# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:20:30 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (Z)-1-{2,2-difluoro-6-[5-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]-2,3-dihydro-4H-1,4-benzoxazin-4-yl}methanimine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCc1c[nH]c2ncnc(c3ccc4OC(F)(F)CN(C=N)c4c3)c12
#
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
 G4V  G4V  (Z)-1-{2,2-difluoro-6-[5-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]-2,3-dihydro-4H-1,4-benzoxazin-4-yl}methanimine  ligand  44  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G4V
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
 G4V  N3   N  NR15  0  -0.663   5.3722  -0.1885  -0.1063
 G4V  C4   C  CR15  0  -0.037   4.7401  -1.4031  -0.0479
 G4V  N2   N  N     0  -0.420   4.6777   2.0915  -0.0307
 G4V  C7   C  CR6   0   0.010   0.7360   0.6434   0.5927
 G4V  C6   C  CR56  0  -0.006   3.1859   0.1760   0.2043
 G4V  C9   C  CR6   0   0.376  -1.5840   0.6564  -0.0826
 G4V  C8   C  CR5   0  -0.081   3.3971  -1.2467   0.1390
 G4V  C16  C  CH3   0  -0.393  -0.4308  -3.4490  -1.8416
 G4V  C17  C  CH2   0  -0.584   2.4175  -2.3755   0.1859
 G4V  C2   C  CR16  0  -0.332  -0.8704  -0.6676   1.8135
 G4V  C10  C  CR6   0   0.314  -1.8660  -0.2329   0.9580
 G4V  C15  C  CT    0   0.884  -4.1467  -0.2405   0.3976
 G4V  O1   O  O2    0  -0.486  -3.1313  -0.7043   1.1818
 G4V  C5   C  CR16  0   0.023   3.5840   2.8225   0.0771
 G4V  C1   C  CR16  0  -0.295   0.4292  -0.2282   1.6330
 G4V  O2   O  O2    0  -0.483   0.5864  -3.4615  -0.8758
 G4V  N    N  N     0  -0.626  -3.6122   2.5406  -2.3670
 G4V  C14  C  CH2   0  -0.470  -3.7158   0.0863  -1.0149
 G4V  N4   N  NT    0  -0.562  -2.6299   1.0283  -0.9247
 G4V  C3   C  CR16  0  -0.366  -0.2733   1.0871  -0.2531
 G4V  F1   F  F     0  -0.304  -5.0975  -1.1876   0.4173
 G4V  N1   N  N     0  -0.432   2.3404   2.3850   0.2607
 G4V  C12  C  CR56  0   0.502   4.4518   0.7880   0.0254
 G4V  C11  C  CR6   0   0.185   2.1262   1.0753   0.3519
 G4V  H1   H  HNR5  0   0.418   6.3596  -0.0474  -0.2475
 G4V  H2   H  HCR5  0   0.298   5.3050  -2.3157  -0.1546
 G4V  H3   H  H     0   0.255  -1.8687   2.9077  -1.2768
 G4V  H4   H  HCH2  0   0.203   0.8868  -1.4257  -1.0102
 G4V  H5   H  HCH2  0   0.201   2.0230  -2.4080  -1.9351
 G4V  H6   H  HCH3  0   0.234  -1.0530  -4.3307  -1.6911
 G4V  H7   H  HCH3  0   0.196  -1.0669  -2.5581  -1.7559
 G4V  H8   H  HCH3  0   0.203  -0.0338  -3.4771  -2.8635
 G4V  H9   H  HCH2  0   0.256   2.9746  -3.3157   0.1817
 G4V  H10  H  HCH2  0   0.243   1.8420  -2.3589   1.1140
 G4V  H11  H  HCR6  0   0.285  -1.1179  -1.3396   2.6247
 G4V  H12  H  HCR6  0   0.254   3.7100   3.8976   0.0166
 G4V  H13  H  HCR6  0   0.275   1.2018  -0.5576   2.3143
 G4V  H14  H  H     0   0.355  -3.4862   3.4880  -2.7003
 G4V  H15  H  HCH2  0   0.296  -3.4058  -0.8304  -1.5257
 G4V  H16  H  HCH2  0   0.315  -4.5386   0.5289  -1.5729
