# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:42:05 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-(morpholin-4-yl)[4,5'-bipyrimidin]-2'-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(cn1)c2ccnc(n2)N3CCOCC3
#
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
 VYP  VYP  2-(morpholin-4-yl)[4,5'-bipyrimidin]-2'-amine  ligand  33  19  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VYP
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
 VYP  C9   C  CR16  0  -0.425  -18.7095  10.2235  27.3256
 VYP  C10  C  CR16  0  -0.015  -19.2434  11.1683  28.1817
 VYP  C4   C  CR16  0  -0.041  -17.2692   8.4452  25.3903
 VYP  C6   C  CR16  0  -0.009  -15.2798   9.5954  25.8630
 VYP  C5   C  CR6   0  -0.126  -16.6537   9.4839  26.0872
 VYP  C8   C  CR6   0   0.318  -17.3689  10.4010  26.9796
 VYP  C12  C  CR6   0   0.642  -17.2848  12.2880  28.2690
 VYP  C2   C  CR6   0   0.566  -15.3055   7.8275  24.4523
 VYP  C15  C  CH2   0  -0.315  -17.0764  14.2706  29.7076
 VYP  C19  C  CH2   0  -0.321  -15.1456  13.4846  28.4614
 VYP  C16  C  CH2   0  -0.186  -16.6698  15.6867  29.3412
 VYP  C18  C  CH2   0  -0.185  -14.8238  14.9354  28.1499
 VYP  N11  N  N     0  -0.479  -18.5620  12.1939  28.6626
 VYP  N3   N  N     0  -0.450  -16.6248   7.6264  24.5859
 VYP  N7   N  N     0  -0.447  -14.6053   8.7927  25.0683
 VYP  N13  N  N     0  -0.520  -16.6720  11.4249  27.4561
 VYP  N14  N  NT    0  -0.515  -16.5657  13.3443  28.7164
 VYP  N1   N  NH2   0  -0.811  -14.6356   7.0015  23.6450
 VYP  O17  O  O2    0  -0.484  -15.2753  15.8031  29.1656
 VYP  H24  H  HCR6  0   0.265  -19.3126   9.4025  26.9697
 VYP  H25  H  HCR6  0   0.269  -20.2782  11.0891  28.4983
 VYP  H23  H  HCR6  0   0.277  -14.7131  10.3749  26.3594
 VYP  H26  H  HCH2  0   0.271  -18.1597  14.2036  29.7548
 VYP  H27  H  HCH2  0   0.234  -16.6817  14.0119  30.6980
 VYP  H33  H  HCH2  0   0.276  -14.8553  12.8595  27.6211
 VYP  H32  H  HCH2  0   0.234  -14.5737  13.1528  29.3371
 VYP  H28  H  HCH2  0   0.242  -16.9584  16.3708  30.1406
 VYP  H29  H  HCH2  0   0.206  -17.1988  15.9903  28.4268
 VYP  H31  H  HCH2  0   0.242  -13.7439  15.0629  28.0640
 VYP  H30  H  HCH2  0   0.206  -15.2767  15.2064  27.1858
 VYP  H21  H  HNH2  0   0.405  -13.6501   7.1237  23.4941
 VYP  H20  H  HNH2  0   0.406  -15.1153   6.2714  23.1491
 VYP  H22  H  HCR6  0   0.268  -18.3361   8.2691  25.4783

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
 VYP  N1   C2   single    1.335  0.020  1.335
 VYP  C2   N7   aromatic  1.342  0.020  1.342
 VYP  C2   N3   aromatic  1.341  0.020  1.341
 VYP  N7   C6   aromatic  1.316  0.020  1.316
 VYP  N3   C4   aromatic  1.316  0.020  1.316
 VYP  C6   C5   aromatic  1.397  0.020  1.397
 VYP  C4   C5   aromatic  1.394  0.020  1.394
 VYP  C5   C8   single    1.466  0.020  1.466
 VYP  C8   C9   aromatic  1.396  0.020  1.396
 VYP  C8   N13  aromatic  1.327  0.020  1.327
 VYP  C9   C10  aromatic  1.382  0.020  1.382
