# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 04:11:58 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCN(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
 62X  62X  5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine  ligand  64  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_62X
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
 62X  C4   C  CH2   0  -0.252  -4.8157   2.8134   0.7896
 62X  C5   C  CH2   0  -0.464  -3.7213   1.7553   0.7470
 62X  C6   C  CH2   0  -0.265  -3.3246   1.4485  -0.6916
 62X  C8   C  CH2   0  -0.268  -2.4482  -0.8127  -0.4522
 62X  C10  C  CH1   0  -0.200  -1.4329  -2.9922   0.3893
 62X  C15  C  CH2   0  -0.313  -1.4733   0.7340  -2.0574
 62X  C21  C  CH1   0  -0.019   0.4619   1.9417  -3.1985
 62X  C24  C  CR15  0   0.112   2.3855  -1.4660  -1.3558
 62X  C26  C  CR56  0   0.016   3.0334  -1.5815   0.6519
 62X  C1   C  CH3   0  -0.527  -4.4267   3.5380   3.0561
 62X  N2   N  NT    0  -0.406  -5.3886   3.0178   2.1077
 62X  C3   C  CH3   0  -0.518  -6.5454   3.8836   2.0322
 62X  N7   N  NT    0  -0.415  -2.1774   0.5678  -0.8005
 62X  C9   C  CH2   0  -0.447  -1.1791  -1.5358  -0.0224
 62X  N11  N  NH2   0  -0.778  -2.2545  -3.0507   1.5749
 62X  C12  C  C     0   0.525  -0.0700  -3.6487   0.5363
 62X  O13  O  O     0  -0.439   0.5233  -3.7652   1.5801
 62X  O14  O  OH1   0  -0.600   0.4252  -4.0329  -0.6349
 62X  C16  C  CH1   0  -0.000  -0.3583   1.7632  -1.9282
 62X  O17  O  O2    0  -0.477   0.5783   1.3533  -0.9262
 62X  C18  C  CH1   0   0.242   1.8069   1.0152  -1.5014
 62X  C19  C  CH1   0  -0.080   1.5481   0.8813  -2.9994
 62X  O20  O  OH1   0  -0.654   2.7296   1.0904  -3.7127
 62X  O22  O  OH1   0  -0.669   1.0136   3.2334  -3.2077
 62X  N23  N  NR5   0  -0.552   2.3146  -0.1865  -0.8763
 62X  N25  N  N     0  -0.472   2.8164  -2.3249  -0.4793
 62X  C27  C  CR6   0   0.457   3.4663  -1.9122   1.9481
 62X  N28  N  NH2   0  -0.812   3.7855  -3.1613   2.3072
 62X  N29  N  N     0  -0.472   3.5878  -0.9224   2.8371
 62X  C30  C  CR16  0   0.039   3.2879   0.3214   2.4692
 62X  N31  N  N     0  -0.455   2.8490   0.7473   1.2981
 62X  C32  C  CR56  0   0.500   2.7359  -0.2486   0.4234
 62X  H1   H  HCH2  0   0.183  -4.4209   3.7578   0.3717
 62X  H2   H  HCH2  0   0.226  -2.8276   2.0898   1.2787
 62X  H3   H  HCH2  0   0.196  -4.1966   1.0606  -1.2463
 62X  H4   H  HCH2  0   0.226  -3.0625   2.3951  -1.1736
 62X  H5   H  HCH2  0   0.239  -3.1515  -0.8361   0.3797
 62X  H6   H  HCH2  0   0.195  -2.9265  -1.3668  -1.2784
 62X  H7   H  HCH1  0   0.261  -1.9653  -3.4935  -0.4253
 62X  H8   H  HCH2  0   0.238  -1.0558  -0.2238  -2.3800
 62X  H9   H  HCH2  0   0.231  -2.1497   1.0459  -2.8667
 62X  H10  H  HCH1  0   0.249  -0.1322   1.7484  -4.1011
 62X  H11  H  HCR5  0   0.300   2.1216  -1.7183  -2.3705
