# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:14:56 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1CCCCC1)C(=O)CCc2cc3ccccc3nc2N
#
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
 RTM  RTM  3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide  ligand  48  23  .  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_RTM
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
 RTM  N1    N  N     0  -0.498  -3.8113   1.5406  -0.3374
 RTM  N3    N  NT    0  -0.462   2.7444  -0.0618  -0.3113
 RTM  C4    C  CR16  0  -0.321  -5.0466  -1.8972   0.2100
 RTM  C5    C  CR66  0   0.083  -4.1804  -0.7865   0.2230
 RTM  C6    C  CR66  0   0.203  -4.6024   0.4436  -0.3310
 RTM  C7    C  CR6   0   0.386  -2.6054   1.4685   0.1718
 RTM  C8    C  CR6   0   0.024  -2.0647   0.2663   0.7527
 RTM  C10   C  CH2   0  -0.532  -0.6602   0.2142   1.2811
 RTM  C13   C  CH3   0  -0.550   2.4138  -0.2402  -1.7132
 RTM  C15   C  CH2   0  -0.428   4.8010  -1.4439  -0.3871
 RTM  C17   C  CH2   0  -0.432   7.0440  -0.2994  -0.4636
 RTM  C16   C  CH2   0  -0.434   6.2640  -1.5071   0.0429
 RTM  C18   C  CH2   0  -0.435   6.4012   1.0016   0.0033
 RTM  C19   C  CH2   0  -0.425   4.9375   1.0813  -0.4212
 RTM  C14   C  CH1   0  -0.095   4.1541  -0.1361   0.0703
 RTM  C12   C  C     0   0.580   1.7919   0.1145   0.6307
 RTM  O1    O  O     0  -0.510   2.0510   0.2592   1.8203
 RTM  C11   C  CH2   0  -0.594   0.3551   0.1293   0.1435
 RTM  C9    C  CR16  0  -0.259  -2.8722  -0.8284   0.7668
 RTM  C1    C  CR16  0  -0.270  -6.2995  -1.7949  -0.3397
 RTM  C2    C  CR16  0  -0.263  -6.7228  -0.5717  -0.8930
 RTM  C3    C  CR16  0  -0.304  -5.8967   0.5240  -0.8901
 RTM  N2    N  NH2   0  -0.833  -1.8304   2.5854   0.0974
 RTM  H4    H  HCR6  0   0.254  -4.7078  -2.8339   0.6373
 RTM  H10   H  HCH2  0   0.248  -0.4531   1.0792   1.9174
 RTM  H10A  H  HCH2  0   0.266  -0.5587  -0.6583   1.9279
 RTM  H13   H  HCH3  0   0.247   2.0814  -1.2556  -1.9387
 RTM  H13A  H  HCH3  0   0.257   1.6412   0.4530  -2.0377
 RTM  H13B  H  HCH3  0   0.261   3.2885  -0.0324  -2.3236
 RTM  H15   H  HCH2  0   0.217   4.7504  -1.5363  -1.4768
 RTM  H15A  H  HCH2  0   0.236   4.2469  -2.2898   0.0281
 RTM  H17   H  HCH2  0   0.230   8.0828  -0.3517  -0.1295
 RTM  H17A  H  HCH2  0   0.210   7.0663  -0.3181  -1.5588
 RTM  H16   H  HCH2  0   0.214   6.3243  -1.5480   1.1358
 RTM  H16A  H  HCH2  0   0.232   6.7139  -2.4324  -0.3244
 RTM  H18   H  HCH2  0   0.213   6.4692   1.0697   1.0946
 RTM  H18A  H  HCH2  0   0.231   6.9467   1.8608  -0.3939
 RTM  H19   H  HCH2  0   0.235   4.4763   1.9906  -0.0276
 RTM  H19A  H  HCH2  0   0.215   4.8871   1.1496  -1.5132
 RTM  H14   H  HCH1  0   0.247   4.1812  -0.1230   1.1605
 RTM  H11   H  HCH2  0   0.278   0.1569  -0.7696  -0.4477
 RTM  H11A  H  HCH2  0   0.274   0.2195   0.9678  -0.5457
 RTM  H9    H  HCR6  0   0.258  -2.5110  -1.7571   1.1959
 RTM  H1    H  HCR6  0   0.254  -6.9630  -2.6492  -0.3521
