# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 05:47:55 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](3-ethoxy-2,3-dioxopropyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C(=O)CN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 6CZ  6CZ  5'-{[(3S)-3-amino-3-carboxypropyl](3-ethoxy-2,3-dioxopropyl)amino}-5'-deoxyadenosine  ligand  61  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_6CZ
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
 6CZ  N1   N  N     0  -0.475  22.7184  27.9901  114.8371
 6CZ  C1   C  CR56  0   0.492  23.5364  25.6563  115.7848
 6CZ  C2   C  CR56  0  -0.012  22.6848  26.4090  116.5773
 6CZ  C3   C  CR16  0   0.046  23.5324  27.1623  114.1880
 6CZ  C4   C  CR15  0   0.112  23.0831  24.6506  117.6735
 6CZ  C5   C  CR6   0   0.460  22.2689  27.6446  116.0491
 6CZ  N2   N  N     0  -0.456  23.9926  25.9867  114.5794
 6CZ  C6   C  C     0   0.534  21.7395  15.9177  116.9550
 6CZ  C7   C  CH1   0  -0.183  23.1742  16.4046  116.9975
 6CZ  N3   N  NH2   0  -0.803  23.7840  16.4097  115.6823
 6CZ  C8   C  CH2   0  -0.461  23.1590  17.8189  117.5947
 6CZ  C9   C  CH2   0  -0.331  24.5709  18.3592  117.8348
 6CZ  N4   N  NT    0  -0.414  24.6529  19.6084  118.5732
 6CZ  C11  C  CR15  0  -0.029  24.5913  21.1493  116.6407
 6CZ  O2   O  O     0  -0.494  23.8434  22.2422  116.0949
 6CZ  C12  C  CR15  0   0.201  24.6120  23.4139  116.0994
 6CZ  C13  C  CR15  0  -0.015  25.7884  23.1357  117.0348
 6CZ  O3   O  OH1   0  -0.653  26.8329  24.0062  116.7418
 6CZ  C14  C  CR15  0  -0.032  26.0306  21.6509  116.7738
 6CZ  O4   O  OH1   0  -0.670  26.7512  21.5384  115.5732
 6CZ  N5   N  NR5   0  -0.539  23.7907  24.5250  116.5074
 6CZ  N6   N  N     0  -0.448  22.4119  25.7596  117.7540
 6CZ  N7   N  NH2   0  -0.816  21.4602  28.4762  116.7068
 6CZ  C15  C  CH2   0  -0.402  24.3507  19.4710  119.9719
 6CZ  C16  C  C     0   0.277  25.1332  20.4317  120.8299
 6CZ  C17  C  C     0   0.533  24.8394  20.3262  122.3355
 6CZ  O6   O  O     0  -0.331  25.9373  21.2257  120.4258
 6CZ  O7   O  O2    0  -0.435  25.5251  21.2021  123.0231
 6CZ  O8   O  O     0  -0.419  24.0696  19.5165  122.7834
 6CZ  C18  C  CH2   0  -0.191  25.3626  21.2114  124.4565
 6CZ  C19  C  CH3   0  -0.689  26.2443  22.2998  125.0144
 6CZ  H1   H  HCR6  0   0.253  23.8581  27.5009  113.2104
 6CZ  H2   H  HCR5  0   0.295  23.0913  23.8820  118.4313
 6CZ  H3   H  HCH1  0   0.249  23.6835  15.7474  117.7180
 6CZ  H4   H  HNH2  0   0.360  24.7548  16.6813  115.7666
 6CZ  H5   H  HNH2  0   0.355  23.8069  15.4698  115.3059
 6CZ  H7   H  HCH2  0   0.242  22.6024  18.4792  116.9237
 6CZ  H8   H  HCH2  0   0.252  22.6174  17.7898  118.5437
 6CZ  H9   H  HCH2  0   0.255  25.1515  17.6141  118.3859
 6CZ  H10  H  HCH2  0   0.241  25.0885  18.4908  116.8815