 62X  H12  H  HCH3  0   0.188  -4.0063   4.5119   2.7553
 62X  H13  H  HCH3  0   0.233  -4.9018   3.6689   4.0293
 62X  H14  H  HCH3  0   0.236  -3.5963   2.8456   3.1895
 62X  H15  H  HCH3  0   0.230  -7.2958   3.4549   1.3661
 62X  H16  H  HCH3  0   0.231  -6.9986   3.9913   3.0190
 62X  H17  H  HCH3  0   0.188  -6.3092   4.8947   1.6632
 62X  H19  H  HCH2  0   0.238  -0.4528  -1.5159  -0.8366
 62X  H20  H  HCH2  0   0.234  -0.7204  -0.9937   0.8095
 62X  H21  H  HNH2  0   0.354  -2.4497  -4.0122   1.8228
 62X  H22  H  HNH2  0   0.343  -1.7592  -2.6478   2.3611
 62X  H24  H  HOH1  0   0.474   1.3808  -4.1889  -0.5529
 62X  H25  H  HCH1  0   0.251  -0.7901   2.7209  -1.6187
 62X  H26  H  HCH1  0   0.253   2.5486   1.8004  -1.3177
 62X  H27  H  HCH1  0   0.248   1.1060  -0.0961  -3.2264
 62X  H28  H  HOH1  0   0.471   2.6187   0.7510  -4.6066
 62X  H29  H  HOH1  0   0.449   1.7676   3.2332  -3.8090
 62X  H30  H  HNH2  0   0.403   3.4808  -3.9294   1.7343
 62X  H31  H  HNH2  0   0.399   3.9335  -3.3595   3.2826
 62X  H32  H  HCR6  0   0.252   3.4160   1.0779   3.2359
 62X  H33  H  HCH2  0   0.223  -5.6274   2.5018   0.1241
 62X  H34  H  HCH2  0   0.222  -4.0814   0.8568   1.2554

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
 62X  N29  C30  aromatic  1.331  0.020  1.331
 62X  N29  C27  aromatic  1.336  0.020  1.336
 62X  N28  C27  single    1.338  0.020  1.338
 62X  C30  N31  aromatic  1.321  0.020  1.321
 62X  C27  C26  aromatic  1.406  0.020  1.406
 62X  N31  C32  aromatic  1.330  0.020  1.330
 62X  C26  C32  aromatic  1.385  0.020  1.385
 62X  C26  N25  aromatic  1.371  0.020  1.371
 62X  C32  N23  aromatic  1.368  0.020  1.368
 62X  N25  C24  aromatic  1.301  0.020  1.301
 62X  N23  C24  aromatic  1.368  0.020  1.368
 62X  N23  C18  single    1.447  0.020  1.447
 62X  C18  C19  single    1.526  0.020  1.526
 62X  C18  O17  single    1.398  0.020  1.398
 62X  N11  C10  single    1.444  0.020  1.444
 62X  C19  O20  single    1.396  0.020  1.396
 62X  C19  C21  single    1.531  0.020  1.531
 62X  O17  C16  single    1.431  0.020  1.431
 62X  O13  C12  double    1.206  0.020  1.206
 62X  C10  C9   single    1.535  0.020  1.535
 62X  C10  C12  single    1.520  0.020  1.520
 62X  C21  C16  single    1.523  0.020  1.523
 62X  C21  O22  single    1.405  0.020  1.405
 62X  C16  C15  single    1.523  0.020  1.523
 62X  C9   C8   single    1.523  0.020  1.523
 62X  C12  O14  single    1.328  0.020  1.328
 62X  C8   N7   single    1.449  0.020  1.449
 62X  C15  N7   single    1.450  0.020  1.450
 62X  N7   C6   single    1.450  0.020  1.450
 62X  C6   C5   single    1.524  0.020  1.524
 62X  C5   C4   single    1.523  0.020  1.523
 62X  C3   N2   single    1.447  0.020  1.447
 62X  C4   N2   single    1.452  0.020  1.452
 62X  N2   C1   single    1.448  0.020  1.448
