# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 18:23:01 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2,3-dihydroxanthosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=O)Nc23
#
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
 4UO  4UO  '2,3-dihydroxanthosine    '  ligand  32  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4UO
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
 4UO  O6   O  O     0  -0.452   3.8845  -2.3403  -0.4091
 4UO  C6   C  CR6   0   0.526   3.1586  -1.3756  -0.2732
 4UO  N1   N  NR16  0  -0.735   3.6413  -0.0799  -0.4693
 4UO  C2   C  CR6   0   0.665   2.9795   1.1271  -0.3889
 4UO  O2   O  O     0  -0.473   3.5262   2.1850  -0.6212
 4UO  N3   N  NR16  0  -0.749   1.6594   1.0422  -0.0246
 4UO  C4   C  CR56  0   0.633   1.1035  -0.1777   0.1953
 4UO  C5   C  CR56  0  -0.073   1.7715  -1.3706   0.0893
 4UO  N7   N  N     0  -0.439   0.9239  -2.4069   0.3709
 4UO  C8   C  CR15  0   0.100  -0.2156  -1.8489   0.6410
 4UO  N9   N  NR5   0  -0.537  -0.1635  -0.4753   0.5492
 4UO  C1'  C  CH1   0   0.212  -1.2316   0.4874   0.8375
 4UO  O4'  O  O2    0  -0.483  -2.3660  -0.1957   1.2345
 4UO  C4'  C  CH1   0  -0.076  -3.4268   0.0068   0.2934
 4UO  C5'  C  CH2   0  -0.160  -3.4865  -1.1118  -0.7292
 4UO  O5'  O  OH1   0  -0.663  -3.6495  -2.3252  -0.0383
 4UO  C3'  C  CH1   0  -0.009  -3.1279   1.3755  -0.3165
 4UO  O3'  O  OH1   0  -0.662  -3.4706   2.4252   0.5441
 4UO  C2'  C  CH1   0  -0.040  -1.5996   1.3180  -0.4043
 4UO  O2'  O  OH1   0  -0.657  -0.9283   2.5431  -0.3493
 4UO  H1   H  HNR6  0   0.428   4.6167  -0.0071  -0.7300
 4UO  H2   H  HNR6  0   0.437   1.0990   1.8892  -0.0312
 4UO  H3   H  HCR5  0   0.296  -1.1281  -2.3623   0.8976
 4UO  H4   H  HCH1  0   0.288  -0.8736   1.1316   1.6481
 4UO  H5   H  HCH1  0   0.274  -4.3602   0.0151   0.8635
 4UO  H6   H  HCH2  0   0.226  -4.3280  -0.9060  -1.4033
 4UO  H7   H  HCH2  0   0.203  -2.5811  -1.1181  -1.3507
 4UO  H8   H  HOH1  0   0.462  -3.6447  -3.0407  -0.6803
 4UO  H9   H  HCH1  0   0.256  -3.5833   1.4906  -1.3077
 4UO  H10  H  HOH1  0   0.460  -4.4303   2.4829   0.5863
 4UO  H11  H  HCH1  0   0.269  -1.3273   0.7618  -1.3091
 4UO  H12  H  HOH1  0   0.474  -0.9693   2.9631  -1.2152

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
 4UO  N7   C8   aromatic  1.297  0.020  1.297
 4UO  N7   C5   aromatic  1.368  0.020  1.368
 4UO  C8   N9   aromatic  1.378  0.020  1.378
 4UO  O6   C6   double    1.215  0.020  1.215
 4UO  C5   C6   single    1.434  0.020  1.434
 4UO  C5   C4   aromatic  1.371  0.020  1.371
 4UO  C6   N1   single    1.397  0.020  1.397
 4UO  N9   C4   aromatic  1.349  0.020  1.349
 4UO  N9   C1'  single    1.467  0.020  1.467
 4UO  C4   N3   single    1.359  0.020  1.359
 4UO  C1'  C2'  single    1.539  0.020  1.539
 4UO  C1'  O4'  single    1.382  0.020  1.382
 4UO  O2'  C2'  single    1.398  0.020  1.398
 4UO  N1   C2   single    1.379  0.020  1.379
 4UO  C2'  C3'  single    1.532  0.020  1.532
 4UO  O4'  C4'  single    1.432  0.020  1.432
 4UO  N3   C2   single    1.372  0.020  1.372
 4UO  C2   O2   double    1.213  0.020  1.213
 4UO  C3'  C4'  single    1.528  0.020  1.528
 4UO  C3'  O3'  single    1.400  0.020  1.400
 4UO  C4'  C5'  single    1.517  0.020  1.517
 4UO  O5'  C5'  single    1.406  0.020  1.406
 4UO  N1   H1   single    0.860  0.020  1.020
 4UO  N3   H2   single    0.860  0.020  1.020
 4UO  C8   H3   single    0.930  0.020  1.080
 4UO  C1'  H4   single    0.970  0.020  1.090
 4UO  C4'  H5   single    0.970  0.020  1.090
 4UO  C5'  H6   single    0.970  0.020  1.090
 4UO  C5'  H7   single    0.970  0.020  1.090
 4UO  O5'  H8   single    0.850  0.020  0.980
 4UO  C3'  H9   single    0.970  0.020  1.090