 6CZ  H14  H  HCR5  0   0.253  24.5325  20.3223  115.9253
 6CZ  H15  H  HCR5  0   0.263  24.9778  23.6610  115.0969
 6CZ  H16  H  HCR5  0   0.236  25.4560  23.2438  118.0774
 6CZ  H17  H  HOH1  0   0.463  27.5207  23.9001  117.4063
 6CZ  H18  H  HCR5  0   0.260  26.5424  21.1601  117.6088
 6CZ  H19  H  HOH1  0   0.455  26.8848  20.6042  115.3856
 6CZ  H20  H  HNH2  0   0.404  21.1488  29.3279  116.2728
 6CZ  H21  H  HNH2  0   0.411  21.0697  28.2259  117.5980
 6CZ  H22  H  HOH1  0   0.481  20.2530  15.7201  115.8160
 6CZ  H23  H  HCH2  0   0.265  23.2824  19.5818  120.2169
 6CZ  H24  H  HCH2  0   0.299  24.6155  18.4645  120.3122
 6CZ  H25  H  HCH2  0   0.246  24.3135  21.3906  124.6977
 6CZ  H26  H  HCH2  0   0.247  25.6412  20.2343  124.8548
 6CZ  H27  H  HCH3  0   0.244  26.1389  22.3157  126.0987
 6CZ  H28  H  HCH3  0   0.240  27.2948  22.1257  124.7827
 6CZ  H29  H  HCH3  0   0.240  25.9595  23.2812  124.6363
 6CZ  C10  C  CH2   0  -0.314  23.9654  20.7330  117.9683
 6CZ  O5   O  OH1   0  -0.578  21.1722  16.0230  115.7637
 6CZ  O1   O  O     0  -0.452  21.1611  15.5025  117.9301
 6CZ  H12  H  HCH2  0   0.240  24.0208  21.5745  118.6620
 6CZ  H13  H  HCH2  0   0.240  22.8927  20.5440  117.8117

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
 6CZ  C3   N1   aromatic  1.330  0.020  1.330
 6CZ  C3   N2   aromatic  1.322  0.020  1.322
 6CZ  N1   C5   aromatic  1.338  0.020  1.338
 6CZ  N2   C1   aromatic  1.331  0.020  1.331
 6CZ  C5   N7   single    1.333  0.020  1.333
 6CZ  C5   C2   aromatic  1.407  0.020  1.407
 6CZ  C1   C2   aromatic  1.386  0.020  1.386
 6CZ  C1   N5   aromatic  1.366  0.020  1.366
 6CZ  C2   N6   aromatic  1.371  0.020  1.371
 6CZ  O3   C13  single    1.391  0.020  1.391
 6CZ  O4   C14  single    1.405  0.020  1.405
 6CZ  C12  N5   single    1.441  0.020  1.441
 6CZ  C12  O2   single    1.401  0.020  1.401
 6CZ  C12  C13  single    1.528  0.020  1.528
 6CZ  N5   C4   aromatic  1.370  0.020  1.370
 6CZ  N3   C7   single    1.450  0.020  1.450
 6CZ  O2   C11  single    1.432  0.020  1.432
 6CZ  C13  C14  single    1.527  0.020  1.527
 6CZ  O1   C6   double    1.207  0.020  1.207
 6CZ  C14  C11  single    1.530  0.020  1.530
 6CZ  N6   C4   aromatic  1.299  0.020  1.299
 6CZ  C7   C6   single    1.516  0.020  1.516
 6CZ  C7   C8   single    1.535  0.020  1.535
 6CZ  C11  C10  single    1.526  0.020  1.526
 6CZ  C6   O5   single    1.324  0.020  1.324
 6CZ  C8   C9   single    1.531  0.020  1.531
 6CZ  C9   N4   single    1.453  0.020  1.453
 6CZ  C10  N4   single    1.450  0.020  1.450
 6CZ  N4   C15  single    1.438  0.020  1.438
 6CZ  C15  C16  single    1.507  0.020  1.507
 6CZ  O6   C16  double    1.200  0.020  1.200
 6CZ  C16  C17  single    1.538  0.020  1.538
