# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 13:35:38 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](3-bromo-2-oxopropyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)CC(=O)CBr)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
 6D0  6D0  5'-{[(3S)-3-amino-3-carboxypropyl](3-bromo-2-oxopropyl)amino}-5'-deoxyadenosine  ligand  55  31  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6D0
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
 6D0  O1   O   O     0  -0.435  21.3678  17.0433  121.6713
 6D0  C1   C   C     0   0.540  21.9970  16.7690  120.6817
 6D0  C2   C   CH1   0  -0.190  22.5231  17.7605  119.6542
 6D0  N1   N   NH2   0  -0.799  21.9045  19.0533  119.8384
 6D0  C3   C   CH2   0  -0.463  24.0575  17.8152  119.7264
 6D0  C4   C   CH2   0  -0.318  24.6594  18.2810  121.0511
 6D0  N2   N   NT    0  -0.399  24.3868  19.6699  121.3858
 6D0  C5   C   CH2   0  -0.300  25.4842  20.5892  121.2151
 6D0  C6   C   CH1   0  -0.035  25.8443  20.8116  119.7500
 6D0  O2   O   O2    0  -0.491  24.7010  21.2029  118.9816
 6D0  C7   C   CH1   0   0.213  24.7917  22.5461  118.6082
 6D0  C8   C   CH1   0  -0.011  25.9231  23.1398  119.4492
 6D0  O3   O   OH1   0  -0.653  26.4284  24.2738  118.8235
 6D0  C9   C   CH1   0  -0.026  26.8611  21.9399  119.5699
 6D0  O4   O   OH1   0  -0.667  27.5795  21.8345  118.3694
 6D0  N3   N   NR5   0  -0.538  23.5148  23.1846  118.8256
 6D0  C10  C   CR15  0   0.112  22.7052  23.0594  119.9211
 6D0  N4   N   N     0  -0.450  21.6267  23.7813  119.8519
 6D0  C11  C   CR56  0  -0.013  21.7268  24.4264  118.6463
 6D0  C12  C   CR6   0   0.457  20.8947  25.3465  117.9820
 6D0  N5   N   NH2   0  -0.816  19.7509  25.7911  118.5048
 6D0  C13  C   CR56  0   0.492  22.8940  24.0670  117.9899
 6D0  N6   N   N     0  -0.455  23.2961  24.5009  116.7977
 6D0  C14  C   CR16  0   0.043  22.4339  25.3532  116.2721
 6D0  N7   N   N     0  -0.474  21.2868  25.7930  116.7835
 6D0  C15  C   CH2   0  -0.446  23.5550  19.8891  122.5260
 6D0  C16  C   C     0   0.410  24.1826  19.5827  123.8767
 6D0  C17  C   CH2   0  -0.631  23.2815  19.9059  125.0477
 6D0  O5   O   O     0  -0.372  25.2916  19.1325  124.0003
 6D0  BR1  BR  BR    0  -0.095  24.0092  19.3076  126.7414
 6D0  O6   O   OH1   0  -0.600  22.3262  15.5191  120.3604
 6D0  H1   H   HCH1  0   0.263  22.2873  17.3312  118.6709
 6D0  H2   H   HNH2  0   0.360  22.5686  19.7906  119.6525
 6D0  H3   H   HNH2  0   0.350  21.1251  19.1686  119.2064
 6D0  H5   H   HCH2  0   0.246  24.4526  16.8206  119.5085
 6D0  H6   H   HCH2  0   0.251  24.3997  18.4585  118.9131
 6D0  H7   H   HCH2  0   0.241  24.3134  17.6252  121.8559
 6D0  H8   H   HCH2  0   0.240  25.7417  18.1174  121.0034
 6D0  H10  H   HCH2  0   0.228  26.4017  20.2619  121.7266
 6D0  H11  H   HCH2  0   0.238  25.2041  21.5455  121.6685
 6D0  H12  H   HCH1  0   0.259  26.2274  19.8781  119.3247
 6D0  H13  H   HCH1  0   0.262  25.0121  22.6590  117.5409
 6D0  H14  H   HCH1  0   0.243  25.5357  23.3702  120.4516
 6D0  H15  H   HOH1  0   0.463  27.0275  24.7217  119.4288
 6D0  H16  H   HCH1  0   0.252  27.5284  22.0194  120.4379
 6D0  H17  H   HOH1  0   0.457  28.1155  21.0356  118.4044
