# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:32:54 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2S)-1-(2,3-dihydro-1H-inden-2-ylamino)-3-(3,4-dimethylphenoxy)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(OC[C@@H](O)CNC2Cc3ccccc3C2)cc1C
#
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
 38F  38F  (2S)-1-(2,3-dihydro-1H-inden-2-ylamino)-3-(3,4-dimethylphenoxy)propan-2-ol  ligand  48  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_38F
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
 38F  CAO  C  CH2   0  -0.503  -3.6724   0.6673   0.4208
 38F  CAP  C  CR56  0   0.097  -5.1694   0.7004   0.2942
 38F  CAS  C  CR16  0  -0.331  -6.0654   1.6621   0.7325
 38F  CAT  C  CR16  0  -0.261  -7.4261   1.4706   0.5083
 38F  CAU  C  CR16  0  -0.261  -7.8783   0.3298  -0.1453
 38F  CAV  C  CR16  0  -0.328  -6.9766  -0.6354  -0.5855
 38F  CAQ  C  CR56  0   0.092  -5.6227  -0.4418  -0.3637
 38F  CAR  C  CH2   0  -0.504  -4.4606  -1.3235  -0.7213
 38F  CAN  C  CR15  0  -0.059  -3.2657  -0.3593  -0.6517
 38F  NAM  N  NH1   0  -0.608  -2.0274  -1.0482  -0.3551
 38F  CAL  C  CH2   0  -0.291  -0.8716  -0.1765  -0.3587
 38F  CAI  C  CH1   0  -0.035   0.4143  -0.9525  -0.0923
 38F  OAH  O  OH1   0  -0.654   0.3727  -1.6831   1.1087
 38F  CAJ  C  CH2   0  -0.180   1.5952   0.0036  -0.1371
 38F  OAK  O  O2    0  -0.478   2.7807  -0.7513  -0.0016
 38F  CAF  C  CR6   0   0.387   3.9660  -0.1057  -0.0368
 38F  CAG  C  CR16  0  -0.402   5.1052  -0.9031   0.0900
 38F  CAB  C  CR6   0   0.089   6.3788  -0.3563   0.0615
 38F  CAA  C  CH3   0  -0.737   7.5795  -1.2452   0.2023
 38F  CAC  C  CR6   0   0.046   6.5359   1.0310  -0.0979
 38F  CAW  C  CH3   0  -0.733   7.9009   1.6536  -0.1434
 38F  CAD  C  CR16  0  -0.286   5.3948   1.8096  -0.2177
 38F  CAE  C  CR16  0  -0.388   4.1134   1.2666  -0.1903
 38F  H1   H  HCH2  0   0.252  -3.2100   1.6456   0.2822
 38F  H2   H  HCH2  0   0.245  -3.3778   0.3027   1.4120
 38F  H3   H  HCR6  0   0.245  -5.7168   2.5557   1.2366
 38F  H4   H  HCR6  0   0.250  -8.1364   2.2175   0.8396
 38F  H5   H  HCR6  0   0.251  -8.9383   0.1936  -0.3183
 38F  H6   H  HCR6  0   0.245  -7.3340  -1.5211  -1.0970
 38F  H7   H  HCH2  0   0.244  -4.3384  -2.1127   0.0294
 38F  H8   H  HCH2  0   0.252  -4.5585  -1.8099  -1.6936
 38F  H9   H  HCR5  0   0.212  -3.2173   0.1806  -1.6133
 38F  H10  H  HNH1  0   0.345  -1.8890  -1.7692  -1.0547
 38F  H12  H  HCH2  0   0.205  -0.7586   0.3776  -1.3043
 38F  H13  H  HCH2  0   0.230  -0.9965   0.5801   0.4239
 38F  H14  H  HCH1  0   0.234   0.5453  -1.6951  -0.8878
 38F  H15  H  HOH1  0   0.443   0.1074  -1.0889   1.8190
 38F  H16  H  HCH2  0   0.225   1.5902   0.5517  -1.0864
 38F  H17  H  HCH2  0   0.221   1.5085   0.7420   0.6709
 38F  H18  H  HCR6  0   0.249   4.9830  -1.9740   0.2097
