# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 00:07:20 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](Cl)[P](O)(O)=O)O3
#
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
 VA4  VA4  5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine  ligand  44  31  .  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_VA4
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
 VA4  N1   N   N      0  -0.463  -4.7163  -3.4591  -0.4970
 VA4  C2   C   CR16   0   0.086  -4.6432  -2.6302  -1.5359
 VA4  N3   N   N      0  -0.494  -4.1856  -1.3914  -1.5665
 VA4  C4   C   CR56   0   0.440  -3.7461  -0.9951  -0.3738
 VA4  C5   C   CR56   0   0.184  -3.7682  -1.7381   0.7965
 VA4  C6   C   CR6    0   0.297  -4.2810  -3.0404   0.6973
 VA4  N6   N   NH2    0  -0.848  -4.3837  -3.8583   1.7566
 VA4  N7   N   N      0  -0.486  -3.2343  -1.0250   1.8351
 VA4  C8   C   CR15   0   0.137  -2.8908   0.1127   1.3080
 VA4  N9   N   NR5    0  -0.553  -3.2085   0.2072  -0.0206
 VA4  PA   P   P      0   1.327   0.5819   2.0609   1.8012
 VA4  PB   P   P      0   1.274   1.7584  -0.2911   0.5002
 VA4  PG   P   P      0   1.175   1.9761  -2.4975  -1.7434
 VA4  C1'  C   CR15   0   0.243  -3.0576   1.3562  -0.8832
 VA4  O1A  O   OP    -1  -0.870  -0.5039   1.7797   2.7999
 VA4  O2B  O   O      0  -0.847   1.8162  -1.0183   1.8114
 VA4  O1G  O   OP    -1  -0.959   2.6789  -3.3257  -0.6695
 VA4  C2'  C   CH2    0  -0.529  -3.9313   2.5364  -0.4672
 VA4  O2A  O   O      0  -0.839   1.9608   2.4062   2.2780
 VA4  O1B  O   OP    -1  -0.838   3.0001   0.3097  -0.0949
 VA4  O2G  O   OP    -1  -0.960   0.9757  -3.2958  -2.5822
 VA4  C3'  C   CR15   0  -0.020  -3.1298   3.7173  -0.9900
 VA4  O3'  O   OH1    0  -0.693  -3.2910   3.8929  -2.3796
 VA4  O3A  O   O2     0  -0.719   0.6282   0.9332   0.6395
 VA4  C3B  C   CH1    0  -0.710   0.9100  -1.2542  -0.8053
 VA4  CL1  CL  CL     0  -0.211  -0.5161  -2.0850  -0.0559
 VA4  O3G  O   O      0  -0.758   2.8947  -1.6111  -2.5846
 VA4  C4'  C   CR15   0  -0.026  -1.6983   3.2372  -0.7333
 VA4  O4'  O   O      0  -0.520  -1.7324   1.8209  -0.8571
 VA4  C5'  C   CH2    0  -0.128  -1.2204   3.6795   0.6364
 VA4  O5'  O   O2     0  -0.586   0.1204   3.3462   0.8641
 VA4  H1   H   HCR6   0   0.272  -5.0289  -3.0202  -2.4723
 VA4  H2   H   HNH2   0   0.381  -4.5523  -4.8350   1.5797
 VA4  H3   H   HNH2   0   0.387  -3.8370  -3.6507   2.5759
 VA4  H4   H   HCR5   0   0.316  -2.3828   0.9103   1.8367
 VA4  H5   H   HCR5   0   0.320  -3.3231   1.0095  -1.8853
 VA4  H8   H   HCH2   0   0.248  -4.9417   2.4747  -0.8717
 VA4  H9   H   HCH2   0   0.310  -4.0164   2.5857   0.6209
 VA4  H12  H   HCR5   0   0.263  -3.3526   4.6430  -0.4435
 VA4  H13  H   HOH1   0   0.450  -4.2232   4.0563  -2.5535
 VA4  H14  H   HCH1   0   0.183   0.4637  -0.5572  -1.5183
 VA4  H15  H   HCR5   0   0.243  -1.0181   3.6328  -1.4952
 VA4  H16  H   HCH2   0   0.306  -1.3007   4.7725   0.6621
 VA4  H17  H   HCH2   0   0.215  -1.8731   3.2858   1.4241

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
 VA4  C2   N1   aromatic  1.331  0.020  1.331
 VA4  C2   N3   aromatic  1.321  0.020  1.321
 VA4  N1   C6   aromatic  1.338  0.020  1.338
 VA4  N3   C4   aromatic  1.331  0.020  1.331
 VA4  C6   N6   single    1.342  0.020  1.342
 VA4  C6   C5   aromatic  1.403  0.020  1.403
 VA4  C4   C5   aromatic  1.386  0.020  1.386
 VA4  C4   N9   aromatic  1.364  0.020  1.364
 VA4  C2'  C1'  single    1.526  0.020  1.526
