# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 22:25:07 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 5'-(D-alanylamino)-5'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)C(=O)NC[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
 48C  48C  5'-(D-alanylamino)-5'-deoxyuridine  ligand  40  22  .  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_48C
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
 48C  OAZ  O  O     0  -0.479   3.5779   0.7408   1.7406
 48C  CAU  C  CR6   0   0.740   3.3062  -0.0551   0.8648
 48C  NAT  N  NR16  0  -0.731   4.2398  -0.8866   0.3089
 48C  CAV  C  CR6   0   0.567   4.0531  -1.8247  -0.6959
 48C  OBA  O  O     0  -0.465   4.9866  -2.4938  -1.0986
 48C  CAX  C  CR16  0  -0.509   2.6918  -1.8957  -1.1628
 48C  CAY  C  CR16  0   0.091   1.7583  -1.0925  -0.6241
 48C  NAW  N  NR6   0  -0.568   2.0318  -0.1850   0.3540
 48C  CBB  C  CR15  0   0.186   0.9984   0.6990   0.9370
 48C  OBE  O  O     0  -0.496  -0.2653   0.2066   0.6202
 48C  CBD  C  CR15  0  -0.040   1.0821   2.1173   0.3690
 48C  OBG  O  OH1   0  -0.664   0.6278   3.0001   1.3572
 48C  CBC  C  CR15  0  -0.034   0.0844   2.0338  -0.7925
 48C  OBH  O  OH1   0  -0.655  -0.4758   3.2648  -1.1484
 48C  CBF  C  CR15  0   0.028  -0.9850   1.1137  -0.2161
 48C  CAA  C  CH2   0  -0.320  -1.7666   0.3471  -1.2661
 48C  NAB  N  NH1   0  -0.633  -2.7261  -0.5713  -0.7037
 48C  C    C  C     0   0.562  -3.9368  -0.1894  -0.2669
 48C  O    O  O     0  -0.498  -4.3501   0.9570  -0.3712
 48C  CA   C  CH1   0  -0.224  -4.7576  -1.2708   0.4201
 48C  N    N  NH2   0  -0.786  -6.1238  -1.1856  -0.0643
 48C  CB   C  CH3   0  -0.666  -4.6012  -1.1089   1.9349
 48C  H1   H  HNR6  0   0.427   5.1771  -0.7935   0.6812
 48C  H2   H  HCR6  0   0.292   2.4269  -2.6010  -1.9348
 48C  H3   H  HCR6  0   0.323   0.7306  -1.1485  -0.9466
 48C  H4   H  HCR5  0   0.287   1.1458   0.6896   2.0183
 48C  H5   H  HCR5  0   0.262   2.0929   2.3709   0.0304
 48C  H6   H  HOH1  0   0.452   0.2054   3.7464   0.9136
 48C  H7   H  HCR5  0   0.246   0.5707   1.5512  -1.6519
 48C  H8   H  HOH1  0   0.470   0.1117   3.7086  -1.7686
 48C  H9   H  HCR5  0   0.256  -1.6802   1.6951   0.4009
 48C  H10  H  HCH2  0   0.272  -2.2782   1.0675  -1.9064
 48C  H11  H  HCH2  0   0.262  -1.0887  -0.2208  -1.9058
 48C  H12  H  HNH1  0   0.406  -2.4428  -1.5287  -0.5763
 48C  H13  H  HCH1  0   0.251  -4.3668  -2.2527   0.1376
 48C  H14  H  HNH2  0   0.352  -6.6865  -1.8815   0.4094
 48C  H15  H  HNH2  0   0.341  -6.5158  -0.2870   0.1922
 48C  H17  H  HCH3  0   0.229  -3.5588  -1.1939   2.2476
 48C  H18  H  HCH3  0   0.228  -4.9759  -0.1371   2.2603
 48C  H19  H  HCH3  0   0.241  -5.1679  -1.8830   2.4535

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
 48C  OBG  CBD  single  1.401  0.020  1.401
 48C  OBH  CBC  single  1.399  0.020  1.399
