# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 21:08:37 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC#CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)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
 0KL  0KL  '5-(5-aminopent-1-yn-1-yl)-2'-deoxyuridine 5'-(tetrahydrogen triphosphate)'  ligand  56  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0KL
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
 0KL  O3G  O  OH1   0  -0.763  18.7017  -14.9855  -14.7869
 0KL  PG   P  P     0   1.417  17.2305  -14.4600  -14.6434
 0KL  O2G  O  OH1   0  -0.697  17.4044  -12.9007  -14.4010
 0KL  O1G  O  O     0  -0.679  16.2919  -14.8652  -15.6998
 0KL  O3B  O  O2    0  -0.685  16.7569  -14.9339  -13.1388
 0KL  PB   P  P     0   1.395  16.5635  -16.4399  -12.6084
 0KL  O1B  O  OH1   0  -0.611  15.1857  -16.4254  -11.8465
 0KL  O2B  O  O     0  -0.694  16.8433  -17.4681  -13.6179
 0KL  O3A  O  O2    0  -0.707  17.5213  -16.4371  -11.3067
 0KL  PA   P  P     0   1.501  19.1431  -16.3736  -11.2799
 0KL  O1A  O  O     0  -0.693  19.6866  -15.9523  -12.5936
 0KL  O2A  O  OH1   0  -0.707  19.4815  -15.5079  -10.0156
 0KL  O5'  O  O2    0  -0.497  19.5808  -17.7870  -10.7434
 0KL  C5'  C  CH2   0  -0.214  19.3147  -19.0022  -11.4707
 0KL  C4'  C  CH1   0  -0.005  18.5540  -19.9819  -10.6165
 0KL  C3'  C  CH1   0   0.077  17.2526  -19.5108   -9.9772
 0KL  O3'  O  OH1   0  -0.639  16.2373  -19.4939  -10.9371
 0KL  C2'  C  CH2   0  -0.597  17.1049  -20.5463   -8.8661
 0KL  O4'  O  O2    0  -0.470  19.3554  -20.4130   -9.5216
 0KL  C1'  C  CH1   0   0.207  18.5523  -20.7653   -8.4327
 0KL  N1   N  NR6   0  -0.436  18.9254  -19.9255   -7.2691
 0KL  C2   C  CR6   0   0.684  18.5527  -20.3978   -6.0278
 0KL  O2   O  O     0  -0.523  17.9761  -21.4547   -5.8771
 0KL  N3   N  NR16  0  -0.709  18.8828  -19.5820   -4.9797
 0KL  C6   C  CR16  0  -0.012  19.5418  -18.7262   -7.4103
 0KL  C5   C  CR6   0  -0.414  19.8421  -17.9141   -6.3681
 0KL  C4   C  CR6   0   0.520  19.4936  -18.3418   -5.0230
 0KL  O4   O  O     0  -0.332  19.6948  -17.7095   -4.0058
 0KL  C29  C  CSP   0   0.139  20.4748  -16.6595   -6.5511
 0KL  C30  C  CSP   0   0.038  21.0083  -15.5857   -6.6712
 0KL  C31  C  CH2   0  -0.594  21.5591  -14.2458   -6.8133
 0KL  C32  C  CH2   0  -0.460  21.0455  -13.2791   -5.7365
 0KL  C33  C  CH2   0  -0.232  21.7921  -13.3712   -4.4131
 0KL  N34  N  NH2   0  -0.811  21.9360  -14.7402   -3.9502
 0KL  H1   H  HOH1  0   0.497  19.1545  -15.3172  -13.9629
 0KL  H2   H  HOH1  0   0.494  16.6165  -12.3776  -14.6038
 0KL  H3   H  HOH1  0   0.530  14.4239  -16.6957  -12.3796
 0KL  H4   H  HOH1  0   0.486  19.5414  -14.5540  -10.1701
 0KL  H5   H  HCH2  0   0.268  18.7409  -18.8156  -12.3803
 0KL  H6   H  HCH2  0   0.341  20.2771  -19.4171  -11.7676
 0KL  H7   H  HCH1  0   0.267  18.3275  -20.8337  -11.2712
