# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 05:18:00 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-1~{H}-imidazo[2,1-f]purin-3-yl)oxolan-2-yl]methyl dihydrogen phosphite
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1COP(O)O)N2C(=O)Nc3c4nccn4cnc23
#
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
 U7T  U7T  "[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-1~{H}-imidazo[2,1-f]purin-3-yl)oxolan-2-yl]methyl dihydrogen phosphite"  ligand  38  24  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U7T
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
 U7T  P     P  P     0   0.896  20.3667  25.0670  27.3245
 U7T  OP1   O  OH1   0  -0.768  20.8393  25.8539  28.6868
 U7T  OP2   O  OH1   0  -0.759  20.6139  23.5105  27.7679
 U7T  O5'   O  O2    0  -0.598  18.7564  25.0238  27.6353
 U7T  C4    C  CR15  0  -0.105  18.6301  19.0291  24.6912
 U7T  N3    N  N     0  -0.523  17.9376  20.0717  25.2684
 U7T  C2    C  CR16  0   0.147  18.3707  21.1141  26.0290
 U7T  N1    N  NR5   0  -0.624  15.2290  22.7125  26.5449
 U7T  C6    C  CR56  0   0.203  15.7395  20.8670  25.4273
 U7T  C5    C  CR15  0  -0.199  17.6836  18.2881  24.0481
 U7T  C2'   C  CH2   0  -0.520  15.9251  23.8412  28.6837
 U7T  C5'   C  CH2   0  -0.185  17.9740  26.1536  27.2991
 U7T  C4'   C  CH1   0   0.025  16.5120  25.8589  27.5448
 U7T  O4'   O  O2    0  -0.497  16.0296  24.8940  26.6167
 U7T  C1'   C  CH1   0   0.236  15.2784  23.9241  27.3102
 U7T  C3'   C  CH1   0  -0.031  16.2015  25.3153  28.9532
 U7T  O3'   O  OH1   0  -0.669  15.0579  25.9966  29.4226
 U7T  C1    C  CR56  0   0.453  16.2722  21.8802  26.1820
 U7T  N2    N  N     0  -0.428  17.5676  22.0158  26.4903
 U7T  C3    C  CR56  0   0.523  16.6007  19.8842  24.9258
 U7T  N4    N  N     0  -0.464  16.4326  18.8126  24.1916
 U7T  N5    N  NR15  0  -0.748  14.3917  21.0817  25.3274
 U7T  C7    C  CR5   0   0.662  14.0456  22.2262  25.9989
 U7T  H1    H  HOH1  0   0.479  21.5588  26.4692  28.5031
 U7T  H3    H  HOH1  0   0.485  21.2539  23.0849  27.1858
 U7T  H5    H  HCR5  0   0.306  19.6962  18.9215  24.7936
 U7T  H4    H  HCR6  0   0.303  19.4313  21.1610  26.2352
 U7T  H6    H  HCR5  0   0.264  17.8504  17.3861  23.4796
 U7T  H2'   H  HCH2  0   0.266  15.2721  23.3836  29.4275
 U7T  H2''  H  HCH2  0   0.264  16.8566  23.2772  28.6477
 U7T  H5''  H  HCH2  0   0.237  18.1205  26.4393  26.2504
 U7T  H5'   H  HCH2  0   0.226  18.2454  27.0207  27.9115
 U7T  H4'   H  HCH1  0   0.248  15.9749  26.8052  27.4037
 U7T  H1'   H  HCH1  0   0.248  14.2367  24.2434  27.4141
 U7T  H3'   H  HCH1  0   0.246  17.0471  25.4529  29.6357
 U7T  H7    H  HOH1  0   0.451  14.8238  25.6333  30.2827
 U7T  H2    H  HNR5  0   0.428  13.7291  20.5029  24.8348
