# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:17:04 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCNCc1ccc(c(Cl)c1)c2ccccc2
#
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
 54R  54R  N-(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)acetamide  ligand  43  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_54R
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
 54R  C1   C   C     0   0.521  -7.9336  -0.0020   0.7482
 54R  C3   C   CH2   0  -0.500  -4.2909  -0.1939   0.0284
 54R  C4   C   CH2   0  -0.251  -3.3459   0.1517  -1.1113
 54R  C5   C   CH2   0  -0.315  -1.0220   0.1927  -1.7840
 54R  C7   C   CR16  0  -0.290   1.3311  -0.6780  -2.0736
 54R  C8   C   CR16  0  -0.296   2.6348  -0.8266  -1.6253
 54R  C9   C   CR6   0   0.139   3.0534  -0.3055  -0.4026
 54R  C10  C   CR6   0  -0.106   2.0944   0.3670   0.3565
 54R  C11  C   CR16  0  -0.226   0.7894   0.5206  -0.0784
 54R  C12  C   CR6   0   0.061   4.4519  -0.4977   0.0390
 54R  C14  C   CR16  0  -0.243   6.6011   0.3933   0.6858
 54R  C15  C   CR16  0  -0.263   7.1064  -0.8945   0.8164
 54R  C16  C   CR16  0  -0.242   6.2873  -1.9835   0.5522
 54R  C17  C   CR16  0  -0.292   4.9692  -1.7857   0.1633
 54R  CL   CL  CL    0  -0.132   2.5041   0.9973   1.9223
 54R  C13  C   CR16  0  -0.284   5.2832   0.5908   0.3017
 54R  C6   C   CR6   0   0.068   0.3938   0.0047  -1.3087
 54R  N1   N   NH1   0  -0.596  -1.9723  -0.1215  -0.7370
 54R  C2   C   CH2   0  -0.235  -5.7343   0.1246  -0.3225
 54R  N    N   NH1   0  -0.633  -6.6126  -0.2282   0.7731
 54R  O    O   O     0  -0.514  -8.4923   0.5144  -0.2128
 54R  C    C   CH3   0  -0.777  -8.6926  -0.4152   1.9843
 54R  H1   H   HCH2  0   0.235  -4.1985  -1.2588   0.2669
 54R  H2   H   HCH2  0   0.237  -3.9926   0.3616   0.9220
 54R  H3   H   HCH2  0   0.195  -3.6566  -0.3873  -2.0206
 54R  H4   H   HCH2  0   0.223  -3.4301   1.2180  -1.3442
 54R  H5   H   HCH2  0   0.244  -1.1677   1.2412  -2.0649
 54R  H6   H   HCH2  0   0.219  -1.1768  -0.3911  -2.7036
 54R  H7   H   HCR6  0   0.257   1.0448  -1.0986  -3.0297
 54R  H8   H   HCR6  0   0.261   3.3526  -1.3581  -2.2375
 54R  H9   H   HCR6  0   0.269   0.0683   1.0332   0.5445
 54R  H10  H   HCR6  0   0.258   7.2360   1.2482   0.8798
 54R  H11  H   HCR6  0   0.258   8.1339  -1.0480   1.1198
 54R  H12  H   HCR6  0   0.258   6.6718  -2.9902   0.6517
 54R  H13  H   HCR6  0   0.254   4.3335  -2.6404  -0.0337
 54R  H14  H   HCR6  0   0.254   4.9039   1.5984   0.1903
 54R  H15  H   HNH1  0   0.344  -1.8819  -1.1019  -0.4961
 54R  H17  H   HCH2  0   0.232  -5.8341   1.1897  -0.5497
 54R  H18  H   HCH2  0   0.231  -6.0287  -0.4192  -1.2251
 54R  H19  H   HNH1  0   0.401  -6.2048  -0.6462   1.5930
 54R  H20  H   HCH3  0   0.248  -8.0813  -0.9344   2.7199
 54R  H21  H   HCH3  0   0.265  -9.1208   0.4686   2.4576
 54R  H22  H   HCH3  0   0.263  -9.5211  -1.0644   1.7025

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
 54R  C16  C17  aromatic  1.388  0.020  1.388
 54R  C16  C15  aromatic  1.388  0.020  1.388
 54R  C17  C12  aromatic  1.394  0.020  1.394
 54R  C15  C14  aromatic  1.390  0.020  1.390
 54R  C8   C7   aromatic  1.387  0.020  1.387
 54R  C8   C9   aromatic  1.393  0.020  1.393
 54R  C12  C9   single    1.479  0.020  1.479
 54R  C12  C13  aromatic  1.395  0.020  1.395
 54R  C7   C6   aromatic  1.389  0.020  1.389
 54R  C14  C13  aromatic  1.387  0.020  1.387
 54R  C9   C10  aromatic  1.396  0.020  1.396
 54R  C6   C5   single    1.505  0.020  1.505