 0KL  H8   H  HCH1  0   0.193  17.3856  -18.5170   -9.5297
 0KL  H9   H  HOH1  0   0.463  15.4581  -19.0803  -10.5532
 0KL  H10  H  HCH2  0   0.267  16.4557  -20.2311   -8.0507
 0KL  H11  H  HCH2  0   0.299  16.7073  -21.4756   -9.2802
 0KL  H12  H  HCH1  0   0.279  18.7509  -21.7961   -8.1429
 0KL  H13  H  HNR6  0   0.397  18.6205  -19.9275   -4.0643
 0KL  H14  H  HCR6  0   0.293  19.8028  -18.4373   -8.4155
 0KL  H15  H  HCH2  0   0.270  22.6522  -14.2810   -6.7948
 0KL  H16  H  HCH2  0   0.295  21.2830  -13.8704   -7.8023
 0KL  H17  H  HCH2  0   0.268  21.1402  -12.2567   -6.1076
 0KL  H18  H  HCH2  0   0.201  19.9772  -13.4522   -5.5813
 0KL  H19  H  HCH2  0   0.241  22.7959  -12.9576   -4.5513
 0KL  H20  H  HCH2  0   0.138  21.2853  -12.7085   -3.6971
 0KL  H21  H  HNH2  0   0.361  22.3317  -14.7410   -3.0191
 0KL  H22  H  HNH2  0   0.351  21.0327  -15.1916   -3.8764

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
 0KL  O1G  PG   double  1.470  0.020  1.470
 0KL  O3G  PG   single  1.569  0.020  1.569
 0KL  PG   O2G  single  1.588  0.020  1.588
 0KL  PG   O3B  single  1.647  0.020  1.647
 0KL  O2B  PB   double  1.468  0.020  1.468
 0KL  O1A  PA   double  1.483  0.020  1.483
 0KL  O3B  PB   single  1.608  0.020  1.608
 0KL  PB   O1B  single  1.574  0.020  1.574
 0KL  PB   O3A  single  1.616  0.020  1.616
 0KL  C5'  O5'  single  1.441  0.020  1.441
 0KL  C5'  C4'  single  1.506  0.020  1.506
 0KL  PA   O3A  single  1.623  0.020  1.623
 0KL  PA   O5'  single  1.574  0.020  1.574
 0KL  PA   O2A  single  1.569  0.020  1.569
 0KL  O3'  C3'  single  1.397  0.020  1.397
 0KL  C4'  C3'  single  1.525  0.020  1.525
 0KL  C4'  O4'  single  1.424  0.020  1.424
 0KL  C3'  C2'  single  1.526  0.020  1.526
 0KL  O4'  C1'  single  1.398  0.020  1.398
 0KL  C2'  C1'  single  1.527  0.020  1.527
 0KL  C1'  N1   single  1.483  0.020  1.483
 0KL  C6   N1   single  1.356  0.020  1.356
 0KL  C6   C5   double  1.355  0.020  1.355
 0KL  N1   C2   single  1.379  0.020  1.379
 0KL  C31  C30  single  1.456  0.020  1.456
 0KL  C31  C32  single  1.536  0.020  1.536
 0KL  C30  C29  triple  1.205  0.020  1.205
 0KL  C29  C5   single  1.417  0.020  1.417
 0KL  C5   C4   single  1.454  0.020  1.454
 0KL  C32  C33  single  1.522  0.020  1.522
 0KL  C2   O2   double  1.213  0.020  1.213
 0KL  C2   N3   single  1.369  0.020  1.369
 0KL  C4   N3   single  1.383  0.020  1.383
 0KL  C4   O4   double  1.215  0.020  1.215
 0KL  C33  N34  single  1.452  0.020  1.452
 0KL  O3G  H1   single  0.850  0.020  0.980
 0KL  O2G  H2   single  0.850  0.020  0.980
 0KL  O1B  H3   single  0.850  0.020  0.980
 0KL  O2A  H4   single  0.850  0.020  0.980
 0KL  C5'  H5   single  0.970  0.020  1.090
 0KL  C5'  H6   single  0.970  0.020  1.090
 0KL  C4'  H7   single  0.970  0.020  1.090
