# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:40:40 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 6-[(E)-iminomethyl]uridine 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
 U1P  U1P  '6-[(E)-iminomethyl]uridine 5'-(dihydrogen phosphate)'  ligand  35  23  .  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_U1P
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
 U1P  O1P   O  O      0  -0.905  -4.4604   1.6549   0.2550
 U1P  P     P  P      0   1.221  -4.3678   0.5979  -0.8401
 U1P  O2P   O  OP    -1  -0.904  -5.1555  -0.6744  -0.5460
 U1P  O3P   O  OP    -1  -0.897  -4.4974   1.1229  -2.2633
 U1P  N1    N  NR6    0  -0.626   2.2400  -0.0136   0.0535
 U1P  C2    C  CR6    0   0.737   2.2059   0.6529   1.2643
 U1P  O2    O  O      0  -0.464   1.3481   0.4612   2.0973
 U1P  N3    N  NR16   0  -0.730   3.2303   1.5359   1.4735
 U1P  C4    C  CR6    0   0.578   4.2524   1.8694   0.6034
 U1P  O4    O  O      0  -0.455   5.1154   2.6616   0.9287
 U1P  C6    C  CR6    0   0.435   3.1526   0.3412  -0.9169
 U1P  C5    C  CR16   0  -0.506   4.1441   1.2205  -0.6803
 U1P  O5'   O  O2     0  -0.657  -2.7296   0.1095  -0.8364
 U1P  C5'   C  CH2    0  -0.128  -2.2144  -0.3918   0.3557
 U1P  C4'   C  CH1    0   0.005  -1.0182  -1.2692   0.0738
 U1P  C3'   C  CH1    0  -0.024  -0.4060  -1.9044   1.3190
 U1P  O3'   O  OH1    0  -0.664  -1.0705  -3.1065   1.6166
 U1P  C2'   C  CH1    0  -0.045   1.0615  -2.1273   0.9029
 U1P  O2'   O  OH1    0  -0.676   1.2154  -3.3926   0.3113
 U1P  O4'   O  O2     0  -0.489   0.0304  -0.4883  -0.4834
 U1P  C1'   C  CH1    0   0.179   1.2678  -1.0703  -0.2034
 U1P  C7    C  C1     0  -0.129   2.9720  -0.2004  -2.2872
 U1P  N8    N  N      0  -0.505   3.9804  -0.5240  -2.9709
 U1P  HN3   H  HNR6   0   0.430   3.2199   2.0023   2.3728
 U1P  H5    H  HCR6   0   0.298   4.8321   1.4888  -1.4669
 U1P  H5'   H  HCH2   0   0.173  -1.9047   0.4096   1.0441
 U1P  H5'A  H  HCH2   0   0.180  -2.9446  -1.0073   0.8993
 U1P  H4'   H  HCH1   0   0.222  -1.3082  -2.0667  -0.6267
 U1P  H3'   H  HCH1   0   0.254  -0.4504  -1.2077   2.1586
 U1P  HO3'  H  HOH1   0   0.469  -0.9751  -3.2907   2.5565
 U1P  H2'   H  HCH1   0   0.250   1.7593  -2.0094   1.7369
 U1P  HO2'  H  HOH1   0   0.449   0.5068  -3.9509   0.6612
 U1P  H1'   H  HCH1   0   0.274   1.6545  -1.6156  -1.0692
 U1P  H7    H  H      0   0.286   1.9466  -0.2297  -2.6590
 U1P  HN8   H  H      0   0.368   3.6974  -0.8112  -3.9037

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
 U1P  O1P  P     deloc   1.525  0.020  1.525
 U1P  O2P  P     deloc   1.525  0.020  1.525
 U1P  P    O5'   single  1.710  0.020  1.710
 U1P  P    O3P   deloc   1.523  0.020  1.523
 U1P  C2   N1    single  1.382  0.020  1.382
 U1P  C6   N1    single  1.379  0.020  1.379
 U1P  N1   C1'   single  1.459  0.020  1.459
 U1P  N3   C2    single  1.368  0.020  1.368
 U1P  C2   O2    double  1.211  0.020  1.211
 U1P  C4   N3    single  1.383  0.020  1.383
 U1P  N3   HN3   single  0.860  0.020  1.020
 U1P  O4   C4    double  1.216  0.020  1.216
 U1P  C4   C5    single  1.442  0.020  1.442
 U1P  C5   C6    double  1.346  0.020  1.346
 U1P  C6   C7    single  1.484  0.020  1.484
 U1P  C5   H5    single  0.930  0.020  1.080
 U1P  C5'  O5'   single  1.392  0.020  1.392
 U1P  C5'  C4'   single  1.510  0.020  1.510
 U1P  C5'  H5'   single  0.970  0.020  1.090
 U1P  C5'  H5'A  single  0.970  0.020  1.090
 U1P  O4'  C4'   single  1.421  0.020  1.421
 U1P  C4'  C3'   single  1.526  0.020  1.526
 U1P  C4'  H4'   single  0.970  0.020  1.090
 U1P  C3'  C2'   single  1.542  0.020  1.542
 U1P  C3'  O3'   single  1.406  0.020  1.406
 U1P  C3'  H3'   single  0.970  0.020  1.090
 U1P  O3'  HO3'  single  0.850  0.020  0.980
 U1P  C1'  C2'   single  1.544  0.020  1.544
 U1P  C2'  O2'   single  1.405  0.020  1.405
 U1P  C2'  H2'   single  0.970  0.020  1.090
 U1P  O2'  HO2'  single  0.850  0.020  0.980
 U1P  O4'  C1'   single  1.396  0.020  1.396
 U1P  C1'  H1'   single  0.970  0.020  1.090
 U1P  N8   C7    double  1.261  0.020  1.261
 U1P  C7   H7    single  0.930  0.020  1.080
 U1P  N8   HN8   single  0.890  0.020  1.040