 54R  C6   C11  aromatic  1.392  0.020  1.392
 54R  C10  C11  aromatic  1.384  0.020  1.384
 54R  C10  CL   single    1.737  0.020  1.737
 54R  C5   N1   single    1.448  0.020  1.448
 54R  C4   N1   single    1.450  0.020  1.450
 54R  C4   C3   single    1.520  0.020  1.520
 54R  C2   C3   single    1.519  0.020  1.519
 54R  C2   N    single    1.448  0.020  1.448
 54R  N    C1   single    1.340  0.020  1.340
 54R  O    C1   double    1.226  0.020  1.226
 54R  C1   C    single    1.508  0.020  1.508
 54R  C3   H1   single    0.970  0.020  1.090
 54R  C3   H2   single    0.970  0.020  1.090
 54R  C4   H3   single    0.970  0.020  1.090
 54R  C4   H4   single    0.970  0.020  1.090
 54R  C5   H5   single    0.970  0.020  1.090
 54R  C5   H6   single    0.970  0.020  1.090
 54R  C7   H7   single    0.930  0.020  1.080
 54R  C8   H8   single    0.930  0.020  1.080
 54R  C11  H9   single    0.930  0.020  1.080
 54R  C14  H10  single    0.930  0.020  1.080
 54R  C15  H11  single    0.930  0.020  1.080
 54R  C16  H12  single    0.930  0.020  1.080
 54R  C17  H13  single    0.930  0.020  1.080
 54R  C13  H14  single    0.930  0.020  1.080
 54R  N1   H15  single    0.890  0.020  1.040
 54R  C2   H17  single    0.970  0.020  1.090
 54R  C2   H18  single    0.970  0.020  1.090
 54R  N    H19  single    0.860  0.020  1.020
 54R  C    H20  single    0.970  0.020  1.090
 54R  C    H21  single    0.970  0.020  1.090
 54R  C    H22  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
 54R  C    C1   O    121.91  3.000
 54R  C    C1   N    115.76  3.000
 54R  O    C1   N    122.33  3.000
 54R  H2   C3   H1   107.04  3.000
 54R  H2   C3   C2   109.96  3.000
 54R  H1   C3   C2   109.53  3.000
 54R  H2   C3   C4   109.12  3.000
 54R  H1   C3   C4   109.38  3.000
 54R  C2   C3   C4   111.70  3.000
 54R  H4   C4   H3   106.22  3.000
 54R  H4   C4   N1   108.14  3.000
 54R  H3   C4   N1   112.84  3.000
 54R  H4   C4   C3   109.46  3.000
 54R  H3   C4   C3   109.40  3.000
 54R  N1   C4   C3   110.64  3.000
 54R  H6   C5   H5   105.95  3.000
 54R  H6   C5   N1   113.38  3.000
 54R  H5   C5   N1   107.80  3.000
 54R  H6   C5   C6   109.27  3.000
 54R  H5   C5   C6   109.01  3.000
 54R  N1   C5   C6   111.21  3.000
 54R  H7   C7   C6   119.90  3.000
 54R  H7   C7   C8   119.50  3.000
 54R  C6   C7   C8   120.60  3.000
 54R  H8   C8   C9   118.72  3.000
 54R  H8   C8   C7   119.54  3.000
 54R  C9   C8   C7   121.74  3.000
 54R  C12  C9   C10  123.36  3.000
 54R  C10  C9   C8   116.81  3.000
 54R  C12  C9   C8   119.83  3.000
 54R  CL   C10  C11  117.74  3.000
 54R  CL   C10  C9   120.20  3.000
 54R  C11  C10  C9   122.03  3.000
 54R  H9   C11  C6   119.69  3.000
 54R  H9   C11  C10  120.00  3.000
 54R  C6   C11  C10  120.31  3.000
 54R  C13  C12  C17  118.90  3.000
 54R  C13  C12  C9   121.23  3.000
 54R  C17  C12  C9   119.85  3.000
 54R  H10  C14  C13  119.64  3.000
 54R  H10  C14  C15  120.13  3.000
 54R  C13  C14  C15  120.23  3.000
 54R  H11  C15  C16  120.16  3.000
 54R  H11  C15  C14  120.20  3.000
 54R  C16  C15  C14  119.65  3.000
 54R  H12  C16  C17  119.71  3.000
 54R  H12  C16  C15  120.17  3.000
 54R  C17  C16  C15  120.12  3.000
 54R  H13  C17  C16  119.71  3.000
 54R  H13  C17  C12  119.68  3.000
 54R  C16  C17  C12  120.60  3.000
 54R  H14  C13  C14  119.61  3.000
 54R  H14  C13  C12  119.89  3.000
 54R  C14  C13  C12  120.50  3.000
 54R  C11  C6   C7   118.51  3.000
 54R  C11  C6   C5   120.01  3.000
 54R  C7   C6   C5   121.48  3.000
 54R  H15  N1   C5   108.85  3.000
