# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:03:07 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 6-[(4-methyl-1,4-diazepan-1-yl)methyl]quinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCN(CC1)Cc2ccc3ncccc3c2
#
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
 5R9  5R9  6-[(4-methyl-1,4-diazepan-1-yl)methyl]quinoline  ligand  40  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5R9
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
 5R9  N7   N  NT    0  -0.406   3.2186  -1.4148   0.5739
 5R9  C5   C  CH2   0  -0.341   2.0243   0.0672  -1.0683
 5R9  C6   C  CH2   0  -0.234   2.2865  -1.3317  -0.5324
 5R9  C2   C  CH2   0  -0.414   3.9746   0.8696   1.1165
 5R9  C1   C  CH2   0  -0.299   4.3334  -0.4869   0.5179
 5R9  C3   C  CH2   0  -0.284   3.0203   1.7458   0.3201
 5R9  N4   N  NT    0  -0.409   1.7821   1.0828  -0.0539
 5R9  C18  C  CH3   0  -0.517   3.6176  -2.7856   0.7915
 5R9  C22  C  CH2   0  -0.308   0.7679   2.0267  -0.4717
 5R9  C23  C  CR6   0   0.073  -0.6186   1.4341  -0.4852
 5R9  C26  C  CR16  0  -0.297  -1.6058   2.0128  -1.3182
 5R9  C27  C  CR16  0  -0.279  -2.8878   1.5392  -1.3449
 5R9  C28  C  CR66  0   0.192  -3.2603   0.4415  -0.5366
 5R9  C29  C  CR66  0   0.098  -2.2782  -0.1456   0.2988
 5R9  C30  C  CR16  0  -0.395  -0.9641   0.3721   0.3096
 5R9  N34  N  N     0  -0.429  -4.5350  -0.0136  -0.5925
 5R9  C35  C  CR16  0  -0.084  -4.8588  -1.0339   0.1568
 5R9  C36  C  CR16  0  -0.325  -3.9605  -1.6922   1.0230
 5R9  C37  C  CR16  0  -0.202  -2.6715  -1.2456   1.0925
 5R9  H2   H  HCH2  0   0.217   2.8504   0.3780  -1.7256
 5R9  H3   H  HCH2  0   0.252   1.1531  -0.0160  -1.7217
 5R9  H4   H  HCH2  0   0.187   2.6271  -1.9306  -1.3959
 5R9  H5   H  HCH2  0   0.205   1.3390  -1.7757  -0.2081
 5R9  H6   H  HCH2  0   0.214   3.5569   0.6908   2.1108
 5R9  H7   H  HCH2  0   0.220   4.8956   1.4418   1.2597
 5R9  H8   H  HCH2  0   0.236   5.1417  -0.9016   1.1239
 5R9  H9   H  HCH2  0   0.200   4.7511  -0.3776  -0.4960
 5R9  H10  H  HCH2  0   0.232   2.7762   2.6173   0.9322
 5R9  H11  H  HCH2  0   0.188   3.5426   2.1309  -0.5727
 5R9  H13  H  HCH3  0   0.188   4.1865  -3.2208  -0.0459
 5R9  H14  H  HCH3  0   0.230   4.2306  -2.8665   1.6901
 5R9  H15  H  HCH3  0   0.227   2.7332  -3.4092   0.9393
 5R9  H16  H  HCH2  0   0.258   0.7689   2.8673   0.2296
 5R9  H17  H  HCH2  0   0.215   0.9786   2.4665  -1.4612
 5R9  H18  H  HCR6  0   0.255  -1.3331   2.8488  -1.9518
 5R9  H19  H  HCR6  0   0.260  -3.6327   1.9876  -1.9899
 5R9  H20  H  HCR6  0   0.265  -0.2219  -0.0884   0.9511
 5R9  H21  H  HCR6  0   0.264  -5.8856  -1.3791   0.0932
 5R9  H22  H  HCR6  0   0.273  -4.3012  -2.5321   1.6125
 5R9  H23  H  HCR6  0   0.276  -1.9501  -1.7212   1.7458

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
 5R9  C2   C3   single    1.521  0.020  1.521
 5R9  C2   C1   single    1.526  0.020  1.526
 5R9  C3   N4   single    1.454  0.020  1.454
 5R9  C1   N7   single    1.452  0.020  1.452
 5R9  C22  N4   single    1.447  0.020  1.447
 5R9  C22  C23  single    1.508  0.020  1.508
 5R9  N4   C5   single    1.456  0.020  1.456
