# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 15:40:30 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: [4-[(4-fluorophenyl)methyl]piperazin-1-yl]-(2-methylphenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1C(=O)N2CCN(CC2)Cc3ccc(F)cc3
#
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
 B5N  B5N  '[4-[(4-fluorophenyl)methyl]piperazin-1-yl]-(2-methylphenyl)methanone'  ligand  44  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B5N
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
 B5N  C01  C  CR16  0  -0.294   3.8067   0.0436   1.8377
 B5N  C02  C  CR16  0  -0.397   4.8345   0.9620   1.6586
 B5N  C03  C  CR6   0   0.075   3.2769  -0.6648   0.7659
 B5N  C04  C  CR6   0   0.509   5.3199   1.1636   0.3832
 B5N  C05  C  CR16  0  -0.262   3.7922  -0.4302  -0.5078
 B5N  C06  C  CR16  0  -0.398   4.8155   0.4825  -0.7100
 B5N  C08  C  CH2   0  -0.324   2.1798  -1.6765   0.9670
 B5N  C10  C  CH2   0  -0.311  -0.8980  -2.4428  -1.0211
 B5N  C11  C  CH2   0  -0.284   0.1681  -2.6102   0.0465
 B5N  C13  C  CH2   0  -0.309  -0.7073  -0.0381  -0.7695
 B5N  C14  C  CH2   0  -0.283   0.3699  -0.2499   0.2798
 B5N  C15  C  C     0   0.486  -2.9392  -1.1228  -0.8224
 B5N  C16  C  CR6   0  -0.112  -3.5604   0.2258  -0.6053
 B5N  C17  C  CR16  0  -0.303  -4.4434   1.9124   0.8439
 B5N  C18  C  CR6   0   0.106  -3.7921   0.6915   0.6925
 B5N  C19  C  CR16  0  -0.242  -4.8556   2.6525  -0.2562
 B5N  C20  C  CR16  0  -0.266  -4.6237   2.1764  -1.5381
 B5N  C21  C  CR16  0  -0.252  -3.9810   0.9582  -1.7087
 B5N  C23  C  CH3   0  -0.750  -3.3390  -0.0924   1.8902
 B5N  F07  F  F     0  -0.318   6.3105   2.0529   0.1948
 B5N  N09  N  NT    0  -0.419   1.0847  -1.4867   0.0365
 B5N  N12  N  NT    0  -0.440  -1.5961  -1.1840  -0.8333
 B5N  O22  O  O     0  -0.487  -3.6607  -2.1008  -0.9752
 B5N  H1   H  HCR6  0   0.261   3.4118  -0.1146   2.8339
 B5N  H2   H  HCR6  0   0.277   5.2398   1.5143   2.4963
 B5N  H3   H  HCR6  0   0.257   3.3799  -0.9615  -1.3562
 B5N  H4   H  HCR6  0   0.277   5.2147   0.6617  -1.6999
 B5N  H5   H  HCH2  0   0.255   2.5824  -2.6806   0.8033
 B5N  H6   H  HCH2  0   0.218   1.8409  -1.6480   2.0158
 B5N  H7   H  HCH2  0   0.244  -0.4332  -2.4521  -2.0123
 B5N  H8   H  HCH2  0   0.268  -1.6061  -3.2654  -0.9727
 B5N  H9   H  HCH2  0   0.202  -0.3211  -2.7337   1.0279
 B5N  H10  H  HCH2  0   0.249   0.7244  -3.5283  -0.1541
 B5N  H11  H  HCH2  0   0.275  -1.2650   0.8675  -0.5447
 B5N  H12  H  HCH2  0   0.249  -0.2352   0.1000  -1.7479
 B5N  H13  H  HCH2  0   0.255   1.0641   0.5909   0.2302
 B5N  H14  H  HCH2  0   0.207  -0.0842  -0.2358   1.2866
 B5N  H15  H  HCR6  0   0.252  -4.6309   2.2898   1.8421
 B5N  H16  H  HCR6  0   0.257  -5.3595   3.5990  -0.1088
