# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 06:40:51 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{S},3~{R})-8,9-dimethoxy-3-[2,4,5-tris(fluoranyl)phenyl]-2,3-dihydro-1~{H}-benzo[f]chromen-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ccc3O[C@@H]([C@@H](N)Cc3c2cc1OC)c4cc(F)c(F)cc4F
#
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
 HL1  HL1  (2~{S},3~{R})-8,9-dimethoxy-3-[2,4,5-tris(fluoranyl)phenyl]-2,3-dihydro-1~{H}-benzo[f]chromen-2-amine  ligand  46  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HL1
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
 HL1  C1   C  CR6   0   0.540  -4.0745  -0.7278  -1.1708
 HL1  C2   C  CR6   0  -0.134  -3.1869  -0.0865  -0.3237
 HL1  C3   C  CR16  0  -0.433  -3.7240   0.7085   0.6879
 HL1  C4   C  CR6   0   0.410  -5.0865   0.8415   0.8245
 HL1  C5   C  CR6   0   0.409  -5.9456   0.1875  -0.0433
 HL1  C6   C  CR16  0  -0.557  -5.4478  -0.6062  -1.0523
 HL1  F7   F  F     0  -0.299  -3.6040  -1.5015  -2.1568
 HL1  F8   F  F     0  -0.298  -7.2619   0.3336   0.1057
 HL1  F9   F  F     0  -0.304  -5.5987   1.6048   1.7948
 HL1  C10  C  CH1   0   0.015  -1.7000  -0.2602  -0.4463
 HL1  O11  O  O2    0  -0.494  -1.1201   1.0275  -0.3300
 HL1  C12  C  CR6   0   0.344   0.2354   1.0719  -0.2753
 HL1  C13  C  CR6   0  -0.044   1.0073  -0.0227   0.0419
 HL1  C14  C  CH2   0  -0.515   0.3599  -1.3331   0.3911
 HL1  C15  C  CH1   0  -0.096  -1.1366  -1.1904   0.6287
 HL1  N16  N  NH2   0  -0.802  -1.7805  -2.4858   0.5276
 HL1  C17  C  CR66  0   0.120   2.4223   0.1160   0.0249
 HL1  C20  C  CR66  0   0.089   3.0087   1.3647  -0.2832
 HL1  C21  C  CR16  0  -0.328   2.1704   2.4643  -0.5670
 HL1  C22  C  CR16  0  -0.362   0.8125   2.3238  -0.5704
 HL1  C23  C  CR16  0  -0.524   3.2818  -0.9782   0.3023
 HL1  C24  C  CR6   0   0.363   4.6436  -0.8415   0.2666
 HL1  C25  C  CR6   0   0.311   5.2312   0.4239  -0.0499
 HL1  C26  C  CR16  0  -0.465   4.4202   1.4916  -0.3113
 HL1  O27  O  O2    0  -0.461   5.5256  -1.8229   0.5083
 HL1  C28  C  CH3   0  -0.441   5.0265  -3.1027   0.8421
 HL1  O30  O  O2    0  -0.461   6.5745   0.4370  -0.0614
 HL1  C31  C  CH3   0  -0.438   7.2202   1.6578  -0.3599
 HL1  H1   H  HCR6  0   0.301  -3.0755   1.2334   1.3777
 HL1  H2   H  HCR6  0   0.317  -6.1137  -1.1182  -1.7345
 HL1  H3   H  HCH1  0   0.256  -1.4450  -0.6846  -1.4246
 HL1  H4   H  HCH2  0   0.256   0.5198  -2.0624  -0.4114
 HL1  H5   H  HCH2  0   0.262   0.8192  -1.7560   1.2891
 HL1  H6   H  HCH1  0   0.232  -1.2934  -0.7068   1.6055
 HL1  H7   H  HNH2  0   0.358  -1.2731  -3.1587   1.0894
 HL1  H8   H  HNH2  0   0.353  -2.7085  -2.4426   0.9307
 HL1  H10  H  HCR6  0   0.254   2.6148   3.4242  -0.8010
 HL1  H11  H  HCR6  0   0.261   0.1680   3.1617  -0.8045
 HL1  H12  H  HCR6  0   0.281   2.8484  -1.9395   0.5387
 HL1  H13  H  HCR6  0   0.281   4.8370   2.4606  -0.5547
 HL1  H14  H  HCH3  0   0.263   5.8924  -3.7416   0.9951
 HL1  H15  H  HCH3  0   0.230   4.4368  -3.0809   1.7625
