# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:41:36 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 3-[2-amino-6-(2-methylphenyl)quinolin-3-yl]-N-cyclohexylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2ccc3nc(N)c(CCC(=O)NC4CCCCC4)cc3c2
#
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
 RTN  RTN  3-[2-amino-6-(2-methylphenyl)quinolin-3-yl]-N-cyclohexylpropanamide  ligand  58  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RTN
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
 RTN  C4    C  CR66  0   0.195  -2.1628  -1.6116   0.6588
 RTN  C5    C  CR66  0   0.108  -2.1112  -0.4625  -0.1599
 RTN  C6    C  CR16  0  -0.382  -3.2621   0.3268  -0.3393
 RTN  C8    C  CR6   0   0.389   0.0495  -2.1076   0.2768
 RTN  C10   C  CR16  0  -0.263  -0.8654  -0.1633  -0.7657
 RTN  C13   C  CR16  0  -0.260  -6.6297   3.0729   0.2558
 RTN  C15   C  CR16  0  -0.293  -7.9441   1.2225  -0.5171
 RTN  C17   C  CH3   0  -0.747  -7.0371  -1.0940  -0.7609
 RTN  C20   C  C     0   0.568   3.8438   0.3976  -0.6647
 RTN  C22   C  CR16  0  -0.062   6.2114   0.7866  -0.0586
 RTN  C24   C  C     0  -0.437   8.2164   2.0583   0.7741
 RTN  C26   C  C     0  -0.439   8.5368  -0.0478  -0.5623
 RTN  C23   C  C     0  -0.437   6.7704   1.6627   1.0595
 RTN  C25   C  C     0  -0.432   9.0970   0.8333   0.5495
 RTN  C27   C  C     0  -0.423   7.0910  -0.4446  -0.2788
 RTN  N21   N  NH1   0  -0.644   4.8408   0.4150   0.2335
 RTN  O29   O  O     0  -0.506   3.9940   0.6888  -1.8445
 RTN  C19   C  CH2   0  -0.578   2.4882   0.0236  -0.0973
 RTN  C9    C  CR6   0   0.025   0.2254  -0.9505  -0.5626
 RTN  N7    N  N     0  -0.497  -1.0899  -2.4105   0.8521
 RTN  N28   N  NH2   0  -0.833   1.1113  -2.9180   0.5330
 RTN  C3    C  CR16  0  -0.296  -3.3868  -1.9298   1.2862
 RTN  C2    C  CR16  0  -0.292  -4.4940  -1.1456   1.0953
 RTN  C1    C  CR6   0   0.032  -4.4532   0.0020   0.2709
 RTN  C11   C  CR6   0   0.051  -5.6480   0.8597   0.0971
 RTN  C12   C  CR16  0  -0.291  -5.5479   2.2183   0.4013
 RTN  C14   C  CR16  0  -0.253  -7.8379   2.5695  -0.2031
 RTN  C16   C  CR6   0   0.065  -6.8669   0.3491  -0.3766
 RTN  H6    H  HCR6  0   0.252  -3.2029   1.1982  -0.9823
 RTN  H10   H  HCR6  0   0.258  -0.7851   0.7149  -1.3975
 RTN  H13   H  HCR6  0   0.253  -6.5286   4.1219   0.5022
 RTN  H15   H  HCR6  0   0.248  -8.8854   0.8378  -0.8920
 RTN  H17   H  HCH3  0   0.249  -7.2454  -1.7233   0.1062
 RTN  H17A  H  HCH3  0   0.251  -7.8727  -1.2123  -1.4500
 RTN  H17B  H  HCH3  0   0.245  -6.1463  -1.4977  -1.2416
 RTN  H22   H  HCR6  0   0.235   6.1958   1.3731  -0.9811
 RTN  H24   H  H     0   0.214   8.2477   2.6948  -0.1164
 RTN  H24A  H  H     0   0.232   8.6047   2.6604   1.5986
 RTN  H26   H  H     0   0.213   8.5818   0.4947  -1.5129
 RTN  H26A  H  H     0   0.232   9.1511  -0.9422  -0.6864
 RTN  H23   H  H     0   0.239   6.1464   2.5515   1.1776
 RTN  H23A  H  H     0   0.216   6.7265   1.1122   2.0070
 RTN  H25   H  H     0   0.230  10.1177   1.1415   0.3110
