# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:19:06 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2',3'-O-(phosphonomethylidene)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](O[C@@H]34)[P](O)(O)=O
#
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
 P2G  P2G  2',3'-O-(phosphonomethylidene)guanosine  ligand  37  25  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P2G
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
 P2G  O6    O  OC     0  -0.474  -5.8979   0.1805   1.0254
 P2G  C6    C  CR6    0   0.506  -4.8138   0.3586   0.4960
 P2G  N1    N  NR16   0  -0.730  -4.6413   1.3783  -0.4492
 P2G  C2    C  CR6    0   0.704  -3.4839   1.6760  -1.1116
 P2G  N2    N  NH2    0  -0.836  -3.5260   2.6816  -1.9883
 P2G  N3    N  N      0  -0.516  -2.3630   1.0227  -0.9178
 P2G  C4    C  CR56   0   0.508  -2.4767   0.0392  -0.0179
 P2G  C5    C  CR56   0  -0.099  -3.5951  -0.3511   0.6949
 P2G  N7    N  N      0  -0.441  -3.3027  -1.4104   1.5168
 P2G  C8    C  CR15   0   0.092  -2.0458  -1.6494   1.3122
 P2G  N9    N  NR5    0  -0.549  -1.4833  -0.7971   0.3911
 P2G  C1'   C  CH1    0   0.195  -0.1214  -0.7992  -0.0591
 P2G  O4'   O  O2     0  -0.491   0.1543  -2.0600  -0.6068
 P2G  C2'   C  CH1    0  -0.071   0.9196  -0.5888   1.0594
 P2G  O2'   O  O2     0  -0.498   1.5194   0.6728   1.0571
 P2G  C1    C  CH1    0  -0.034   2.6793   0.5657   0.2472
 P2G  P     P  P      0   1.152   3.9359   1.9066   0.6146
 P2G  O3    O  OP    -1  -0.895   5.0671   1.5830  -0.3624
 P2G  O4    O  OP    -1  -0.894   3.1677   3.1883   0.2904
 P2G  O2    O  O      0  -0.890   4.2923   1.7304   2.0885
 P2G  O3'   O  O2     0  -0.499   3.1745  -0.7294   0.5257
 P2G  C3'   C  CH1    0  -0.054   2.0559  -1.5566   0.6831
 P2G  C4'   C  CH1    0   0.003   1.5640  -2.2333  -0.6072
 P2G  C5'   C  CH2    0  -0.168   1.8988  -3.7021  -0.6588
 P2G  O5'   O  OH1    0  -0.669   1.4520  -4.2401  -1.8779
 P2G  HN1   H  HNR6   0   0.425  -5.4629   1.9361  -0.6454
 P2G  HN21  H  HNH2   0   0.417  -2.6967   2.9146  -2.5059
 P2G  HN22  H  HNH2   0   0.419  -4.3634   3.2038  -2.1756
 P2G  H8    H  HCR5   0   0.294  -1.4716  -2.4300   1.7880
 P2G  H1'   H  HCH1   0   0.264  -0.0315   0.0012  -0.8040
 P2G  H2'   H  HCH1   0   0.282   0.4873  -0.7816   2.0444
 P2G  H1    H  HCH1   0   0.169   2.3745   0.6145  -0.8178
 P2G  H3'   H  HCH1   0   0.267   2.2611  -2.2953   1.4630
 P2G  H4'   H  HCH1   0   0.242   2.0046  -1.7239  -1.4765
 P2G  H5'1  H  HCH2   0   0.209   2.9868  -3.7940  -0.5420
 P2G  H5'2  H  HCH2   0   0.203   1.4408  -4.2012   0.2061
 P2G  H5'   H  HOH1   0   0.458   1.6523  -5.1803  -1.8821

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
 P2G  O6   C6    double    1.220  0.020  1.220
 P2G  C6   N1    aromatic  1.401  0.020  1.401
 P2G  C6   C5    aromatic  1.424  0.020  1.424
 P2G  N1   C2    aromatic  1.366  0.020  1.366
 P2G  N1   HN1   single    0.860  0.020  1.020
 P2G  C2   N2    single    1.335  0.020  1.335
 P2G  C2   N3    aromatic  1.312  0.020  1.312
 P2G  N2   HN21  single    0.860  0.020  1.020
 P2G  N2   HN22  single    0.860  0.020  1.020
 P2G  N3   C4    aromatic  1.338  0.020  1.338