 6D0  H18  H   HCR5  0   0.290  22.9575  22.4035  120.7405
 6D0  H19  H   HNH2  0   0.403  19.1577  26.4071  117.9762
 6D0  H20  H   HNH2  0   0.411  19.4013  25.4223  119.3716
 6D0  H21  H   HCR6  0   0.252  22.6906  25.7507  115.2960
 6D0  H22  H   HCH2  0   0.277  23.2074  20.9285  122.5511
 6D0  H23  H   HCH2  0   0.297  22.6393  19.2967  122.4292
 6D0  H24  H   HCH2  0   0.328  23.1319  20.9865  125.1024
 6D0  H25  H   HCH2  0   0.319  22.3000  19.4482  124.9123
 6D0  H26  H   HOH1  0   0.478  22.0087  14.9085  121.0421

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
 6D0  C14  N7   aromatic  1.331  0.020  1.331
 6D0  C14  N6   aromatic  1.321  0.020  1.321
 6D0  N7   C12  aromatic  1.338  0.020  1.338
 6D0  N6   C13  aromatic  1.331  0.020  1.331
 6D0  C12  N5   single    1.334  0.020  1.334
 6D0  C12  C11  aromatic  1.407  0.020  1.407
 6D0  C13  C11  aromatic  1.387  0.020  1.387
 6D0  C13  N3   aromatic  1.365  0.020  1.365
 6D0  O3   C8   single    1.390  0.020  1.390
 6D0  O4   C9   single    1.403  0.020  1.403
 6D0  C11  N4   aromatic  1.371  0.020  1.371
 6D0  C7   N3   single    1.444  0.020  1.444
 6D0  C7   C8   single    1.530  0.020  1.530
 6D0  C7   O2   single    1.397  0.020  1.397
 6D0  N3   C10  aromatic  1.368  0.020  1.368
 6D0  C8   C9   single    1.528  0.020  1.528
 6D0  O2   C6   single    1.432  0.020  1.432
 6D0  C9   C6   single    1.530  0.020  1.530
 6D0  C2   C1   single    1.522  0.020  1.522
 6D0  C2   C3   single    1.537  0.020  1.537
 6D0  C2   N1   single    1.445  0.020  1.445
 6D0  N4   C10  aromatic  1.300  0.020  1.300
 6D0  C6   C5   single    1.525  0.020  1.525
 6D0  C1   O1   double    1.204  0.020  1.204
 6D0  C1   O6   single    1.332  0.020  1.332
 6D0  C3   C4   single    1.528  0.020  1.528
 6D0  C5   N2   single    1.442  0.020  1.442
 6D0  C4   N2   single    1.454  0.020  1.454
 6D0  N2   C15  single    1.428  0.020  1.428
 6D0  C15  C16  single    1.521  0.020  1.521
 6D0  O5   C16  double    1.203  0.020  1.203
 6D0  C16  C17  single    1.512  0.020  1.512
 6D0  C17  BR1  single    1.938  0.020  1.938
 6D0  C2   H1   single    0.970  0.020  1.090
 6D0  N1   H2   single    0.890  0.020  1.040
 6D0  N1   H3   single    0.890  0.020  1.040
 6D0  C3   H5   single    0.970  0.020  1.090
 6D0  C3   H6   single    0.970  0.020  1.090
 6D0  C4   H7   single    0.970  0.020  1.090
 6D0  C4   H8   single    0.970  0.020  1.090
 6D0  C5   H10  single    0.970  0.020  1.090
 6D0  C5   H11  single    0.970  0.020  1.090
 6D0  C6   H12  single    0.970  0.020  1.090
 6D0  C7   H13  single    0.970  0.020  1.090
 6D0  C8   H14  single    0.970  0.020  1.090
 6D0  O3   H15  single    0.850  0.020  0.980
 6D0  C9   H16  single    0.970  0.020  1.090
 6D0  O4   H17  single    0.850  0.020  0.980
 6D0  C10  H18  single    0.930  0.020  1.080
 6D0  N5   H19  single    0.860  0.020  1.020
 6D0  N5   H20  single    0.860  0.020  1.020
 6D0  C14  H21  single    0.930  0.020  1.080
 6D0  C15  H22  single    0.970  0.020  1.090
 6D0  C15  H23  single    0.970  0.020  1.090
 6D0  C17  H24  single    0.970  0.020  1.090
 6D0  C17  H25  single    0.970  0.020  1.090
