# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 12:52:12 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2S,3R)-2-amino-9-methoxy-3-(2,4,5-trifluorophenyl)-2,3-dihydro-1H-naphtho[2,1-b]pyran-8-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2c(ccc3O[C@@H]([C@@H](N)Cc23)c4cc(F)c(F)cc4F)cc1C#N
#
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
 9EL  9EL  (2S,3R)-2-amino-9-methoxy-3-(2,4,5-trifluorophenyl)-2,3-dihydro-1H-naphtho[2,1-b]pyran-8-carbonitrile  ligand  43  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9EL
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
 9EL  C1   C  CR6   0   0.540  -4.0001  -0.7291  -1.1674
 9EL  C2   C  CR6   0  -0.132  -3.1028  -0.0849  -0.3333
 9EL  C3   C  CR16  0  -0.430  -3.6266   0.7116   0.6843
 9EL  C4   C  CR6   0   0.410  -4.9869   0.8444   0.8381
 9EL  C5   C  CR6   0   0.411  -5.8566   0.1875  -0.0174
 9EL  C6   C  CR16  0  -0.556  -5.3719  -0.6083  -1.0310
 9EL  F7   F  F     0  -0.298  -3.5412  -1.5036  -2.1580
 9EL  F8   F  F     0  -0.297  -7.1707   0.3333   0.1481
 9EL  F9   F  F     0  -0.304  -5.4875   1.6089   1.8132
 9EL  C10  C  CH1   0   0.009  -1.6179  -0.2543  -0.4767
 9EL  O11  O  O2    0  -0.485  -1.0452   1.0447  -0.4123
 9EL  C12  C  CR6   0   0.373   0.2997   1.1140  -0.3504
 9EL  C13  C  CR6   0  -0.052   1.0909   0.0370  -0.0173
 9EL  C14  C  CH2   0  -0.515   0.4671  -1.2773   0.3570
 9EL  C15  C  CH1   0  -0.098  -1.0272  -1.1469   0.6141
 9EL  N16  N  NH2   0  -0.802  -1.6566  -2.4509   0.5519
 9EL  C17  C  CR66  0   0.162   2.5017   0.2027  -0.0362
 9EL  C20  C  CR66  0   0.058   3.0560   1.4695  -0.3608
 9EL  C21  C  CR16  0  -0.306   2.1962   2.5534  -0.6576
 9EL  C22  C  CR16  0  -0.359   0.8472   2.3821  -0.6578
 9EL  C23  C  CR16  0  -0.523   3.3742  -0.8738   0.2542
 9EL  C24  C  CR6   0   0.465   4.7355  -0.7077   0.2216
 9EL  C25  C  CR6   0  -0.108   5.2808   0.5654  -0.1039
 9EL  C26  C  CR16  0  -0.289   4.4508   1.6231  -0.3864
 9EL  O27  O  O2    0  -0.459   5.6401  -1.6567   0.4725
 9EL  C28  C  CH3   0  -0.444   5.1863  -2.9555   0.8160
 9EL  C30  C  CSP   0   0.062   6.6934   0.7275  -0.1359
 9EL  N31  N  NS    0  -0.254   7.8367   0.8702  -0.1757
 9EL  H1   H  HCR6  0   0.302  -2.9699   1.2389   1.3647
 9EL  H2   H  HCR6  0   0.318  -6.0465  -1.1216  -1.7035
 9EL  H3   H  HCH1  0   0.264  -1.3742  -0.7024  -1.4463
 9EL  H4   H  HCH2  0   0.262   0.6254  -2.0145  -0.4384
 9EL  H5   H  HCH2  0   0.267   0.9433  -1.6798   1.2551
 9EL  H6   H  HCH1  0   0.237  -1.1738  -0.6410   1.5809
 9EL  H7   H  HNH2  0   0.359  -1.1298  -3.1074   1.1152
 9EL  H8   H  HNH2  0   0.355  -2.5772  -2.4122   0.9714
 9EL  H10  H  HCR6  0   0.267   2.6235   3.5181  -0.8998
 9EL  H11  H  HCR6  0   0.272   0.1801   3.1997  -0.8984
 9EL  H12  H  HCR6  0   0.291   2.9571  -1.8401   0.4972