 5R9  C18  N7   single    1.444  0.020  1.444
 5R9  C5   C6   single    1.521  0.020  1.521
 5R9  N7   C6   single    1.449  0.020  1.449
 5R9  C23  C30  aromatic  1.371  0.020  1.371
 5R9  C23  C26  aromatic  1.415  0.020  1.415
 5R9  C30  C29  aromatic  1.412  0.020  1.412
 5R9  C26  C27  aromatic  1.367  0.020  1.367
 5R9  C29  C37  aromatic  1.412  0.020  1.412
 5R9  C29  C28  aromatic  1.417  0.020  1.417
 5R9  C37  C36  aromatic  1.366  0.020  1.366
 5R9  C27  C28  aromatic  1.413  0.020  1.413
 5R9  C28  N34  aromatic  1.355  0.020  1.355
 5R9  C36  C35  aromatic  1.411  0.020  1.411
 5R9  N34  C35  aromatic  1.307  0.020  1.307
 5R9  C5   H2   single    0.970  0.020  1.090
 5R9  C5   H3   single    0.970  0.020  1.090
 5R9  C6   H4   single    0.970  0.020  1.090
 5R9  C6   H5   single    0.970  0.020  1.090
 5R9  C2   H6   single    0.970  0.020  1.090
 5R9  C2   H7   single    0.970  0.020  1.090
 5R9  C1   H8   single    0.970  0.020  1.090
 5R9  C1   H9   single    0.970  0.020  1.090
 5R9  C3   H10  single    0.970  0.020  1.090
 5R9  C3   H11  single    0.970  0.020  1.090
 5R9  C18  H13  single    0.970  0.020  1.090
 5R9  C18  H14  single    0.970  0.020  1.090
 5R9  C18  H15  single    0.970  0.020  1.090
 5R9  C22  H16  single    0.970  0.020  1.090
 5R9  C22  H17  single    0.970  0.020  1.090
 5R9  C26  H18  single    0.930  0.020  1.080
 5R9  C27  H19  single    0.930  0.020  1.080
 5R9  C30  H20  single    0.930  0.020  1.080
 5R9  C35  H21  single    0.930  0.020  1.080
 5R9  C36  H22  single    0.930  0.020  1.080
 5R9  C37  H23  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
 5R9  C18  N7   C1   113.60  3.000
 5R9  C18  N7   C6   110.31  3.000
 5R9  C1   N7   C6   115.34  3.000
 5R9  H3   C5   H2   105.25  3.000
 5R9  H3   C5   N4   109.71  3.000
 5R9  H2   C5   N4   110.13  3.000
 5R9  H3   C5   C6   106.15  3.000
 5R9  H2   C5   C6   109.93  3.000
 5R9  N4   C5   C6   115.14  3.000
 5R9  H5   C6   H4   106.16  3.000
 5R9  H5   C6   C5   109.15  3.000
 5R9  H4   C6   C5   106.04  3.000
 5R9  H5   C6   N7   107.89  3.000
 5R9  H4   C6   N7   111.56  3.000
 5R9  C5   C6   N7   115.64  3.000
 5R9  H7   C2   H6   106.76  3.000
 5R9  H7   C2   C3   107.19  3.000
 5R9  H6   C2   C3   109.32  3.000
 5R9  H7   C2   C1   108.57  3.000
 5R9  H6   C2   C1   107.54  3.000
 5R9  C3   C2   C1   117.03  3.000
 5R9  H9   C1   H8   105.53  3.000
 5R9  H9   C1   C2   111.22  3.000
 5R9  H8   C1   C2   107.10  3.000
 5R9  H9   C1   N7   112.96  3.000
 5R9  H8   C1   N7   107.71  3.000
 5R9  C2   C1   N7   111.88  3.000
 5R9  H11  C3   H10  106.30  3.000
 5R9  H11  C3   N4   110.74  3.000
 5R9  H10  C3   N4   108.52  3.000
 5R9  H11  C3   C2   109.13  3.000
 5R9  H10  C3   C2   107.84  3.000
 5R9  N4   C3   C2   113.99  3.000
 5R9  C22  N4   C3   111.95  3.000
 5R9  C22  N4   C5   111.75  3.000
 5R9  C3   N4   C5   110.84  3.000
 5R9  H15  C18  H14  107.54  3.000
 5R9  H15  C18  H13  107.18  3.000
 5R9  H14  C18  H13  107.86  3.000
 5R9  H15  C18  N7   109.79  3.000
 5R9  H14  C18  N7   110.47  3.000
 5R9  H13  C18  N7   113.77  3.000
