# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:16:40 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: 5'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=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
 U4P  U4P  '5'-deoxyuridine          '  ligand  28  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U4P
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
 U4P  OAC  O  O     0  -0.462  2.7849  -56.7086  25.2935
 U4P  CAM  C  CR6   0   0.740  2.7676  -57.2956  24.2340
 U4P  NAI  N  NR16  0  -0.735  2.0302  -58.4352  24.0456
 U4P  CAL  C  CR6   0   0.564  1.9067  -59.1997  22.8931
 U4P  OAB  O  O     0  -0.452  1.1965  -60.1858  22.8772
 U4P  CAK  C  CR16  0  -0.509  2.6888  -58.6958  21.7909
 U4P  CAG  C  CR16  0   0.100  3.4235  -57.5852  21.9552
 U4P  NAR  N  NR6   0  -0.572  3.4739  -56.8750  23.1228
 U4P  C1'  C  CH1   0   0.213  4.3146  -55.6875  23.2001
 U4P  O4'  O  O2    0  -0.487  5.3608  -55.9196  24.0958
 U4P  C4'  C  CH1   0   0.034  5.6502  -54.7285  24.8173
 U4P  C5'  C  CH3   0  -0.688  6.3000  -55.0730  26.1352
 U4P  C3'  C  CH1   0   0.007  4.3018  -54.0180  24.9366
 U4P  O3'  O  OH1   0  -0.668  4.4475  -52.6285  25.0774
 U4P  C2'  C  CH1   0  -0.056  3.6086  -54.3817  23.6149
 U4P  O2'  O  OH1   0  -0.666  3.8825  -53.4350  22.6142
 U4P  H1   H  HNR6  0   0.424  1.5039  -58.7428  24.8549
 U4P  H2   H  HCR6  0   0.292  2.6811  -59.2150  20.8452
 U4P  H3   H  HCR6  0   0.327  4.0203  -57.1873  21.1465
 U4P  H4   H  HCH1  0   0.258  4.6965  -55.5485  22.1830
 U4P  H5   H  HCH1  0   0.222  6.3266  -54.0933  24.2274
 U4P  H6   H  HCH3  0   0.235  6.5041  -54.1576  26.6910
 U4P  H7   H  HCH3  0   0.229  5.6464  -55.7020  26.7413
 U4P  H8   H  HCH3  0   0.242  7.2491  -55.5905  25.9943
 U4P  H9   H  HCH1  0   0.247  3.7350  -54.4469  25.7654
 U4P  H10  H  HOH1  0   0.465  4.1004  -52.3576  25.9307
 U4P  H11  H  HCH1  0   0.245  2.5285  -54.5166  23.7412
 U4P  H12  H  HOH1  0   0.450  3.7673  -52.5605  23.0052

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
 U4P  CAK  CAG  double  1.342  0.020  1.342
 U4P  CAK  CAL  single  1.442  0.020  1.442
 U4P  CAG  NAR  single  1.368  0.020  1.368
 U4P  O2'  C2'  single  1.404  0.020  1.404
 U4P  OAB  CAL  double  1.215  0.020  1.215
 U4P  CAL  NAI  single  1.388  0.020  1.388
 U4P  NAR  C1'  single  1.457  0.020  1.457
 U4P  NAR  CAM  single  1.382  0.020  1.382
 U4P  C1'  C2'  single  1.541  0.020  1.541
 U4P  C1'  O4'  single  1.397  0.020  1.397
 U4P  C2'  C3'  single  1.536  0.020  1.536
 U4P  O4'  C4'  single  1.422  0.020  1.422
 U4P  NAI  CAM  single  1.370  0.020  1.370
 U4P  CAM  OAC  double  1.211  0.020  1.211
 U4P  C4'  C3'  single  1.529  0.020  1.529
 U4P  C4'  C5'  single  1.509  0.020  1.509
 U4P  C3'  O3'  single  1.404  0.020  1.404
 U4P  NAI  H1   single  0.860  0.020  1.020
 U4P  CAK  H2   single  0.930  0.020  1.080
 U4P  CAG  H3   single  0.930  0.020  1.080
 U4P  C1'  H4   single  0.970  0.020  1.090
 U4P  C4'  H5   single  0.970  0.020  1.090
