# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:44:39 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-[(2-chloranylphenoxazin-10-yl)methyl]cyclohexan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CC[C@H](CC1)CN2c3ccccc3Oc4ccc(Cl)cc24
#
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
 E2R  E2R  4-[(2-chloranylphenoxazin-10-yl)methyl]cyclohexan-1-amine  ligand  44  23  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E2R
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
 E2R  C4   C   CR16  0  -0.365  16.8907  -34.8761  -0.6573
 E2R  C5   C   CR16  0  -0.253  15.9329  -34.3636   0.2116
 E2R  C6   C   CR16  0  -0.277  15.8599  -34.8091   1.5175
 E2R  C7   C   CR16  0  -0.372  16.7594  -35.7770   1.9503
 E2R  C8   C   CR66  0   0.325  17.7113  -36.2780   1.0866
 E2R  C10  C   CR66  0   0.343  19.4867  -37.7783   0.7687
 E2R  C13  C   CR6   0  -0.047  21.4119  -38.9780  -0.7755
 E2R  C15  C   CR16  0  -0.386  20.3014  -38.7489   1.3084
 E2R  C17  C   CH2   0  -0.434  18.2278  -37.2244  -5.9965
 E2R  C20  C   CH2   0  -0.429  16.8267  -36.8226  -3.4556
 E2R  C21  C   CH2   0  -0.427  16.2393  -37.6868  -4.5656
 E2R  C22  C   CH1   0  -0.053  16.7047  -37.2269  -5.9421
 E2R  N2   N   NR6   0  -0.632  18.7873  -36.3831  -1.0716
 E2R  C19  C   CH1   0  -0.246  18.3534  -36.8115  -3.5070
 E2R  C11  C   CR66  0   0.358  19.6132  -37.3778  -0.5698
 E2R  C3   C   CR66  0   0.356  17.8038  -35.8426  -0.2422
 E2R  C12  C   CR16  0  -0.321  20.5936  -38.0044  -1.3367
 E2R  CL1  CL  CL    0  -0.132  22.6179  -39.7180  -1.7791
 E2R  C14  C   CR16  0  -0.243  21.2840  -39.3659   0.5399
 E2R  N23  N   NH2   0  -0.806  16.1722  -38.1139  -6.9670
 E2R  C18  C   CH2   0  -0.429  18.8292  -36.3665  -4.8894
 E2R  O9   O   O     0  -0.498  18.5622  -37.2172   1.5932
 E2R  H1   H   HCR6  0   0.268  16.9030  -34.5107  -1.6730
 E2R  H2   H   HCR6  0   0.257  15.2436  -33.6139  -0.1533
 E2R  H3   H   HCR6  0   0.258  15.1168  -34.4181   2.1985
 E2R  H4   H   HCR6  0   0.270  16.7289  -36.1475   2.9671
 E2R  H5   H   HCR6  0   0.280  20.1721  -39.0263   2.3467
 E2R  H7   H   HCH2  0   0.229  18.5674  -36.8649  -6.9725
 E2R  H8   H   HCH2  0   0.211  16.4564  -35.7967  -3.5641
 E2R  H9   H   HCH2  0   0.238  16.4765  -37.1812  -2.4849
 E2R  H10  H   HCH2  0   0.228  15.1465  -37.6645  -4.5123
 E2R  H11  H   HCH2  0   0.211  16.5398  -38.7310  -4.4249
 E2R  H12  H   HCH1  0   0.185  16.3682  -36.1844  -6.0762
 E2R  H15  H   HCH1  0   0.230  18.6980  -37.8417  -3.3495
 E2R  H16  H   HCR6  0   0.290  20.7349  -37.7474  -2.3754
 E2R  H17  H   HCR6  0   0.279  21.9206  -40.1254   0.9708
 E2R  H18  H   HNH2  0   0.339  15.1607  -38.0547  -6.9678
 E2R  H20  H   HNH2  0   0.339  16.4618  -37.7855  -7.8808
 E2R  H21  H   HCH2  0   0.233  19.9212  -36.4059  -4.9418
 E2R  H22  H   HCH2  0   0.216  18.5497  -35.3175  -5.0431
 E2R  C1   C   CH2   0  -0.349  18.9851  -35.9227  -2.4332
 E2R  H6   H   HCH2  0   0.211  18.5822  -38.2566  -5.9000
 E2R  H13  H   HCH2  0   0.269  20.0614  -35.8398  -2.6092
 E2R  H14  H   HCH2  0   0.276  18.6148  -34.9019  -2.5230

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
 E2R  N23  C22  single    1.456  0.020  1.456
 E2R  C17  C22  single    1.524  0.020  1.524
 E2R  C17  C18  single    1.524  0.020  1.524
 E2R  C22  C21  single    1.524  0.020  1.524
 E2R  C18  C19  single    1.528  0.020  1.528
 E2R  C21  C20  single    1.524  0.020  1.524
 E2R  C19  C20  single    1.528  0.020  1.528
 E2R  C19  C1   single    1.530  0.020  1.530
