# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 21:41:16 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-methanoyl-~{N}-(oxan-4-ylmethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=Cc1ccc(cc1)C(=O)NCC2CCOCC2
#
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
 V3N  V3N  4-methanoyl-~{N}-(oxan-4-ylmethyl)benzamide  ligand  35  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_V3N
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
 V3N  C01  C  C1    0   0.120  -20.0261  21.8251  -4.3482
 V3N  C02  C  CR6   0  -0.016  -18.9627  21.4554  -3.3967
 V3N  C03  C  CR16  0  -0.260  -19.2185  20.4600  -2.4597
 V3N  C04  C  CR16  0  -0.271  -18.2372  20.0804  -1.5572
 V3N  C05  C  CR6   0  -0.031  -16.9914  20.7005  -1.5827
 V3N  C06  C  C     0   0.516  -15.9026  20.3517  -0.6116
 V3N  C08  C  CH2   0  -0.265  -14.8665  18.5022   0.6568
 V3N  C09  C  CR16  0  -0.253  -14.0665  17.3600   0.0261
 V3N  C10  C  C     0  -0.459  -13.1097  17.8534  -1.0782
 V3N  C11  C  C     0  -0.185  -11.6794  17.9569  -0.5543
 V3N  C13  C  C     0  -0.164  -12.1865  17.5025   1.6986
 V3N  C14  C  C     0  -0.520  -13.2652  16.6070   1.0858
 V3N  C16  C  CR16  0  -0.257  -16.7453  21.7163  -2.5078
 V3N  C17  C  CR16  0  -0.252  -17.7174  22.0834  -3.4171
 V3N  N07  N  NH1   0  -0.640  -15.8283  19.0558  -0.2718
 V3N  O12  O  O     0  -0.491  -11.6631  18.4377   0.7714
 V3N  O15  O  O     0  -0.477  -15.1458  21.2159  -0.1930
 V3N  H1   H  H     0   0.201  -20.9574  21.2407  -4.2419
 V3N  H4   H  HCR6  0   0.276  -20.1880  19.9764  -2.4352
 V3N  H5   H  HCR6  0   0.273  -18.4633  19.3196  -0.8209
 V3N  H6   H  HCH2  0   0.251  -14.2133  19.3095   0.9821
 V3N  H7   H  HCH2  0   0.247  -15.3960  18.1346   1.5413
 V3N  H8   H  HCR6  0   0.247  -14.7910  16.6657  -0.4108
 V3N  H9   H  H     0   0.234  -13.4381  18.8249  -1.4565
 V3N  H10  H  H     0   0.235  -13.1247  17.1770  -1.9358
 V3N  H11  H  H     0   0.201  -11.1725  16.9851  -0.6239
 V3N  H12  H  H     0   0.236  -11.0958  18.6545  -1.1554
 V3N  H13  H  H     0   0.211  -11.3817  16.8818   2.1136
 V3N  H14  H  H     0   0.221  -12.6012  18.0858   2.5245
 V3N  H15  H  H     0   0.251  -13.9107  16.2259   1.8801
 V3N  H16  H  H     0   0.247  -12.8093  15.7312   0.6174
 V3N  H17  H  HCR6  0   0.268  -15.7836  22.2113  -2.5201
 V3N  H18  H  HCR6  0   0.270  -17.5142  22.8606  -4.1425
 V3N  H19  H  HNH1  0   0.405  -16.4411  18.3990  -0.7307
 V3N  O1   O  O     0  -0.369  -19.9224  22.6882  -5.1865

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
 V3N  C01  C02  single    1.474  0.020  1.474
 V3N  C02  C17  aromatic  1.395  0.020  1.395
 V3N  C02  C03  aromatic  1.391  0.020  1.391
 V3N  C17  C16  aromatic  1.381  0.020  1.381
 V3N  C03  C04  aromatic  1.386  0.020  1.386
 V3N  C16  C05  aromatic  1.396  0.020  1.396