 54R  H15  N1   C4   109.15  3.000
 54R  C5   N1   C4   113.21  3.000
 54R  H18  C2   H17  106.74  3.000
 54R  H18  C2   N    109.87  3.000
 54R  H17  C2   N    109.83  3.000
 54R  H18  C2   C3   110.00  3.000
 54R  H17  C2   C3   109.81  3.000
 54R  N    C2   C3   110.52  3.000
 54R  H19  N    C2   118.15  3.000
 54R  H19  N    C1   118.97  3.000
 54R  C2   N    C1   122.87  3.000
 54R  H22  C    H21  107.26  3.000
 54R  H22  C    H20  108.53  3.000
 54R  H21  C    H20  108.29  3.000
 54R  H22  C    C1   109.51  3.000
 54R  H21  C    C1   109.35  3.000
 54R  H20  C    C1   113.70  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
 54R  CONST_01  C12  C9   C8   C7    180.00   0.0  0
 54R  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 54R  CONST_03  C10  C11  C6   C7      0.00   0.0  0
 54R  CONST_04  C11  C6   C7   C8      0.00   0.0  0
 54R  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 54R  CONST_08  C6   C7   C8   C9      0.00   0.0  0
 54R  CONST_09  C16  C17  C12  C9    180.00   0.0  0
 54R  CONST_10  C14  C13  C12  C9    180.00   0.0  0
 54R  CONST_11  C6   C11  C10  C9      0.00   0.0  0
 54R  CONST_14  C12  C9   C10  C11   180.00   0.0  0
 54R  CONST_15  C15  C16  C17  C12     0.00   0.0  0
 54R  CONST_16  C15  C14  C13  C12     0.00   0.0  0
 54R  CONST_17  C17  C16  C15  C14     0.00   0.0  0
 54R  CONST_18  C17  C12  C13  C14     0.00   0.0  0
 54R  CONST_19  C13  C12  C17  C16     0.00   0.0  0
 54R  CONST_20  C13  C14  C15  C16     0.00   0.0  0
 54R  CONST_21  C8   C7   C6   C5    180.00   0.0  0
 54R  CONST_22  C10  C11  C6   C5    180.00   0.0  0
 54R  CONST_23  CL   C10  C9   C8    180.00   0.0  0
 54R  CONST_24  CL   C10  C9   C12     0.00   0.0  0
 54R  CONST_25  C6   C11  C10  CL    180.00   0.0  0
 54R  CONST_26  H9   C11  C6   C7    180.00   0.0  0
 54R  CONST_27  H7   C7   C8   C9    180.00   0.0  0
 54R  CONST_28  H13  C17  C12  C9      0.00   0.0  0
 54R  CONST_29  H14  C13  C12  C9      0.00   0.0  0
 54R  CONST_30  H8   C8   C9   C10   180.00   0.0  0
 54R  CONST_31  H12  C16  C17  C12   180.00   0.0  0
 54R  CONST_32  H10  C14  C13  C12   180.00   0.0  0
 54R  CONST_33  H11  C15  C16  C17   180.00   0.0  0
 54R  CONST_34  O    C1   N    C2      0.00   0.0  0
 54R  CONST_35  C    C1   N    C2    180.00   0.0  0
 54R  CONST_36  H19  N    C1   O     180.00   0.0  0
 54R  Var_01    N1   C5   C6   C7    133.30  30.0  2
 54R  Var_02    C6   C5   N1   C4    175.14  30.0  2
 54R  Var_03    C3   C2   N    C1    177.27  30.0  2
 54R  Var_04    C5   N1   C4   C3   -179.82  30.0  3
 54R  Var_05    N    C2   C3   C4    179.34  30.0  2
 54R  Var_06    C2   C3   C4   N1    178.20  30.0  3
 54R  Var_07    H20  C    C1   N      -5.22  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
 54R  plan-1  C5   0.020
 54R  plan-1  C7   0.020
 54R  plan-1  C8   0.020
 54R  plan-1  C9   0.020
 54R  plan-1  C10  0.020
 54R  plan-1  C11  0.020
 54R  plan-1  C12  0.020
 54R  plan-1  CL   0.020
 54R  plan-1  C6   0.020
 54R  plan-1  H7   0.020
 54R  plan-1  H8   0.020
 54R  plan-1  H9   0.020
 54R  plan-2  C9   0.020
 54R  plan-2  C12  0.020
 54R  plan-2  C14  0.020
 54R  plan-2  C15  0.020
 54R  plan-2  C16  0.020
 54R  plan-2  C17  0.020
 54R  plan-2  C13  0.020
 54R  plan-2  H10  0.020
 54R  plan-2  H11  0.020
 54R  plan-2  H12  0.020
 54R  plan-2  H13  0.020
 54R  plan-2  H14  0.020
 54R  plan-3  C1   0.020
 54R  plan-3  C2   0.020
 54R  plan-3  N    0.020
 54R  plan-3  O    0.020
 54R  plan-3  C    0.020
 54R  plan-3  H19  0.020

