# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:24:19 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 6-cyanouridine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C#N
#
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
 6CN  6CN  '6-cyanouridine 5'-(dihydrogen phosphate)'  ligand  35  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6CN
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
 6CN  O3P   O  O     0  -0.705  -4.0691   2.0467   0.7668
 6CN  P     P  P     0   1.458  -4.1095   0.9935  -0.2628
 6CN  O1P   O  OH1   0  -0.740  -5.2227  -0.0864   0.1184
 6CN  O2P   O  OH1   0  -0.719  -4.3532   1.4322  -1.7771
 6CN  O5'   O  O2    0  -0.586  -2.7543   0.1874  -0.5174
 6CN  C5'   C  CH2   0  -0.177  -2.0757  -0.3940   0.5973
 6CN  C4'   C  CH1   0   0.019  -1.0051  -1.3206   0.0830
 6CN  C3'   C  CH1   0  -0.040  -0.2910  -2.0560   1.2184
 6CN  O3'   O  OH1   0  -0.648  -0.9209  -3.2894   1.4519
 6CN  C2'   C  CH1   0  -0.025   1.1416  -2.2258   0.6754
 6CN  O2'   O  OH1   0  -0.662   1.2694  -3.4584   0.0217
 6CN  O4'   O  O2    0  -0.474  -0.0113  -0.5759  -0.5971
 6CN  C1'   C  CH1   0   0.175   1.2562  -1.1183  -0.3894
 6CN  N1    N  NR6   0  -0.632   2.1953  -0.0352  -0.0918
 6CN  C6    C  CR6   0   0.463   3.1808   0.3328  -0.9793
 6CN  C5    C  CR16  0  -0.452   4.0185   1.3647  -0.7817
 6CN  C4    C  CR6   0   0.605   3.8974   2.1661   0.4199
 6CN  O4    O  O     0  -0.425   4.5922   3.1169   0.7000
 6CN  N3    N  NR16  0  -0.728   2.8803   1.7414   1.2515
 6CN  C2    C  CR6   0   0.764   2.0160   0.6941   1.0714
 6CN  O2    O  O     0  -0.449   1.1624   0.4265   1.8828
 6CN  C7    C  CSP   0   0.046   3.3355  -0.4303  -2.1806
 6CN  N8    N  NS    0  -0.186   3.5117  -1.0023  -3.1625
 6CN  HO1P  H  HOH1  0   0.498  -5.3718  -0.7865  -0.5315
 6CN  HO2P  H  HOH1  0   0.486  -5.0859   2.0510  -1.8819
 6CN  H5'   H  HCH2  0   0.249  -1.6309   0.3857   1.2194
 6CN  H5'A  H  HCH2  0   0.241  -2.7667  -0.9770   1.2128
 6CN  H4'   H  HCH1  0   0.250  -1.4566  -2.0567  -0.5957
 6CN  H3'   H  HCH1  0   0.269  -0.2751  -1.4477   2.1229
 6CN  HO3'  H  HOH1  0   0.456  -0.8084  -3.5221   2.3773
 6CN  H2'   H  HCH1  0   0.244   1.8978  -2.1206   1.4598
 6CN  HO2'  H  HOH1  0   0.441   0.5810  -4.0336   0.3834
 6CN  H1'   H  HCH1  0   0.275   1.6240  -1.5888  -1.3046
 6CN  H5    H  HCR6  0   0.298   4.7791   1.6056  -1.5067
 6CN  HN3   H  HNR6  0   0.410   2.7484   2.2574   2.1109

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
 6CN  O3P  P     double  1.473  0.020  1.473
 6CN  P    O5'   single  1.597  0.020  1.597
 6CN  P    O1P   single  1.597  0.020  1.597
 6CN  O1P  HO1P  single  0.850  0.020  0.980
 6CN  O2P  P     single  1.595  0.020  1.595
 6CN  O2P  HO2P  single  0.850  0.020  0.980
 6CN  C5'  O5'   single  1.429  0.020  1.429
 6CN  C5'  C4'   single  1.506  0.020  1.506
 6CN  C5'  H5'   single  0.970  0.020  1.090
 6CN  C5'  H5'A  single  0.970  0.020  1.090
 6CN  C4'  C3'   single  1.530  0.020  1.530
 6CN  C4'  H4'   single  0.970  0.020  1.090
 6CN  C3'  O3'   single  1.405  0.020  1.405
 6CN  C3'  H3'   single  0.970  0.020  1.090
 6CN  O3'  HO3'  single  0.850  0.020  0.980
 6CN  C2'  C3'   single  1.541  0.020  1.541
 6CN  C2'  O2'   single  1.401  0.020  1.401
 6CN  C2'  H2'   single  0.970  0.020  1.090
 6CN  O2'  HO2'  single  0.850  0.020  0.980
 6CN  O4'  C4'   single  1.416  0.020  1.416
 6CN  O4'  C1'   single  1.394  0.020  1.394
 6CN  C1'  C2'   single  1.541  0.020  1.541
 6CN  C1'  H1'   single  0.970  0.020  1.090
 6CN  N1   C1'   single  1.464  0.020  1.464
 6CN  C6   N1    single  1.376  0.020  1.376
 6CN  C5   C6    double  1.344  0.020  1.344
 6CN  C5   H5    single  0.930  0.020  1.080
 6CN  C4   C5    single  1.449  0.020  1.449
 6CN  C4   N3    single  1.381  0.020  1.381
