# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 21:38:59 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](2-chloroethyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN(CCCl)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=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
 6D1  6D1  5'-{[(3S)-3-amino-3-carboxypropyl](2-chloroethyl)amino}-5'-deoxyadenosine  ligand  52  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6D1
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
 6D1  N1   N   NH2    0  -0.785  -4.3798  -2.9374  -0.2753
 6D1  C1   C   CH1    0  -0.214  -4.7668  -1.6666  -0.8704
 6D1  C2   C   CH2    0  -0.439  -3.6218  -0.6608  -0.7416
 6D1  C3   C   CH2    0  -0.269  -3.2082  -0.4090   0.7008
 6D1  N2   N   NT     0  -0.422  -2.1197   0.5507   0.8073
 6D1  C4   C   CH2    0  -0.284  -2.5288   1.9198   0.5676
 6D1  C5   C   CH2    0  -0.455  -1.4190   2.6604  -0.1545
 6D1  CL1  CL  CL     0  -0.180  -1.9022   4.3685  -0.4597
 6D1  C6   C   CH2    0  -0.296  -1.3471   0.4123   2.0233
 6D1  C7   C   CH1    0  -0.001  -0.4090  -0.7845   1.9966
 6D1  O1   O   O2     0  -0.483   0.4358  -0.7245   0.8417
 6D1  C8   C   CH1    0   0.212   1.7807  -0.7319   1.2279
 6D1  C9   C   CH1    0  -0.042   1.7870  -0.1701   2.6452
 6D1  O2   O   OH1    0  -0.653   2.9721  -0.5143   3.2966
 6D1  C10  C   CH1    0  -0.037   0.5207  -0.8220   3.2090
 6D1  O3   O   OH1    0  -0.668   0.7616  -2.1608   3.5587
 6D1  N3   N   NR5    0  -0.543   2.5521   0.0248   0.2797
 6D1  C11  C   CR15   0   0.116   2.4199   1.3515  -0.0318
 6D1  N4   N   N      0  -0.447   3.2332   1.7494  -0.9624
 6D1  C12  C   CR56   0  -0.011   3.9453   0.6249  -1.2948
 6D1  C13  C   CR6    0   0.460   4.9708   0.3831  -2.2274
 6D1  N5   N   NH2    0  -0.816   5.4576   1.3325  -3.0270
 6D1  N6   N   N      0  -0.474   5.4616  -0.8588  -2.3097
 6D1  C14  C   CR16   0   0.047   4.9658  -1.8053  -1.5173
 6D1  N7   N   N      0  -0.457   4.0113  -1.7000  -0.6089
 6D1  C15  C   CR56   0   0.492   3.5343  -0.4602  -0.5378
 6D1  C16  C   C      0   0.385  -5.2329  -1.7329  -2.3475
 6D1  O4   O   OC    -1  -0.624  -5.7280  -0.6832  -2.8104
 6D1  O5   O   O      0  -0.607  -5.0743  -2.8079  -2.9584
 6D1  H1   H   HNH2   0   0.334  -5.1572  -3.5818  -0.3572
 6D1  H2   H   HNH2   0   0.323  -3.6558  -3.3466  -0.8557
 6D1  H4   H   HCH1   0   0.209  -5.6115  -1.2776  -0.2869
 6D1  H5   H   HCH2   0   0.211  -2.7482  -1.0199  -1.2983
 6D1  H6   H   HCH2   0   0.225  -3.9332   0.2709  -1.2176
 6D1  H7   H   HCH2   0   0.194  -4.0846  -0.0939   1.2922
 6D1  H8   H   HCH2   0   0.234  -2.8807  -1.3560   1.1289
 6D1  H10  H   HCH2   0   0.253  -3.4166   1.9303  -0.0651
 6D1  H11  H   HCH2   0   0.226  -2.7980   2.4498   1.4923
 6D1  H12  H   HCH2   0   0.271  -0.5033   2.7004   0.4320
 6D1  H13  H   HCH2   0   0.283  -1.2048   2.2007  -1.1165
 6D1  H14  H   HCH2   0   0.234  -0.7541   1.3197   2.1704
 6D1  H15  H   HCH2   0   0.222  -1.9858   0.3223   2.9172
 6D1  H16  H   HCH1   0   0.253  -0.9896  -1.7119   1.9577
