# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:00:00 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-(2-aminoquinolin-3-yl)-N-(cyclohexylmethyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2ccccc2cc1CCC(=O)NCC3CCCCC3
#
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
 3RU  3RU  3-(2-aminoquinolin-3-yl)-N-(cyclohexylmethyl)propanamide  ligand  48  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3RU
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
 3RU  C4    C  CR16  0  -0.321  -4.7093  -2.2135   0.6395
 3RU  C5    C  CR66  0   0.082  -4.0590  -1.0000   0.3422
 3RU  C6    C  CR66  0   0.204  -4.6620  -0.0734  -0.5389
 3RU  C8    C  CR6   0   0.386  -2.9163   1.4104  -0.3313
 3RU  C10   C  CR16  0  -0.258  -2.7993  -0.6417   0.8834
 3RU  C13   C  CH2   0  -0.578   0.2492   0.7108   0.0475
 3RU  C17   C  CH2   0  -0.270   3.9665   1.4540  -0.0659
 3RU  C20   C  CH2   0  -0.430   7.1827  -0.6235  -0.6266
 3RU  C21   C  CH2   0  -0.429   6.7294  -1.9305   0.0150
 3RU  C22   C  CH2   0  -0.429   5.2641  -2.2120  -0.2985
 3RU  C19   C  CH2   0  -0.420   6.2855   0.5385  -0.2122
 3RU  C23   C  CH2   0  -0.414   4.3703  -1.0502   0.1261
 3RU  C18   C  CH1   0  -0.239   4.8128   0.2636  -0.5158
 3RU  N15   N  NH1   0  -0.638   2.5537   1.3033  -0.3322
 3RU  C14   C  C     0   0.568   1.6382   0.9749   0.5950
 3RU  O16   O  O     0  -0.503   1.8946   0.8705   1.7870
 3RU  C9    C  CR6   0   0.026  -2.2028   0.5389   0.5663
 3RU  C1    C  CR16  0  -0.270  -5.9265  -2.5058   0.0778
 3RU  C2    C  CR16  0  -0.263  -6.5293  -1.5861  -0.8009
 3RU  C3    C  CR16  0  -0.305  -5.9147  -0.3973  -1.1045
 3RU  N7    N  N     0  -0.498  -4.0829   1.1091  -0.8486
 3RU  N11   N  NH2   0  -0.832  -2.3527   2.5899  -0.7088
 3RU  H4    H  HCR6  0   0.255  -4.2338  -2.9128   1.3173
 3RU  H10   H  HCR6  0   0.259  -2.3018  -1.3292   1.5592
 3RU  H13   H  HCH2  0   0.262   0.0588   1.3360  -0.8271
 3RU  H13A  H  HCH2  0   0.281   0.2314  -0.3229  -0.3129
 3RU  H17   H  HCH2  0   0.236   4.0948   1.6163   1.0049
 3RU  H17A  H  HCH2  0   0.245   4.3180   2.3589  -0.5685
 3RU  H20   H  HCH2  0   0.226   8.2205  -0.4084  -0.3606
 3RU  H20A  H  HCH2  0   0.209   7.1566  -0.7278  -1.7167
 3RU  H21   H  HCH2  0   0.225   7.3574  -2.7582  -0.3242
 3RU  H21A  H  HCH2  0   0.207   6.8594  -1.8637   1.1010
 3RU  H22   H  HCH2  0   0.207   5.1509  -2.3803  -1.3752
 3RU  H22A  H  HCH2  0   0.226   4.9386  -3.1317   0.1940
 3RU  H19   H  HCH2  0   0.208   6.3982   0.7167   0.8642
 3RU  H19A  H  HCH2  0   0.226   6.6057   1.4571  -0.7127
 3RU  H23   H  HCH2  0   0.224   3.3323  -1.2673  -0.1381
 3RU  H23A  H  HCH2  0   0.206   4.4021  -0.9458   1.2169
 3RU  H18   H  HCH1  0   0.212   4.7043   0.1595  -1.6045
 3RU  HN15  H  HNH1  0   0.396   2.2578   1.3545  -1.2941
 3RU  H12   H  HCH2  0   0.269  -0.6270   0.2578   1.9571
 3RU  H12A  H  HCH2  0   0.249  -0.8305   1.9201   1.4796
 3RU  H1    H  HCR6  0   0.254  -6.4237  -3.4391   0.3070
 3RU  H2    H  HCR6  0   0.256  -7.4902  -1.8209  -1.2407