 G4V  H17  H  HCR6  0   0.284  -0.0234   1.7372  -1.0815
 G4V  C13  C  C1    0   0.118  -2.6862   2.2449  -1.5559
 G4V  F2   F  F     0  -0.323  -4.6849   0.8564   0.9852
 G4V  C18  C  CH2   0  -0.118   1.4565  -2.3641  -0.9934

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
 G4V  N2   C5   aromatic  1.320  0.020  1.320
 G4V  N2   C12  aromatic  1.324  0.020  1.324
 G4V  C5   N1   aromatic  1.331  0.020  1.331
 G4V  N1   C11  aromatic  1.330  0.020  1.330
 G4V  C12  N3   aromatic  1.348  0.020  1.348
 G4V  C12  C6   aromatic  1.417  0.020  1.417
 G4V  N3   C4   aromatic  1.370  0.020  1.370
 G4V  C1   C2   aromatic  1.384  0.020  1.384
 G4V  C1   C7   aromatic  1.391  0.020  1.391
 G4V  C11  C6   aromatic  1.398  0.020  1.398
 G4V  C11  C7   single    1.476  0.020  1.476
 G4V  C6   C8   aromatic  1.440  0.020  1.440
 G4V  C2   C10  aromatic  1.383  0.020  1.383
 G4V  C4   C8   aromatic  1.365  0.020  1.365
 G4V  C7   C3   aromatic  1.390  0.020  1.390
 G4V  C8   C17  single    1.495  0.020  1.495
 G4V  C10  O1   single    1.369  0.020  1.369
 G4V  C10  C9   aromatic  1.398  0.020  1.398
 G4V  C3   C9   aromatic  1.390  0.020  1.390
 G4V  C17  C18  single    1.521  0.020  1.521
 G4V  O1   C15  single    1.364  0.020  1.364
 G4V  C9   N4   single    1.393  0.020  1.393
 G4V  F2   C15  single    1.356  0.020  1.356
 G4V  C14  N4   single    1.440  0.020  1.440
 G4V  C14  C15  single    1.512  0.020  1.512
 G4V  N4   C13  single    1.372  0.020  1.372
 G4V  C15  F1   single    1.342  0.020  1.342
 G4V  N    C13  double    1.266  0.020  1.266
 G4V  C18  O2   single    1.405  0.020  1.405
 G4V  O2   C16  single    1.403  0.020  1.403
 G4V  N3   H1   single    0.860  0.020  1.020
 G4V  C4   H2   single    0.930  0.020  1.080
 G4V  C13  H3   single    0.930  0.020  1.080
 G4V  C18  H4   single    0.970  0.020  1.090
 G4V  C18  H5   single    0.970  0.020  1.090
 G4V  C16  H6   single    0.970  0.020  1.090
 G4V  C16  H7   single    0.970  0.020  1.090
 G4V  C16  H8   single    0.970  0.020  1.090
 G4V  C17  H9   single    0.970  0.020  1.090
 G4V  C17  H10  single    0.970  0.020  1.090
 G4V  C2   H11  single    0.930  0.020  1.080
 G4V  C5   H12  single    0.930  0.020  1.080
 G4V  C1   H13  single    0.930  0.020  1.080
 G4V  N    H14  single    0.890  0.020  1.040
 G4V  C14  H15  single    0.970  0.020  1.090
 G4V  C14  H16  single    0.970  0.020  1.090
 G4V  C3   H17  single    0.930  0.020  1.080

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
 G4V  H1   N3   C12  125.54  3.000
 G4V  H1   N3   C4   125.60  3.000
 G4V  C12  N3   C4   108.83  3.000
 G4V  H2   C4   C8   128.74  3.000
 G4V  H2   C4   N3   120.27  3.000
 G4V  C8   C4   N3   110.99  3.000
 G4V  C12  N2   C5   113.61  3.000
 G4V  C11  C7   C3   119.44  3.000
 G4V  C3   C7   C1   119.67  3.000
 G4V  C11  C7   C1   120.87  3.000
 G4V  C11  C6   C12  114.38  3.000
 G4V  C11  C6   C8   138.75  3.000
 G4V  C12  C6   C8   106.85  3.000
