# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 00:31:25 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-[(2S)-4-(7H-purin-6-yl)morpholin-2-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CN(CCO1)c2ncnc3nc[nH]c23
#
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
 ZYV  ZYV  1-[(2S)-4-(7H-purin-6-yl)morpholin-2-yl]methanamine  ligand  31  17  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZYV
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
 ZYV  C5    C  CR56  0   0.156   1.6999  -0.4079   0.0519
 ZYV  N7    N  NR15  0  -0.658   1.8567  -1.7718  -0.0022
 ZYV  C8    C  CR15  0   0.115   3.1189  -2.0363   0.3848
 ZYV  N9    N  N     0  -0.457   3.8062  -0.9668   0.6883
 ZYV  C4    C  CR56  0   0.276   2.9372   0.0657   0.4994
 ZYV  N3    N  N     0  -0.441   3.2013   1.3550   0.7412
 ZYV  C2    C  CR16  0   0.029   2.1654   2.1367   0.5351
 ZYV  N1    N  N     0  -0.487   0.9541   1.7979   0.0992
 ZYV  C6    C  CR6   0   0.554   0.6674   0.5257  -0.1770
 ZYV  N6    N  NT    0  -0.500  -0.5789   0.2289  -0.6100
 ZYV  CAG   C  CH2   0  -0.330  -1.6143   1.2462  -0.6668
 ZYV  CAF   C  CH2   0  -0.331  -0.9087  -0.9113  -1.4449
 ZYV  CAE   C  CH2   0  -0.185  -2.2453  -1.4863  -1.0160
 ZYV  OAL   O  O2    0  -0.489  -3.2570  -0.5038  -1.0340
 ZYV  CAP   C  CH1   0   0.002  -2.9529   0.6432  -0.2548
 ZYV  CAD   C  CH2   0  -0.305  -3.0193   0.3640   1.2423
 ZYV  NAA   N  NH2   0  -0.801  -4.3267  -0.1528   1.6111
 ZYV  H7    H  HNR5  0   0.434   1.1706  -2.4772  -0.2141
 ZYV  H8    H  HCR5  0   0.296   3.4872  -3.0498   0.4300
 ZYV  H2    H  HCR6  0   0.250   2.3062   3.1944   0.7329
 ZYV  HAG1  H  HCH2  0   0.275  -1.3587   2.0698  -0.0054
 ZYV  HAG2  H  HCH2  0   0.252  -1.6835   1.6519  -1.6835
 ZYV  HAF1  H  HCH2  0   0.256  -0.9605  -0.5852  -2.4907
 ZYV  HAF2  H  HCH2  0   0.249  -0.1522  -1.6878  -1.4041
 ZYV  HAP   H  HCH1  0   0.246  -3.7347   1.3699  -0.4930
 ZYV  HAE1  H  HCH2  0   0.250  -2.5474  -2.2703  -1.7114
 ZYV  HAE2  H  HCH2  0   0.216  -2.1437  -1.9449  -0.0246
 ZYV  HAD1  H  HCH2  0   0.204  -2.1824  -0.2771   1.5528
 ZYV  HAD2  H  HCH2  0   0.234  -2.8693   1.3185   1.7528
 ZYV  HAA1  H  HNH2  0   0.342  -4.4381  -1.0920   1.2506
 ZYV  HAA2  H  HNH2  0   0.349  -4.3763  -0.2410   2.6176

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
 ZYV  C5   N7    aromatic  1.374  0.020  1.374
 ZYV  C5   C4    aromatic  1.398  0.020  1.398
 ZYV  C5   C6    aromatic  1.411  0.020  1.411
 ZYV  N7   C8    aromatic  1.346  0.020  1.346
 ZYV  C8   N9    aromatic  1.307  0.020  1.307
 ZYV  N9   C4    aromatic  1.363  0.020  1.363
 ZYV  C4   N3    aromatic  1.338  0.020  1.338
 ZYV  N3   C2    aromatic  1.314  0.020  1.314