 5R9  H17  C22  H16  105.56  3.000
 5R9  H17  C22  C23  108.92  3.000
 5R9  H16  C22  C23  107.96  3.000
 5R9  H17  C22  N4   112.66  3.000
 5R9  H16  C22  N4   108.38  3.000
 5R9  C23  C22  N4   112.99  3.000
 5R9  C30  C23  C26  118.83  3.000
 5R9  C26  C23  C22  119.07  3.000
 5R9  C30  C23  C22  122.08  3.000
 5R9  H18  C26  C27  119.46  3.000
 5R9  H18  C26  C23  118.94  3.000
 5R9  C27  C26  C23  121.60  3.000
 5R9  H19  C27  C28  118.76  3.000
 5R9  H19  C27  C26  120.89  3.000
 5R9  C28  C27  C26  120.34  3.000
 5R9  N34  C28  C29  122.50  3.000
 5R9  N34  C28  C27  119.04  3.000
 5R9  C29  C28  C27  118.46  3.000
 5R9  C37  C29  C30  122.70  3.000
 5R9  C37  C29  C28  117.46  3.000
 5R9  C30  C29  C28  119.84  3.000
 5R9  H20  C30  C29  119.07  3.000
 5R9  H20  C30  C23  119.99  3.000
 5R9  C29  C30  C23  120.93  3.000
 5R9  C35  N34  C28  118.16  3.000
 5R9  H21  C35  C36  119.34  3.000
 5R9  H21  C35  N34  116.70  3.000
 5R9  C36  C35  N34  123.96  3.000
 5R9  H22  C36  C37  121.57  3.000
 5R9  H22  C36  C35  119.77  3.000
 5R9  C37  C36  C35  118.65  3.000
 5R9  H23  C37  C36  121.04  3.000
 5R9  H23  C37  C29  119.70  3.000
 5R9  C36  C37  C29  119.27  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
 5R9  CONST_01  C37  C29  C30  C23  180.00   0.0  0
 5R9  CONST_02  C28  C29  C30  C23    0.00   0.0  0
 5R9  CONST_03  C28  C27  C26  C23    0.00   0.0  0
 5R9  CONST_04  C29  C30  C23  C26    0.00   0.0  0
 5R9  CONST_05  C29  C28  C27  C26    0.00   0.0  0
 5R9  CONST_06  N34  C28  C27  C26  180.00   0.0  0
 5R9  CONST_07  C30  C23  C26  C27    0.00   0.0  0
 5R9  CONST_08  C30  C29  C28  C27    0.00   0.0  0
 5R9  CONST_09  C37  C29  C28  C27  180.00   0.0  0
 5R9  CONST_10  C35  N34  C28  C27  180.00   0.0  0
 5R9  CONST_11  C36  C37  C29  C28    0.00   0.0  0
 5R9  CONST_12  C36  C35  N34  C28    0.00   0.0  0
 5R9  CONST_13  C35  C36  C37  C29    0.00   0.0  0
 5R9  CONST_14  C35  N34  C28  C29    0.00   0.0  0
 5R9  CONST_15  C36  C37  C29  C30  180.00   0.0  0
 5R9  CONST_16  N34  C28  C29  C30  180.00   0.0  0
 5R9  CONST_17  C37  C29  C28  N34    0.00   0.0  0
 5R9  CONST_18  C37  C36  C35  N34    0.00   0.0  0
 5R9  CONST_19  C29  C30  C23  C22  180.00   0.0  0
 5R9  CONST_20  C27  C26  C23  C22  180.00   0.0  0
 5R9  CONST_21  H19  C27  C26  C23  180.00   0.0  0
 5R9  CONST_22  H20  C30  C23  C26  180.00   0.0  0
 5R9  CONST_23  H23  C37  C29  C28  180.00   0.0  0
 5R9  CONST_24  H18  C26  C27  C28  180.00   0.0  0
 5R9  CONST_25  H21  C35  N34  C28  180.00   0.0  0
 5R9  CONST_26  H22  C36  C37  C29  180.00   0.0  0
 5R9  Var_01    C30  C23  C22  N4    25.58  30.0  2

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
 5R9  plan-1  C22  0.020
 5R9  plan-1  C23  0.020
 5R9  plan-1  C26  0.020
 5R9  plan-1  C27  0.020
 5R9  plan-1  C28  0.020
 5R9  plan-1  C29  0.020
 5R9  plan-1  C30  0.020
 5R9  plan-1  N34  0.020
 5R9  plan-1  C35  0.020
 5R9  plan-1  C36  0.020
 5R9  plan-1  C37  0.020
 5R9  plan-1  H18  0.020
 5R9  plan-1  H19  0.020
 5R9  plan-1  H20  0.020
 5R9  plan-1  H21  0.020
 5R9  plan-1  H22  0.020
 5R9  plan-1  H23  0.020