 6CZ  C17  O8   double    1.204  0.020  1.204
 6CZ  C17  O7   single    1.308  0.020  1.308
 6CZ  O7   C18  single    1.443  0.020  1.443
 6CZ  C18  C19  single    1.508  0.020  1.508
 6CZ  C3   H1   single    0.930  0.020  1.080
 6CZ  C4   H2   single    0.930  0.020  1.080
 6CZ  C7   H3   single    0.970  0.020  1.090
 6CZ  N3   H4   single    0.890  0.020  1.040
 6CZ  N3   H5   single    0.890  0.020  1.040
 6CZ  C8   H7   single    0.970  0.020  1.090
 6CZ  C8   H8   single    0.970  0.020  1.090
 6CZ  C9   H9   single    0.970  0.020  1.090
 6CZ  C9   H10  single    0.970  0.020  1.090
 6CZ  C10  H12  single    0.970  0.020  1.090
 6CZ  C10  H13  single    0.970  0.020  1.090
 6CZ  C11  H14  single    0.970  0.020  1.090
 6CZ  C12  H15  single    0.970  0.020  1.090
 6CZ  C13  H16  single    0.970  0.020  1.090
 6CZ  O3   H17  single    0.850  0.020  0.980
 6CZ  C14  H18  single    0.970  0.020  1.090
 6CZ  O4   H19  single    0.850  0.020  0.980
 6CZ  N7   H20  single    0.860  0.020  1.020
 6CZ  N7   H21  single    0.860  0.020  1.020
 6CZ  O5   H22  single    0.850  0.020  0.980
 6CZ  C15  H23  single    0.970  0.020  1.090
 6CZ  C15  H24  single    0.970  0.020  1.090
 6CZ  C18  H25  single    0.970  0.020  1.090
 6CZ  C18  H26  single    0.970  0.020  1.090
 6CZ  C19  H27  single    0.970  0.020  1.090
 6CZ  C19  H28  single    0.970  0.020  1.090
 6CZ  C19  H29  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
 6CZ  C5   N1   C3   119.14  3.000
 6CZ  N5   C1   N2   128.38  3.000
 6CZ  N5   C1   C2   105.17  3.000
 6CZ  N2   C1   C2   126.45  3.000
 6CZ  N6   C2   C5   132.79  3.000
 6CZ  N6   C2   C1   110.85  3.000
 6CZ  C5   C2   C1   116.37  3.000
 6CZ  H1   C3   N2   116.11  3.000
 6CZ  H1   C3   N1   115.42  3.000
 6CZ  N2   C3   N1   128.47  3.000
 6CZ  H2   C4   N6   124.64  3.000
 6CZ  H2   C4   N5   121.90  3.000
 6CZ  N6   C4   N5   113.46  3.000
 6CZ  N7   C5   C2   122.81  3.000
 6CZ  C2   C5   N1   117.88  3.000
 6CZ  N7   C5   N1   119.31  3.000
 6CZ  C3   N2   C1   111.70  3.000
 6CZ  O5   C6   C7   113.92  3.000
 6CZ  O5   C6   O1   123.29  3.000
 6CZ  C7   C6   O1   122.77  3.000
 6CZ  H3   C7   C8   107.47  3.000
 6CZ  H3   C7   N3   113.67  3.000
 6CZ  C8   C7   N3   110.72  3.000
 6CZ  H3   C7   C6   105.35  3.000
 6CZ  C8   C7   C6   107.31  3.000
 6CZ  N3   C7   C6   111.95  3.000
 6CZ  H5   N3   H4   104.98  3.000
 6CZ  H5   N3   C7   110.09  3.000
 6CZ  H4   N3   C7   109.21  3.000
 6CZ  H8   C8   H7   107.25  3.000
 6CZ  H8   C8   C9   109.28  3.000
 6CZ  H7   C8   C9   110.65  3.000
 6CZ  H8   C8   C7   108.55  3.000
 6CZ  H7   C8   C7   108.82  3.000
 6CZ  C9   C8   C7   112.15  3.000
 6CZ  H10  C9   H9   105.68  3.000
 6CZ  H10  C9   N4   108.24  3.000
 6CZ  H9   C9   N4   107.44  3.000
