# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:04:32 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (1R)-1-(4-chloro-2-fluoro-3-phenoxyphenyl)propan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]([NH3+])c1ccc(Cl)c(Oc2ccccc2)c1F
#
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
 DJL  DJL  (1R)-1-(4-chloro-2-fluoro-3-phenoxyphenyl)propan-1-aminium  ligand  35  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJL
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
 DJL  C1    C   CR16  0  -0.247  -3.1920  -1.8816  -1.3424
 DJL  C2    C   CR16  0  -0.268  -4.3146  -2.1731  -0.5830
 DJL  C3    C   CR16  0  -0.246  -4.4558  -1.5934   0.6725
 DJL  C4    C   CR16  0  -0.323  -3.4875  -0.7336   1.1653
 DJL  C5    C   CR6   0   0.368  -2.3683  -0.4528   0.3917
 DJL  C6    C   CR16  0  -0.337  -2.2110  -1.0200  -0.8644
 DJL  O7    O   O2    0  -0.490  -1.4610   0.4142   0.9479
 DJL  C8    C   CR6   0   0.245  -0.3100   0.6795   0.2882
 DJL  C9    C   CR6   0  -0.124  -0.1958   1.7731  -0.5584
 DJL  C10   C   CR16  0  -0.223   1.0141   2.0710  -1.1668
 DJL  C11   C   CR16  0  -0.299   2.1081   1.2569  -0.9372
 DJL  C12   C   CR6   0  -0.066   2.0279   0.1440  -0.1032
 DJL  C13   C   CR6   0   0.531   0.8069  -0.1194   0.4932
 DJL  CL1   CL  CL    0  -0.069  -1.5789   2.7545  -0.8280
 DJL  N20   N   NT3   1  -0.778   4.1630   0.0088   1.0649
 DJL  C23   C   CH2   0  -0.427   3.9495  -1.1660  -1.1115
 DJL  F23   F   F     0  -0.283   0.6672  -1.1712   1.3002
 DJL  C30   C   CH1   0  -0.236   3.2259  -0.7319   0.1572
 DJL  H30   H   HCH1  0   0.332   2.9363  -1.6181   0.7200
 DJL  HN20  H   HNT3  0   0.480   4.9848  -0.5499   1.2992
 DJL  HN2A  H   HNT3  0   0.472   4.5018   0.8791   0.6525
 DJL  HN2B  H   HNT3  0   0.484   3.7180   0.2519   1.9505
 DJL  H22   H   HCH3  0   0.230   5.9565  -1.6111  -0.3559
 DJL  H22A  H   HCH3  0   0.241   4.8232  -2.9631  -0.2564
 DJL  H22B  H   HCH3  0   0.262   5.5062  -2.4791  -1.8046
 DJL  H23   H   HCH2  0   0.254   4.2843  -0.2931  -1.6766
 DJL  H23A  H   HCH2  0   0.278   3.2063  -1.6689  -1.7314
 DJL  H11   H   HCR6  0   0.288   3.0433   1.5039  -1.4235
 DJL  H10   H   HCR6  0   0.298   1.0976   2.9270  -1.8209
 DJL  H4    H   HCR6  0   0.274  -3.5962  -0.2828   2.1435
 DJL  H3    H   HCR6  0   0.264  -5.3258  -1.8120   1.2779
 DJL  H2    H   HCR6  0   0.259  -5.0730  -2.8435  -0.9642
 DJL  H1    H   HCR6  0   0.266  -3.0679  -2.3236  -2.3222
 DJL  H6    H   HCR6  0   0.280  -1.3472  -0.8065  -1.4810
 DJL  C22   C   CH3   0  -0.689   5.1222  -2.1036  -0.8576

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
 DJL  C1   C2    aromatic  1.386  0.020  1.386
 DJL  C1   C6    aromatic  1.390  0.020  1.390
 DJL  C1   H1    single    0.930  0.020  1.080
 DJL  C2   C3    aromatic  1.390  0.020  1.390
 DJL  C2   H2    single    0.930  0.020  1.080
 DJL  C3   C4    aromatic  1.386  0.020  1.386
 DJL  C3   H3    single    0.930  0.020  1.080
 DJL  C4   C5    aromatic  1.389  0.020  1.389
