# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 11:18:20 2021
#   Inital geometry file: a 147 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC#CC1=C(N)NC(=O)N(C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
#
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
 0L6  0L6  '5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate)'  ligand  59  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 PERFECT
;

data_comp_0L6
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
 0L6  O2   O  O     0  -0.510  18.3041  -21.7485   -5.7677
 0L6  C2   C  C     0   0.711  18.4159  -20.5327   -5.7816
 0L6  N3   N  NH1   0  -0.743  18.5124  -19.8334   -4.6015
 0L6  C4   C  C     0   0.523  18.9024  -18.5123   -4.5078
 0L6  N4   N  NH2   0  -0.839  19.2482  -18.0955   -3.2571
 0L6  C5   C  C     0  -0.332  18.8645  -17.7420   -5.6206
 0L6  C29  C  CSP   0   0.126  19.2792  -16.3936   -5.6152
 0L6  C30  C  CSP   0   0.027  19.6179  -15.2324   -5.6505
 0L6  C31  C  CH2   0  -0.615  20.0510  -13.8409   -5.6893
 0L6  C32  C  CH2   0  -0.434  21.5660  -13.6712   -5.8328
 0L6  C33  C  CH2   0  -0.270  22.1044  -14.2195   -7.1437
 0L6  N34  N  NH2   0  -0.800  23.5478  -14.0492   -7.2182
 0L6  C6   C  CH2   0  -0.315  18.2762  -18.3318   -6.8696
 0L6  N1   N  NT    0  -0.518  18.4659  -19.7775   -6.9117
 0L6  C1'  C  CR15  0   0.191  18.3436  -20.4370   -8.1896
 0L6  O4'  O  O     0  -0.495  19.3560  -19.9414   -9.0518
 0L6  C2'  C  CH2   0  -0.561  17.0108  -20.1963   -8.9142
 0L6  C3'  C  CR15  0   0.022  17.3670  -19.1734   -9.9828
 0L6  O3'  O  OH1   0  -0.695  16.5180  -19.1432  -11.1062
 0L6  C4'  C  CR15  0   0.019  18.8115  -19.5742  -10.3005
 0L6  C5'  C  CH2   0  -0.245  19.6965  -18.5560  -10.9769
 0L6  O5'  O  O2    0  -0.560  19.7689  -17.3384  -10.2118
 0L6  PA   P  P     0   1.521  19.3040  -15.9272  -10.7269
 0L6  O1A  O  OH1   0  -0.684  19.2829  -15.1616   -9.3531
 0L6  O2A  O  O     0  -0.703  20.0452  -15.3107  -11.8579
 0L6  O3A  O  O2    0  -0.700  17.7354  -16.0970  -11.0949
 0L6  PB   P  P     0   1.462  17.0732  -16.3241  -12.5701
 0L6  O1B  O  O     0  -0.671  17.9603  -17.0539  -13.4872
 0L6  O2B  O  OH1   0  -0.723  15.6655  -16.9024  -12.2016
 0L6  O3B  O  O2    0  -0.679  16.6944  -14.8362  -13.0105
 0L6  PG   P  P     0   1.452  17.5582  -13.8394  -14.0041
 0L6  O1G  O  OH1   0  -0.713  16.6819  -12.5239  -13.9269
 0L6  O2G  O  OH1   0  -0.762  18.7927  -13.3925  -13.1390
 0L6  O3G  O  O     0  -0.681  17.7858  -14.4392  -15.3267
 0L6  H1   H  HNH1  0   0.416  18.4695  -20.3919   -3.7623
 0L6  H2   H  HNH2  0   0.395  19.7549  -18.7539   -2.6840
 0L6  H3   H  HNH2  0   0.394  19.6419  -17.1680   -3.2136
 0L6  H4   H  HCH2  0   0.255  19.5448  -13.3364   -6.5187
 0L6  H5   H  HCH2  0   0.268  19.7124  -13.3326   -4.7824
 0L6  H6   H  HCH2  0   0.229  21.7958  -12.6038   -5.7595
 0L6  H7   H  HCH2  0   0.223  22.0717  -14.1614   -4.9974
 0L6  H8   H  HCH2  0   0.221  21.8802  -15.2871   -7.2051