 P2G  C4   C5    aromatic  1.382  0.020  1.382
 P2G  C4   N9    aromatic  1.361  0.020  1.361
 P2G  C5   N7    aromatic  1.372  0.020  1.372
 P2G  N7   C8    aromatic  1.296  0.020  1.296
 P2G  C8   N9    aromatic  1.375  0.020  1.375
 P2G  C8   H8    single    0.930  0.020  1.080
 P2G  N9   C1'   single    1.434  0.020  1.434
 P2G  C1'  O4'   single    1.402  0.020  1.402
 P2G  C1'  C2'   single    1.542  0.020  1.542
 P2G  C1'  H1'   single    0.970  0.020  1.090
 P2G  O4'  C4'   single    1.420  0.020  1.420
 P2G  C2'  O2'   single    1.397  0.020  1.397
 P2G  C2'  C3'   single    1.539  0.020  1.539
 P2G  C2'  H2'   single    0.970  0.020  1.090
 P2G  O2'  C1    single    1.419  0.020  1.419
 P2G  C1   P     single    1.874  0.020  1.874
 P2G  C1   O3'   single    1.414  0.020  1.414
 P2G  C1   H1    single    0.970  0.020  1.090
 P2G  P    O3    deloc     1.529  0.020  1.529
 P2G  P    O4    deloc     1.529  0.020  1.529
 P2G  P    O2    deloc     1.527  0.020  1.527
 P2G  O3'  C3'   single    1.400  0.020  1.400
 P2G  C3'  C4'   single    1.538  0.020  1.538
 P2G  C3'  H3'   single    0.970  0.020  1.090
 P2G  C4'  C5'   single    1.507  0.020  1.507
 P2G  C4'  H4'   single    0.970  0.020  1.090
 P2G  C5'  O5'   single    1.405  0.020  1.405
 P2G  C5'  H5'1  single    0.970  0.020  1.090
 P2G  C5'  H5'2  single    0.970  0.020  1.090
 P2G  O5'  H5'   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
 P2G  C5    C6   N1    110.58  3.000
 P2G  C5    C6   O6    128.85  3.000
 P2G  N1    C6   O6    120.57  3.000
 P2G  HN1   N1   C2    118.26  3.000
 P2G  HN1   N1   C6    115.59  3.000
 P2G  C2    N1   C6    126.15  3.000
 P2G  N3    C2   N2    119.95  3.000
 P2G  N3    C2   N1    122.93  3.000
 P2G  N2    C2   N1    117.12  3.000
 P2G  HN22  N2   HN21  118.12  3.000
 P2G  HN22  N2   C2    122.71  3.000
 P2G  HN21  N2   C2    119.14  3.000
 P2G  C4    N3   C2    113.13  3.000
 P2G  N9    C4   C5    105.19  3.000
 P2G  N9    C4   N3    126.27  3.000
 P2G  C5    C4   N3    128.54  3.000
 P2G  N7    C5   C4    110.76  3.000
 P2G  N7    C5   C6    130.59  3.000
 P2G  C4    C5   C6    118.66  3.000
 P2G  C8    N7   C5    104.75  3.000
 P2G  H8    C8   N9    121.72  3.000
 P2G  H8    C8   N7    125.44  3.000
 P2G  N9    C8   N7    112.84  3.000
 P2G  C1'   N9   C8    126.70  3.000
 P2G  C1'   N9   C4    126.83  3.000
 P2G  C8    N9   C4    106.47  3.000
 P2G  H1'   C1'  C2'   109.73  3.000
 P2G  H1'   C1'  O4'   112.01  3.000
 P2G  C2'   C1'  O4'   105.86  3.000
 P2G  H1'   C1'  N9    106.85  3.000
 P2G  C2'   C1'  N9    114.40  3.000
 P2G  O4'   C1'  N9    108.09  3.000
 P2G  C4'   O4'  C1'   107.76  3.000
 P2G  H2'   C2'  C3'   113.67  3.000
 P2G  H2'   C2'  O2'   109.31  3.000
 P2G  C3'   C2'  O2'   104.51  3.000
 P2G  H2'   C2'  C1'   111.25  3.000
 P2G  C3'   C2'  C1'   103.60  3.000
 P2G  O2'   C2'  C1'   114.32  3.000
 P2G  C1    O2'  C2'   106.48  3.000
 P2G  H1    C1   O3'   109.01  3.000
 P2G  H1    C1   P     109.94  3.000
 P2G  O3'   C1   P     112.45  3.000
 P2G  H1    C1   O2'   108.67  3.000
 P2G  O3'   C1   O2'   104.06  3.000
 P2G  P     C1   O2'   112.47  3.000
 P2G  O2    P    O4    114.76  3.000
