# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:05:00 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: N-[(2S)-2-aminopropyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CN(CC(O)=O)C(=O)Cn1cnc2c(N)ncnc12
#
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
 40A  40A  N-[(2S)-2-aminopropyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine  peptide  39  22  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_40A
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
 40A  C'    C  C     0   0.552  -3.4141  -1.8385   0.4162
 40A  N1    N  N     0  -0.474   4.6032   0.8278   0.9582
 40A  C2    C  CR16  0   0.041   3.4923   1.0240   1.6643
 40A  N3    N  N     0  -0.453   2.3007   0.4803   1.4886
 40A  C4    C  CR56  0   0.483   2.2934  -0.3605   0.4573
 40A  C5    C  CR56  0  -0.005   3.3642  -0.6683  -0.3676
 40A  C6    C  CR6   0   0.452   4.5783  -0.0210  -0.0756
 40A  N6    N  NH2   0  -0.817   5.6968  -0.2305  -0.7743
 40A  N7    N  N     0  -0.452   2.9929  -1.5725  -1.3299
 40A  C8    C  CR15  0   0.113   1.7356  -1.7978  -1.0863
 40A  N9    N  NR5   0  -0.487   1.2576  -1.1130  -0.0066
 40A  N1'   N  NH2   0  -0.772  -1.8961   3.0734   0.3409
 40A  O1'   O  O     0  -0.430  -3.2177  -2.2526  -0.6956
 40A  C2'   C  CH1   0  -0.104  -3.1775   2.4839  -0.0100
 40A  C2M   C  CH3   0  -0.668  -4.0920   3.3944  -0.8262
 40A  C3'   C  CH2   0  -0.308  -2.9578   1.1802  -0.7755
 40A  N4'   N  NT    0  -0.438  -2.1538   0.2153  -0.0456
 40A  C5'   C  CH2   0  -0.478  -2.8363  -0.5469   0.9622
 40A  C7'   C  C     0   0.565  -0.8623   0.0190  -0.3743
 40A  O7'   O  O     0  -0.475  -0.2924   0.6205  -1.2660
 40A  C8'   C  CH2   0  -0.464  -0.1047  -1.0401   0.4308
 40A  H2    H  HCR6  0   0.251   3.5821   1.7228   2.4890
 40A  H8    H  HCR5  0   0.293   1.0997  -2.4654  -1.6489
 40A  H22'  H  HCH1  0   0.225  -3.6894   2.2486   0.9302
 40A  H13'  H  HCH2  0   0.257  -3.9247   0.7244  -1.0031
 40A  H23'  H  HCH2  0   0.257  -2.4775   1.3907  -1.7306
 40A  H15'  H  HCH2  0   0.324  -3.6464   0.0543   1.3798
 40A  H25'  H  HCH2  0   0.317  -2.1954  -0.7786   1.8150
 40A  HN6   H  HNH2  0   0.410   5.6851  -0.7847  -1.6125
 40A  HN6A  H  HNH2  0   0.402   6.5180   0.3170  -0.5819
 40A  H18'  H  HCH2  0   0.314  -0.5640  -2.0229   0.3160
 40A  H28'  H  HCH2  0   0.312  -0.1102  -0.8032   1.4959
 40A  H2M   H  HCH3  0   0.234  -4.2908   4.3222  -0.2882
 40A  H2MA  H  HCH3  0   0.220  -3.6274   3.6541  -1.7804
 40A  H2MB  H  HCH3  0   0.223  -5.0523   2.9205  -1.0383
 40A  OXT   O  OH1   0  -0.585  -4.1490  -2.4517   1.3293
 40A  HNXT  H  HNH2  0   0.346  -2.0562   3.9363   0.8469
 40A  HXT   H  HOH1  0   0.488  -4.4965  -3.2870   0.9813
 40A  HN1'  H  HNH2  0   0.334  -1.4022   3.3383  -0.5042

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
 40A  C'    O1'   double    1.203  0.020  1.203
 40A  C'    C5'   single    1.517  0.020  1.517
 40A  C'    OXT   single    1.323  0.020  1.323
 40A  N1    C2    aromatic  1.331  0.020  1.331
 40A  N1    C6    aromatic  1.338  0.020  1.338
 40A  C2    N3    aromatic  1.322  0.020  1.322
 40A  N3    C4    aromatic  1.331  0.020  1.331
 40A  C4    N9    aromatic  1.362  0.020  1.362
 40A  C5    C4    aromatic  1.386  0.020  1.386
 40A  C5    N7    aromatic  1.372  0.020  1.372
 40A  C6    C5    aromatic  1.407  0.020  1.407
 40A  N6    C6    single    1.335  0.020  1.335
