# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:57:48 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 G2P  G2P  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine  ligand  46  32  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G2P
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
 G2P  PG    P  P      0   1.212  -4.6779  -0.0938   4.4043
 G2P  O1G   O  OP    -1  -0.953  -3.4007  -0.9136   4.2909
 G2P  O2G   O  O      0  -0.843  -5.0169   0.3064   5.8427
 G2P  O3G   O  OP    -1  -0.858  -5.8692  -0.6166   3.6144
 G2P  O3B   O  O2     0  -0.629  -4.2542   1.4016   3.6775
 G2P  PB    P  P      0   1.255  -5.1814   2.2865   2.6999
 G2P  O1B   O  OP    -1  -0.961  -5.1561   1.7830   1.2767
 G2P  O2B   O  O      0  -0.870  -6.5369   2.5522   3.3265
 G2P  C3A   C  CH2    0  -0.955  -4.2750   3.8967   2.7833
 G2P  PA    P  P      0   1.242  -2.7610   4.1647   1.8135
 G2P  O1A   O  OP    -1  -0.959  -3.0097   4.1190   0.3281
 G2P  O2A   O  O      0  -0.756  -2.0306   5.3712   2.3624
 G2P  O5'   O  O2     0  -0.598  -1.9155   2.8147   2.2669
 G2P  C5'   C  CH2    0  -0.073  -0.8196   2.4122   1.4962
 G2P  C4'   C  CR15   0  -0.072   0.0281   1.4747   2.3371
 G2P  O4'   O  O      0  -0.451  -0.7438   0.3869   2.8401
 G2P  C3'   C  CR15   0  -0.107   1.1679   0.8300   1.5534
 G2P  O3'   O  OH1    0  -0.681   2.2042   0.3785   2.3871
 G2P  C2'   C  CR15   0   0.009   0.4536  -0.3940   0.9825
 G2P  O2'   O  OH1    0  -0.648   1.2622  -1.4731   0.6332
 G2P  C1'   C  CR15   0   0.221  -0.4888  -0.7815   2.1330
 G2P  N9    N  NR5    0  -0.465  -1.7297  -1.3588   1.6603
 G2P  C8    C  CR15   0   0.122  -2.8985  -0.7077   1.3467
 G2P  N7    N  N      0  -0.497  -3.7860  -1.5043   0.8346
 G2P  C5    C  CR56   0  -0.073  -3.1982  -2.7411   0.8430
 G2P  C6    C  CR6    0   0.493  -3.6942  -4.0045   0.4242
 G2P  O6    O  OC     0  -0.399  -4.7788  -4.2836  -0.0678
 G2P  N1    N  NR16   0  -0.759  -2.7416  -5.0095   0.6437
 G2P  C2    C  CR6    0   0.628  -1.5011  -4.8346   1.1855
 G2P  N2    N  NH2    0  -0.822  -0.7578  -5.9471   1.3702
 G2P  N3    N  N      0  -0.531  -1.0426  -3.6707   1.5568
 G2P  C4    C  CR56   0   0.449  -1.9201  -2.6688   1.3685
 G2P  H3A1  H  HCH2   0   0.182  -4.0694   4.1310   3.8318
 G2P  H3A2  H  HCH2   0   0.273  -4.9780   4.6658   2.4442
 G2P  H5'1  H  HCH2   0   0.179  -1.1470   1.9195   0.5719
 G2P  H5'2  H  HCH2   0   0.179  -0.1825   3.2562   1.1959
 G2P  H4'   H  HCR5   0   0.262   0.4067   2.0355   3.1987
 G2P  H3'   H  HCR5   0   0.310   1.5450   1.4915   0.7621
 G2P  HA    H  HOH1   0   0.442   2.6253   1.1464   2.7855
 G2P  H2'   H  HCR5   0   0.247  -0.1549  -0.0605   0.1310
 G2P  HB    H  HOH1   0   0.451   1.7216  -1.2559  -0.1836
 G2P  H1'   H  HCR5   0   0.292  -0.0105  -1.5350   2.7698
 G2P  H8    H  HCR5   0   0.273  -3.0482   0.3411   1.5476
 G2P  H1    H  HNR6   0   0.399  -3.0277  -5.9460   0.3899
 G2P  H2N1  H  HNH2   0   0.429   0.2157  -5.8004   1.5793
 G2P  H2N2  H  HNH2   0   0.411  -0.9548  -6.7702   0.8255

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
 G2P  PG   O1G   deloc     1.522  0.020  1.522
 G2P  PG   O2G   deloc     1.531  0.020  1.531
 G2P  PG   O3G   deloc     1.522  0.020  1.522
 G2P  PG   O3B   single    1.716  0.020  1.716
 G2P  O3B  PB    single    1.612  0.020  1.612
 G2P  PB   O1B   deloc     1.510  0.020  1.510
 G2P  PB   O2B   deloc     1.517  0.020  1.517
 G2P  PB   C3A   single    1.850  0.020  1.850
 G2P  C3A  PA    single    1.818  0.020  1.818
 G2P  C3A  H3A1  single    0.970  0.020  1.090
 G2P  C3A  H3A2  single    0.970  0.020  1.090
 G2P  PA   O1A   deloc     1.507  0.020  1.507
 G2P  PA   O2A   deloc     1.513  0.020  1.513