 HL1  H16  H  HCH3  0   0.231   4.4128  -3.5221   0.0405
 HL1  H17  H  HCH3  0   0.228   6.9509   2.0302  -1.3521
 HL1  H18  H  HCH3  0   0.229   6.9901   2.4307   0.3785
 HL1  H19  H  HCH3  0   0.261   8.2884   1.4570  -0.3374

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
 HL1  C31  O30  single    1.413  0.020  1.413
 HL1  O30  C25  single    1.343  0.020  1.343
 HL1  O27  C28  single    1.414  0.020  1.414
 HL1  O27  C24  single    1.341  0.020  1.341
 HL1  C25  C24  aromatic  1.431  0.020  1.431
 HL1  C25  C26  aromatic  1.366  0.020  1.366
 HL1  C24  C23  aromatic  1.369  0.020  1.369
 HL1  C26  C20  aromatic  1.417  0.020  1.417
 HL1  C23  C17  aromatic  1.419  0.020  1.419
 HL1  C20  C17  aromatic  1.413  0.020  1.413
 HL1  C20  C21  aromatic  1.411  0.020  1.411
 HL1  C17  C13  aromatic  1.422  0.020  1.422
 HL1  C21  C22  aromatic  1.365  0.020  1.365
 HL1  C13  C12  aromatic  1.376  0.020  1.376
 HL1  C13  C14  single    1.503  0.020  1.503
 HL1  C22  C12  aromatic  1.410  0.020  1.410
 HL1  C12  O11  single    1.357  0.020  1.357
 HL1  C14  C15  single    1.522  0.020  1.522
 HL1  O11  C10  single    1.417  0.020  1.417
 HL1  C15  C10  single    1.529  0.020  1.529
 HL1  C15  N16  single    1.450  0.020  1.450
 HL1  C10  C2   single    1.502  0.020  1.502
 HL1  C2   C3   aromatic  1.394  0.020  1.394
 HL1  C2   C1   aromatic  1.384  0.020  1.384
 HL1  F7   C1   single    1.339  0.020  1.339
 HL1  C3   C4   aromatic  1.376  0.020  1.376
 HL1  C1   C6   aromatic  1.384  0.020  1.384
 HL1  C4   F9   single    1.337  0.020  1.337
 HL1  C4   C5   aromatic  1.385  0.020  1.385
 HL1  C6   C5   aromatic  1.377  0.020  1.377
 HL1  C5   F8   single    1.333  0.020  1.333
 HL1  C3   H1   single    0.930  0.020  1.080
 HL1  C6   H2   single    0.930  0.020  1.080
 HL1  C10  H3   single    0.970  0.020  1.090
 HL1  C14  H4   single    0.970  0.020  1.090
 HL1  C14  H5   single    0.970  0.020  1.090
 HL1  C15  H6   single    0.970  0.020  1.090
 HL1  N16  H7   single    0.890  0.020  1.040
 HL1  N16  H8   single    0.890  0.020  1.040
 HL1  C21  H10  single    0.930  0.020  1.080
 HL1  C22  H11  single    0.930  0.020  1.080
 HL1  C23  H12  single    0.930  0.020  1.080
 HL1  C26  H13  single    0.930  0.020  1.080
 HL1  C28  H14  single    0.970  0.020  1.090
 HL1  C28  H15  single    0.970  0.020  1.090
 HL1  C28  H16  single    0.970  0.020  1.090
 HL1  C31  H17  single    0.970  0.020  1.090
 HL1  C31  H18  single    0.970  0.020  1.090
 HL1  C31  H19  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
 HL1  F7   C1   C6   117.56  3.000
 HL1  C6   C1   C2   122.90  3.000
 HL1  F7   C1   C2   119.54  3.000
 HL1  C10  C2   C3   120.43  3.000
 HL1  C3   C2   C1   117.46  3.000
 HL1  C10  C2   C1   122.08  3.000
 HL1  H1   C3   C4   118.89  3.000
 HL1  H1   C3   C2   120.54  3.000
 HL1  C4   C3   C2   120.57  3.000
 HL1  F9   C4   C5   119.12  3.000
 HL1  C5   C4   C3   120.43  3.000
 HL1  F9   C4   C3   120.45  3.000