 6CN  O4   C4    double  1.210  0.020  1.210
 6CN  N3   C2    single  1.370  0.020  1.370
 6CN  N3   HN3   single  0.860  0.020  1.020
 6CN  C2   N1    single  1.385  0.020  1.385
 6CN  O2   C2    double  1.208  0.020  1.208
 6CN  C7   C6    single  1.432  0.020  1.432
 6CN  N8   C7    triple  1.150  0.020  1.150

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
 6CN  O5'   P    O2P   96.73  3.000
 6CN  O2P   P    O1P  107.82  3.000
 6CN  O5'   P    O1P  106.75  3.000
 6CN  O2P   P    O3P  118.10  3.000
 6CN  O1P   P    O3P  109.61  3.000
 6CN  O5'   P    O3P  116.67  3.000
 6CN  HO1P  O1P  P    115.88  3.000
 6CN  HO2P  O2P  P    113.30  3.000
 6CN  C5'   O5'  P    118.95  3.000
 6CN  H5'A  C5'  H5'  108.49  3.000
 6CN  H5'A  C5'  C4'  108.26  3.000
 6CN  H5'   C5'  C4'  110.13  3.000
 6CN  H5'A  C5'  O5'  110.85  3.000
 6CN  H5'   C5'  O5'  110.33  3.000
 6CN  C4'   C5'  O5'  108.75  3.000
 6CN  H4'   C4'  O4'  110.14  3.000
 6CN  O4'   C4'  C3'  106.36  3.000
 6CN  H4'   C4'  C3'  109.17  3.000
 6CN  O4'   C4'  C5'  109.84  3.000
 6CN  H4'   C4'  C5'  109.33  3.000
 6CN  C3'   C4'  C5'  111.97  3.000
 6CN  H3'   C3'  C2'  109.89  3.000
 6CN  C2'   C3'  O3'  112.25  3.000
 6CN  H3'   C3'  O3'  111.01  3.000
 6CN  C2'   C3'  C4'  103.03  3.000
 6CN  H3'   C3'  C4'  110.76  3.000
 6CN  O3'   C3'  C4'  109.65  3.000
 6CN  HO3'  O3'  C3'  108.69  3.000
 6CN  H2'   C2'  C1'  112.01  3.000
 6CN  C1'   C2'  O2'  107.64  3.000
 6CN  H2'   C2'  O2'  110.85  3.000
 6CN  C1'   C2'  C3'  103.49  3.000
 6CN  H2'   C2'  C3'  112.28  3.000
 6CN  O2'   C2'  C3'  110.25  3.000
 6CN  HO2'  O2'  C2'  106.48  3.000
 6CN  C1'   O4'  C4'  111.22  3.000
 6CN  H1'   C1'  N1   105.84  3.000
 6CN  N1    C1'  O4'  109.00  3.000
 6CN  H1'   C1'  O4'  110.41  3.000
 6CN  N1    C1'  C2'  116.04  3.000
 6CN  H1'   C1'  C2'  107.11  3.000
 6CN  O4'   C1'  C2'  108.36  3.000
 6CN  C2    N1   C6   119.58  3.000
 6CN  C2    N1   C1'  118.51  3.000
 6CN  C6    N1   C1'  121.74  3.000
 6CN  C7    C6   C5   117.74  3.000
 6CN  C7    C6   N1   118.42  3.000
 6CN  C5    C6   N1   123.84  3.000
 6CN  H5    C5   C4   119.53  3.000
 6CN  C4    C5   C6   119.64  3.000
 6CN  H5    C5   C6   120.83  3.000
 6CN  N3    C4   O4   121.67  3.000
 6CN  O4    C4   C5   125.33  3.000
 6CN  N3    C4   C5   113.00  3.000
 6CN  HN3   N3   C2   114.81  3.000
 6CN  HN3   N3   C4   116.81  3.000
 6CN  C2    N3   C4   128.38  3.000
 6CN  O2    C2   N3   121.81  3.000
 6CN  O2    C2   N1   122.63  3.000
 6CN  N3    C2   N1   115.55  3.000
 6CN  N8    C7   C6   180.00  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
 6CN  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 6CN  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 6CN  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 6CN  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 6CN  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 6CN  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 6CN  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 6CN  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 6CN  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 6CN  Var_01    C4'  C5'  O5'  P    168.60  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
 6CN  chir_01  C4'  C5'  C3'  O4'  positiv
 6CN  chir_02  C3'  O3'  C2'  C4'  negativ
 6CN  chir_03  C2'  O2'  C1'  C3'  negativ
 6CN  chir_04  C1'  O4'  N1   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
 6CN  plan-1  C1'  0.020
 6CN  plan-1  N1   0.020
 6CN  plan-1  C6   0.020
 6CN  plan-1  C5   0.020
 6CN  plan-1  C4   0.020
 6CN  plan-1  O4   0.020
 6CN  plan-1  N3   0.020
 6CN  plan-1  C2   0.020
 6CN  plan-1  O2   0.020
 6CN  plan-1  C7   0.020
 6CN  plan-1  N8   0.020
 6CN  plan-1  H5   0.020
 6CN  plan-1  HN3  0.020