 6D1  H17  H   HCH1   0   0.255   2.2054  -1.7426   1.2251
 6D1  H18  H   HCH1   0   0.246   1.6424   0.9177   2.6160
 6D1  H19  H   HOH1   0   0.470   3.0988   0.0759   4.0462
 6D1  H20  H   HCH1   0   0.250   0.1097  -0.2514   4.0523
 6D1  H21  H   HOH1   0   0.449   1.5676  -2.1899   4.0878
 6D1  H22  H   HCR5   0   0.286   1.7014   1.9841   0.4662
 6D1  H23  H   HNH2   0   0.412   5.1422   2.2837  -2.9552
 6D1  H24  H   HNH2   0   0.404   6.2265   1.1311  -3.6426
 6D1  H25  H   HCR6   0   0.253   5.4059  -2.7896  -1.6361

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
 6D1  N5   C13  single    1.333  0.020  1.333
 6D1  C13  C12  aromatic  1.407  0.020  1.407
 6D1  C13  N6   aromatic  1.338  0.020  1.338
 6D1  N4   C12  aromatic  1.372  0.020  1.372
 6D1  N4   C11  aromatic  1.298  0.020  1.298
 6D1  C12  C15  aromatic  1.385  0.020  1.385
 6D1  N6   C14  aromatic  1.330  0.020  1.330
 6D1  C11  N3   aromatic  1.369  0.020  1.369
 6D1  C15  N3   aromatic  1.367  0.020  1.367
 6D1  C15  N7   aromatic  1.330  0.020  1.330
 6D1  C14  N7   aromatic  1.322  0.020  1.322
 6D1  N3   C8   single    1.438  0.020  1.438
 6D1  C9   O2   single    1.395  0.020  1.395
 6D1  C9   C8   single    1.525  0.020  1.525
 6D1  C9   C10  single    1.532  0.020  1.532
 6D1  C8   O1   single    1.399  0.020  1.399
 6D1  CL1  C5   single    1.801  0.020  1.801
 6D1  C5   C4   single    1.517  0.020  1.517
 6D1  O1   C7   single    1.432  0.020  1.432
 6D1  C6   C7   single    1.521  0.020  1.521
 6D1  C6   N2   single    1.447  0.020  1.447
 6D1  C10  C7   single    1.528  0.020  1.528
 6D1  C10  O3   single    1.405  0.020  1.405
 6D1  C4   N2   single    1.449  0.020  1.449
 6D1  N2   C3   single    1.455  0.020  1.455
 6D1  C3   C2   single    1.521  0.020  1.521
 6D1  C2   C1   single    1.530  0.020  1.530
 6D1  N1   C1   single    1.456  0.020  1.456
 6D1  C1   C16  single    1.550  0.020  1.550
 6D1  C16  O5   deloc     1.247  0.020  1.247
 6D1  C16  O4   deloc     1.250  0.020  1.250
 6D1  N1   H1   single    0.890  0.020  1.040
 6D1  N1   H2   single    0.890  0.020  1.040
 6D1  C1   H4   single    0.970  0.020  1.090
 6D1  C2   H5   single    0.970  0.020  1.090
 6D1  C2   H6   single    0.970  0.020  1.090
 6D1  C3   H7   single    0.970  0.020  1.090
 6D1  C3   H8   single    0.970  0.020  1.090
 6D1  C4   H10  single    0.970  0.020  1.090
 6D1  C4   H11  single    0.970  0.020  1.090
 6D1  C5   H12  single    0.970  0.020  1.090
 6D1  C5   H13  single    0.970  0.020  1.090
 6D1  C6   H14  single    0.970  0.020  1.090
 6D1  C6   H15  single    0.970  0.020  1.090
 6D1  C7   H16  single    0.970  0.020  1.090
 6D1  C8   H17  single    0.970  0.020  1.090
 6D1  C9   H18  single    0.970  0.020  1.090
 6D1  O2   H19  single    0.850  0.020  0.980
 6D1  C10  H20  single    0.970  0.020  1.090
 6D1  O3   H21  single    0.850  0.020  0.980
 6D1  C11  H22  single    0.930  0.020  1.080
 6D1  N5   H23  single    0.860  0.020  1.020
 6D1  N5   H24  single    0.860  0.020  1.020