 3RU  H3    H  HCR6  0   0.251  -6.3786   0.3105  -1.7800
 3RU  HN11  H  HNH2  0   0.387  -2.9604   3.2439  -1.1747
 3RU  HN1A  H  HNH2  0   0.396  -1.6643   3.0183  -0.1141
 3RU  C12   C  CH2   0  -0.539  -0.8449   0.8937   1.0990

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
 3RU  C5   C4    aromatic  1.408  0.020  1.408
 3RU  C4   C1    aromatic  1.372  0.020  1.372
 3RU  C4   H4    single    0.930  0.020  1.080
 3RU  C6   C5    aromatic  1.414  0.020  1.414
 3RU  C10  C5    aromatic  1.417  0.020  1.417
 3RU  N7   C6    aromatic  1.353  0.020  1.353
 3RU  C6   C3    aromatic  1.412  0.020  1.412
 3RU  N11  C8    single    1.361  0.020  1.361
 3RU  C8   N7    aromatic  1.311  0.020  1.311
 3RU  C8   C9    aromatic  1.440  0.020  1.440
 3RU  C9   C10   aromatic  1.360  0.020  1.360
 3RU  C10  H10   single    0.930  0.020  1.080
 3RU  C13  C14   single    1.516  0.020  1.516
 3RU  C13  C12   single    1.528  0.020  1.528
 3RU  C13  H13   single    0.970  0.020  1.090
 3RU  C13  H13A  single    0.970  0.020  1.090
 3RU  N15  C17   single    1.446  0.020  1.446
 3RU  C18  C17   single    1.528  0.020  1.528
 3RU  C17  H17   single    0.970  0.020  1.090
 3RU  C17  H17A  single    0.970  0.020  1.090
 3RU  C20  C19   single    1.525  0.020  1.525
 3RU  C20  C21   single    1.525  0.020  1.525
 3RU  C20  H20   single    0.970  0.020  1.090
 3RU  C20  H20A  single    0.970  0.020  1.090
 3RU  C21  C22   single    1.525  0.020  1.525
 3RU  C21  H21   single    0.970  0.020  1.090
 3RU  C21  H21A  single    0.970  0.020  1.090
 3RU  C22  C23   single    1.526  0.020  1.526
 3RU  C22  H22   single    0.970  0.020  1.090
 3RU  C22  H22A  single    0.970  0.020  1.090
 3RU  C19  C18   single    1.529  0.020  1.529
 3RU  C19  H19   single    0.970  0.020  1.090
 3RU  C19  H19A  single    0.970  0.020  1.090
 3RU  C18  C23   single    1.528  0.020  1.528
 3RU  C23  H23   single    0.970  0.020  1.090
 3RU  C23  H23A  single    0.970  0.020  1.090
 3RU  C18  H18   single    0.970  0.020  1.090
 3RU  N15  C14   single    1.344  0.020  1.344
 3RU  N15  HN15  single    0.860  0.020  1.020
 3RU  C14  O16   double    1.224  0.020  1.224
 3RU  C12  C9    single    1.501  0.020  1.501
 3RU  C12  H12   single    0.970  0.020  1.090
 3RU  C12  H12A  single    0.970  0.020  1.090
 3RU  C2   C1    aromatic  1.408  0.020  1.408
 3RU  C1   H1    single    0.930  0.020  1.080
 3RU  C3   C2    aromatic  1.372  0.020  1.372
 3RU  C2   H2    single    0.930  0.020  1.080
 3RU  C3   H3    single    0.930  0.020  1.080
 3RU  N11  HN11  single    0.890  0.020  1.040
 3RU  N11  HN1A  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
 3RU  H4    C4   C1    120.52  3.000
 3RU  H4    C4   C5    119.04  3.000
 3RU  C1    C4   C5    120.45  3.000
 3RU  C10   C5   C6    116.84  3.000
 3RU  C10   C5   C4    123.20  3.000
 3RU  C6    C5   C4    119.96  3.000
 3RU  N7    C6   C3    119.25  3.000
 3RU  C3    C6   C5    118.54  3.000
 3RU  N7    C6   C5    122.22  3.000