 4UO  O3'  H10  single    0.850  0.020  0.980
 4UO  C2'  H11  single    0.970  0.020  1.090
 4UO  O2'  H12  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
 4UO  C5   C6   N1   111.51  3.000
 4UO  N1   C6   O6   120.96  3.000
 4UO  C5   C6   O6   127.53  3.000
 4UO  H1   N1   C2   114.49  3.000
 4UO  H1   N1   C6   115.85  3.000
 4UO  C2   N1   C6   129.65  3.000
 4UO  N3   C2   O2   122.57  3.000
 4UO  O2   C2   N1   122.40  3.000
 4UO  N3   C2   N1   115.03  3.000
 4UO  H2   N3   C4   121.61  3.000
 4UO  H2   N3   C2   118.53  3.000
 4UO  C4   N3   C2   119.49  3.000
 4UO  N9   C4   C5   106.61  3.000
 4UO  N9   C4   N3   128.68  3.000
 4UO  C5   C4   N3   124.70  3.000
 4UO  N7   C5   C4   109.95  3.000
 4UO  C4   C5   C6   119.60  3.000
 4UO  N7   C5   C6   130.45  3.000
 4UO  C8   N7   C5   105.15  3.000
 4UO  H3   C8   N9   121.51  3.000
 4UO  H3   C8   N7   126.04  3.000
 4UO  N9   C8   N7   112.44  3.000
 4UO  C1'  N9   C8   127.87  3.000
 4UO  C1'  N9   C4   126.22  3.000
 4UO  C8   N9   C4   105.84  3.000
 4UO  H4   C1'  C2'  110.97  3.000
 4UO  H4   C1'  O4'  110.26  3.000
 4UO  C2'  C1'  O4'  107.59  3.000
 4UO  H4   C1'  N9   107.06  3.000
 4UO  O4'  C1'  N9   109.25  3.000
 4UO  C2'  C1'  N9   111.71  3.000
 4UO  C4'  O4'  C1'  110.44  3.000
 4UO  H5   C4'  C3'  111.61  3.000
 4UO  H5   C4'  C5'  108.87  3.000
 4UO  C3'  C4'  C5'  113.53  3.000
 4UO  H5   C4'  O4'  106.90  3.000
 4UO  C5'  C4'  O4'  111.58  3.000
 4UO  C3'  C4'  O4'  104.13  3.000
 4UO  H7   C5'  H6   106.59  3.000
 4UO  H7   C5'  O5'  111.64  3.000
 4UO  H6   C5'  O5'  112.01  3.000
 4UO  H7   C5'  C4'  110.69  3.000
 4UO  H6   C5'  C4'  107.81  3.000
 4UO  O5'  C5'  C4'  108.05  3.000
 4UO  H8   O5'  C5'  108.28  3.000
 4UO  H9   C3'  C2'  111.49  3.000
 4UO  H9   C3'  O3'  112.03  3.000
 4UO  C2'  C3'  O3'  107.91  3.000
 4UO  H9   C3'  C4'  111.94  3.000
 4UO  O3'  C3'  C4'  112.24  3.000
 4UO  C2'  C3'  C4'  100.63  3.000
 4UO  H10  O3'  C3'  108.42  3.000
 4UO  H11  C2'  O2'  110.96  3.000
 4UO  H11  C2'  C3'  108.31  3.000
 4UO  O2'  C2'  C3'  116.35  3.000
 4UO  H11  C2'  C1'  109.43  3.000
 4UO  C3'  C2'  C1'  102.27  3.000
 4UO  O2'  C2'  C1'  109.06  3.000
 4UO  H12  O2'  C2'  109.05  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
 4UO  CONST_01  C8   N7  C5  C4    0.00  0.0  0
 4UO  CONST_02  N7   C8  N9  C4    0.00  0.0  0
 4UO  CONST_03  N9   C8  N7  C5    0.00  0.0  0
 4UO  CONST_04  C8   N9  C4  C5    0.00  0.0  0
 4UO  CONST_05  N9   C4  C5  N7    0.00  0.0  0
 4UO  CONST_06  C1'  N9  C4  N3    0.00  0.0  0
 4UO  CONST_07  C1'  N9  C4  C5  180.00  0.0  0
 4UO  CONST_08  C1'  N9  C8  N7  180.00  0.0  0
 4UO  CONST_09  N3   C2  N1  C6    0.00  0.0  0
 4UO  CONST_10  C4   N3  C2  N1    0.00  0.0  0
 4UO  CONST_11  C5   C6  N1  C2    0.00  0.0  0
 4UO  CONST_12  C2   N1  C6  O6  180.00  0.0  0
 4UO  CONST_13  O2   C2  N1  C6  180.00  0.0  0
 4UO  CONST_14  C4   N3  C2  O2  180.00  0.0  0
 4UO  CONST_15  H3   C8  N9  C4  180.00  0.0  0
 4UO  CONST_16  H2   N3  C2  N1  180.00  0.0  0
 4UO  CONST_17  H1   N1  C2  N3  180.00  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
 4UO  chir_01  C1'  N9   C2'  O4'  negativ
 4UO  chir_02  C4'  O4'  C3'  C5'  negativ
 4UO  chir_03  C3'  O3'  C4'  C2'  positiv
 4UO  chir_04  C2'  O2'  C3'  C1'  positiv

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
 4UO  plan-1  O6   0.020
 4UO  plan-1  C6   0.020
 4UO  plan-1  N1   0.020
 4UO  plan-1  C2   0.020
 4UO  plan-1  O2   0.020
 4UO  plan-1  N3   0.020
 4UO  plan-1  C4   0.020
 4UO  plan-1  C5   0.020
 4UO  plan-1  N7   0.020
 4UO  plan-1  C8   0.020
 4UO  plan-1  N9   0.020
 4UO  plan-1  C1'  0.020
 4UO  plan-1  H1   0.020
 4UO  plan-1  H2   0.020
 4UO  plan-1  H3   0.020