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
 U1P  O5'   P    O3P  100.49  3.000
 U1P  O3P   P    O2P  115.08  3.000
 U1P  O5'   P    O2P  104.85  3.000
 U1P  O3P   P    O1P  115.29  3.000
 U1P  O5'   P    O1P  104.76  3.000
 U1P  O2P   P    O1P  114.11  3.000
 U1P  C1'   N1   C6   120.24  3.000
 U1P  C1'   N1   C2   119.15  3.000
 U1P  C6    N1   C2   120.58  3.000
 U1P  N3    C2   O2   121.82  3.000
 U1P  O2    C2   N1   122.93  3.000
 U1P  N3    C2   N1   115.24  3.000
 U1P  HN3   N3   C4   117.07  3.000
 U1P  HN3   N3   C2   115.15  3.000
 U1P  C4    N3   C2   127.78  3.000
 U1P  C5    C4   O4   125.77  3.000
 U1P  C5    C4   N3   113.32  3.000
 U1P  O4    C4   N3   120.89  3.000
 U1P  C7    C6   C5   119.35  3.000
 U1P  C7    C6   N1   118.38  3.000
 U1P  C5    C6   N1   122.14  3.000
 U1P  H5    C5   C6   120.26  3.000
 U1P  H5    C5   C4   119.28  3.000
 U1P  C6    C5   C4   120.37  3.000
 U1P  C5'   O5'  P    117.35  3.000
 U1P  H5'A  C5'  H5'  106.58  3.000
 U1P  H5'A  C5'  C4'  107.05  3.000
 U1P  H5'   C5'  C4'  108.47  3.000
 U1P  H5'A  C5'  O5'  112.30  3.000
 U1P  H5'   C5'  O5'  112.18  3.000
 U1P  C4'   C5'  O5'  110.03  3.000
 U1P  H4'   C4'  O4'  110.06  3.000
 U1P  H4'   C4'  C3'  108.87  3.000
 U1P  O4'   C4'  C3'  104.63  3.000
 U1P  H4'   C4'  C5'  109.34  3.000
 U1P  C3'   C4'  C5'  114.04  3.000
 U1P  O4'   C4'  C5'  109.78  3.000
 U1P  H3'   C3'  C2'  109.79  3.000
 U1P  H3'   C3'  O3'  111.33  3.000
 U1P  C2'   C3'  O3'  112.55  3.000
 U1P  H3'   C3'  C4'  110.22  3.000
 U1P  O3'   C3'  C4'  109.82  3.000
 U1P  C2'   C3'  C4'  102.82  3.000
 U1P  HO3'  O3'  C3'  108.87  3.000
 U1P  H2'   C2'  C1'  112.79  3.000
 U1P  H2'   C2'  O2'  110.38  3.000
 U1P  C1'   C2'  O2'  107.47  3.000
 U1P  H2'   C2'  C3'  112.70  3.000
 U1P  O2'   C2'  C3'  110.37  3.000
 U1P  C1'   C2'  C3'  102.80  3.000
 U1P  HO2'  O2'  C2'  106.68  3.000
 U1P  C1'   O4'  C4'  110.26  3.000
 U1P  H1'   C1'  O4'  111.25  3.000
 U1P  H1'   C1'  C2'  105.85  3.000
 U1P  O4'   C1'  C2'  108.10  3.000
 U1P  H1'   C1'  N1   105.36  3.000
 U1P  O4'   C1'  N1   108.91  3.000
 U1P  C2'   C1'  N1   117.31  3.000
 U1P  H7    C7   N8   124.06  3.000
 U1P  H7    C7   C6   116.02  3.000
 U1P  N8    C7   C6   119.80  3.000
 U1P  HN8   N8   C7   110.34  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
 U1P  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 U1P  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 U1P  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 U1P  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 U1P  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 U1P  CONST_06  C6   N1   C2   O2   180.00   0.0  0
 U1P  CONST_07  C1'  N1   C2   O2     0.00   0.0  0
 U1P  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 U1P  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 U1P  CONST_10  HN8  N8   C7   C6   180.00   0.0  0
 U1P  Var_01    N8   C7   C6   N1  -142.91  30.0  2
 U1P  Var_02    C4'  C5'  O5'  P    156.87  30.0  2

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
 U1P  chir_01  C4'  C5'  O4'  C3'  negativ
 U1P  chir_02  C3'  O3'  C4'  C2'  positiv
 U1P  chir_03  C2'  O2'  C3'  C1'  positiv
 U1P  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
 U1P  plan-1  N1   0.020
 U1P  plan-1  C2   0.020
 U1P  plan-1  O2   0.020
 U1P  plan-1  N3   0.020
 U1P  plan-1  C4   0.020
 U1P  plan-1  O4   0.020
 U1P  plan-1  C6   0.020
 U1P  plan-1  C5   0.020
 U1P  plan-1  C1'  0.020
 U1P  plan-1  C7   0.020
 U1P  plan-1  HN3  0.020
 U1P  plan-1  H5   0.020
 U1P  plan-2  C6   0.020
 U1P  plan-2  C7   0.020
 U1P  plan-2  N8   0.020
 U1P  plan-2  H7   0.020
 U1P  plan-2  HN8  0.020