 48C  N    CA   single  1.452  0.020  1.452
 48C  CBD  CBC  single  1.534  0.020  1.534
 48C  CBD  CBB  single  1.530  0.020  1.530
 48C  CBC  CBF  single  1.524  0.020  1.524
 48C  CBF  CAA  single  1.517  0.020  1.517
 48C  CBF  OBE  single  1.428  0.020  1.428
 48C  CA   CB   single  1.531  0.020  1.531
 48C  CA   C    single  1.522  0.020  1.522
 48C  CAA  NAB  single  1.442  0.020  1.442
 48C  OBE  CBB  single  1.393  0.020  1.393
 48C  CBB  NAW  single  1.480  0.020  1.480
 48C  NAB  C    single  1.342  0.020  1.342
 48C  C    O    double  1.223  0.020  1.223
 48C  OAZ  CAU  double  1.214  0.020  1.214
 48C  NAW  CAU  single  1.379  0.020  1.379
 48C  NAW  CAY  single  1.362  0.020  1.362
 48C  CAU  NAT  single  1.368  0.020  1.368
 48C  CAY  CAX  double  1.344  0.020  1.344
 48C  NAT  CAV  single  1.387  0.020  1.387
 48C  CAX  CAV  single  1.441  0.020  1.441
 48C  CAV  OBA  double  1.217  0.020  1.217
 48C  NAT  H1   single  0.860  0.020  1.020
 48C  CAX  H2   single  0.930  0.020  1.080
 48C  CAY  H3   single  0.930  0.020  1.080
 48C  CBB  H4   single  0.970  0.020  1.090
 48C  CBD  H5   single  0.970  0.020  1.090
 48C  OBG  H6   single  0.850  0.020  0.980
 48C  CBC  H7   single  0.970  0.020  1.090
 48C  OBH  H8   single  0.850  0.020  0.980
 48C  CBF  H9   single  0.970  0.020  1.090
 48C  CAA  H10  single  0.970  0.020  1.090
 48C  CAA  H11  single  0.970  0.020  1.090
 48C  NAB  H12  single  0.860  0.020  1.020
 48C  CA   H13  single  0.970  0.020  1.090
 48C  N    H14  single  0.890  0.020  1.040
 48C  N    H15  single  0.890  0.020  1.040
 48C  CB   H17  single  0.970  0.020  1.090
 48C  CB   H18  single  0.970  0.020  1.090
 48C  CB   H19  single  0.970  0.020  1.090

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
 48C  NAW  CAU  NAT  115.01  3.000
 48C  NAT  CAU  OAZ  122.60  3.000
 48C  NAW  CAU  OAZ  122.39  3.000
 48C  H1   NAT  CAV  116.93  3.000
 48C  H1   NAT  CAU  115.23  3.000
 48C  CAV  NAT  CAU  127.83  3.000
 48C  CAX  CAV  OBA  126.18  3.000
 48C  OBA  CAV  NAT  120.54  3.000
 48C  CAX  CAV  NAT  113.28  3.000
 48C  H2   CAX  CAY  120.46  3.000
 48C  H2   CAX  CAV  119.74  3.000
 48C  CAY  CAX  CAV  119.79  3.000
 48C  H3   CAY  NAW  116.15  3.000
 48C  H3   CAY  CAX  120.72  3.000
 48C  NAW  CAY  CAX  123.13  3.000
 48C  CBB  NAW  CAY  122.74  3.000
 48C  CAY  NAW  CAU  120.95  3.000
 48C  CBB  NAW  CAU  116.31  3.000
 48C  H4   CBB  CBD  111.61  3.000
 48C  H4   CBB  OBE  110.17  3.000
 48C  CBD  CBB  OBE  107.03  3.000
 48C  H4   CBB  NAW  106.91  3.000
 48C  OBE  CBB  NAW  109.44  3.000
 48C  CBD  CBB  NAW  111.68  3.000
 48C  CBF  OBE  CBB  111.46  3.000
 48C  H5   CBD  CBC  112.25  3.000
 48C  H5   CBD  OBG  111.80  3.000
 48C  CBC  CBD  OBG  110.96  3.000
 48C  H5   CBD  CBB  112.31  3.000
 48C  CBC  CBD  CBB  101.25  3.000
