# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:27:17 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 4-(1-ethyl-6-methyl-1H-imidazo[4,5-c]pyridin-2-yl)-1,2,5-oxadiazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c2cc(C)ncc2nc1c3nonc3N
#
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
 VUP  VUP  4-(1-ethyl-6-methyl-1H-imidazo[4,5-c]pyridin-2-yl)-1,2,5-oxadiazol-3-amine  ligand  30  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VUP
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
 VUP  C     C  CR6   0   0.223  -3.8000  -0.0993  -0.1074
 VUP  C1    C  CR16  0  -0.396  -2.7727   0.8243  -0.2091
 VUP  C2    C  CR56  0   0.433  -1.4823   0.3142  -0.1266
 VUP  N2    N  NR5   0  -0.557  -0.2460   0.8867  -0.1926
 VUP  C6    C  CH2   0  -0.336   0.0081   2.3144  -0.3297
 VUP  C7    C  CH3   0  -0.662   0.2182   2.9984   1.0082
 VUP  C5    C  CR5   0   0.541   0.6484  -0.1368  -0.0344
 VUP  N1    N  N     0  -0.507   0.0816  -1.3067   0.1074
 VUP  C3    C  CR56  0   0.081  -1.2601  -1.0547   0.0534
 VUP  C4    C  CR16  0  -0.129  -2.3660  -1.8966   0.1421
 VUP  N     N  N     0  -0.435  -3.5916  -1.4210   0.0627
 VUP  C8    C  CR5   0   0.090   2.0888  -0.0075  -0.0319
 VUP  C9    C  CR5   0   0.352   3.0379  -1.0825   0.0974
 VUP  N5    N  NH2   0  -0.849   2.7751  -2.3851   0.3013
 VUP  N4    N  N     0  -0.189   4.2282  -0.5588   0.0304
 VUP  O     O  O     0  -0.215   4.0388   0.7792  -0.1229
 VUP  C10   C  CH3   0  -0.712  -5.2322   0.3342  -0.1842
 VUP  N3    N  N     0  -0.124   2.7536   1.0964  -0.1579
 VUP  H51N  H  HNH2  0   0.404   3.5068  -3.0493   0.1105
 VUP  H52N  H  HNH2  0   0.413   1.8307  -2.6881   0.1197
 VUP  HA    H  HCR6  0   0.267  -2.2458  -2.9667   0.2770
 VUP  H61C  H  HCH2  0   0.281   0.8664   2.4535  -0.9822
 VUP  H62C  H  HCH2  0   0.277  -0.8496   2.7406  -0.8485
 VUP  H71C  H  HCH3  0   0.247   0.3815   4.0636   0.8482
 VUP  H72C  H  HCH3  0   0.239  -0.6523   2.8828   1.6535
 VUP  H73C  H  HCH3  0   0.238   1.0896   2.6019   1.5284
 VUP  H1    H  HCR6  0   0.280  -2.9794   1.8773  -0.3446
 VUP  H101  H  HCH3  0   0.250  -5.7355  -0.1451  -1.0253
 VUP  H102  H  HCH3  0   0.250  -5.7726   0.0473   0.7190
 VUP  H103  H  HCH3  0   0.243  -5.3220   1.4124  -0.3054

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
 VUP  N5   C9    single    1.344  0.020  1.344
 VUP  C9   N4    aromatic  1.302  0.020  1.302
 VUP  C9   C8    aromatic  1.440  0.020  1.440
 VUP  N4   O     aromatic  1.360  0.020  1.360
 VUP  O    N3    aromatic  1.324  0.020  1.324
 VUP  N3   C8    aromatic  1.295  0.020  1.295
 VUP  C8   C5    single    1.446  0.020  1.446
 VUP  C5   N1    aromatic  1.308  0.020  1.308
 VUP  C5   N2    aromatic  1.368  0.020  1.368
 VUP  N1   C3    aromatic  1.366  0.020  1.366
 VUP  C3   C4    aromatic  1.393  0.020  1.393
 VUP  C3   C2    aromatic  1.398  0.020  1.398
 VUP  C4   N     aromatic  1.317  0.020  1.317
 VUP  N    C     aromatic  1.349  0.020  1.349