 E2R  C1   N2   single    1.451  0.020  1.451
 E2R  N2   C11  single    1.387  0.020  1.387
 E2R  N2   C3   single    1.396  0.020  1.396
 E2R  CL1  C13  single    1.735  0.020  1.735
 E2R  C12  C11  aromatic  1.393  0.020  1.393
 E2R  C12  C13  aromatic  1.390  0.020  1.390
 E2R  C4   C3   aromatic  1.393  0.020  1.393
 E2R  C4   C5   aromatic  1.391  0.020  1.391
 E2R  C11  C10  aromatic  1.403  0.020  1.403
 E2R  C13  C14  aromatic  1.377  0.020  1.377
 E2R  C3   C8   aromatic  1.401  0.020  1.401
 E2R  C5   C6   aromatic  1.382  0.020  1.382
 E2R  C10  O9   single    1.360  0.020  1.360
 E2R  C10  C15  aromatic  1.377  0.020  1.377
 E2R  C8   O9   single    1.365  0.020  1.365
 E2R  C8   C7   aromatic  1.379  0.020  1.379
 E2R  C14  C15  aromatic  1.392  0.020  1.392
 E2R  C6   C7   aromatic  1.390  0.020  1.390
 E2R  C4   H1   single    0.930  0.020  1.080
 E2R  C5   H2   single    0.930  0.020  1.080
 E2R  C6   H3   single    0.930  0.020  1.080
 E2R  C7   H4   single    0.930  0.020  1.080
 E2R  C15  H5   single    0.930  0.020  1.080
 E2R  C17  H6   single    0.970  0.020  1.090
 E2R  C17  H7   single    0.970  0.020  1.090
 E2R  C20  H8   single    0.970  0.020  1.090
 E2R  C20  H9   single    0.970  0.020  1.090
 E2R  C21  H10  single    0.970  0.020  1.090
 E2R  C21  H11  single    0.970  0.020  1.090
 E2R  C22  H12  single    0.970  0.020  1.090
 E2R  C1   H13  single    0.970  0.020  1.090
 E2R  C1   H14  single    0.970  0.020  1.090
 E2R  C19  H15  single    0.970  0.020  1.090
 E2R  C12  H16  single    0.930  0.020  1.080
 E2R  C14  H17  single    0.930  0.020  1.080
 E2R  N23  H18  single    0.890  0.020  1.040
 E2R  N23  H20  single    0.890  0.020  1.040
 E2R  C18  H21  single    0.970  0.020  1.090
 E2R  C18  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
 E2R  H1   C4   C3   120.52  3.000
 E2R  H1   C4   C5   118.09  3.000
 E2R  C3   C4   C5   121.39  3.000
 E2R  H2   C5   C6   120.57  3.000
 E2R  H2   C5   C4   118.90  3.000
 E2R  C6   C5   C4   120.52  3.000
 E2R  H3   C6   C7   120.02  3.000
 E2R  H3   C6   C5   121.00  3.000
 E2R  C7   C6   C5   118.98  3.000
 E2R  H4   C7   C8   118.89  3.000
 E2R  H4   C7   C6   120.82  3.000
 E2R  C8   C7   C6   120.29  3.000
 E2R  O9   C8   C3   121.64  3.000
 E2R  O9   C8   C7   116.60  3.000
 E2R  C3   C8   C7   121.76  3.000
 E2R  O9   C10  C11  121.47  3.000
 E2R  O9   C10  C15  117.08  3.000
 E2R  C11  C10  C15  121.45  3.000
 E2R  C14  C13  CL1  119.80  3.000
 E2R  C14  C13  C12  121.88  3.000
 E2R  CL1  C13  C12  118.33  3.000
 E2R  H5   C15  C14  120.03  3.000
 E2R  H5   C15  C10  119.07  3.000
 E2R  C14  C15  C10  120.91  3.000
 E2R  H7   C17  H6   106.72  3.000
 E2R  H7   C17  C18  109.91  3.000
 E2R  H6   C17  C18  109.80  3.000
 E2R  H7   C17  C22  110.03  3.000
 E2R  H6   C17  C22  108.58  3.000
 E2R  C18  C17  C22  111.67  3.000
 E2R  H9   C20  H8   106.67  3.000
 E2R  H9   C20  C19  110.65  3.000
 E2R  H8   C20  C19  109.12  3.000
 E2R  H9   C20  C21  109.72  3.000
 E2R  H8   C20  C21  109.17  3.000
 E2R  C19  C20  C21  111.39  3.000
 E2R  H11  C21  H10  106.68  3.000
 E2R  H11  C21  C22  108.65  3.000
 E2R  H10  C21  C22  110.04  3.000
 E2R  H11  C21  C20  109.95  3.000
 E2R  H10  C21  C20  109.75  3.000
 E2R  C22  C21  C20  111.65  3.000
 E2R  H12  C22  N23  112.23  3.000
 E2R  H12  C22  C21  107.55  3.000
 E2R  N23  C22  C21  109.89  3.000
 E2R  H12  C22  C17  107.39  3.000
 E2R  C21  C22  C17  109.75  3.000
 E2R  N23  C22  C17  109.96  3.000
 E2R  C3   N2   C11  118.84  3.000
 E2R  C3   N2   C1   122.07  3.000