 6D0  O6   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
 6D0  O6   C1   C2   111.30  3.000
 6D0  O6   C1   O1   122.75  3.000
 6D0  C2   C1   O1   125.95  3.000
 6D0  H1   C2   C3   105.67  3.000
 6D0  H1   C2   N1   111.83  3.000
 6D0  C3   C2   N1   112.92  3.000
 6D0  H1   C2   C1   106.00  3.000
 6D0  N1   C2   C1   110.42  3.000
 6D0  C3   C2   C1   109.67  3.000
 6D0  H3   N1   H2   108.00  3.000
 6D0  H3   N1   C2   110.65  3.000
 6D0  H2   N1   C2   110.38  3.000
 6D0  H6   C3   H5   105.93  3.000
 6D0  H6   C3   C4   110.04  3.000
 6D0  H5   C3   C4   107.95  3.000
 6D0  H6   C3   C2   107.39  3.000
 6D0  H5   C3   C2   108.62  3.000
 6D0  C4   C3   C2   116.42  3.000
 6D0  H8   C4   H7   104.76  3.000
 6D0  H8   C4   N2   109.74  3.000
 6D0  H7   C4   N2   110.11  3.000
 6D0  H8   C4   C3   107.81  3.000
 6D0  H7   C4   C3   109.29  3.000
 6D0  N2   C4   C3   114.64  3.000
 6D0  C15  N2   C5   116.10  3.000
 6D0  C15  N2   C4   116.07  3.000
 6D0  C5   N2   C4   116.04  3.000
 6D0  H11  C5   H10  106.30  3.000
 6D0  H11  C5   C6   109.33  3.000
 6D0  H10  C5   C6   107.04  3.000
 6D0  H11  C5   N2   108.26  3.000
 6D0  H10  C5   N2   112.95  3.000
 6D0  C6   C5   N2   112.74  3.000
 6D0  H12  C6   C9   110.52  3.000
 6D0  H12  C6   O2   107.69  3.000
 6D0  C9   C6   O2   105.42  3.000
 6D0  H12  C6   C5   109.36  3.000
 6D0  C9   C6   C5   112.19  3.000
 6D0  O2   C6   C5   111.52  3.000
 6D0  C7   O2   C6   110.75  3.000
 6D0  H13  C7   N3   106.20  3.000
 6D0  H13  C7   C8   110.29  3.000
 6D0  N3   C7   C8   113.56  3.000
 6D0  H13  C7   O2   111.87  3.000
 6D0  C8   C7   O2   105.92  3.000
 6D0  N3   C7   O2   109.11  3.000
 6D0  H14  C8   C9   108.00  3.000
 6D0  H14  C8   O3   111.56  3.000
 6D0  C9   C8   O3   116.94  3.000
 6D0  H14  C8   C7   108.79  3.000
 6D0  C9   C8   C7   101.12  3.000
 6D0  O3   C8   C7   109.76  3.000
 6D0  H15  O3   C8   108.84  3.000
 6D0  H16  C9   O4   111.76  3.000
 6D0  H16  C9   C8   112.26  3.000
 6D0  O4   C9   C8   107.80  3.000
 6D0  H16  C9   C6   111.37  3.000
 6D0  C8   C9   C6   100.40  3.000
 6D0  O4   C9   C6   112.69  3.000
 6D0  H17  O4   C9   108.44  3.000
 6D0  C13  N3   C10  106.28  3.000
 6D0  C10  N3   C7   127.12  3.000
 6D0  C13  N3   C7   126.58  3.000
 6D0  H18  C10  N4   124.88  3.000
 6D0  H18  C10  N3   121.68  3.000
 6D0  N4   C10  N3   113.43  3.000
 6D0  C11  N4   C10  104.34  3.000
 6D0  C13  C11  C12  116.34  3.000
 6D0  C13  C11  N4   110.85  3.000
 6D0  C12  C11  N4   132.81  3.000
 6D0  N7   C12  N5   119.42  3.000
 6D0  N5   C12  C11  122.68  3.000
 6D0  N7   C12  C11  117.90  3.000
 6D0  H20  N5   H19  118.24  3.000
 6D0  H20  N5   C12  120.93  3.000
 6D0  H19  N5   C12  120.28  3.000
 6D0  N6   C13  C11  126.44  3.000
 6D0  C11  C13  N3   105.10  3.000
 6D0  N6   C13  N3   128.46  3.000
 6D0  C14  N6   C13  111.68  3.000
 6D0  H21  C14  N7   115.39  3.000
 6D0  H21  C14  N6   116.09  3.000
 6D0  N7   C14  N6   128.52  3.000
 6D0  C14  N7   C12  119.12  3.000
 6D0  H23  C15  H22  104.46  3.000
 6D0  H23  C15  C16  108.34  3.000
 6D0  H22  C15  C16  107.55  3.000
 6D0  H23  C15  N2   109.48  3.000
 6D0  H22  C15  N2   110.40  3.000
