# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:26:51 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  63  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  -4.9437   2.9244   0.6852
 62X  C5   C  CH2    0  -0.460  -3.8573   1.8581   0.6826
 62X  C6   C  CH2    0  -0.269  -3.3906   1.5510  -0.7344
 62X  C8   C  CH2    0  -0.262  -2.8532  -0.8123  -0.5915
 62X  C10  C  CH1    0  -0.215  -2.2085  -3.2099   0.0121
 62X  C15  C  CH2    0  -0.311  -1.5051   0.6773  -1.9478
 62X  C21  C  CH1    0  -0.043   0.6067   1.7285  -2.8867
 62X  C24  C  CR15   0   0.107   2.0525  -1.4434  -0.2072
 62X  C26  C  CR5    0  -0.012   3.7904  -1.2600   0.9816
 62X  C1   C  CH3    0  -0.527  -4.6272   3.6804   2.9531
 62X  N2   N  NT     0  -0.407  -5.5557   3.1372   1.9849
 62X  C3   C  CH3    0  -0.518  -6.7216   3.9861   1.8689
 62X  N7   N  NT     0  -0.417  -2.3520   0.5381  -0.7809
 62X  C9   C  CH2    0  -0.441  -1.7605  -1.7578  -0.1211
 62X  N11  N  NH2    0  -0.787  -3.2808  -3.3138   0.9899
 62X  C12  C  C      0   0.395  -0.9744  -4.1150   0.2656
 62X  O13  O  O      0  -0.606  -0.9594  -4.7993   1.3067
 62X  O14  O  OC    -1  -0.615  -0.0859  -4.0853  -0.6144
 62X  C16  C  CH1    0   0.016  -0.3284   1.6024  -1.6840
 62X  O17  O  O2     0  -0.485   0.4680   1.0884  -0.6057
 62X  C18  C  CH1    0   0.220   1.7933   0.9389  -1.0273
 62X  C19  C  CH1    0  -0.040   1.7007   0.7171  -2.5315
 62X  O20  O  OH1    0  -0.655   2.9387   0.9449  -3.1348
 62X  O22  O  OH1    0  -0.670   1.1260   3.0340  -2.9308
 62X  N23  N  NR5    0  -0.547   2.4245  -0.1256  -0.2948
 62X  N25  N  N      0  -0.450   2.8423  -2.1492   0.5454
 62X  C27  C  C      0   0.456   4.9162  -1.3928   1.8145
 62X  N28  N  NH2    0  -0.817   5.2638  -2.5509   2.3784
 62X  N29  N  N      0  -0.475   5.6544  -0.3018   2.0495
 62X  C30  C  C1     0   0.045   5.2964   0.8532   1.4949
 62X  N31  N  N      0  -0.458   4.2694   1.0997   0.7004
 62X  C32  C  CR5    0   0.487   3.5473   0.0051   0.4739
 62X  H1   H  HCH2   0   0.182  -4.5334   3.8655   0.2754
 62X  H2   H  HCH2   0   0.224  -2.9873   2.1776   1.2611
 62X  H3   H  HCH2   0   0.194  -4.2535   1.2736  -1.3647
 62X  H4   H  HCH2   0   0.227  -2.9903   2.4732  -1.1659
 62X  H5   H  HCH2   0   0.229  -3.6461  -0.7882   0.1564
 62X  H6   H  HCH2   0   0.182  -3.3170  -1.2092  -1.5124
 62X  H7   H  HCH1   0   0.209  -2.6222  -3.5120  -0.9595
 62X  H8   H  HCH2   0   0.239  -1.1274  -0.3008  -2.2554
 62X  H9   H  HCH2   0   0.225  -2.0586   1.0686  -2.8152
 62X  H10  H  HCH1   0   0.246   0.0984   1.4669  -3.8238
 62X  H11  H  HCR5   0   0.297   1.1812  -1.8380  -0.7080
 62X  H12  H  HCH3   0   0.188  -4.2144   4.6582   2.6542
 62X  H13  H  HCH3   0   0.233  -5.1293   3.8122   3.9126
 62X  H14  H  HCH3   0   0.236  -3.7893   3.0030   3.1142
 62X  H15  H  HCH3   0   0.230  -7.4481   3.5391   1.1883
 62X  H16  H  HCH3   0   0.230  -7.2020   4.0984   2.8422
 62X  H17  H  HCH3   0   0.188  -6.4902   4.9965   1.4947
 62X  H19  H  HCH2   0   0.225  -0.9279  -1.7349  -0.8227
 62X  H20  H  HCH2   0   0.208  -1.3636  -1.3987   0.8352
 62X  H21  H  HNH2   0   0.333  -3.5558  -4.2856   1.0694
 62X  H22  H  HNH2   0   0.322  -2.8993  -3.0882   1.9022
 62X  H25  H  HCH1   0   0.244  -0.7023   2.5928  -1.4001
 62X  H26  H  HCH1   0   0.250   2.3946   1.8328  -0.8217
 62X  H27  H  HCH1   0   0.246   1.3295  -0.2965  -2.7328
 62X  H28  H  HOH1   0   0.469   2.9451   0.5237  -4.0000
