# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 21:10:42 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-methanoyl-~{N}-[(1-methylpyrazol-4-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(CNC(=O)c2ccc(C=O)cc2)cn1
#
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
 V3K  V3K  4-methanoyl-~{N}-[(1-methylpyrazol-4-yl)methyl]benzamide  ligand  31  18  .  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_V3K
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
 V3K  C01  C  CH3   0  -0.516  11.5188  15.9183   2.0061
 V3K  C03  C  CR15  0   0.036  13.4279  16.8417   0.6917
 V3K  C04  C  CR5   0  -0.131  13.7485  18.0844   0.1899
 V3K  C05  C  CR15  0  -0.081  12.6713  18.8940   0.5926
 V3K  C07  C  CH2   0  -0.415  14.9769  18.4666  -0.5705
 V3K  C09  C  C     0   0.538  16.0312  20.3234   0.6280
 V3K  C10  C  CR6   0  -0.028  17.1283  20.7394   1.5612
 V3K  C11  C  CR16  0  -0.272  18.3675  20.1056   1.5933
 V3K  C12  C  CR16  0  -0.260  19.3488  20.5461   2.4674
 V3K  C13  C  CR6   0  -0.015  19.1020  21.6193   3.3164
 V3K  C14  C  CR16  0  -0.252  17.8645  22.2617   3.2782
 V3K  C15  C  CR16  0  -0.254  16.8909  21.8298   2.3996
 V3K  C16  C  C1    0   0.120  20.1641  22.0573   4.2396
 V3K  N02  N  NR5   0  -0.261  12.2512  16.9633   1.3287
 V3K  N06  N  N     0  -0.285  11.7765  18.2043   1.2765
 V3K  N08  N  NH1   0  -0.627  16.0184  19.0305   0.2698
 V3K  O17  O  O     0  -0.476  15.2096  21.1375   0.2312
 V3K  H1   H  HCH3  0   0.265  10.6090  16.3477   2.4136
 V3K  H2   H  HCH3  0   0.257  11.2553  15.1214   1.3129
 V3K  H3   H  HCH3  0   0.257  12.1089  15.5002   2.8195
 V3K  H4   H  HCR5  0   0.286  13.9499  15.8988   0.6327
 V3K  H5   H  HCR5  0   0.252  12.5225  19.9464   0.4033
 V3K  H6   H  HCH2  0   0.273  15.3992  17.5908  -1.0624
 V3K  H7   H  HCH2  0   0.265  14.7370  19.1841  -1.3541
 V3K  H8   H  HCR6  0   0.270  18.5904  19.2836   0.9253
 V3K  H9   H  HCR6  0   0.276  20.3138  20.0533   2.4849
 V3K  H10  H  HCR6  0   0.270  17.6669  23.0987   3.9352
 V3K  H11  H  HCR6  0   0.267  15.9348  22.3342   2.3687
 V3K  H12  H  H     0   0.202  21.0960  21.4676   4.1783
 V3K  H15  H  HNH1  0   0.407  16.6109  18.3775   0.7570
 V3K  O1   O  O     0  -0.368  20.0593  22.9790   5.0126

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
 V3K  C07  C04  single    1.494  0.020  1.494
 V3K  C07  N08  single    1.452  0.020  1.452
 V3K  O17  C09  double    1.223  0.020  1.223
 V3K  C04  C05  aromatic  1.406  0.020  1.406
 V3K  C04  C03  aromatic  1.378  0.020  1.378
 V3K  N08  C09  single    1.342  0.020  1.342
 V3K  C09  C10  single    1.499  0.020  1.499
 V3K  C05  N06  aromatic  1.321  0.020  1.321
 V3K  C03  N02  aromatic  1.344  0.020  1.344
 V3K  N06  N02  aromatic  1.330  0.020  1.330