 0L6  H9   H  HCH2  0   0.182  21.5623  -13.7456   -7.9758
 0L6  H10  H  HNH2  0   0.346  23.8949  -14.4781   -8.0663
 0L6  H11  H  HNH2  0   0.337  23.7654  -13.0638   -7.3041
 0L6  H13  H  HCH2  0   0.257  18.7827  -17.8986   -7.7305
 0L6  H14  H  HCH2  0   0.244  17.2089  -18.0858   -6.9641
 0L6  H15  H  HCR5  0   0.269  18.4999  -21.4998   -8.0159
 0L6  H16  H  HCH2  0   0.283  16.2170  -19.8686   -8.2444
 0L6  H17  H  HCH2  0   0.279  16.6824  -21.1256   -9.3863
 0L6  H18  H  HCR5  0   0.265  17.3270  -18.1676   -9.5619
 0L6  H19  H  HOH1  0   0.477  16.4735  -20.0085  -11.5319
 0L6  H20  H  HCR5  0   0.251  18.7902  -20.4383  -10.9844
 0L6  H21  H  HCH2  0   0.267  19.3340  -18.3815  -11.9902
 0L6  H22  H  HCH2  0   0.290  20.7140  -18.9378  -11.0559
 0L6  H23  H  HOH1  0   0.515  19.3185  -14.1969   -9.4158
 0L6  H24  H  HOH1  0   0.519  15.7594  -17.8035  -11.7894
 0L6  H25  H  HOH1  0   0.511  16.0673  -12.4142  -14.6656
 0L6  H26  H  HOH1  0   0.500  19.3710  -14.0990  -12.7404

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
 0L6  O3G  PG   double  1.470  0.020  1.470
 0L6  O2G  PG   single  1.572  0.020  1.572
 0L6  PG   O1G  single  1.582  0.020  1.582
 0L6  PG   O3B  single  1.651  0.020  1.651
 0L6  O1B  PB   double  1.470  0.020  1.470
 0L6  O2A  PA   double  1.486  0.020  1.486
 0L6  O3B  PB   single  1.597  0.020  1.597
 0L6  PB   O2B  single  1.566  0.020  1.566
 0L6  PB   O3A  single  1.633  0.020  1.633
 0L6  PA   O3A  single  1.620  0.020  1.620
 0L6  PA   O5'  single  1.573  0.020  1.573
 0L6  PA   O1A  single  1.573  0.020  1.573
 0L6  C5'  O5'  single  1.440  0.020  1.440
 0L6  C5'  C4'  single  1.509  0.020  1.509
 0L6  O3'  C3'  single  1.408  0.020  1.408
 0L6  C4'  C3'  single  1.532  0.020  1.532
 0L6  C4'  O4'  single  1.411  0.020  1.411
 0L6  C3'  C2'  single  1.522  0.020  1.522
 0L6  O4'  C1'  single  1.419  0.020  1.419
 0L6  C2'  C1'  single  1.536  0.020  1.536
 0L6  C1'  N1   single  1.443  0.020  1.443
 0L6  C6   N1   single  1.459  0.020  1.459
 0L6  C6   C5   single  1.501  0.020  1.501
 0L6  N1   C2   single  1.360  0.020  1.360
 0L6  C31  C30  single  1.458  0.020  1.458
 0L6  C31  C32  single  1.531  0.020  1.531
 0L6  C30  C29  triple  1.210  0.020  1.210
 0L6  C29  C5   single  1.411  0.020  1.411
 0L6  C5   C4   double  1.354  0.020  1.354
 0L6  C2   O2   double  1.221  0.020  1.221
 0L6  C2   N3   single  1.375  0.020  1.375
 0L6  C33  C32  single  1.520  0.020  1.520
 0L6  C33  N34  single  1.455  0.020  1.455
 0L6  C4   N3   single  1.381  0.020  1.381
 0L6  C4   N4   single  1.363  0.020  1.363
 0L6  N3   H1   single  0.860  0.020  1.020
 0L6  N4   H2   single  0.890  0.020  1.040
 0L6  N4   H3   single  0.890  0.020  1.040
 0L6  C31  H4   single  0.970  0.020  1.090
 0L6  C31  H5   single  0.970  0.020  1.090
 0L6  C32  H6   single  0.970  0.020  1.090
 0L6  C32  H7   single  0.970  0.020  1.090
 0L6  C33  H8   single  0.970  0.020  1.090
 0L6  C33  H9   single  0.970  0.020  1.090