 G4V  C3   C9   N4   123.43  3.000
 G4V  N4   C9   C10  117.93  3.000
 G4V  C3   C9   C10  118.60  3.000
 G4V  C17  C8   C6   130.42  3.000
 G4V  C17  C8   C4   124.23  3.000
 G4V  C6   C8   C4   105.29  3.000
 G4V  H8   C16  H7   107.65  3.000
 G4V  H8   C16  H6   108.34  3.000
 G4V  H7   C16  H6   108.36  3.000
 G4V  H8   C16  O2   112.26  3.000
 G4V  H7   C16  O2   111.93  3.000
 G4V  H6   C16  O2   108.17  3.000
 G4V  H10  C17  H9   106.55  3.000
 G4V  H10  C17  C18  109.01  3.000
 G4V  H9   C17  C18  108.99  3.000
 G4V  H10  C17  C8   111.13  3.000
 G4V  H9   C17  C8   108.39  3.000
 G4V  C18  C17  C8   112.57  3.000
 G4V  H11  C2   C1   120.66  3.000
 G4V  H11  C2   C10  119.62  3.000
 G4V  C1   C2   C10  119.71  3.000
 G4V  O1   C10  C2   117.14  3.000
 G4V  O1   C10  C9   121.83  3.000
 G4V  C2   C10  C9   121.02  3.000
 G4V  F1   C15  C14  111.60  3.000
 G4V  F1   C15  O1   106.20  3.000
 G4V  C14  C15  O1   113.47  3.000
 G4V  F1   C15  F2   106.46  3.000
 G4V  C14  C15  F2   110.06  3.000
 G4V  O1   C15  F2   108.74  3.000
 G4V  C15  O1   C10  118.49  3.000
 G4V  H12  C5   N1   116.25  3.000
 G4V  H12  C5   N2   116.64  3.000
 G4V  N1   C5   N2   127.11  3.000
 G4V  H13  C1   C2   119.47  3.000
 G4V  H13  C1   C7   120.29  3.000
 G4V  C2   C1   C7   120.24  3.000
 G4V  C16  O2   C18  112.61  3.000
 G4V  H14  N    C13  109.78  3.000
 G4V  H16  C14  H15  108.40  3.000
 G4V  H16  C14  N4   109.64  3.000
 G4V  H15  C14  N4   111.32  3.000
 G4V  H16  C14  C15  110.57  3.000
 G4V  H15  C14  C15  109.61  3.000
 G4V  N4   C14  C15  107.32  3.000
 G4V  C14  N4   C13  121.35  3.000
 G4V  C13  N4   C9   123.07  3.000
 G4V  C14  N4   C9   115.41  3.000
 G4V  H17  C3   C9   119.85  3.000
 G4V  H17  C3   C7   119.34  3.000
 G4V  C9   C3   C7   120.75  3.000
 G4V  C11  N1   C5   118.91  3.000
 G4V  C6   C12  N2   125.64  3.000
 G4V  C6   C12  N3   108.02  3.000
 G4V  N2   C12  N3   126.33  3.000
 G4V  N1   C11  C6   120.28  3.000
 G4V  C6   C11  C7   122.91  3.000
 G4V  N1   C11  C7   116.81  3.000
 G4V  H3   C13  N4   113.02  3.000
 G4V  H3   C13  N    124.84  3.000
 G4V  N4   C13  N    122.14  3.000
 G4V  H5   C18  H4   106.76  3.000
 G4V  H5   C18  O2   111.06  3.000
 G4V  H4   C18  O2   110.33  3.000
 G4V  H5   C18  C17  109.76  3.000
 G4V  H4   C18  C17  110.25  3.000
 G4V  O2   C18  C17  108.69  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
 G4V  CONST_01  C5   N2   C12  N3    180.00   0.0  0
 G4V  CONST_02  C11  C6   C12  N3    180.00   0.0  0
 G4V  CONST_03  C8   C6   C12  N3      0.00   0.0  0
 G4V  CONST_04  C6   C8   C4   N3      0.00   0.0  0
 G4V  CONST_05  N2   C12  N3   C4    180.00   0.0  0
 G4V  CONST_06  C6   C12  N3   C4      0.00   0.0  0
 G4V  CONST_07  C12  C6   C8   C4      0.00   0.0  0
 G4V  CONST_08  C11  C6   C8   C4    180.00   0.0  0
 G4V  CONST_09  C11  N1   C5   N2      0.00   0.0  0
 G4V  CONST_10  C11  C6   C12  N2      0.00   0.0  0
