# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:40:10 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCN(CC1)Cc2ccc(cc2)c3ccc(CN4CCCN(C)CC4)cc3C#N
#
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
 5RA  5RA  5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile  ligand  69  32  .  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_5RA
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
 5RA  C1   C  CH3   0  -0.524  -7.1337   3.3528   1.7234
 5RA  C51  C  CH2   0  -0.238   5.2294   2.2145   0.3508
 5RA  C6   C  CH2   0  -0.278  -6.5729   2.6199  -0.4935
 5RA  C8   C  CH2   0  -0.277  -6.7970   0.1625  -1.2311
 5RA  C10  C  CH2   0  -0.289  -5.6463   0.0112   0.8747
 5RA  N2   N  NT    0  -0.415  -6.8597   2.2096   0.8750
 5RA  C7   C  CH2   0  -0.420  -7.0495   1.6320  -1.5515
 5RA  N9   N  NT    0  -0.422  -5.5210  -0.0732  -0.5706
 5RA  C11  C  CH2   0  -0.275  -5.7735   1.4198   1.4275
 5RA  C22  C  CH2   0  -0.316  -4.8856  -1.3074  -0.9778
 5RA  C23  C  CR6   0   0.074  -3.4105  -1.3308  -0.6650
 5RA  C26  C  CR16  0  -0.297  -2.7767  -2.5292  -0.3810
 5RA  C27  C  CR6   0  -0.004  -1.3999  -2.5731  -0.1560
 5RA  C28  C  CR6   0   0.134  -0.6188  -1.4098  -0.1924
 5RA  C29  C  CR16  0  -0.293  -1.2743  -0.2137  -0.4757
 5RA  C30  C  CR16  0  -0.251  -2.6389  -0.1720  -0.7087
 5RA  C34  C  CR6   0   0.025   0.8370  -1.4246   0.0462
 5RA  C35  C  CR16  0  -0.282   1.6978  -0.7865  -0.8479
 5RA  C36  C  CR16  0  -0.269   3.0664  -0.7799  -0.6352
 5RA  C37  C  CR6   0   0.069   3.6172  -1.4068   0.4804
 5RA  C38  C  CR16  0  -0.301   2.7569  -2.0259   1.3809
 5RA  C39  C  CR16  0  -0.277   1.3862  -2.0400   1.1693
 5RA  C44  C  CSP   0   0.001  -0.8054  -3.8526   0.0652
 5RA  N45  N  NS    0  -0.246  -0.3597  -4.8995   0.2492
 5RA  C46  C  CH2   0  -0.316   5.1098  -1.4464   0.6896
 5RA  N47  N  NT    0  -0.406   5.7593  -0.2335   0.2385
 5RA  C50  C  CH2   0  -0.335   5.4430   0.9034   1.0892
 5RA  N52  N  NT    0  -0.405   6.2239   2.5358  -0.6525
 5RA  C53  C  CH2   0  -0.298   7.5831   2.1340  -0.3390
 5RA  C54  C  CH2   0  -0.411   7.8576   0.6868  -0.7387
 5RA  C55  C  CH2   0  -0.284   7.1953  -0.3970   0.0987
 5RA  C66  C  CH3   0  -0.518   6.1062   3.9186  -1.0501
 5RA  H1   H  HCH3  0   0.232  -7.9936   3.9049   1.3422
 5RA  H2   H  HCH3  0   0.230  -7.3769   3.0190   2.7332
 5RA  H3   H  HCH3  0   0.190  -6.2914   4.0582   1.8008
 5RA  H4   H  HCH2  0   0.215   4.2492   2.1938  -0.1387
 5RA  H5   H  HCH2  0   0.182   5.1694   2.9979   1.1276
 5RA  H6   H  HCH2  0   0.230  -7.0640   3.5761  -0.6875
 5RA  H7   H  HCH2  0   0.198  -5.4953   2.8048  -0.6208
 5RA  H8   H  HCH2  0   0.200  -7.6239  -0.2312  -0.6229
 5RA  H9   H  HCH2  0   0.232  -6.8240  -0.4013  -2.1652
 5RA  H10  H  HCH2  0   0.200  -6.4973  -0.5952   1.2268
 5RA  H11  H  HCH2  0   0.237  -4.7521  -0.4167   1.3346
 5RA  H13  H  HCH2  0   0.215  -8.1224   1.7601  -1.7183
 5RA  H14  H  HCH2  0   0.216  -6.5577   1.8957  -2.4917