 VA4  C2'  C3'  single    1.520  0.020  1.520
 VA4  C1'  N9   single    1.445  0.020  1.445
 VA4  C1'  O4'  single    1.405  0.020  1.405
 VA4  C5   N7   aromatic  1.368  0.020  1.368
 VA4  N9   C8   aromatic  1.369  0.020  1.369
 VA4  O3'  C3'  single    1.410  0.020  1.410
 VA4  C3'  C4'  single    1.531  0.020  1.531
 VA4  O4'  C4'  single    1.422  0.020  1.422
 VA4  N7   C8   aromatic  1.300  0.020  1.300
 VA4  C4'  C5'  single    1.517  0.020  1.517
 VA4  O2B  PB   deloc     1.500  0.020  1.500
 VA4  C5'  O5'  single    1.400  0.020  1.400
 VA4  O5'  PA   single    1.656  0.020  1.656
 VA4  PB   O3A  single    1.672  0.020  1.672
 VA4  PB   O1B  deloc     1.502  0.020  1.502
 VA4  PB   C3B  single    1.831  0.020  1.831
 VA4  O3A  PA   single    1.620  0.020  1.620
 VA4  CL1  C3B  single    1.813  0.020  1.813
 VA4  PA   O2A  deloc     1.499  0.020  1.499
 VA4  PA   O1A  deloc     1.502  0.020  1.502
 VA4  C3B  PG   single    1.887  0.020  1.887
 VA4  PG   O3G  deloc     1.529  0.020  1.529
 VA4  PG   O1G  deloc     1.527  0.020  1.527
 VA4  PG   O2G  deloc     1.530  0.020  1.530
 VA4  C2   H1   single    0.930  0.020  1.080
 VA4  N6   H2   single    0.890  0.020  1.040
 VA4  N6   H3   single    0.890  0.020  1.040
 VA4  C8   H4   single    0.930  0.020  1.080
 VA4  C1'  H5   single    0.970  0.020  1.090
 VA4  C2'  H8   single    0.970  0.020  1.090
 VA4  C2'  H9   single    0.970  0.020  1.090
 VA4  C3'  H12  single    0.970  0.020  1.090
 VA4  O3'  H13  single    0.850  0.020  0.980
 VA4  C3B  H14  single    0.970  0.020  1.090
 VA4  C4'  H15  single    0.970  0.020  1.090
 VA4  C5'  H16  single    0.970  0.020  1.090
 VA4  C5'  H17  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
 VA4  C6   N1   C2   118.94  3.000
 VA4  H1   C2   N3   116.12  3.000
 VA4  H1   C2   N1   115.47  3.000
 VA4  N3   C2   N1   128.40  3.000
 VA4  C4   N3   C2   111.88  3.000
 VA4  N9   C4   C5   105.08  3.000
 VA4  N9   C4   N3   128.65  3.000
 VA4  C5   C4   N3   126.26  3.000
 VA4  N7   C5   C6   132.83  3.000
 VA4  N7   C5   C4   110.81  3.000
 VA4  C6   C5   C4   116.33  3.000
 VA4  N6   C6   C5   122.53  3.000
 VA4  C5   C6   N1   118.18  3.000
 VA4  N6   C6   N1   119.26  3.000
 VA4  H3   N6   H2   115.72  3.000
 VA4  H3   N6   C6   118.37  3.000
 VA4  H2   N6   C6   117.73  3.000
 VA4  C8   N7   C5   104.56  3.000
 VA4  H4   C8   N9   122.11  3.000
 VA4  H4   C8   N7   124.77  3.000
 VA4  N9   C8   N7   113.11  3.000
 VA4  C1'  N9   C8   127.58  3.000
 VA4  C8   N9   C4   106.38  3.000
 VA4  C1'  N9   C4   126.00  3.000
 VA4  O5'  PA   O3A   98.19  3.000
 VA4  O3A  PA   O2A  111.23  3.000
 VA4  O5'  PA   O2A  104.92  3.000
 VA4  O2A  PA   O1A  119.78  3.000
 VA4  O3A  PA   O1A  111.54  3.000
 VA4  O5'  PA   O1A  108.67  3.000
 VA4  C3B  PB   O3A   97.55  3.000
 VA4  C3B  PB   O1B  108.11  3.000
 VA4  O3A  PB   O1B  107.39  3.000
 VA4  C3B  PB   O2B  112.71  3.000
 VA4  O1B  PB   O2B  120.54  3.000
 VA4  O3A  PB   O2B  107.95  3.000
 VA4  O3G  PG   C3B  103.35  3.000
 VA4  O3G  PG   O2G  113.19  3.000
 VA4  C3B  PG   O2G  104.29  3.000
 VA4  O2G  PG   O1G  113.78  3.000
 VA4  O3G  PG   O1G  115.14  3.000
 VA4  C3B  PG   O1G  105.52  3.000
 VA4  H5   C1'  O4'  110.55  3.000
 VA4  H5   C1'  C2'  110.87  3.000
 VA4  O4'  C1'  C2'  106.22  3.000
 VA4  H5   C1'  N9   105.64  3.000
 VA4  O4'  C1'  N9   110.52  3.000
 VA4  C2'  C1'  N9   113.11  3.000
 VA4  H9   C2'  H8   107.45  3.000
