# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:40:13 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: [3-(aminomethyl)-5-[3-(1,3-dihydroisoindol-2-yl)propoxy]-4-methoxy-phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(CN)cc(CN)cc1OCCCN2Cc3ccccc3C2
#
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
 JC5  JC5  '[3-(aminomethyl)-5-[3-(1,3-dihydroisoindol-2-yl)propoxy]-4-methoxy-phenyl]methanamine'  ligand  52  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JC5
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
 JC5  N1   N  NH2   0  -0.789   3.8751   4.2653   0.5278
 JC5  C4   C  CR16  0  -0.367   4.7494   1.3268   0.1380
 JC5  C5   C  CR6   0   0.135   3.6356   2.0017  -0.3409
 JC5  C6   C  CH2   0  -0.363   3.7132   3.4667  -0.6804
 JC5  C7   C  CR16  0  -0.456   2.4274   1.3205  -0.4483
 JC5  C8   C  CR6   0   0.356   2.3394  -0.0239  -0.0994
 JC5  C10  C  CH2   0  -0.470  -1.1169  -1.1287  -0.4444
 JC5  C13  C  CR56  0   0.073  -5.5349  -0.2040  -0.5765
 JC5  C15  C  CR16  0  -0.260  -7.1483   1.3187   0.3049
 JC5  C17  C  CR16  0  -0.327  -5.6901   0.1128   1.8088
 JC5  N    N  NH2   0  -0.779   6.5809  -1.4193  -0.1815
 JC5  C    C  CH3   0  -0.412   3.4812  -2.9307  -0.3732
 JC5  C1   C  CR6   0   0.213   3.4819  -0.7002   0.3514
 JC5  C11  C  CH2   0  -0.277  -2.4294  -0.5274  -0.9245
 JC5  C12  C  CH2   0  -0.351  -4.7211  -1.0297  -1.5395
 JC5  C14  C  CR16  0  -0.325  -6.5611   0.6984  -0.7955
 JC5  C16  C  CR16  0  -0.259  -6.7162   1.0300   1.5946
 JC5  C18  C  CR56  0   0.080  -5.1069  -0.4967   0.7118
 JC5  C19  C  CH2   0  -0.365  -4.0057  -1.5215   0.6216
 JC5  C2   C  CR6   0   0.043   4.6930  -0.0237   0.4709
 JC5  C3   C  CH2   0  -0.358   5.9355  -0.7350   0.9336
 JC5  C9   C  CH2   0  -0.173   0.0051  -0.1158  -0.5471
 JC5  N2   N  NR5   0  -0.430  -3.5446  -1.4543  -0.7708
 JC5  O1   O  O2    0  -0.469   1.2096  -0.7533  -0.1600
 JC5  H27  H  HNH2  0   0.349   3.9566   5.2412   0.2703
 JC5  H11  H  HNH2  0   0.340   3.0336   4.1990   1.0872
 JC5  H7   H  HCR6  0   0.236   5.6889   1.8576   0.2493
 JC5  H9   H  HCH2  0   0.211   2.8347   3.7423  -1.2791
 JC5  H8   H  HCH2  0   0.233   4.5853   3.6450  -1.3143
 JC5  H12  H  HCR6  0   0.274   1.5578   1.8531  -0.8128
 JC5  H15  H  HCH2  0   0.236  -1.1996  -1.4606   0.5941
 JC5  H16  H  HCH2  0   0.236  -0.8825  -2.0078  -1.0498
 JC5  H24  H  HCR6  0   0.248  -5.3564  -0.1089   2.8154
 JC5  H5   H  HNH2  0   0.341   6.9511  -0.7306  -0.8253
 JC5  H6   H  HNH2  0   0.349   7.3825  -1.9335   0.1626
 JC5  H2   H  HCH3  0   0.230   3.3879  -3.9291   0.0515
 JC5  H1   H  HCH3  0   0.217   2.6818  -2.7903  -1.1041
 JC5  H    H  HCH3  0   0.226   4.4496  -2.8422  -0.8692
 JC5  H17  H  HCH2  0   0.201  -2.6108   0.4336  -0.4147
 JC5  H18  H  HCH2  0   0.238  -2.3296  -0.2959  -1.9872
 JC5  H20  H  HCH2  0   0.254  -5.2916  -1.9083  -1.8630
 JC5  H19  H  HCH2  0   0.251  -4.4307  -0.4907  -2.4425