 G2P  PA   O5'   single    1.656  0.020  1.656
 G2P  O5'  C5'   single    1.399  0.020  1.399
 G2P  C5'  C4'   single    1.518  0.020  1.518
 G2P  C5'  H5'1  single    0.970  0.020  1.090
 G2P  C5'  H5'2  single    0.970  0.020  1.090
 G2P  C4'  O4'   single    1.426  0.020  1.426
 G2P  C4'  C3'   single    1.526  0.020  1.526
 G2P  C4'  H4'   single    0.970  0.020  1.090
 G2P  O4'  C1'   single    1.389  0.020  1.389
 G2P  C3'  O3'   single    1.405  0.020  1.405
 G2P  C3'  C2'   single    1.528  0.020  1.528
 G2P  C3'  H3'   single    0.970  0.020  1.090
 G2P  O3'  HA    single    0.850  0.020  0.980
 G2P  C2'  O2'   single    1.393  0.020  1.393
 G2P  C2'  C1'   single    1.537  0.020  1.537
 G2P  C2'  H2'   single    0.970  0.020  1.090
 G2P  O2'  HB    single    0.850  0.020  0.980
 G2P  C1'  N9    single    1.448  0.020  1.448
 G2P  C1'  H1'   single    0.970  0.020  1.090
 G2P  N9   C8    aromatic  1.374  0.020  1.374
 G2P  N9   C4    aromatic  1.356  0.020  1.356
 G2P  C8   N7    aromatic  1.298  0.020  1.298
 G2P  C8   H8    single    0.930  0.020  1.080
 G2P  N7   C5    aromatic  1.369  0.020  1.369
 G2P  C5   C6    aromatic  1.420  0.020  1.420
 G2P  C5   C4    aromatic  1.384  0.020  1.384
 G2P  C6   O6    double    1.223  0.020  1.223
 G2P  C6   N1    aromatic  1.402  0.020  1.402
 G2P  N1   C2    aromatic  1.365  0.020  1.365
 G2P  N1   H1    single    0.860  0.020  1.020
 G2P  C2   N2    single    1.351  0.020  1.351
 G2P  C2   N3    aromatic  1.305  0.020  1.305
 G2P  N2   H2N1  single    0.890  0.020  1.040
 G2P  N2   H2N2  single    0.890  0.020  1.040
 G2P  N3   C4    aromatic  1.345  0.020  1.345

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
 G2P  O3B   PG   O3G   105.83  3.000
 G2P  O3B   PG   O2G   102.99  3.000
 G2P  O3G   PG   O2G   113.83  3.000
 G2P  O3B   PG   O1G   103.34  3.000
 G2P  O3G   PG   O1G   115.67  3.000
 G2P  O2G   PG   O1G   113.37  3.000
 G2P  PB    O3B  PG    126.39  3.000
 G2P  C3A   PB   O2B   105.48  3.000
 G2P  C3A   PB   O1B   108.94  3.000
 G2P  O2B   PB   O1B   117.57  3.000
 G2P  C3A   PB   O3B    99.71  3.000
 G2P  O2B   PB   O3B   111.08  3.000
 G2P  O1B   PB   O3B   112.27  3.000
 G2P  H3A2  C3A  H3A1  105.47  3.000
 G2P  H3A2  C3A  PA    105.41  3.000
 G2P  H3A1  C3A  PA    108.86  3.000
 G2P  H3A2  C3A  PB    106.42  3.000
 G2P  H3A1  C3A  PB    108.77  3.000
 G2P  PA    C3A  PB    120.83  3.000
 G2P  O5'   PA   O2A   107.71  3.000
 G2P  O5'   PA   O1A   109.23  3.000
 G2P  O2A   PA   O1A   117.48  3.000
 G2P  O5'   PA   C3A    99.14  3.000
 G2P  O2A   PA   C3A   109.03  3.000
 G2P  O1A   PA   C3A   112.58  3.000
 G2P  C5'   O5'  PA    118.93  3.000
 G2P  H5'2  C5'  H5'1  106.71  3.000
 G2P  H5'2  C5'  C4'   107.57  3.000
 G2P  H5'1  C5'  C4'   110.85  3.000
 G2P  H5'2  C5'  O5'   112.56  3.000
 G2P  H5'1  C5'  O5'   111.07  3.000
 G2P  C4'   C5'  O5'   108.06  3.000
 G2P  H4'   C4'  C3'   111.23  3.000
 G2P  H4'   C4'  O4'   107.47  3.000
 G2P  C3'   C4'  O4'   105.26  3.000
 G2P  H4'   C4'  C5'   108.21  3.000
 G2P  C3'   C4'  C5'   113.17  3.000
 G2P  O4'   C4'  C5'   111.36  3.000
 G2P  C1'   O4'  C4'   111.27  3.000
 G2P  H3'   C3'  C2'   111.96  3.000
 G2P  H3'   C3'  O3'   111.59  3.000
 G2P  C2'   C3'  O3'   108.01  3.000
 G2P  H3'   C3'  C4'   111.84  3.000
 G2P  C2'   C3'  C4'   100.44  3.000
 G2P  O3'   C3'  C4'   112.46  3.000
 G2P  HA    O3'  C3'   108.18  3.000
 G2P  H2'   C2'  C1'   108.49  3.000
 G2P  H2'   C2'  O2'   111.25  3.000
 G2P  C1'   C2'  O2'   110.39  3.000
 G2P  H2'   C2'  C3'   107.78  3.000
 G2P  C1'   C2'  C3'   102.06  3.000
 G2P  O2'   C2'  C3'   116.29  3.000
 G2P  HB    O2'  C2'   108.38  3.000
 G2P  H1'   C1'  N9    106.83  3.000
 G2P  H1'   C1'  C2'   109.91  3.000