 B5N  H17  H  HCR6  0   0.258  -4.9415   2.7462  -2.4014
 B5N  H18  H  HCR6  0   0.260  -3.7956   0.5821  -2.7075
 B5N  H19  H  HCH3  0   0.251  -2.2496  -0.1290   1.9565
 B5N  H20  H  HCH3  0   0.257  -3.7071   0.3526   2.8129
 B5N  H21  H  HCH3  0   0.249  -3.6909  -1.1243   1.8545

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
 B5N  C14  N09  single    1.449  0.020  1.449
 B5N  C14  C13  single    1.519  0.020  1.519
 B5N  C11  N09  single    1.450  0.020  1.450
 B5N  C11  C10  single    1.518  0.020  1.518
 B5N  N09  C08  single    1.450  0.020  1.450
 B5N  C21  C20  aromatic  1.388  0.020  1.388
 B5N  C21  C16  aromatic  1.389  0.020  1.389
 B5N  C20  C19  aromatic  1.387  0.020  1.387
 B5N  C13  N12  single    1.452  0.020  1.452
 B5N  F07  C04  single    1.345  0.020  1.345
 B5N  C06  C04  aromatic  1.383  0.020  1.383
 B5N  C06  C05  aromatic  1.386  0.020  1.386
 B5N  C04  C02  aromatic  1.379  0.020  1.379
 B5N  C10  N12  single    1.452  0.020  1.452
 B5N  C05  C03  aromatic  1.394  0.020  1.394
 B5N  N12  C15  single    1.345  0.020  1.345
 B5N  C02  C01  aromatic  1.390  0.020  1.390
 B5N  C03  C01  aromatic  1.390  0.020  1.390
 B5N  C03  C08  single    1.506  0.020  1.506
 B5N  C15  C16  single    1.501  0.020  1.501
 B5N  C15  O22  double    1.225  0.020  1.225
 B5N  C16  C18  aromatic  1.398  0.020  1.398
 B5N  C19  C17  aromatic  1.389  0.020  1.389
 B5N  C18  C17  aromatic  1.392  0.020  1.392
 B5N  C18  C23  single    1.501  0.020  1.501
 B5N  C01  H1   single    0.930  0.020  1.080
 B5N  C02  H2   single    0.930  0.020  1.080
 B5N  C05  H3   single    0.930  0.020  1.080
 B5N  C06  H4   single    0.930  0.020  1.080
 B5N  C08  H5   single    0.970  0.020  1.090
 B5N  C08  H6   single    0.970  0.020  1.090
 B5N  C10  H7   single    0.970  0.020  1.090
 B5N  C10  H8   single    0.970  0.020  1.090
 B5N  C11  H9   single    0.970  0.020  1.090
 B5N  C11  H10  single    0.970  0.020  1.090
 B5N  C13  H11  single    0.970  0.020  1.090
 B5N  C13  H12  single    0.970  0.020  1.090
 B5N  C14  H13  single    0.970  0.020  1.090
 B5N  C14  H14  single    0.970  0.020  1.090
 B5N  C17  H15  single    0.930  0.020  1.080
 B5N  C19  H16  single    0.930  0.020  1.080
 B5N  C20  H17  single    0.930  0.020  1.080
 B5N  C21  H18  single    0.930  0.020  1.080
 B5N  C23  H19  single    0.970  0.020  1.090
 B5N  C23  H20  single    0.970  0.020  1.090
 B5N  C23  H21  single    0.970  0.020  1.090

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
 B5N  H1   C01  C03  119.72  3.000
 B5N  H1   C01  C02  118.98  3.000
 B5N  C03  C01  C02  121.29  3.000
 B5N  H2   C02  C04  120.63  3.000
 B5N  H2   C02  C01  120.96  3.000
 B5N  C04  C02  C01  118.42  3.000
 B5N  C08  C03  C05  120.30  3.000
 B5N  C08  C03  C01  121.15  3.000