 RTN  H25A  H  H     0   0.211   9.1538   0.2535   1.4772
 RTN  H27   H  H     0   0.212   7.0495  -1.0743   0.6170
 RTN  H27A  H  H     0   0.234   6.6869  -1.0377  -1.1025
 RTN  HN21  H  HNH1  0   0.393   4.6343   0.1213   1.1756
 RTN  H19   H  HCH2  0   0.261   2.6045  -0.6420   0.7609
 RTN  H19A  H  HCH2  0   0.282   2.0256   0.9376   0.2884
 RTN  H18   H  HCH2  0   0.268   1.4189   0.1081  -1.9615
 RTN  H18A  H  HCH2  0   0.251   2.0414  -1.4759  -1.5910
 RTN  HN28  H  HNH2  0   0.388   0.8996  -3.8028   0.9652
 RTN  HN2A  H  HNH2  0   0.397   1.8777  -2.9487  -0.1175
 RTN  H3    H  HCR6  0   0.252  -3.4320  -2.8019   1.9264
 RTN  H2    H  HCR6  0   0.254  -5.4172  -1.4027   1.5996
 RTN  H12   H  HCR6  0   0.249  -4.6072   2.6062   0.7729
 RTN  H14   H  HCR6  0   0.253  -8.6927   3.2225  -0.3237
 RTN  C18   C  CH2   0  -0.538   1.5636  -0.5986  -1.1449

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
 RTN  N7   C4    aromatic  1.352  0.020  1.352
 RTN  C4   C3    aromatic  1.412  0.020  1.412
 RTN  C4   C5    aromatic  1.412  0.020  1.412
 RTN  C10  C5    aromatic  1.417  0.020  1.417
 RTN  C5   C6    aromatic  1.407  0.020  1.407
 RTN  C6   C1    aromatic  1.377  0.020  1.377
 RTN  C6   H6    single    0.930  0.020  1.080
 RTN  N28  C8    single    1.360  0.020  1.360
 RTN  C8   N7    aromatic  1.312  0.020  1.312
 RTN  C8   C9    aromatic  1.440  0.020  1.440
 RTN  C9   C10   aromatic  1.360  0.020  1.360
 RTN  C10  H10   single    0.930  0.020  1.080
 RTN  C12  C13   aromatic  1.386  0.020  1.386
 RTN  C13  C14   aromatic  1.387  0.020  1.387
 RTN  C13  H13   single    0.930  0.020  1.080
 RTN  C16  C15   aromatic  1.394  0.020  1.394
 RTN  C15  C14   aromatic  1.387  0.020  1.387
 RTN  C15  H15   single    0.930  0.020  1.080
 RTN  C17  C16   single    1.503  0.020  1.503
 RTN  C17  H17   single    0.970  0.020  1.090
 RTN  C17  H17A  single    0.970  0.020  1.090
 RTN  C17  H17B  single    0.970  0.020  1.090
 RTN  C19  C20   single    1.516  0.020  1.516
 RTN  N21  C20   single    1.342  0.020  1.342
 RTN  C20  O29   double    1.224  0.020  1.224
 RTN  N21  C22   single    1.450  0.020  1.450
 RTN  C22  C23   single    1.526  0.020  1.526
 RTN  C22  C27   single    1.529  0.020  1.529
 RTN  C22  H22   single    0.970  0.020  1.090
 RTN  C23  C24   single    1.526  0.020  1.526
 RTN  C24  C25   single    1.525  0.020  1.525
 RTN  C24  H24   single    0.970  0.020  1.090
 RTN  C24  H24A  single    0.970  0.020  1.090
 RTN  C27  C26   single    1.526  0.020  1.526
 RTN  C26  C25   single    1.525  0.020  1.525
 RTN  C26  H26   single    0.970  0.020  1.090
 RTN  C26  H26A  single    0.970  0.020  1.090
 RTN  C23  H23   single    0.970  0.020  1.090
 RTN  C23  H23A  single    0.970  0.020  1.090
 RTN  C25  H25   single    0.970  0.020  1.090
 RTN  C25  H25A  single    0.970  0.020  1.090
 RTN  C27  H27   single    0.970  0.020  1.090
 RTN  C27  H27A  single    0.970  0.020  1.090
 RTN  N21  HN21  single    0.860  0.020  1.020