 6D1  C14  H25  single    0.930  0.020  1.080

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
 6D1  H2   N1   H1   104.18  3.000
 6D1  H2   N1   C1   107.95  3.000
 6D1  H1   N1   C1   108.56  3.000
 6D1  H4   C1   C16  106.87  3.000
 6D1  H4   C1   C2   107.35  3.000
 6D1  C16  C1   C2   109.47  3.000
 6D1  H4   C1   N1   107.26  3.000
 6D1  C16  C1   N1   115.60  3.000
 6D1  C2   C1   N1   109.92  3.000
 6D1  H6   C2   H5   106.59  3.000
 6D1  H6   C2   C3   110.47  3.000
 6D1  H5   C2   C3   108.60  3.000
 6D1  H6   C2   C1   108.12  3.000
 6D1  H5   C2   C1   109.77  3.000
 6D1  C3   C2   C1   113.09  3.000
 6D1  H8   C3   H7   106.05  3.000
 6D1  H8   C3   N2   108.64  3.000
 6D1  H7   C3   N2   111.50  3.000
 6D1  H8   C3   C2   108.08  3.000
 6D1  H7   C3   C2   109.85  3.000
 6D1  N2   C3   C2   112.45  3.000
 6D1  C6   N2   C4   112.34  3.000
 6D1  C4   N2   C3   113.58  3.000
 6D1  C6   N2   C3   113.44  3.000
 6D1  H11  C4   H10  106.51  3.000
 6D1  H11  C4   C5   110.13  3.000
 6D1  H10  C4   C5   108.35  3.000
 6D1  H11  C4   N2   112.67  3.000
 6D1  H10  C4   N2   109.57  3.000
 6D1  C5   C4   N2   109.48  3.000
 6D1  H13  C5   H12  109.07  3.000
 6D1  H13  C5   CL1  107.68  3.000
 6D1  H12  C5   CL1  106.39  3.000
 6D1  H13  C5   C4   111.02  3.000
 6D1  H12  C5   C4   112.15  3.000
 6D1  CL1  C5   C4   110.32  3.000
 6D1  H15  C6   H14  105.83  3.000
 6D1  H15  C6   C7   107.90  3.000
 6D1  H14  C6   C7   108.70  3.000
 6D1  H15  C6   N2   112.32  3.000
 6D1  H14  C6   N2   108.85  3.000
 6D1  C7   C6   N2   112.94  3.000
 6D1  H16  C7   C10  109.27  3.000
 6D1  H16  C7   O1   108.64  3.000
 6D1  C10  C7   O1   106.37  3.000
 6D1  H16  C7   C6   109.88  3.000
 6D1  C10  C7   C6   112.37  3.000
 6D1  O1   C7   C6   110.18  3.000
 6D1  C8   O1   C7   110.13  3.000
 6D1  H17  C8   N3   106.01  3.000
 6D1  H17  C8   C9   109.91  3.000
 6D1  N3   C8   C9   114.65  3.000
 6D1  H17  C8   O1   112.11  3.000
 6D1  C9   C8   O1   104.99  3.000
 6D1  N3   C8   O1   109.32  3.000
 6D1  H18  C9   C10  108.82  3.000
 6D1  H18  C9   O2   111.64  3.000
 6D1  C10  C9   O2   115.17  3.000
 6D1  H18  C9   C8   109.86  3.000
 6D1  C10  C9   C8   100.48  3.000
 6D1  O2   C9   C8   110.28  3.000
 6D1  H19  O2   C9   108.91  3.000
 6D1  H20  C10  O3   111.61  3.000
 6D1  H20  C10  C9   111.78  3.000
 6D1  O3   C10  C9   110.83  3.000
 6D1  H20  C10  C7   111.64  3.000
 6D1  O3   C10  C7   108.98  3.000
 6D1  C9   C10  C7   101.56  3.000
 6D1  H21  O3   C10  107.97  3.000
 6D1  C15  N3   C11  106.09  3.000
 6D1  C15  N3   C8   126.39  3.000
 6D1  C11  N3   C8   127.47  3.000
 6D1  H22  C11  N4   124.63  3.000
 6D1  H22  C11  N3   121.82  3.000
 6D1  N4   C11  N3   113.55  3.000
 6D1  C12  N4   C11  104.34  3.000
 6D1  C15  C12  C13  116.35  3.000
 6D1  C15  C12  N4   110.83  3.000
 6D1  C13  C12  N4   132.82  3.000
 6D1  N6   C13  N5   119.35  3.000
 6D1  N6   C13  C12  117.88  3.000
 6D1  N5   C13  C12  122.77  3.000
 6D1  H24  N5   H23  118.27  3.000