 U7T  O4    O  O     0  -0.479  12.9377  22.7118  26.1021

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
 U7T  C5   N4    aromatic  1.364  0.020  1.364
 U7T  C5   C4    aromatic  1.363  0.020  1.363
 U7T  N4   C3    aromatic  1.310  0.020  1.310
 U7T  C4   N3    aromatic  1.378  0.020  1.378
 U7T  C3   C6    aromatic  1.400  0.020  1.400
 U7T  C3   N3    aromatic  1.393  0.020  1.393
 U7T  N5   C6    single    1.368  0.020  1.368
 U7T  N5   C7    single    1.371  0.020  1.371
 U7T  C6   C1    aromatic  1.371  0.020  1.371
 U7T  N3   C2    aromatic  1.361  0.020  1.361
 U7T  O4   C7    double    1.214  0.020  1.214
 U7T  C7   N1    single    1.391  0.020  1.391
 U7T  C1   N1    single    1.383  0.020  1.383
 U7T  C1   N2    aromatic  1.339  0.020  1.339
 U7T  C2   N2    aromatic  1.293  0.020  1.293
 U7T  N1   C1'   single    1.434  0.020  1.434
 U7T  O4'  C1'   single    1.409  0.020  1.409
 U7T  O4'  C4'   single    1.423  0.020  1.423
 U7T  C5'  C4'   single    1.511  0.020  1.511
 U7T  C5'  O5'   single    1.415  0.020  1.415
 U7T  C1'  C2'   single    1.520  0.020  1.520
 U7T  P    O5'   single    1.641  0.020  1.641
 U7T  P    OP1   single    1.643  0.020  1.643
 U7T  P    OP2   single    1.637  0.020  1.637
 U7T  C4'  C3'   single    1.541  0.020  1.541
 U7T  C2'  C3'   single    1.524  0.020  1.524
 U7T  C3'  O3'   single    1.411  0.020  1.411
 U7T  OP1  H1    single    0.850  0.020  0.980
 U7T  OP2  H3    single    0.850  0.020  0.980
 U7T  C4   H5    single    0.930  0.020  1.080
 U7T  C2   H4    single    0.930  0.020  1.080
 U7T  C5   H6    single    0.930  0.020  1.080
 U7T  C2'  H2'   single    0.970  0.020  1.090
 U7T  C2'  H2''  single    0.970  0.020  1.090
 U7T  C5'  H5''  single    0.970  0.020  1.090
 U7T  C5'  H5'   single    0.970  0.020  1.090
 U7T  C4'  H4'   single    0.970  0.020  1.090
 U7T  C1'  H1'   single    0.970  0.020  1.090
 U7T  C3'  H3'   single    0.970  0.020  1.090
 U7T  O3'  H7    single    0.850  0.020  0.980
 U7T  N5   H2    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
 U7T  O5'   P    OP2    94.12  3.000
 U7T  OP2   P    OP1   100.80  3.000
 U7T  O5'   P    OP1    97.93  3.000
 U7T  H1    OP1  P     111.25  3.000
 U7T  H3    OP2  P     110.88  3.000
 U7T  C5'   O5'  P     118.48  3.000
 U7T  H5    C4   C5    132.71  3.000
 U7T  H5    C4   N3    122.23  3.000
 U7T  C5    C4   N3    105.06  3.000
 U7T  C3    N3   C2    123.09  3.000
 U7T  C2    N3   C4    130.81  3.000
 U7T  C3    N3   C4    106.11  3.000
 U7T  H4    C2   N2    120.73  3.000
 U7T  H4    C2   N3    116.86  3.000
 U7T  N2    C2   N3    122.42  3.000
 U7T  C7    N1   C1    109.16  3.000
 U7T  C1    N1   C1'   128.51  3.000