 V3K  N02  C01  single    1.445  0.020  1.445
 V3K  C10  C11  aromatic  1.392  0.020  1.392
 V3K  C10  C15  aromatic  1.396  0.020  1.396
 V3K  C11  C12  aromatic  1.386  0.020  1.386
 V3K  C15  C14  aromatic  1.381  0.020  1.381
 V3K  C12  C13  aromatic  1.391  0.020  1.391
 V3K  C14  C13  aromatic  1.395  0.020  1.395
 V3K  C13  C16  single    1.474  0.020  1.474
 V3K  C01  H1   single    0.970  0.020  1.090
 V3K  C01  H2   single    0.970  0.020  1.090
 V3K  C01  H3   single    0.970  0.020  1.090
 V3K  C03  H4   single    0.930  0.020  1.080
 V3K  C05  H5   single    0.930  0.020  1.080
 V3K  C07  H6   single    0.970  0.020  1.090
 V3K  C07  H7   single    0.970  0.020  1.090
 V3K  C11  H8   single    0.930  0.020  1.080
 V3K  C12  H9   single    0.930  0.020  1.080
 V3K  C14  H10  single    0.930  0.020  1.080
 V3K  C15  H11  single    0.930  0.020  1.080
 V3K  C16  H12  single    0.930  0.020  1.080
 V3K  N08  H15  single    0.860  0.020  1.020
 V3K  C16  O1   double    1.208  0.020  1.208

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
 V3K  H3   C01  H2   109.02  3.000
 V3K  H3   C01  H1   109.02  3.000
 V3K  H2   C01  H1   109.02  3.000
 V3K  H3   C01  N02  110.69  3.000
 V3K  H2   C01  N02  110.71  3.000
 V3K  H1   C01  N02  108.35  3.000
 V3K  H4   C03  N02  121.91  3.000
 V3K  H4   C03  C04  130.95  3.000
 V3K  N02  C03  C04  107.14  3.000
 V3K  C07  C04  C05  128.91  3.000
 V3K  C05  C04  C03  103.69  3.000
 V3K  C07  C04  C03  127.38  3.000
 V3K  H5   C05  N06  120.43  3.000
 V3K  H5   C05  C04  128.07  3.000
 V3K  N06  C05  C04  111.50  3.000
 V3K  H7   C07  H6   106.86  3.000
 V3K  H7   C07  N08  108.57  3.000
 V3K  H6   C07  N08  107.18  3.000
 V3K  H7   C07  C04  110.70  3.000
 V3K  H6   C07  C04  110.05  3.000
 V3K  N08  C07  C04  113.23  3.000
 V3K  O17  C09  N08  123.27  3.000
 V3K  N08  C09  C10  116.14  3.000
 V3K  O17  C09  C10  120.60  3.000
 V3K  C15  C10  C11  119.55  3.000
 V3K  C15  C10  C09  117.79  3.000
 V3K  C11  C10  C09  122.64  3.000
 V3K  H8   C11  C12  119.00  3.000
 V3K  H8   C11  C10  120.98  3.000
 V3K  C12  C11  C10  120.00  3.000
 V3K  H9   C12  C13  119.95  3.000
 V3K  H9   C12  C11  119.74  3.000
 V3K  C13  C12  C11  120.31  3.000
 V3K  C16  C13  C14  121.31  3.000
 V3K  C16  C13  C12  118.94  3.000
 V3K  C14  C13  C12  119.75  3.000
 V3K  H10  C14  C15  119.96  3.000
 V3K  H10  C14  C13  120.11  3.000
 V3K  C15  C14  C13  119.93  3.000
 V3K  H11  C15  C14  119.72  3.000
 V3K  H11  C15  C10  119.84  3.000
 V3K  C14  C15  C10  120.44  3.000
 V3K  O1   C16  H12  121.08  3.000
 V3K  O1   C16  C13  124.42  3.000
 V3K  H12  C16  C13  114.50  3.000
 V3K  N06  N02  C03  112.24  3.000
 V3K  N06  N02  C01  120.83  3.000
 V3K  C03  N02  C01  126.93  3.000