 U4P  C5'  H6   single  0.970  0.020  1.090
 U4P  C5'  H7   single  0.970  0.020  1.090
 U4P  C5'  H8   single  0.970  0.020  1.090
 U4P  C3'  H9   single  0.970  0.020  1.090
 U4P  O3'  H10  single  0.850  0.020  0.980
 U4P  C2'  H11  single  0.970  0.020  1.090
 U4P  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
 U4P  NAR  CAM  NAI  114.68  3.000
 U4P  NAI  CAM  OAC  122.07  3.000
 U4P  NAR  CAM  OAC  123.25  3.000
 U4P  H1   NAI  CAL  116.72  3.000
 U4P  H1   NAI  CAM  114.97  3.000
 U4P  CAL  NAI  CAM  128.31  3.000
 U4P  CAK  CAL  OAB  126.18  3.000
 U4P  OAB  CAL  NAI  120.64  3.000
 U4P  CAK  CAL  NAI  113.18  3.000
 U4P  H2   CAK  CAG  120.64  3.000
 U4P  H2   CAK  CAL  119.85  3.000
 U4P  CAG  CAK  CAL  119.51  3.000
 U4P  H3   CAG  NAR  115.29  3.000
 U4P  H3   CAG  CAK  121.02  3.000
 U4P  NAR  CAG  CAK  123.68  3.000
 U4P  C1'  NAR  CAG  119.33  3.000
 U4P  C1'  NAR  CAM  120.01  3.000
 U4P  CAG  NAR  CAM  120.63  3.000
 U4P  H4   C1'  C2'  107.58  3.000
 U4P  H4   C1'  O4'  110.82  3.000
 U4P  C2'  C1'  O4'  108.13  3.000
 U4P  H4   C1'  NAR  104.80  3.000
 U4P  O4'  C1'  NAR  109.32  3.000
 U4P  C2'  C1'  NAR  116.13  3.000
 U4P  C4'  O4'  C1'  109.79  3.000
 U4P  H5   C4'  C3'  108.42  3.000
 U4P  H5   C4'  C5'  109.60  3.000
 U4P  C3'  C4'  C5'  114.69  3.000
 U4P  H5   C4'  O4'  109.68  3.000
 U4P  C5'  C4'  O4'  109.84  3.000
 U4P  C3'  C4'  O4'  104.43  3.000
 U4P  H8   C5'  H7   108.65  3.000
 U4P  H8   C5'  H6   107.54  3.000
 U4P  H7   C5'  H6   108.24  3.000
 U4P  H8   C5'  C4'  111.74  3.000
 U4P  H7   C5'  C4'  111.03  3.000
 U4P  H6   C5'  C4'  109.52  3.000
 U4P  H9   C3'  C2'  109.02  3.000
 U4P  H9   C3'  O3'  111.49  3.000
 U4P  C2'  C3'  O3'  111.55  3.000
 U4P  H9   C3'  C4'  109.54  3.000
 U4P  O3'  C3'  C4'  112.10  3.000
 U4P  C2'  C3'  C4'  102.76  3.000
 U4P  H10  O3'  C3'  109.32  3.000
 U4P  H11  C2'  O2'  110.93  3.000
 U4P  H11  C2'  C3'  112.01  3.000
 U4P  O2'  C2'  C3'  111.44  3.000
 U4P  H11  C2'  C1'  112.22  3.000
 U4P  C3'  C2'  C1'  103.03  3.000
 U4P  O2'  C2'  C1'  106.86  3.000
 U4P  H12  O2'  C2'  107.39  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
 U4P  CONST_01  CAG  NAR  CAM  NAI    0.00  0.0  0
 U4P  CONST_02  C1'  NAR  CAM  NAI  180.00  0.0  0
 U4P  CONST_03  NAR  CAM  NAI  CAL    0.00  0.0  0
 U4P  CONST_04  CAG  NAR  CAM  OAC  180.00  0.0  0
 U4P  CONST_05  C1'  NAR  CAM  OAC    0.00  0.0  0
 U4P  CONST_06  CAL  NAI  CAM  OAC  180.00  0.0  0
 U4P  CONST_07  H1   NAI  CAM  NAR  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
 U4P  chir_01  C1'  NAR  C2'  O4'  negativ
 U4P  chir_02  C4'  O4'  C3'  C5'  negativ
 U4P  chir_03  C3'  O3'  C4'  C2'  positiv
 U4P  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
 U4P  plan-1  OAC  0.020
 U4P  plan-1  CAM  0.020
 U4P  plan-1  NAI  0.020
 U4P  plan-1  CAL  0.020
 U4P  plan-1  OAB  0.020
 U4P  plan-1  CAK  0.020
 U4P  plan-1  CAG  0.020
 U4P  plan-1  NAR  0.020
 U4P  plan-1  C1'  0.020
 U4P  plan-1  H1   0.020
 U4P  plan-1  H2   0.020
 U4P  plan-1  H3   0.020