 VA4  H9   C2'  C3'  110.40  3.000
 VA4  H8   C2'  C3'  113.90  3.000
 VA4  H9   C2'  C1'  110.55  3.000
 VA4  H8   C2'  C1'  112.69  3.000
 VA4  C3'  C2'  C1'  101.84  3.000
 VA4  H12  C3'  C4'  111.75  3.000
 VA4  H12  C3'  O3'  111.25  3.000
 VA4  C4'  C3'  O3'  108.13  3.000
 VA4  H12  C3'  C2'  112.13  3.000
 VA4  C4'  C3'  C2'  101.05  3.000
 VA4  O3'  C3'  C2'  112.05  3.000
 VA4  H13  O3'  C3'  108.06  3.000
 VA4  PB   O3A  PA   126.08  3.000
 VA4  H14  C3B  CL1  103.94  3.000
 VA4  H14  C3B  PG   109.07  3.000
 VA4  CL1  C3B  PG   110.37  3.000
 VA4  H14  C3B  PB   108.61  3.000
 VA4  PG   C3B  PB   116.05  3.000
 VA4  CL1  C3B  PB   108.11  3.000
 VA4  H15  C4'  C5'  109.10  3.000
 VA4  H15  C4'  O4'  108.31  3.000
 VA4  C5'  C4'  O4'  112.12  3.000
 VA4  H15  C4'  C3'  110.52  3.000
 VA4  C5'  C4'  C3'  110.76  3.000
 VA4  O4'  C4'  C3'  105.98  3.000
 VA4  C4'  O4'  C1'  110.71  3.000
 VA4  H17  C5'  H16  107.31  3.000
 VA4  H17  C5'  O5'  111.59  3.000
 VA4  H16  C5'  O5'  107.68  3.000
 VA4  H17  C5'  C4'  110.89  3.000
 VA4  H16  C5'  C4'  106.79  3.000
 VA4  O5'  C5'  C4'  112.28  3.000
 VA4  C5'  O5'  PA   122.93  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
 VA4  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 VA4  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 VA4  CONST_03  N7   C5   C6   N1   180.00   0.0  0
 VA4  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 VA4  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 VA4  CONST_06  N9   C4   N3   C2   180.00   0.0  0
 VA4  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 VA4  CONST_08  C6   C5   C4   N3     0.00   0.0  0
 VA4  CONST_09  N7   C5   C4   N3   180.00   0.0  0
 VA4  CONST_10  C8   N9   C4   N3   180.00   0.0  0
 VA4  CONST_11  C8   N7   C5   C4     0.00   0.0  0
 VA4  CONST_12  N7   C8   N9   C4     0.00   0.0  0
 VA4  CONST_13  C8   N9   C4   C5     0.00   0.0  0
 VA4  CONST_14  N9   C8   N7   C5     0.00   0.0  0
 VA4  CONST_15  N9   C4   C5   C6   180.00   0.0  0
 VA4  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 VA4  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 VA4  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 VA4  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 VA4  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 VA4  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 VA4  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 VA4  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 VA4  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 VA4  CONST_25  H4   C8   N9   C4   180.00   0.0  0
 VA4  Var_01    C4'  C5'  O5'  PA  -102.37  30.0  2
 VA4  Var_02    O2B  PB   O3A  PA    52.35  30.0  1
 VA4  Var_03    O5'  PA   O3A  PB   141.44  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
 VA4  chir_03  C1'  C2'  N9   O4'  positiv
 VA4  chir_04  C3'  O3'  C4'  C2'  positiv
 VA4  chir_05  C3B  PB   CL1  PG   positiv
 VA4  chir_06  C4'  O4'  C3'  C5'  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
 VA4  plan-1  N1   0.020
 VA4  plan-1  C2   0.020
 VA4  plan-1  N3   0.020
 VA4  plan-1  C4   0.020
 VA4  plan-1  C5   0.020
 VA4  plan-1  C6   0.020
 VA4  plan-1  N6   0.020
 VA4  plan-1  N7   0.020
 VA4  plan-1  C8   0.020
 VA4  plan-1  N9   0.020
 VA4  plan-1  C1'  0.020
 VA4  plan-1  H1   0.020
 VA4  plan-1  H4   0.020
 VA4  plan-2  C6   0.020
 VA4  plan-2  N6   0.020
 VA4  plan-2  H2   0.020
 VA4  plan-2  H3   0.020

