# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 19:43:27 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-methanoyl-~{N}-[(1-methylimidazol-2-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccnc1CNC(=O)c2ccc(C=O)cc2
#
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
 V3T  V3T  4-methanoyl-~{N}-[(1-methylimidazol-2-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_V3T
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
 V3T  C01  C  CH3   0  -0.534  24.1680  22.3850   2.8667
 V3T  C03  C  CR15  0  -0.105  25.2337  24.5228   3.6169
 V3T  C04  C  CR15  0  -0.223  26.4170  25.1377   3.3269
 V3T  C06  C  CR5   0   0.440  26.4025  23.3171   2.2157
 V3T  C07  C  CH2   0  -0.389  26.7875  22.2051   1.2985
 V3T  C09  C  C     0   0.533  25.1913  21.0050  -0.1524
 V3T  C10  C  CR6   0  -0.026  24.3193  21.1339  -1.3644
 V3T  C11  C  CR16  0  -0.255  23.1087  20.4471  -1.3759
 V3T  C12  C  CR16  0  -0.263  22.2677  20.5462  -2.4710
 V3T  C13  C  CR6   0  -0.015  22.6379  21.3104  -3.5738
 V3T  C14  C  CR16  0  -0.247  23.8622  21.9758  -3.5755
 V3T  C15  C  CR16  0  -0.274  24.6947  21.8911  -2.4754
 V3T  C16  C  C1    0   0.120  21.7199  21.3961  -4.7233
 V3T  N02  N  NR5   0  -0.428  25.2376  23.3571   2.9053
 V3T  N05  N  N     0  -0.453  27.1358  24.3785   2.4511
 V3T  N08  N  NH1   0  -0.637  25.8983  22.1052   0.1612
 V3T  O17  O  O     0  -0.471  25.2181  19.9692   0.4944
 V3T  H1   H  HCH3  0   0.272  23.5646  22.4834   3.7651
 V3T  H2   H  HCH3  0   0.259  23.5293  22.5364   1.9974
 V3T  H3   H  HCH3  0   0.261  24.5729  21.3761   2.8353
 V3T  H4   H  HCR5  0   0.285  24.4101  24.7993   4.2544
 V3T  H5   H  HCR5  0   0.247  26.7845  26.0797   3.7038
 V3T  H6   H  HCH2  0   0.281  26.7884  21.2457   1.8158
 V3T  H7   H  HCH2  0   0.285  27.8079  22.3937   0.9619
 V3T  H8   H  HCR6  0   0.270  22.8178  19.8466  -0.5247
 V3T  H9   H  HCR6  0   0.275  21.3173  20.0252  -2.4704
 V3T  H10  H  HCR6  0   0.273  24.1646  22.5579  -4.4361
 V3T  H11  H  HCR6  0   0.273  25.6494  22.4011  -2.5014
 V3T  H12  H  H     0   0.202  20.7824  20.8243  -4.6055
 V3T  H15  H  HNH1  0   0.413  25.7757  22.9400  -0.3899
 V3T  O1   O  O     0  -0.368  21.9410  22.0305  -5.7266

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
 V3T  C16  C13  single    1.474  0.020  1.474
 V3T  C13  C14  aromatic  1.393  0.020  1.393
 V3T  C13  C12  aromatic  1.392  0.020  1.392
 V3T  C14  C15  aromatic  1.382  0.020  1.382
 V3T  C12  C11  aromatic  1.384  0.020  1.384
 V3T  C15  C10  aromatic  1.396  0.020  1.396
 V3T  C11  C10  aromatic  1.392  0.020  1.392
 V3T  C10  C09  single    1.499  0.020  1.499
 V3T  C09  O17  double    1.221  0.020  1.221
 V3T  C09  N08  single    1.345  0.020  1.345