 V3N  C04  C05  aromatic  1.392  0.020  1.392
 V3N  C05  C06  single    1.500  0.020  1.500
 V3N  C10  C11  single    1.527  0.020  1.527
 V3N  C10  C09  single    1.542  0.020  1.542
 V3N  C11  O12  single    1.410  0.020  1.410
 V3N  C06  N07  single    1.342  0.020  1.342
 V3N  C06  O15  double    1.223  0.020  1.223
 V3N  N07  C08  single    1.447  0.020  1.447
 V3N  C09  C08  single    1.530  0.020  1.530
 V3N  C09  C14  single    1.527  0.020  1.527
 V3N  O12  C13  single    1.417  0.020  1.417
 V3N  C14  C13  single    1.530  0.020  1.530
 V3N  C01  H1   single    0.930  0.020  1.080
 V3N  C03  H4   single    0.930  0.020  1.080
 V3N  C04  H5   single    0.930  0.020  1.080
 V3N  C08  H6   single    0.970  0.020  1.090
 V3N  C08  H7   single    0.970  0.020  1.090
 V3N  C09  H8   single    0.970  0.020  1.090
 V3N  C10  H9   single    0.970  0.020  1.090
 V3N  C10  H10  single    0.970  0.020  1.090
 V3N  C11  H11  single    0.970  0.020  1.090
 V3N  C11  H12  single    0.970  0.020  1.090
 V3N  C13  H13  single    0.970  0.020  1.090
 V3N  C13  H14  single    0.970  0.020  1.090
 V3N  C14  H15  single    0.970  0.020  1.090
 V3N  C14  H16  single    0.970  0.020  1.090
 V3N  C16  H17  single    0.930  0.020  1.080
 V3N  C17  H18  single    0.930  0.020  1.080
 V3N  N07  H19  single    0.860  0.020  1.020
 V3N  C01  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
 V3N  O1   C01  H1   121.15  3.000
 V3N  O1   C01  C02  124.43  3.000
 V3N  H1   C01  C02  114.42  3.000
 V3N  C17  C02  C03  119.76  3.000
 V3N  C03  C02  C01  118.79  3.000
 V3N  C17  C02  C01  121.44  3.000
 V3N  H4   C03  C04  119.77  3.000
 V3N  H4   C03  C02  119.95  3.000
 V3N  C04  C03  C02  120.29  3.000
 V3N  H5   C04  C05  120.83  3.000
 V3N  H5   C04  C03  119.17  3.000
 V3N  C05  C04  C03  119.98  3.000
 V3N  C16  C05  C06  118.05  3.000
 V3N  C06  C05  C04  122.29  3.000
 V3N  C16  C05  C04  119.62  3.000
 V3N  O15  C06  N07  124.17  3.000
 V3N  O15  C06  C05  120.43  3.000
 V3N  N07  C06  C05  115.39  3.000
 V3N  H7   C08  H6   107.34  3.000
 V3N  H7   C08  N07  109.00  3.000
 V3N  H6   C08  N07  107.88  3.000
 V3N  H7   C08  C09  109.58  3.000
 V3N  H6   C08  C09  111.29  3.000
 V3N  N07  C08  C09  111.62  3.000
 V3N  H8   C09  C14  108.15  3.000
 V3N  H8   C09  C10  109.13  3.000
 V3N  C14  C09  C10  109.21  3.000
 V3N  H8   C09  C08  106.98  3.000
 V3N  C14  C09  C08  110.88  3.000
 V3N  C10  C09  C08  112.37  3.000
 V3N  H10  C10  H9   105.93  3.000
 V3N  H10  C10  C11  108.92  3.000
 V3N  H9   C10  C11  109.87  3.000
 V3N  H10  C10  C09  110.83  3.000
 V3N  H9   C10  C09  110.23  3.000
 V3N  C11  C10  C09  110.93  3.000
 V3N  H12  C11  H11  106.51  3.000
 V3N  H12  C11  O12  107.10  3.000
 V3N  H11  C11  O12  110.85  3.000
 V3N  H12  C11  C10  110.83  3.000
