# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 21:33:14 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
#   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)C[P@@](O)(=O)O[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
 F2A  F2A  2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine  ligand  48  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F2A
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
 F2A  PA    P  P     0   1.294  -3.4439  -3.1320  33.2531
 F2A  O1A   O  OH1   0  -0.649  -4.4372  -3.0896  34.5186
 F2A  O2A   O  O     0  -0.591  -2.6345  -1.9128  33.0512
 F2A  C3A   C  CH2   0  -1.079  -2.4867  -4.6544  33.4580
 F2A  O5'   O  O2    0  -0.588  -4.4356  -3.5740  32.0885
 F2A  PB    P  P     0   1.320  -3.3950  -6.1937  33.2019
 F2A  O1B   O  O     0  -0.728  -3.6329  -6.6073  31.8082
 F2A  O2B   O  OH1   0  -0.700  -4.7446  -6.1334  34.0487
 F2A  O3B   O  O2    0  -0.566  -2.4415  -7.2955  33.9436
 F2A  PG    P  P     0   1.394  -2.3808  -7.8782  35.4456
 F2A  O1G   O  O     0  -0.727  -1.1081  -8.5680  35.6998
 F2A  O2G   O  OH1   0  -0.578  -3.7038  -8.7379  35.6315
 F2A  O3G   O  OH1   0  -0.794  -2.7130  -6.5487  36.2538
 F2A  C5'   C  CH2   0  -0.218  -5.5930  -2.8354  31.6907
 F2A  C4'   C  CH1   0   0.047  -5.6362  -2.7464  30.1836
 F2A  O4'   O  O2    0  -0.550  -4.5751  -1.9307  29.7112
 F2A  C1'   C  CH1   0   0.180  -3.7743  -2.6162  28.7893
 F2A  N9    N  NR5   0  -0.531  -2.5537  -3.0768  29.4342
 F2A  C4    C  CR56  0   0.534  -1.5825  -2.2404  29.9090
 F2A  N3    N  N     0  -0.500  -1.5099  -0.9170  29.7987
 F2A  C2    C  CR16  0   0.064  -0.4373  -0.4358  30.4010
 F2A  N1    N  N     0  -0.497   0.5094  -1.0977  31.0622
 F2A  C6    C  CR6   0   0.350   0.4247  -2.4281  31.1569
 F2A  N6    N  NH2   0  -0.780   1.3570  -3.0974  31.8409
 F2A  C5    C  CR56  0   0.039  -0.6660  -3.0625  30.5396
 F2A  N7    N  N     0  -0.417  -1.0594  -4.3741  30.4656
 F2A  C8    C  CR15  0   0.085  -2.1863  -4.3374  29.8164
 F2A  C2'   C  CH2   0  -0.543  -4.6377  -3.7437  28.2535
 F2A  C3'   C  CH1   0  -0.019  -5.5261  -4.0980  29.4473
 F2A  O3'   O  OH1   0  -0.686  -6.7632  -4.6675  29.1265
 F2A  HO1A  H  HOH1  0   0.533  -4.1227  -2.5374  35.2474
 F2A  H3A   H  HCH2  0   0.344  -1.6647  -4.6577  32.7378
 F2A  H3AA  H  HCH2  0   0.342  -2.0386  -4.6291  34.4543
 F2A  HO2B  H  HOH1  0   0.496  -4.7328  -5.6418  34.8818
 F2A  HO2G  H  HOH1  0   0.538  -3.5978  -9.6813  35.4465
 F2A  HO3G  H  HOH1  0   0.527  -2.6995  -6.6260  37.2182
 F2A  H5'   H  HCH2  0   0.220  -6.4790  -3.3604  32.0523
 F2A  H5'A  H  HCH2  0   0.257  -5.5982  -1.8313  32.1215
 F2A  H4'   H  HCH1  0   0.297  -6.5897  -2.2703  29.9198
 F2A  H1'   H  HCH1  0   0.279  -3.4715  -1.9146  28.0120
 F2A  H2    H  HCR6  0   0.272  -0.3039   0.6400  30.3535
 F2A  HN6   H  HNH2  0   0.384   2.1572  -2.6118  32.2075
 F2A  HN6A  H  HNH2  0   0.393   1.3682  -4.1020  31.8514
 F2A  H8    H  HCR5  0   0.310  -2.7837  -5.2056  29.5894
 F2A  H2'   H  HCH2  0   0.248  -5.2495  -3.3401  27.4427
 F2A  H2'A  H  HCH2  0   0.302  -4.0777  -4.5860  27.8506
 F2A  H3'   H  HCH1  0   0.248  -5.0292  -4.8383  30.0795
 F2A  HO3'  H  HOH1  0   0.445  -7.2374  -4.0740  28.5330

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
 F2A  O5'  PA    single    1.592  0.020  1.592
 F2A  PA   C3A   single    1.810  0.020  1.810
 F2A  PA   O2A   double    1.477  0.020  1.477
 F2A  PA   O1A   single    1.609  0.020  1.609
 F2A  O1A  HO1A  single    0.850  0.020  0.980
 F2A  PB   C3A   single    1.806  0.020  1.806
 F2A  C3A  H3A   single    0.970  0.020  1.090
 F2A  C3A  H3AA  single    0.970  0.020  1.090
 F2A  C5'  O5'   single    1.429  0.020  1.429
 F2A  O1B  PB    double    1.473  0.020  1.473
 F2A  PB   O2B   single    1.594  0.020  1.594