 6D0  C16  C15  N2   115.97  3.000
 6D0  O5   C16  C17  123.33  3.000
 6D0  C17  C16  C15  113.51  3.000
 6D0  O5   C16  C15  123.16  3.000
 6D0  H25  C17  H24  107.33  3.000
 6D0  H25  C17  BR1  108.46  3.000
 6D0  H24  C17  BR1  108.25  3.000
 6D0  H25  C17  C16  110.49  3.000
 6D0  H24  C17  C16  109.37  3.000
 6D0  BR1  C17  C16  112.77  3.000
 6D0  H26  O6   C1   109.93  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
 6D0  CONST_01  C14  N6   C13  N3    180.00   0.0  0
 6D0  CONST_02  C12  C11  C13  N3    180.00   0.0  0
 6D0  CONST_03  N4   C11  C13  N3      0.00   0.0  0
 6D0  CONST_04  C11  N4   C10  N3      0.00   0.0  0
 6D0  CONST_05  N6   C13  N3   C10   180.00   0.0  0
 6D0  CONST_06  C11  C13  N3   C10     0.00   0.0  0
 6D0  CONST_07  C12  C11  N4   C10   180.00   0.0  0
 6D0  CONST_08  C13  C11  N4   C10     0.00   0.0  0
 6D0  CONST_09  N7   C12  C11  N4    180.00   0.0  0
 6D0  CONST_10  N6   C13  C11  N4    180.00   0.0  0
 6D0  CONST_11  C13  N3   C10  N4      0.00   0.0  0
 6D0  CONST_12  C14  N7   C12  C11     0.00   0.0  0
 6D0  CONST_13  C14  N6   C13  C11     0.00   0.0  0
 6D0  CONST_14  N6   C14  N7   C12     0.00   0.0  0
 6D0  CONST_15  N6   C13  C11  C12     0.00   0.0  0
 6D0  CONST_16  N7   C14  N6   C13     0.00   0.0  0
 6D0  CONST_17  N7   C12  C11  C13     0.00   0.0  0
 6D0  CONST_18  N6   C13  N3   C7      0.00   0.0  0
 6D0  CONST_19  C11  C13  N3   C7    180.00   0.0  0
 6D0  CONST_20  N4   C10  N3   C7    180.00   0.0  0
 6D0  CONST_21  N5   C12  C11  N4      0.00   0.0  0
 6D0  CONST_22  C14  N7   C12  N5    180.00   0.0  0
 6D0  CONST_23  C13  C11  C12  N5    180.00   0.0  0
 6D0  CONST_24  H18  C10  N3   C7      0.00   0.0  0
 6D0  CONST_25  H21  C14  N7   C12   180.00   0.0  0
 6D0  CONST_26  H19  N5   C12  C11   180.00   0.0  0
 6D0  CONST_27  H20  N5   C12  C11     0.00   0.0  0
 6D0  CONST_28  H26  O6   C1   O1      0.00   0.0  0
 6D0  Var_01    C6   C5   N2   C4     69.08  30.0  1
 6D0  Var_02    N2   C4   C3   C2    -66.26  30.0  3
 6D0  Var_03    C5   N2   C4   C3   -104.80  30.0  3
 6D0  Var_04    C16  C15  N2   C4     71.39  30.0  3
 6D0  Var_05    O5   C16  C15  N2     -2.85  30.0  3
 6D0  Var_06    BR1  C17  C16  C15   172.91  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
 6D0  chir_01  C2  C1  C3  N1  positiv
 6D0  chir_02  C6  O2  C9  C5  negativ
 6D0  chir_03  C7  O2  N3  C8  negativ
 6D0  chir_04  C8  O3  C7  C9  negativ
 6D0  chir_05  C9  O4  C6  C8  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
 6D0  plan-1  C7   0.020
 6D0  plan-1  N3   0.020
 6D0  plan-1  C10  0.020
 6D0  plan-1  N4   0.020
 6D0  plan-1  C11  0.020
 6D0  plan-1  C12  0.020
 6D0  plan-1  N5   0.020
 6D0  plan-1  C13  0.020
 6D0  plan-1  N6   0.020
 6D0  plan-1  C14  0.020
 6D0  plan-1  N7   0.020
 6D0  plan-1  H18  0.020
 6D0  plan-1  H21  0.020
 6D0  plan-2  C12  0.020
 6D0  plan-2  N5   0.020
 6D0  plan-2  H19  0.020
 6D0  plan-2  H20  0.020
 6D0  plan-3  C15  0.020
 6D0  plan-3  C16  0.020
 6D0  plan-3  C17  0.020
 6D0  plan-3  O5   0.020
 6D0  plan-4  O1   0.020
 6D0  plan-4  C1   0.020
 6D0  plan-4  C2   0.020
 6D0  plan-4  O6   0.020
 6D0  plan-4  H26  0.020

