  N    C    C3    180.00   0.0  0
 V47  CONST_41  H19  N    C    C3      0.00   0.0  0
 V47  CONST_42  H5   O2   C15  C14   180.00   0.0  0
 V47  Var_01    C16  C14  C15  O3      0.26  30.0  2
 V47  Var_02    C11  C10  C9   O1    176.20  30.0  2
 V47  Var_03    C9   C8   C7   C6     70.36  30.0  3
 V47  Var_04    C10  C9   C8   C7   -174.36  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
 V47  chir_01  C5   N4  C18  O    negativ
 V47  chir_02  C6   O   C17  C7   negativ
 V47  chir_03  C17  O4  C6   C18  positiv
 V47  chir_04  C18  O5  C17  C5   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
 V47  plan-1  C9   0.020
 V47  plan-1  C10  0.020
 V47  plan-1  C11  0.020
 V47  plan-1  C12  0.020
 V47  plan-1  C13  0.020
 V47  plan-1  C14  0.020
 V47  plan-1  C15  0.020
 V47  plan-1  C16  0.020
 V47  plan-1  H11  0.020
 V47  plan-1  H12  0.020
 V47  plan-1  H13  0.020
 V47  plan-1  H14  0.020
 V47  plan-2  C4   0.020
 V47  plan-2  C5   0.020
 V47  plan-2  C3   0.020
 V47  plan-2  C2   0.020
 V47  plan-2  C1   0.020
 V47  plan-2  N1   0.020
 V47  plan-2  N2   0.020
 V47  plan-2  N4   0.020
 V47  plan-2  N3   0.020
 V47  plan-2  C    0.020
 V47  plan-2  N    0.020
 V47  plan-2  H6   0.020
 V47  plan-2  H2   0.020
 V47  plan-3  C    0.020
 V47  plan-3  N    0.020
 V47  plan-3  H18  0.020
 V47  plan-3  H19  0.020
 V47  plan-4  C8   0.020
 V47  plan-4  C9   0.020
 V47  plan-4  C10  0.020
 V47  plan-4  O1   0.020
 V47  plan-5  C14  0.020
 V47  plan-5  C15  0.020
 V47  plan-5  H5   0.020
 V47  plan-5  O3   0.020
 V47  plan-5  O2   0.020

