# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:27:24 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-{[(6-amino-9H-purin-9-yl)acetyl](carboxymethyl)amino}ethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CC(=O)N(CC[NH3+])CC(O)=O)cnc12
#
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
 APN  APN  2-{[(6-amino-9H-purin-9-yl)acetyl](carboxymethyl)amino}ethanaminium  peptide  37  21  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_APN
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
 APN  C8'   C  CH2   0  -0.460  -0.2375   0.3324   1.1908
 APN  C7'   C  C     0   0.573  -1.0726  -0.5218   0.2403
 APN  O7'   O  O     0  -0.462  -0.5599  -1.4185  -0.4003
 APN  C5'   C  CH2   0  -0.483  -3.0175   0.8459   0.8769
 APN  C'    C  C     0   0.554  -2.9416   2.1544   0.1137
 APN  O1'   O  O     0  -0.425  -2.3489   2.2956  -0.9226
 APN  OXT   O  OH1   0  -0.583  -3.6022   3.1095   0.7448
 APN  N4'   N  NT    0  -0.453  -2.3922  -0.2338   0.1610
 APN  C3'   C  CH2   0  -0.342  -3.2019  -0.9538  -0.8018
 APN  C2'   C  CH2   0  -0.304  -3.7000  -2.2599  -0.2011
 APN  N1'   N  NT3   1  -0.778  -4.5416  -2.9927  -1.1781
 APN  N9    N  NR5   0  -0.491   1.1366  -0.0646   1.1353
 APN  C8    C  CR15  0   0.111   1.7697  -0.9638   1.9454
 APN  N7    N  N     0  -0.450   2.9945  -1.2113   1.5872
 APN  C5    C  CR56  0  -0.005   3.1775  -0.4463   0.4633
 APN  C6    C  CR6   0   0.454   4.2691  -0.2605  -0.4044
 APN  N6    N  NH2   0  -0.817   5.4359  -0.8887  -0.2444
 APN  N1    N  N     0  -0.474   4.1114   0.5730  -1.4390
 APN  C2    C  CR16  0   0.040   2.9430   1.1878  -1.6061
 APN  N3    N  N     0  -0.449   1.8533   1.0974  -0.8635
 APN  C4    C  CR56  0   0.486   2.0278   0.2655   0.1597
 APN  H8'1  H  HCH2  0   0.311  -0.3115   1.3885   0.9286
 APN  H8'2  H  HCH2  0   0.325  -0.5895   0.2292   2.2186
 APN  H5'1  H  HCH2  0   0.325  -2.5834   0.9836   1.8688
 APN  H5'2  H  HCH2  0   0.332  -4.0648   0.5983   1.0620
 APN  HXT   H  HOH1  0   0.490  -3.5379   3.9458   0.2586
 APN  H3'1  H  HCH2  0   0.289  -4.0459  -0.3239  -1.0871
 APN  H3'2  H  HCH2  0   0.289  -2.6263  -1.1451  -1.7074
 APN  H2'1  H  HCH2  0   0.305  -2.8746  -2.9160   0.0625
 APN  H2'2  H  HCH2  0   0.302  -4.3123  -2.0895   0.6813
 APN  H1'1  H  HNT3  0   0.474  -4.0371  -3.2040  -2.0391
 APN  H1'2  H  HNT3  0   0.484  -4.8570  -3.8836  -0.7962
 APN  H1'3  H  HNT3  0   0.474  -5.3784  -2.4705  -1.4370
 APN  H8    H  HCR5  0   0.296   1.2677  -1.3927   2.8002
 APN  HN61  H  HNH2  0   0.410   5.6118  -1.4512   0.5695
 APN  HN62  H  HNH2  0   0.403   6.2135  -0.6641  -0.8410
 APN  H2    H  HCR6  0   0.251   2.8836   1.8476  -2.4650

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
 APN  C8'  C7'   single    1.527  0.020  1.527
 APN  C8'  N9    single    1.431  0.020  1.431
 APN  C8'  H8'1  single    0.970  0.020  1.090
 APN  C8'  H8'2  single    0.970  0.020  1.090
 APN  C7'  O7'   double    1.215  0.020  1.215
 APN  C7'  N4'   single    1.353  0.020  1.353
 APN  C5'  C'    single    1.517  0.020  1.517
 APN  C5'  N4'   single    1.439  0.020  1.439
 APN  C5'  H5'1  single    0.970  0.020  1.090
 APN  C5'  H5'2  single    0.970  0.020  1.090
 APN  C'   O1'   double    1.202  0.020  1.202
 APN  C'   OXT   single    1.322  0.020  1.322
 APN  OXT  HXT   single    0.850  0.020  0.980