 5RA  H16  H  HCH2  0   0.229  -5.9360   1.3159   2.5036
 5RA  H17  H  HCH2  0   0.186  -4.8076   1.9405   1.3052
 5RA  H18  H  HCH2  0   0.217  -5.3593  -2.2027  -0.5426
 5RA  H19  H  HCH2  0   0.264  -4.9951  -1.4081  -2.0615
 5RA  H20  H  HCR6  0   0.273  -3.3507  -3.4471  -0.3430
 5RA  H21  H  HCR6  0   0.266  -0.7032   0.7054  -0.4975
 5RA  H22  H  HCR6  0   0.264  -3.1205   0.7749  -0.9158
 5RA  H23  H  HCR6  0   0.255   1.2949  -0.3052  -1.7307
 5RA  H24  H  HCR6  0   0.250   3.7184  -0.2757  -1.3368
 5RA  H25  H  HCR6  0   0.251   3.1592  -2.4952   2.2709
 5RA  H26  H  HCR6  0   0.257   0.7446  -2.5100   1.9042
 5RA  H27  H  HCH2  0   0.213   5.3222  -1.6819   1.7461
 5RA  H28  H  HCH2  0   0.255   5.5131  -2.2839   0.1119
 5RA  H30  H  HCH2  0   0.213   6.2173   1.0290   1.8613
 5RA  H31  H  HCH2  0   0.250   4.5173   0.7087   1.6352
 5RA  H33  H  HCH2  0   0.235   8.2560   2.7626  -0.9262
 5RA  H34  H  HCH2  0   0.199   7.8560   2.3114   0.7140
 5RA  H35  H  HCH2  0   0.213   7.5557   0.5704  -1.7828
 5RA  H36  H  HCH2  0   0.218   8.9369   0.5134  -0.7007
 5RA  H37  H  HCH2  0   0.186   7.6831  -0.4386   1.0885
 5RA  H38  H  HCH2  0   0.231   7.3914  -1.3595  -0.3799
 5RA  H39  H  HCH3  0   0.187   6.3268   4.6336  -0.2411
 5RA  H40  H  HCH3  0   0.230   6.7790   4.1366  -1.8806
 5RA  H41  H  HCH3  0   0.227   5.0877   4.1202  -1.3894

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
 5RA  C51  C50  single    1.520  0.020  1.520
 5RA  C51  N52  single    1.449  0.020  1.449
 5RA  C6   N2   single    1.457  0.020  1.457
 5RA  C6   C7   single    1.524  0.020  1.524
 5RA  C8   C7   single    1.525  0.020  1.525
 5RA  C8   N9   single    1.456  0.020  1.456
 5RA  C10  N9   single    1.453  0.020  1.453
 5RA  C10  C11  single    1.519  0.020  1.519
 5RA  N2   C11  single    1.452  0.020  1.452
 5RA  N9   C22  single    1.447  0.020  1.447
 5RA  C22  C23  single    1.508  0.020  1.508
 5RA  C23  C26  aromatic  1.385  0.020  1.385
 5RA  C23  C30  aromatic  1.393  0.020  1.393
 5RA  C26  C27  aromatic  1.396  0.020  1.396
 5RA  C27  C28  aromatic  1.402  0.020  1.402
 5RA  C27  C44  single    1.428  0.020  1.428
 5RA  C28  C29  aromatic  1.393  0.020  1.393
 5RA  C28  C34  single    1.475  0.020  1.475
 5RA  C29  C30  aromatic  1.385  0.020  1.385
 5RA  C34  C35  aromatic  1.396  0.020  1.396
 5RA  C34  C39  aromatic  1.393  0.020  1.393
 5RA  C35  C36  aromatic  1.385  0.020  1.385
 5RA  C36  C37  aromatic  1.393  0.020  1.393
 5RA  C37  C38  aromatic  1.391  0.020  1.391
 5RA  C37  C46  single    1.508  0.020  1.508
 5RA  C38  C39  aromatic  1.387  0.020  1.387
 5RA  C44  N45  triple    1.153  0.020  1.153
 5RA  C46  N47  single    1.448  0.020  1.448
 5RA  N47  C50  single    1.455  0.020  1.455
 5RA  N47  C55  single    1.452  0.020  1.452
 5RA  N52  C53  single    1.452  0.020  1.452
 5RA  N52  C66  single    1.444  0.020  1.444
 5RA  C53  C54  single    1.526  0.020  1.526
