# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 23:05:38 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[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
 M5T  M5T  '5-methyluridine 5'-(tetrahydrogen triphosphate)'  ligand  47  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M5T
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
 M5T  C15  C  CH2   0  -0.212  93.6036  18.0694  -12.9339
 M5T  C10  C  CH1   0   0.178  96.4367  18.9870  -11.1805
 M5T  C11  C  CH1   0  -0.011  96.6095  17.5273  -11.6119
 M5T  C12  C  CH1   0  -0.048  96.1223  17.5990  -13.0592
 M5T  C13  C  CH1   0   0.000  95.0005  18.6403  -12.9689
 M5T  C02  C  CR6   0  -0.183  94.9938  18.8608   -7.7726
 M5T  C03  C  CR16  0   0.070  95.1982  18.7339   -9.0933
 M5T  N04  N  NR6   0  -0.571  96.3171  19.1855   -9.7475
 M5T  C05  C  CR6   0   0.733  97.3247  19.8364   -9.0694
 M5T  O06  O  O     0  -0.479  98.3271  20.2676   -9.6007
 M5T  N07  N  NR16  0  -0.735  97.1080  19.9567   -7.7222
 M5T  C08  C  CR6   0   0.564  96.0197  19.5209   -6.9880
 M5T  O09  O  O     0  -0.450  95.9705  19.7020   -5.7860
 M5T  O14  O  O2    0  -0.494  95.2493  19.4104  -11.7927
 M5T  O16  O  O2    0  -0.577  93.5452  16.9973  -11.9801
 M5T  P17  P  P     0   1.476  92.2378  16.6433  -11.1627
 M5T  O18  O  O     0  -0.662  91.7479  17.6404  -10.1996
 M5T  O19  O  OH1   0  -0.714  92.6391  15.2162  -10.6101
 M5T  O20  O  O2    0  -0.682  91.1837  16.3503  -12.3665
 M5T  P21  P  P     0   1.513  89.9102  15.3657  -12.4108
 M5T  O22  O  OH1   0  -0.740  89.4530  15.1892  -10.9033
 M5T  O23  O  O     0  -0.644  88.9262  15.7964  -13.4060
 M5T  O24  O  O2    0  -0.691  90.6514  13.9709  -12.6815
 M5T  P25  P  P     0   1.468  90.1080  12.4743  -12.3024
 M5T  O26  O  OH1   0  -0.710  91.0388  11.5801  -13.2145
 M5T  O27  O  O     0  -0.684  88.6468  12.3601  -12.4210
 M5T  O28  O  OH1   0  -0.718  90.7664  12.2027  -10.8898
 M5T  O29  O  OH1   0  -0.666  97.1168  18.1132  -13.9082
 M5T  O30  O  OH1   0  -0.658  97.9271  17.0756  -11.5339
 M5T  H1   H  HCH2  0   0.272  92.8894  18.8590  -12.6880
 M5T  H2   H  HCH2  0   0.271  93.3529  17.6742  -13.9192
 M5T  H4   H  HCH1  0   0.250  95.9279  16.8878  -11.0383
 M5T  H5   H  HCH1  0   0.261  95.7572  16.6285  -13.4151
 M5T  H6   H  HCH1  0   0.277  95.0400  19.2961  -13.8452
 M5T  H7   H  HCH3  0   0.249  93.2232  19.1834   -6.6035
 M5T  H8   H  HCH3  0   0.245  93.0851  17.8994   -7.8009
 M5T  H9   H  HCH3  0   0.248  94.0000  17.6345   -6.3177
 M5T  H10  H  HCR6  0   0.293  94.4511  18.2684   -9.7188
 M5T  H11  H  HNR6  0   0.427  97.8442  20.4264   -7.2092
 M5T  H12  H  HOH1  0   0.511  92.3535  15.0322   -9.7047
 M5T  H13  H  HOH1  0   0.517  88.7025  15.7377  -10.6309
 M5T  H14  H  HOH1  0   0.513  90.8085  11.5749  -14.1543
 M5T  H15  H  HOH1  0   0.512  90.1311  12.0497  -10.1772
 M5T  H16  H  HOH1  0   0.456  97.8814  17.5284  -13.8693
 M5T  H17  H  HOH1  0   0.469  98.0685  16.6552  -10.6812
 M5T  H3   H  HCH1  0   0.274  97.2954  19.5744  -11.5121
 M5T  C01  C  CH3   0  -0.716  93.7615  18.3683   -7.0886

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
 M5T  O29  C12  single  1.405  0.020  1.405