 F2A  PB   O3B   single    1.635  0.020  1.635
 F2A  O2B  HO2B  single    0.850  0.020  0.980
 F2A  O3B  PG    single    1.612  0.020  1.612
 F2A  PG   O1G   double    1.470  0.020  1.470
 F2A  PG   O3G   single    1.591  0.020  1.591
 F2A  PG   O2G   single    1.589  0.020  1.589
 F2A  O2G  HO2G  single    0.850  0.020  0.980
 F2A  O3G  HO3G  single    0.850  0.020  0.980
 F2A  C4'  C5'   single    1.510  0.020  1.510
 F2A  C5'  H5'   single    0.970  0.020  1.090
 F2A  C5'  H5'A  single    0.970  0.020  1.090
 F2A  C3'  C4'   single    1.543  0.020  1.543
 F2A  O4'  C4'   single    1.419  0.020  1.419
 F2A  C4'  H4'   single    0.970  0.020  1.090
 F2A  C1'  O4'   single    1.400  0.020  1.400
 F2A  C2'  C1'   single    1.518  0.020  1.518
 F2A  C1'  N9    single    1.455  0.020  1.455
 F2A  C1'  H1'   single    0.970  0.020  1.090
 F2A  C4   N9    aromatic  1.367  0.020  1.367
 F2A  N9   C8    aromatic  1.368  0.020  1.368
 F2A  N3   C4    aromatic  1.330  0.020  1.330
 F2A  C4   C5    aromatic  1.383  0.020  1.383
 F2A  C2   N3    aromatic  1.321  0.020  1.321
 F2A  C2   N1    aromatic  1.331  0.020  1.331
 F2A  C2   H2    single    0.930  0.020  1.080
 F2A  N1   C6    aromatic  1.336  0.020  1.336
 F2A  C6   N6    single    1.336  0.020  1.336
 F2A  C6   C5    aromatic  1.405  0.020  1.405
 F2A  N6   HN6   single    0.860  0.020  1.020
 F2A  N6   HN6A  single    0.860  0.020  1.020
 F2A  C5   N7    aromatic  1.371  0.020  1.371
 F2A  C8   N7    aromatic  1.301  0.020  1.301
 F2A  C8   H8    single    0.930  0.020  1.080
 F2A  C2'  C3'   single    1.530  0.020  1.530
 F2A  C2'  H2'   single    0.970  0.020  1.090
 F2A  C2'  H2'A  single    0.970  0.020  1.090
 F2A  O3'  C3'   single    1.399  0.020  1.399
 F2A  C3'  H3'   single    0.970  0.020  1.090
 F2A  O3'  HO3'  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
 F2A  O5'   PA   C3A  100.30  3.000
 F2A  C3A   PA   O2A  114.83  3.000
 F2A  O5'   PA   O2A  118.06  3.000
 F2A  O2A   PA   O1A  115.08  3.000
 F2A  C3A   PA   O1A  105.04  3.000
 F2A  O5'   PA   O1A  101.42  3.000
 F2A  HO1A  O1A  PA   114.02  3.000
 F2A  H3AA  C3A  H3A  107.01  3.000
 F2A  H3AA  C3A  PB   110.81  3.000
 F2A  H3A   C3A  PB   106.40  3.000
 F2A  H3AA  C3A  PA   107.50  3.000
 F2A  H3A   C3A  PA   109.01  3.000
 F2A  PB    C3A  PA   115.78  3.000
 F2A  C5'   O5'  PA   124.36  3.000
 F2A  O3B   PB   O2B  106.16  3.000
 F2A  O3B   PB   O1B  109.52  3.000
 F2A  O2B   PB   O1B  112.11  3.000
 F2A  O3B   PB   C3A  102.52  3.000
 F2A  O2B   PB   C3A  108.56  3.000
 F2A  O1B   PB   C3A  117.05  3.000
 F2A  HO2B  O2B  PB   117.79  3.000
 F2A  PG    O3B  PB   133.48  3.000
 F2A  O3G   PG   O2G  102.65  3.000
 F2A  O2G   PG   O1G  116.55  3.000
 F2A  O3G   PG   O1G  119.02  3.000
 F2A  O2G   PG   O3B  105.86  3.000
 F2A  O3G   PG   O3B   99.40  3.000
 F2A  O1G   PG   O3B  111.31  3.000
 F2A  HO2G  O2G  PG   114.47  3.000
 F2A  HO3G  O3G  PG   115.89  3.000
 F2A  H5'A  C5'  H5'  107.91  3.000
 F2A  H5'A  C5'  C4'  109.82  3.000
 F2A  H5'   C5'  C4'  109.62  3.000
 F2A  H5'A  C5'  O5'  111.65  3.000
 F2A  H5'   C5'  O5'  108.45  3.000
 F2A  C4'   C5'  O5'  109.35  3.000
 F2A  H4'   C4'  C3'  109.09  3.000
 F2A  H4'   C4'  O4'  108.67  3.000
 F2A  C3'   C4'  O4'  106.93  3.000
 F2A  H4'   C4'  C5'  106.87  3.000
 F2A  O4'   C4'  C5'  110.16  3.000
 F2A  C3'   C4'  C5'  114.99  3.000
 F2A  C1'   O4'  C4'  111.43  3.000
 F2A  H1'   C1'  C2'  112.61  3.000
 F2A  H1'   C1'  N9   106.66  3.000
 F2A  C2'   C1'  N9   113.48  3.000
 F2A  H1'   C1'  O4'  108.25  3.000
 F2A  N9    C1'  O4'  110.05  3.000
 F2A  C2'   C1'  O4'  105.71  3.000
 F2A  C8    N9   C4   106.02  3.000
 F2A  C8    N9   C1'  129.86  3.000
 F2A  C4    N9   C1'  123.80  3.000
 F2A  C5    C4   N3   126.37  3.000