 VYP  N13  C12  aromatic  1.335  0.020  1.335
 VYP  C10  N11  aromatic  1.322  0.020  1.322
 VYP  C12  N14  single    1.354  0.020  1.354
 VYP  C12  N11  aromatic  1.340  0.020  1.340
 VYP  C18  C19  single    1.518  0.020  1.518
 VYP  C18  O17  single    1.410  0.020  1.410
 VYP  C19  N14  single    1.450  0.020  1.450
 VYP  N14  C15  single    1.450  0.020  1.450
 VYP  O17  C16  single    1.410  0.020  1.410
 VYP  C16  C15  single    1.518  0.020  1.518
 VYP  C9   H24  single    0.930  0.020  1.080
 VYP  C10  H25  single    0.930  0.020  1.080
 VYP  C4   H22  single    0.930  0.020  1.080
 VYP  C6   H23  single    0.930  0.020  1.080
 VYP  C15  H26  single    0.970  0.020  1.090
 VYP  C15  H27  single    0.970  0.020  1.090
 VYP  C19  H33  single    0.970  0.020  1.090
 VYP  C19  H32  single    0.970  0.020  1.090
 VYP  C16  H28  single    0.970  0.020  1.090
 VYP  C16  H29  single    0.970  0.020  1.090
 VYP  C18  H31  single    0.970  0.020  1.090
 VYP  C18  H30  single    0.970  0.020  1.090
 VYP  N1   H21  single    0.860  0.020  1.020
 VYP  N1   H20  single    0.860  0.020  1.020

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
 VYP  H24  C9   C8   123.49  3.000
 VYP  H24  C9   C10  120.56  3.000
 VYP  C8   C9   C10  115.95  3.000
 VYP  H25  C10  N11  116.24  3.000
 VYP  H25  C10  C9   119.94  3.000
 VYP  N11  C10  C9   123.82  3.000
 VYP  H22  C4   N3   115.47  3.000
 VYP  H22  C4   C5   120.97  3.000
 VYP  N3   C4   C5   123.56  3.000
 VYP  H23  C6   N7   116.56  3.000
 VYP  H23  C6   C5   119.88  3.000
 VYP  N7   C6   C5   123.55  3.000
 VYP  C8   C5   C6   121.85  3.000
 VYP  C8   C5   C4   123.71  3.000
 VYP  C6   C5   C4   114.43  3.000
 VYP  N13  C8   C5   116.43  3.000
 VYP  N13  C8   C9   120.89  3.000
 VYP  C5   C8   C9   122.68  3.000
 VYP  N14  C12  N13  117.51  3.000
 VYP  N14  C12  N11  117.65  3.000
 VYP  N13  C12  N11  124.84  3.000
 VYP  N1   C2   N7   117.43  3.000
 VYP  N7   C2   N3   125.12  3.000
 VYP  N1   C2   N3   117.45  3.000
 VYP  H27  C15  H26  107.75  3.000
 VYP  H27  C15  N14  109.86  3.000
 VYP  H26  C15  N14  109.98  3.000
 VYP  H27  C15  C16  109.97  3.000
 VYP  H26  C15  C16  109.58  3.000
 VYP  N14  C15  C16  109.67  3.000
 VYP  H32  C19  H33  107.69  3.000
 VYP  H32  C19  N14  109.94  3.000
 VYP  H33  C19  N14  110.01  3.000
 VYP  H32  C19  C18  110.01  3.000
 VYP  H33  C19  C18  109.53  3.000
 VYP  N14  C19  C18  109.64  3.000
 VYP  H29  C16  H28  108.00  3.000
 VYP  H29  C16  O17  110.46  3.000
 VYP  H28  C16  O17  107.52  3.000
 VYP  H29  C16  C15  109.24  3.000
 VYP  H28  C16  C15  109.71  3.000
 VYP  O17  C16  C15  111.83  3.000
 VYP  H30  C18  H31  108.06  3.000
 VYP  H30  C18  O17  110.38  3.000
 VYP  H31  C18  O17  107.56  3.000
 VYP  H30  C18  C19  109.16  3.000
 VYP  H31  C18  C19  109.74  3.000
 VYP  O17  C18  C19  111.86  3.000
 VYP  C12  N11  C10  116.04  3.000
 VYP  C2   N3   C4   116.69  3.000
 VYP  C2   N7   C6   116.65  3.000
