# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 09:34:09 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(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
 AN6  AN6  5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine  L-peptide  52  28  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AN6
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
 AN6  C'    C  C      0   0.407  -2.8716  -2.9541  -0.5040
 AN6  N'    N  NH2    0  -0.794  -4.4967  -1.9583   1.1725
 AN6  O'    O  O      0  -0.611  -3.1650  -4.0643  -0.0156
 AN6  C1    C  CH3    0  -0.665  -3.6117   2.6530   2.9090
 AN6  N1    N  N      0  -0.475   4.9865  -2.0210   0.8468
 AN6  C2    C  CR16   0   0.044   4.9740  -0.6915   0.9012
 AN6  C3    C  CH2    0  -0.284  -3.3282   2.9715   1.4502
 AN6  N3    N  N      0  -0.458   3.9846   0.1341   0.6086
 AN6  C4    C  CR56   0   0.486   2.8931  -0.5219   0.2207
 AN6  C5    C  CR56   0  -0.012   2.7553  -1.8955   0.1125
 AN6  C6    C  CR6    0   0.455   3.8827  -2.6654   0.4513
 AN6  N6    N  NH2    0  -0.817   3.8912  -3.9978   0.3872
 AN6  N7    N  N      0  -0.449   1.4962  -2.2261  -0.3160
 AN6  C8    C  CR15   0   0.104   0.8912  -1.0856  -0.4662
 AN6  N9    N  NR5    0  -0.546   1.6843  -0.0092  -0.1576
 AN6  C1'   C  CH1    0   0.221   1.3526   1.3903  -0.2003
 AN6  N10   N  NT     0  -0.414  -2.6859   1.8762   0.7428
 AN6  C2'   C  CH1    0  -0.034   1.0609   1.9366  -1.5935
 AN6  O2'   O  OH1    0  -0.656   2.2476   2.1381  -2.3006
 AN6  C3'   C  CH1    0  -0.045   0.3025   3.2157  -1.2264
 AN6  O3'   O  OH1    0  -0.670   1.1943   4.2196  -0.8094
 AN6  C4'   C  CH1    0   0.012  -0.5163   2.7506  -0.0235
 AN6  O4'   O  O2     0  -0.488   0.1844   1.6250   0.5305
 AN6  C5'   C  CH2    0  -0.302  -1.9320   2.3457  -0.4018
 AN6  O5'   O  OC    -1  -0.601  -1.9938  -2.7368  -1.3652
 AN6  CA'   C  CH1    0  -0.220  -3.7111  -1.7329  -0.0346
 AN6  CB'   C  CH2    0  -0.452  -2.8345  -0.4984   0.1204
 AN6  CG'   C  CH2    0  -0.259  -3.5917   0.7863   0.4202
 AN6  HN'   H  HNH2   0   0.332  -4.8551  -2.9054   1.1311
 AN6  HN'A  H  HNH2   0   0.323  -3.8641  -1.9659   1.9660
 AN6  H1    H  HCH3   0   0.222  -4.2637   1.7871   3.0280
 AN6  H1A   H  HCH3   0   0.221  -2.6837   2.4465   3.4429
 AN6  H1B   H  HCH3   0   0.224  -4.1046   3.4966   3.3933
 AN6  H3    H  HCH2   0   0.194  -4.2534   3.2931   0.9438
 AN6  H3A   H  HCH2   0   0.227  -2.6585   3.8348   1.4210
 AN6  HN6   H  HNH2   0   0.411   3.0664  -4.5103   0.1292
 AN6  HN6A  H  HNH2   0   0.403   4.7021  -4.5154   0.6790
 AN6  H1'   H  HCH1   0   0.249   2.2192   1.9126   0.2236
 AN6  H2'   H  HCH1   0   0.247   0.3828   1.2544  -2.1220
 AN6  HO2'  H  HOH1   0   0.468   2.0713   2.0412  -3.2407
 AN6  H3'   H  HCH1   0   0.247  -0.3400   3.5651  -2.0449
 AN6  HO3'  H  HOH1   0   0.449   1.8437   4.3499  -1.5097
 AN6  H4'   H  HCH1   0   0.245  -0.5502   3.5449   0.7302
 AN6  H5'   H  HCH2   0   0.238  -1.8782   1.5613  -1.1594
 AN6  H5'A  H  HCH2   0   0.221  -2.4188   3.2039  -0.8922