 9EL  H13  H  HCR6  0   0.285   4.8745   2.5874  -0.6369
 9EL  H14  H  HCH3  0   0.269   6.0759  -3.5594   0.9694
 9EL  H15  H  HCH3  0   0.238   4.6002  -2.9440   1.7377
 9EL  H16  H  HCH3  0   0.238   4.5871  -3.3961   0.0163

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
 9EL  F8   C5   single    1.333  0.020  1.333
 9EL  C5   C6   aromatic  1.377  0.020  1.377
 9EL  C5   C4   aromatic  1.386  0.020  1.386
 9EL  C6   C1   aromatic  1.384  0.020  1.384
 9EL  F9   C4   single    1.336  0.020  1.336
 9EL  C4   C3   aromatic  1.375  0.020  1.375
 9EL  C1   F7   single    1.339  0.020  1.339
 9EL  C1   C2   aromatic  1.384  0.020  1.384
 9EL  C3   C2   aromatic  1.394  0.020  1.394
 9EL  C2   C10  single    1.501  0.020  1.501
 9EL  N16  C15  single    1.449  0.020  1.449
 9EL  C15  C10  single    1.528  0.020  1.528
 9EL  C15  C14  single    1.522  0.020  1.522
 9EL  C10  O11  single    1.421  0.020  1.421
 9EL  O11  C12  single    1.348  0.020  1.348
 9EL  C14  C13  single    1.502  0.020  1.502
 9EL  C12  C13  aromatic  1.377  0.020  1.377
 9EL  C12  C22  aromatic  1.415  0.020  1.415
 9EL  C13  C17  aromatic  1.421  0.020  1.421
 9EL  C22  C21  aromatic  1.360  0.020  1.360
 9EL  C17  C23  aromatic  1.416  0.020  1.416
 9EL  C17  C20  aromatic  1.420  0.020  1.420
 9EL  C23  C24  aromatic  1.372  0.020  1.372
 9EL  C28  O27  single    1.418  0.020  1.418
 9EL  C21  C20  aromatic  1.415  0.020  1.415
 9EL  C20  C26  aromatic  1.403  0.020  1.403
 9EL  C24  O27  single    1.335  0.020  1.335
 9EL  C24  C25  aromatic  1.423  0.020  1.423
 9EL  C26  C25  aromatic  1.374  0.020  1.374
 9EL  C25  C30  single    1.422  0.020  1.422
 9EL  C30  N31  triple    1.153  0.020  1.153
 9EL  C3   H1   single    0.930  0.020  1.080
 9EL  C6   H2   single    0.930  0.020  1.080
 9EL  C10  H3   single    0.970  0.020  1.090
 9EL  C14  H4   single    0.970  0.020  1.090
 9EL  C14  H5   single    0.970  0.020  1.090
 9EL  C15  H6   single    0.970  0.020  1.090
 9EL  N16  H7   single    0.890  0.020  1.040
 9EL  N16  H8   single    0.890  0.020  1.040
 9EL  C21  H10  single    0.930  0.020  1.080
 9EL  C22  H11  single    0.930  0.020  1.080
 9EL  C23  H12  single    0.930  0.020  1.080
 9EL  C26  H13  single    0.930  0.020  1.080
 9EL  C28  H14  single    0.970  0.020  1.090
 9EL  C28  H15  single    0.970  0.020  1.090
 9EL  C28  H16  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
 9EL  F7   C1   C6   117.60  3.000
 9EL  F7   C1   C2   119.54  3.000
 9EL  C6   C1   C2   122.86  3.000
 9EL  C10  C2   C3   120.38  3.000
 9EL  C10  C2   C1   122.07  3.000
 9EL  C3   C2   C1   117.53  3.000
 9EL  H1   C3   C4   118.85  3.000
 9EL  H1   C3   C2   120.60  3.000
 9EL  C4   C3   C2   120.55  3.000
 9EL  F9   C4   C5   119.12  3.000
 9EL  F9   C4   C3   120.48  3.000
 9EL  C5   C4   C3   120.40  3.000
 9EL  F8   C5   C6   120.13  3.000