 3RU  N11   C8   N7    117.27  3.000
 3RU  N7    C8   C9    123.21  3.000
 3RU  N11   C8   C9    119.49  3.000
 3RU  H10   C10  C9    119.61  3.000
 3RU  H10   C10  C5    119.04  3.000
 3RU  C9    C10  C5    121.35  3.000
 3RU  H13A  C13  H13   105.92  3.000
 3RU  H13A  C13  C12   109.14  3.000
 3RU  H13   C13  C12   110.96  3.000
 3RU  H13A  C13  C14   107.35  3.000
 3RU  H13   C13  C14   110.44  3.000
 3RU  C12   C13  C14   112.73  3.000
 3RU  H17A  C17  H17   106.89  3.000
 3RU  H17A  C17  N15   108.41  3.000
 3RU  H17   C17  N15   108.14  3.000
 3RU  H17A  C17  C18   109.35  3.000
 3RU  H17   C17  C18   109.86  3.000
 3RU  N15   C17  C18   113.94  3.000
 3RU  H20A  C20  H20   106.48  3.000
 3RU  H20A  C20  C19   109.20  3.000
 3RU  H20   C20  C19   110.03  3.000
 3RU  H20A  C20  C21   109.27  3.000
 3RU  H20   C20  C21   110.40  3.000
 3RU  C19   C20  C21   111.33  3.000
 3RU  H21A  C21  H21   106.60  3.000
 3RU  H21A  C21  C22   109.21  3.000
 3RU  H21   C21  C22   110.40  3.000
 3RU  H21A  C21  C20   109.24  3.000
 3RU  H21   C21  C20   110.34  3.000
 3RU  C22   C21  C20   110.94  3.000
 3RU  H22A  C22  H22   106.43  3.000
 3RU  H22A  C22  C23   109.93  3.000
 3RU  H22   C22  C23   109.26  3.000
 3RU  H22A  C22  C21   110.43  3.000
 3RU  H22   C22  C21   109.25  3.000
 3RU  C23   C22  C21   111.42  3.000
 3RU  H19A  C19  H19   106.40  3.000
 3RU  H19A  C19  C18   110.01  3.000
 3RU  H19   C19  C18   108.85  3.000
 3RU  H19A  C19  C20   110.07  3.000
 3RU  H19   C19  C20   109.27  3.000
 3RU  C18   C19  C20   112.07  3.000
 3RU  H23A  C23  H23   106.68  3.000
 3RU  H23A  C23  C18   109.13  3.000
 3RU  H23   C23  C18   110.14  3.000
 3RU  H23A  C23  C22   109.41  3.000
 3RU  H23   C23  C22   109.75  3.000
 3RU  C18   C23  C22   111.60  3.000
 3RU  H18   C18  C23   107.83  3.000
 3RU  H18   C18  C19   107.99  3.000
 3RU  C23   C18  C19   110.51  3.000
 3RU  H18   C18  C17   108.10  3.000
 3RU  C23   C18  C17   112.69  3.000
 3RU  C19   C18  C17   109.57  3.000
 3RU  HN15  N15  C14   118.10  3.000
 3RU  HN15  N15  C17   117.23  3.000
 3RU  C14   N15  C17   124.34  3.000
 3RU  O16   C14  N15   123.38  3.000
 3RU  O16   C14  C13   121.93  3.000
 3RU  N15   C14  C13   114.68  3.000
 3RU  C12   C9   C10   121.27  3.000
 3RU  C12   C9   C8    121.76  3.000
 3RU  C10   C9   C8    116.95  3.000
 3RU  H1    C1   C2    119.93  3.000
 3RU  H1    C1   C4    120.31  3.000
 3RU  C2    C1   C4    119.76  3.000
 3RU  H2    C2   C3    119.70  3.000
 3RU  H2    C2   C1    119.48  3.000
 3RU  C3    C2   C1    120.82  3.000
 3RU  H3    C3   C2    120.83  3.000
 3RU  H3    C3   C6    118.68  3.000
 3RU  C2    C3   C6    120.49  3.000
 3RU  C8    N7   C6    119.43  3.000
 3RU  HN1A  N11  HN11  114.21  3.000
 3RU  HN1A  N11  C8    119.26  3.000
 3RU  HN11  N11  C8    116.20  3.000
 3RU  H12A  C12  H12   105.70  3.000
 3RU  H12A  C12  C9    110.91  3.000
 3RU  H12   C12  C9    108.81  3.000
 3RU  H12A  C12  C13   110.00  3.000
 3RU  H12   C12  C13   109.18  3.000