 5RA  C54  C55  single    1.521  0.020  1.521
 5RA  N2   C1   single    1.450  0.020  1.450
 5RA  C1   H1   single    0.970  0.020  1.090
 5RA  C1   H2   single    0.970  0.020  1.090
 5RA  C1   H3   single    0.970  0.020  1.090
 5RA  C51  H4   single    0.970  0.020  1.090
 5RA  C51  H5   single    0.970  0.020  1.090
 5RA  C6   H6   single    0.970  0.020  1.090
 5RA  C6   H7   single    0.970  0.020  1.090
 5RA  C8   H8   single    0.970  0.020  1.090
 5RA  C8   H9   single    0.970  0.020  1.090
 5RA  C10  H10  single    0.970  0.020  1.090
 5RA  C10  H11  single    0.970  0.020  1.090
 5RA  C7   H13  single    0.970  0.020  1.090
 5RA  C7   H14  single    0.970  0.020  1.090
 5RA  C11  H16  single    0.970  0.020  1.090
 5RA  C11  H17  single    0.970  0.020  1.090
 5RA  C22  H18  single    0.970  0.020  1.090
 5RA  C22  H19  single    0.970  0.020  1.090
 5RA  C26  H20  single    0.930  0.020  1.080
 5RA  C29  H21  single    0.930  0.020  1.080
 5RA  C30  H22  single    0.930  0.020  1.080
 5RA  C35  H23  single    0.930  0.020  1.080
 5RA  C36  H24  single    0.930  0.020  1.080
 5RA  C38  H25  single    0.930  0.020  1.080
 5RA  C39  H26  single    0.930  0.020  1.080
 5RA  C46  H27  single    0.970  0.020  1.090
 5RA  C46  H28  single    0.970  0.020  1.090
 5RA  C50  H30  single    0.970  0.020  1.090
 5RA  C50  H31  single    0.970  0.020  1.090
 5RA  C53  H33  single    0.970  0.020  1.090
 5RA  C53  H34  single    0.970  0.020  1.090
 5RA  C54  H35  single    0.970  0.020  1.090
 5RA  C54  H36  single    0.970  0.020  1.090
 5RA  C55  H37  single    0.970  0.020  1.090
 5RA  C55  H38  single    0.970  0.020  1.090
 5RA  C66  H39  single    0.970  0.020  1.090
 5RA  C66  H40  single    0.970  0.020  1.090
 5RA  C66  H41  single    0.970  0.020  1.090

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
 5RA  H3   C1   H2   107.54  3.000
 5RA  H3   C1   H1   107.65  3.000
 5RA  H2   C1   H1   107.62  3.000
 5RA  H3   C1   N2   113.68  3.000
 5RA  H2   C1   N2   110.04  3.000
 5RA  H1   C1   N2   110.09  3.000
 5RA  H5   C51  H4   106.20  3.000
 5RA  H5   C51  N52  111.52  3.000
 5RA  H4   C51  N52  107.99  3.000
 5RA  H5   C51  C50  106.13  3.000
 5RA  H4   C51  C50  109.05  3.000
 5RA  N52  C51  C50  115.55  3.000
 5RA  H7   C6   H6   105.82  3.000
 5RA  H7   C6   C7   109.56  3.000
 5RA  H6   C6   C7   107.67  3.000
 5RA  H7   C6   N2   110.40  3.000
 5RA  H6   C6   N2   108.95  3.000
 5RA  C7   C6   N2   114.07  3.000
 5RA  H9   C8   H8   105.65  3.000
 5RA  H9   C8   N9   109.05  3.000
 5RA  H8   C8   N9   110.50  3.000
 5RA  H9   C8   C7   108.29  3.000
 5RA  H8   C8   C7   109.68  3.000
 5RA  N9   C8   C7   113.35  3.000
 5RA  H11  C10  H10  106.37  3.000
 5RA  H11  C10  C11  106.17  3.000
 5RA  H10  C10  C11  109.22  3.000
 5RA  H11  C10  N9   108.98  3.000
 5RA  H10  C10  N9   110.62  3.000
 5RA  C11  C10  N9   115.03  3.000
 5RA  C11  N2   C6   111.30  3.000
 5RA  C11  N2   C1   110.33  3.000