 ZYV  C2   N1    aromatic  1.331  0.020  1.331
 ZYV  N1   C6    aromatic  1.333  0.020  1.333
 ZYV  C6   N6    single    1.352  0.020  1.352
 ZYV  N6   CAG   single    1.453  0.020  1.453
 ZYV  N6   CAF   single    1.451  0.020  1.451
 ZYV  CAG  CAP   single    1.525  0.020  1.525
 ZYV  CAF  CAE   single    1.517  0.020  1.517
 ZYV  CAE  OAL   single    1.410  0.020  1.410
 ZYV  OAL  CAP   single    1.420  0.020  1.420
 ZYV  CAP  CAD   single    1.524  0.020  1.524
 ZYV  CAD  NAA   single    1.453  0.020  1.453
 ZYV  N7   H7    single    0.860  0.020  1.020
 ZYV  C8   H8    single    0.930  0.020  1.080
 ZYV  C2   H2    single    0.930  0.020  1.080
 ZYV  CAG  HAG1  single    0.970  0.020  1.090
 ZYV  CAG  HAG2  single    0.970  0.020  1.090
 ZYV  CAF  HAF1  single    0.970  0.020  1.090
 ZYV  CAF  HAF2  single    0.970  0.020  1.090
 ZYV  CAP  HAP   single    0.970  0.020  1.090
 ZYV  CAE  HAE1  single    0.970  0.020  1.090
 ZYV  CAE  HAE2  single    0.970  0.020  1.090
 ZYV  CAD  HAD1  single    0.970  0.020  1.090
 ZYV  CAD  HAD2  single    0.970  0.020  1.090
 ZYV  NAA  HAA1  single    0.890  0.020  1.040
 ZYV  NAA  HAA2  single    0.890  0.020  1.040

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
 ZYV  C6    C5   C4    118.39  3.000
 ZYV  C6    C5   N7    137.23  3.000
 ZYV  C4    C5   N7    104.35  3.000
 ZYV  H7    N7   C8    124.18  3.000
 ZYV  H7    N7   C5    128.77  3.000
 ZYV  C8    N7   C5    106.89  3.000
 ZYV  H8    C8   N9    125.39  3.000
 ZYV  H8    C8   N7    121.09  3.000
 ZYV  N9    C8   N7    113.52  3.000
 ZYV  C4    N9   C8    104.62  3.000
 ZYV  N3    C4   N9    125.39  3.000
 ZYV  N3    C4   C5    123.97  3.000
 ZYV  N9    C4   C5    110.61  3.000
 ZYV  C2    N3   C4    112.91  3.000
 ZYV  H2    C2   N1    115.20  3.000
 ZYV  H2    C2   N3    116.67  3.000
 ZYV  N1    C2   N3    128.12  3.000
 ZYV  C6    N1   C2    120.43  3.000
 ZYV  N6    C6   N1    118.30  3.000
 ZYV  N6    C6   C5    125.54  3.000
 ZYV  N1    C6   C5    116.14  3.000
 ZYV  CAF   N6   CAG   111.45  3.000
 ZYV  CAF   N6   C6    124.48  3.000
 ZYV  CAG   N6   C6    121.04  3.000
 ZYV  HAG2  CAG  HAG1  107.38  3.000
 ZYV  HAG2  CAG  CAP   109.95  3.000
 ZYV  HAG1  CAG  CAP   109.98  3.000
 ZYV  HAG2  CAG  N6    109.89  3.000
 ZYV  HAG1  CAG  N6    109.83  3.000
 ZYV  CAP   CAG  N6    109.77  3.000
 ZYV  HAF2  CAF  HAF1  106.35  3.000
 ZYV  HAF2  CAF  CAE   109.42  3.000
 ZYV  HAF1  CAF  CAE   109.92  3.000
 ZYV  HAF2  CAF  N6    112.47  3.000
 ZYV  HAF1  CAF  N6    109.01  3.000
 ZYV  CAE   CAF  N6    109.60  3.000
 ZYV  HAE2  CAE  HAE1  107.54  3.000
 ZYV  HAE2  CAE  OAL   111.67  3.000
 ZYV  HAE1  CAE  OAL   107.09  3.000
 ZYV  HAE2  CAE  CAF   109.41  3.000