 62X  C4   H1   single    0.970  0.020  1.090
 62X  C5   H2   single    0.970  0.020  1.090
 62X  C6   H3   single    0.970  0.020  1.090
 62X  C6   H4   single    0.970  0.020  1.090
 62X  C8   H5   single    0.970  0.020  1.090
 62X  C8   H6   single    0.970  0.020  1.090
 62X  C10  H7   single    0.970  0.020  1.090
 62X  C15  H8   single    0.970  0.020  1.090
 62X  C15  H9   single    0.970  0.020  1.090
 62X  C21  H10  single    0.970  0.020  1.090
 62X  C24  H11  single    0.930  0.020  1.080
 62X  C1   H12  single    0.970  0.020  1.090
 62X  C1   H13  single    0.970  0.020  1.090
 62X  C1   H14  single    0.970  0.020  1.090
 62X  C3   H15  single    0.970  0.020  1.090
 62X  C3   H16  single    0.970  0.020  1.090
 62X  C3   H17  single    0.970  0.020  1.090
 62X  C9   H19  single    0.970  0.020  1.090
 62X  C9   H20  single    0.970  0.020  1.090
 62X  N11  H21  single    0.890  0.020  1.040
 62X  N11  H22  single    0.890  0.020  1.040
 62X  O14  H24  single    0.850  0.020  0.980
 62X  C16  H25  single    0.970  0.020  1.090
 62X  C18  H26  single    0.970  0.020  1.090
 62X  C19  H27  single    0.970  0.020  1.090
 62X  O20  H28  single    0.850  0.020  0.980
 62X  O22  H29  single    0.850  0.020  0.980
 62X  N28  H30  single    0.890  0.020  1.040
 62X  N28  H31  single    0.890  0.020  1.040
 62X  C30  H32  single    0.930  0.020  1.080
 62X  C4   H33  single    0.970  0.020  1.090
 62X  C5   H34  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
 62X  H33  C4   H1   106.14  3.000
 62X  H33  C4   N2   107.42  3.000
 62X  H1   C4   N2   111.34  3.000
 62X  H33  C4   C5   108.54  3.000
 62X  H1   C4   C5   109.04  3.000
 62X  N2   C4   C5   114.00  3.000
 62X  H34  C5   H2   107.15  3.000
 62X  H34  C5   C6   111.06  3.000
 62X  H2   C5   C6   107.95  3.000
 62X  H34  C5   C4   108.74  3.000
 62X  H2   C5   C4   111.20  3.000
 62X  C6   C5   C4   110.70  3.000
 62X  H4   C6   H3   105.78  3.000
 62X  H4   C6   N7   107.63  3.000
 62X  H3   C6   N7   111.95  3.000
 62X  H4   C6   C5   107.71  3.000
 62X  H3   C6   C5   109.85  3.000
 62X  N7   C6   C5   113.52  3.000
 62X  H6   C8   H5   106.32  3.000
 62X  H6   C8   C9   109.52  3.000
 62X  H5   C8   C9   108.20  3.000
 62X  H6   C8   N7   112.28  3.000
 62X  H5   C8   N7   108.94  3.000
 62X  C9   C8   N7   111.38  3.000
 62X  H7   C10  C12  108.08  3.000
 62X  H7   C10  N11  108.41  3.000
 62X  C12  C10  N11  114.42  3.000
 62X  H7   C10  C9   108.38  3.000
 62X  C12  C10  C9   106.71  3.000
 62X  N11  C10  C9   110.67  3.000
 62X  H9   C15  H8   105.44  3.000
 62X  H9   C15  C16  108.73  3.000
 62X  H8   C15  C16  109.72  3.000
 62X  H9   C15  N7   111.82  3.000
 62X  H8   C15  N7   109.92  3.000
 62X  C16  C15  N7   111.06  3.000
 62X  H10  C21  O22  111.66  3.000
