# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 04:27:04 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: ~{N}5-cyclopropyl-~{N}3-methyl-1-(phenylmethyl)pyrazole-3,5-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(n(Cc2ccccc2)n1)C(=O)NC3CC3
#
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
 VE5  VE5  ~{N}5-cyclopropyl-~{N}3-methyl-1-(phenylmethyl)pyrazole-3,5-dicarboxamide  ligand  40  22  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VE5
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
 VE5  N1   N  NH1   0  -0.649  45.4907  16.3644  10.1980
 VE5  N3   N  N     0  -0.278  41.6073  17.2153   7.9570
 VE5  C4   C  CR5   0   0.330  43.5752  17.0099   8.9536
 VE5  C5   C  C     0   0.518  44.7287  17.3968   9.8033
 VE5  C6   C  CH1   0  -0.084  46.6937  16.5534  10.9404
 VE5  C7   C  CH2   0  -0.509  47.8398  15.6451  10.6349
 VE5  C8   C  CH2   0  -0.481  47.9008  17.0869  10.2360
 VE5  C10  C  CR6   0   0.118  41.3359  18.4221  10.9062
 VE5  C13  C  CR16  0  -0.260  40.1359  17.5334  13.2627
 VE5  C15  C  CR16  0  -0.288  40.0394  17.9134  10.8892
 VE5  O1   O  O     0  -0.467  44.9739  18.5606  10.0811
 VE5  C3   C  CR15  0  -0.510  43.4527  15.9492   8.0826
 VE5  N2   N  NR5   0  -0.311  42.4399  17.7443   8.8273
 VE5  C2   C  CR5   0   0.169  42.2030  16.1321   7.4822
 VE5  C1   C  C     0   0.510  41.5893  15.2809   6.4366
 VE5  O    O  O     0  -0.483  42.1434  14.2552   6.0634
 VE5  N    N  NH1   0  -0.637  40.4229  15.7168   5.9477
 VE5  C    C  CH3   0  -0.513  39.7080  15.0107   4.9122
 VE5  C9   C  CH2   0  -0.420  41.9851  18.8766   9.6251
 VE5  C14  C  CR16  0  -0.239  39.4419  17.4713  12.0603
 VE5  C12  C  CR16  0  -0.238  41.4267  18.0426  13.2876
 VE5  C11  C  CR16  0  -0.294  42.0239  18.4843  12.1134
 VE5  H1   H  HNH1  0   0.413  45.1633  15.4223  10.0513
 VE5  H2   H  HCH1  0   0.271  46.5543  16.8465  11.9762
 VE5  H3   H  HCH2  0   0.260  47.7001  14.9117   9.8502
 VE5  H4   H  HCH2  0   0.261  48.4445  15.3063  11.4653
 VE5  H5   H  HCH2  0   0.257  47.8017  17.3216   9.1843
 VE5  H6   H  HCH2  0   0.257  48.5508  17.7528  10.7879
 VE5  H7   H  HCR6  0   0.257  39.6692  17.1908  14.1773
 VE5  H8   H  HCR6  0   0.254  39.4917  17.8667   9.9553
 VE5  H9   H  HCR5  0   0.288  44.1781  15.1780   7.8804
 VE5  H10  H  HNH1  0   0.408  40.0399  16.5776   6.3037
 VE5  H11  H  HCH3  0   0.251  38.8060  15.5680   4.6762
 VE5  H12  H  HCH3  0   0.239  40.3027  14.9191   4.0027
 VE5  H13  H  HCH3  0   0.239  39.4182  14.0094   5.2324
 VE5  H14  H  HCH2  0   0.299  42.8314  19.5279   9.8199
 VE5  H15  H  HCH2  0   0.296  41.2781  19.4209   9.0012
 VE5  H16  H  HCR6  0   0.257  38.4320  17.0825  12.0363
 VE5  H17  H  HCR6  0   0.256  41.9709  18.0987  14.2215
 VE5  H18  H  HCR6  0   0.255  43.0305  18.8831  12.1380

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
 VE5  C    N    single    1.443  0.020  1.443
 VE5  O    C1   double    1.224  0.020  1.224
 VE5  N    C1   single    1.338  0.020  1.338
 VE5  C1   C2   single    1.481  0.020  1.481
 VE5  C2   C3   aromatic  1.399  0.020  1.399
 VE5  C2   N3   aromatic  1.324  0.020  1.324
 VE5  C3   C4   aromatic  1.378  0.020  1.378
 VE5  N3   N2   aromatic  1.316  0.020  1.316
 VE5  C4   N2   aromatic  1.358  0.020  1.358
 VE5  C4   C5   single    1.484  0.020  1.484
 VE5  N2   C9   single    1.458  0.020  1.458
 VE5  C5   N1   single    1.342  0.020  1.342
 VE5  C5   O1   double    1.221  0.020  1.221
 VE5  C9   C10  single    1.506  0.020  1.506