 APN  N4'  C3'   single    1.449  0.020  1.449
 APN  C3'  C2'   single    1.521  0.020  1.521
 APN  C3'  H3'1  single    0.970  0.020  1.090
 APN  C3'  H3'2  single    0.970  0.020  1.090
 APN  C2'  N1'   single    1.483  0.020  1.483
 APN  C2'  H2'1  single    0.970  0.020  1.090
 APN  C2'  H2'2  single    0.970  0.020  1.090
 APN  N1'  H1'1  single    0.890  0.020  1.040
 APN  N1'  H1'2  single    0.890  0.020  1.040
 APN  N1'  H1'3  single    0.890  0.020  1.040
 APN  N9   C8    aromatic  1.366  0.020  1.366
 APN  N9   C4    aromatic  1.362  0.020  1.362
 APN  C8   N7    aromatic  1.300  0.020  1.300
 APN  C8   H8    single    0.930  0.020  1.080
 APN  N7   C5    aromatic  1.372  0.020  1.372
 APN  C5   C6    aromatic  1.407  0.020  1.407
 APN  C5   C4    aromatic  1.386  0.020  1.386
 APN  C6   N6    single    1.335  0.020  1.335
 APN  C6   N1    aromatic  1.338  0.020  1.338
 APN  N6   HN61  single    0.860  0.020  1.020
 APN  N6   HN62  single    0.860  0.020  1.020
 APN  N1   C2    aromatic  1.331  0.020  1.331
 APN  C2   N3    aromatic  1.322  0.020  1.322
 APN  C2   H2    single    0.930  0.020  1.080
 APN  N3   C4    aromatic  1.330  0.020  1.330

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
 APN  H8'2  C8'  H8'1  107.22  3.000
 APN  H8'2  C8'  N9    108.66  3.000
 APN  H8'1  C8'  N9    108.93  3.000
 APN  H8'2  C8'  C7'   110.92  3.000
 APN  H8'1  C8'  C7'   110.79  3.000
 APN  N9    C8'  C7'   110.23  3.000
 APN  N4'   C7'  O7'   122.52  3.000
 APN  N4'   C7'  C8'   116.80  3.000
 APN  O7'   C7'  C8'   120.68  3.000
 APN  H5'2  C5'  H5'1  104.84  3.000
 APN  H5'2  C5'  N4'   109.33  3.000
 APN  H5'1  C5'  N4'   111.96  3.000
 APN  H5'2  C5'  C'    109.20  3.000
 APN  H5'1  C5'  C'    109.18  3.000
 APN  N4'   C5'  C'    112.04  3.000
 APN  OXT   C'   O1'   124.97  3.000
 APN  OXT   C'   C5'   110.99  3.000
 APN  O1'   C'   C5'   124.04  3.000
 APN  HXT   OXT  C'    110.54  3.000
 APN  C3'   N4'  C5'   117.42  3.000
 APN  C3'   N4'  C7'   118.55  3.000
 APN  C5'   N4'  C7'   123.68  3.000
 APN  H3'2  C3'  H3'1  107.00  3.000
 APN  H3'2  C3'  C2'   110.50  3.000
 APN  H3'1  C3'  C2'   110.22  3.000
 APN  H3'2  C3'  N4'   110.13  3.000
 APN  H3'1  C3'  N4'   108.60  3.000
 APN  C2'   C3'  N4'   110.31  3.000
 APN  H2'2  C2'  H2'1  108.99  3.000
 APN  H2'2  C2'  N1'   107.00  3.000
 APN  H2'1  C2'  N1'   107.00  3.000
 APN  H2'2  C2'  C3'   111.73  3.000
 APN  H2'1  C2'  C3'   111.43  3.000
 APN  N1'   C2'  C3'   110.48  3.000
 APN  H1'3  N1'  H1'2  106.78  3.000
 APN  H1'3  N1'  H1'1  107.32  3.000
 APN  H1'2  N1'  H1'1  106.75  3.000
 APN  H1'3  N1'  C2'   112.32  3.000
 APN  H1'2  N1'  C2'   111.14  3.000
 APN  H1'1  N1'  C2'   112.19  3.000
 APN  C4    N9   C8    106.33  3.000
 APN  C4    N9   C8'   126.06  3.000
 APN  C8    N9   C8'   127.20  3.000
 APN  H8    C8   N7    125.48  3.000
 APN  H8    C8   N9    121.03  3.000
 APN  N7    C8   N9    113.49  3.000
 APN  C5    N7   C8    104.20  3.000
 APN  C4    C5   C6    116.15  3.000
 APN  C4    C5   N7    110.81  3.000
 APN  C6    C5   N7    133.04  3.000
 APN  N1    C6   N6    119.27  3.000
 APN  N1    C6   C5    117.89  3.000
 APN  N6    C6   C5    122.83  3.000
 APN  HN62  N6   HN61  118.05  3.000
 APN  HN62  N6   C6    119.98  3.000
 APN  HN61  N6   C6    120.90  3.000