 9EL  C6   C5   C4   120.51  3.000
 9EL  F8   C5   C4   119.37  3.000
 9EL  H2   C6   C5   120.82  3.000
 9EL  H2   C6   C1   121.02  3.000
 9EL  C5   C6   C1   118.17  3.000
 9EL  H3   C10  C15  107.87  3.000
 9EL  H3   C10  O11  108.92  3.000
 9EL  C15  C10  O11  110.23  3.000
 9EL  H3   C10  C2   110.53  3.000
 9EL  O11  C10  C2   106.92  3.000
 9EL  C15  C10  C2   112.33  3.000
 9EL  C12  O11  C10  116.81  3.000
 9EL  C22  C12  C13  122.07  3.000
 9EL  C22  C12  O11  114.97  3.000
 9EL  C13  C12  O11  122.96  3.000
 9EL  C17  C13  C14  121.18  3.000
 9EL  C17  C13  C12  118.43  3.000
 9EL  C14  C13  C12  120.39  3.000
 9EL  H5   C14  H4   106.60  3.000
 9EL  H5   C14  C15  108.69  3.000
 9EL  H4   C14  C15  108.79  3.000
 9EL  H5   C14  C13  110.23  3.000
 9EL  H4   C14  C13  110.35  3.000
 9EL  C15  C14  C13  112.01  3.000
 9EL  H6   C15  N16  113.16  3.000
 9EL  H6   C15  C14  108.57  3.000
 9EL  N16  C15  C14  110.00  3.000
 9EL  H6   C15  C10  107.87  3.000
 9EL  C14  C15  C10  107.99  3.000
 9EL  N16  C15  C10  109.09  3.000
 9EL  H8   N16  H7   105.50  3.000
 9EL  H8   N16  C15  110.05  3.000
 9EL  H7   N16  C15  109.48  3.000
 9EL  C23  C17  C20  118.98  3.000
 9EL  C20  C17  C13  119.65  3.000
 9EL  C23  C17  C13  121.37  3.000
 9EL  C26  C20  C21  121.08  3.000
 9EL  C26  C20  C17  119.32  3.000
 9EL  C21  C20  C17  119.60  3.000
 9EL  H10  C21  C22  120.25  3.000
 9EL  H10  C21  C20  119.32  3.000
 9EL  C22  C21  C20  120.42  3.000
 9EL  H11  C22  C21  121.09  3.000
 9EL  H11  C22  C12  119.13  3.000
 9EL  C21  C22  C12  119.78  3.000
 9EL  H12  C23  C24  119.79  3.000
 9EL  H12  C23  C17  119.23  3.000
 9EL  C24  C23  C17  120.97  3.000
 9EL  O27  C24  C25  114.80  3.000
 9EL  C25  C24  C23  119.61  3.000
 9EL  O27  C24  C23  125.58  3.000
 9EL  C30  C25  C26  120.51  3.000
 9EL  C30  C25  C24  119.20  3.000
 9EL  C26  C25  C24  120.30  3.000
 9EL  H13  C26  C25  119.79  3.000
 9EL  H13  C26  C20  119.39  3.000
 9EL  C25  C26  C20  120.82  3.000
 9EL  C28  O27  C24  118.68  3.000
 9EL  H16  C28  H15  109.13  3.000
 9EL  H16  C28  H14  109.18  3.000
 9EL  H15  C28  H14  109.04  3.000
 9EL  H16  C28  O27  111.57  3.000
 9EL  H15  C28  O27  111.50  3.000
 9EL  H14  C28  O27  106.34  3.000
 9EL  N31  C30  C25  180.00  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
 9EL  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 9EL  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 9EL  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 9EL  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 9EL  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 9EL  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 9EL  CONST_07  C23  C17  C13  C12  180.00   0.0  0
 9EL  CONST_08  C20  C17  C13  C12    0.00   0.0  0
 9EL  CONST_09  C20  C21  C22  C12    0.00   0.0  0