 5RA  C6   N2   C1   111.40  3.000
 5RA  H14  C7   H13  106.38  3.000
 5RA  H14  C7   C8   109.79  3.000
 5RA  H13  C7   C8   107.90  3.000
 5RA  H14  C7   C6   107.46  3.000
 5RA  H13  C7   C6   109.69  3.000
 5RA  C8   C7   C6   115.27  3.000
 5RA  C22  N9   C10  111.56  3.000
 5RA  C22  N9   C8   113.29  3.000
 5RA  C10  N9   C8   111.48  3.000
 5RA  H17  C11  H16  106.50  3.000
 5RA  H17  C11  N2   110.84  3.000
 5RA  H16  C11  N2   108.36  3.000
 5RA  H17  C11  C10  108.90  3.000
 5RA  H16  C11  C10  106.41  3.000
 5RA  N2   C11  C10  115.38  3.000
 5RA  H19  C22  H18  105.86  3.000
 5RA  H19  C22  C23  107.57  3.000
 5RA  H18  C22  C23  109.01  3.000
 5RA  H19  C22  N9   108.27  3.000
 5RA  H18  C22  N9   113.15  3.000
 5RA  C23  C22  N9   112.61  3.000
 5RA  C30  C23  C26  118.21  3.000
 5RA  C30  C23  C22  121.50  3.000
 5RA  C26  C23  C22  120.23  3.000
 5RA  H20  C26  C27  119.36  3.000
 5RA  H20  C26  C23  119.86  3.000
 5RA  C27  C26  C23  120.77  3.000
 5RA  C44  C27  C28  121.04  3.000
 5RA  C44  C27  C26  117.63  3.000
 5RA  C28  C27  C26  121.29  3.000
 5RA  C34  C28  C29  120.39  3.000
 5RA  C34  C28  C27  122.50  3.000
 5RA  C29  C28  C27  117.11  3.000
 5RA  H21  C29  C30  119.40  3.000
 5RA  H21  C29  C28  119.01  3.000
 5RA  C30  C29  C28  121.58  3.000
 5RA  H22  C30  C29  119.80  3.000
 5RA  H22  C30  C23  119.16  3.000
 5RA  C29  C30  C23  121.03  3.000
 5RA  C39  C34  C35  118.37  3.000
 5RA  C39  C34  C28  121.58  3.000
 5RA  C35  C34  C28  120.03  3.000
 5RA  H23  C35  C36  119.38  3.000
 5RA  H23  C35  C34  119.73  3.000
 5RA  C36  C35  C34  120.88  3.000
 5RA  H24  C36  C37  119.38  3.000
 5RA  H24  C36  C35  119.86  3.000
 5RA  C37  C36  C35  120.76  3.000
 5RA  C46  C37  C38  120.72  3.000
 5RA  C46  C37  C36  120.95  3.000
 5RA  C38  C37  C36  118.31  3.000
 5RA  H25  C38  C39  119.19  3.000
 5RA  H25  C38  C37  119.67  3.000
 5RA  C39  C38  C37  121.13  3.000
 5RA  H26  C39  C38  119.10  3.000
 5RA  H26  C39  C34  120.35  3.000
 5RA  C38  C39  C34  120.53  3.000
 5RA  N45  C44  C27  180.00  3.000
 5RA  H28  C46  H27  105.74  3.000
 5RA  H28  C46  N47  108.13  3.000
 5RA  H27  C46  N47  113.01  3.000
 5RA  H28  C46  C37  108.16  3.000
 5RA  H27  C46  C37  109.22  3.000
 5RA  N47  C46  C37  112.26  3.000
 5RA  C55  N47  C50  111.06  3.000
 5RA  C55  N47  C46  112.29  3.000
 5RA  C50  N47  C46  112.02  3.000
 5RA  H31  C50  H30  105.42  3.000
 5RA  H31  C50  N47  109.71  3.000
 5RA  H30  C50  N47  110.27  3.000
 5RA  H31  C50  C51  106.11  3.000
 5RA  H30  C50  C51  109.95  3.000
 5RA  N47  C50  C51  114.88  3.000
 5RA  C66  N52  C53  113.63  3.000
 5RA  C66  N52  C51  110.31  3.000
 5RA  C53  N52  C51  115.59  3.000
 5RA  H34  C53  H33  105.57  3.000
 5RA  H34  C53  C54  110.99  3.000
 5RA  H33  C53  C54  107.11  3.000
 5RA  H34  C53  N52  113.18  3.000
 5RA  H33  C53  N52  107.55  3.000
 5RA  C54  C53  N52  111.98  3.000
 5RA  H36  C54  H35  106.79  3.000
