# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:39:18 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 5-(aminomethyl)quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc2nc(N)ccc12
#
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
 RP8  RP8  5-(aminomethyl)quinolin-2-amine  ligand  24  13  .  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_RP8
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
 RP8  C1    C  CR66  0   0.208  -0.5523  -0.9683   0.0227
 RP8  C2    C  CR16  0  -0.323   0.0391  -2.2486   0.1134
 RP8  C3    C  CR16  0  -0.246   1.3987  -2.3877   0.0348
 RP8  C4    C  CR16  0  -0.338   2.2252  -1.2628  -0.1405
 RP8  C5    C  CR6   0   0.088   1.6925   0.0013  -0.2318
 RP8  C6    C  CR66  0   0.029   0.2862   0.1619  -0.1381
 RP8  N7    N  N     0  -0.506  -1.9024  -0.8818   0.0956
 RP8  C8    C  CR6   0   0.432  -2.4702   0.2972   0.0076
 RP8  C9    C  CR16  0  -0.372  -1.7165   1.5004  -0.1494
 RP8  N10   N  NH2   0  -0.835  -3.8266   0.3639   0.0286
 RP8  C11   C  CR16  0  -0.177  -0.3634   1.4233  -0.2158
 RP8  C12   C  CH2   0  -0.394   2.6000   1.1887  -0.4219
 RP8  N13   N  NH2   0  -0.787   2.5876   2.0567   0.7479
 RP8  H2    H  HCR6  0   0.249  -0.6057  -3.1087   0.2436
 RP8  H3    H  HCR6  0   0.254   1.8463  -3.3711   0.1051
 RP8  H4    H  HCR6  0   0.248   3.2981  -1.3966  -0.2081
 RP8  H121  H  HCH2  0   0.228   3.5990   0.8186  -0.6847
 RP8  H122  H  HCH2  0   0.234   2.2603   1.7747  -1.2802
 RP8  H11   H  HCR6  0   0.266   0.2237   2.3259  -0.3123
 RP8  H9    H  HCR6  0   0.270  -2.2264   2.4534  -0.2117
 RP8  H101  H  HNH2  0   0.385  -4.3229  -0.4491   0.3542
 RP8  H102  H  HNH2  0   0.395  -4.2612   1.2438   0.2493
 RP8  H13   H  HNH2  0   0.342   3.0064   1.5679   1.5295
 RP8  H1    H  HNH2  0   0.352   3.1824   2.8567   0.5711

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
 RP8  C1   C2    aromatic  1.413  0.020  1.413
 RP8  C1   C6    aromatic  1.416  0.020  1.416
 RP8  C1   N7    aromatic  1.355  0.020  1.355
 RP8  C2   C3    aromatic  1.369  0.020  1.369
 RP8  C3   C4    aromatic  1.407  0.020  1.407
 RP8  C4   C5    aromatic  1.375  0.020  1.375
 RP8  C5   C6    aromatic  1.419  0.020  1.419
 RP8  C5   C12   single    1.506  0.020  1.506
 RP8  C6   C11   aromatic  1.421  0.020  1.421
 RP8  N7   C8    aromatic  1.312  0.020  1.312
 RP8  C8   C9    aromatic  1.428  0.020  1.428
 RP8  C8   N10   single    1.358  0.020  1.358
 RP8  C9   C11   aromatic  1.357  0.020  1.357
 RP8  C12  N13   single    1.457  0.020  1.457
 RP8  C2   H2    single    0.930  0.020  1.080
 RP8  C3   H3    single    0.930  0.020  1.080
 RP8  C4   H4    single    0.930  0.020  1.080
 RP8  C12  H121  single    0.970  0.020  1.090
 RP8  C12  H122  single    0.970  0.020  1.090
 RP8  C11  H11   single    0.930  0.020  1.080
 RP8  C9   H9    single    0.930  0.020  1.080
 RP8  N10  H101  single    0.890  0.020  1.040
 RP8  N10  H102  single    0.890  0.020  1.040
 RP8  N13  H13   single    0.890  0.020  1.040
 RP8  N13  H1    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
 RP8  N7    C1   C6    123.03  3.000
 RP8  N7    C1   C2    118.12  3.000
 RP8  C6    C1   C2    118.85  3.000
 RP8  H2    C2   C3    121.17  3.000
 RP8  H2    C2   C1    118.57  3.000
 RP8  C3    C2   C1    120.26  3.000
 RP8  H3    C3   C4    119.44  3.000
 RP8  H3    C3   C2    119.94  3.000
 RP8  C4    C3   C2    120.63  3.000