 VUP  N2   C6    single    1.457  0.020  1.457
 VUP  N2   C2    aromatic  1.364  0.020  1.364
 VUP  C6   C7    single    1.517  0.020  1.517
 VUP  C2   C1    aromatic  1.390  0.020  1.390
 VUP  C1   C     aromatic  1.385  0.020  1.385
 VUP  C    C10   single    1.498  0.020  1.498
 VUP  N5   H51N  single    0.890  0.020  1.040
 VUP  N5   H52N  single    0.890  0.020  1.040
 VUP  C4   HA    single    0.930  0.020  1.080
 VUP  C6   H61C  single    0.970  0.020  1.090
 VUP  C6   H62C  single    0.970  0.020  1.090
 VUP  C7   H71C  single    0.970  0.020  1.090
 VUP  C7   H72C  single    0.970  0.020  1.090
 VUP  C7   H73C  single    0.970  0.020  1.090
 VUP  C1   H1    single    0.930  0.020  1.080
 VUP  C10  H101  single    0.970  0.020  1.090
 VUP  C10  H102  single    0.970  0.020  1.090
 VUP  C10  H103  single    0.970  0.020  1.090

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
 VUP  C10   C    N     115.96  3.000
 VUP  C10   C    C1    120.81  3.000
 VUP  N     C    C1    123.23  3.000
 VUP  H1    C1   C2    122.83  3.000
 VUP  H1    C1   C     121.10  3.000
 VUP  C2    C1   C     116.07  3.000
 VUP  C3    C2   N2    105.85  3.000
 VUP  N2    C2   C1    133.20  3.000
 VUP  C3    C2   C1    120.95  3.000
 VUP  C5    N2   C6    129.04  3.000
 VUP  C6    N2   C2    125.04  3.000
 VUP  C5    N2   C2    105.84  3.000
 VUP  H62C  C6   H61C  106.60  3.000
 VUP  H62C  C6   C7    110.65  3.000
 VUP  H61C  C6   C7    111.24  3.000
 VUP  H62C  C6   N2    106.92  3.000
 VUP  H61C  C6   N2    108.64  3.000
 VUP  C7    C6   N2    112.52  3.000
 VUP  H73C  C7   H72C  108.52  3.000
 VUP  H73C  C7   H71C  107.82  3.000
 VUP  H72C  C7   H71C  108.08  3.000
 VUP  H73C  C7   C6    111.57  3.000
 VUP  H72C  C7   C6    111.33  3.000
 VUP  H71C  C7   C6    109.39  3.000
 VUP  C8    C5   N1    120.76  3.000
 VUP  N1    C5   N2    113.48  3.000
 VUP  C8    C5   N2    125.76  3.000
 VUP  C3    N1   C5    104.85  3.000
 VUP  C4    C3   N1    131.74  3.000
 VUP  C4    C3   C2    118.28  3.000
 VUP  N1    C3   C2    109.98  3.000
 VUP  HA    C4   N     117.81  3.000
 VUP  HA    C4   C3    121.07  3.000
 VUP  N     C4   C3    121.11  3.000
 VUP  C4    N    C     120.35  3.000
 VUP  N3    C8   C9    107.87  3.000
 VUP  N3    C8   C5    125.97  3.000
 VUP  C9    C8   C5    126.15  3.000
 VUP  N4    C9   N5    125.18  3.000
 VUP  N4    C9   C8    107.32  3.000
 VUP  N5    C9   C8    127.46  3.000
 VUP  H52N  N5   H51N  116.65  3.000
 VUP  H52N  N5   C9    116.54  3.000
 VUP  H51N  N5   C9    117.94  3.000
 VUP  O     N4   C9    105.91  3.000
 VUP  N3    O    N4    111.95  3.000
 VUP  H103  C10  H102  108.17  3.000
 VUP  H103  C10  H101  108.13  3.000
 VUP  H102  C10  H101  107.11  3.000
 VUP  H103  C10  C     111.78  3.000
 VUP  H102  C10  C     110.79  3.000
 VUP  H101  C10  C     110.69  3.000
 VUP  O     N3   C8    106.95  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
 VUP  CONST_01  C3    C4   N   C      0.00   0.0  0