 APN  C2    N1   C6    119.24  3.000
 APN  H2    C2   N3    116.19  3.000
 APN  H2    C2   N1    115.38  3.000
 APN  N3    C2   N1    128.44  3.000
 APN  C4    N3   C2    111.52  3.000
 APN  N3    C4   C5    126.77  3.000
 APN  N3    C4   N9    128.08  3.000
 APN  C5    C4   N9    105.15  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
 APN  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 APN  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 APN  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 APN  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 APN  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 APN  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 APN  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 APN  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 APN  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 APN  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 APN  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 APN  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 APN  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 APN  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 APN  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 APN  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 APN  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 APN  CONST_18  N7    C8   N9   C8'  180.00   0.0  0
 APN  CONST_19  C5    C4   N9   C8'  180.00   0.0  0
 APN  CONST_20  N3    C4   N9   C8'    0.00   0.0  0
 APN  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 APN  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 APN  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 APN  CONST_24  H8    C8   N7   C5   180.00   0.0  0
 APN  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 APN  CONST_26  HN61  N6   C6   C5     0.00   0.0  0
 APN  CONST_27  HN62  N6   C6   C5   180.00   0.0  0
 APN  CONST_28  C5'   N4'  C7'  C8'    0.00   0.0  0
 APN  CONST_29  C3'   N4'  C7'  C8'  180.00   0.0  0
 APN  CONST_30  C5'   N4'  C7'  O7'  180.00   0.0  0
 APN  CONST_31  C3'   N4'  C7'  O7'    0.00   0.0  0
 APN  CONST_32  HXT   OXT  C'   C5'  180.00   0.0  0
 APN  Var_01    C8    N9   C8'  C7'  -93.49  30.0  2
 APN  Var_02    N9    C8'  C7'  O7'    2.13  30.0  1
 APN  Var_03    C'    C5'  N4'  C7'   86.74  30.0  2
 APN  Var_04    C2'   C3'  N4'  C7'   86.35  30.0  3
 APN  Var_05    N4'   C5'  C'   O1'   -4.85  30.0  1
 APN  Var_06    N1'   C2'  C3'  N4'  179.37  30.0  3
 APN  Var_07    H1'1  N1'  C2'  C3'   58.79  30.0  3

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
 APN  plan-1  C8'   0.020
 APN  plan-1  N9    0.020
 APN  plan-1  C8    0.020
 APN  plan-1  N7    0.020
 APN  plan-1  C5    0.020
 APN  plan-1  C6    0.020
 APN  plan-1  N6    0.020
 APN  plan-1  N1    0.020
 APN  plan-1  C2    0.020
 APN  plan-1  N3    0.020
 APN  plan-1  C4    0.020
 APN  plan-1  H8    0.020
 APN  plan-1  H2    0.020
 APN  plan-2  C8'   0.020
 APN  plan-2  C7'   0.020
 APN  plan-2  O7'   0.020
 APN  plan-2  C5'   0.020
 APN  plan-2  N4'   0.020
 APN  plan-2  C3'   0.020
 APN  plan-3  C6    0.020
 APN  plan-3  N6    0.020
 APN  plan-3  HN61  0.020
 APN  plan-3  HN62  0.020
 APN  plan-4  C5'   0.020
 APN  plan-4  C'    0.020
 APN  plan-4  O1'   0.020
 APN  plan-4  OXT   0.020
 APN  plan-4  HXT   0.020