 38F  H19  H  HCH3  0   0.243   8.2549  -1.1441  -0.6493
 38F  H20  H  HCH3  0   0.244   8.1584  -0.9945   1.0939
 38F  H21  H  HCH3  0   0.250   7.2933  -2.2930   0.2778
 38F  H22  H  HCH3  0   0.238   8.4724   1.4543   0.7657
 38F  H23  H  HCH3  0   0.239   8.4936   1.2682  -0.9762
 38F  H24  H  HCH3  0   0.247   7.8351   2.7348  -0.2602
 38F  H25  H  HCR6  0   0.246   5.4979   2.8820  -0.3374
 38F  H26  H  HCR6  0   0.273   3.2626   1.9264  -0.2908

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
 38F  CAW  CAC  single    1.501  0.020  1.501
 38F  CAC  CAD  aromatic  1.387  0.020  1.387
 38F  CAC  CAB  aromatic  1.405  0.020  1.405
 38F  CAD  CAE  aromatic  1.392  0.020  1.392
 38F  CAA  CAB  single    1.501  0.020  1.501
 38F  CAB  CAG  aromatic  1.386  0.020  1.386
 38F  CAE  CAF  aromatic  1.389  0.020  1.389
 38F  CAG  CAF  aromatic  1.396  0.020  1.396
 38F  CAF  OAK  single    1.350  0.020  1.350
 38F  CAJ  OAK  single    1.412  0.020  1.412
 38F  CAJ  CAI  single    1.520  0.020  1.520
 38F  CAI  OAH  single    1.406  0.020  1.406
 38F  CAI  CAL  single    1.525  0.020  1.525
 38F  CAL  NAM  single    1.448  0.020  1.448
 38F  CAR  CAN  single    1.537  0.020  1.537
 38F  CAR  CAQ  single    1.502  0.020  1.502
 38F  NAM  CAN  single    1.448  0.020  1.448
 38F  CAN  CAO  single    1.539  0.020  1.539
 38F  CAV  CAQ  aromatic  1.386  0.020  1.386
 38F  CAV  CAU  aromatic  1.392  0.020  1.392
 38F  CAQ  CAP  aromatic  1.394  0.020  1.394
 38F  CAU  CAT  aromatic  1.390  0.020  1.390
 38F  CAO  CAP  single    1.503  0.020  1.503
 38F  CAP  CAS  aromatic  1.386  0.020  1.386
 38F  CAT  CAS  aromatic  1.392  0.020  1.392
 38F  CAO  H1   single    0.970  0.020  1.090
 38F  CAO  H2   single    0.970  0.020  1.090
 38F  CAS  H3   single    0.930  0.020  1.080
 38F  CAT  H4   single    0.930  0.020  1.080
 38F  CAU  H5   single    0.930  0.020  1.080
 38F  CAV  H6   single    0.930  0.020  1.080
 38F  CAR  H7   single    0.970  0.020  1.090
 38F  CAR  H8   single    0.970  0.020  1.090
 38F  CAN  H9   single    0.970  0.020  1.090
 38F  NAM  H10  single    0.890  0.020  1.040
 38F  CAL  H12  single    0.970  0.020  1.090
 38F  CAL  H13  single    0.970  0.020  1.090
 38F  CAI  H14  single    0.970  0.020  1.090
 38F  OAH  H15  single    0.850  0.020  0.980
 38F  CAJ  H16  single    0.970  0.020  1.090
 38F  CAJ  H17  single    0.970  0.020  1.090
 38F  CAG  H18  single    0.930  0.020  1.080
 38F  CAA  H19  single    0.970  0.020  1.090
 38F  CAA  H20  single    0.970  0.020  1.090
 38F  CAA  H21  single    0.970  0.020  1.090
 38F  CAW  H22  single    0.970  0.020  1.090
 38F  CAW  H23  single    0.970  0.020  1.090
 38F  CAW  H24  single    0.970  0.020  1.090
 38F  CAD  H25  single    0.930  0.020  1.080
 38F  CAE  H26  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
