# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:59:03 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2S)-2-[(4-chlorobenzyl)oxy]-2-phenylethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](OCc1ccc(Cl)cc1)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
 VU2  VU2  (2S)-2-[(4-chlorobenzyl)oxy]-2-phenylethanamine  ligand  34  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VU2
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
 VU2  C1    C   CH2   0  -0.273   2.1482  -1.9573   0.7793
 VU2  C2    C   CR16  0  -0.270   5.2470   1.9457   0.3534
 VU2  C3    C   CR16  0  -0.242   5.4476   0.8133  -0.4255
 VU2  C7    C   CR16  0  -0.239   3.9962   2.1807   0.9089
 VU2  C9    C   CH2   0  -0.195  -0.1032  -0.5229  -1.2734
 VU2  C10   C   CR6   0   0.074  -1.5103  -0.3865  -0.7658
 VU2  C11   C   CR16  0  -0.317  -2.4068   0.4995  -1.3477
 VU2  C12   C   CR16  0  -0.199  -3.7095   0.6155  -0.8771
 VU2  C13   C   CR6   0  -0.052  -4.1045  -0.1634   0.1963
 VU2  C14   C   CR16  0  -0.201  -3.2259  -1.0536   0.7997
 VU2  C15   C   CR16  0  -0.296  -1.9332  -1.1598   0.3146
 VU2  N2    N   NH2   0  -0.782   1.1575  -2.9963   0.5679
 VU2  C4    C   CR16  0  -0.301   4.4029  -0.0746  -0.6415
 VU2  C5    C   CR6   0   0.091   3.1462   0.1518  -0.0859
 VU2  C6    C   CR16  0  -0.308   2.9525   1.2900   0.6922
 VU2  O1    O   O2    0  -0.493   0.7853  -0.2442  -0.2165
 VU2  CL    CL  CL    0  -0.134  -5.7257  -0.0274   0.8001
 VU2  C8    C   CH1   0  -0.005   2.0478  -0.8647  -0.2854
 VU2  H11C  H   HCH2  0   0.225   1.9721  -1.4990   1.7565
 VU2  H12C  H   HCH2  0   0.203   3.1829  -2.3272   0.7915
 VU2  H21N  H   HNH2  0   0.343   1.4224  -3.5656  -0.2264
 VU2  H22N  H   HNH2  0   0.352   1.1491  -3.6186   1.3651
 VU2  H8    H   HCH1  0   0.228   2.1937  -1.3291  -1.2710
 VU2  H3    H   HCR6  0   0.254   6.4165   0.6232  -0.8695
 VU2  H7    H   HCR6  0   0.253   3.8301   3.0623   1.5151
 VU2  H4    H   HCR6  0   0.248   4.5667  -0.9531  -1.2559
 VU2  H6    H   HCR6  0   0.248   1.9835   1.4908   1.1302
 VU2  H91C  H   HCH2  0   0.221   0.0445  -1.5412  -1.6481
 VU2  H92C  H   HCH2  0   0.221   0.0596   0.1578  -2.1192
 VU2  H11   H   HCR6  0   0.262  -2.0934   1.1137  -2.1831
 VU2  H15   H   HCR6  0   0.277  -1.2424  -1.8606   0.7694
 VU2  H12   H   HCR6  0   0.278  -4.3975   1.3107  -1.3386
 VU2  H14   H   HCR6  0   0.276  -3.5457  -1.6543   1.6410
 VU2  H2    H   HCR6  0   0.254   6.0590   2.6407   0.5241

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
 VU2  C1   N2    single    1.451  0.020  1.451
 VU2  C1   C8    single    1.529  0.020  1.529
 VU2  C2   C3    aromatic  1.389  0.020  1.389
 VU2  C2   C7    aromatic  1.389  0.020  1.389
 VU2  C3   C4    aromatic  1.388  0.020  1.388
 VU2  C7   C6    aromatic  1.389  0.020  1.389
 VU2  C9   C10   single    1.502  0.020  1.502
 VU2  C9   O1    single    1.409  0.020  1.409