 6CZ  H10  C9   C8   110.03  3.000
 6CZ  H9   C9   C8   109.16  3.000
 6CZ  N4   C9   C8   115.79  3.000
 6CZ  C15  N4   C10  112.35  3.000
 6CZ  C15  N4   C9   113.60  3.000
 6CZ  C10  N4   C9   115.33  3.000
 6CZ  H14  C11  C14  110.79  3.000
 6CZ  H14  C11  O2   107.41  3.000
 6CZ  C14  C11  O2   105.92  3.000
 6CZ  H14  C11  C10  109.90  3.000
 6CZ  C14  C11  C10  113.56  3.000
 6CZ  O2   C11  C10  109.00  3.000
 6CZ  C12  O2   C11  110.51  3.000
 6CZ  H15  C12  N5   106.00  3.000
 6CZ  H15  C12  C13  110.13  3.000
 6CZ  N5   C12  C13  113.95  3.000
 6CZ  H15  C12  O2   111.64  3.000
 6CZ  C13  C12  O2   105.78  3.000
 6CZ  N5   C12  O2   109.46  3.000
 6CZ  H16  C13  C14  107.79  3.000
 6CZ  H16  C13  O3   111.42  3.000
 6CZ  C14  C13  O3   116.97  3.000
 6CZ  H16  C13  C12  109.25  3.000
 6CZ  C14  C13  C12  101.22  3.000
 6CZ  O3   C13  C12  109.58  3.000
 6CZ  H17  O3   C13  108.80  3.000
 6CZ  H18  C14  O4   112.08  3.000
 6CZ  H18  C14  C13  112.30  3.000
 6CZ  O4   C14  C13  107.77  3.000
 6CZ  H18  C14  C11  111.04  3.000
 6CZ  C13  C14  C11  100.63  3.000
 6CZ  O4   C14  C11  112.46  3.000
 6CZ  H19  O4   C14  108.39  3.000
 6CZ  C12  N5   C4   127.32  3.000
 6CZ  C4   N5   C1   106.15  3.000
 6CZ  C12  N5   C1   126.51  3.000
 6CZ  C4   N6   C2   104.38  3.000
 6CZ  H21  N7   H20  118.27  3.000
 6CZ  H21  N7   C5   121.19  3.000
 6CZ  H20  N7   C5   120.22  3.000
 6CZ  H24  C15  H23  104.94  3.000
 6CZ  H24  C15  C16  106.47  3.000
 6CZ  H23  C15  C16  108.23  3.000
 6CZ  H24  C15  N4   109.84  3.000
 6CZ  H23  C15  N4   114.25  3.000
 6CZ  C16  C15  N4   112.57  3.000
 6CZ  O6   C16  C17  120.21  3.000
 6CZ  C17  C16  C15  114.49  3.000
 6CZ  O6   C16  C15  125.30  3.000
 6CZ  O8   C17  O7   126.17  3.000
 6CZ  O7   C17  C16  111.63  3.000
 6CZ  O8   C17  C16  122.19  3.000
 6CZ  C18  O7   C17  117.88  3.000
 6CZ  H26  C18  H25  108.17  3.000
 6CZ  H26  C18  C19  111.22  3.000
 6CZ  H25  C18  C19  111.21  3.000
 6CZ  H26  C18  O7   109.15  3.000
 6CZ  H25  C18  O7   109.21  3.000
 6CZ  C19  C18  O7   107.84  3.000
 6CZ  H29  C19  H28  108.79  3.000
 6CZ  H29  C19  H27  107.87  3.000
 6CZ  H28  C19  H27  107.89  3.000
 6CZ  H29  C19  C18  111.65  3.000
 6CZ  H28  C19  C18  111.70  3.000
 6CZ  H27  C19  C18  108.80  3.000
 6CZ  H13  C10  H12  105.80  3.000
 6CZ  H13  C10  C11  108.84  3.000
 6CZ  H12  C10  C11  108.76  3.000
 6CZ  H13  C10  N4   112.85  3.000
 6CZ  H12  C10  N4   107.98  3.000
 6CZ  C11  C10  N4   112.34  3.000
 6CZ  H22  O5   C6   109.45  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
 6CZ  CONST_01  C1   N2   C3   N1      0.00   0.0  0
 6CZ  CONST_02  C1   C2   C5   N1      0.00   0.0  0
 6CZ  CONST_03  N6   C2   C5   N1    180.00   0.0  0
 6CZ  CONST_04  C4   N6   C2   C1      0.00   0.0  0