 RTM  H2    H  HCR6  0   0.256  -7.7120  -0.4965  -1.3268
 RTM  H3    H  HCR6  0   0.251  -6.2207   1.4656  -1.3153
 RTM  HN2   H  HNH2  0   0.388  -2.3113   3.4443  -0.1157
 RTM  HN2A  H  HNH2  0   0.395  -1.0611   2.6940   0.7359

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
 RTM  C7   N1    aromatic  1.311  0.020  1.311
 RTM  N1   C6    aromatic  1.353  0.020  1.353
 RTM  C12  N3    single    1.351  0.020  1.351
 RTM  C14  N3    single    1.462  0.020  1.462
 RTM  N3   C13   single    1.451  0.020  1.451
 RTM  C5   C4    aromatic  1.409  0.020  1.409
 RTM  C4   C1    aromatic  1.372  0.020  1.372
 RTM  C4   H4    single    0.930  0.020  1.080
 RTM  C6   C5    aromatic  1.414  0.020  1.414
 RTM  C9   C5    aromatic  1.417  0.020  1.417
 RTM  C6   C3    aromatic  1.412  0.020  1.412
 RTM  N2   C7    single    1.361  0.020  1.361
 RTM  C7   C8    aromatic  1.440  0.020  1.440
 RTM  C10  C8    single    1.502  0.020  1.502
 RTM  C8   C9    aromatic  1.360  0.020  1.360
 RTM  C11  C10   single    1.527  0.020  1.527
 RTM  C10  H10   single    0.970  0.020  1.090
 RTM  C10  H10A  single    0.970  0.020  1.090
 RTM  C13  H13   single    0.970  0.020  1.090
 RTM  C13  H13A  single    0.970  0.020  1.090
 RTM  C13  H13B  single    0.970  0.020  1.090
 RTM  C14  C15   single    1.529  0.020  1.529
 RTM  C16  C15   single    1.526  0.020  1.526
 RTM  C15  H15   single    0.970  0.020  1.090
 RTM  C15  H15A  single    0.970  0.020  1.090
 RTM  C18  C17   single    1.524  0.020  1.524
 RTM  C17  C16   single    1.524  0.020  1.524
 RTM  C17  H17   single    0.970  0.020  1.090
 RTM  C17  H17A  single    0.970  0.020  1.090
 RTM  C16  H16   single    0.970  0.020  1.090
 RTM  C16  H16A  single    0.970  0.020  1.090
 RTM  C18  C19   single    1.526  0.020  1.526
 RTM  C18  H18   single    0.970  0.020  1.090
 RTM  C18  H18A  single    0.970  0.020  1.090
 RTM  C19  C14   single    1.529  0.020  1.529
 RTM  C19  H19   single    0.970  0.020  1.090
 RTM  C19  H19A  single    0.970  0.020  1.090
 RTM  C14  H14   single    0.970  0.020  1.090
 RTM  O1   C12   double    1.226  0.020  1.226
 RTM  C12  C11   single    1.517  0.020  1.517
 RTM  C11  H11   single    0.970  0.020  1.090
 RTM  C11  H11A  single    0.970  0.020  1.090
 RTM  C9   H9    single    0.930  0.020  1.080
 RTM  C2   C1    aromatic  1.408  0.020  1.408
 RTM  C1   H1    single    0.930  0.020  1.080
 RTM  C3   C2    aromatic  1.372  0.020  1.372
 RTM  C2   H2    single    0.930  0.020  1.080
 RTM  C3   H3    single    0.930  0.020  1.080
 RTM  N2   HN2   single    0.890  0.020  1.040
 RTM  N2   HN2A  single    0.890  0.020  1.040

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
 RTM  C7    N1   C6    119.44  3.000
 RTM  C12   N3   C14   120.29  3.000
 RTM  C14   N3   C13   117.73  3.000
 RTM  C12   N3   C13   121.93  3.000
 RTM  H4    C4   C1    120.52  3.000
 RTM  H4    C4   C5    119.06  3.000
 RTM  C1    C4   C5    120.43  3.000
 RTM  C9    C5   C6    116.85  3.000
 RTM  C9    C5   C4    123.22  3.000