 VYP  C12  N13  C8   118.46  3.000
 VYP  C19  N14  C15  113.80  3.000
 VYP  C15  N14  C12  122.50  3.000
 VYP  C19  N14  C12  122.53  3.000
 VYP  H20  N1   H21  118.87  3.000
 VYP  H20  N1   C2   120.56  3.000
 VYP  H21  N1   C2   120.52  3.000
 VYP  C18  O17  C16  110.83  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
 VYP  CONST_01  C6   C5   C8   C9    180.00   0.0  0
 VYP  CONST_02  C4   C5   C8   C9      0.00   0.0  0
 VYP  CONST_03  C12  N13  C8   C9      0.00   0.0  0
 VYP  CONST_04  C12  N11  C10  C9      0.00   0.0  0
 VYP  CONST_05  C5   C8   C9   C10   180.00   0.0  0
 VYP  CONST_06  N13  C8   C9   C10     0.00   0.0  0
 VYP  CONST_07  N13  C12  N11  C10     0.00   0.0  0
 VYP  CONST_08  N7   C2   N3   C4      0.00   0.0  0
 VYP  CONST_09  N7   C6   C5   C4      0.00   0.0  0
 VYP  CONST_10  N13  C8   C5   C4    180.00   0.0  0
 VYP  CONST_11  N3   C2   N7   C6      0.00   0.0  0
 VYP  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 VYP  CONST_13  N13  C8   C5   C6      0.00   0.0  0
 VYP  CONST_14  C2   N7   C6   C5      0.00   0.0  0
 VYP  CONST_15  C2   N3   C4   C5      0.00   0.0  0
 VYP  CONST_16  C12  N13  C8   C5    180.00   0.0  0
 VYP  CONST_17  N7   C6   C5   C8    180.00   0.0  0
 VYP  CONST_18  N3   C4   C5   C8    180.00   0.0  0
 VYP  CONST_19  N11  C10  C9   C8      0.00   0.0  0
 VYP  CONST_20  N11  C12  N13  C8      0.00   0.0  0
 VYP  CONST_21  N14  C12  N11  C10   180.00   0.0  0
 VYP  CONST_22  N14  C12  N13  C8    180.00   0.0  0
 VYP  CONST_23  N1   C2   N3   C4    180.00   0.0  0
 VYP  CONST_24  N1   C2   N7   C6    180.00   0.0  0
 VYP  CONST_25  H23  C6   C5   C4    180.00   0.0  0
 VYP  CONST_26  H22  C4   C5   C6    180.00   0.0  0
 VYP  CONST_27  H24  C9   C8   C5      0.00   0.0  0
 VYP  CONST_28  H25  C10  C9   C8    180.00   0.0  0
 VYP  CONST_29  H21  N1   C2   N3    180.00   0.0  0
 VYP  CONST_30  H20  N1   C2   N3      0.00   0.0  0
 VYP  Var_01    C18  C19  N14  C12   140.14  30.0  1
 VYP  Var_02    C16  C15  N14  C12  -140.11  30.0  1
 VYP  Var_03    N13  C12  N14  C15  -173.55  30.0  1
 VYP  Var_04    O17  C18  C19  N14    54.63  30.0  1
 VYP  Var_05    O17  C16  C15  N14   -54.63  30.0  1
 VYP  Var_06    H31  C18  O17  C16  -179.61  30.0  1
 VYP  Var_07    H28  C16  O17  C18   179.52  30.0  1

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
 VYP  plan-1  C9   0.020
 VYP  plan-1  C10  0.020
 VYP  plan-1  C5   0.020
 VYP  plan-1  C8   0.020
 VYP  plan-1  C12  0.020
 VYP  plan-1  N11  0.020
 VYP  plan-1  N13  0.020
 VYP  plan-1  N14  0.020
 VYP  plan-1  H24  0.020
 VYP  plan-1  H25  0.020
 VYP  plan-2  C4   0.020
 VYP  plan-2  C6   0.020
 VYP  plan-2  C5   0.020
 VYP  plan-2  C8   0.020
 VYP  plan-2  C2   0.020
 VYP  plan-2  N3   0.020
 VYP  plan-2  N7   0.020
 VYP  plan-2  N1   0.020
 VYP  plan-2  H23  0.020
 VYP  plan-2  H22  0.020
 VYP  plan-3  C2   0.020
 VYP  plan-3  N1   0.020
 VYP  plan-3  H21  0.020
 VYP  plan-3  H20  0.020