 0L6  N34  H10  single  0.890  0.020  1.040
 0L6  N34  H11  single  0.890  0.020  1.040
 0L6  C6   H13  single  0.970  0.020  1.090
 0L6  C6   H14  single  0.970  0.020  1.090
 0L6  C1'  H15  single  0.970  0.020  1.090
 0L6  C2'  H16  single  0.970  0.020  1.090
 0L6  C2'  H17  single  0.970  0.020  1.090
 0L6  C3'  H18  single  0.970  0.020  1.090
 0L6  O3'  H19  single  0.850  0.020  0.980
 0L6  C4'  H20  single  0.970  0.020  1.090
 0L6  C5'  H21  single  0.970  0.020  1.090
 0L6  C5'  H22  single  0.970  0.020  1.090
 0L6  O1A  H23  single  0.850  0.020  0.980
 0L6  O2B  H24  single  0.850  0.020  0.980
 0L6  O1G  H25  single  0.850  0.020  0.980
 0L6  O2G  H26  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
 0L6  N1   C2   N3   115.34  3.000
 0L6  N3   C2   O2   120.20  3.000
 0L6  N1   C2   O2   124.45  3.000
 0L6  H1   N3   C4   119.03  3.000
 0L6  H1   N3   C2   115.42  3.000
 0L6  C4   N3   C2   124.38  3.000
 0L6  C5   C4   N4   125.97  3.000
 0L6  N4   C4   N3   115.25  3.000
 0L6  C5   C4   N3   118.73  3.000
 0L6  H3   N4   H2   112.30  3.000
 0L6  H3   N4   C4   114.83  3.000
 0L6  H2   N4   C4   116.68  3.000
 0L6  C6   C5   C29  119.60  3.000
 0L6  C29  C5   C4   122.17  3.000
 0L6  C6   C5   C4   118.11  3.000
 0L6  C30  C29  C5   180.00  3.000
 0L6  C31  C30  C29  180.00  3.000
 0L6  H5   C31  H4   105.72  3.000
 0L6  H5   C31  C32  109.42  3.000
 0L6  H4   C31  C32  109.59  3.000
 0L6  H5   C31  C30  109.24  3.000
 0L6  H4   C31  C30  108.83  3.000
 0L6  C32  C31  C30  113.72  3.000
 0L6  H7   C32  H6   106.81  3.000
 0L6  H7   C32  C33  109.49  3.000
 0L6  H6   C32  C33  109.59  3.000
 0L6  H7   C32  C31  109.67  3.000
 0L6  H6   C32  C31  108.04  3.000
 0L6  C33  C32  C31  113.04  3.000
 0L6  H9   C33  H8   106.10  3.000
 0L6  H9   C33  N34  113.55  3.000
 0L6  H8   C33  N34  108.36  3.000
 0L6  H9   C33  C32  108.80  3.000
 0L6  H8   C33  C32  109.16  3.000
 0L6  N34  C33  C32  110.69  3.000
 0L6  H11  N34  H10  105.52  3.000
 0L6  H11  N34  C33  109.35  3.000
 0L6  H10  N34  C33  109.48  3.000
 0L6  H14  C6   H13  107.13  3.000
 0L6  H14  C6   N1   110.22  3.000
 0L6  H13  C6   N1   108.12  3.000
 0L6  H14  C6   C5   111.35  3.000
 0L6  H13  C6   C5   108.62  3.000
 0L6  N1   C6   C5   111.25  3.000
 0L6  C1'  N1   C6   117.86  3.000
 0L6  C6   N1   C2   121.44  3.000
 0L6  C1'  N1   C2   118.61  3.000
 0L6  H15  C1'  C2'  110.67  3.000
 0L6  H15  C1'  O4'  109.61  3.000
 0L6  C2'  C1'  O4'  106.12  3.000
 0L6  H15  C1'  N1   107.02  3.000
 0L6  C2'  C1'  N1   114.81  3.000
 0L6  O4'  C1'  N1   108.54  3.000
 0L6  C4'  O4'  C1'  110.69  3.000
 0L6  H17  C2'  H16  107.61  3.000
 0L6  H17  C2'  C3'  109.79  3.000
 0L6  H16  C2'  C3'  113.59  3.000
 0L6  H17  C2'  C1'  109.35  3.000
 0L6  H16  C2'  C1'  112.92  3.000
 0L6  C3'  C2'  C1'  103.50  3.000
 0L6  H18  C3'  C4'  110.83  3.000
 0L6  H18  C3'  O3'  105.41  3.000
 0L6  C4'  C3'  O3'  114.11  3.000
 0L6  H18  C3'  C2'  109.89  3.000
 0L6  C4'  C3'  C2'  100.98  3.000