 VE5  N1   C6   single    1.426  0.020  1.426
 VE5  C8   C6   single    1.496  0.020  1.496
 VE5  C8   C7   single    1.497  0.020  1.497
 VE5  C6   C7   single    1.494  0.020  1.494
 VE5  C15  C10  aromatic  1.393  0.020  1.393
 VE5  C15  C14  aromatic  1.387  0.020  1.387
 VE5  C10  C11  aromatic  1.391  0.020  1.391
 VE5  C14  C13  aromatic  1.390  0.020  1.390
 VE5  C11  C12  aromatic  1.389  0.020  1.389
 VE5  C13  C12  aromatic  1.388  0.020  1.388
 VE5  N1   H1   single    0.860  0.020  1.020
 VE5  C6   H2   single    0.970  0.020  1.090
 VE5  C7   H3   single    0.970  0.020  1.090
 VE5  C7   H4   single    0.970  0.020  1.090
 VE5  C8   H5   single    0.970  0.020  1.090
 VE5  C8   H6   single    0.970  0.020  1.090
 VE5  C13  H7   single    0.930  0.020  1.080
 VE5  C15  H8   single    0.930  0.020  1.080
 VE5  C3   H9   single    0.930  0.020  1.080
 VE5  N    H10  single    0.860  0.020  1.020
 VE5  C    H11  single    0.970  0.020  1.090
 VE5  C    H12  single    0.970  0.020  1.090
 VE5  C    H13  single    0.970  0.020  1.090
 VE5  C9   H14  single    0.970  0.020  1.090
 VE5  C9   H15  single    0.970  0.020  1.090
 VE5  C14  H16  single    0.930  0.020  1.080
 VE5  C12  H17  single    0.930  0.020  1.080
 VE5  C11  H18  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
 VE5  H1   N1   C6   118.26  3.000
 VE5  H1   N1   C5   119.45  3.000
 VE5  C6   N1   C5   122.00  3.000
 VE5  C2   N3   N2   106.34  3.000
 VE5  N2   C4   C3   106.45  3.000
 VE5  N2   C4   C5   124.20  3.000
 VE5  C3   C4   C5   129.18  3.000
 VE5  O1   C5   C4   122.32  3.000
 VE5  O1   C5   N1   123.50  3.000
 VE5  C4   C5   N1   114.14  3.000
 VE5  H2   C6   C8   117.17  3.000
 VE5  H2   C6   C7   117.25  3.000
 VE5  C8   C6   C7    60.10  3.000
 VE5  H2   C6   N1   115.10  3.000
 VE5  C7   C6   N1   117.40  3.000
 VE5  C8   C6   N1   118.87  3.000
 VE5  H4   C7   H3   114.59  3.000
 VE5  H4   C7   C8   118.91  3.000
 VE5  H3   C7   C8   117.67  3.000
 VE5  H4   C7   C6   117.54  3.000
 VE5  H3   C7   C6   117.44  3.000
 VE5  C8   C7   C6    60.02  3.000
 VE5  H6   C8   H5   114.66  3.000
 VE5  H6   C8   C7   118.77  3.000
 VE5  H5   C8   C7   117.65  3.000
 VE5  H6   C8   C6   117.65  3.000
 VE5  H5   C8   C6   117.46  3.000
 VE5  C7   C8   C6    59.88  3.000
 VE5  C11  C10  C9   120.77  3.000
 VE5  C11  C10  C15  119.16  3.000
 VE5  C9   C10  C15  120.06  3.000
 VE5  H7   C13  C12  120.14  3.000
 VE5  H7   C13  C14  120.11  3.000
 VE5  C12  C13  C14  119.76  3.000
 VE5  H8   C15  C14  119.75  3.000
 VE5  H8   C15  C10  119.78  3.000
 VE5  C14  C15  C10  120.47  3.000
 VE5  H9   C3   C2   127.91  3.000
 VE5  H9   C3   C4   127.56  3.000
 VE5  C2   C3   C4   104.48  3.000
 VE5  C9   N2   C4   129.05  3.000
 VE5  C9   N2   N3   118.48  3.000
 VE5  C4   N2   N3   111.91  3.000
 VE5  C1   C2   C3   126.73  3.000
 VE5  C3   C2   N3   110.80  3.000
 VE5  C1   C2   N3   122.46  3.000
 VE5  N    C1   O    123.80  3.000
 VE5  N    C1   C2   115.59  3.000
 VE5  O    C1   C2   120.61  3.000
 VE5  H10  N    C    118.91  3.000
 VE5  H10  N    C1   118.74  3.000
 VE5  C    N    C1   122.33  3.000
 VE5  H13  C    H12  108.22  3.000
 VE5  H13  C    H11  108.32  3.000
 VE5  H12  C    H11  108.34  3.000
 VE5  H13  C    N    111.73  3.000
 VE5  H12  C    N    111.68  3.000
 VE5  H11  C    N    108.43  3.000
 VE5  H15  C9   H14  108.01  3.000
 VE5  H15  C9   N2   106.10  3.000
 VE5  H14  C9   N2   108.72  3.000
 VE5  H15  C9   C10  111.00  3.000