 0KL  C3'  H8   single  0.970  0.020  1.090
 0KL  O3'  H9   single  0.850  0.020  0.980
 0KL  C2'  H10  single  0.970  0.020  1.090
 0KL  C2'  H11  single  0.970  0.020  1.090
 0KL  C1'  H12  single  0.970  0.020  1.090
 0KL  N3   H13  single  0.860  0.020  1.020
 0KL  C6   H14  single  0.930  0.020  1.080
 0KL  C31  H15  single  0.970  0.020  1.090
 0KL  C31  H16  single  0.970  0.020  1.090
 0KL  C32  H17  single  0.970  0.020  1.090
 0KL  C32  H18  single  0.970  0.020  1.090
 0KL  C33  H19  single  0.970  0.020  1.090
 0KL  C33  H20  single  0.970  0.020  1.090
 0KL  N34  H21  single  0.890  0.020  1.040
 0KL  N34  H22  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
 0KL  H1   O3G  PG   117.50  3.000
 0KL  O3B  PG   O1G  113.18  3.000
 0KL  O3B  PG   O2G  100.06  3.000
 0KL  O1G  PG   O2G  116.77  3.000
 0KL  O3B  PG   O3G  104.88  3.000
 0KL  O2G  PG   O3G  103.90  3.000
 0KL  O1G  PG   O3G  116.15  3.000
 0KL  H2   O2G  PG   114.20  3.000
 0KL  PB   O3B  PG   127.25  3.000
 0KL  O3A  PB   O2B  116.24  3.000
 0KL  O3A  PB   O1B   97.40  3.000
 0KL  O2B  PB   O1B  120.40  3.000
 0KL  O3A  PB   O3B  101.11  3.000
 0KL  O1B  PB   O3B  104.85  3.000
 0KL  O2B  PB   O3B  113.96  3.000
 0KL  H3   O1B  PB   114.80  3.000
 0KL  PA   O3A  PB   127.27  3.000
 0KL  O5'  PA   O2A   99.25  3.000
 0KL  O2A  PA   O1A  118.55  3.000
 0KL  O5'  PA   O1A  117.08  3.000
 0KL  O2A  PA   O3A  104.50  3.000
 0KL  O5'  PA   O3A  104.38  3.000
 0KL  O1A  PA   O3A  111.26  3.000
 0KL  H4   O2A  PA   115.37  3.000
 0KL  C5'  O5'  PA   122.27  3.000
 0KL  H6   C5'  H5   107.60  3.000
 0KL  H6   C5'  C4'  110.68  3.000
 0KL  H5   C5'  C4'  108.56  3.000
 0KL  H6   C5'  O5'  107.19  3.000
 0KL  H5   C5'  O5'  111.93  3.000
 0KL  C4'  C5'  O5'  110.83  3.000
 0KL  H7   C4'  O4'  109.87  3.000
 0KL  H7   C4'  C3'  108.28  3.000
 0KL  O4'  C4'  C3'  104.57  3.000
 0KL  H7   C4'  C5'  105.70  3.000
 0KL  O4'  C4'  C5'  110.42  3.000
 0KL  C3'  C4'  C5'  117.90  3.000
 0KL  H8   C3'  C2'  109.22  3.000
 0KL  H8   C3'  O3'  110.92  3.000
 0KL  C2'  C3'  O3'  115.98  3.000
 0KL  H8   C3'  C4'  110.32  3.000
 0KL  C2'  C3'  C4'  100.26  3.000
 0KL  O3'  C3'  C4'  109.63  3.000
 0KL  H9   O3'  C3'  108.63  3.000
 0KL  H11  C2'  H10  108.25  3.000
 0KL  H11  C2'  C1'  109.31  3.000
 0KL  H10  C2'  C1'  113.21  3.000
 0KL  H11  C2'  C3'  109.67  3.000
 0KL  H10  C2'  C3'  113.99  3.000
 0KL  C1'  C2'  C3'  102.26  3.000
 0KL  C1'  O4'  C4'  110.61  3.000
 0KL  H12  C1'  N1   106.35  3.000
 0KL  H12  C1'  O4'  109.94  3.000
 0KL  N1   C1'  O4'  108.90  3.000
 0KL  H12  C1'  C2'  112.59  3.000
 0KL  N1   C1'  C2'  112.34  3.000
 0KL  O4'  C1'  C2'  106.69  3.000
 0KL  C6   N1   C2   121.29  3.000
 0KL  C2   N1   C1'  116.38  3.000
 0KL  C6   N1   C1'  122.25  3.000
 0KL  N3   C2   O2   122.60  3.000
 0KL  N3   C2   N1   114.83  3.000