 62X  H10  C21  C19  111.66  3.000
 62X  O22  C21  C19  111.04  3.000
 62X  H10  C21  C16  111.96  3.000
 62X  O22  C21  C16  108.96  3.000
 62X  C19  C21  C16  101.10  3.000
 62X  H11  C24  N25  124.10  3.000
 62X  H11  C24  N23  122.40  3.000
 62X  N25  C24  N23  113.49  3.000
 62X  C32  C26  C27  116.40  3.000
 62X  C32  C26  N25  110.60  3.000
 62X  C27  C26  N25  132.99  3.000
 62X  H14  C1   H13  107.40  3.000
 62X  H14  C1   H12  107.71  3.000
 62X  H13  C1   H12  107.67  3.000
 62X  H14  C1   N2   111.00  3.000
 62X  H13  C1   N2   109.77  3.000
 62X  H12  C1   N2   113.08  3.000
 62X  C3   N2   C1   110.51  3.000
 62X  C1   N2   C4   112.54  3.000
 62X  C3   N2   C4   110.63  3.000
 62X  H17  C3   H16  107.54  3.000
 62X  H17  C3   H15  107.67  3.000
 62X  H16  C3   H15  107.77  3.000
 62X  H17  C3   N2   113.28  3.000
 62X  H16  C3   N2   110.12  3.000
 62X  H15  C3   N2   110.28  3.000
 62X  C15  N7   C8   114.09  3.000
 62X  C15  N7   C6   112.30  3.000
 62X  C8   N7   C6   114.37  3.000
 62X  H20  C9   H19  106.22  3.000
 62X  H20  C9   C10  109.62  3.000
 62X  H19  C9   C10  109.12  3.000
 62X  H20  C9   C8   109.20  3.000
 62X  H19  C9   C8   109.60  3.000
 62X  C10  C9   C8   112.87  3.000
 62X  H22  N11  H21  106.40  3.000
 62X  H22  N11  C10  110.06  3.000
 62X  H21  N11  C10  110.46  3.000
 62X  O14  C12  O13  123.48  3.000
 62X  O14  C12  C10  111.96  3.000
 62X  O13  C12  C10  124.50  3.000
 62X  H24  O14  C12  109.80  3.000
 62X  H25  C16  O17  108.09  3.000
 62X  H25  C16  C21  110.22  3.000
 62X  O17  C16  C21  105.37  3.000
 62X  H25  C16  C15  109.04  3.000
 62X  C21  C16  C15  113.75  3.000
 62X  O17  C16  C15  110.18  3.000
 62X  C18  O17  C16  110.87  3.000
 62X  H26  C18  N23  106.57  3.000
 62X  H26  C18  C19  110.01  3.000
 62X  N23  C18  C19  114.25  3.000
 62X  H26  C18  O17  110.65  3.000
 62X  C19  C18  O17  106.03  3.000
 62X  N23  C18  O17  109.36  3.000
 62X  H27  C19  O20  111.66  3.000
 62X  H27  C19  C18  110.47  3.000
 62X  O20  C19  C18  110.18  3.000
 62X  H27  C19  C21  107.72  3.000
 62X  O20  C19  C21  115.49  3.000
 62X  C18  C19  C21  100.79  3.000
 62X  H28  O20  C19  108.92  3.000
 62X  H29  O22  C21  108.12  3.000
 62X  C32  N23  C18  123.82  3.000
 62X  C18  N23  C24  130.06  3.000
 62X  C32  N23  C24  105.93  3.000
 62X  C26  N25  C24  104.50  3.000
 62X  N29  C27  N28  119.42  3.000
 62X  N28  C27  C26  122.70  3.000
 62X  N29  C27  C26  117.86  3.000
 62X  H31  N28  H30  116.51  3.000
 62X  H31  N28  C27  118.62  3.000
 62X  H30  N28  C27  119.20  3.000
 62X  C30  N29  C27  119.19  3.000
 62X  H32  C30  N31  116.17  3.000
 62X  H32  C30  N29  115.45  3.000
 62X  N31  C30  N29  128.39  3.000
 62X  C32  N31  C30  111.70  3.000
 62X  N31  C32  N23  128.09  3.000
 62X  N23  C32  C26  105.47  3.000