 V3T  N08  C07  single    1.447  0.020  1.447
 V3T  C07  C06  single    1.492  0.020  1.492
 V3T  C01  N02  single    1.446  0.020  1.446
 V3T  C06  N02  aromatic  1.354  0.020  1.354
 V3T  C06  N05  aromatic  1.311  0.020  1.311
 V3T  N02  C03  aromatic  1.366  0.020  1.366
 V3T  N05  C04  aromatic  1.364  0.020  1.364
 V3T  C03  C04  aromatic  1.365  0.020  1.365
 V3T  C01  H1   single    0.970  0.020  1.090
 V3T  C01  H2   single    0.970  0.020  1.090
 V3T  C01  H3   single    0.970  0.020  1.090
 V3T  C03  H4   single    0.930  0.020  1.080
 V3T  C04  H5   single    0.930  0.020  1.080
 V3T  C07  H6   single    0.970  0.020  1.090
 V3T  C07  H7   single    0.970  0.020  1.090
 V3T  C11  H8   single    0.930  0.020  1.080
 V3T  C12  H9   single    0.930  0.020  1.080
 V3T  C14  H10  single    0.930  0.020  1.080
 V3T  C15  H11  single    0.930  0.020  1.080
 V3T  C16  H12  single    0.930  0.020  1.080
 V3T  N08  H15  single    0.860  0.020  1.020
 V3T  C16  O1   double    1.207  0.020  1.207

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
 V3T  H3   C01  H2   108.92  3.000
 V3T  H3   C01  H1   108.34  3.000
 V3T  H2   C01  H1   108.76  3.000
 V3T  H3   C01  N02  110.43  3.000
 V3T  H2   C01  N02  111.20  3.000
 V3T  H1   C01  N02  109.14  3.000
 V3T  H4   C03  N02  121.97  3.000
 V3T  H4   C03  C04  132.29  3.000
 V3T  N02  C03  C04  105.74  3.000
 V3T  H5   C04  N05  122.06  3.000
 V3T  H5   C04  C03  127.91  3.000
 V3T  N05  C04  C03  110.04  3.000
 V3T  N05  C06  N02  111.45  3.000
 V3T  N05  C06  C07  124.70  3.000
 V3T  N02  C06  C07  123.85  3.000
 V3T  H7   C07  H6   107.33  3.000
 V3T  H7   C07  N08  110.13  3.000
 V3T  H6   C07  N08  108.22  3.000
 V3T  H7   C07  C06  107.59  3.000
 V3T  H6   C07  C06  111.38  3.000
 V3T  N08  C07  C06  112.09  3.000
 V3T  O17  C09  N08  123.96  3.000
 V3T  N08  C09  C10  115.09  3.000
 V3T  O17  C09  C10  120.94  3.000
 V3T  C15  C10  C11  119.67  3.000
 V3T  C11  C10  C09  118.05  3.000
 V3T  C15  C10  C09  122.27  3.000
 V3T  H8   C11  C12  119.93  3.000
 V3T  H8   C11  C10  120.09  3.000
 V3T  C12  C11  C10  119.98  3.000
 V3T  H9   C12  C13  119.84  3.000
 V3T  H9   C12  C11  119.87  3.000
 V3T  C13  C12  C11  120.30  3.000
 V3T  C16  C13  C14  121.24  3.000
 V3T  C14  C13  C12  119.79  3.000
 V3T  C16  C13  C12  118.97  3.000
 V3T  H10  C14  C15  119.84  3.000
 V3T  H10  C14  C13  120.22  3.000
 V3T  C15  C14  C13  119.93  3.000
 V3T  H11  C15  C14  118.89  3.000
 V3T  H11  C15  C10  120.78  3.000
 V3T  C14  C15  C10  120.31  3.000
 V3T  O1   C16  H12  121.07  3.000
 V3T  O1   C16  C13  124.38  3.000
 V3T  H12  C16  C13  114.55  3.000
 V3T  C06  N02  C03  107.04  3.000
 V3T  C03  N02  C01  125.85  3.000
 V3T  C06  N02  C01  127.07  3.000
 V3T  C06  N05  C04  105.73  3.000