 48C  OBG  CBD  CBB  107.73  3.000
 48C  H6   OBG  CBD  107.76  3.000
 48C  H7   CBC  CBF  109.95  3.000
 48C  H7   CBC  OBH  111.39  3.000
 48C  CBF  CBC  OBH  110.28  3.000
 48C  H7   CBC  CBD  109.16  3.000
 48C  CBF  CBC  CBD  101.71  3.000
 48C  OBH  CBC  CBD  113.92  3.000
 48C  H8   OBH  CBC  108.99  3.000
 48C  H9   CBF  CAA  109.32  3.000
 48C  H9   CBF  CBC  109.73  3.000
 48C  CAA  CBF  CBC  113.88  3.000
 48C  H9   CBF  OBE  109.08  3.000
 48C  CAA  CBF  OBE  110.12  3.000
 48C  CBC  CBF  OBE  104.56  3.000
 48C  H11  CAA  H10  106.91  3.000
 48C  H11  CAA  NAB  108.09  3.000
 48C  H10  CAA  NAB  109.71  3.000
 48C  H11  CAA  CBF  110.40  3.000
 48C  H10  CAA  CBF  108.30  3.000
 48C  NAB  CAA  CBF  113.24  3.000
 48C  H12  NAB  C    118.90  3.000
 48C  H12  NAB  CAA  117.89  3.000
 48C  C    NAB  CAA  123.07  3.000
 48C  CA   C    O    121.49  3.000
 48C  O    C    NAB  122.94  3.000
 48C  CA   C    NAB  115.54  3.000
 48C  H13  CA   CB   108.29  3.000
 48C  H13  CA   N    107.62  3.000
 48C  CB   CA   N    114.82  3.000
 48C  H13  CA   C    109.19  3.000
 48C  CB   CA   C    108.44  3.000
 48C  N    CA   C    108.37  3.000
 48C  H15  N    H14  106.02  3.000
 48C  H15  N    CA   109.37  3.000
 48C  H14  N    CA   109.06  3.000
 48C  H19  CB   H18  108.17  3.000
 48C  H19  CB   H17  107.74  3.000
 48C  H18  CB   H17  108.17  3.000
 48C  H19  CB   CA   110.01  3.000
 48C  H18  CB   CA   110.74  3.000
 48C  H17  CB   CA   111.88  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
 48C  CONST_01  CBB  NAW  CAU  NAT  180.00   0.0  0
 48C  CONST_02  CAY  NAW  CAU  NAT    0.00   0.0  0
 48C  CONST_03  NAW  CAU  NAT  CAV    0.00   0.0  0
 48C  CONST_04  CBB  NAW  CAU  OAZ    0.00   0.0  0
 48C  CONST_05  CAY  NAW  CAU  OAZ  180.00   0.0  0
 48C  CONST_06  CAV  NAT  CAU  OAZ  180.00   0.0  0
 48C  CONST_07  H1   NAT  CAU  NAW  180.00   0.0  0
 48C  CONST_08  CA   C    NAB  CAA  180.00   0.0  0
 48C  CONST_09  O    C    NAB  CAA    0.00   0.0  0
 48C  CONST_10  H12  NAB  C    O    180.00   0.0  0
 48C  Var_01    C    NAB  CAA  CBF   81.06  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
 48C  chir_01  CBB  CBD  OBE  NAW  negativ
 48C  chir_02  CBD  OBG  CBB  CBC  negativ
 48C  chir_03  CBC  OBH  CBD  CBF  negativ
 48C  chir_04  CBF  OBE  CBC  CAA  negativ
 48C  chir_05  CA   N    CB   C    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
 48C  plan-1  OAZ  0.020
 48C  plan-1  CAU  0.020
 48C  plan-1  NAT  0.020
 48C  plan-1  CAV  0.020
 48C  plan-1  OBA  0.020
 48C  plan-1  CAX  0.020
 48C  plan-1  CAY  0.020
 48C  plan-1  NAW  0.020
 48C  plan-1  CBB  0.020
 48C  plan-1  H1   0.020
 48C  plan-1  H2   0.020
 48C  plan-1  H3   0.020
 48C  plan-2  CAA  0.020
 48C  plan-2  NAB  0.020
 48C  plan-2  C    0.020
 48C  plan-2  O    0.020
 48C  plan-2  CA   0.020
 48C  plan-2  H12  0.020

