# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:21:57 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-(4-methanoylphenyl)carbonyl-~{N},~{N}-dimethyl-piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)N1CCN(CC1)C(=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
 V3B  V3B  4-(4-methanoylphenyl)carbonyl-~{N},~{N}-dimethyl-piperazine-1-carboxamide  ligand  40  21  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V3B
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
 V3B  C01  C  CH3   0  -0.518  -11.9832  14.0290   0.0969
 V3B  C03  C  C     0   0.714  -12.8381  16.1534   0.8499
 V3B  C05  C  CH2   0  -0.311  -13.7809  18.2475   1.5801
 V3B  C06  C  CH2   0  -0.301  -14.0416  19.6497   1.0667
 V3B  C08  C  C     0   0.529  -15.5773  20.8061  -0.3816
 V3B  C09  C  CR6   0  -0.066  -16.6846  20.7748  -1.3903
 V3B  C10  C  CR16  0  -0.256  -16.5854  21.5902  -2.5178
 V3B  C11  C  CR16  0  -0.254  -17.6200  21.6415  -3.4316
 V3B  C12  C  CR6   0  -0.015  -18.7819  20.9020  -3.2100
 V3B  C13  C  CR16  0  -0.266  -18.8907  20.1095  -2.0719
 V3B  C14  C  CR16  0  -0.236  -17.8428  20.0379  -1.1676
 V3B  C15  C  C1    0   0.119  -19.9068  20.9401  -4.1610
 V3B  C17  C  CH2   0  -0.318  -15.2381  18.3644  -0.6709
 V3B  C18  C  CH2   0  -0.297  -13.8984  17.6607  -0.8101
 V3B  C20  C  CH3   0  -0.536  -11.4439  16.0275  -1.1903
 V3B  N02  N  NT    0  -0.480  -12.2613  15.4257  -0.1539
 V3B  N04  N  NT    0  -0.495  -13.3240  17.3872   0.5020
 V3B  N07  N  NT    0  -0.457  -15.0587  19.6322   0.0221
 V3B  O16  O  O     0  -0.477  -15.1982  21.8821   0.0597
 V3B  O19  O  O     0  -0.523  -12.9287  15.7298   1.9970
 V3B  H1   H  HCH3  0   0.247  -12.7783  13.5709   0.6790
 V3B  H2   H  HCH3  0   0.239  -11.9244  13.5066  -0.8577
 V3B  H3   H  HCH3  0   0.223  -11.0353  13.8771   0.6226
 V3B  H4   H  HCH2  0   0.237  -14.6852  17.8570   2.0601
 V3B  H5   H  HCH2  0   0.266  -13.0140  18.3131   2.3513
 V3B  H6   H  HCH2  0   0.249  -13.1129  20.0933   0.6946
 V3B  H7   H  HCH2  0   0.266  -14.3825  20.2644   1.8999
 V3B  H8   H  HCR6  0   0.269  -15.6903  22.1752  -2.6849
 V3B  H9   H  HCR6  0   0.270  -17.5311  22.2614  -4.3143
 V3B  H10  H  HCR6  0   0.274  -19.7971  19.5436  -1.8919
 V3B  H11  H  HCR6  0   0.275  -17.9353  19.4164  -0.2858
 V3B  H12  H  H     0   0.200  -20.7728  20.3194  -3.8689
 V3B  H15  H  HCH2  0   0.285  -15.6334  18.5358  -1.6699
 V3B  H16  H  HCH2  0   0.258  -15.9490  17.7228  -0.1428
 V3B  H17  H  HCH2  0   0.271  -14.0570  16.7260  -1.3472
 V3B  H18  H  HCH2  0   0.244  -13.2369  18.2821  -1.4210
 V3B  H19  H  HCH3  0   0.252  -11.3693  17.1039  -1.0637
 V3B  H20  H  HCH3  0   0.250  -10.4286  15.6276  -1.1330
 V3B  H21  H  HCH3  0   0.237  -11.8310  15.8203  -2.1900
 V3B  O1   O  O     0  -0.370  -19.9174  21.5829  -5.1833

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
 V3B  C15  C12  single    1.474  0.020  1.474
 V3B  C11  C12  aromatic  1.395  0.020  1.395
 V3B  C11  C10  aromatic  1.381  0.020  1.381
 V3B  C12  C13  aromatic  1.391  0.020  1.391
 V3B  C10  C09  aromatic  1.395  0.020  1.395
 V3B  C13  C14  aromatic  1.386  0.020  1.386
 V3B  C20  N02  single    1.451  0.020  1.451
 V3B  C09  C14  aromatic  1.391  0.020  1.391
 V3B  C09  C08  single    1.498  0.020  1.498