 V3T  H15  N08  C09  119.09  3.000
 V3T  H15  N08  C07  116.57  3.000
 V3T  C09  N08  C07  124.25  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
 V3T  CONST_01  N05  C06  N02  C03     0.00   0.0  0
 V3T  CONST_02  C06  N05  C04  C03     0.00   0.0  0
 V3T  CONST_03  N02  C06  N05  C04     0.00   0.0  0
 V3T  CONST_04  C06  N02  C03  C04     0.00   0.0  0
 V3T  CONST_05  C13  C14  C15  C10     0.00   0.0  0
 V3T  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 V3T  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 V3T  CONST_08  C14  C15  C10  C11     0.00   0.0  0
 V3T  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 V3T  CONST_10  C15  C10  C11  C12     0.00   0.0  0
 V3T  CONST_11  N05  C04  C03  N02     0.00   0.0  0
 V3T  CONST_12  N05  C06  N02  C01   180.00   0.0  0
 V3T  CONST_13  C04  C03  N02  C01   180.00   0.0  0
 V3T  CONST_14  C07  C06  N02  C03   180.00   0.0  0
 V3T  CONST_15  C07  C06  N05  C04   180.00   0.0  0
 V3T  CONST_16  C14  C15  C10  C09   180.00   0.0  0
 V3T  CONST_17  C12  C11  C10  C09   180.00   0.0  0
 V3T  CONST_18  C16  C13  C12  C11   180.00   0.0  0
 V3T  CONST_19  C16  C13  C14  C15   180.00   0.0  0
 V3T  CONST_20  H4   C03  N02  C06   180.00   0.0  0
 V3T  CONST_21  H5   C04  N05  C06   180.00   0.0  0
 V3T  CONST_22  H10  C14  C15  C10   180.00   0.0  0
 V3T  CONST_23  H9   C12  C11  C10   180.00   0.0  0
 V3T  CONST_24  H11  C15  C10  C11   180.00   0.0  0
 V3T  CONST_25  H8   C11  C12  C13   180.00   0.0  0
 V3T  CONST_26  C10  C09  N08  C07   180.00   0.0  0
 V3T  CONST_27  H15  N08  C09  C10     0.00   0.0  0
 V3T  CONST_28  O17  C09  N08  C07     0.00   0.0  0
 V3T  Var_01    O17  C09  C10  C11    32.75  30.0  2
 V3T  Var_02    O1   C16  C13  C12   179.89  30.0  2
 V3T  Var_03    N08  C07  C06  N02    64.13  30.0  1
 V3T  Var_04    H1   C01  N02  C03   -23.61  30.0  2
 V3T  Var_05    C09  N08  C07  C06  -121.99  30.0  2

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
 V3T  plan-1  C01  0.020
 V3T  plan-1  C03  0.020
 V3T  plan-1  C04  0.020
 V3T  plan-1  C06  0.020
 V3T  plan-1  C07  0.020
 V3T  plan-1  N02  0.020
 V3T  plan-1  N05  0.020
 V3T  plan-1  H4   0.020
 V3T  plan-1  H5   0.020
 V3T  plan-2  C09  0.020
 V3T  plan-2  C10  0.020
 V3T  plan-2  C11  0.020
 V3T  plan-2  C12  0.020
 V3T  plan-2  C13  0.020
 V3T  plan-2  C14  0.020
 V3T  plan-2  C15  0.020
 V3T  plan-2  C16  0.020
 V3T  plan-2  H8   0.020
 V3T  plan-2  H9   0.020
 V3T  plan-2  H10  0.020
 V3T  plan-2  H11  0.020
 V3T  plan-3  C07  0.020
 V3T  plan-3  C09  0.020
 V3T  plan-3  C10  0.020
 V3T  plan-3  N08  0.020
 V3T  plan-3  O17  0.020
 V3T  plan-3  H15  0.020
 V3T  plan-4  C13  0.020
 V3T  plan-4  C16  0.020
 V3T  plan-4  H12  0.020
 V3T  plan-4  O1   0.020