 5RA  H36  C54  C55  107.30  3.000
 5RA  H35  C54  C55  109.25  3.000
 5RA  H36  C54  C53  108.59  3.000
 5RA  H35  C54  C53  107.54  3.000
 5RA  C55  C54  C53  116.94  3.000
 5RA  H38  C55  H37  106.27  3.000
 5RA  H38  C55  C54  107.95  3.000
 5RA  H37  C55  C54  109.14  3.000
 5RA  H38  C55  N47  108.59  3.000
 5RA  H37  C55  N47  110.79  3.000
 5RA  C54  C55  N47  113.78  3.000
 5RA  H41  C66  H40  107.56  3.000
 5RA  H41  C66  H39  107.15  3.000
 5RA  H40  C66  H39  107.80  3.000
 5RA  H41  C66  N52  109.78  3.000
 5RA  H40  C66  N52  110.54  3.000
 5RA  H39  C66  N52  113.77  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
 5RA  CONST_01  C28  C27  C26  C23    0.00   0.0  0
 5RA  CONST_02  C28  C29  C30  C23    0.00   0.0  0
 5RA  CONST_03  C29  C30  C23  C26    0.00   0.0  0
 5RA  CONST_04  C29  C28  C27  C26    0.00   0.0  0
 5RA  CONST_05  C34  C28  C27  C26  180.00   0.0  0
 5RA  CONST_06  C30  C23  C26  C27    0.00   0.0  0
 5RA  CONST_07  C30  C29  C28  C27    0.00   0.0  0
 5RA  CONST_10  C36  C35  C34  C28  180.00   0.0  0
 5RA  CONST_11  C38  C39  C34  C28  180.00   0.0  0
 5RA  CONST_14  C34  C28  C29  C30  180.00   0.0  0
 5RA  CONST_15  C37  C36  C35  C34    0.00   0.0  0
 5RA  CONST_16  C37  C38  C39  C34    0.00   0.0  0
 5RA  CONST_17  C38  C39  C34  C35    0.00   0.0  0
 5RA  CONST_18  C38  C37  C36  C35    0.00   0.0  0
 5RA  CONST_19  C39  C34  C35  C36    0.00   0.0  0
 5RA  CONST_20  C39  C38  C37  C36    0.00   0.0  0
 5RA  CONST_21  C27  C26  C23  C22  180.00   0.0  0
 5RA  CONST_22  C29  C30  C23  C22  180.00   0.0  0
 5RA  CONST_23  C44  C27  C26  C23  180.00   0.0  0
 5RA  CONST_24  C44  C27  C28  C29  180.00   0.0  0
 5RA  CONST_25  C44  C27  C28  C34    0.00   0.0  0
 5RA  CONST_26  C46  C37  C36  C35  180.00   0.0  0
 5RA  CONST_27  C46  C37  C38  C39  180.00   0.0  0
 5RA  CONST_28  H21  C29  C30  C23  180.00   0.0  0
 5RA  CONST_29  H22  C30  C23  C26  180.00   0.0  0
 5RA  CONST_30  H20  C26  C27  C28  180.00   0.0  0
 5RA  CONST_31  H23  C35  C34  C28    0.00   0.0  0
 5RA  CONST_32  H26  C39  C34  C28    0.00   0.0  0
 5RA  CONST_33  H24  C36  C35  C34  180.00   0.0  0
 5RA  CONST_34  H25  C38  C39  C34  180.00   0.0  0
 5RA  Var_01    C26  C23  C22  N9   149.58  30.0  2
 5RA  Var_02    N47  C46  C37  C36   35.77  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
 5RA  plan-1  C22  0.020
 5RA  plan-1  C23  0.020
 5RA  plan-1  C26  0.020
 5RA  plan-1  C27  0.020
 5RA  plan-1  C28  0.020
 5RA  plan-1  C29  0.020
 5RA  plan-1  C30  0.020
 5RA  plan-1  C34  0.020
 5RA  plan-1  C44  0.020
 5RA  plan-1  N45  0.020
 5RA  plan-1  H20  0.020
 5RA  plan-1  H21  0.020
 5RA  plan-1  H22  0.020
 5RA  plan-2  C28  0.020
 5RA  plan-2  C34  0.020
 5RA  plan-2  C35  0.020
 5RA  plan-2  C36  0.020
 5RA  plan-2  C37  0.020
 5RA  plan-2  C38  0.020
 5RA  plan-2  C39  0.020
 5RA  plan-2  C46  0.020
 5RA  plan-2  H23  0.020
 5RA  plan-2  H24  0.020
 5RA  plan-2  H25  0.020
 5RA  plan-2  H26  0.020