 AN6  HA'   H  HCH1   0   0.209  -4.4212  -1.5329  -0.8518
 AN6  HB'   H  HCH2   0   0.208  -2.0994  -0.6580   0.9174
 AN6  HB'A  H  HCH2   0   0.226  -2.2673  -0.3883  -0.8032
 AN6  HG'   H  HCH2   0   0.227  -4.2499   0.6150   1.2729
 AN6  HG'A  H  HCH2   0   0.182  -4.2538   1.0359  -0.4279
 AN6  H2    H  HCR6   0   0.251   5.9002  -0.2303   1.2270
 AN6  H8    H  HCR5   0   0.302  -0.1330  -0.9806  -0.7917

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
 AN6  O'   C'    deloc     1.248  0.020  1.248
 AN6  C'   O5'   deloc     1.249  0.020  1.249
 AN6  C'   CA'   single    1.555  0.020  1.555
 AN6  N'   CA'   single    1.458  0.020  1.458
 AN6  N'   HN'   single    0.890  0.020  1.040
 AN6  N'   HN'A  single    0.890  0.020  1.040
 AN6  C1   C3    single    1.520  0.020  1.520
 AN6  C1   H1    single    0.970  0.020  1.090
 AN6  C1   H1A   single    0.970  0.020  1.090
 AN6  C1   H1B   single    0.970  0.020  1.090
 AN6  C6   N1    aromatic  1.338  0.020  1.338
 AN6  N1   C2    aromatic  1.331  0.020  1.331
 AN6  N3   C2    aromatic  1.321  0.020  1.321
 AN6  C2   H2    single    0.930  0.020  1.080
 AN6  C3   N10   single    1.453  0.020  1.453
 AN6  C3   H3    single    0.970  0.020  1.090
 AN6  C3   H3A   single    0.970  0.020  1.090
 AN6  C4   N3    aromatic  1.331  0.020  1.331
 AN6  N9   C4    aromatic  1.366  0.020  1.366
 AN6  C5   C4    aromatic  1.385  0.020  1.385
 AN6  N7   C5    aromatic  1.371  0.020  1.371
 AN6  C5   C6    aromatic  1.407  0.020  1.407
 AN6  N6   C6    single    1.334  0.020  1.334
 AN6  N6   HN6   single    0.860  0.020  1.020
 AN6  N6   HN6A  single    0.860  0.020  1.020
 AN6  C8   N7    aromatic  1.300  0.020  1.300
 AN6  C8   N9    aromatic  1.372  0.020  1.372
 AN6  C8   H8    single    0.930  0.020  1.080
 AN6  N9   C1'   single    1.439  0.020  1.439
 AN6  O4'  C1'   single    1.398  0.020  1.398
 AN6  C2'  C1'   single    1.525  0.020  1.525
 AN6  C1'  H1'   single    0.970  0.020  1.090
 AN6  CG'  N10   single    1.453  0.020  1.453
 AN6  N10  C5'   single    1.449  0.020  1.449
 AN6  C3'  C2'   single    1.532  0.020  1.532
 AN6  C2'  O2'   single    1.396  0.020  1.396
 AN6  C2'  H2'   single    0.970  0.020  1.090
 AN6  O2'  HO2'  single    0.850  0.020  0.980
 AN6  C4'  C3'   single    1.528  0.020  1.528
 AN6  C3'  O3'   single    1.406  0.020  1.406
 AN6  C3'  H3'   single    0.970  0.020  1.090
 AN6  O3'  HO3'  single    0.850  0.020  0.980
 AN6  C5'  C4'   single    1.520  0.020  1.520
 AN6  O4'  C4'   single    1.437  0.020  1.437
 AN6  C4'  H4'   single    0.970  0.020  1.090
 AN6  C5'  H5'   single    0.970  0.020  1.090
 AN6  C5'  H5'A  single    0.970  0.020  1.090
 AN6  CB'  CA'   single    1.522  0.020  1.522
 AN6  CA'  HA'   single    0.970  0.020  1.090
 AN6  CG'  CB'   single    1.521  0.020  1.521
 AN6  CB'  HB'   single    0.970  0.020  1.090
 AN6  CB'  HB'A  single    0.970  0.020  1.090
 AN6  CG'  HG'   single    0.970  0.020  1.090
 AN6  CG'  HG'A  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
 AN6  CA'   C'   O5'  116.82  3.000