 0KL  O2   C2   N1   122.57  3.000
 0KL  H13  N3   C4   116.65  3.000
 0KL  H13  N3   C2   115.23  3.000
 0KL  C4   N3   C2   128.10  3.000
 0KL  H14  C6   C5   120.20  3.000
 0KL  H14  C6   N1   116.37  3.000
 0KL  C5   C6   N1   123.42  3.000
 0KL  C29  C5   C4   119.14  3.000
 0KL  C4   C5   C6   118.83  3.000
 0KL  C29  C5   C6   122.03  3.000
 0KL  O4   C4   C5   125.60  3.000
 0KL  O4   C4   N3   120.91  3.000
 0KL  C5   C4   N3   113.49  3.000
 0KL  C30  C29  C5   180.00  3.000
 0KL  C31  C30  C29  180.00  3.000
 0KL  H16  C31  H15  106.18  3.000
 0KL  H16  C31  C32  109.49  3.000
 0KL  H15  C31  C32  110.04  3.000
 0KL  H16  C31  C30  107.99  3.000
 0KL  H15  C31  C30  110.30  3.000
 0KL  C32  C31  C30  112.61  3.000
 0KL  H18  C32  H17  106.33  3.000
 0KL  H18  C32  C33  110.26  3.000
 0KL  H17  C32  C33  108.03  3.000
 0KL  H18  C32  C31  109.07  3.000
 0KL  H17  C32  C31  108.79  3.000
 0KL  C33  C32  C31  114.05  3.000
 0KL  H20  C33  H19  106.09  3.000
 0KL  H20  C33  N34  113.97  3.000
 0KL  H19  C33  N34  107.80  3.000
 0KL  H20  C33  C32  107.68  3.000
 0KL  H19  C33  C32  108.50  3.000
 0KL  N34  C33  C32  112.50  3.000
 0KL  H22  N34  H21  106.35  3.000
 0KL  H22  N34  C33  110.80  3.000
 0KL  H21  N34  C33  109.44  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
 0KL  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 0KL  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 0KL  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 0KL  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 0KL  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 0KL  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 0KL  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 0KL  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 0KL  CONST_09  H13  N3   C2   N1    180.00   0.0  0
 0KL  Var_01    C4'  C5'  O5'  PA   -124.47  30.0  2
 0KL  Var_02    O2B  PB   O3B  PG     -0.46  30.0  3
 0KL  Var_03    O1A  PA   O3A  PB     15.27  30.0  2
 0KL  Var_04    C32  C31  C30  C29    51.62  30.0  1
 0KL  Var_05    C33  C32  C31  C30    82.39  30.0  3
 0KL  Var_06    N34  C33  C32  C31   -48.50  30.0  3
 0KL  Var_07    H21  N34  C33  C32  -172.95  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
 0KL  chir_03  C4'  C5'  C3'  O4'  positiv
 0KL  chir_04  C3'  O3'  C2'  C4'  negativ
 0KL  chir_05  C1'  O4'  N1   C2'  negativ
 0KL  chir_06  PB   O3B  O1B  O3A  both
 0KL  chir_07  PA   O3A  O5'  O2A  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
 0KL  plan-1  C1'  0.020
 0KL  plan-1  N1   0.020
 0KL  plan-1  C2   0.020
 0KL  plan-1  O2   0.020
 0KL  plan-1  N3   0.020
 0KL  plan-1  C6   0.020
 0KL  plan-1  C5   0.020
 0KL  plan-1  C4   0.020
 0KL  plan-1  O4   0.020
 0KL  plan-1  C29  0.020
 0KL  plan-1  C30  0.020
 0KL  plan-1  H13  0.020
 0KL  plan-1  H14  0.020