 ZYV  HAE1  CAE  CAF   109.65  3.000
 ZYV  OAL   CAE  CAF   111.37  3.000
 ZYV  CAP   OAL  CAE   113.71  3.000
 ZYV  HAP   CAP  CAD   107.73  3.000
 ZYV  HAP   CAP  OAL   105.32  3.000
 ZYV  CAD   CAP  OAL   112.45  3.000
 ZYV  HAP   CAP  CAG   107.81  3.000
 ZYV  CAD   CAP  CAG   112.08  3.000
 ZYV  OAL   CAP  CAG   111.05  3.000
 ZYV  HAD2  CAD  HAD1  105.84  3.000
 ZYV  HAD2  CAD  NAA   108.39  3.000
 ZYV  HAD1  CAD  NAA   113.94  3.000
 ZYV  HAD2  CAD  CAP   107.03  3.000
 ZYV  HAD1  CAD  CAP   110.56  3.000
 ZYV  NAA   CAD  CAP   110.70  3.000
 ZYV  HAA2  NAA  HAA1  105.56  3.000
 ZYV  HAA2  NAA  CAD   109.12  3.000
 ZYV  HAA1  NAA  CAD   109.79  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
 ZYV  CONST_01  N9    C8   N7   C5      0.00   0.0  0
 ZYV  CONST_02  C8    N9   C4   C5      0.00   0.0  0
 ZYV  CONST_03  C2    N3   C4   C5      0.00   0.0  0
 ZYV  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 ZYV  CONST_05  N9    C4   C5   N7      0.00   0.0  0
 ZYV  CONST_06  N3    C4   C5   N7    180.00   0.0  0
 ZYV  CONST_07  N1    C6   C5   N7    180.00   0.0  0
 ZYV  CONST_08  C4    N9   C8   N7      0.00   0.0  0
 ZYV  CONST_09  C4    C5   N7   C8      0.00   0.0  0
 ZYV  CONST_10  C6    C5   N7   C8    180.00   0.0  0
 ZYV  CONST_11  N3    C4   N9   C8    180.00   0.0  0
 ZYV  CONST_12  C6    C5   C4   N9    180.00   0.0  0
 ZYV  CONST_13  C2    N3   C4   N9    180.00   0.0  0
 ZYV  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 ZYV  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 ZYV  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 ZYV  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 ZYV  CONST_18  N6    C6   C5   N7      0.00   0.0  0
 ZYV  CONST_19  N6    C6   C5   C4    180.00   0.0  0
 ZYV  CONST_20  N6    C6   N1   C2    180.00   0.0  0
 ZYV  CONST_21  H8    C8   N7   C5    180.00   0.0  0
 ZYV  CONST_22  H7    N7   C8   N9    180.00   0.0  0
 ZYV  CONST_23  H2    C2   N3   C4    180.00   0.0  0
 ZYV  Var_01    CAG   N6   C6   C5    172.84  30.0  2
 ZYV  Var_02    CAP   CAG  N6   C6   -141.95  30.0  1
 ZYV  Var_03    CAE   CAF  N6   C6    142.34  30.0  1
 ZYV  Var_04    OAL   CAE  CAF  N6     55.32  30.0  1
 ZYV  Var_05    HAA1  NAA  CAD  CAP    70.43  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
 ZYV  chir_01  CAP  CAG  OAL  CAD  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
 ZYV  plan-1  C5  0.020
 ZYV  plan-1  N7  0.020
 ZYV  plan-1  C8  0.020
 ZYV  plan-1  N9  0.020
 ZYV  plan-1  C4  0.020
 ZYV  plan-1  N3  0.020
 ZYV  plan-1  C2  0.020
 ZYV  plan-1  N1  0.020
 ZYV  plan-1  C6  0.020
 ZYV  plan-1  N6  0.020
 ZYV  plan-1  H7  0.020
 ZYV  plan-1  H8  0.020
 ZYV  plan-1  H2  0.020