 V3B  C18  C17  single    1.520  0.020  1.520
 V3B  C18  N04  single    1.458  0.020  1.458
 V3B  C17  N07  single    1.456  0.020  1.456
 V3B  C08  N07  single    1.345  0.020  1.345
 V3B  C08  O16  double    1.223  0.020  1.223
 V3B  N02  C01  single    1.446  0.020  1.446
 V3B  N02  C03  single    1.367  0.020  1.367
 V3B  N07  C06  single    1.458  0.020  1.458
 V3B  N04  C03  single    1.371  0.020  1.371
 V3B  N04  C05  single    1.453  0.020  1.453
 V3B  C03  O19  double    1.226  0.020  1.226
 V3B  C06  C05  single    1.516  0.020  1.516
 V3B  C01  H1   single    0.970  0.020  1.090
 V3B  C01  H2   single    0.970  0.020  1.090
 V3B  C01  H3   single    0.970  0.020  1.090
 V3B  C05  H4   single    0.970  0.020  1.090
 V3B  C05  H5   single    0.970  0.020  1.090
 V3B  C06  H6   single    0.970  0.020  1.090
 V3B  C06  H7   single    0.970  0.020  1.090
 V3B  C10  H8   single    0.930  0.020  1.080
 V3B  C11  H9   single    0.930  0.020  1.080
 V3B  C13  H10  single    0.930  0.020  1.080
 V3B  C14  H11  single    0.930  0.020  1.080
 V3B  C15  H12  single    0.930  0.020  1.080
 V3B  C17  H15  single    0.970  0.020  1.090
 V3B  C17  H16  single    0.970  0.020  1.090
 V3B  C18  H17  single    0.970  0.020  1.090
 V3B  C18  H18  single    0.970  0.020  1.090
 V3B  C20  H19  single    0.970  0.020  1.090
 V3B  C20  H20  single    0.970  0.020  1.090
 V3B  C20  H21  single    0.970  0.020  1.090
 V3B  C15  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
 V3B  H3   C01  H2   107.91  3.000
 V3B  H3   C01  H1   108.53  3.000
 V3B  H2   C01  H1   107.85  3.000
 V3B  H3   C01  N02  112.58  3.000
 V3B  H2   C01  N02  108.75  3.000
 V3B  H1   C01  N02  111.06  3.000
 V3B  O19  C03  N04  121.48  3.000
 V3B  O19  C03  N02  122.28  3.000
 V3B  N04  C03  N02  116.24  3.000
 V3B  H5   C05  H4   106.99  3.000
 V3B  H5   C05  N04  109.85  3.000
 V3B  H4   C05  N04  111.94  3.000
 V3B  H5   C05  C06  107.76  3.000
 V3B  H4   C05  C06  109.64  3.000
 V3B  N04  C05  C06  110.52  3.000
 V3B  H7   C06  H6   107.26  3.000
 V3B  H7   C06  N07  109.64  3.000
 V3B  H6   C06  N07  110.68  3.000
 V3B  H7   C06  C05  108.46  3.000
 V3B  H6   C06  C05  110.13  3.000
 V3B  N07  C06  C05  110.57  3.000
 V3B  O16  C08  N07  122.67  3.000
 V3B  O16  C08  C09  119.36  3.000
 V3B  N07  C08  C09  117.95  3.000
 V3B  C14  C09  C10  119.90  3.000
 V3B  C14  C09  C08  121.25  3.000
 V3B  C10  C09  C08  118.65  3.000
 V3B  H8   C10  C11  119.82  3.000
 V3B  H8   C10  C09  119.97  3.000
 V3B  C11  C10  C09  120.20  3.000
 V3B  H9   C11  C12  120.11  3.000
 V3B  H9   C11  C10  119.95  3.000
 V3B  C12  C11  C10  119.94  3.000
 V3B  C15  C12  C13  118.89  3.000
 V3B  C13  C12  C11  119.80  3.000
 V3B  C15  C12  C11  121.31  3.000
 V3B  H10  C13  C14  119.81  3.000
 V3B  H10  C13  C12  119.92  3.000
 V3B  C14  C13  C12  120.28  3.000
 V3B  H11  C14  C13  119.76  3.000
 V3B  H11  C14  C09  120.38  3.000
 V3B  C13  C14  C09  119.85  3.000
 V3B  O1   C15  H12  121.07  3.000
 V3B  O1   C15  C12  124.53  3.000
 V3B  H12  C15  C12  114.41  3.000
 V3B  H16  C17  H15  107.44  3.000
 V3B  H16  C17  N07  111.17  3.000
 V3B  H15  C17  N07  110.16  3.000
 V3B  H16  C17  C18  110.22  3.000
 V3B  H15  C17  C18  108.01  3.000
