# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 15:56:32 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 2',3'-O-[(1R)-2-phosphonoethylidene]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@H]4O[C@@H](C[P](O)(O)=O)O[C@@H]34
#
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
 P1G  P1G  2',3'-O-[(1R)-2-phosphonoethylidene]guanosine  ligand  40  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1G
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
 P1G  O3    O  OP    -1  -0.883   3.9063   0.4176  -1.0772
 P1G  P     P  P      0   1.190   3.1455   1.6131  -0.4876
 P1G  O4    O  OP    -1  -0.912   3.8590   2.9520  -0.7275
 P1G  O2    O  O      0  -0.859   1.6557   1.6463  -0.8523
 P1G  C1P   C  CH2    0  -0.771   3.2519   1.4493   1.3792
 P1G  C1    C  CH1    0   0.310   2.5580   0.3220   2.1113
 P1G  O3'   O  O2     0  -0.505   2.9532  -0.9559   1.6624
 P1G  O2'   O  O2     0  -0.504   1.1526   0.3896   1.9862
 P1G  C2'   C  CH1    0  -0.050   0.6305  -0.8274   1.5443
 P1G  C3'   C  CH1    0  -0.035   1.8454  -1.7088   1.2595
 P1G  C4'   C  CH1    0  -0.034   1.7878  -1.9728  -0.2520
 P1G  C5'   C  CH2    0  -0.166   2.1637  -3.3917  -0.5952
 P1G  O5'   O  OH1    0  -0.655   2.1272  -3.5665  -1.9908
 P1G  O4'   O  O2     0  -0.505   0.4308  -1.7439  -0.6147
 P1G  C1'   C  CH1    0   0.141  -0.0831  -0.7083   0.1829
 P1G  N9    N  NR5    0  -0.534  -1.5087  -0.9020   0.2579
 P1G  C8    C  CR15   0   0.112  -2.1553  -2.0539   0.6332
 P1G  N7    N  N      0  -0.441  -3.4472  -1.9449   0.6004
 P1G  C5    C  CR56   0  -0.093  -3.6744  -0.6582   0.1833
 P1G  C4    C  CR56   0   0.503  -2.4789   0.0032  -0.0380
 P1G  N3    N  N      0  -0.491  -2.2920   1.2630  -0.4516
 P1G  C2    C  CR6    0   0.709  -3.4114   1.9099  -0.6571
 P1G  N2    N  NH2    0  -0.811  -3.3802   3.1929  -1.0398
 P1G  N1    N  NR16   0  -0.718  -4.6427   1.3477  -0.4719
 P1G  C6    C  CR6    0   0.513  -4.8951   0.0381  -0.0444
 P1G  O6    O  OC     0  -0.484  -6.0411  -0.3608   0.0856
 P1G  H1P1  H  HCH2   0   0.203   2.8871   2.3794   1.8297
 P1G  H1P2  H  HCH2   0   0.206   4.3117   1.4002   1.6552
 P1G  H1    H  HCH1   0   0.189   2.8017   0.3862   3.1843
 P1G  H2'   H  HCH1   0   0.260  -0.0322  -1.2554   2.3051
 P1G  H3'   H  HCH1   0   0.254   1.8111  -2.6457   1.8279
 P1G  H4'   H  HCH1   0   0.290   2.4555  -1.2609  -0.7546
 P1G  H5'1  H  HCH2   0   0.217   3.1674  -3.5729  -0.1879
 P1G  H5'2  H  HCH2   0   0.174   1.4811  -4.0819  -0.0789
 P1G  H5'   H  HOH1   0   0.431   2.3761  -4.4744  -2.1841
 P1G  H1'   H  HCH1   0   0.320   0.1271   0.2840  -0.2356
 P1G  H8    H  HCR5   0   0.264  -1.6126  -2.9442   0.9126
 P1G  HN21  H  HNH2   0   0.398  -2.4927   3.5916  -1.2924
 P1G  HN22  H  HNH2   0   0.381  -4.2041   3.6734  -1.3557
 P1G  HN1   H  HNR6   0   0.385  -5.4622   1.9142  -0.6483

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
 P1G  O3   P     deloc     1.535  0.020  1.535
 P1G  P    O4    deloc     1.536  0.020  1.536
 P1G  P    O2    deloc     1.534  0.020  1.534
 P1G  P    C1P   single    1.877  0.020  1.877
 P1G  C1P  C1    single    1.513  0.020  1.513
 P1G  C1P  H1P1  single    0.970  0.020  1.090
 P1G  C1P  H1P2  single    0.970  0.020  1.090
 P1G  C1   O3'   single    1.411  0.020  1.411
 P1G  C1   O2'   single    1.413  0.020  1.413
 P1G  C1   H1    single    0.970  0.020  1.090
 P1G  O3'  C3'   single    1.399  0.020  1.399