 G2P  N9    C1'  C2'   112.44  3.000
 G2P  H1'   C1'  O4'   111.25  3.000
 G2P  N9    C1'  O4'   110.13  3.000
 G2P  C2'   C1'  O4'   106.35  3.000
 G2P  C4    N9   C8    106.82  3.000
 G2P  C4    N9   C1'   125.17  3.000
 G2P  C8    N9   C1'   127.92  3.000
 G2P  H8    C8   N7    125.14  3.000
 G2P  H8    C8   N9    122.43  3.000
 G2P  N7    C8   N9    112.39  3.000
 G2P  C5    N7   C8    104.97  3.000
 G2P  C4    C5   C6    118.75  3.000
 G2P  C4    C5   N7    110.59  3.000
 G2P  C6    C5   N7    130.66  3.000
 G2P  N1    C6   O6    120.12  3.000
 G2P  N1    C6   C5    110.74  3.000
 G2P  O6    C6   C5    129.13  3.000
 G2P  H1    N1   C2    118.38  3.000
 G2P  H1    N1   C6    115.61  3.000
 G2P  C2    N1   C6    126.00  3.000
 G2P  N3    C2   N2    120.15  3.000
 G2P  N3    C2   N1    123.14  3.000
 G2P  N2    C2   N1    116.68  3.000
 G2P  H2N2  N2   H2N1  114.89  3.000
 G2P  H2N2  N2   C2    119.46  3.000
 G2P  H2N1  N2   C2    116.15  3.000
 G2P  C4    N3   C2    113.28  3.000
 G2P  N3    C4   C5    128.08  3.000
 G2P  N3    C4   N9    126.73  3.000
 G2P  C5    C4   N9    105.19  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
 G2P  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 G2P  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 G2P  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 G2P  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 G2P  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 G2P  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 G2P  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 G2P  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 G2P  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 G2P  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 G2P  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 G2P  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 G2P  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 G2P  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 G2P  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 G2P  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 G2P  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 G2P  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 G2P  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 G2P  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 G2P  CONST_21  O6    C6   C5   N7     0.00   0.0  0
 G2P  CONST_22  N2    C2   N1   C6   180.00   0.0  0
 G2P  CONST_23  C4    C5   C6   O6   180.00   0.0  0
 G2P  CONST_24  C2    N1   C6   O6   180.00   0.0  0
 G2P  CONST_25  C4    N3   C2   N2   180.00   0.0  0
 G2P  CONST_26  H8    C8   N9   C1'    0.00   0.0  0
 G2P  CONST_27  H1    N1   C6   C5   180.00   0.0  0
 G2P  CONST_28  H2N1  N2   C2   N1   180.00   0.0  0
 G2P  Var_01    C4'   C5'  O5'  PA   161.72  30.0  3
 G2P  Var_02    O1B   PB   O3B  PG   -81.35  30.0  3
 G2P  Var_03    PA    C3A  PB   O3B   79.03  30.0  3
 G2P  Var_04    O1A   PA   C3A  PB    63.92  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
 G2P  chir_03  C4'  C5'  O4'  C3'  negativ
 G2P  chir_04  C3'  O3'  C4'  C2'  positiv
 G2P  chir_05  C2'  O2'  C3'  C1'  positiv
 G2P  chir_06  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
 G2P  plan-1  C1'   0.020
 G2P  plan-1  N9    0.020
 G2P  plan-1  C8    0.020
 G2P  plan-1  N7    0.020
 G2P  plan-1  C5    0.020
 G2P  plan-1  C6    0.020
 G2P  plan-1  O6    0.020
 G2P  plan-1  N1    0.020
 G2P  plan-1  C2    0.020
 G2P  plan-1  N2    0.020
 G2P  plan-1  N3    0.020
 G2P  plan-1  C4    0.020
 G2P  plan-1  H8    0.020
 G2P  plan-1  H1    0.020
 G2P  plan-2  C2    0.020
 G2P  plan-2  N2    0.020
 G2P  plan-2  H2N1  0.020
 G2P  plan-2  H2N2  0.020