 38F  H2   CAO  H1   107.40  3.000
 38F  H2   CAO  CAN  109.70  3.000
 38F  H1   CAO  CAN  113.43  3.000
 38F  H2   CAO  CAP  110.56  3.000
 38F  H1   CAO  CAP  113.07  3.000
 38F  CAN  CAO  CAP  102.66  3.000
 38F  CAQ  CAP  CAS  120.51  3.000
 38F  CAS  CAP  CAO  129.26  3.000
 38F  CAQ  CAP  CAO  110.23  3.000
 38F  H3   CAS  CAT  120.18  3.000
 38F  H3   CAS  CAP  120.77  3.000
 38F  CAT  CAS  CAP  119.05  3.000
 38F  H4   CAT  CAU  119.76  3.000
 38F  H4   CAT  CAS  119.81  3.000
 38F  CAU  CAT  CAS  120.43  3.000
 38F  H5   CAU  CAV  119.76  3.000
 38F  H5   CAU  CAT  119.79  3.000
 38F  CAV  CAU  CAT  120.45  3.000
 38F  H6   CAV  CAQ  120.81  3.000
 38F  H6   CAV  CAU  120.15  3.000
 38F  CAQ  CAV  CAU  119.04  3.000
 38F  CAR  CAQ  CAV  129.49  3.000
 38F  CAV  CAQ  CAP  120.52  3.000
 38F  CAR  CAQ  CAP  109.99  3.000
 38F  H8   CAR  H7   107.41  3.000
 38F  H8   CAR  CAN  112.93  3.000
 38F  H7   CAR  CAN  109.51  3.000
 38F  H8   CAR  CAQ  113.85  3.000
 38F  H7   CAR  CAQ  110.24  3.000
 38F  CAN  CAR  CAQ  102.85  3.000
 38F  H9   CAN  NAM  111.94  3.000
 38F  H9   CAN  CAR  107.55  3.000
 38F  NAM  CAN  CAR  112.07  3.000
 38F  H9   CAN  CAO  106.99  3.000
 38F  NAM  CAN  CAO  113.62  3.000
 38F  CAR  CAN  CAO  104.15  3.000
 38F  H10  NAM  CAL  108.51  3.000
 38F  H10  NAM  CAN  108.28  3.000
 38F  CAL  NAM  CAN  113.32  3.000
 38F  H13  CAL  H12  106.11  3.000
 38F  H13  CAL  CAI  108.82  3.000
 38F  H12  CAL  CAI  108.62  3.000
 38F  H13  CAL  NAM  108.85  3.000
 38F  H12  CAL  NAM  112.76  3.000
 38F  CAI  CAL  NAM  111.49  3.000
 38F  H14  CAI  CAJ  108.17  3.000
 38F  H14  CAI  OAH  105.74  3.000
 38F  CAJ  CAI  OAH  112.02  3.000
 38F  H14  CAI  CAL  108.58  3.000
 38F  OAH  CAI  CAL  112.86  3.000
 38F  CAJ  CAI  CAL  109.26  3.000
 38F  H15  OAH  CAI  108.50  3.000
 38F  H17  CAJ  H16  107.50  3.000
 38F  H17  CAJ  OAK  110.81  3.000
 38F  H16  CAJ  OAK  110.75  3.000
 38F  H17  CAJ  CAI  109.87  3.000
 38F  H16  CAJ  CAI  109.66  3.000
 38F  OAK  CAJ  CAI  108.25  3.000
 38F  CAF  OAK  CAJ  118.61  3.000
 38F  CAE  CAF  CAG  119.19  3.000
 38F  CAG  CAF  OAK  116.15  3.000
 38F  CAE  CAF  OAK  124.65  3.000
 38F  H18  CAG  CAB  119.69  3.000
 38F  H18  CAG  CAF  118.82  3.000
 38F  CAB  CAG  CAF  121.50  3.000
 38F  CAC  CAB  CAA  120.40  3.000
 38F  CAA  CAB  CAG  119.97  3.000
 38F  CAC  CAB  CAG  119.63  3.000
 38F  H21  CAA  H20  107.68  3.000
 38F  H21  CAA  H19  107.81  3.000
 38F  H20  CAA  H19  106.72  3.000
 38F  H21  CAA  CAB  111.48  3.000
 38F  H20  CAA  CAB  111.40  3.000
 38F  H19  CAA  CAB  111.53  3.000
 38F  CAD  CAC  CAW  120.85  3.000
 38F  CAD  CAC  CAB  118.18  3.000
 38F  CAW  CAC  CAB  120.97  3.000
 38F  H24  CAW  H23  107.53  3.000
 38F  H24  CAW  H22  107.57  3.000
 38F  H23  CAW  H22  106.64  3.000
