# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:00:39 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}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)O[P@@](O)(=O)C[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
 GCP  GCP  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}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_GCP
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
 GCP  PG    P  P      0   1.153  -2.6563   1.0085   2.9060
 GCP  O1G   O  O      0  -0.945  -2.2822   1.5700   4.2819
 GCP  O2G   O  OP    -1  -0.900  -3.2374   2.0756   1.9626
 GCP  O3G   O  OP    -1  -0.951  -3.4991  -0.2708   2.9679
 GCP  C3B   C  CH2    0  -0.975  -1.0462   0.5195   2.0870
 GCP  PB    P  P      0   1.172  -0.3159  -1.0348   2.6479
 GCP  O1B   O  O      0  -0.793  -0.1421  -1.0974   4.1423
 GCP  O2B   O  OP    -1  -0.827  -0.9117  -2.2154   1.9278
 GCP  O3A   O  O2     0  -0.636   1.2420  -0.9595   1.9789
 GCP  PA    P  P      0   1.343   2.5316  -0.1151   2.4799
 GCP  O1A   O  O      0  -0.826   2.1373   1.1716   3.1401
 GCP  O2A   O  OP    -1  -0.833   3.5184  -1.0367   3.1306
 GCP  O5'   O  O2     0  -0.614   3.1865   0.2225   0.9991
 GCP  C5'   C  CH2    0  -0.187   2.4657   1.0577   0.1255
 GCP  C4'   C  CH1    0  -0.027   2.8093   0.7013  -1.3003
 GCP  O4'   O  O2     0  -0.528   2.4054  -0.6368  -1.5980
 GCP  C3'   C  CH1    0  -0.037   2.0852   1.5710  -2.3235
 GCP  O3'   O  OH1    0  -0.670   2.8189   2.7366  -2.5775
 GCP  C2'   C  CH1    0   0.014   1.9844   0.6295  -3.5262
 GCP  O2'   O  OH1    0  -0.656   3.2084   0.5453  -4.2046
 GCP  C1'   C  CH1    0   0.190   1.7582  -0.7103  -2.8287
 GCP  N9    N  NR5    0  -0.592   0.3346  -0.9685  -2.6118
 GCP  C8    C  CR15   0   0.146  -0.3311  -1.1679  -1.4238
 GCP  N7    N  N      0  -0.425  -1.5898  -1.4373  -1.5971
 GCP  C5    C  CR56   0  -0.139  -1.7681  -1.4340  -2.9543
 GCP  C6    C  CR6    0   0.528  -2.9331  -1.6754  -3.7388
 GCP  O6    O  OC     0  -0.479  -4.0668  -1.9312  -3.3693
 GCP  N1    N  NR16   0  -0.688  -2.6342  -1.5856  -5.1050
 GCP  C2    C  CR6    0   0.641  -1.4101  -1.3149  -5.6455
 GCP  N2    N  NH2    0  -0.804  -1.3217  -1.3251  -6.9860
 GCP  N3    N  N      0  -0.491  -0.3441  -1.0891  -4.9212
 GCP  C4    C  CR56   0   0.502  -0.5788  -1.1565  -3.6010
 GCP  H3B1  H  HCH2   0   0.194  -0.3177   1.3215   2.2289
 GCP  H3B2  H  HCH2   0   0.231  -1.2154   0.4232   1.0101
 GCP  H5'2  H  HCH2   0   0.227   1.3811   0.9722   0.2651
 GCP  H5'1  H  HCH2   0   0.246   2.7248   2.1116   0.2836
 GCP  H4'   H  HCH1   0   0.258   3.8935   0.7844  -1.4483
 GCP  H3'   H  HCH1   0   0.253   1.0734   1.8036  -1.9656
 GCP  HO3'  H  HOH1   0   0.440   2.2365   3.3865  -2.9837
 GCP  H2'   H  HCH1   0   0.258   1.1636   0.8914  -4.2019
 GCP  HO2'  H  HOH1   0   0.439   3.5913   1.4310  -4.2309
 GCP  H1'   H  HCH1   0   0.255   2.1593  -1.5412  -3.4162
 GCP  H8    H  HCR5   0   0.278   0.1629  -1.1167  -0.4663
 GCP  HN1   H  HNR6   0   0.432  -3.4093  -1.7537  -5.7340
 GCP  HN21  H  HNH2   0   0.419  -0.4751  -0.9637  -7.3921
 GCP  HN22  H  HNH2   0   0.404  -2.1495  -1.2451  -7.5515

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
 GCP  PG   O1G   deloc     1.532  0.020  1.532
 GCP  PG   O2G   deloc     1.538  0.020  1.538
 GCP  PG   O3G   deloc     1.533  0.020  1.533
 GCP  PG   C3B   single    1.871  0.020  1.871
 GCP  C3B  PB    single    1.807  0.020  1.807
 GCP  C3B  H3B1  single    0.970  0.020  1.090
 GCP  C3B  H3B2  single    0.970  0.020  1.090
 GCP  PB   O1B   deloc     1.506  0.020  1.506
 GCP  PB   O2B   deloc     1.506  0.020  1.506
 GCP  PB   O3A   single    1.697  0.020  1.697
 GCP  O3A  PA    single    1.621  0.020  1.621
 GCP  PA   O1A   deloc     1.499  0.020  1.499