 40A  N6    HN6A  single    0.860  0.020  1.020
 40A  N7    C8    aromatic  1.300  0.020  1.300
 40A  C8    H8    single    0.930  0.020  1.080
 40A  N9    C8    aromatic  1.365  0.020  1.365
 40A  N9    C8'   single    1.433  0.020  1.433
 40A  N1'   HNXT  single    0.890  0.020  1.040
 40A  C2'   N1'   single    1.453  0.020  1.453
 40A  C2'   H22'  single    0.970  0.020  1.090
 40A  C2'   C2M   single    1.527  0.020  1.527
 40A  C2M   H2MA  single    0.970  0.020  1.090
 40A  C3'   C2'   single    1.528  0.020  1.528
 40A  N4'   C3'   single    1.453  0.020  1.453
 40A  N4'   C5'   single    1.436  0.020  1.436
 40A  C5'   H15'  single    0.970  0.020  1.090
 40A  C5'   H25'  single    0.970  0.020  1.090
 40A  C7'   N4'   single    1.347  0.020  1.347
 40A  O7'   C7'   double    1.217  0.020  1.217
 40A  C8'   C7'   single    1.531  0.020  1.531
 40A  C8'   H18'  single    0.970  0.020  1.090
 40A  H2    C2    single    0.930  0.020  1.080
 40A  HN1'  N1'   single    0.890  0.020  1.040
 40A  H13'  C3'   single    0.970  0.020  1.090
 40A  H23'  C3'   single    0.970  0.020  1.090
 40A  HN6   N6    single    0.860  0.020  1.020
 40A  H28'  C8'   single    0.970  0.020  1.090
 40A  H2M   C2M   single    0.970  0.020  1.090
 40A  H2MB  C2M   single    0.970  0.020  1.090
 40A  OXT   HXT   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
 40A  OXT   C'   C5'   110.97  3.000
 40A  OXT   C'   O1'   124.70  3.000
 40A  C5'   C'   O1'   124.32  3.000
 40A  C6    N1   C2    119.21  3.000
 40A  H2    C2   N3    116.15  3.000
 40A  H2    C2   N1    115.42  3.000
 40A  N3    C2   N1    128.43  3.000
 40A  C4    N3   C2    111.59  3.000
 40A  N9    C4   C5    105.19  3.000
 40A  C5    C4   N3    126.68  3.000
 40A  N9    C4   N3    128.13  3.000
 40A  N7    C5   C6    133.05  3.000
 40A  C6    C5   C4    116.17  3.000
 40A  N7    C5   C4    110.78  3.000
 40A  N6    C6   C5    122.83  3.000
 40A  N6    C6   N1    119.23  3.000
 40A  C5    C6   N1    117.93  3.000
 40A  HN6A  N6   HN6   117.99  3.000
 40A  HN6   N6   C6    120.88  3.000
 40A  HN6A  N6   C6    119.90  3.000
 40A  C8    N7   C5    104.15  3.000
 40A  H8    C8   N9    121.06  3.000
 40A  N9    C8   N7    113.57  3.000
 40A  H8    C8   N7    125.37  3.000
 40A  C8'   N9   C8    126.87  3.000
 40A  C8'   N9   C4    126.23  3.000
 40A  C8    N9   C4    106.28  3.000
 40A  HNXT  N1'  HN1'  105.71  3.000
 40A  HN1'  N1'  C2'   109.52  3.000
 40A  HNXT  N1'  C2'   109.07  3.000
 40A  H22'  C2'  C3'   108.29  3.000
 40A  C3'   C2'  C2M   109.10  3.000
 40A  H22'  C2'  C2M   107.86  3.000
 40A  C3'   C2'  N1'   109.90  3.000
 40A  C2M   C2'  N1'   114.53  3.000
 40A  H22'  C2'  N1'   106.96  3.000
 40A  H2MB  C2M  H2MA  107.92  3.000
 40A  H2MB  C2M  H2M   107.74  3.000
 40A  H2MA  C2M  H2M   107.82  3.000
 40A  H2MB  C2M  C2'   111.83  3.000
 40A  H2M   C2M  C2'   110.65  3.000
 40A  H2MA  C2M  C2'   110.72  3.000
 40A  H23'  C3'  H13'  106.74  3.000
 40A  H23'  C3'  N4'   108.96  3.000
 40A  H13'  C3'  N4'   108.50  3.000
 40A  H23'  C3'  C2'   109.74  3.000
 40A  H13'  C3'  C2'   109.45  3.000
 40A  N4'   C3'  C2'   113.24  3.000
 40A  C7'   N4'  C5'   123.33  3.000
 40A  C7'   N4'  C3'   120.32  3.000
 40A  C5'   N4'  C3'   116.24  3.000
 40A  H25'  C5'  H15'  104.69  3.000
 40A  H25'  C5'  N4'   112.45  3.000
 40A  H15'  C5'  N4'   109.20  3.000
 40A  H25'  C5'  C'    108.91  3.000
 40A  H15'  C5'  C'    108.90  3.000