 0L6  O3'  C3'  C2'  115.69  3.000
 0L6  H19  O3'  C3'  111.12  3.000
 0L6  H20  C4'  C5'  105.20  3.000
 0L6  H20  C4'  C3'  108.39  3.000
 0L6  C5'  C4'  C3'  117.99  3.000
 0L6  H20  C4'  O4'  110.65  3.000
 0L6  C3'  C4'  O4'  104.38  3.000
 0L6  C5'  C4'  O4'  110.24  3.000
 0L6  H22  C5'  H21  107.41  3.000
 0L6  H22  C5'  O5'  106.73  3.000
 0L6  H21  C5'  O5'  112.04  3.000
 0L6  H22  C5'  C4'  110.10  3.000
 0L6  H21  C5'  C4'  109.24  3.000
 0L6  O5'  C5'  C4'  111.22  3.000
 0L6  PA   O5'  C5'  124.75  3.000
 0L6  O3A  PA   O2A  110.70  3.000
 0L6  O3A  PA   O1A  103.68  3.000
 0L6  O2A  PA   O1A  118.00  3.000
 0L6  O1A  PA   O5'   98.90  3.000
 0L6  O3A  PA   O5'  105.46  3.000
 0L6  O2A  PA   O5'  118.30  3.000
 0L6  H23  O1A  PA   115.36  3.000
 0L6  PB   O3A  PA   127.77  3.000
 0L6  O3B  PB   O2B  101.29  3.000
 0L6  O2B  PB   O1B  120.40  3.000
 0L6  O3B  PB   O1B  115.70  3.000
 0L6  O2B  PB   O3A  101.73  3.000
 0L6  O3B  PB   O3A  102.45  3.000
 0L6  O1B  PB   O3A  112.83  3.000
 0L6  H24  O2B  PB   110.31  3.000
 0L6  PG   O3B  PB   127.17  3.000
 0L6  O3G  PG   O2G  119.30  3.000
 0L6  O2G  PG   O1G   99.88  3.000
 0L6  O3G  PG   O1G  117.96  3.000
 0L6  O1G  PG   O3B  100.53  3.000
 0L6  O2G  PG   O3B  104.55  3.000
 0L6  O3G  PG   O3B  112.09  3.000
 0L6  H25  O1G  PG   114.14  3.000
 0L6  H26  O2G  PG   118.32  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
 0L6  CONST_02  C1'  N1   C2   N3    180.00   0.0  0
 0L6  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 0L6  CONST_05  C1'  N1   C2   O2      0.00   0.0  0
 0L6  CONST_07  C4   N3   C2   O2    180.00   0.0  0
 0L6  CONST_09  H1   N3   C4   C5    180.00   0.0  0
 0L6  CONST_11  H3   N4   C4   N3    180.00   0.0  0
 0L6  Var_01    C29  C5   C4   N3   -178.33  30.0  1
 0L6  Var_02    N1   C6   C5   C29   154.30  30.0  1
 0L6  Var_03    H13  C6   N1   C2    154.65  30.0  1
 0L6  Var_04    C6   C5   C29  C30     6.40  30.0  3
 0L6  Var_05    C32  C31  C30  C29    13.25  30.0  1
 0L6  Var_06    C33  C32  C31  C30    63.67  30.0  3
 0L6  Var_07    N34  C33  C32  C31  -179.19  30.0  1
 0L6  Var_08    O2A  PA   O5'  C5'   -65.61  30.0  1
 0L6  Var_09    O1B  PB   O3A  PA     30.44  30.0  1
 0L6  Var_10    O3G  PG   O3B  PB     57.57  30.0  1
 0L6  Var_11    H10  N34  C33  C32   176.02  30.0  3
 0L6  Var_12    H21  C5'  O5'  PA      3.48  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
 0L6  chir_01  C1'  O4'  C2'  N1   positiv
 0L6  chir_02  C3'  O3'  C4'  C2'  positiv
 0L6  chir_03  C4'  O4'  C3'  C5'  negativ
 0L6  chir_04  PA   O3A  O5'  O1A  both
 0L6  chir_05  PB   O2B  O3B  O1B  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
 0L6  plan-1  O2   0.020
 0L6  plan-1  C2   0.020
 0L6  plan-1  N3   0.020
 0L6  plan-1  C4   0.020
 0L6  plan-1  N4   0.020
 0L6  plan-1  C5   0.020
 0L6  plan-1  C6   0.020
 0L6  plan-1  N1   0.020
 0L6  plan-1  C1'  0.020
 0L6  plan-1  H1   0.020
 0L6  plan-1  H2   0.020
 0L6  plan-1  H3   0.020

