# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:42:09 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 5-methyluridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=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
 38T  38T  '5-methyluridine          '  ligand  32  18  .  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_38T
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
 38T  OAC  O  O     0  -0.474  -0.0437  -0.7895  -1.6090
 38T  CAM  C  CR6   0   0.744   0.8951  -0.4913  -0.9005
 38T  NAI  N  NR16  0  -0.734   2.1692  -0.9182  -1.1653
 38T  CAL  C  CR6   0   0.560   3.3239  -0.6523  -0.4512
 38T  OAB  O  O     0  -0.453   4.3949  -1.1012  -0.8154
 38T  CAK  C  CR6   0  -0.185   3.1234   0.1761   0.7210
 38T  CAA  C  CH3   0  -0.707   4.3000   0.5177   1.5745
 38T  CAG  C  CR16  0   0.063   1.8752   0.5949   0.9884
 38T  NAR  N  NR6   0  -0.570   0.7783   0.3009   0.2176
 38T  C1'  C  CH1   0   0.204  -0.5343   0.7750   0.6391
 38T  O4'  O  O2    0  -0.490  -1.3203  -0.3152   1.0254
 38T  C4'  C  CH1   0   0.020  -2.6366  -0.2049   0.5081
 38T  C5'  C  CH2   0  -0.162  -3.1858  -1.5737   0.1943
 38T  O5'  O  OH1   0  -0.671  -3.3606  -2.2935   1.3911
 38T  C3'  C  CH1   0  -0.034  -2.5236   0.6803  -0.7318
 38T  O3'  O  OH1   0  -0.663  -3.7175   1.3990  -0.9149
 38T  C2'  C  CH1   0  -0.046  -1.3284   1.5917  -0.3959
 38T  O2'  O  OH1   0  -0.675  -1.7697   2.7644   0.2386
 38T  H1   H  HNR6  0   0.426   2.2665  -1.4986  -1.9897
 38T  H2   H  HCH3  0   0.248   4.7811  -0.3802   1.9644
 38T  H3   H  HCH3  0   0.248   5.0533   1.0691   1.0105
 38T  H4   H  HCH3  0   0.248   4.0005   1.1324   2.4218
 38T  H5   H  HCR6  0   0.318   1.6703   1.2111   1.8534
 38T  H6   H  HCH1  0   0.260  -0.3318   1.4261   1.4945
 38T  H7   H  HCH1  0   0.234  -3.2868   0.2918   1.2432
 38T  H8   H  HCH2  0   0.206  -4.1361  -1.4339  -0.3379
 38T  H9   H  HCH2  0   0.202  -2.4974  -2.0805  -0.4950
 38T  H10  H  HOH1  0   0.457  -3.7378  -3.1499   1.1712
 38T  H11  H  HCH1  0   0.259  -2.2890   0.0755  -1.6088
 38T  H12  H  HOH1  0   0.470  -3.8227   1.5931  -1.8515
 38T  H13  H  HCH1  0   0.249  -0.7274   1.8313  -1.2803
 38T  H14  H  HOH1  0   0.448  -2.6747   2.9225  -0.0645

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
 38T  OAC  CAM  double  1.213  0.020  1.213
 38T  NAI  CAM  single  1.370  0.020  1.370
 38T  NAI  CAL  single  1.383  0.020  1.383
 38T  OAB  CAL  double  1.217  0.020  1.217
 38T  CAM  NAR  single  1.375  0.020  1.375
 38T  O2'  C2'  single  1.405  0.020  1.405
 38T  C2'  C3'  single  1.540  0.020  1.540
 38T  C2'  C1'  single  1.539  0.020  1.539
 38T  CAL  CAK  single  1.449  0.020  1.449
 38T  O3'  C3'  single  1.406  0.020  1.406
 38T  NAR  C1'  single  1.458  0.020  1.458
 38T  NAR  CAG  single  1.373  0.020  1.373
 38T  C3'  C4'  single  1.528  0.020  1.528
 38T  C1'  O4'  single  1.398  0.020  1.398
 38T  CAK  CAG  double  1.343  0.020  1.343
 38T  CAK  CAA  single  1.493  0.020  1.493
 38T  C4'  O4'  single  1.419  0.020  1.419
 38T  C4'  C5'  single  1.508  0.020  1.508
 38T  O5'  C5'  single  1.407  0.020  1.407
 38T  NAI  H1   single  0.860  0.020  1.020
 38T  CAA  H2   single  0.970  0.020  1.090
 38T  CAA  H3   single  0.970  0.020  1.090
 38T  CAA  H4   single  0.970  0.020  1.090
 38T  CAG  H5   single  0.930  0.020  1.080
 38T  C1'  H6   single  0.970  0.020  1.090