 P2G  O2    P    O3    114.81  3.000
 P2G  O4    P    O3    114.43  3.000
 P2G  O2    P    C1    105.26  3.000
 P2G  O4    P    C1    102.79  3.000
 P2G  O3    P    C1    102.67  3.000
 P2G  C3'   O3'  C1    106.46  3.000
 P2G  H3'   C3'  C4'   111.17  3.000
 P2G  H3'   C3'  O3'   109.23  3.000
 P2G  C4'   C3'  O3'   114.91  3.000
 P2G  H3'   C3'  C2'   112.88  3.000
 P2G  C4'   C3'  C2'   104.22  3.000
 P2G  O3'   C3'  C2'   104.23  3.000
 P2G  H4'   C4'  C5'   109.59  3.000
 P2G  H4'   C4'  C3'   109.34  3.000
 P2G  C5'   C4'  C3'   112.73  3.000
 P2G  H4'   C4'  O4'   109.96  3.000
 P2G  C5'   C4'  O4'   109.84  3.000
 P2G  C3'   C4'  O4'   105.28  3.000
 P2G  H5'2  C5'  H5'1  106.93  3.000
 P2G  H5'2  C5'  O5'   112.11  3.000
 P2G  H5'1  C5'  O5'   112.04  3.000
 P2G  H5'2  C5'  C4'   108.85  3.000
 P2G  H5'1  C5'  C4'   107.34  3.000
 P2G  O5'   C5'  C4'   109.39  3.000
 P2G  H5'   O5'  C5'   108.18  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
 P2G  CONST_01  N3    C2  N1  C6    0.00  0.0  0
 P2G  CONST_02  N3    C4  C5  C6    0.00  0.0  0
 P2G  CONST_03  N9    C4  C5  C6  180.00  0.0  0
 P2G  CONST_04  C8    N7  C5  C6  180.00  0.0  0
 P2G  CONST_05  C4    C5  C6  N1    0.00  0.0  0
 P2G  CONST_06  N7    C5  C6  N1  180.00  0.0  0
 P2G  CONST_07  C4    N3  C2  N1    0.00  0.0  0
 P2G  CONST_08  C5    C6  N1  C2    0.00  0.0  0
 P2G  CONST_09  C5    C4  N3  C2    0.00  0.0  0
 P2G  CONST_10  N9    C4  N3  C2  180.00  0.0  0
 P2G  CONST_11  N7    C5  C4  N3  180.00  0.0  0
 P2G  CONST_12  C8    N9  C4  N3  180.00  0.0  0
 P2G  CONST_13  C8    N7  C5  C4    0.00  0.0  0
 P2G  CONST_14  N7    C8  N9  C4    0.00  0.0  0
 P2G  CONST_15  C8    N9  C4  C5    0.00  0.0  0
 P2G  CONST_16  N9    C8  N7  C5    0.00  0.0  0
 P2G  CONST_17  N9    C4  C5  N7    0.00  0.0  0
 P2G  CONST_18  C1'   N9  C4  N3    0.00  0.0  0
 P2G  CONST_19  C1'   N9  C4  C5  180.00  0.0  0
 P2G  CONST_20  C1'   N9  C8  N7  180.00  0.0  0
 P2G  CONST_21  C2    N1  C6  O6  180.00  0.0  0
 P2G  CONST_22  C4    C5  C6  O6  180.00  0.0  0
 P2G  CONST_23  N7    C5  C6  O6    0.00  0.0  0
 P2G  CONST_24  N2    C2  N1  C6  180.00  0.0  0
 P2G  CONST_25  C4    N3  C2  N2  180.00  0.0  0
 P2G  CONST_26  HN1   N1  C2  N3  180.00  0.0  0
 P2G  CONST_27  H8    C8  N9  C4  180.00  0.0  0
 P2G  CONST_28  HN21  N2  C2  N1  180.00  0.0  0
 P2G  CONST_29  HN22  N2  C2  N1    0.00  0.0  0

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
 P2G  chir_01  C1'  N9   O4'  C2'  positiv
 P2G  chir_02  C2'  O2'  C3'  C1'  positiv
 P2G  chir_03  C1   P    O2'  O3'  positiv
 P2G  chir_04  C3'  O3'  C2'  C4'  negativ
 P2G  chir_05  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
 P2G  plan-1  O6    0.020
 P2G  plan-1  C6    0.020
 P2G  plan-1  N1    0.020
 P2G  plan-1  C2    0.020
 P2G  plan-1  N2    0.020
 P2G  plan-1  N3    0.020
 P2G  plan-1  C4    0.020
 P2G  plan-1  C5    0.020
 P2G  plan-1  N7    0.020
 P2G  plan-1  C8    0.020
 P2G  plan-1  N9    0.020
 P2G  plan-1  C1'   0.020
 P2G  plan-1  HN1   0.020
 P2G  plan-1  H8    0.020
 P2G  plan-2  C2    0.020
 P2G  plan-2  N2    0.020
 P2G  plan-2  HN21  0.020
 P2G  plan-2  HN22  0.020