 RP8  H4    C4   C5    119.54  3.000
 RP8  H4    C4   C3    119.40  3.000
 RP8  C5    C4   C3    121.06  3.000
 RP8  C12   C5   C6    121.08  3.000
 RP8  C12   C5   C4    119.98  3.000
 RP8  C6    C5   C4    118.93  3.000
 RP8  C11   C6   C5    123.37  3.000
 RP8  C11   C6   C1    116.35  3.000
 RP8  C5    C6   C1    120.27  3.000
 RP8  C8    N7   C1    119.03  3.000
 RP8  N10   C8   C9    119.16  3.000
 RP8  N10   C8   N7    118.39  3.000
 RP8  C9    C8   N7    122.42  3.000
 RP8  H9    C9   C11   121.12  3.000
 RP8  H9    C9   C8    119.95  3.000
 RP8  C11   C9   C8    118.93  3.000
 RP8  H102  N10  H101  115.00  3.000
 RP8  H102  N10  C8    118.54  3.000
 RP8  H101  N10  C8    117.24  3.000
 RP8  H11   C11  C9    119.90  3.000
 RP8  H11   C11  C6    119.85  3.000
 RP8  C9    C11  C6    120.24  3.000
 RP8  H122  C12  H121  106.00  3.000
 RP8  H122  C12  N13   107.96  3.000
 RP8  H121  C12  N13   113.64  3.000
 RP8  H122  C12  C5    109.53  3.000
 RP8  H121  C12  C5    108.23  3.000
 RP8  N13   C12  C5    111.30  3.000
 RP8  H1    N13  H13   105.86  3.000
 RP8  H1    N13  C12   109.01  3.000
 RP8  H13   N13  C12   109.19  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
 RP8  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 RP8  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 RP8  CONST_03  C9   C11  C6   C1      0.00   0.0  0
 RP8  CONST_04  C9   C8   N7   C1      0.00   0.0  0
 RP8  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 RP8  CONST_06  C11  C6   C1   C2    180.00   0.0  0
 RP8  CONST_07  C8   N7   C1   C2    180.00   0.0  0
 RP8  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 RP8  CONST_09  C6   C1   C2   C3      0.00   0.0  0
 RP8  CONST_10  N7   C1   C2   C3    180.00   0.0  0
 RP8  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 RP8  CONST_12  C11  C6   C5   C4    180.00   0.0  0
 RP8  CONST_13  N7   C1   C6   C5    180.00   0.0  0
 RP8  CONST_14  C9   C11  C6   C5    180.00   0.0  0
 RP8  CONST_15  C8   N7   C1   C6      0.00   0.0  0
 RP8  CONST_16  C8   C9   C11  C6      0.00   0.0  0
 RP8  CONST_17  C11  C6   C1   N7      0.00   0.0  0
 RP8  CONST_18  C11  C9   C8   N7      0.00   0.0  0
 RP8  CONST_19  C12  C5   C6   C1    180.00   0.0  0
 RP8  CONST_20  N10  C8   N7   C1    180.00   0.0  0
 RP8  CONST_21  C12  C5   C4   C3    180.00   0.0  0
 RP8  CONST_22  C11  C9   C8   N10   180.00   0.0  0
 RP8  CONST_23  C12  C5   C6   C11     0.00   0.0  0
 RP8  CONST_24  H3   C3   C2   C1    180.00   0.0  0
 RP8  CONST_25  H11  C11  C6   C1    180.00   0.0  0
 RP8  CONST_26  H4   C4   C3   C2    180.00   0.0  0
 RP8  CONST_27  H2   C2   C3   C4    180.00   0.0  0
 RP8  CONST_28  H9   C9   C11  C6    180.00   0.0  0
 RP8  Var_01    N13  C12  C5   C4   -113.08  30.0  2
 RP8  Var_02    H13  N13  C12  C5     66.69  30.0  3

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
 RP8  plan-1  C1    0.020
 RP8  plan-1  C2    0.020
 RP8  plan-1  C3    0.020
 RP8  plan-1  C4    0.020
 RP8  plan-1  C5    0.020
 RP8  plan-1  C6    0.020
 RP8  plan-1  N7    0.020
 RP8  plan-1  C8    0.020
 RP8  plan-1  C9    0.020
 RP8  plan-1  N10   0.020
 RP8  plan-1  C11   0.020
 RP8  plan-1  C12   0.020
 RP8  plan-1  H2    0.020
 RP8  plan-1  H3    0.020
 RP8  plan-1  H4    0.020
 RP8  plan-1  H11   0.020
 RP8  plan-1  H9    0.020
 RP8  plan-2  C8    0.020
 RP8  plan-2  N10   0.020
 RP8  plan-2  H101  0.020
 RP8  plan-2  H102  0.020