 V3N  H11  C11  C10  110.53  3.000
 V3N  O12  C11  C10  110.89  3.000
 V3N  H14  C13  H13  107.11  3.000
 V3N  H14  C13  O12  106.40  3.000
 V3N  H13  C13  O12  110.47  3.000
 V3N  H14  C13  C14  110.34  3.000
 V3N  H13  C13  C14  109.71  3.000
 V3N  O12  C13  C14  112.62  3.000
 V3N  H16  C14  H15  106.17  3.000
 V3N  H16  C14  C13  110.28  3.000
 V3N  H15  C14  C13  109.25  3.000
 V3N  H16  C14  C09  108.46  3.000
 V3N  H15  C14  C09  111.51  3.000
 V3N  C13  C14  C09  111.06  3.000
 V3N  H17  C16  C17  119.78  3.000
 V3N  H17  C16  C05  119.82  3.000
 V3N  C17  C16  C05  120.39  3.000
 V3N  H18  C17  C16  120.01  3.000
 V3N  H18  C17  C02  120.05  3.000
 V3N  C16  C17  C02  119.94  3.000
 V3N  H19  N07  C08  116.53  3.000
 V3N  H19  N07  C06  118.68  3.000
 V3N  C08  N07  C06  124.67  3.000
 V3N  C13  O12  C11  112.69  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
 V3N  CONST_01  C05  C16  C17  C02     0.00   0.0  0
 V3N  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 V3N  CONST_03  C16  C17  C02  C03     0.00   0.0  0
 V3N  CONST_04  C16  C05  C04  C03     0.00   0.0  0
 V3N  CONST_05  C17  C02  C03  C04     0.00   0.0  0
 V3N  CONST_06  C17  C16  C05  C04     0.00   0.0  0
 V3N  CONST_07  C16  C17  C02  C01   180.00   0.0  0
 V3N  CONST_08  C04  C03  C02  C01   180.00   0.0  0
 V3N  CONST_09  C06  C05  C04  C03   180.00   0.0  0
 V3N  CONST_10  C17  C16  C05  C06   180.00   0.0  0
 V3N  CONST_11  H17  C16  C17  C02   180.00   0.0  0
 V3N  CONST_12  H5   C04  C03  C02   180.00   0.0  0
 V3N  CONST_13  H18  C17  C02  C03   180.00   0.0  0
 V3N  CONST_14  H4   C03  C04  C05   180.00   0.0  0
 V3N  CONST_15  C08  N07  C06  C05   180.00   0.0  0
 V3N  CONST_16  H19  N07  C06  C05     0.00   0.0  0
 V3N  CONST_17  O15  C06  N07  C08     0.00   0.0  0
 V3N  Var_01    O12  C11  C10  C09   -38.36  30.0  1
 V3N  Var_02    O12  C13  C14  C09   -32.84  30.0  1
 V3N  Var_03    C14  C13  O12  C11   -30.66  30.0  1
 V3N  Var_04    O1   C01  C02  C03   178.69  30.0  2
 V3N  Var_05    N07  C06  C05  C04    36.44  30.0  2
 V3N  Var_06    C09  C08  N07  C06  -124.75  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
 V3N  chir_01  C09  C10  C08  C14  positiv

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
 V3N  plan-1  C01  0.020
 V3N  plan-1  C02  0.020
 V3N  plan-1  C03  0.020
 V3N  plan-1  C04  0.020
 V3N  plan-1  C05  0.020
 V3N  plan-1  C06  0.020
 V3N  plan-1  C16  0.020
 V3N  plan-1  C17  0.020
 V3N  plan-1  H4   0.020
 V3N  plan-1  H5   0.020
 V3N  plan-1  H17  0.020
 V3N  plan-1  H18  0.020
 V3N  plan-2  C05  0.020
 V3N  plan-2  C06  0.020
 V3N  plan-2  C08  0.020
 V3N  plan-2  N07  0.020
 V3N  plan-2  O15  0.020
 V3N  plan-2  H19  0.020
 V3N  plan-3  C01  0.020
 V3N  plan-3  C02  0.020
 V3N  plan-3  H1   0.020
 V3N  plan-3  O1   0.020