 38F  H24  CAW  CAC  111.10  3.000
 38F  H23  CAW  CAC  111.72  3.000
 38F  H22  CAW  CAC  112.02  3.000
 38F  H25  CAD  CAE  118.40  3.000
 38F  H25  CAD  CAC  119.13  3.000
 38F  CAE  CAD  CAC  122.47  3.000
 38F  H26  CAE  CAD  118.98  3.000
 38F  H26  CAE  CAF  121.98  3.000
 38F  CAD  CAE  CAF  119.04  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
 38F  CONST_01  CAU  CAV  CAQ  CAP     0.00   0.0  0
 38F  CONST_02  CAU  CAT  CAS  CAP     0.00   0.0  0
 38F  CONST_03  CAV  CAQ  CAP  CAS     0.00   0.0  0
 38F  CONST_04  CAV  CAU  CAT  CAS     0.00   0.0  0
 38F  CONST_05  CAQ  CAV  CAU  CAT     0.00   0.0  0
 38F  CONST_06  CAQ  CAP  CAS  CAT     0.00   0.0  0
 38F  CONST_07  CAC  CAD  CAE  CAF     0.00   0.0  0
 38F  CONST_08  CAC  CAB  CAG  CAF     0.00   0.0  0
 38F  CONST_09  CAD  CAC  CAB  CAG     0.00   0.0  0
 38F  CONST_10  CAD  CAE  CAF  CAG     0.00   0.0  0
 38F  CONST_11  CAE  CAD  CAC  CAB     0.00   0.0  0
 38F  CONST_12  CAE  CAF  CAG  CAB     0.00   0.0  0
 38F  CONST_13  CAD  CAE  CAF  OAK   180.00   0.0  0
 38F  CONST_14  CAB  CAG  CAF  OAK   180.00   0.0  0
 38F  CONST_15  CAA  CAB  CAG  CAF   180.00   0.0  0
 38F  CONST_16  CAW  CAC  CAB  CAG   180.00   0.0  0
 38F  CONST_17  CAD  CAC  CAB  CAA   180.00   0.0  0
 38F  CONST_18  CAE  CAD  CAC  CAW   180.00   0.0  0
 38F  CONST_19  H3   CAS  CAP  CAO     0.00   0.0  0
 38F  CONST_20  H6   CAV  CAQ  CAP   180.00   0.0  0
 38F  CONST_21  H4   CAT  CAS  CAP   180.00   0.0  0
 38F  CONST_22  H5   CAU  CAT  CAS   180.00   0.0  0
 38F  CONST_23  H25  CAD  CAE  CAF   180.00   0.0  0
 38F  CONST_24  H26  CAE  CAF  CAG   180.00   0.0  0
 38F  CONST_25  H18  CAG  CAB  CAC   180.00   0.0  0
 38F  Var_01    CAN  CAR  CAQ  CAP   -19.38  30.0  1
 38F  Var_02    CAN  CAO  CAP  CAS  -161.27  30.0  1
 38F  Var_03    CAE  CAF  OAK  CAJ     0.41  30.0  2
 38F  Var_04    H19  CAA  CAB  CAG   122.89  30.0  2
 38F  Var_05    H22  CAW  CAC  CAB   -59.03  30.0  2
 38F  Var_06    CAI  CAL  NAM  CAN  -177.93  30.0  1
 38F  Var_07    H16  CAJ  OAK  CAF    58.63  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
 38F  chir_01  CAN  CAR  NAM  CAO  positiv
 38F  chir_02  CAI  OAH  CAL  CAJ  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
 38F  plan-1  OAK  0.020
 38F  plan-1  CAF  0.020
 38F  plan-1  CAG  0.020
 38F  plan-1  CAB  0.020
 38F  plan-1  CAA  0.020
 38F  plan-1  CAC  0.020
 38F  plan-1  CAW  0.020
 38F  plan-1  CAD  0.020
 38F  plan-1  CAE  0.020
 38F  plan-1  H18  0.020
 38F  plan-1  H25  0.020
 38F  plan-1  H26  0.020
 38F  plan-2  CAO  0.020
 38F  plan-2  CAP  0.020
 38F  plan-2  CAS  0.020
 38F  plan-2  CAT  0.020
 38F  plan-2  CAU  0.020
 38F  plan-2  CAV  0.020
 38F  plan-2  CAQ  0.020
 38F  plan-2  CAR  0.020
 38F  plan-2  H3   0.020
 38F  plan-2  H4   0.020
 38F  plan-2  H5   0.020
 38F  plan-2  H6   0.020