 RTN  C18  C19   single    1.530  0.020  1.530
 RTN  C19  H19   single    0.970  0.020  1.090
 RTN  C19  H19A  single    0.970  0.020  1.090
 RTN  C18  C9    single    1.501  0.020  1.501
 RTN  C18  H18   single    0.970  0.020  1.090
 RTN  C18  H18A  single    0.970  0.020  1.090
 RTN  N28  HN28  single    0.890  0.020  1.040
 RTN  N28  HN2A  single    0.890  0.020  1.040
 RTN  C3   C2    aromatic  1.370  0.020  1.370
 RTN  C3   H3    single    0.930  0.020  1.080
 RTN  C2   C1    aromatic  1.414  0.020  1.414
 RTN  C2   H2    single    0.930  0.020  1.080
 RTN  C1   C11   single    1.481  0.020  1.481
 RTN  C11  C16   aromatic  1.404  0.020  1.404
 RTN  C11  C12   aromatic  1.396  0.020  1.396
 RTN  C12  H12   single    0.930  0.020  1.080
 RTN  C14  H14   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
 RTN  C3    C4   N7    119.44  3.000
 RTN  C3    C4   C5    118.21  3.000
 RTN  N7    C4   C5    122.35  3.000
 RTN  C10   C5   C6    123.10  3.000
 RTN  C6    C5   C4    120.04  3.000
 RTN  C10   C5   C4    116.86  3.000
 RTN  H6    C6   C1    119.96  3.000
 RTN  H6    C6   C5    118.79  3.000
 RTN  C1    C6   C5    121.24  3.000
 RTN  N28   C8   N7    117.25  3.000
 RTN  N7    C8   C9    123.17  3.000
 RTN  N28   C8   C9    119.54  3.000
 RTN  H10   C10  C9    119.74  3.000
 RTN  H10   C10  C5    119.00  3.000
 RTN  C9    C10  C5    121.26  3.000
 RTN  H13   C13  C14   120.56  3.000
 RTN  H13   C13  C12   120.05  3.000
 RTN  C14   C13  C12   119.39  3.000
 RTN  H15   C15  C16   118.93  3.000
 RTN  H15   C15  C14   119.30  3.000
 RTN  C16   C15  C14   121.76  3.000
 RTN  H17B  C17  H17A  107.92  3.000
 RTN  H17B  C17  H17   107.02  3.000
 RTN  H17A  C17  H17   107.07  3.000
 RTN  H17B  C17  C16   112.08  3.000
 RTN  H17A  C17  C16   110.66  3.000
 RTN  H17   C17  C16   111.85  3.000
 RTN  C19   C20  O29   121.92  3.000
 RTN  O29   C20  N21   123.41  3.000
 RTN  C19   C20  N21   114.64  3.000
 RTN  H22   C22  N21   107.10  3.000
 RTN  H22   C22  C27   108.58  3.000
 RTN  N21   C22  C27   111.49  3.000
 RTN  H22   C22  C23   108.39  3.000
 RTN  C27   C22  C23   110.91  3.000
 RTN  N21   C22  C23   110.23  3.000
 RTN  H24A  C24  H24   106.46  3.000
 RTN  H24A  C24  C25   110.40  3.000
 RTN  H24   C24  C25   109.30  3.000
 RTN  H24A  C24  C23   109.80  3.000
 RTN  H24   C24  C23   109.26  3.000
 RTN  C25   C24  C23   111.49  3.000
 RTN  H26A  C26  H26   106.49  3.000
 RTN  H26A  C26  C27   109.94  3.000
 RTN  H26   C26  C27   109.20  3.000
 RTN  H26A  C26  C25   110.45  3.000
 RTN  H26   C26  C25   109.35  3.000
 RTN  C27   C26  C25   111.27  3.000
 RTN  H23A  C23  H23   106.98  3.000
 RTN  H23A  C23  C24   109.25  3.000
 RTN  H23   C23  C24   110.52  3.000
 RTN  H23A  C23  C22   109.28  3.000
 RTN  H23   C23  C22   109.69  3.000
 RTN  C24   C23  C22   111.03  3.000
 RTN  H25A  C25  H25   106.60  3.000
 RTN  H25A  C25  C26   109.30  3.000
 RTN  H25   C25  C26   110.30  3.000
 RTN  H25A  C25  C24   109.29  3.000
 RTN  H25   C25  C24   110.18  3.000