 VUP  CONST_02  C3    C2   C1  C      0.00   0.0  0
 VUP  CONST_03  N2    C2   C1  C    180.00   0.0  0
 VUP  CONST_04  N1    C3   C2  C1   180.00   0.0  0
 VUP  CONST_05  C4    C3   C2  C1     0.00   0.0  0
 VUP  CONST_06  C5    N2   C2  C1   180.00   0.0  0
 VUP  CONST_07  C4    N    C   C1     0.00   0.0  0
 VUP  CONST_08  C5    N1   C3  C2     0.00   0.0  0
 VUP  CONST_09  N     C4   C3  C2     0.00   0.0  0
 VUP  CONST_10  C8    C5   N2  C2   180.00   0.0  0
 VUP  CONST_11  N1    C5   N2  C2     0.00   0.0  0
 VUP  CONST_12  N     C    C1  C2     0.00   0.0  0
 VUP  CONST_13  C9    C8   C5  N2   180.00   0.0  0
 VUP  CONST_14  N3    C8   C5  N2     0.00   0.0  0
 VUP  CONST_15  C3    N1   C5  N2     0.00   0.0  0
 VUP  CONST_16  N1    C3   C2  N2     0.00   0.0  0
 VUP  CONST_17  C4    C3   C2  N2   180.00   0.0  0
 VUP  CONST_18  N4    C9   C8  C5   180.00   0.0  0
 VUP  CONST_19  O     N3   C8  C5   180.00   0.0  0
 VUP  CONST_20  C4    C3   N1  C5   180.00   0.0  0
 VUP  CONST_21  C3    C2   N2  C5     0.00   0.0  0
 VUP  CONST_22  C9    C8   C5  N1     0.00   0.0  0
 VUP  CONST_23  N3    C8   C5  N1   180.00   0.0  0
 VUP  CONST_24  N     C4   C3  N1   180.00   0.0  0
 VUP  CONST_25  C8    C5   N1  C3   180.00   0.0  0
 VUP  CONST_26  O     N4   C9  C8     0.00   0.0  0
 VUP  CONST_27  N4    O    N3  C8     0.00   0.0  0
 VUP  CONST_28  N3    O    N4  C9     0.00   0.0  0
 VUP  CONST_29  O     N3   C8  C9     0.00   0.0  0
 VUP  CONST_30  N3    C8   C9  N4     0.00   0.0  0
 VUP  CONST_31  C6    N2   C2  C1     0.00   0.0  0
 VUP  CONST_32  C10   C    C1  C2   180.00   0.0  0
 VUP  CONST_33  C8    C5   N2  C6     0.00   0.0  0
 VUP  CONST_34  N1    C5   N2  C6   180.00   0.0  0
 VUP  CONST_35  C3    C2   N2  C6   180.00   0.0  0
 VUP  CONST_36  N5    C9   C8  C5     0.00   0.0  0
 VUP  CONST_37  C10   C    N   C4   180.00   0.0  0
 VUP  CONST_38  O     N4   C9  N5   180.00   0.0  0
 VUP  CONST_39  N3    C8   C9  N5   180.00   0.0  0
 VUP  CONST_40  HA    C4   N   C    180.00   0.0  0
 VUP  CONST_41  H1    C1   C2  N2     0.00   0.0  0
 VUP  Var_01    C7    C6   N2  C2    93.95  30.0  2
 VUP  Var_02    H101  C10  C   C1   119.64  30.0  2
 VUP  Var_03    H71C  C7   C6  N2  -178.75  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
 VUP  plan-1  C5    0.020
 VUP  plan-1  C8    0.020
 VUP  plan-1  C9    0.020
 VUP  plan-1  N5    0.020
 VUP  plan-1  N4    0.020
 VUP  plan-1  O     0.020
 VUP  plan-1  N3    0.020
 VUP  plan-2  C     0.020
 VUP  plan-2  C1    0.020
 VUP  plan-2  C2    0.020
 VUP  plan-2  N2    0.020
 VUP  plan-2  C6    0.020
 VUP  plan-2  C5    0.020
 VUP  plan-2  N1    0.020
 VUP  plan-2  C3    0.020
 VUP  plan-2  C4    0.020
 VUP  plan-2  N     0.020
 VUP  plan-2  C8    0.020
 VUP  plan-2  C10   0.020
 VUP  plan-2  HA    0.020
 VUP  plan-2  H1    0.020
 VUP  plan-3  C9    0.020
 VUP  plan-3  N5    0.020
 VUP  plan-3  H51N  0.020
 VUP  plan-3  H52N  0.020