 VU2  C10  C11   aromatic  1.388  0.020  1.388
 VU2  C10  C15   aromatic  1.394  0.020  1.394
 VU2  C11  C12   aromatic  1.390  0.020  1.390
 VU2  C12  C13   aromatic  1.384  0.020  1.384
 VU2  C13  C14   aromatic  1.389  0.020  1.389
 VU2  C13  CL    single    1.735  0.020  1.735
 VU2  C14  C15   aromatic  1.385  0.020  1.385
 VU2  C4   C5    aromatic  1.393  0.020  1.393
 VU2  C5   C6    aromatic  1.392  0.020  1.392
 VU2  C5   C8    single    1.510  0.020  1.510
 VU2  O1   C8    single    1.408  0.020  1.408
 VU2  C1   H11C  single    0.970  0.020  1.090
 VU2  C1   H12C  single    0.970  0.020  1.090
 VU2  N2   H21N  single    0.890  0.020  1.040
 VU2  N2   H22N  single    0.890  0.020  1.040
 VU2  C8   H8    single    0.970  0.020  1.090
 VU2  C2   H2    single    0.930  0.020  1.080
 VU2  C3   H3    single    0.930  0.020  1.080
 VU2  C7   H7    single    0.930  0.020  1.080
 VU2  C4   H4    single    0.930  0.020  1.080
 VU2  C6   H6    single    0.930  0.020  1.080
 VU2  C9   H91C  single    0.970  0.020  1.090
 VU2  C9   H92C  single    0.970  0.020  1.090
 VU2  C11  H11   single    0.930  0.020  1.080
 VU2  C15  H15   single    0.930  0.020  1.080
 VU2  C12  H12   single    0.930  0.020  1.080
 VU2  C14  H14   single    0.930  0.020  1.080

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
 VU2  H12C  C1   H11C  106.42  3.000
 VU2  H12C  C1   C8    108.07  3.000
 VU2  H11C  C1   C8    108.19  3.000
 VU2  H12C  C1   N2    113.80  3.000
 VU2  H11C  C1   N2    108.68  3.000
 VU2  C8    C1   N2    111.44  3.000
 VU2  H2    C2   C7    120.26  3.000
 VU2  H2    C2   C3    120.24  3.000
 VU2  C7    C2   C3    119.50  3.000
 VU2  H3    C3   C4    119.82  3.000
 VU2  H3    C3   C2    120.17  3.000
 VU2  C4    C3   C2    120.01  3.000
 VU2  H7    C7   C6    119.61  3.000
 VU2  H7    C7   C2    120.00  3.000
 VU2  C6    C7   C2    120.39  3.000
 VU2  H92C  C9   H91C  107.03  3.000
 VU2  H92C  C9   O1    111.22  3.000
 VU2  H91C  C9   O1    110.83  3.000
 VU2  H92C  C9   C10   110.06  3.000
 VU2  H91C  C9   C10   109.05  3.000
 VU2  O1    C9   C10   108.63  3.000
 VU2  C15   C10  C11   118.87  3.000
 VU2  C15   C10  C9    119.71  3.000
 VU2  C11   C10  C9    121.42  3.000
 VU2  H11   C11  C12   119.01  3.000
 VU2  H11   C11  C10   119.89  3.000
 VU2  C12   C11  C10   121.10  3.000
 VU2  H12   C12  C13   120.75  3.000
 VU2  H12   C12  C11   120.36  3.000
 VU2  C13   C12  C11   118.89  3.000
 VU2  CL    C13  C14   119.35  3.000
 VU2  CL    C13  C12   119.50  3.000
 VU2  C14   C13  C12   121.15  3.000
 VU2  H14   C14  C15   120.38  3.000
 VU2  H14   C14  C13   120.45  3.000
 VU2  C15   C14  C13   119.17  3.000
 VU2  H15   C15  C14   119.83  3.000
 VU2  H15   C15  C10   119.36  3.000
 VU2  C14   C15  C10   120.80  3.000
 VU2  H22N  N2   H21N  105.94  3.000
 VU2  H22N  N2   C1    109.36  3.000
 VU2  H21N  N2   C1    109.77  3.000
 VU2  H4    C4   C5    119.61  3.000