 AN6  CA'   C'   O'   116.98  3.000
 AN6  O5'   C'   O'   126.16  3.000
 AN6  HN'A  N'   HN'  104.20  3.000
 AN6  HN'A  N'   CA'  108.22  3.000
 AN6  HN'   N'   CA'  107.54  3.000
 AN6  H1B   C1   H1A  108.29  3.000
 AN6  H1B   C1   H1   107.19  3.000
 AN6  H1A   C1   H1   107.76  3.000
 AN6  H1B   C1   C3   110.40  3.000
 AN6  H1A   C1   C3   110.54  3.000
 AN6  H1    C1   C3   112.50  3.000
 AN6  C6    N1   C2   119.05  3.000
 AN6  H2    C2   N3   116.11  3.000
 AN6  H2    C2   N1   115.41  3.000
 AN6  N3    C2   N1   128.48  3.000
 AN6  H3A   C3   H3   105.76  3.000
 AN6  H3A   C3   N10  108.15  3.000
 AN6  H3    C3   N10  111.53  3.000
 AN6  H3A   C3   C1   107.78  3.000
 AN6  H3    C3   C1   110.20  3.000
 AN6  N10   C3   C1   113.06  3.000
 AN6  C4    N3   C2   111.75  3.000
 AN6  N9    C4   C5   105.22  3.000
 AN6  C5    C4   N3   126.38  3.000
 AN6  N9    C4   N3   128.40  3.000
 AN6  N7    C5   C6   132.81  3.000
 AN6  C6    C5   C4   116.38  3.000
 AN6  N7    C5   C4   110.80  3.000
 AN6  N6    C6   C5   122.70  3.000
 AN6  N6    C6   N1   119.34  3.000
 AN6  C5    C6   N1   117.96  3.000
 AN6  HN6A  N6   HN6  118.30  3.000
 AN6  HN6A  N6   C6   120.36  3.000
 AN6  HN6   N6   C6   121.10  3.000
 AN6  C8    N7   C5   104.60  3.000
 AN6  H8    C8   N9   122.67  3.000
 AN6  H8    C8   N7   124.17  3.000
 AN6  N9    C8   N7   113.16  3.000
 AN6  C1'   N9   C8   128.54  3.000
 AN6  C1'   N9   C4   125.24  3.000
 AN6  C8    N9   C4   106.22  3.000
 AN6  H1'   C1'  O4'  112.22  3.000
 AN6  H1'   C1'  C2'  109.49  3.000
 AN6  O4'   C1'  C2'  104.93  3.000
 AN6  H1'   C1'  N9   105.63  3.000
 AN6  C2'   C1'  N9   114.82  3.000
 AN6  O4'   C1'  N9   109.90  3.000
 AN6  CG'   N10  C5'  113.08  3.000
 AN6  C5'   N10  C3   111.73  3.000
 AN6  CG'   N10  C3   113.44  3.000
 AN6  H2'   C2'  C3'  109.18  3.000
 AN6  H2'   C2'  O2'  111.78  3.000
 AN6  C3'   C2'  O2'  114.95  3.000
 AN6  H2'   C2'  C1'  109.60  3.000
 AN6  O2'   C2'  C1'  110.61  3.000
 AN6  C3'   C2'  C1'  100.08  3.000
 AN6  HO2'  O2'  C2'  108.96  3.000
 AN6  H3'   C3'  C4'  111.74  3.000
 AN6  H3'   C3'  O3'  111.41  3.000
 AN6  C4'   C3'  O3'  108.90  3.000
 AN6  H3'   C3'  C2'  112.14  3.000
 AN6  O3'   C3'  C2'  110.69  3.000
 AN6  C4'   C3'  C2'  101.53  3.000
 AN6  HO3'  O3'  C3'  107.96  3.000
 AN6  H4'   C4'  C5'  109.60  3.000
 AN6  H4'   C4'  O4'  108.53  3.000
 AN6  C5'   C4'  O4'  109.96  3.000
 AN6  H4'   C4'  C3'  109.73  3.000
 AN6  O4'   C4'  C3'  106.30  3.000
 AN6  C5'   C4'  C3'  112.60  3.000
 AN6  C4'   O4'  C1'  109.72  3.000
 AN6  H5'A  C5'  H5'  105.81  3.000
 AN6  H5'A  C5'  C4'  108.35  3.000
 AN6  H5'   C5'  C4'  108.55  3.000
 AN6  H5'A  C5'  N10  111.97  3.000
 AN6  H5'   C5'  N10  109.94  3.000
 AN6  C4'   C5'  N10  111.98  3.000
 AN6  HA'   CA'  CB'  107.44  3.000
 AN6  HA'   CA'  N'   107.16  3.000
 AN6  CB'   CA'  N'   110.58  3.000
 AN6  HA'   CA'  C'   105.48  3.000
 AN6  CB'   CA'  C'   110.91  3.000
 AN6  N'    CA'  C'   114.81  3.000
 AN6  HB'A  CB'  HB'  106.38  3.000
 AN6  HB'A  CB'  CG'  109.93  3.000