 DJL  C4   H4    single    0.930  0.020  1.080
 DJL  C5   C6    aromatic  1.387  0.020  1.387
 DJL  C5   O7    single    1.373  0.020  1.373
 DJL  C6   H6    single    0.930  0.020  1.080
 DJL  O7   C8    single    1.353  0.020  1.353
 DJL  C8   C9    aromatic  1.388  0.020  1.388
 DJL  C8   C13   aromatic  1.388  0.020  1.388
 DJL  C9   C10   aromatic  1.387  0.020  1.387
 DJL  C9   CL1   single    1.717  0.020  1.717
 DJL  C10  C11   aromatic  1.383  0.020  1.383
 DJL  C10  H10   single    0.930  0.020  1.080
 DJL  C11  C12   aromatic  1.393  0.020  1.393
 DJL  C11  H11   single    0.930  0.020  1.080
 DJL  C12  C13   aromatic  1.384  0.020  1.384
 DJL  C12  C30   single    1.507  0.020  1.507
 DJL  C13  F23   single    1.333  0.020  1.333
 DJL  N20  C30   single    1.500  0.020  1.500
 DJL  N20  HN20  single    0.890  0.020  1.040
 DJL  N20  HN2A  single    0.890  0.020  1.040
 DJL  N20  HN2B  single    0.890  0.020  1.040
 DJL  C22  C23   single    1.523  0.020  1.523
 DJL  C22  H22   single    0.970  0.020  1.090
 DJL  C22  H22A  single    0.970  0.020  1.090
 DJL  C22  H22B  single    0.970  0.020  1.090
 DJL  C23  C30   single    1.524  0.020  1.524
 DJL  C23  H23   single    0.970  0.020  1.090
 DJL  C23  H23A  single    0.970  0.020  1.090
 DJL  C30  H30   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
 DJL  H1    C1   C6    118.92  3.000
 DJL  H1    C1   C2    120.20  3.000
 DJL  C6    C1   C2    120.89  3.000
 DJL  H2    C2   C3    120.37  3.000
 DJL  H2    C2   C1    120.34  3.000
 DJL  C3    C2   C1    119.29  3.000
 DJL  H3    C3   C4    119.22  3.000
 DJL  H3    C3   C2    120.18  3.000
 DJL  C4    C3   C2    120.60  3.000
 DJL  H4    C4   C5    119.99  3.000
 DJL  H4    C4   C3    120.64  3.000
 DJL  C5    C4   C3    119.37  3.000
 DJL  O7    C5   C6    123.38  3.000
 DJL  O7    C5   C4    115.76  3.000
 DJL  C6    C5   C4    120.86  3.000
 DJL  H6    C6   C5    121.71  3.000
 DJL  H6    C6   C1    119.30  3.000
 DJL  C5    C6   C1    118.99  3.000
 DJL  C8    O7   C5    119.25  3.000
 DJL  C13   C8   C9    118.51  3.000
 DJL  C13   C8   O7    119.97  3.000
 DJL  C9    C8   O7    121.47  3.000
 DJL  CL1   C9   C10   120.74  3.000
 DJL  CL1   C9   C8    118.68  3.000
 DJL  C10   C9   C8    120.59  3.000
 DJL  H10   C10  C11   120.38  3.000
 DJL  H10   C10  C9    120.21  3.000
 DJL  C11   C10  C9    119.40  3.000
 DJL  H11   C11  C12   120.06  3.000
 DJL  H11   C11  C10   118.33  3.000
 DJL  C12   C11  C10   121.62  3.000
 DJL  C30   C12  C13   121.09  3.000
 DJL  C30   C12  C11   121.48  3.000
 DJL  C13   C12  C11   117.43  3.000
 DJL  F23   C13  C12   120.22  3.000
 DJL  F23   C13  C8    117.33  3.000
 DJL  C12   C13  C8    122.45  3.000
 DJL  HN2B  N20  HN2A  106.99  3.000
 DJL  HN2B  N20  HN20  106.39  3.000
 DJL  HN2A  N20  HN20  106.97  3.000
 DJL  HN2B  N20  C30   111.74  3.000
 DJL  HN2A  N20  C30   112.57  3.000
 DJL  HN20  N20  C30   111.81  3.000
 DJL  H23A  C23  H23   106.45  3.000
 DJL  H23A  C23  C30   106.32  3.000
 DJL  H23   C23  C30   110.40  3.000