 G4V  CONST_11  C8   C6   C12  N2    180.00   0.0  0
 G4V  CONST_12  C10  C2   C1   C7      0.00   0.0  0
 G4V  CONST_13  C5   N1   C11  C7    180.00   0.0  0
 G4V  CONST_14  C12  C6   C11  C7    180.00   0.0  0
 G4V  CONST_15  C8   C6   C11  C7      0.00   0.0  0
 G4V  CONST_16  C10  C9   C3   C7      0.00   0.0  0
 G4V  CONST_17  C5   N2   C12  C6      0.00   0.0  0
 G4V  CONST_18  C5   N1   C11  C6      0.00   0.0  0
 G4V  CONST_21  C1   C2   C10  C9      0.00   0.0  0
 G4V  CONST_22  C1   C7   C3   C9      0.00   0.0  0
 G4V  CONST_23  C11  C7   C3   C9    180.00   0.0  0
 G4V  CONST_24  N1   C11  C6   C8    180.00   0.0  0
 G4V  CONST_25  C12  N3   C4   C8      0.00   0.0  0
 G4V  CONST_26  C11  C7   C1   C2    180.00   0.0  0
 G4V  CONST_27  C3   C7   C1   C2      0.00   0.0  0
 G4V  CONST_28  C3   C9   C10  C2      0.00   0.0  0
 G4V  CONST_31  C12  N2   C5   N1      0.00   0.0  0
 G4V  CONST_32  C12  C6   C11  N1      0.00   0.0  0
 G4V  CONST_33  C17  C8   C4   N3    180.00   0.0  0
 G4V  CONST_34  C12  C6   C8   C17   180.00   0.0  0
 G4V  CONST_35  C11  C6   C8   C17     0.00   0.0  0
 G4V  CONST_36  H1   N3   C12  N2      0.00   0.0  0
 G4V  CONST_37  H11  C2   C1   C7    180.00   0.0  0
 G4V  CONST_38  H2   C4   C8   C6    180.00   0.0  0
 G4V  CONST_39  H13  C1   C2   C10   180.00   0.0  0
 G4V  CONST_40  H17  C3   C9   C10   180.00   0.0  0
 G4V  CONST_41  H12  C5   N2   C12   180.00   0.0  0
 G4V  CONST_42  N    C13  N4   C9    180.00   0.0  0
 G4V  CONST_43  C14  N4   C13  N       0.00   0.0  0
 G4V  CONST_44  H3   C13  N4   C9      0.00   0.0  0
 G4V  CONST_45  H14  N    C13  N4    180.00   0.0  0
 G4V  Var_01    C15  C14  N4   C9     51.57  30.0  1
 G4V  Var_02    C14  C15  O1   C10    32.43  30.0  1
 G4V  Var_03    C14  N4   C9   C10   -25.10  30.0  1
 G4V  Var_04    N4   C14  C15  O1    -55.71  30.0  1
 G4V  Var_05    C18  C17  C8   C4   -113.17  30.0  2
 G4V  Var_06    O2   C18  C17  C8    179.37  30.0  3
 G4V  Var_07    C17  C18  O2   C16   173.41  30.0  1
 G4V  Var_08    H6   C16  O2   C18   179.44  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
 G4V  plan-1  N3   0.020
 G4V  plan-1  C4   0.020
 G4V  plan-1  N2   0.020
 G4V  plan-1  C7   0.020
 G4V  plan-1  C6   0.020
 G4V  plan-1  C8   0.020
 G4V  plan-1  C17  0.020
 G4V  plan-1  C5   0.020
 G4V  plan-1  N1   0.020
 G4V  plan-1  C12  0.020
 G4V  plan-1  C11  0.020
 G4V  plan-1  H1   0.020
 G4V  plan-1  H2   0.020
 G4V  plan-1  H12  0.020
 G4V  plan-2  C7   0.020
 G4V  plan-2  C9   0.020
 G4V  plan-2  C2   0.020
 G4V  plan-2  C10  0.020
 G4V  plan-2  O1   0.020
 G4V  plan-2  C1   0.020
 G4V  plan-2  N4   0.020
 G4V  plan-2  C3   0.020
 G4V  plan-2  C11  0.020
 G4V  plan-2  H11  0.020
 G4V  plan-2  H13  0.020
 G4V  plan-2  H17  0.020
 G4V  plan-3  C9   0.020
 G4V  plan-3  N    0.020
 G4V  plan-3  C14  0.020
 G4V  plan-3  N4   0.020
 G4V  plan-3  H3   0.020
 G4V  plan-3  H14  0.020
 G4V  plan-3  C13  0.020