 GCP  PA   O2A   deloc     1.499  0.020  1.499
 GCP  PA   O5'   single    1.654  0.020  1.654
 GCP  O5'  C5'   single    1.407  0.020  1.407
 GCP  C5'  C4'   single    1.509  0.020  1.509
 GCP  C5'  H5'2  single    0.970  0.020  1.090
 GCP  C5'  H5'1  single    0.970  0.020  1.090
 GCP  C4'  O4'   single    1.429  0.020  1.429
 GCP  C4'  C3'   single    1.526  0.020  1.526
 GCP  C4'  H4'   single    0.970  0.020  1.090
 GCP  O4'  C1'   single    1.392  0.020  1.392
 GCP  C3'  O3'   single    1.401  0.020  1.401
 GCP  C3'  C2'   single    1.531  0.020  1.531
 GCP  C3'  H3'   single    0.970  0.020  1.090
 GCP  O3'  HO3'  single    0.850  0.020  0.980
 GCP  C2'  O2'   single    1.402  0.020  1.402
 GCP  C2'  C1'   single    1.527  0.020  1.527
 GCP  C2'  H2'   single    0.970  0.020  1.090
 GCP  O2'  HO2'  single    0.850  0.020  0.980
 GCP  C1'  N9    single    1.463  0.020  1.463
 GCP  C1'  H1'   single    0.970  0.020  1.090
 GCP  N9   C8    aromatic  1.376  0.020  1.376
 GCP  N9   C4    aromatic  1.359  0.020  1.359
 GCP  C8   N7    aromatic  1.299  0.020  1.299
 GCP  C8   H8    single    0.930  0.020  1.080
 GCP  N7   C5    aromatic  1.369  0.020  1.369
 GCP  C5   C6    aromatic  1.425  0.020  1.425
 GCP  C5   C4    aromatic  1.382  0.020  1.382
 GCP  C6   O6    double    1.220  0.020  1.220
 GCP  C6   N1    aromatic  1.401  0.020  1.401
 GCP  N1   C2    aromatic  1.365  0.020  1.365
 GCP  N1   HN1   single    0.860  0.020  1.020
 GCP  C2   N2    single    1.343  0.020  1.343
 GCP  C2   N3    aromatic  1.308  0.020  1.308
 GCP  N2   HN21  single    0.890  0.020  1.040
 GCP  N2   HN22  single    0.890  0.020  1.040
 GCP  N3   C4    aromatic  1.343  0.020  1.343

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
 GCP  C3B   PG   O3G   105.82  3.000
 GCP  C3B   PG   O2G   103.76  3.000
 GCP  O3G   PG   O2G   113.32  3.000
 GCP  C3B   PG   O1G   106.18  3.000
 GCP  O3G   PG   O1G   113.81  3.000
 GCP  O2G   PG   O1G   112.87  3.000
 GCP  H3B2  C3B  H3B1  107.19  3.000
 GCP  H3B2  C3B  PB    107.00  3.000
 GCP  H3B1  C3B  PB    108.76  3.000
 GCP  H3B2  C3B  PG    108.70  3.000
 GCP  H3B1  C3B  PG    108.96  3.000
 GCP  PB    C3B  PG    115.89  3.000
 GCP  O3A   PB   O2B   102.09  3.000
 GCP  O3A   PB   O1B   106.68  3.000
 GCP  O2B   PB   O1B   119.18  3.000
 GCP  O3A   PB   C3B   102.15  3.000
 GCP  O2B   PB   C3B   111.48  3.000
 GCP  O1B   PB   C3B   112.99  3.000
 GCP  PA    O3A  PB    129.17  3.000
 GCP  O5'   PA   O2A   104.69  3.000
 GCP  O5'   PA   O1A   108.86  3.000
 GCP  O2A   PA   O1A   120.65  3.000
 GCP  O5'   PA   O3A    98.32  3.000
 GCP  O2A   PA   O3A   109.73  3.000
 GCP  O1A   PA   O3A   111.97  3.000
 GCP  C5'   O5'  PA    118.30  3.000
 GCP  H5'1  C5'  H5'2  106.87  3.000
 GCP  H5'1  C5'  C4'   108.02  3.000
 GCP  H5'2  C5'  C4'   109.08  3.000
 GCP  H5'1  C5'  O5'   111.08  3.000
 GCP  H5'2  C5'  O5'   112.41  3.000
 GCP  C4'   C5'  O5'   109.25  3.000
 GCP  H4'   C4'  C3'   109.59  3.000
 GCP  H4'   C4'  O4'   108.78  3.000
 GCP  C3'   C4'  O4'   105.06  3.000
 GCP  H4'   C4'  C5'   109.54  3.000
 GCP  C3'   C4'  C5'   113.01  3.000
 GCP  O4'   C4'  C5'   110.70  3.000
 GCP  C1'   O4'  C4'   111.40  3.000
 GCP  H3'   C3'  C2'   109.01  3.000
 GCP  H3'   C3'  O3'   111.44  3.000
 GCP  C2'   C3'  O3'   113.82  3.000
 GCP  H3'   C3'  C4'   109.84  3.000
 GCP  C2'   C3'  C4'   101.98  3.000
 GCP  O3'   C3'  C4'   110.33  3.000
 GCP  HO3'  O3'  C3'   108.75  3.000
 GCP  H2'   C2'  C1'   112.37  3.000
 GCP  H2'   C2'  O2'   111.73  3.000
 GCP  C1'   C2'  O2'   107.31  3.000
 GCP  H2'   C2'  C3'   112.78  3.000
 GCP  C1'   C2'  C3'   100.98  3.000
 GCP  O2'   C2'  C3'   111.08  3.000
 GCP  HO2'  O2'  C2'   107.72  3.000