 38T  C4'  H7   single  0.970  0.020  1.090
 38T  C5'  H8   single  0.970  0.020  1.090
 38T  C5'  H9   single  0.970  0.020  1.090
 38T  O5'  H10  single  0.850  0.020  0.980
 38T  C3'  H11  single  0.970  0.020  1.090
 38T  O3'  H12  single  0.850  0.020  0.980
 38T  C2'  H13  single  0.970  0.020  1.090
 38T  O2'  H14  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
 38T  NAR  CAM  NAI  114.57  3.000
 38T  NAR  CAM  OAC  123.40  3.000
 38T  NAI  CAM  OAC  122.02  3.000
 38T  H1   NAI  CAL  116.75  3.000
 38T  H1   NAI  CAM  115.17  3.000
 38T  CAL  NAI  CAM  128.08  3.000
 38T  CAK  CAL  OAB  125.07  3.000
 38T  CAK  CAL  NAI  114.32  3.000
 38T  OAB  CAL  NAI  120.60  3.000
 38T  CAG  CAK  CAA  123.16  3.000
 38T  CAA  CAK  CAL  118.95  3.000
 38T  CAG  CAK  CAL  117.89  3.000
 38T  H4   CAA  H3   107.87  3.000
 38T  H4   CAA  H2   107.94  3.000
 38T  H3   CAA  H2   107.24  3.000
 38T  H4   CAA  CAK  110.93  3.000
 38T  H3   CAA  CAK  111.36  3.000
 38T  H2   CAA  CAK  111.32  3.000
 38T  H5   CAG  NAR  114.82  3.000
 38T  H5   CAG  CAK  120.85  3.000
 38T  NAR  CAG  CAK  124.33  3.000
 38T  C1'  NAR  CAG  119.17  3.000
 38T  CAG  NAR  CAM  120.80  3.000
 38T  C1'  NAR  CAM  119.93  3.000
 38T  H6   C1'  C2'  107.79  3.000
 38T  H6   C1'  O4'  110.62  3.000
 38T  C2'  C1'  O4'  108.03  3.000
 38T  H6   C1'  NAR  104.65  3.000
 38T  O4'  C1'  NAR  109.41  3.000
 38T  C2'  C1'  NAR  116.27  3.000
 38T  C4'  O4'  C1'  111.11  3.000
 38T  H7   C4'  C3'  108.94  3.000
 38T  H7   C4'  C5'  109.49  3.000
 38T  C3'  C4'  C5'  112.59  3.000
 38T  H7   C4'  O4'  109.87  3.000
 38T  C5'  C4'  O4'  110.07  3.000
 38T  C3'  C4'  O4'  105.81  3.000
 38T  H9   C5'  H8   107.28  3.000
 38T  H9   C5'  O5'  112.06  3.000
 38T  H8   C5'  O5'  111.71  3.000
 38T  H9   C5'  C4'  108.73  3.000
 38T  H8   C5'  C4'  107.48  3.000
 38T  O5'  C5'  C4'  109.42  3.000
 38T  H10  O5'  C5'  108.05  3.000
 38T  H11  C3'  C2'  109.67  3.000
 38T  H11  C3'  O3'  111.19  3.000
 38T  C2'  C3'  O3'  112.64  3.000
 38T  H11  C3'  C4'  110.32  3.000
 38T  O3'  C3'  C4'  109.83  3.000
 38T  C2'  C3'  C4'  102.90  3.000
 38T  H12  O3'  C3'  108.83  3.000
 38T  H13  C2'  O2'  110.75  3.000
 38T  H13  C2'  C3'  112.27  3.000
 38T  O2'  C2'  C3'  110.42  3.000
 38T  H13  C2'  C1'  112.07  3.000
 38T  C3'  C2'  C1'  103.48  3.000
 38T  O2'  C2'  C1'  107.54  3.000
 38T  H14  O2'  C2'  106.79  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
 38T  CONST_01  C1'  NAR  CAM  NAI  180.00   0.0  0
 38T  CONST_02  CAG  NAR  CAM  NAI    0.00   0.0  0
 38T  CONST_03  NAR  CAM  NAI  CAL    0.00   0.0  0
 38T  CONST_04  CAL  NAI  CAM  OAC  180.00   0.0  0
 38T  CONST_05  C1'  NAR  CAM  OAC    0.00   0.0  0
 38T  CONST_06  CAG  NAR  CAM  OAC  180.00   0.0  0
 38T  CONST_07  H1   NAI  CAM  NAR  180.00   0.0  0
 38T  Var_01    H2   CAA  CAK  CAL  -59.11  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
 38T  chir_01  C1'  C2'  NAR  O4'  positiv
 38T  chir_02  C4'  O4'  C5'  C3'  positiv
 38T  chir_03  C3'  O3'  C4'  C2'  positiv
 38T  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
 38T  plan-1  OAC  0.020
 38T  plan-1  CAM  0.020
 38T  plan-1  NAI  0.020
 38T  plan-1  CAL  0.020
 38T  plan-1  OAB  0.020
 38T  plan-1  CAK  0.020
 38T  plan-1  CAA  0.020
 38T  plan-1  CAG  0.020
 38T  plan-1  NAR  0.020
 38T  plan-1  C1'  0.020
 38T  plan-1  H1   0.020
 38T  plan-1  H5   0.020