 RTN  C26   C25  C24   111.05  3.000
 RTN  H27A  C27  H27   106.88  3.000
 RTN  H27A  C27  C26   110.58  3.000
 RTN  H27   C27  C26   109.71  3.000
 RTN  H27A  C27  C22   109.45  3.000
 RTN  H27   C27  C22   108.86  3.000
 RTN  C26   C27  C22   111.25  3.000
 RTN  HN21  N21  C22   117.17  3.000
 RTN  HN21  N21  C20   118.00  3.000
 RTN  C22   N21  C20   124.80  3.000
 RTN  H19A  C19  H19   106.08  3.000
 RTN  H19A  C19  C18   108.99  3.000
 RTN  H19   C19  C18   110.77  3.000
 RTN  H19A  C19  C20   107.68  3.000
 RTN  H19   C19  C20   110.43  3.000
 RTN  C18   C19  C20   112.61  3.000
 RTN  C18   C9   C10   121.41  3.000
 RTN  C18   C9   C8    121.55  3.000
 RTN  C10   C9   C8    117.00  3.000
 RTN  C8    N7   C4    119.36  3.000
 RTN  HN2A  N28  HN28  114.26  3.000
 RTN  HN2A  N28  C8    119.42  3.000
 RTN  HN28  N28  C8    116.11  3.000
 RTN  H3    C3   C2    120.64  3.000
 RTN  H3    C3   C4    118.71  3.000
 RTN  C2    C3   C4    120.64  3.000
 RTN  H2    C2   C1    119.27  3.000
 RTN  H2    C2   C3    119.22  3.000
 RTN  C1    C2   C3    121.50  3.000
 RTN  C11   C1   C2    121.02  3.000
 RTN  C11   C1   C6    120.61  3.000
 RTN  C2    C1   C6    118.35  3.000
 RTN  C16   C11  C12   119.32  3.000
 RTN  C12   C11  C1    118.71  3.000
 RTN  C16   C11  C1    121.97  3.000
 RTN  H12   C12  C11   119.05  3.000
 RTN  H12   C12  C13   119.53  3.000
 RTN  C11   C12  C13   121.42  3.000
 RTN  H14   C14  C15   120.01  3.000
 RTN  H14   C14  C13   120.38  3.000
 RTN  C15   C14  C13   119.60  3.000
 RTN  C11   C16  C17   122.26  3.000
 RTN  C11   C16  C15   118.50  3.000
 RTN  C17   C16  C15   119.22  3.000
 RTN  H18A  C18  H18   105.82  3.000
 RTN  H18A  C18  C9    111.06  3.000
 RTN  H18   C18  C9    108.93  3.000
 RTN  H18A  C18  C19   109.96  3.000
 RTN  H18   C18  C19   109.25  3.000
 RTN  C9    C18  C19   111.63  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
 RTN  CONST_01  C9    C8   N7   C4      0.00   0.0  0
 RTN  CONST_02  C1    C2   C3   C4      0.00   0.0  0
 RTN  CONST_03  C9    C10  C5   C4      0.00   0.0  0
 RTN  CONST_04  C1    C6   C5   C4      0.00   0.0  0
 RTN  CONST_05  C8    N7   C4   C5      0.00   0.0  0
 RTN  CONST_06  C2    C3   C4   C5      0.00   0.0  0
 RTN  CONST_07  C8    C9   C10  C5      0.00   0.0  0
 RTN  CONST_08  C2    C1   C6   C5      0.00   0.0  0
 RTN  CONST_09  C11   C1   C6   C5    180.00   0.0  0
 RTN  CONST_10  N7    C4   C5   C6    180.00   0.0  0
 RTN  CONST_11  C3    C4   C5   C6      0.00   0.0  0
 RTN  CONST_12  C9    C10  C5   C6    180.00   0.0  0
 RTN  CONST_13  C3    C2   C1   C6      0.00   0.0  0
 RTN  CONST_16  C3    C4   N7   C8    180.00   0.0  0
 RTN  CONST_17  N7    C4   C5   C10     0.00   0.0  0
 RTN  CONST_18  C3    C4   C5   C10   180.00   0.0  0
 RTN  CONST_19  C1    C6   C5   C10   180.00   0.0  0
 RTN  CONST_20  N7    C8   C9   C10     0.00   0.0  0
 RTN  CONST_21  C1    C11  C12  C13   180.00   0.0  0
 RTN  CONST_22  C16   C11  C12  C13     0.00   0.0  0
 RTN  CONST_23  C16   C15  C14  C13     0.00   0.0  0