 V3B  N07  C17  C18  109.77  3.000
 V3B  H18  C18  H17  107.45  3.000
 V3B  H18  C18  N04  111.77  3.000
 V3B  H17  C18  N04  109.87  3.000
 V3B  H18  C18  C17  108.73  3.000
 V3B  H17  C18  C17  108.30  3.000
 V3B  N04  C18  C17  110.59  3.000
 V3B  H21  C20  H20  107.93  3.000
 V3B  H21  C20  H19  108.61  3.000
 V3B  H20  C20  H19  107.02  3.000
 V3B  H21  C20  N02  112.07  3.000
 V3B  H20  C20  N02  109.53  3.000
 V3B  H19  C20  N02  111.50  3.000
 V3B  C20  N02  C03  122.77  3.000
 V3B  C03  N02  C01  117.89  3.000
 V3B  C20  N02  C01  114.60  3.000
 V3B  C18  N04  C05  115.64  3.000
 V3B  C05  N04  C03  117.13  3.000
 V3B  C18  N04  C03  122.47  3.000
 V3B  C17  N07  C08  124.71  3.000
 V3B  C08  N07  C06  118.25  3.000
 V3B  C17  N07  C06  115.94  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
 V3B  CONST_01  C12  C11  C10  C09     0.00   0.0  0
 V3B  CONST_02  C12  C13  C14  C09     0.00   0.0  0
 V3B  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 V3B  CONST_04  C13  C14  C09  C10     0.00   0.0  0
 V3B  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 V3B  CONST_06  C14  C09  C10  C11     0.00   0.0  0
 V3B  CONST_07  C11  C10  C09  C08   180.00   0.0  0
 V3B  CONST_08  C13  C14  C09  C08   180.00   0.0  0
 V3B  CONST_09  C15  C12  C11  C10   180.00   0.0  0
 V3B  CONST_10  C15  C12  C13  C14   180.00   0.0  0
 V3B  CONST_11  C09  C08  N07  C06   180.00   0.0  0
 V3B  CONST_13  H9   C11  C10  C09   180.00   0.0  0
 V3B  CONST_14  H10  C13  C14  C09   180.00   0.0  0
 V3B  CONST_15  H11  C14  C09  C10   180.00   0.0  0
 V3B  CONST_16  H8   C10  C11  C12   180.00   0.0  0
 V3B  CONST_17  O19  C03  N04  C05     0.00   0.0  0
 V3B  CONST_18  O16  C08  N07  C06     0.00   0.0  0
 V3B  CONST_19  O16  C08  N07  C17   180.00   0.0  0
 V3B  CONST_21  N02  C03  N04  C05   180.00   0.0  0
 V3B  CONST_23  N04  C03  N02  C01   180.00   0.0  0
 V3B  CONST_25  O19  C03  N02  C01     0.00   0.0  0
 V3B  Var_01    C17  C18  N04  C05   -23.90  30.0  1
 V3B  Var_02    C17  N07  C06  C05   -22.66  30.0  1
 V3B  Var_03    C18  C17  N07  C06   -35.18  30.0  1
 V3B  Var_04    C18  N04  C05  C06   -34.28  30.0  1
 V3B  Var_05    N07  C17  C18  N04    60.60  30.0  1
 V3B  Var_06    N07  C06  C05  N04    59.69  30.0  1
 V3B  Var_07    N07  C08  C09  C10  -130.20  30.0  2
 V3B  Var_08    O1   C15  C12  C11     0.58  30.0  2
 V3B  Var_09    H19  C20  N02  C01  -155.70  30.0  3
 V3B  Var_10    H1   C01  N02  C03    38.49  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
 V3B  plan-1  C08  0.020
 V3B  plan-1  C09  0.020
 V3B  plan-1  C10  0.020
 V3B  plan-1  C11  0.020
 V3B  plan-1  C12  0.020
 V3B  plan-1  C13  0.020
 V3B  plan-1  C14  0.020
 V3B  plan-1  C15  0.020
 V3B  plan-1  H8   0.020
 V3B  plan-1  H9   0.020
 V3B  plan-1  H10  0.020
 V3B  plan-1  H11  0.020
 V3B  plan-2  C12  0.020
 V3B  plan-2  C15  0.020
 V3B  plan-2  H12  0.020
 V3B  plan-2  O1   0.020
 V3B  plan-3  C01  0.020
 V3B  plan-3  C03  0.020
 V3B  plan-3  C05  0.020
 V3B  plan-3  C18  0.020
 V3B  plan-3  C20  0.020
 V3B  plan-3  N02  0.020
 V3B  plan-3  N04  0.020
 V3B  plan-3  O19  0.020
 V3B  plan-4  C06  0.020
 V3B  plan-4  C08  0.020
 V3B  plan-4  C09  0.020
 V3B  plan-4  C17  0.020
 V3B  plan-4  N07  0.020
 V3B  plan-4  O16  0.020