 U7T  C7    N1   C1'   122.29  3.000
 U7T  N5    C6   C3    133.63  3.000
 U7T  N5    C6   C1    107.87  3.000
 U7T  C3    C6   C1    118.49  3.000
 U7T  H6    C5   N4    121.23  3.000
 U7T  H6    C5   C4    126.55  3.000
 U7T  N4    C5   C4    112.22  3.000
 U7T  H2''  C2'  H2'   108.50  3.000
 U7T  H2''  C2'  C3'   110.58  3.000
 U7T  H2'   C2'  C3'   113.21  3.000
 U7T  H2''  C2'  C1'   111.22  3.000
 U7T  H2'   C2'  C1'   112.60  3.000
 U7T  C3'   C2'  C1'   100.61  3.000
 U7T  H5'   C5'  H5''  107.17  3.000
 U7T  H5'   C5'  C4'   107.64  3.000
 U7T  H5''  C5'  C4'   109.60  3.000
 U7T  H5'   C5'  O5'   111.23  3.000
 U7T  H5''  C5'  O5'   111.19  3.000
 U7T  C4'   C5'  O5'   109.92  3.000
 U7T  H4'   C4'  C3'   108.85  3.000
 U7T  H4'   C4'  O4'   109.57  3.000
 U7T  C3'   C4'  O4'   106.77  3.000
 U7T  H4'   C4'  C5'   106.52  3.000
 U7T  C3'   C4'  C5'   114.34  3.000
 U7T  O4'   C4'  C5'   110.73  3.000
 U7T  C1'   O4'  C4'   109.05  3.000
 U7T  H1'   C1'  O4'   110.69  3.000
 U7T  H1'   C1'  C2'   109.57  3.000
 U7T  O4'   C1'  C2'   104.79  3.000
 U7T  H1'   C1'  N1    105.33  3.000
 U7T  C2'   C1'  N1    116.80  3.000
 U7T  O4'   C1'  N1    109.71  3.000
 U7T  H3'   C3'  O3'   110.96  3.000
 U7T  H3'   C3'  C4'   111.69  3.000
 U7T  O3'   C3'  C4'   107.27  3.000
 U7T  H3'   C3'  C2'   111.82  3.000
 U7T  O3'   C3'  C2'   112.26  3.000
 U7T  C4'   C3'  C2'   102.49  3.000
 U7T  H7    O3'  C3'   108.19  3.000
 U7T  N2    C1   C6    125.29  3.000
 U7T  N2    C1   N1    127.48  3.000
 U7T  C6    C1   N1    107.23  3.000
 U7T  C1    N2   C2    116.64  3.000
 U7T  N4    C3   C6    134.14  3.000
 U7T  C6    C3   N3    114.08  3.000
 U7T  N4    C3   N3    111.79  3.000
 U7T  C3    N4   C5    104.82  3.000
 U7T  H2    N5   C7    123.54  3.000
 U7T  H2    N5   C6    126.36  3.000
 U7T  C7    N5   C6    110.10  3.000
 U7T  N5    C7   O4    127.28  3.000
 U7T  O4    C7   N1    127.10  3.000
 U7T  N5    C7   N1    105.62  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
 U7T  CONST_01  C3    N4   C5   C4      0.00   0.0  0
 U7T  CONST_02  N4    C3   N3   C4      0.00   0.0  0
 U7T  CONST_03  C6    C3   N3   C4    180.00   0.0  0
 U7T  CONST_04  N2    C2   N3   C4    180.00   0.0  0
 U7T  CONST_05  N4    C5   C4   N3      0.00   0.0  0
 U7T  CONST_06  C5    N4   C3   N3      0.00   0.0  0
 U7T  CONST_07  C1    C6   C3   N3      0.00   0.0  0
 U7T  CONST_08  C1    N2   C2   N3      0.00   0.0  0
 U7T  CONST_09  C5    C4   N3   C2    180.00   0.0  0
 U7T  CONST_10  N4    C3   N3   C2    180.00   0.0  0
 U7T  CONST_11  C6    C3   N3   C2      0.00   0.0  0
 U7T  CONST_12  C6    C1   N2   C2      0.00   0.0  0
 U7T  CONST_13  C5    N4   C3   C6    180.00   0.0  0