 GCP  H1'   C1'  N9    107.60  3.000
 GCP  H1'   C1'  C2'   111.52  3.000
 GCP  N9    C1'  C2'   111.51  3.000
 GCP  H1'   C1'  O4'   110.15  3.000
 GCP  N9    C1'  O4'   109.30  3.000
 GCP  C2'   C1'  O4'   106.77  3.000
 GCP  C4    N9   C8    106.44  3.000
 GCP  C4    N9   C1'   124.77  3.000
 GCP  C8    N9   C1'   128.62  3.000
 GCP  H8    C8   N7    124.90  3.000
 GCP  H8    C8   N9    122.53  3.000
 GCP  N7    C8   N9    112.56  3.000
 GCP  C5    N7   C8    104.95  3.000
 GCP  C4    C5   C6    118.68  3.000
 GCP  C4    C5   N7    110.64  3.000
 GCP  C6    C5   N7    130.68  3.000
 GCP  N1    C6   O6    120.47  3.000
 GCP  N1    C6   C5    110.57  3.000
 GCP  O6    C6   C5    128.96  3.000
 GCP  HN1   N1   C2    118.26  3.000
 GCP  HN1   N1   C6    115.58  3.000
 GCP  C2    N1   C6    126.15  3.000
 GCP  N3    C2   N2    120.00  3.000
 GCP  N3    C2   N1    123.06  3.000
 GCP  N2    C2   N1    116.91  3.000
 GCP  HN22  N2   HN21  115.91  3.000
 GCP  HN22  N2   C2    120.42  3.000
 GCP  HN21  N2   C2    117.09  3.000
 GCP  C4    N3   C2    113.16  3.000
 GCP  N3    C4   C5    128.37  3.000
 GCP  N3    C4   N9    126.23  3.000
 GCP  C5    C4   N9    105.40  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
 GCP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GCP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GCP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 GCP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 GCP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 GCP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 GCP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 GCP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 GCP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 GCP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 GCP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 GCP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 GCP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 GCP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 GCP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 GCP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 GCP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 GCP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 GCP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 GCP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 GCP  CONST_21  O6    C6   C5   N7      0.00   0.0  0
 GCP  CONST_22  N2    C2   N1   C6    180.00   0.0  0
 GCP  CONST_23  C4    C5   C6   O6    180.00   0.0  0
 GCP  CONST_24  C2    N1   C6   O6    180.00   0.0  0
 GCP  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 GCP  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 GCP  CONST_27  HN1   N1   C6   C5    180.00   0.0  0
 GCP  CONST_28  HN21  N2   C2   N1    180.00   0.0  0
 GCP  Var_01    C4'   C5'  O5'  PA   -151.63  30.0  3
 GCP  Var_02    O1B   PB   C3B  PG    -53.31  30.0  3
 GCP  Var_03    PB    C3B  PG   O1G    77.71  30.0  3
 GCP  Var_04    O1A   PA   O3A  PB    -31.46  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
 GCP  chir_03  C4'  C5'  O4'  C3'  negativ
 GCP  chir_04  C3'  O3'  C4'  C2'  positiv
 GCP  chir_05  C2'  O2'  C3'  C1'  positiv
 GCP  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
 GCP  plan-1  C1'   0.020
 GCP  plan-1  N9    0.020
 GCP  plan-1  C8    0.020
 GCP  plan-1  N7    0.020
 GCP  plan-1  C5    0.020
 GCP  plan-1  C6    0.020
 GCP  plan-1  O6    0.020
 GCP  plan-1  N1    0.020
 GCP  plan-1  C2    0.020
 GCP  plan-1  N2    0.020
 GCP  plan-1  N3    0.020
 GCP  plan-1  C4    0.020
 GCP  plan-1  H8    0.020
 GCP  plan-1  HN1   0.020
 GCP  plan-2  C2    0.020
 GCP  plan-2  N2    0.020
 GCP  plan-2  HN21  0.020
 GCP  plan-2  HN22  0.020