 6D1  H24  N5   C13  120.25  3.000
 6D1  H23  N5   C13  121.11  3.000
 6D1  C14  N6   C13  119.15  3.000
 6D1  H25  C14  N7   116.13  3.000
 6D1  H25  C14  N6   115.42  3.000
 6D1  N7   C14  N6   128.45  3.000
 6D1  C15  N7   C14  111.70  3.000
 6D1  N7   C15  C12  126.47  3.000
 6D1  N7   C15  N3   128.34  3.000
 6D1  C12  C15  N3   105.19  3.000
 6D1  O5   C16  O4   126.39  3.000
 6D1  O4   C16  C1   115.86  3.000
 6D1  O5   C16  C1   117.75  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
 6D1  CONST_01  C12  N4   C11  N3      0.00   0.0  0
 6D1  CONST_02  C13  C12  C15  N3    180.00   0.0  0
 6D1  CONST_03  N4   C12  C15  N3      0.00   0.0  0
 6D1  CONST_04  C14  N7   C15  N3    180.00   0.0  0
 6D1  CONST_05  C13  C12  N4   C11   180.00   0.0  0
 6D1  CONST_06  C15  C12  N4   C11     0.00   0.0  0
 6D1  CONST_07  C12  C15  N3   C11     0.00   0.0  0
 6D1  CONST_08  N7   C15  N3   C11   180.00   0.0  0
 6D1  CONST_09  N6   C13  C12  N4    180.00   0.0  0
 6D1  CONST_10  N7   C15  C12  N4    180.00   0.0  0
 6D1  CONST_11  C15  N3   C11  N4      0.00   0.0  0
 6D1  CONST_12  C14  N6   C13  C12     0.00   0.0  0
 6D1  CONST_13  C14  N7   C15  C12     0.00   0.0  0
 6D1  CONST_14  N7   C15  C12  C13     0.00   0.0  0
 6D1  CONST_15  N7   C14  N6   C13     0.00   0.0  0
 6D1  CONST_16  C15  C12  C13  N6      0.00   0.0  0
 6D1  CONST_17  C15  N7   C14  N6      0.00   0.0  0
 6D1  CONST_18  N4   C11  N3   C8    180.00   0.0  0
 6D1  CONST_19  C12  C15  N3   C8    180.00   0.0  0
 6D1  CONST_20  N7   C15  N3   C8      0.00   0.0  0
 6D1  CONST_21  N5   C13  C12  N4      0.00   0.0  0
 6D1  CONST_22  C15  C12  C13  N5    180.00   0.0  0
 6D1  CONST_23  C14  N6   C13  N5    180.00   0.0  0
 6D1  CONST_24  H22  C11  N3   C8      0.00   0.0  0
 6D1  CONST_25  H25  C14  N6   C13   180.00   0.0  0
 6D1  CONST_26  H23  N5   C13  C12     0.00   0.0  0
 6D1  CONST_27  H24  N5   C13  C12   180.00   0.0  0
 6D1  Var_01    C7   C6   N2   C3     75.33  30.0  2
 6D1  Var_02    N2   C3   C2   C1   -179.93  30.0  1
 6D1  Var_03    C6   N2   C3   C2   -155.87  30.0  1
 6D1  Var_04    C5   C4   N2   C3   -144.22  30.0  3
 6D1  Var_05    CL1  C5   C4   N2   -179.82  30.0  1

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
 6D1  chir_01  C1   C2  N1  C16  positiv
 6D1  chir_02  C7   O1  C6  C10  positiv
 6D1  chir_03  C8   O1  N3  C9   negativ
 6D1  chir_04  C9   O2  C8  C10  negativ
 6D1  chir_05  C10  O3  C7  C9   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
 6D1  plan-1  C8   0.020
 6D1  plan-1  N3   0.020
 6D1  plan-1  C11  0.020
 6D1  plan-1  N4   0.020
 6D1  plan-1  C12  0.020
 6D1  plan-1  C13  0.020
 6D1  plan-1  N5   0.020
 6D1  plan-1  N6   0.020
 6D1  plan-1  C14  0.020
 6D1  plan-1  N7   0.020
 6D1  plan-1  C15  0.020
 6D1  plan-1  H22  0.020
 6D1  plan-1  H25  0.020
 6D1  plan-2  C13  0.020
 6D1  plan-2  N5   0.020
 6D1  plan-2  H23  0.020
 6D1  plan-2  H24  0.020
 6D1  plan-3  C1   0.020
 6D1  plan-3  C16  0.020
 6D1  plan-3  O4   0.020
 6D1  plan-3  O5   0.020