 M5T  O23  P21  double  1.464  0.020  1.464
 M5T  C12  C13  single  1.533  0.020  1.533
 M5T  C12  C11  single  1.529  0.020  1.529
 M5T  C13  C15  single  1.509  0.020  1.509
 M5T  C13  O14  single  1.428  0.020  1.428
 M5T  C15  O16  single  1.436  0.020  1.436
 M5T  O27  P25  double  1.470  0.020  1.470
 M5T  O24  P21  single  1.603  0.020  1.603
 M5T  O24  P25  single  1.637  0.020  1.637
 M5T  O26  P25  single  1.580  0.020  1.580
 M5T  O20  P21  single  1.610  0.020  1.610
 M5T  O20  P17  single  1.627  0.020  1.627
 M5T  P21  O22  single  1.585  0.020  1.585
 M5T  P25  O28  single  1.582  0.020  1.582
 M5T  O16  P17  single  1.582  0.020  1.582
 M5T  C11  O30  single  1.395  0.020  1.395
 M5T  C11  C10  single  1.532  0.020  1.532
 M5T  O14  C10  single  1.401  0.020  1.401
 M5T  P17  O18  double  1.470  0.020  1.470
 M5T  P17  O19  single  1.582  0.020  1.582
 M5T  C10  N04  single  1.452  0.020  1.452
 M5T  N04  C03  single  1.373  0.020  1.373
 M5T  N04  C05  single  1.378  0.020  1.378
 M5T  O06  C05  double  1.214  0.020  1.214
 M5T  C03  C02  double  1.342  0.020  1.342
 M5T  C05  N07  single  1.370  0.020  1.370
 M5T  C02  C01  single  1.493  0.020  1.493
 M5T  C02  C08  single  1.450  0.020  1.450
 M5T  N07  C08  single  1.383  0.020  1.383
 M5T  C08  O09  double  1.217  0.020  1.217
 M5T  C15  H1   single  0.970  0.020  1.090
 M5T  C15  H2   single  0.970  0.020  1.090
 M5T  C10  H3   single  0.970  0.020  1.090
 M5T  C11  H4   single  0.970  0.020  1.090
 M5T  C12  H5   single  0.970  0.020  1.090
 M5T  C13  H6   single  0.970  0.020  1.090
 M5T  C01  H7   single  0.970  0.020  1.090
 M5T  C01  H8   single  0.970  0.020  1.090
 M5T  C01  H9   single  0.970  0.020  1.090
 M5T  C03  H10  single  0.930  0.020  1.080
 M5T  N07  H11  single  0.860  0.020  1.020
 M5T  O19  H12  single  0.850  0.020  0.980
 M5T  O22  H13  single  0.850  0.020  0.980
 M5T  O26  H14  single  0.850  0.020  0.980
 M5T  O28  H15  single  0.850  0.020  0.980
 M5T  O29  H16  single  0.850  0.020  0.980
 M5T  O30  H17  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
 M5T  H2   C15  H1   108.36  3.000
 M5T  H2   C15  O16  108.67  3.000
 M5T  H1   C15  O16  111.30  3.000
 M5T  H2   C15  C13  109.20  3.000
 M5T  H1   C15  C13  109.68  3.000
 M5T  O16  C15  C13  109.59  3.000
 M5T  H3   C10  O14  111.78  3.000
 M5T  H3   C10  N04  106.92  3.000
 M5T  O14  C10  N04  108.67  3.000
 M5T  H3   C10  C11  109.78  3.000
 M5T  N04  C10  C11  114.68  3.000
 M5T  O14  C10  C11  105.10  3.000
 M5T  H4   C11  O30  111.65  3.000
 M5T  H4   C11  C12  108.93  3.000
 M5T  O30  C11  C12  111.66  3.000
 M5T  H4   C11  C10  109.77  3.000
 M5T  O30  C11  C10  113.54  3.000
 M5T  C12  C11  C10  100.72  3.000
 M5T  H5   C12  O29  111.32  3.000
 M5T  H5   C12  C13  112.13  3.000
 M5T  O29  C12  C13  107.75  3.000
 M5T  H5   C12  C11  111.84  3.000
 M5T  C13  C12  C11  102.08  3.000
 M5T  O29  C12  C11  111.32  3.000
 M5T  H6   C13  O14  109.26  3.000
 M5T  H6   C13  C12  109.46  3.000
 M5T  O14  C13  C12  106.70  3.000
 M5T  H6   C13  C15  106.16  3.000
 M5T  O14  C13  C15  110.25  3.000
 M5T  C12  C13  C15  114.93  3.000
 M5T  C08  C02  C03  117.88  3.000
 M5T  C08  C02  C01  119.08  3.000