 3RU  C9    C12  C13   112.03  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
 3RU  CONST_01  N7    C6   C5   C4    180.00   0.0  0
 3RU  CONST_02  C3    C6   C5   C4      0.00   0.0  0
 3RU  CONST_03  C9    C10  C5   C4    180.00   0.0  0
 3RU  CONST_04  C3    C2   C1   C4      0.00   0.0  0
 3RU  CONST_05  C2    C1   C4   C5      0.00   0.0  0
 3RU  CONST_06  C8    N7   C6   C5      0.00   0.0  0
 3RU  CONST_07  C2    C3   C6   C5      0.00   0.0  0
 3RU  CONST_08  C8    C9   C10  C5      0.00   0.0  0
 3RU  CONST_09  C1    C4   C5   C6      0.00   0.0  0
 3RU  CONST_10  C9    C10  C5   C6      0.00   0.0  0
 3RU  CONST_11  C9    C8   N7   C6      0.00   0.0  0
 3RU  CONST_12  C1    C2   C3   C6      0.00   0.0  0
 3RU  CONST_13  C3    C6   N7   C8    180.00   0.0  0
 3RU  CONST_14  C1    C4   C5   C10   180.00   0.0  0
 3RU  CONST_15  N7    C6   C5   C10     0.00   0.0  0
 3RU  CONST_16  C3    C6   C5   C10   180.00   0.0  0
 3RU  CONST_17  N7    C8   C9   C10     0.00   0.0  0
 3RU  CONST_18  N7    C6   C3   C2    180.00   0.0  0
 3RU  CONST_19  C12   C9   C10  C5    180.00   0.0  0
 3RU  CONST_20  N11   C8   N7   C6    180.00   0.0  0
 3RU  CONST_21  N11   C8   C9   C10   180.00   0.0  0
 3RU  CONST_22  N7    C8   C9   C12   180.00   0.0  0
 3RU  CONST_23  H10   C10  C5   C4      0.00   0.0  0
 3RU  CONST_24  H2    C2   C1   C4    180.00   0.0  0
 3RU  CONST_25  H1    C1   C4   C5    180.00   0.0  0
 3RU  CONST_26  H3    C3   C6   C5    180.00   0.0  0
 3RU  CONST_27  H4    C4   C5   C6    180.00   0.0  0
 3RU  CONST_28  HN11  N11  C8   C9    180.00   0.0  0
 3RU  CONST_30  C17   N15  C14  C13   180.00   0.0  0
 3RU  CONST_31  O16   C14  N15  C17     0.00   0.0  0
 3RU  CONST_32  HN15  N15  C14  C13     0.00   0.0  0
 3RU  Var_01    C23   C22  C21  C20   -55.55  30.0  1
 3RU  Var_02    C18   C19  C20  C21   -55.12  30.0  1
 3RU  Var_03    C18   C23  C22  C21    55.90  30.0  1
 3RU  Var_04    C19   C20  C21  C22    55.02  30.0  1
 3RU  Var_05    C13   C12  C9   C8    -75.37  30.0  3
 3RU  Var_06    C14   N15  C17  C18   102.32  30.0  1
 3RU  Var_07    C9    C12  C13  C14  -176.14  30.0  3
 3RU  Var_08    C12   C13  C14  N15  -157.05  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
 3RU  chir_01  C18  C17  C19  C23  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
 3RU  plan-1  C4    0.020
 3RU  plan-1  C5    0.020
 3RU  plan-1  C6    0.020
 3RU  plan-1  C8    0.020
 3RU  plan-1  C10   0.020
 3RU  plan-1  C9    0.020
 3RU  plan-1  C1    0.020
 3RU  plan-1  C2    0.020
 3RU  plan-1  C3    0.020
 3RU  plan-1  N7    0.020
 3RU  plan-1  N11   0.020
 3RU  plan-1  H4    0.020
 3RU  plan-1  H10   0.020
 3RU  plan-1  H1    0.020
 3RU  plan-1  H2    0.020
 3RU  plan-1  H3    0.020
 3RU  plan-1  C12   0.020
 3RU  plan-2  C8    0.020
 3RU  plan-2  N11   0.020
 3RU  plan-2  HN11  0.020
 3RU  plan-2  HN1A  0.020
 3RU  plan-3  C13   0.020
 3RU  plan-3  C17   0.020
 3RU  plan-3  N15   0.020
 3RU  plan-3  C14   0.020
 3RU  plan-3  O16   0.020
 3RU  plan-3  HN15  0.020