 E2R  C11  N2   C1   119.08  3.000
 E2R  H15  C19  C18  107.78  3.000
 E2R  H15  C19  C1   108.35  3.000
 E2R  C18  C19  C1   109.70  3.000
 E2R  H15  C19  C20  107.58  3.000
 E2R  C1   C19  C20  113.15  3.000
 E2R  C18  C19  C20  110.10  3.000
 E2R  C12  C11  N2   122.84  3.000
 E2R  C12  C11  C10  117.40  3.000
 E2R  N2   C11  C10  119.75  3.000
 E2R  N2   C3   C8   119.33  3.000
 E2R  C8   C3   C4   117.06  3.000
 E2R  N2   C3   C4   123.61  3.000
 E2R  H16  C12  C11  120.98  3.000
 E2R  H16  C12  C13  118.56  3.000
 E2R  C11  C12  C13  120.46  3.000
 E2R  H17  C14  C15  120.49  3.000
 E2R  H17  C14  C13  121.60  3.000
 E2R  C15  C14  C13  117.91  3.000
 E2R  H20  N23  H18  105.41  3.000
 E2R  H20  N23  C22  109.44  3.000
 E2R  H18  N23  C22  109.27  3.000
 E2R  H22  C18  H21  106.39  3.000
 E2R  H22  C18  C19  109.03  3.000
 E2R  H21  C18  C19  110.10  3.000
 E2R  H22  C18  C17  109.64  3.000
 E2R  H21  C18  C17  109.80  3.000
 E2R  C19  C18  C17  111.73  3.000
 E2R  C10  O9   C8   118.86  3.000
 E2R  H14  C1   H13  104.49  3.000
 E2R  H14  C1   C19  110.25  3.000
 E2R  H13  C1   C19  109.71  3.000
 E2R  H14  C1   N2   109.16  3.000
 E2R  H13  C1   N2   108.01  3.000
 E2R  C19  C1   N2   114.70  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
 E2R  CONST_01  C7   C8   C3   C4      0.00   0.0  0
 E2R  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 E2R  CONST_03  C8   C3   C4   C5      0.00   0.0  0
 E2R  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 E2R  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 E2R  CONST_06  C3   C8   C7   C6      0.00   0.0  0
 E2R  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 E2R  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 E2R  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 E2R  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 E2R  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 E2R  CONST_12  C14  C15  C10  C11     0.00   0.0  0
 E2R  CONST_13  CL1  C13  C14  C15   180.00   0.0  0
 E2R  CONST_14  CL1  C13  C12  C11   180.00   0.0  0
 E2R  CONST_15  H3   C6   C5   C4    180.00   0.0  0
 E2R  CONST_16  H4   C7   C6   C5    180.00   0.0  0
 E2R  CONST_17  H1   C4   C5   C6    180.00   0.0  0
 E2R  CONST_18  H2   C5   C6   C7    180.00   0.0  0
 E2R  CONST_19  H16  C12  C11  C10   180.00   0.0  0
 E2R  CONST_20  H17  C14  C15  C10   180.00   0.0  0
 E2R  CONST_21  H5   C15  C14  C13   180.00   0.0  0
 E2R  Var_01    C11  N2   C3   C4   -177.59  30.0  1
 E2R  Var_02    C11  C10  O9   C8      2.34  30.0  1
 E2R  Var_03    C3   N2   C11  C10    -2.81  30.0  1
 E2R  Var_04    C3   C8   O9   C10    -2.60  30.0  1
 E2R  Var_05    C19  C18  C17  C22    56.17  30.0  1
 E2R  Var_06    C19  C20  C21  C22   -56.93  30.0  1

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
 E2R  chir_01  C22  N23  C17  C21  positiv
 E2R  chir_02  C19  C18  C20  C1   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
 E2R  plan-1  C4   0.020
 E2R  plan-1  C5   0.020
 E2R  plan-1  C6   0.020
 E2R  plan-1  C7   0.020
 E2R  plan-1  C8   0.020
 E2R  plan-1  N2   0.020
 E2R  plan-1  C3   0.020
 E2R  plan-1  O9   0.020
 E2R  plan-1  H1   0.020
 E2R  plan-1  H2   0.020
 E2R  plan-1  H3   0.020
 E2R  plan-1  H4   0.020
 E2R  plan-2  C10  0.020
 E2R  plan-2  C13  0.020
 E2R  plan-2  C15  0.020
 E2R  plan-2  N2   0.020
 E2R  plan-2  C11  0.020
 E2R  plan-2  C12  0.020
 E2R  plan-2  CL1  0.020
 E2R  plan-2  C14  0.020
 E2R  plan-2  O9   0.020
 E2R  plan-2  H5   0.020
 E2R  plan-2  H16  0.020
 E2R  plan-2  H17  0.020

