# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 22:41:12 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 6-methyluridine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
#
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
 U6M  U6M  '6-methyluridine 5'-(dihydrogen phosphate)'  ligand  37  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U6M
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
 U6M  O2   O  O     0  -0.523   0.1966   0.9238   0.9645
 U6M  C2   C  CR6   0   0.801   1.2452   1.0366   0.3478
 U6M  N3   N  NR16  0  -0.727   1.9142   2.2171   0.3079
 U6M  C4   C  CR6   0   0.575   3.1342   2.4672  -0.3014
 U6M  O4   O  O     0  -0.457   3.6311   3.5762  -0.2582
 U6M  C5   C  CR16  0  -0.535   3.6940   1.3083  -0.9385
 U6M  C6   C  CR6   0   0.457   3.0469   0.1248  -0.9517
 U6M  C7   C  CH3   0  -0.772   3.6611  -1.0537  -1.6319
 U6M  N1   N  NR6   0  -0.622   1.8151  -0.0180  -0.3294
 U6M  C1'  C  CH1   0   0.213   1.0571  -1.2637  -0.4373
 U6M  O4'  O  O2    0  -0.481  -0.1976  -1.0175  -0.9954
 U6M  C2'  C  CH1   0  -0.047   0.8197  -2.0376   0.8590
 U6M  O2'  O  OH1   0  -0.656   1.9547  -2.8012   1.1530
 U6M  C3'  C  CH1   0  -0.043  -0.4124  -2.8665   0.4626
 U6M  O3'  O  OH1   0  -0.666  -0.0449  -3.9748  -0.3149
 U6M  C4'  C  CH1   0  -0.018  -1.1744  -1.8822  -0.4189
 U6M  C5'  C  CH2   0  -0.179  -2.2065  -1.1064   0.3801
 U6M  O5'  O  O2    0  -0.586  -2.6699  -0.0338  -0.4329
 U6M  P    P  P     0   1.431  -3.2613   1.3246   0.1632
 U6M  O3P  O  O     0  -0.714  -4.6397   1.2872   0.6920
 U6M  O1P  O  OH1   0  -0.778  -2.2476   1.8343   1.2729
 U6M  O2P  O  OH1   0  -0.737  -3.0492   2.2096  -1.1511
 U6M  H1   H  HNR6  0   0.433   1.4785   2.9827   0.8087
 U6M  H2   H  HCR6  0   0.291   4.6559   1.4011  -1.4185
 U6M  H5   H  HCH3  0   0.288   4.6506  -0.7844  -1.9901
 U6M  H6   H  HCH3  0   0.277   3.7624  -1.9036  -0.9575
 U6M  H7   H  HCH3  0   0.284   3.0741  -1.3732  -2.4941
 U6M  H8   H  HCH1  0   0.286   1.6356  -1.9073  -1.1003
 U6M  H9   H  HCH1  0   0.268   0.5614  -1.3701   1.6838
 U6M  H10  H  HOH1  0   0.471   1.9650  -2.9948   2.0954
 U6M  H11  H  HCH1  0   0.253  -0.9984  -3.1663   1.3422
 U6M  H12  H  HOH1  0   0.450   0.6886  -4.4174   0.1288
 U6M  H13  H  HCH1  0   0.268  -1.6824  -2.4097  -1.2323
 U6M  H14  H  HCH2  0   0.256  -3.0356  -1.7770   0.6189
 U6M  H15  H  HCH2  0   0.239  -1.7918  -0.7462   1.3233
 U6M  H16  H  HOH1  0   0.500  -1.2896   1.6430   1.1307
 U6M  H17  H  HOH1  0   0.499  -3.6392   2.9730  -1.1997

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
 U6M  C7   C6   single  1.493  0.020  1.493
 U6M  C6   C5   double  1.349  0.020  1.349
 U6M  C6   N1   single  1.387  0.020  1.387
 U6M  C5   C4   single  1.436  0.020  1.436
 U6M  O4'  C1'  single  1.395  0.020  1.395
 U6M  O4'  C4'  single  1.426  0.020  1.426
 U6M  O4   C4   double  1.216  0.020  1.216
 U6M  C4   N3   single  1.386  0.020  1.386
 U6M  N1   C1'  single  1.462  0.020  1.462
 U6M  N1   C2   single  1.377  0.020  1.377
 U6M  C1'  C2'  single  1.528  0.020  1.528
 U6M  C4'  C5'  single  1.518  0.020  1.518
 U6M  C4'  C3'  single  1.525  0.020  1.525
 U6M  N3   C2   single  1.357  0.020  1.357
 U6M  C2   O2   double  1.222  0.020  1.222
 U6M  O3'  C3'  single  1.403  0.020  1.403
 U6M  C5'  O5'  single  1.423  0.020  1.423
 U6M  C3'  C2'  single  1.537  0.020  1.537
 U6M  C2'  O2'  single  1.399  0.020  1.399
 U6M  O3P  P    double  1.477  0.020  1.477
 U6M  O5'  P    single  1.597  0.020  1.597
 U6M  P    O1P  single  1.587  0.020  1.587
 U6M  P    O2P  single  1.599  0.020  1.599
 U6M  N3   H1   single  0.860  0.020  1.020
 U6M  C5   H2   single  0.930  0.020  1.080
 U6M  C7   H5   single  0.970  0.020  1.090
 U6M  C7   H6   single  0.970  0.020  1.090
 U6M  C7   H7   single  0.970  0.020  1.090
 U6M  C1'  H8   single  0.970  0.020  1.090