 DJL  H23A  C23  C22   109.62  3.000
 DJL  H23   C23  C22   110.01  3.000
 DJL  C30   C23  C22   113.73  3.000
 DJL  H30   C30  C23   108.95  3.000
 DJL  H30   C30  N20   104.78  3.000
 DJL  C23   C30  N20   110.35  3.000
 DJL  H30   C30  C12   110.54  3.000
 DJL  C23   C30  C12   113.54  3.000
 DJL  N20   C30  C12   108.31  3.000
 DJL  H22B  C22  H22A  107.72  3.000
 DJL  H22B  C22  H22   106.62  3.000
 DJL  H22A  C22  H22   108.17  3.000
 DJL  H22B  C22  C23   109.81  3.000
 DJL  H22A  C22  C23   111.47  3.000
 DJL  H22   C22  C23   112.81  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
 DJL  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 DJL  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 DJL  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 DJL  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 DJL  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 DJL  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 DJL  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 DJL  CONST_08  C11  C12  C13  C8     0.00   0.0  0
 DJL  CONST_09  C12  C13  C8   C9     0.00   0.0  0
 DJL  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 DJL  CONST_11  C13  C8   C9   C10    0.00   0.0  0
 DJL  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 DJL  CONST_13  O7   C5   C6   C1   180.00   0.0  0
 DJL  CONST_14  O7   C5   C4   C3   180.00   0.0  0
 DJL  CONST_15  C10  C9   C8   O7   180.00   0.0  0
 DJL  CONST_16  C12  C13  C8   O7   180.00   0.0  0
 DJL  CONST_17  C30  C12  C13  C8   180.00   0.0  0
 DJL  CONST_18  F23  C13  C8   C9   180.00   0.0  0
 DJL  CONST_19  C30  C12  C11  C10  180.00   0.0  0
 DJL  CONST_20  CL1  C9   C10  C11  180.00   0.0  0
 DJL  CONST_21  F23  C13  C12  C11  180.00   0.0  0
 DJL  CONST_22  CL1  C9   C8   C13  180.00   0.0  0
 DJL  CONST_23  H3   C3   C2   C1   180.00   0.0  0
 DJL  CONST_24  H6   C6   C1   C2   180.00   0.0  0
 DJL  CONST_25  H4   C4   C3   C2   180.00   0.0  0
 DJL  CONST_26  H1   C1   C2   C3   180.00   0.0  0
 DJL  CONST_27  H2   C2   C3   C4   180.00   0.0  0
 DJL  CONST_28  H10  C10  C9   C8   180.00   0.0  0
 DJL  CONST_29  H11  C11  C10  C9   180.00   0.0  0
 DJL  Var_01    C9   C8   O7   C5    93.84  30.0  2
 DJL  Var_02    H22  C22  C23  C30  -68.86  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
 DJL  chir_01  C30  C12  N20  C23  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
 DJL  plan-1  C1   0.020
 DJL  plan-1  C2   0.020
 DJL  plan-1  C3   0.020
 DJL  plan-1  C4   0.020
 DJL  plan-1  C5   0.020
 DJL  plan-1  C6   0.020
 DJL  plan-1  O7   0.020
 DJL  plan-1  H4   0.020
 DJL  plan-1  H3   0.020
 DJL  plan-1  H2   0.020
 DJL  plan-1  H1   0.020
 DJL  plan-1  H6   0.020
 DJL  plan-2  O7   0.020
 DJL  plan-2  C8   0.020
 DJL  plan-2  C9   0.020
 DJL  plan-2  C10  0.020
 DJL  plan-2  C11  0.020
 DJL  plan-2  C12  0.020
 DJL  plan-2  C13  0.020
 DJL  plan-2  CL1  0.020
 DJL  plan-2  F23  0.020
 DJL  plan-2  C30  0.020
 DJL  plan-2  H11  0.020
 DJL  plan-2  H10  0.020