 VE5  H14  C9   C10  111.37  3.000
 VE5  N2   C9   C10  111.43  3.000
 VE5  H16  C14  C15  119.85  3.000
 VE5  H16  C14  C13  120.07  3.000
 VE5  C15  C14  C13  120.08  3.000
 VE5  H17  C12  C11  119.78  3.000
 VE5  H17  C12  C13  120.14  3.000
 VE5  C11  C12  C13  120.08  3.000
 VE5  H18  C11  C12  119.83  3.000
 VE5  H18  C11  C10  119.73  3.000
 VE5  C12  C11  C10  120.45  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
 VE5  CONST_01  C4   C3   C2   N3      0.00   0.0  0
 VE5  CONST_02  C3   C4   N2   N3      0.00   0.0  0
 VE5  CONST_03  C2   N3   N2   C4      0.00   0.0  0
 VE5  CONST_04  C13  C14  C15  C10     0.00   0.0  0
 VE5  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 VE5  CONST_06  C12  C11  C10  C15     0.00   0.0  0
 VE5  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 VE5  CONST_08  N2   N3   C2   C3      0.00   0.0  0
 VE5  CONST_09  C2   C3   C4   N2      0.00   0.0  0
 VE5  CONST_10  C11  C10  C15  C14     0.00   0.0  0
 VE5  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 VE5  CONST_12  C5   C4   N2   N3    180.00   0.0  0
 VE5  CONST_13  C1   C2   C3   C4    180.00   0.0  0
 VE5  CONST_14  C2   C3   C4   C5    180.00   0.0  0
 VE5  CONST_15  C9   N2   C4   C3    180.00   0.0  0
 VE5  CONST_16  C1   C2   N3   N2    180.00   0.0  0
 VE5  CONST_17  C9   N2   N3   C2    180.00   0.0  0
 VE5  CONST_18  C14  C15  C10  C9    180.00   0.0  0
 VE5  CONST_19  C12  C11  C10  C9    180.00   0.0  0
 VE5  CONST_20  H9   C3   C2   N3    180.00   0.0  0
 VE5  CONST_21  H16  C14  C15  C10   180.00   0.0  0
 VE5  CONST_22  H17  C12  C11  C10   180.00   0.0  0
 VE5  CONST_23  H8   C15  C14  C13   180.00   0.0  0
 VE5  CONST_24  H18  C11  C12  C13   180.00   0.0  0
 VE5  CONST_25  H7   C13  C14  C15   180.00   0.0  0
 VE5  CONST_26  C6   N1   C5   C4    180.00   0.0  0
 VE5  CONST_27  O1   C5   N1   C6      0.00   0.0  0
 VE5  CONST_28  C    N    C1   C2    180.00   0.0  0
 VE5  CONST_29  H1   N1   C5   C4      0.00   0.0  0
 VE5  CONST_30  H10  N    C1   C2      0.00   0.0  0
 VE5  CONST_31  C    N    C1   O       0.00   0.0  0
 VE5  Var_01    C7   C8   C6   N1   -106.80  30.0  1
 VE5  Var_02    C10  C9   N2   N3     89.60  30.0  2
 VE5  Var_03    N2   C9   C10  C15   -76.87  30.0  2
 VE5  Var_04    H3   C7   C8   C6    107.36  30.0  1
 VE5  Var_05    C3   C4   C5   N1    -29.77  30.0  1
 VE5  Var_06    O    C1   C2   N3   -176.82  30.0  2
 VE5  Var_07    C8   C6   N1   C5    -73.53  30.0  3
 VE5  Var_08    H11  C    N    C1   -179.05  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
 VE5  chir_01  C6  N1  C8  C7  both

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
 VE5  plan-1  N3   0.020
 VE5  plan-1  C4   0.020
 VE5  plan-1  C5   0.020
 VE5  plan-1  C3   0.020
 VE5  plan-1  N2   0.020
 VE5  plan-1  C2   0.020
 VE5  plan-1  C1   0.020
 VE5  plan-1  C9   0.020
 VE5  plan-1  H9   0.020
 VE5  plan-2  C10  0.020
 VE5  plan-2  C13  0.020
 VE5  plan-2  C15  0.020
 VE5  plan-2  C9   0.020
 VE5  plan-2  C14  0.020
 VE5  plan-2  C12  0.020
 VE5  plan-2  C11  0.020
 VE5  plan-2  H7   0.020
 VE5  plan-2  H8   0.020
 VE5  plan-2  H16  0.020
 VE5  plan-2  H17  0.020
 VE5  plan-2  H18  0.020
 VE5  plan-3  C2   0.020
 VE5  plan-3  C1   0.020
 VE5  plan-3  O    0.020
 VE5  plan-3  N    0.020
 VE5  plan-3  C    0.020
 VE5  plan-3  H10  0.020
 VE5  plan-4  N1   0.020
 VE5  plan-4  C4   0.020
 VE5  plan-4  C5   0.020
 VE5  plan-4  C6   0.020
 VE5  plan-4  O1   0.020
 VE5  plan-4  H1   0.020