 V3K  N02  N06  C05  105.42  3.000
 V3K  H15  N08  C09  119.33  3.000
 V3K  H15  N08  C07  116.74  3.000
 V3K  C09  N08  C07  122.38  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
 V3K  CONST_01  N06  C05  C04  C03     0.00   0.0  0
 V3K  CONST_02  C05  N06  N02  C03     0.00   0.0  0
 V3K  CONST_03  N02  N06  C05  C04     0.00   0.0  0
 V3K  CONST_04  N06  N02  C03  C04     0.00   0.0  0
 V3K  CONST_05  N02  C03  C04  C05     0.00   0.0  0
 V3K  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 V3K  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 V3K  CONST_08  C14  C15  C10  C11     0.00   0.0  0
 V3K  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 V3K  CONST_10  C15  C10  C11  C12     0.00   0.0  0
 V3K  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 V3K  CONST_12  C04  C03  N02  C01   180.00   0.0  0
 V3K  CONST_13  C05  N06  N02  C01   180.00   0.0  0
 V3K  CONST_14  N06  C05  C04  C07   180.00   0.0  0
 V3K  CONST_15  N02  C03  C04  C07   180.00   0.0  0
 V3K  CONST_16  C12  C11  C10  C09   180.00   0.0  0
 V3K  CONST_17  C14  C15  C10  C09   180.00   0.0  0
 V3K  CONST_18  C16  C13  C12  C11   180.00   0.0  0
 V3K  CONST_19  C16  C13  C14  C15   180.00   0.0  0
 V3K  CONST_20  H5   C05  C04  C03   180.00   0.0  0
 V3K  CONST_21  H4   C03  C04  C05   180.00   0.0  0
 V3K  CONST_22  H9   C12  C11  C10   180.00   0.0  0
 V3K  CONST_23  H10  C14  C15  C10   180.00   0.0  0
 V3K  CONST_24  H11  C15  C10  C11   180.00   0.0  0
 V3K  CONST_25  H8   C11  C12  C13   180.00   0.0  0
 V3K  CONST_26  C10  C09  N08  C07   180.00   0.0  0
 V3K  CONST_27  H15  N08  C09  C10     0.00   0.0  0
 V3K  CONST_28  O17  C09  N08  C07     0.00   0.0  0
 V3K  Var_01    N08  C07  C04  C03   -95.26  30.0  2
 V3K  Var_02    O17  C09  C10  C11  -151.01  30.0  2
 V3K  Var_03    O1   C16  C13  C12   179.63  30.0  2
 V3K  Var_04    H1   C01  N02  C03  -179.96  30.0  2
 V3K  Var_05    C09  N08  C07  C04   -83.13  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
 V3K  plan-1  C01  0.020
 V3K  plan-1  C03  0.020
 V3K  plan-1  C04  0.020
 V3K  plan-1  C05  0.020
 V3K  plan-1  C07  0.020
 V3K  plan-1  N02  0.020
 V3K  plan-1  N06  0.020
 V3K  plan-1  H4   0.020
 V3K  plan-1  H5   0.020
 V3K  plan-2  C09  0.020
 V3K  plan-2  C10  0.020
 V3K  plan-2  C11  0.020
 V3K  plan-2  C12  0.020
 V3K  plan-2  C13  0.020
 V3K  plan-2  C14  0.020
 V3K  plan-2  C15  0.020
 V3K  plan-2  C16  0.020
 V3K  plan-2  H8   0.020
 V3K  plan-2  H9   0.020
 V3K  plan-2  H10  0.020
 V3K  plan-2  H11  0.020
 V3K  plan-3  C07  0.020
 V3K  plan-3  C09  0.020
 V3K  plan-3  C10  0.020
 V3K  plan-3  N08  0.020
 V3K  plan-3  O17  0.020
 V3K  plan-3  H15  0.020
 V3K  plan-4  C13  0.020
 V3K  plan-4  C16  0.020
 V3K  plan-4  H12  0.020
 V3K  plan-4  O1   0.020