 AN6  HB'   CB'  CG'  108.27  3.000
 AN6  HB'A  CB'  CA'  107.19  3.000
 AN6  HB'   CB'  CA'  110.02  3.000
 AN6  CG'   CB'  CA'  114.74  3.000
 AN6  HG'A  CG'  HG'  105.90  3.000
 AN6  HG'A  CG'  CB'  109.75  3.000
 AN6  HG'   CG'  CB'  108.78  3.000
 AN6  HG'A  CG'  N10  112.00  3.000
 AN6  HG'   CG'  N10  108.69  3.000
 AN6  CB'   CG'  N10  111.53  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
 AN6  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 AN6  CONST_02  N7    C5   C6   N1    180.00   0.0  0
 AN6  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 AN6  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 AN6  CONST_05  N9    C4   N3   C2    180.00   0.0  0
 AN6  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 AN6  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 AN6  CONST_08  C8    N9   C4   N3    180.00   0.0  0
 AN6  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 AN6  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 AN6  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 AN6  CONST_12  C8    N7   C5   C4      0.00   0.0  0
 AN6  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 AN6  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 AN6  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 AN6  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 AN6  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 AN6  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 AN6  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 AN6  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 AN6  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 AN6  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 AN6  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 AN6  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 AN6  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 AN6  CONST_26  HN6   N6   C6   N1    180.00   0.0  0
 AN6  CONST_27  HN6A  N6   C6   N1      0.00   0.0  0
 AN6  Var_01    C4'   C5'  N10  C3     86.75  30.0  3
 AN6  Var_02    CB'   CG'  N10  C3   -160.88  30.0  3
 AN6  Var_03    CA'   CB'  CG'  N10   171.80  30.0  3
 AN6  Var_04    H1    C1   C3   N10   -59.53  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
 AN6  chir_01  C1'  N9   O4'  C2'  positiv
 AN6  chir_02  C2'  O2'  C1'  C3'  negativ
 AN6  chir_03  C3'  O3'  C4'  C2'  positiv
 AN6  chir_04  C4'  O4'  C3'  C5'  negativ
 AN6  chir_05  CA'  N'   C'   CB'  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
 AN6  plan-1  N1    0.020
 AN6  plan-1  C2    0.020
 AN6  plan-1  N3    0.020
 AN6  plan-1  C4    0.020
 AN6  plan-1  C5    0.020
 AN6  plan-1  C6    0.020
 AN6  plan-1  N6    0.020
 AN6  plan-1  N7    0.020
 AN6  plan-1  C8    0.020
 AN6  plan-1  N9    0.020
 AN6  plan-1  C1'   0.020
 AN6  plan-1  H2    0.020
 AN6  plan-1  H8    0.020
 AN6  plan-2  C6    0.020
 AN6  plan-2  N6    0.020
 AN6  plan-2  HN6   0.020
 AN6  plan-2  HN6A  0.020
 AN6  plan-3  C'    0.020
 AN6  plan-3  O'    0.020
 AN6  plan-3  O5'   0.020
 AN6  plan-3  CA'   0.020