 6CZ  CONST_05  N6   C4   N5   C1      0.00   0.0  0
 6CZ  CONST_06  C3   N1   C5   C2      0.00   0.0  0
 6CZ  CONST_07  C3   N2   C1   C2      0.00   0.0  0
 6CZ  CONST_08  C4   N5   C1   C2      0.00   0.0  0
 6CZ  CONST_09  N5   C4   N6   C2      0.00   0.0  0
 6CZ  CONST_10  N5   C1   N2   C3    180.00   0.0  0
 6CZ  CONST_11  N2   C1   N5   C4    180.00   0.0  0
 6CZ  CONST_12  C5   C2   N6   C4    180.00   0.0  0
 6CZ  CONST_13  N2   C3   N1   C5      0.00   0.0  0
 6CZ  CONST_14  N2   C1   C2   C5      0.00   0.0  0
 6CZ  CONST_15  N5   C1   C2   C5    180.00   0.0  0
 6CZ  CONST_16  N6   C2   C1   N2    180.00   0.0  0
 6CZ  CONST_17  N6   C2   C1   N5      0.00   0.0  0
 6CZ  CONST_18  C12  N5   C1   C2    180.00   0.0  0
 6CZ  CONST_19  C12  N5   C1   N2      0.00   0.0  0
 6CZ  CONST_20  N6   C4   N5   C12   180.00   0.0  0
 6CZ  CONST_21  N7   C5   C2   C1    180.00   0.0  0
 6CZ  CONST_22  N7   C5   N1   C3    180.00   0.0  0
 6CZ  CONST_23  N7   C5   C2   N6      0.00   0.0  0
 6CZ  CONST_24  H1   C3   N2   C1    180.00   0.0  0
 6CZ  CONST_25  H2   C4   N5   C1    180.00   0.0  0
 6CZ  CONST_26  H20  N7   C5   N1      0.00   0.0  0
 6CZ  CONST_27  H21  N7   C5   N1    180.00   0.0  0
 6CZ  CONST_28  H22  O5   C6   O1      0.00   0.0  0
 6CZ  Var_01    C11  C10  N4   C9    -65.48  30.0  1
 6CZ  Var_02    N4   C9   C8   C7   -171.49  30.0  3
 6CZ  Var_03    C10  N4   C9   C8    -59.33  30.0  3
 6CZ  Var_04    C16  C15  N4   C9    147.38  30.0  3
 6CZ  Var_05    O6   C16  C15  N4     -0.77  30.0  3
 6CZ  Var_06    O8   C17  C16  C15     1.71  30.0  2
 6CZ  Var_07    C19  C18  O7   C17  -179.83  30.0  3
 6CZ  Var_08    H27  C19  C18  O7   -179.59  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
 6CZ  chir_01  C7   N3  C6   C8   positiv
 6CZ  chir_02  C11  O2  C14  C10  negativ
 6CZ  chir_03  C12  O2  N5   C13  negativ
 6CZ  chir_04  C13  O3  C12  C14  negativ
 6CZ  chir_05  C14  O4  C11  C13  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
 6CZ  plan-1  N1   0.020
 6CZ  plan-1  C1   0.020
 6CZ  plan-1  C2   0.020
 6CZ  plan-1  C3   0.020
 6CZ  plan-1  C4   0.020
 6CZ  plan-1  C5   0.020
 6CZ  plan-1  N2   0.020
 6CZ  plan-1  C12  0.020
 6CZ  plan-1  N5   0.020
 6CZ  plan-1  N6   0.020
 6CZ  plan-1  N7   0.020
 6CZ  plan-1  H1   0.020
 6CZ  plan-1  H2   0.020
 6CZ  plan-2  C5   0.020
 6CZ  plan-2  N7   0.020
 6CZ  plan-2  H20  0.020
 6CZ  plan-2  H21  0.020
 6CZ  plan-3  C15  0.020
 6CZ  plan-3  C16  0.020
 6CZ  plan-3  C17  0.020
 6CZ  plan-3  O6   0.020
 6CZ  plan-4  C6   0.020
 6CZ  plan-4  C7   0.020
 6CZ  plan-4  H22  0.020
 6CZ  plan-4  O5   0.020
 6CZ  plan-4  O1   0.020
 6CZ  plan-5  C16  0.020
 6CZ  plan-5  C17  0.020
 6CZ  plan-5  O7   0.020
 6CZ  plan-5  O8   0.020