 B5N  C05  C03  C01  118.55  3.000
 B5N  F07  C04  C06  118.92  3.000
 B5N  C06  C04  C02  122.04  3.000
 B5N  F07  C04  C02  119.04  3.000
 B5N  H3   C05  C06  119.34  3.000
 B5N  H3   C05  C03  119.52  3.000
 B5N  C06  C05  C03  121.14  3.000
 B5N  H4   C06  C05  120.98  3.000
 B5N  H4   C06  C04  120.45  3.000
 B5N  C05  C06  C04  118.56  3.000
 B5N  H6   C08  H5   106.21  3.000
 B5N  H6   C08  N09  112.03  3.000
 B5N  H5   C08  N09  107.58  3.000
 B5N  H6   C08  C03  109.49  3.000
 B5N  H5   C08  C03  109.18  3.000
 B5N  N09  C08  C03  112.13  3.000
 B5N  H8   C10  H7   108.10  3.000
 B5N  H8   C10  N12  109.72  3.000
 B5N  H7   C10  N12  109.18  3.000
 B5N  H8   C10  C11  110.05  3.000
 B5N  H7   C10  C11  109.73  3.000
 B5N  N12  C10  C11  110.02  3.000
 B5N  H10  C11  H9   107.16  3.000
 B5N  H10  C11  N09  109.15  3.000
 B5N  H9   C11  N09  111.91  3.000
 B5N  H10  C11  C10  108.74  3.000
 B5N  H9   C11  C10  109.06  3.000
 B5N  N09  C11  C10  110.71  3.000
 B5N  H12  C13  H11  107.51  3.000
 B5N  H12  C13  N12  108.93  3.000
 B5N  H11  C13  N12  110.65  3.000
 B5N  H12  C13  C14  109.21  3.000
 B5N  H11  C13  C14  109.70  3.000
 B5N  N12  C13  C14  110.76  3.000
 B5N  H14  C14  H13  107.04  3.000
 B5N  H14  C14  N09  111.52  3.000
 B5N  H13  C14  N09  109.64  3.000
 B5N  H14  C14  C13  109.66  3.000
 B5N  H13  C14  C13  108.19  3.000
 B5N  N09  C14  C13  110.66  3.000
 B5N  O22  C15  N12  123.44  3.000
 B5N  O22  C15  C16  119.45  3.000
 B5N  N12  C15  C16  117.10  3.000
 B5N  C21  C16  C18  120.75  3.000
 B5N  C18  C16  C15  120.15  3.000
 B5N  C21  C16  C15  118.96  3.000
 B5N  H15  C17  C19  119.53  3.000
 B5N  H15  C17  C18  119.12  3.000
 B5N  C19  C17  C18  121.34  3.000
 B5N  C23  C18  C17  120.82  3.000
 B5N  C23  C18  C16  121.10  3.000
 B5N  C17  C18  C16  118.08  3.000
 B5N  H16  C19  C20  120.26  3.000
 B5N  H16  C19  C17  119.76  3.000
 B5N  C20  C19  C17  119.98  3.000
 B5N  H17  C20  C21  120.01  3.000
 B5N  H17  C20  C19  120.50  3.000
 B5N  C21  C20  C19  119.49  3.000
 B5N  H18  C21  C20  119.82  3.000
 B5N  H18  C21  C16  119.83  3.000
 B5N  C20  C21  C16  120.35  3.000
 B5N  H21  C23  H20  107.78  3.000
 B5N  H21  C23  H19  106.99  3.000
 B5N  H20  C23  H19  107.43  3.000
 B5N  H21  C23  C18  111.74  3.000
 B5N  H20  C23  C18  111.14  3.000
 B5N  H19  C23  C18  111.53  3.000
 B5N  C14  N09  C11  110.38  3.000
 B5N  C11  N09  C08  111.82  3.000
 B5N  C14  N09  C08  112.12  3.000
 B5N  C15  N12  C13  125.13  3.000
 B5N  C15  N12  C10  121.39  3.000
 B5N  C13  N12  C10  113.32  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
 B5N  CONST_01  C06  C04  C02  C01    0.00   0.0  0
 B5N  CONST_02  C06  C05  C03  C01    0.00   0.0  0
 B5N  CONST_03  C05  C06  C04  C02    0.00   0.0  0