 40A  N4'   C5'  C'    112.36  3.000
 40A  C8'   C7'  O7'   119.70  3.000
 40A  C8'   C7'  N4'   116.55  3.000
 40A  O7'   C7'  N4'   123.75  3.000
 40A  H28'  C8'  H18'  107.23  3.000
 40A  H28'  C8'  C7'   111.14  3.000
 40A  H18'  C8'  C7'   111.07  3.000
 40A  H28'  C8'  N9    108.30  3.000
 40A  H18'  C8'  N9    108.81  3.000
 40A  C7'   C8'  N9    110.20  3.000
 40A  HXT   OXT  C'    110.54  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
 40A  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 40A  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 40A  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 40A  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 40A  CONST_05  N9    C4   N3   C2    180.00   0.0  0
 40A  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 40A  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 40A  CONST_08  C8    N9   C4   N3    180.00   0.0  0
 40A  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 40A  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 40A  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 40A  CONST_12  C8    N7   C5   C4      0.00   0.0  0
 40A  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 40A  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 40A  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 40A  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 40A  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 40A  CONST_18  N6    C6   N1   C2    180.00   0.0  0
 40A  CONST_19  C8'   N9   C4   N3      0.00   0.0  0
 40A  CONST_20  N6    C6   C5   C4    180.00   0.0  0
 40A  CONST_21  C8'   N9   C4   C5    180.00   0.0  0
 40A  CONST_22  N7    C5   C6   N6      0.00   0.0  0
 40A  CONST_23  C8'   N9   C8   N7    180.00   0.0  0
 40A  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 40A  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 40A  CONST_26  HN6A  N6   C6   N1      0.00   0.0  0
 40A  CONST_27  HN6   N6   C6   N1    180.00   0.0  0
 40A  CONST_28  O7'   C7'  N4'  C3'     0.00   0.0  0
 40A  CONST_29  C8'   C7'  N4'  C3'   180.00   0.0  0
 40A  CONST_30  O7'   C7'  N4'  C5'   180.00   0.0  0
 40A  CONST_31  C8'   C7'  N4'  C5'     0.00   0.0  0
 40A  CONST_32  HXT   OXT  C'   O1'     0.00   0.0  0
 40A  Var_01    C7'   C8'  N9   C4     87.67  30.0  2
 40A  Var_02    N4'   C7'  C8'  N9   -178.56  30.0  3
 40A  Var_03    C3'   N4'  C5'  C'     90.40  30.0  2
 40A  Var_04    N4'   C5'  C'   O1'     6.96  30.0  3
 40A  Var_05    C5'   N4'  C3'  C2'    80.11  30.0  2

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
 40A  chir_01  C2'  N1'  C2M  C3'  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
 40A  plan-1  N1    0.020
 40A  plan-1  C2    0.020
 40A  plan-1  N3    0.020
 40A  plan-1  C4    0.020
 40A  plan-1  C5    0.020
 40A  plan-1  C6    0.020
 40A  plan-1  N6    0.020
 40A  plan-1  N7    0.020
 40A  plan-1  C8    0.020
 40A  plan-1  N9    0.020
 40A  plan-1  C8'   0.020
 40A  plan-1  H2    0.020
 40A  plan-1  H8    0.020
 40A  plan-2  C3'   0.020
 40A  plan-2  N4'   0.020
 40A  plan-2  C5'   0.020
 40A  plan-2  C7'   0.020
 40A  plan-2  O7'   0.020
 40A  plan-2  C8'   0.020
 40A  plan-3  C6    0.020
 40A  plan-3  N6    0.020
 40A  plan-3  HN6   0.020
 40A  plan-3  HN6A  0.020
 40A  plan-4  C'    0.020
 40A  plan-4  O1'   0.020
 40A  plan-4  C5'   0.020
 40A  plan-4  OXT   0.020
 40A  plan-4  HXT   0.020