 VU2  H4    C4   C3    119.52  3.000
 VU2  C5    C4   C3    120.87  3.000
 VU2  C8    C5   C6    121.53  3.000
 VU2  C8    C5   C4    119.63  3.000
 VU2  C6    C5   C4    118.78  3.000
 VU2  H6    C6   C5    120.16  3.000
 VU2  H6    C6   C7    119.38  3.000
 VU2  C5    C6   C7    120.45  3.000
 VU2  C8    O1   C9    116.20  3.000
 VU2  H8    C8   O1    110.42  3.000
 VU2  H8    C8   C5    107.84  3.000
 VU2  O1    C8   C5    110.43  3.000
 VU2  H8    C8   C1    108.28  3.000
 VU2  O1    C8   C1    109.85  3.000
 VU2  C5    C8   C1    109.96  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
 VU2  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 VU2  CONST_02  C5    C6   C7   C2     0.00   0.0  0
 VU2  CONST_03  C6    C7   C2   C3     0.00   0.0  0
 VU2  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 VU2  CONST_05  C4    C3   C2   C7     0.00   0.0  0
 VU2  CONST_06  C4    C5   C6   C7     0.00   0.0  0
 VU2  CONST_07  C13   C12  C11  C10    0.00   0.0  0
 VU2  CONST_08  C13   C14  C15  C10    0.00   0.0  0
 VU2  CONST_09  C14   C15  C10  C11    0.00   0.0  0
 VU2  CONST_10  C14   C13  C12  C11    0.00   0.0  0
 VU2  CONST_11  C15   C10  C11  C12    0.00   0.0  0
 VU2  CONST_12  C15   C14  C13  C12    0.00   0.0  0
 VU2  CONST_13  C8    C5   C4   C3   180.00   0.0  0
 VU2  CONST_14  C8    C5   C6   C7   180.00   0.0  0
 VU2  CONST_15  C12   C11  C10  C9   180.00   0.0  0
 VU2  CONST_16  C14   C15  C10  C9   180.00   0.0  0
 VU2  CONST_17  CL    C13  C12  C11  180.00   0.0  0
 VU2  CONST_18  CL    C13  C14  C15  180.00   0.0  0
 VU2  CONST_19  H4    C4   C3   C2   180.00   0.0  0
 VU2  CONST_20  H6    C6   C7   C2   180.00   0.0  0
 VU2  CONST_21  H7    C7   C2   C3   180.00   0.0  0
 VU2  CONST_22  H3    C3   C2   C7   180.00   0.0  0
 VU2  CONST_23  H12   C12  C11  C10  180.00   0.0  0
 VU2  CONST_24  H14   C14  C15  C10  180.00   0.0  0
 VU2  CONST_25  H15   C15  C10  C11  180.00   0.0  0
 VU2  CONST_26  H11   C11  C12  C13  180.00   0.0  0
 VU2  CONST_27  H2    C2   C3   C4   180.00   0.0  0
 VU2  Var_01    O1    C9   C10  C11  122.05  30.0  2
 VU2  Var_02    H21N  N2   C1   C8    73.36  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
 VU2  chir_01  C8  C1  C5  O1  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
 VU2  plan-1  C2   0.020
 VU2  plan-1  C3   0.020
 VU2  plan-1  C7   0.020
 VU2  plan-1  C4   0.020
 VU2  plan-1  C5   0.020
 VU2  plan-1  C6   0.020
 VU2  plan-1  C8   0.020
 VU2  plan-1  H3   0.020
 VU2  plan-1  H7   0.020
 VU2  plan-1  H4   0.020
 VU2  plan-1  H6   0.020
 VU2  plan-1  H2   0.020
 VU2  plan-2  C9   0.020
 VU2  plan-2  C10  0.020
 VU2  plan-2  C11  0.020
 VU2  plan-2  C12  0.020
 VU2  plan-2  C13  0.020
 VU2  plan-2  C14  0.020
 VU2  plan-2  C15  0.020
 VU2  plan-2  CL   0.020
 VU2  plan-2  H11  0.020
 VU2  plan-2  H15  0.020
 VU2  plan-2  H12  0.020
 VU2  plan-2  H14  0.020