 B5N  CONST_04  C05  C03  C01  C02    0.00   0.0  0
 B5N  CONST_05  C04  C06  C05  C03    0.00   0.0  0
 B5N  CONST_06  C04  C02  C01  C03    0.00   0.0  0
 B5N  CONST_07  C19  C20  C21  C16    0.00   0.0  0
 B5N  CONST_08  C19  C17  C18  C16    0.00   0.0  0
 B5N  CONST_09  C21  C20  C19  C17    0.00   0.0  0
 B5N  CONST_10  C21  C16  C18  C17    0.00   0.0  0
 B5N  CONST_11  C20  C21  C16  C18    0.00   0.0  0
 B5N  CONST_12  C20  C19  C17  C18    0.00   0.0  0
 B5N  CONST_13  F07  C04  C02  C01  180.00   0.0  0
 B5N  CONST_14  C08  C03  C01  C02  180.00   0.0  0
 B5N  CONST_15  F07  C04  C06  C05  180.00   0.0  0
 B5N  CONST_16  C08  C03  C05  C06  180.00   0.0  0
 B5N  CONST_17  C20  C21  C16  C15  180.00   0.0  0
 B5N  CONST_18  C17  C18  C16  C15  180.00   0.0  0
 B5N  CONST_19  C23  C18  C17  C19  180.00   0.0  0
 B5N  CONST_20  C23  C18  C16  C21  180.00   0.0  0
 B5N  CONST_21  C16  C15  N12  C10  180.00   0.0  0
 B5N  CONST_22  C16  C15  N12  C13    0.00   0.0  0
 B5N  CONST_23  H3   C05  C03  C01  180.00   0.0  0
 B5N  CONST_24  H4   C06  C04  C02  180.00   0.0  0
 B5N  CONST_25  H2   C02  C01  C03  180.00   0.0  0
 B5N  CONST_26  H1   C01  C02  C04  180.00   0.0  0
 B5N  CONST_27  H17  C20  C21  C16  180.00   0.0  0
 B5N  CONST_28  H15  C17  C18  C16  180.00   0.0  0
 B5N  CONST_29  H18  C21  C16  C18  180.00   0.0  0
 B5N  CONST_30  H16  C19  C17  C18  180.00   0.0  0
 B5N  CONST_31  O22  C15  N12  C10    0.00   0.0  0
 B5N  CONST_32  O22  C15  N12  C13  180.00   0.0  0
 B5N  Var_01    C14  N09  C11  C10   59.45  30.0  1
 B5N  Var_02    C14  C13  N12  C10  -53.32  30.0  1
 B5N  Var_03    C13  C14  N09  C11  -58.49  30.0  1
 B5N  Var_04    C13  N12  C10  C11   53.82  30.0  1
 B5N  Var_05    N12  C13  C14  N09   54.81  30.0  1
 B5N  Var_06    N12  C10  C11  N09  -56.26  30.0  1
 B5N  Var_07    N09  C08  C03  C01  131.14  30.0  2
 B5N  Var_08    N12  C15  C16  C18  -86.97  30.0  2
 B5N  Var_09    H19  C23  C18  C16   67.12  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
 B5N  plan-1  C01  0.020
 B5N  plan-1  C02  0.020
 B5N  plan-1  C03  0.020
 B5N  plan-1  C04  0.020
 B5N  plan-1  C05  0.020
 B5N  plan-1  C06  0.020
 B5N  plan-1  C08  0.020
 B5N  plan-1  F07  0.020
 B5N  plan-1  H1   0.020
 B5N  plan-1  H2   0.020
 B5N  plan-1  H3   0.020
 B5N  plan-1  H4   0.020
 B5N  plan-2  C15  0.020
 B5N  plan-2  C16  0.020
 B5N  plan-2  C17  0.020
 B5N  plan-2  C18  0.020
 B5N  plan-2  C19  0.020
 B5N  plan-2  C20  0.020
 B5N  plan-2  C21  0.020
 B5N  plan-2  C23  0.020
 B5N  plan-2  H15  0.020
 B5N  plan-2  H16  0.020
 B5N  plan-2  H17  0.020
 B5N  plan-2  H18  0.020
 B5N  plan-3  C10  0.020
 B5N  plan-3  C13  0.020
 B5N  plan-3  C15  0.020
 B5N  plan-3  C16  0.020
 B5N  plan-3  N12  0.020
 B5N  plan-3  O22  0.020