 62X  H29  H  HOH1   0   0.448   1.9206   3.0204  -3.4773
 62X  H30  H  HNH2   0   0.411   4.7600  -3.3965   2.1773
 62X  H31  H  HNH2   0   0.403   6.1085  -2.6170   2.9195
 62X  H32  H  H      0   0.251   5.9345   1.6991   1.7273
 62X  H33  H  HCH2   0   0.222  -5.7365   2.6134  -0.0027
 62X  H34  H  HCH2   0   0.222  -4.2480   0.9580   1.1651

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  1.330  0.020  1.330
 62X  N29  C27  aromatic  1.338  0.020  1.338
 62X  N28  C27  single    1.334  0.020  1.334
 62X  C30  N31  aromatic  1.322  0.020  1.322
 62X  C27  C26  aromatic  1.407  0.020  1.407
 62X  N31  C32  aromatic  1.331  0.020  1.331
 62X  C26  C32  aromatic  1.385  0.020  1.385
 62X  C26  N25  aromatic  1.371  0.020  1.371
 62X  C32  N23  aromatic  1.367  0.020  1.367
 62X  N25  C24  aromatic  1.299  0.020  1.299
 62X  N23  C24  aromatic  1.372  0.020  1.372
 62X  N23  C18  single    1.438  0.020  1.438
 62X  C18  C19  single    1.523  0.020  1.523
 62X  C18  O17  single    1.399  0.020  1.399
 62X  N11  C10  single    1.455  0.020  1.455
 62X  C19  O20  single    1.396  0.020  1.396
 62X  C19  C21  single    1.532  0.020  1.532
 62X  O17  C16  single    1.436  0.020  1.436
 62X  O13  C12  deloc     1.246  0.020  1.246
 62X  C10  C9   single    1.525  0.020  1.525
 62X  C10  C12  single    1.551  0.020  1.551
 62X  C21  C16  single    1.529  0.020  1.529
 62X  C21  O22  single    1.406  0.020  1.406
 62X  C16  C15  single    1.520  0.020  1.520
 62X  C9   C8   single    1.520  0.020  1.520
 62X  C12  O14  deloc     1.251  0.020  1.251
 62X  C8   N7   single    1.453  0.020  1.453
 62X  C15  N7   single    1.449  0.020  1.449
 62X  N7   C6   single    1.451  0.020  1.451
 62X  C6   C5   single    1.523  0.020  1.523
 62X  C5   C4   single    1.522  0.020  1.522
 62X  C3   N2   single    1.447  0.020  1.447
 62X  C4   N2   single    1.452  0.020  1.452
 62X  N2   C1   single    1.447  0.020  1.447
 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  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    0.860  0.020  1.020
 62X  N28  H31  single    0.860  0.020  1.020
 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   106.12  3.000
 62X  H33  C4   N2   107.39  3.000
 62X  H1   C4   N2   111.31  3.000
 62X  H33  C4   C5   108.47  3.000
 62X  H1   C4   C5   109.32  3.000
 62X  N2   C4   C5   113.88  3.000
 62X  H34  C5   H2   106.96  3.000
 62X  H34  C5   C6   110.73  3.000
 62X  H2   C5   C6   107.91  3.000
 62X  H34  C5   C4   108.72  3.000
 62X  H2   C5   C4   111.26  3.000
 62X  C6   C5   C4   111.19  3.000
 62X  H4   C6   H3   105.82  3.000
 62X  H4   C6   N7   108.28  3.000
 62X  H3   C6   N7   111.44  3.000
 62X  H4   C6   C5   108.01  3.000
 62X  H3   C6   C5   110.02  3.000
 62X  N7   C6   C5   112.94  3.000
 62X  H6   C8   H5   105.93  3.000
 62X  H6   C8   C9   109.65  3.000
 62X  H5   C8   C9   108.93  3.000
 62X  H6   C8   N7   111.72  3.000
 62X  H5   C8   N7   108.64  3.000
 62X  C9   C8   N7   111.75  3.000
 62X  H7   C10  C12  106.48  3.000
 62X  H7   C10  N11  107.29  3.000
 62X  C12  C10  N11  115.78  3.000
 62X  H7   C10  C9   107.17  3.000
 62X  C12  C10  C9   109.64  3.000
 62X  N11  C10  C9   110.06  3.000
 62X  H9   C15  H8   105.68  3.000
 62X  H9   C15  C16  108.04  3.000
 62X  H8   C15  C16  109.03  3.000
 62X  H9   C15  N7   112.02  3.000
 62X  H8   C15  N7   110.05  3.000
 62X  C16  C15  N7   111.79  3.000
 62X  H10  C21  O22  111.44  3.000