 RTN  CONST_24  C1    C11  C16  C15   180.00   0.0  0
 RTN  CONST_25  C12   C11  C16  C15     0.00   0.0  0
 RTN  CONST_26  C12   C13  C14  C15     0.00   0.0  0
 RTN  CONST_27  C2    C3   C4   N7    180.00   0.0  0
 RTN  CONST_28  C11   C1   C2   C3    180.00   0.0  0
 RTN  CONST_31  C14   C15  C16  C11     0.00   0.0  0
 RTN  CONST_32  C14   C13  C12  C11     0.00   0.0  0
 RTN  CONST_33  N28   C8   N7   C4    180.00   0.0  0
 RTN  CONST_34  C18   C9   C10  C5    180.00   0.0  0
 RTN  CONST_35  N28   C8   C9   C10   180.00   0.0  0
 RTN  CONST_36  C14   C15  C16  C17   180.00   0.0  0
 RTN  CONST_37  C1    C11  C16  C17     0.00   0.0  0
 RTN  CONST_38  C12   C11  C16  C17   180.00   0.0  0
 RTN  CONST_39  N7    C8   C9   C18   180.00   0.0  0
 RTN  CONST_40  H2    C2   C3   C4    180.00   0.0  0
 RTN  CONST_41  H10   C10  C5   C4    180.00   0.0  0
 RTN  CONST_42  H6    C6   C5   C4    180.00   0.0  0
 RTN  CONST_43  H3    C3   C4   C5    180.00   0.0  0
 RTN  CONST_44  H15   C15  C14  C13   180.00   0.0  0
 RTN  CONST_45  H13   C13  C14  C15   180.00   0.0  0
 RTN  CONST_46  H12   C12  C11  C1      0.00   0.0  0
 RTN  CONST_47  H14   C14  C13  C12   180.00   0.0  0
 RTN  CONST_48  HN28  N28  C8   C9    180.00   0.0  0
 RTN  CONST_50  C19   C20  N21  C22   180.00   0.0  0
 RTN  CONST_51  O29   C20  N21  C22     0.00   0.0  0
 RTN  CONST_52  HN21  N21  C20  O29   180.00   0.0  0
 RTN  Var_01    C25   C24  C23  C22   -55.75  30.0  1
 RTN  Var_02    C25   C26  C27  C22    55.62  30.0  1
 RTN  Var_03    C27   C26  C25  C24   -55.23  30.0  1
 RTN  Var_04    C23   C24  C25  C26    55.40  30.0  1
 RTN  Var_05    C19   C18  C9   C8    -76.01  30.0  2
 RTN  Var_06    H17   C17  C16  C15   -97.96  30.0  2
 RTN  Var_07    C9    C18  C19  C20  -179.57  30.0  1
 RTN  Var_08    C18   C19  C20  N21  -153.74  30.0  2

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
 RTN  chir_01  C22  N21  C23  C27  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
 RTN  plan-1  C13   0.020
 RTN  plan-1  C15   0.020
 RTN  plan-1  C17   0.020
 RTN  plan-1  C1    0.020
 RTN  plan-1  C11   0.020
 RTN  plan-1  C12   0.020
 RTN  plan-1  C14   0.020
 RTN  plan-1  C16   0.020
 RTN  plan-1  H13   0.020
 RTN  plan-1  H15   0.020
 RTN  plan-1  H12   0.020
 RTN  plan-1  H14   0.020
 RTN  plan-2  C4    0.020
 RTN  plan-2  C5    0.020
 RTN  plan-2  C6    0.020
 RTN  plan-2  C8    0.020
 RTN  plan-2  C10   0.020
 RTN  plan-2  C9    0.020
 RTN  plan-2  N7    0.020
 RTN  plan-2  N28   0.020
 RTN  plan-2  C3    0.020
 RTN  plan-2  C2    0.020
 RTN  plan-2  C1    0.020
 RTN  plan-2  C11   0.020
 RTN  plan-2  H6    0.020
 RTN  plan-2  H10   0.020
 RTN  plan-2  H3    0.020
 RTN  plan-2  H2    0.020
 RTN  plan-2  C18   0.020
 RTN  plan-3  C8    0.020
 RTN  plan-3  N28   0.020
 RTN  plan-3  HN28  0.020
 RTN  plan-3  HN2A  0.020
 RTN  plan-4  C20   0.020
 RTN  plan-4  C22   0.020
 RTN  plan-4  N21   0.020
 RTN  plan-4  O29   0.020
 RTN  plan-4  C19   0.020
 RTN  plan-4  HN21  0.020