 U7T  CONST_14  C3    N3   C4   C5      0.00   0.0  0
 U7T  CONST_15  N4    C3   C6   C1    180.00   0.0  0
 U7T  CONST_16  C3    C6   C1   N2      0.00   0.0  0
 U7T  CONST_17  C3    N3   C2   N2      0.00   0.0  0
 U7T  CONST_18  C6    N5   C7   N1      0.00   0.0  0
 U7T  CONST_19  N5    C6   C1   N1      0.00   0.0  0
 U7T  CONST_20  C7    N1   C1   C6      0.00   0.0  0
 U7T  CONST_21  C1'   N1   C1   C6    180.00   0.0  0
 U7T  CONST_22  N5    C7   N1   C1'   180.00   0.0  0
 U7T  CONST_23  C7    N5   C6   C1      0.00   0.0  0
 U7T  CONST_24  N5    C7   N1   C1      0.00   0.0  0
 U7T  CONST_25  O4    C7   N5   C6    180.00   0.0  0
 U7T  CONST_26  O4    C7   N1   C1'     0.00   0.0  0
 U7T  CONST_27  O4    C7   N1   C1    180.00   0.0  0
 U7T  CONST_28  H4    C2   N3   C4      0.00   0.0  0
 U7T  CONST_29  H6    C5   C4   N3    180.00   0.0  0
 U7T  CONST_30  H5    C4   N3   C2      0.00   0.0  0
 U7T  CONST_31  H4    C2   N2   C1    180.00   0.0  0
 U7T  CONST_32  H6    C5   N4   C3    180.00   0.0  0
 U7T  CONST_33  H5    C4   N3   C3    180.00   0.0  0
 U7T  CONST_34  H4    C2   N3   C3    180.00   0.0  0
 U7T  CONST_35  H5    C4   C5   N4    180.00   0.0  0
 U7T  CONST_36  H2    N5   C7   N1    180.00   0.0  0
 U7T  CONST_37  H2    N5   C6   C1    180.00   0.0  0
 U7T  CONST_38  H2    N5   C7   O4      0.00   0.0  0
 U7T  Var_01    N5    C6   C3   N3    179.10  30.0  1
 U7T  Var_02    N1    C1   N2   C2   -179.48  30.0  1
 U7T  Var_03    C3    C6   C1   N1    179.67  30.0  1
 U7T  Var_04    N2    C1   N1   C1'     1.25  30.0  1
 U7T  Var_05    N5    C6   C1   N2   -179.54  30.0  1
 U7T  Var_06    C7    N1   C1   N2    178.95  30.0  1
 U7T  Var_07    C7    N5   C6   C3   -178.87  30.0  1
 U7T  Var_08    N5    C6   C3   N4     -0.62  30.0  1
 U7T  Var_09    H2    N5   C6   C3      0.81  30.0  1
 U7T  Var_10    C4'   C5'  O5'  P     174.70  30.0  1
 U7T  Var_11    C5'   O5'  P    OP1    83.92  30.0  3
 U7T  Var_12    C5'   O5'  P    OP2  -174.55  30.0  3
 U7T  Var_13    H5''  C5'  O5'  P      53.16  30.0  1
 U7T  Var_14    H5'   C5'  O5'  P     -66.19  30.0  1

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
 U7T  chir_01  C4'  O4'  C5'  C3'  positiv
 U7T  chir_02  C1'  O4'  N1   C2'  negativ
 U7T  chir_03  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
 U7T  plan-1  N1   0.020
 U7T  plan-1  C6   0.020
 U7T  plan-1  C1'  0.020
 U7T  plan-1  C1   0.020
 U7T  plan-1  N5   0.020
 U7T  plan-1  C7   0.020
 U7T  plan-1  H2   0.020
 U7T  plan-1  O4   0.020
 U7T  plan-2  C4   0.020
 U7T  plan-2  N3   0.020
 U7T  plan-2  C2   0.020
 U7T  plan-2  C6   0.020
 U7T  plan-2  C5   0.020
 U7T  plan-2  C3   0.020
 U7T  plan-2  N4   0.020
 U7T  plan-2  H5   0.020
 U7T  plan-2  H6   0.020