 RTM  C6    C5   C4    119.93  3.000
 RTM  C3    C6   C5    118.58  3.000
 RTM  C3    C6   N1    119.21  3.000
 RTM  C5    C6   N1    122.21  3.000
 RTM  N2    C7   C8    119.54  3.000
 RTM  C8    C7   N1    123.22  3.000
 RTM  N2    C7   N1    117.21  3.000
 RTM  C9    C8   C10   121.57  3.000
 RTM  C9    C8   C7    116.93  3.000
 RTM  C10   C8   C7    121.47  3.000
 RTM  H10A  C10  H10   105.67  3.000
 RTM  H10A  C10  C11   109.60  3.000
 RTM  H10   C10  C11   110.58  3.000
 RTM  H10A  C10  C8    108.87  3.000
 RTM  H10   C10  C8    110.76  3.000
 RTM  C11   C10  C8    111.20  3.000
 RTM  H13B  C13  H13A  106.40  3.000
 RTM  H13B  C13  H13   107.87  3.000
 RTM  H13A  C13  H13   108.35  3.000
 RTM  H13B  C13  N3    109.62  3.000
 RTM  H13A  C13  N3    111.82  3.000
 RTM  H13   C13  N3    112.53  3.000
 RTM  H15A  C15  H15   106.82  3.000
 RTM  H15A  C15  C14   109.50  3.000
 RTM  H15   C15  C14   110.51  3.000
 RTM  H15A  C15  C16   110.30  3.000
 RTM  H15   C15  C16   108.74  3.000
 RTM  C14   C15  C16   110.89  3.000
 RTM  H17A  C17  H17   106.59  3.000
 RTM  H17A  C17  C18   109.23  3.000
 RTM  H17   C17  C18   110.38  3.000
 RTM  H17A  C17  C16   109.21  3.000
 RTM  H17   C17  C16   110.30  3.000
 RTM  C18   C17  C16   111.02  3.000
 RTM  H16A  C16  H16   106.34  3.000
 RTM  H16A  C16  C17   110.40  3.000
 RTM  H16   C16  C17   109.45  3.000
 RTM  H16A  C16  C15   109.58  3.000
 RTM  H16   C16  C15   109.60  3.000
 RTM  C17   C16  C15   111.35  3.000
 RTM  H18A  C18  H18   106.40  3.000
 RTM  H18A  C18  C19   109.67  3.000
 RTM  H18   C18  C19   109.47  3.000
 RTM  H18A  C18  C17   110.44  3.000
 RTM  H18   C18  C17   109.39  3.000
 RTM  C19   C18  C17   111.33  3.000
 RTM  H19A  C19  H19   106.73  3.000
 RTM  H19A  C19  C14   110.28  3.000
 RTM  H19   C19  C14   109.30  3.000
 RTM  H19A  C19  C18   108.95  3.000
 RTM  H19   C19  C18   110.37  3.000
 RTM  C14   C19  C18   111.12  3.000
 RTM  H14   C14  C19   107.40  3.000
 RTM  H14   C14  C15   107.38  3.000
 RTM  C19   C14  C15   111.61  3.000
 RTM  H14   C14  N3    106.51  3.000
 RTM  C19   C14  N3    111.69  3.000
 RTM  C15   C14  N3    111.92  3.000
 RTM  C11   C12  O1    120.70  3.000
 RTM  C11   C12  N3    116.42  3.000
 RTM  O1    C12  N3    122.88  3.000
 RTM  H11A  C11  H11   105.48  3.000
 RTM  H11A  C11  C12   109.09  3.000
 RTM  H11   C11  C12   109.70  3.000
 RTM  H11A  C11  C10   110.14  3.000
 RTM  H11   C11  C10   109.14  3.000
 RTM  C12   C11  C10   113.01  3.000
 RTM  H9    C9   C8    119.69  3.000
 RTM  H9    C9   C5    118.97  3.000
 RTM  C8    C9   C5    121.34  3.000
 RTM  H1    C1   C2    119.82  3.000
 RTM  H1    C1   C4    120.38  3.000
 RTM  C2    C1   C4    119.79  3.000
 RTM  H2    C2   C3    119.70  3.000
 RTM  H2    C2   C1    119.51  3.000
 RTM  C3    C2   C1    120.79  3.000
 RTM  H3    C3   C2    120.89  3.000
 RTM  H3    C3   C6    118.64  3.000
 RTM  C2    C3   C6    120.47  3.000
 RTM  HN2A  N2   HN2   114.05  3.000