 U6M  C2'  H9   single  0.970  0.020  1.090
 U6M  O2'  H10  single  0.850  0.020  0.980
 U6M  C3'  H11  single  0.970  0.020  1.090
 U6M  O3'  H12  single  0.850  0.020  0.980
 U6M  C4'  H13  single  0.970  0.020  1.090
 U6M  C5'  H14  single  0.970  0.020  1.090
 U6M  C5'  H15  single  0.970  0.020  1.090
 U6M  O1P  H16  single  0.850  0.020  0.980
 U6M  O2P  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
 U6M  N1   C2   N3   116.59  3.000
 U6M  N3   C2   O2   121.21  3.000
 U6M  N1   C2   O2   122.19  3.000
 U6M  H1   N3   C4   117.33  3.000
 U6M  H1   N3   C2   115.51  3.000
 U6M  C4   N3   C2   127.12  3.000
 U6M  C5   C4   O4   126.33  3.000
 U6M  O4   C4   N3   120.57  3.000
 U6M  C5   C4   N3   113.10  3.000
 U6M  H2   C5   C6   119.92  3.000
 U6M  H2   C5   C4   118.39  3.000
 U6M  C6   C5   C4   121.69  3.000
 U6M  N1   C6   C7   119.23  3.000
 U6M  N1   C6   C5   120.78  3.000
 U6M  C7   C6   C5   119.98  3.000
 U6M  H7   C7   H6   108.11  3.000
 U6M  H7   C7   H5   107.59  3.000
 U6M  H6   C7   H5   108.23  3.000
 U6M  H7   C7   C6   111.71  3.000
 U6M  H6   C7   C6   111.83  3.000
 U6M  H5   C7   C6   109.22  3.000
 U6M  C1'  N1   C6   120.99  3.000
 U6M  C1'  N1   C2   118.31  3.000
 U6M  C6   N1   C2   120.62  3.000
 U6M  H8   C1'  C2'  107.41  3.000
 U6M  H8   C1'  O4'  109.76  3.000
 U6M  C2'  C1'  O4'  106.79  3.000
 U6M  H8   C1'  N1   105.83  3.000
 U6M  C2'  C1'  N1   116.71  3.000
 U6M  O4'  C1'  N1   110.21  3.000
 U6M  C4'  O4'  C1'  110.32  3.000
 U6M  H9   C2'  C3'  109.56  3.000
 U6M  H9   C2'  O2'  111.51  3.000
 U6M  C3'  C2'  O2'  114.22  3.000
 U6M  H9   C2'  C1'  111.58  3.000
 U6M  O2'  C2'  C1'  109.18  3.000
 U6M  C3'  C2'  C1'  100.30  3.000
 U6M  H10  O2'  C2'  108.92  3.000
 U6M  H11  C3'  C4'  111.86  3.000
 U6M  H11  C3'  O3'  111.58  3.000
 U6M  C4'  C3'  O3'  108.69  3.000
 U6M  H11  C3'  C2'  111.61  3.000
 U6M  O3'  C3'  C2'  111.04  3.000
 U6M  C4'  C3'  C2'  101.63  3.000
 U6M  H12  O3'  C3'  107.87  3.000
 U6M  H13  C4'  C5'  108.77  3.000
 U6M  H13  C4'  C3'  110.51  3.000
 U6M  C5'  C4'  C3'  111.42  3.000
 U6M  H13  C4'  O4'  108.04  3.000
 U6M  C3'  C4'  O4'  106.42  3.000
 U6M  C5'  C4'  O4'  111.62  3.000
 U6M  H15  C5'  H14  107.57  3.000
 U6M  H15  C5'  O5'  111.62  3.000
 U6M  H14  C5'  O5'  109.89  3.000
 U6M  H15  C5'  C4'  111.41  3.000
 U6M  H14  C5'  C4'  108.50  3.000
 U6M  O5'  C5'  C4'  107.81  3.000
 U6M  P    O5'  C5'  123.26  3.000
 U6M  O2P  P    O1P  108.19  3.000
 U6M  O2P  P    O3P  115.61  3.000
 U6M  O1P  P    O3P  110.73  3.000
 U6M  O2P  P    O5'   96.60  3.000
 U6M  O1P  P    O5'  107.31  3.000
 U6M  O3P  P    O5'  117.25  3.000
 U6M  H16  O1P  P    117.19  3.000
 U6M  H17  O2P  P    113.44  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
 U6M  CONST_01  C6   N1   C2   N3     0.00   0.0  0
 U6M  CONST_02  C1'  N1   C2   N3   180.00   0.0  0
 U6M  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 U6M  CONST_04  C6   N1   C2   O2   180.00   0.0  0
 U6M  CONST_05  C1'  N1   C2   O2     0.00   0.0  0
 U6M  CONST_06  C4   N3   C2   O2   180.00   0.0  0
 U6M  CONST_07  H1   N3   C2   N1   180.00   0.0  0
 U6M  Var_01    H5   C7   C6   C5     4.07  30.0  3
 U6M  Var_02    O3P  P    O5'  C5'  -76.72  30.0  3
 U6M  Var_03    H14  C5'  O5'  P     88.02  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
 U6M  chir_01  C1'  O4'  N1   C2'  negativ
 U6M  chir_02  C2'  O2'  C1'  C3'  negativ
 U6M  chir_03  C3'  O3'  C4'  C2'  positiv
 U6M  chir_04  C4'  O4'  C3'  C5'  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
 U6M  plan-1  O2   0.020
 U6M  plan-1  C2   0.020
 U6M  plan-1  N3   0.020
 U6M  plan-1  C4   0.020
 U6M  plan-1  O4   0.020
 U6M  plan-1  C5   0.020
 U6M  plan-1  C6   0.020
 U6M  plan-1  C7   0.020
 U6M  plan-1  N1   0.020
 U6M  plan-1  C1'  0.020
 U6M  plan-1  H1   0.020
 U6M  plan-1  H2   0.020