 9EL  CONST_10  C21  C22  C12  C13    0.00   0.0  0
 9EL  CONST_11  C24  C23  C17  C13  180.00   0.0  0
 9EL  CONST_12  C21  C20  C17  C13    0.00   0.0  0
 9EL  CONST_13  C26  C20  C17  C13  180.00   0.0  0
 9EL  CONST_14  C22  C12  C13  C17    0.00   0.0  0
 9EL  CONST_15  C25  C24  C23  C17    0.00   0.0  0
 9EL  CONST_16  C22  C21  C20  C17    0.00   0.0  0
 9EL  CONST_17  C25  C26  C20  C17    0.00   0.0  0
 9EL  CONST_18  C24  C23  C17  C20    0.00   0.0  0
 9EL  CONST_19  C24  C25  C26  C20    0.00   0.0  0
 9EL  CONST_20  C23  C17  C20  C21  180.00   0.0  0
 9EL  CONST_21  C25  C26  C20  C21  180.00   0.0  0
 9EL  CONST_22  C26  C20  C21  C22  180.00   0.0  0
 9EL  CONST_23  C26  C20  C17  C23    0.00   0.0  0
 9EL  CONST_24  C26  C25  C24  C23    0.00   0.0  0
 9EL  CONST_25  C10  C2   C3   C4   180.00   0.0  0
 9EL  CONST_26  C10  C2   C1   C6   180.00   0.0  0
 9EL  CONST_27  F8   C5   C6   C1   180.00   0.0  0
 9EL  CONST_28  F9   C4   C3   C2   180.00   0.0  0
 9EL  CONST_29  F8   C5   C4   C3   180.00   0.0  0
 9EL  CONST_30  F7   C1   C2   C3   180.00   0.0  0
 9EL  CONST_31  F7   C1   C6   C5   180.00   0.0  0
 9EL  CONST_32  F9   C4   C5   C6   180.00   0.0  0
 9EL  CONST_33  C10  C2   C1   F7     0.00   0.0  0
 9EL  CONST_34  O27  C24  C23  C17  180.00   0.0  0
 9EL  CONST_35  C30  C25  C26  C20  180.00   0.0  0
 9EL  CONST_36  C30  C25  C24  C23  180.00   0.0  0
 9EL  CONST_37  O27  C24  C25  C26  180.00   0.0  0
 9EL  CONST_38  H1   C3   C2   C1   180.00   0.0  0
 9EL  CONST_39  H2   C6   C1   C2   180.00   0.0  0
 9EL  CONST_40  H11  C22  C12  O11    0.00   0.0  0
 9EL  CONST_41  H10  C21  C22  C12  180.00   0.0  0
 9EL  CONST_42  H12  C23  C17  C13    0.00   0.0  0
 9EL  CONST_43  H13  C26  C20  C17  180.00   0.0  0
 9EL  Var_01    C13  C12  O11  C10  -16.58  30.0  1
 9EL  Var_02    C15  C14  C13  C12  -12.80  30.0  1
 9EL  Var_03    H14  C28  O27  C24  179.66  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
 9EL  chir_01  C10  C2   C15  O11  positiv
 9EL  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
 9EL  plan-1  C1   0.020
 9EL  plan-1  C2   0.020
 9EL  plan-1  C3   0.020
 9EL  plan-1  C4   0.020
 9EL  plan-1  C5   0.020
 9EL  plan-1  C6   0.020
 9EL  plan-1  F7   0.020
 9EL  plan-1  F8   0.020
 9EL  plan-1  F9   0.020
 9EL  plan-1  C10  0.020
 9EL  plan-1  H1   0.020
 9EL  plan-1  H2   0.020
 9EL  plan-2  O11  0.020
 9EL  plan-2  C12  0.020
 9EL  plan-2  C13  0.020
 9EL  plan-2  C14  0.020
 9EL  plan-2  C17  0.020
 9EL  plan-2  C20  0.020
 9EL  plan-2  C21  0.020
 9EL  plan-2  C22  0.020
 9EL  plan-2  C23  0.020
 9EL  plan-2  C24  0.020
 9EL  plan-2  C25  0.020
 9EL  plan-2  C26  0.020
 9EL  plan-2  O27  0.020
 9EL  plan-2  C30  0.020
 9EL  plan-2  N31  0.020
 9EL  plan-2  H10  0.020
 9EL  plan-2  H11  0.020
 9EL  plan-2  H12  0.020
 9EL  plan-2  H13  0.020