 M5T  C03  C02  C01  123.04  3.000
 M5T  H10  C03  N04  115.46  3.000
 M5T  H10  C03  C02  120.35  3.000
 M5T  N04  C03  C02  124.19  3.000
 M5T  C05  N04  C03  121.13  3.000
 M5T  C05  N04  C10  119.35  3.000
 M5T  C03  N04  C10  119.52  3.000
 M5T  N07  C05  O06  122.01  3.000
 M5T  N07  C05  N04  114.19  3.000
 M5T  O06  C05  N04  123.80  3.000
 M5T  H11  N07  C08  116.70  3.000
 M5T  H11  N07  C05  115.07  3.000
 M5T  C08  N07  C05  128.23  3.000
 M5T  O09  C08  N07  120.62  3.000
 M5T  O09  C08  C02  125.01  3.000
 M5T  N07  C08  C02  114.37  3.000
 M5T  C13  O14  C10  110.15  3.000
 M5T  P17  O16  C15  122.94  3.000
 M5T  O20  P17  O19  105.09  3.000
 M5T  O19  P17  O18  117.87  3.000
 M5T  O20  P17  O18  113.02  3.000
 M5T  O19  P17  O16   99.94  3.000
 M5T  O18  P17  O16  117.52  3.000
 M5T  O20  P17  O16  101.15  3.000
 M5T  H12  O19  P17  115.07  3.000
 M5T  P21  O20  P17  130.01  3.000
 M5T  O24  P21  O23  116.87  3.000
 M5T  O24  P21  O22  101.37  3.000
 M5T  O23  P21  O22  119.03  3.000
 M5T  O22  P21  O20  105.66  3.000
 M5T  O24  P21  O20   99.85  3.000
 M5T  O23  P21  O20  111.74  3.000
 M5T  H13  O22  P21  115.33  3.000
 M5T  P25  O24  P21  127.09  3.000
 M5T  O28  P25  O27  118.18  3.000
 M5T  O28  P25  O26   99.97  3.000
 M5T  O27  P25  O26  119.65  3.000
 M5T  O28  P25  O24  103.04  3.000
 M5T  O26  P25  O24  100.84  3.000
 M5T  O27  P25  O24  112.48  3.000
 M5T  H14  O26  P25  115.05  3.000
 M5T  H15  O28  P25  114.33  3.000
 M5T  H16  O29  C12  108.37  3.000
 M5T  H17  O30  C11  109.28  3.000
 M5T  H9   C01  H8   107.98  3.000
 M5T  H9   C01  H7   107.24  3.000
 M5T  H8   C01  H7   107.83  3.000
 M5T  H9   C01  C02  111.43  3.000
 M5T  H8   C01  C02  110.81  3.000
 M5T  H7   C01  C02  111.38  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
 M5T  CONST_01  N07  C05  N04  C10   180.00   0.0  0
 M5T  CONST_02  C05  N07  C08  C02     0.00   0.0  0
 M5T  CONST_03  N07  C05  N04  C03     0.00   0.0  0
 M5T  CONST_04  C08  N07  C05  N04     0.00   0.0  0
 M5T  CONST_05  O06  C05  N04  C10     0.00   0.0  0
 M5T  CONST_06  O06  C05  N04  C03   180.00   0.0  0
 M5T  CONST_07  O09  C08  N07  C05   180.00   0.0  0
 M5T  CONST_08  C08  N07  C05  O06   180.00   0.0  0
 M5T  CONST_09  H11  N07  C08  C02   180.00   0.0  0
 M5T  Var_01    H7   C01  C02  C03  -119.52  30.0  3
 M5T  Var_02    O20  P17  O16  C15    58.04  30.0  3
 M5T  Var_03    O23  P21  O20  P17   155.49  30.0  3
 M5T  Var_04    O27  P25  O24  P21    34.29  30.0  3
 M5T  Var_05    H1   C15  O16  P17    27.68  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
 M5T  chir_01  C10  C11  O14  N04  negativ
 M5T  chir_02  C11  O30  C12  C10  positiv
 M5T  chir_03  C12  O29  C11  C13  negativ
 M5T  chir_04  C13  O14  C12  C15  negativ
 M5T  chir_05  P17  O16  O18  O19  both
 M5T  chir_06  P21  O24  O20  O22  both

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
 M5T  plan-1  C10  0.020
 M5T  plan-1  C02  0.020
 M5T  plan-1  C03  0.020
 M5T  plan-1  N04  0.020
 M5T  plan-1  C05  0.020
 M5T  plan-1  O06  0.020
 M5T  plan-1  N07  0.020
 M5T  plan-1  C08  0.020
 M5T  plan-1  O09  0.020
 M5T  plan-1  H10  0.020
 M5T  plan-1  H11  0.020
 M5T  plan-1  C01  0.020