 P1G  O2'  C2'   single    1.396  0.020  1.396
 P1G  C2'  C3'   single    1.528  0.020  1.528
 P1G  C2'  C1'   single    1.542  0.020  1.542
 P1G  C2'  H2'   single    0.970  0.020  1.090
 P1G  C3'  C4'   single    1.535  0.020  1.535
 P1G  C3'  H3'   single    0.970  0.020  1.090
 P1G  C4'  C5'   single    1.507  0.020  1.507
 P1G  C4'  O4'   single    1.423  0.020  1.423
 P1G  C4'  H4'   single    0.970  0.020  1.090
 P1G  C5'  O5'   single    1.407  0.020  1.407
 P1G  C5'  H5'1  single    0.970  0.020  1.090
 P1G  C5'  H5'2  single    0.970  0.020  1.090
 P1G  O5'  H5'   single    0.850  0.020  0.980
 P1G  O4'  C1'   single    1.405  0.020  1.405
 P1G  C1'  N9    single    1.441  0.020  1.441
 P1G  C1'  H1'   single    0.970  0.020  1.090
 P1G  N9   C8    aromatic  1.373  0.020  1.373
 P1G  N9   C4    aromatic  1.359  0.020  1.359
 P1G  C8   N7    aromatic  1.297  0.020  1.297
 P1G  C8   H8    single    0.930  0.020  1.080
 P1G  N7   C5    aromatic  1.372  0.020  1.372
 P1G  C5   C4    aromatic  1.384  0.020  1.384
 P1G  C5   C6    aromatic  1.424  0.020  1.424
 P1G  C4   N3    aromatic  1.339  0.020  1.339
 P1G  N3   C2    aromatic  1.309  0.020  1.309
 P1G  C2   N2    single    1.339  0.020  1.339
 P1G  C2   N1    aromatic  1.366  0.020  1.366
 P1G  N2   HN21  single    0.860  0.020  1.020
 P1G  N2   HN22  single    0.860  0.020  1.020
 P1G  N1   C6    aromatic  1.401  0.020  1.401
 P1G  N1   HN1   single    0.860  0.020  1.020
 P1G  C6   O6    double    1.220  0.020  1.220

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
 P1G  C1P   P    O2    107.06  3.000
 P1G  C1P   P    O4    101.84  3.000
 P1G  O2    P    O4    113.27  3.000
 P1G  C1P   P    O3    106.62  3.000
 P1G  O2    P    O3    114.01  3.000
 P1G  O4    P    O3    112.88  3.000
 P1G  H1P2  C1P  H1P1  104.85  3.000
 P1G  H1P2  C1P  C1    106.76  3.000
 P1G  H1P1  C1P  C1    106.31  3.000
 P1G  H1P2  C1P  P     108.01  3.000
 P1G  H1P1  C1P  P     108.41  3.000
 P1G  C1    C1P  P     121.36  3.000
 P1G  H1    C1   O2'   107.66  3.000
 P1G  H1    C1   O3'   107.49  3.000
 P1G  O2'   C1   O3'   107.09  3.000
 P1G  H1    C1   C1P   109.05  3.000
 P1G  O2'   C1   C1P   112.20  3.000
 P1G  O3'   C1   C1P   113.11  3.000
 P1G  C3'   O3'  C1    110.94  3.000
 P1G  C2'   O2'  C1    111.00  3.000
 P1G  H2'   C2'  C1'   111.30  3.000
 P1G  H2'   C2'  C3'   112.64  3.000
 P1G  C1'   C2'  C3'   104.36  3.000
 P1G  H2'   C2'  O2'   110.30  3.000
 P1G  C1'   C2'  O2'   112.66  3.000
 P1G  C3'   C2'  O2'   105.34  3.000
 P1G  H3'   C3'  C4'   111.24  3.000
 P1G  H3'   C3'  C2'   111.81  3.000
 P1G  C4'   C3'  C2'   104.65  3.000
 P1G  H3'   C3'  O3'   109.60  3.000
 P1G  C4'   C3'  O3'   113.94  3.000
 P1G  C2'   C3'  O3'   105.40  3.000
 P1G  H4'   C4'  O4'   111.03  3.000
 P1G  H4'   C4'  C5'   110.76  3.000
 P1G  O4'   C4'  C5'   109.34  3.000
 P1G  H4'   C4'  C3'   108.44  3.000
 P1G  O4'   C4'  C3'   105.01  3.000
 P1G  C5'   C4'  C3'   112.13  3.000
 P1G  H5'2  C5'  H5'1  106.83  3.000
 P1G  H5'2  C5'  O5'   111.82  3.000
 P1G  H5'1  C5'  O5'   111.79  3.000
 P1G  H5'2  C5'  C4'   109.22  3.000
 P1G  H5'1  C5'  C4'   107.38  3.000
 P1G  O5'   C5'  C4'   109.65  3.000
 P1G  H5'   O5'  C5'   108.07  3.000
 P1G  C1'   O4'  C4'   108.83  3.000
 P1G  H1'   C1'  N9    109.34  3.000
 P1G  H1'   C1'  O4'   112.34  3.000
 P1G  N9    C1'  O4'   107.01  3.000
 P1G  H1'   C1'  C2'   108.54  3.000