 RTM  HN2A  N2   C7    119.30  3.000
 RTM  HN2   N2   C7    116.07  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
 RTM  CONST_01  C9   C8   C7   N1     0.00   0.0  0
 RTM  CONST_02  C4   C5   C6   N1   180.00   0.0  0
 RTM  CONST_03  C9   C5   C6   N1     0.00   0.0  0
 RTM  CONST_04  C2   C3   C6   N1   180.00   0.0  0
 RTM  CONST_05  C3   C6   C5   C4     0.00   0.0  0
 RTM  CONST_06  C8   C9   C5   C4   180.00   0.0  0
 RTM  CONST_07  C3   C2   C1   C4     0.00   0.0  0
 RTM  CONST_08  C2   C1   C4   C5     0.00   0.0  0
 RTM  CONST_09  C7   N1   C6   C5     0.00   0.0  0
 RTM  CONST_10  C2   C3   C6   C5     0.00   0.0  0
 RTM  CONST_11  C7   C8   C9   C5     0.00   0.0  0
 RTM  CONST_12  C8   C7   N1   C6     0.00   0.0  0
 RTM  CONST_13  C1   C4   C5   C6     0.00   0.0  0
 RTM  CONST_14  C8   C9   C5   C6     0.00   0.0  0
 RTM  CONST_15  C1   C2   C3   C6     0.00   0.0  0
 RTM  CONST_16  C3   C6   N1   C7   180.00   0.0  0
 RTM  CONST_17  C1   C4   C5   C9   180.00   0.0  0
 RTM  CONST_18  C3   C6   C5   C9   180.00   0.0  0
 RTM  CONST_19  C10  C8   C7   N1   180.00   0.0  0
 RTM  CONST_20  C10  C8   C9   C5   180.00   0.0  0
 RTM  CONST_21  N2   C7   N1   C6   180.00   0.0  0
 RTM  CONST_22  N2   C7   C8   C9   180.00   0.0  0
 RTM  CONST_23  H3   C3   C6   N1     0.00   0.0  0
 RTM  CONST_24  H9   C9   C5   C4     0.00   0.0  0
 RTM  CONST_25  H2   C2   C1   C4   180.00   0.0  0
 RTM  CONST_26  H1   C1   C4   C5   180.00   0.0  0
 RTM  CONST_27  H4   C4   C5   C6   180.00   0.0  0
 RTM  CONST_30  O1   C12  N3   C14    0.00   0.0  0
 RTM  CONST_31  C11  C12  N3   C14  180.00   0.0  0
 RTM  CONST_32  O1   C12  N3   C13  180.00   0.0  0
 RTM  CONST_33  C11  C12  N3   C13    0.00   0.0  0
 RTM  Var_01    C18  C17  C16  C15   56.19  30.0  1
 RTM  Var_02    C14  C19  C18  C17   55.17  30.0  1
 RTM  Var_03    C14  C15  C16  C17  -55.59  30.0  1
 RTM  Var_04    C19  C18  C17  C16  -55.91  30.0  1
 RTM  Var_05    C11  C10  C8   C7   -75.94  30.0  1
 RTM  Var_06    C12  C11  C10  C8   178.35  30.0  1
 RTM  Var_07    H13  C13  N3   C14   98.57  30.0  3
 RTM  Var_08    C10  C11  C12  N3   175.12  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
 RTM  chir_01  C14  N3  C15  C19  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
 RTM  plan-1  N1    0.020
 RTM  plan-1  C4    0.020
 RTM  plan-1  C5    0.020
 RTM  plan-1  C6    0.020
 RTM  plan-1  C7    0.020
 RTM  plan-1  C8    0.020
 RTM  plan-1  C10   0.020
 RTM  plan-1  C9    0.020
 RTM  plan-1  C1    0.020
 RTM  plan-1  C2    0.020
 RTM  plan-1  C3    0.020
 RTM  plan-1  N2    0.020
 RTM  plan-1  H4    0.020
 RTM  plan-1  H9    0.020
 RTM  plan-1  H1    0.020
 RTM  plan-1  H2    0.020
 RTM  plan-1  H3    0.020
 RTM  plan-2  C7    0.020
 RTM  plan-2  N2    0.020
 RTM  plan-2  HN2   0.020
 RTM  plan-2  HN2A  0.020
 RTM  plan-3  N3    0.020
 RTM  plan-3  C13   0.020
 RTM  plan-3  C14   0.020
 RTM  plan-3  C12   0.020
 RTM  plan-3  O1    0.020
 RTM  plan-3  C11   0.020