 62X  H10  C21  C19  111.80  3.000
 62X  O22  C21  C19  110.90  3.000
 62X  H10  C21  C16  111.63  3.000
 62X  O22  C21  C16  109.10  3.000
 62X  C19  C21  C16  101.54  3.000
 62X  H11  C24  N25  124.10  3.000
 62X  H11  C24  N23  122.70  3.000
 62X  N25  C24  N23  113.19  3.000
 62X  C32  C26  C27  116.35  3.000
 62X  C32  C26  N25  110.76  3.000
 62X  C27  C26  N25  132.88  3.000
 62X  H14  C1   H13  107.40  3.000
 62X  H14  C1   H12  107.68  3.000
 62X  H13  C1   H12  107.67  3.000
 62X  H14  C1   N2   111.04  3.000
 62X  H13  C1   N2   109.78  3.000
 62X  H12  C1   N2   113.06  3.000
 62X  C3   N2   C1   110.51  3.000
 62X  C1   N2   C4   112.54  3.000
 62X  C3   N2   C4   110.72  3.000
 62X  H17  C3   H16  107.52  3.000
 62X  H17  C3   H15  107.68  3.000
 62X  H16  C3   H15  107.78  3.000
 62X  H17  C3   N2   113.33  3.000
 62X  H16  C3   N2   110.09  3.000
 62X  H15  C3   N2   110.25  3.000
 62X  C15  N7   C8   113.33  3.000
 62X  C15  N7   C6   112.16  3.000
 62X  C8   N7   C6   113.43  3.000
 62X  H20  C9   H19  106.16  3.000
 62X  H20  C9   C10  110.01  3.000
 62X  H19  C9   C10  107.51  3.000
 62X  H20  C9   C8   109.07  3.000
 62X  H19  C9   C8   109.71  3.000
 62X  C10  C9   C8   114.09  3.000
 62X  H22  N11  H21  104.17  3.000
 62X  H22  N11  C10  108.14  3.000
 62X  H21  N11  C10  108.74  3.000
 62X  O14  C12  O13  126.33  3.000
 62X  O14  C12  C10  115.87  3.000
 62X  O13  C12  C10  117.81  3.000
 62X  H25  C16  O17  108.56  3.000
 62X  H25  C16  C21  109.75  3.000
 62X  O17  C16  C21  106.32  3.000
 62X  H25  C16  C15  109.33  3.000
 62X  C21  C16  C15  112.78  3.000
 62X  O17  C16  C15  110.00  3.000
 62X  C18  O17  C16  109.73  3.000
 62X  H26  C18  N23  105.49  3.000
 62X  H26  C18  C19  109.70  3.000
 62X  N23  C18  C19  114.96  3.000
 62X  H26  C18  O17  112.07  3.000
 62X  C19  C18  O17  104.81  3.000
 62X  N23  C18  O17  109.97  3.000
 62X  H27  C19  O20  111.79  3.000
 62X  H27  C19  C18  109.63  3.000
 62X  O20  C19  C18  110.44  3.000
 62X  H27  C19  C21  109.00  3.000
 62X  O20  C19  C21  115.18  3.000
 62X  C18  C19  C21  100.15  3.000
 62X  H28  O20  C19  108.85  3.000
 62X  H29  O22  C21  108.00  3.000
 62X  C32  N23  C18  125.19  3.000
 62X  C18  N23  C24  128.64  3.000
 62X  C32  N23  C24  106.18  3.000
 62X  C26  N25  C24  104.61  3.000
 62X  N29  C27  N28  119.33  3.000
 62X  N28  C27  C26  122.73  3.000
 62X  N29  C27  C26  117.94  3.000
 62X  H31  N28  H30  118.28  3.000
 62X  H31  N28  C27  120.23  3.000
 62X  H30  N28  C27  121.02  3.000
 62X  C30  N29  C27  119.10  3.000
 62X  H32  C30  N31  116.13  3.000
 62X  H32  C30  N29  115.43  3.000
 62X  N31  C30  N29  128.44  3.000
 62X  C32  N31  C30  111.75  3.000
 62X  N31  C32  N23  128.32  3.000
 62X  N23  C32  C26  105.25  3.000
 62X  N31  C32  C26  126.43  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_26  H30  N28  C27  C26     0.00   0.0  0
 62X  CONST_27  H31  N28  C27  C26   180.00   0.0  0
 62X  Var_01    C16  C15  N7   C6     88.91  30.0  1
 62X  Var_02    N7   C6   C5   C4    179.94  30.0  1
 62X  Var_03    C8   N7   C6   C5     76.69  30.0  1
 62X  Var_04    C3   N2   C4   C5   -170.18  30.0  3
 62X  Var_05    C9   C8   N7   C6   -158.23  30.0  2
 62X  Var_06    N2   C4   C5   C6    172.32  30.0  3
 62X  Var_07    N7   C8   C9   C10  -176.41  30.0  3
 62X  Var_08    H15  C3   N2   C4     58.38  30.0  3
 62X  Var_09    H12  C1   N2   C4     60.34  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