 P1G  N9    C1'  C2'   113.68  3.000
 P1G  O4'   C1'  C2'   105.97  3.000
 P1G  C4    N9   C8    106.38  3.000
 P1G  C4    N9   C1'   127.25  3.000
 P1G  C8    N9   C1'   126.37  3.000
 P1G  H8    C8   N7    125.22  3.000
 P1G  H8    C8   N9    121.72  3.000
 P1G  N7    C8   N9    113.06  3.000
 P1G  C5    N7   C8    104.57  3.000
 P1G  C6    C5   C4    118.77  3.000
 P1G  C6    C5   N7    130.51  3.000
 P1G  C4    C5   N7    110.72  3.000
 P1G  N3    C4   C5    128.28  3.000
 P1G  N3    C4   N9    126.45  3.000
 P1G  C5    C4   N9    105.27  3.000
 P1G  C2    N3   C4    113.21  3.000
 P1G  N1    C2   N2    117.00  3.000
 P1G  N1    C2   N3    123.10  3.000
 P1G  N2    C2   N3    119.89  3.000
 P1G  HN22  N2   HN21  117.09  3.000
 P1G  HN22  N2   C2    121.93  3.000
 P1G  HN21  N2   C2    118.19  3.000
 P1G  HN1   N1   C6    115.52  3.000
 P1G  HN1   N1   C2    118.42  3.000
 P1G  C6    N1   C2    126.05  3.000
 P1G  O6    C6   N1    120.49  3.000
 P1G  O6    C6   C5    128.92  3.000
 P1G  N1    C6   C5    110.59  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
 P1G  CONST_01  C5    N7   C8  N9     0.00   0.0  0
 P1G  CONST_02  N7    C5   C4  N9     0.00   0.0  0
 P1G  CONST_03  C6    C5   C4  N9   180.00   0.0  0
 P1G  CONST_04  C2    N3   C4  N9   180.00   0.0  0
 P1G  CONST_05  C5    C4   N9  C8     0.00   0.0  0
 P1G  CONST_06  N3    C4   N9  C8   180.00   0.0  0
 P1G  CONST_07  C4    C5   N7  C8     0.00   0.0  0
 P1G  CONST_08  C6    C5   N7  C8   180.00   0.0  0
 P1G  CONST_09  C4    N9   C8  N7     0.00   0.0  0
 P1G  CONST_10  N3    C4   C5  N7   180.00   0.0  0
 P1G  CONST_11  N1    C6   C5  N7   180.00   0.0  0
 P1G  CONST_12  C2    N3   C4  C5     0.00   0.0  0
 P1G  CONST_13  C2    N1   C6  C5     0.00   0.0  0
 P1G  CONST_14  N1    C6   C5  C4     0.00   0.0  0
 P1G  CONST_15  N1    C2   N3  C4     0.00   0.0  0
 P1G  CONST_16  C6    C5   C4  N3     0.00   0.0  0
 P1G  CONST_17  C6    N1   C2  N3     0.00   0.0  0
 P1G  CONST_18  N7    C8   N9  C1'  180.00   0.0  0
 P1G  CONST_19  C5    C4   N9  C1'  180.00   0.0  0
 P1G  CONST_20  N3    C4   N9  C1'    0.00   0.0  0
 P1G  CONST_21  O6    C6   C5  N7     0.00   0.0  0
 P1G  CONST_22  O6    C6   C5  C4   180.00   0.0  0
 P1G  CONST_23  N2    C2   N3  C4   180.00   0.0  0
 P1G  CONST_24  O6    C6   N1  C2   180.00   0.0  0
 P1G  CONST_25  C6    N1   C2  N2   180.00   0.0  0
 P1G  CONST_26  H8    C8   N9  C1'    0.00   0.0  0
 P1G  CONST_27  HN1   N1   C6  C5   180.00   0.0  0
 P1G  CONST_28  HN21  N2   C2  N3     0.00   0.0  0
 P1G  CONST_29  HN22  N2   C2  N3   180.00   0.0  0
 P1G  Var_01    C1    C1P  P   O3   -67.29  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
 P1G  chir_01  C1   C1P  O3'  O2'  positiv
 P1G  chir_02  C2'  O2'  C3'  C1'  positiv
 P1G  chir_03  C3'  O3'  C4'  C2'  positiv
 P1G  chir_04  C4'  O4'  C3'  C5'  negativ
 P1G  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
 P1G  plan-1  C1'   0.020
 P1G  plan-1  N9    0.020
 P1G  plan-1  C8    0.020
 P1G  plan-1  N7    0.020
 P1G  plan-1  C5    0.020
 P1G  plan-1  C4    0.020
 P1G  plan-1  N3    0.020
 P1G  plan-1  C2    0.020
 P1G  plan-1  N2    0.020
 P1G  plan-1  N1    0.020
 P1G  plan-1  C6    0.020
 P1G  plan-1  O6    0.020
 P1G  plan-1  H8    0.020
 P1G  plan-1  HN1   0.020
 P1G  plan-2  C2    0.020
 P1G  plan-2  N2    0.020
 P1G  plan-2  HN21  0.020
 P1G  plan-2  HN22  0.020