 HL1  F8   C5   C6   120.15  3.000
 HL1  F8   C5   C4   119.39  3.000
 HL1  C6   C5   C4   120.46  3.000
 HL1  H2   C6   C5   120.81  3.000
 HL1  H2   C6   C1   121.01  3.000
 HL1  C5   C6   C1   118.18  3.000
 HL1  H3   C10  C15  107.82  3.000
 HL1  H3   C10  O11  109.26  3.000
 HL1  C15  C10  O11  110.14  3.000
 HL1  H3   C10  C2   110.36  3.000
 HL1  C15  C10  C2   112.19  3.000
 HL1  O11  C10  C2   107.06  3.000
 HL1  C12  O11  C10  116.22  3.000
 HL1  C22  C12  C13  121.66  3.000
 HL1  C22  C12  O11  115.43  3.000
 HL1  C13  C12  O11  122.91  3.000
 HL1  C17  C13  C14  121.10  3.000
 HL1  C14  C13  C12  120.36  3.000
 HL1  C17  C13  C12  118.54  3.000
 HL1  H5   C14  H4   106.41  3.000
 HL1  H5   C14  C15  108.72  3.000
 HL1  H4   C14  C15  108.67  3.000
 HL1  H5   C14  C13  110.31  3.000
 HL1  H4   C14  C13  110.32  3.000
 HL1  C15  C14  C13  112.22  3.000
 HL1  H6   C15  N16  113.01  3.000
 HL1  H6   C15  C14  108.64  3.000
 HL1  N16  C15  C14  110.00  3.000
 HL1  H6   C15  C10  107.69  3.000
 HL1  N16  C15  C10  109.32  3.000
 HL1  C14  C15  C10  108.03  3.000
 HL1  H8   N16  H7   105.47  3.000
 HL1  H8   N16  C15  109.94  3.000
 HL1  H7   N16  C15  109.41  3.000
 HL1  C23  C17  C20  118.21  3.000
 HL1  C20  C17  C13  120.11  3.000
 HL1  C23  C17  C13  121.68  3.000
 HL1  C26  C20  C21  121.17  3.000
 HL1  C21  C20  C17  119.06  3.000
 HL1  C26  C20  C17  119.77  3.000
 HL1  H10  C21  C22  119.91  3.000
 HL1  H10  C21  C20  119.35  3.000
 HL1  C22  C21  C20  120.73  3.000
 HL1  H11  C22  C21  120.86  3.000
 HL1  H11  C22  C12  119.26  3.000
 HL1  C21  C22  C12  119.88  3.000
 HL1  H12  C23  C24  119.56  3.000
 HL1  H12  C23  C17  119.07  3.000
 HL1  C24  C23  C17  121.36  3.000
 HL1  O27  C24  C25  114.64  3.000
 HL1  C25  C24  C23  120.17  3.000
 HL1  O27  C24  C23  125.19  3.000
 HL1  O30  C25  C26  125.76  3.000
 HL1  C26  C25  C24  119.33  3.000
 HL1  O30  C25  C24  114.91  3.000
 HL1  H13  C26  C25  120.93  3.000
 HL1  H13  C26  C20  117.91  3.000
 HL1  C25  C26  C20  121.16  3.000
 HL1  C28  O27  C24  118.21  3.000
 HL1  H16  C28  H15  108.79  3.000
 HL1  H16  C28  H14  108.96  3.000
 HL1  H15  C28  H14  108.84  3.000
 HL1  H16  C28  O27  111.86  3.000
 HL1  H15  C28  O27  111.79  3.000
 HL1  H14  C28  O27  106.51  3.000
 HL1  C31  O30  C25  117.85  3.000
 HL1  H19  C31  H18  108.87  3.000
 HL1  H19  C31  H17  108.88  3.000
 HL1  H18  C31  H17  108.68  3.000
 HL1  H19  C31  O30  106.56  3.000
 HL1  H18  C31  O30  111.83  3.000
 HL1  H17  C31  O30  111.93  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
 HL1  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 HL1  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 HL1  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 HL1  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 HL1  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 HL1  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 HL1  CONST_07  C23  C17  C13  C12  180.00   0.0  0