 62X  N31  C32  C26  126.44  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
 62X  CONST_01  C27  C26  N25  C24   180.00   0.0  0
 62X  CONST_02  C32  C26  N25  C24     0.00   0.0  0
 62X  CONST_03  N31  C32  N23  C24   180.00   0.0  0
 62X  CONST_04  C26  C32  N23  C24     0.00   0.0  0
 62X  CONST_05  C30  N29  C27  C26     0.00   0.0  0
 62X  CONST_06  C30  N31  C32  C26     0.00   0.0  0
 62X  CONST_07  N23  C24  N25  C26     0.00   0.0  0
 62X  CONST_08  C30  N31  C32  N23   180.00   0.0  0
 62X  CONST_09  C27  C26  C32  N23   180.00   0.0  0
 62X  CONST_10  N25  C26  C32  N23     0.00   0.0  0
 62X  CONST_11  N29  C27  C26  N25   180.00   0.0  0
 62X  CONST_12  N31  C32  C26  N25   180.00   0.0  0
 62X  CONST_13  C32  N23  C24  N25     0.00   0.0  0
 62X  CONST_14  N31  C30  N29  C27     0.00   0.0  0
 62X  CONST_15  N31  C32  C26  C27     0.00   0.0  0
 62X  CONST_16  C32  N31  C30  N29     0.00   0.0  0
 62X  CONST_17  C32  C26  C27  N29     0.00   0.0  0
 62X  CONST_18  C18  N23  C32  C26   180.00   0.0  0
 62X  CONST_19  N31  C32  N23  C18     0.00   0.0  0
 62X  CONST_20  N25  C24  N23  C18   180.00   0.0  0
 62X  CONST_21  N28  C27  C26  N25     0.00   0.0  0
 62X  CONST_22  C30  N29  C27  N28   180.00   0.0  0
 62X  CONST_23  C32  C26  C27  N28   180.00   0.0  0
 62X  CONST_24  H11  C24  N25  C26   180.00   0.0  0
 62X  CONST_25  H32  C30  N29  C27   180.00   0.0  0
 62X  CONST_27  H31  N28  C27  C26   180.00   0.0  0
 62X  Var_01    C16  C15  N7   C6     91.73  30.0  1
 62X  Var_02    N7   C6   C5   C4    173.03  30.0  1
 62X  Var_03    C8   N7   C6   C5     72.69  30.0  1
 62X  Var_04    C3   N2   C4   C5   -171.50  30.0  3
 62X  Var_05    C9   C8   N7   C6   -156.20  30.0  2
 62X  Var_06    N2   C4   C5   C6    171.30  30.0  3
 62X  Var_07    N7   C8   C9   C10   178.52  30.0  3
 62X  Var_08    H15  C3   N2   C4     58.38  30.0  3
 62X  Var_09    H12  C1   N2   C4     60.06  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
 62X  chir_01  C10  N11  C9   C12  negativ
 62X  chir_02  C21  O22  C19  C16  negativ
 62X  chir_03  C16  O17  C21  C15  negativ
 62X  chir_04  C18  O17  N23  C19  negativ
 62X  chir_05  C19  O20  C18  C21  negativ

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
 62X  plan-1  C24  0.020
 62X  plan-1  C26  0.020
 62X  plan-1  C18  0.020
 62X  plan-1  N23  0.020
 62X  plan-1  N25  0.020
 62X  plan-1  C27  0.020
 62X  plan-1  N28  0.020
 62X  plan-1  N29  0.020
 62X  plan-1  C30  0.020
 62X  plan-1  N31  0.020
 62X  plan-1  C32  0.020
 62X  plan-1  H11  0.020
 62X  plan-1  H32  0.020
 62X  plan-2  C27  0.020
 62X  plan-2  N28  0.020
 62X  plan-2  H30  0.020
 62X  plan-2  H31  0.020
 62X  plan-3  C10  0.020
 62X  plan-3  C12  0.020
 62X  plan-3  O13  0.020
 62X  plan-3  O14  0.020
 62X  plan-3  H24  0.020