 F2A  C5    C4   N9   105.39  3.000
 F2A  N3    C4   N9   128.23  3.000
 F2A  C2    N3   C4   111.65  3.000
 F2A  H2    C2   N1   115.30  3.000
 F2A  H2    C2   N3   116.17  3.000
 F2A  N1    C2   N3   128.53  3.000
 F2A  C6    N1   C2   119.02  3.000
 F2A  C5    C6   N6   122.72  3.000
 F2A  C5    C6   N1   117.88  3.000
 F2A  N6    C6   N1   119.39  3.000
 F2A  HN6A  N6   HN6  118.06  3.000
 F2A  HN6A  N6   C6   120.93  3.000
 F2A  HN6   N6   C6   120.01  3.000
 F2A  N7    C5   C6   132.72  3.000
 F2A  N7    C5   C4   110.72  3.000
 F2A  C6    C5   C4   116.51  3.000
 F2A  C8    N7   C5   104.38  3.000
 F2A  H8    C8   N7   124.22  3.000
 F2A  H8    C8   N9   122.31  3.000
 F2A  N7    C8   N9   113.47  3.000
 F2A  H2'A  C2'  H2'  107.40  3.000
 F2A  H2'A  C2'  C3'  114.10  3.000
 F2A  H2'   C2'  C3'  109.84  3.000
 F2A  H2'A  C2'  C1'  114.37  3.000
 F2A  H2'   C2'  C1'  107.82  3.000
 F2A  C3'   C2'  C1'  103.12  3.000
 F2A  H3'   C3'  O3'  105.00  3.000
 F2A  H3'   C3'  C2'  110.14  3.000
 F2A  O3'   C3'  C2'  115.39  3.000
 F2A  H3'   C3'  C4'  110.47  3.000
 F2A  O3'   C3'  C4'  113.76  3.000
 F2A  C2'   C3'  C4'  102.18  3.000
 F2A  HO3'  O3'  C3'  109.00  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
 F2A  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 F2A  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 F2A  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 F2A  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 F2A  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 F2A  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 F2A  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 F2A  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 F2A  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 F2A  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 F2A  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 F2A  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 F2A  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 F2A  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 F2A  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 F2A  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 F2A  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 F2A  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 F2A  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 F2A  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 F2A  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 F2A  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 F2A  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 F2A  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 F2A  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 F2A  CONST_26  HN6   N6   C6   N1      0.00   0.0  0
 F2A  CONST_27  HN6A  N6   C6   N1    180.00   0.0  0
 F2A  Var_01    C4'   C5'  O5'  PA    134.33  30.0  2
 F2A  Var_02    O1B   PB   C3A  PA     78.92  30.0  1
 F2A  Var_03    PB    C3A  PA   O1A    70.56  30.0  3
 F2A  Var_04    O1G   PG   O3B  PB   -163.96  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
 F2A  chir_03  C4'  C5'  C3'  O4'  positiv
 F2A  chir_04  C1'  O4'  N9   C2'  negativ
 F2A  chir_05  C3'  O3'  C4'  C2'  positiv
 F2A  chir_06  PA   C3A  O2A  O1A  both
 F2A  chir_07  PB   O2B  O1B  C3A  both

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
 F2A  plan-1  C1'   0.020
 F2A  plan-1  N9    0.020
 F2A  plan-1  C4    0.020
 F2A  plan-1  N3    0.020
 F2A  plan-1  C2    0.020
 F2A  plan-1  N1    0.020
 F2A  plan-1  C6    0.020
 F2A  plan-1  N6    0.020
 F2A  plan-1  C5    0.020
 F2A  plan-1  N7    0.020
 F2A  plan-1  C8    0.020
 F2A  plan-1  H2    0.020
 F2A  plan-1  H8    0.020
 F2A  plan-2  C6    0.020
 F2A  plan-2  N6    0.020
 F2A  plan-2  HN6   0.020
 F2A  plan-2  HN6A  0.020