 HL1  CONST_08  C20  C17  C13  C12    0.00   0.0  0
 HL1  CONST_09  C20  C21  C22  C12    0.00   0.0  0
 HL1  CONST_10  C24  C23  C17  C13  180.00   0.0  0
 HL1  CONST_11  C26  C20  C17  C13  180.00   0.0  0
 HL1  CONST_12  C21  C20  C17  C13    0.00   0.0  0
 HL1  CONST_13  C21  C22  C12  C13    0.00   0.0  0
 HL1  CONST_14  C25  C24  C23  C17    0.00   0.0  0
 HL1  CONST_15  C25  C26  C20  C17    0.00   0.0  0
 HL1  CONST_16  C22  C21  C20  C17    0.00   0.0  0
 HL1  CONST_17  C22  C12  C13  C17    0.00   0.0  0
 HL1  CONST_18  C24  C25  C26  C20    0.00   0.0  0
 HL1  CONST_19  C24  C23  C17  C20    0.00   0.0  0
 HL1  CONST_20  C25  C26  C20  C21  180.00   0.0  0
 HL1  CONST_21  C23  C17  C20  C21  180.00   0.0  0
 HL1  CONST_22  C26  C20  C21  C22  180.00   0.0  0
 HL1  CONST_23  C26  C25  C24  C23    0.00   0.0  0
 HL1  CONST_24  C26  C20  C17  C23    0.00   0.0  0
 HL1  CONST_25  C10  C2   C3   C4   180.00   0.0  0
 HL1  CONST_26  C10  C2   C1   C6   180.00   0.0  0
 HL1  CONST_27  F8   C5   C6   C1   180.00   0.0  0
 HL1  CONST_28  F9   C4   C3   C2   180.00   0.0  0
 HL1  CONST_29  F7   C1   C2   C3   180.00   0.0  0
 HL1  CONST_30  F8   C5   C4   C3   180.00   0.0  0
 HL1  CONST_31  F7   C1   C6   C5   180.00   0.0  0
 HL1  CONST_32  F9   C4   C5   C6   180.00   0.0  0
 HL1  CONST_33  C10  C2   C1   F7     0.00   0.0  0
 HL1  CONST_34  O27  C24  C23  C17  180.00   0.0  0
 HL1  CONST_35  O30  C25  C26  C20  180.00   0.0  0
 HL1  CONST_36  O30  C25  C24  C23  180.00   0.0  0
 HL1  CONST_37  O27  C24  C25  C26  180.00   0.0  0
 HL1  CONST_38  H1   C3   C2   C1   180.00   0.0  0
 HL1  CONST_39  H2   C6   C1   C2   180.00   0.0  0
 HL1  CONST_40  H11  C22  C12  O11    0.00   0.0  0
 HL1  CONST_41  H10  C21  C22  C12  180.00   0.0  0
 HL1  CONST_42  H12  C23  C17  C13    0.00   0.0  0
 HL1  CONST_43  H13  C26  C20  C17  180.00   0.0  0
 HL1  Var_01    C13  C12  O11  C10  -18.51  30.0  1
 HL1  Var_02    C15  C14  C13  C12  -12.09  30.0  1
 HL1  Var_03    H14  C28  O27  C24  179.94  30.0  3
 HL1  Var_04    H17  C31  O30  C25  -60.04  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
 HL1  chir_01  C10  O11  C15  C2   negativ
 HL1  chir_02  C15  N16  C14  C10  negativ

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
 HL1  plan-1  C1   0.020
 HL1  plan-1  C2   0.020
 HL1  plan-1  C3   0.020
 HL1  plan-1  C4   0.020
 HL1  plan-1  C5   0.020
 HL1  plan-1  C6   0.020
 HL1  plan-1  F7   0.020
 HL1  plan-1  F8   0.020
 HL1  plan-1  F9   0.020
 HL1  plan-1  C10  0.020
 HL1  plan-1  H1   0.020
 HL1  plan-1  H2   0.020
 HL1  plan-2  O11  0.020
 HL1  plan-2  C12  0.020
 HL1  plan-2  C13  0.020
 HL1  plan-2  C14  0.020
 HL1  plan-2  C17  0.020
 HL1  plan-2  C20  0.020
 HL1  plan-2  C21  0.020
 HL1  plan-2  C22  0.020
 HL1  plan-2  C23  0.020
 HL1  plan-2  C24  0.020
 HL1  plan-2  C25  0.020
 HL1  plan-2  C26  0.020
 HL1  plan-2  O27  0.020
 HL1  plan-2  O30  0.020
 HL1  plan-2  H10  0.020
 HL1  plan-2  H11  0.020
 HL1  plan-2  H12  0.020
 HL1  plan-2  H13  0.020