 JC5  H21  H  HCR6  0   0.248  -6.9016   0.9268  -1.7983
 JC5  H23  H  HCR6  0   0.252  -7.1778   1.5270   2.4382
 JC5  H25  H  HCH2  0   0.253  -3.1902  -1.3464   1.3244
 JC5  H26  H  HCH2  0   0.255  -4.3981  -2.5215   0.8387
 JC5  H3   H  HCH2  0   0.235   5.6811  -1.4817   1.6865
 JC5  H4   H  HCH2  0   0.212   6.5870  -0.0029   1.4282
 JC5  H13  H  HCH2  0   0.219   0.0880   0.2610  -1.5737
 JC5  H14  H  HCH2  0   0.222  -0.2017   0.7419   0.1040
 JC5  O    O  O2    0  -0.488   3.3790  -2.0096   0.7065
 JC5  H22  H  HCR6  0   0.252  -7.9463   2.0351   0.1565

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
 JC5  N1   C6   single    1.457  0.020  1.457
 JC5  C6   C5   single    1.506  0.020  1.506
 JC5  C5   C7   aromatic  1.391  0.020  1.391
 JC5  C5   C4   aromatic  1.388  0.020  1.388
 JC5  C7   C8   aromatic  1.392  0.020  1.392
 JC5  C4   C2   aromatic  1.392  0.020  1.392
 JC5  C    O    single    1.423  0.020  1.423
 JC5  C8   O1   single    1.346  0.020  1.346
 JC5  C8   C1   aromatic  1.402  0.020  1.402
 JC5  C2   C1   aromatic  1.392  0.020  1.392
 JC5  C2   C3   single    1.505  0.020  1.505
 JC5  O1   C9   single    1.417  0.020  1.417
 JC5  C1   O    single    1.361  0.020  1.361
 JC5  C9   C10  single    1.515  0.020  1.515
 JC5  C3   N    single    1.459  0.020  1.459
 JC5  C10  C11  single    1.521  0.020  1.521
 JC5  C12  C13  single    1.507  0.020  1.507
 JC5  C12  N2   single    1.468  0.020  1.468
 JC5  C14  C13  aromatic  1.384  0.020  1.384
 JC5  C14  C15  aromatic  1.393  0.020  1.393
 JC5  C13  C18  aromatic  1.389  0.020  1.389
 JC5  C15  C16  aromatic  1.390  0.020  1.390
 JC5  N2   C11  single    1.458  0.020  1.458
 JC5  N2   C19  single    1.468  0.020  1.468
 JC5  C18  C19  single    1.507  0.020  1.507
 JC5  C18  C17  aromatic  1.384  0.020  1.384
 JC5  C16  C17  aromatic  1.393  0.020  1.393
 JC5  N1   H27  single    0.890  0.020  1.040
 JC5  N1   H11  single    0.890  0.020  1.040
 JC5  C4   H7   single    0.930  0.020  1.080
 JC5  C6   H9   single    0.970  0.020  1.090
 JC5  C6   H8   single    0.970  0.020  1.090
 JC5  C7   H12  single    0.930  0.020  1.080
 JC5  C10  H15  single    0.970  0.020  1.090
 JC5  C10  H16  single    0.970  0.020  1.090
 JC5  C15  H22  single    0.930  0.020  1.080
 JC5  C17  H24  single    0.930  0.020  1.080
 JC5  N    H5   single    0.890  0.020  1.040
 JC5  N    H6   single    0.890  0.020  1.040
 JC5  C    H2   single    0.970  0.020  1.090
 JC5  C    H1   single    0.970  0.020  1.090
 JC5  C    H    single    0.970  0.020  1.090
 JC5  C11  H17  single    0.970  0.020  1.090
 JC5  C11  H18  single    0.970  0.020  1.090
 JC5  C12  H20  single    0.970  0.020  1.090
 JC5  C12  H19  single    0.970  0.020  1.090
 JC5  C14  H21  single    0.930  0.020  1.080
 JC5  C16  H23  single    0.930  0.020  1.080
 JC5  C19  H25  single    0.970  0.020  1.090
 JC5  C19  H26  single    0.970  0.020  1.090
 JC5  C3   H3   single    0.970  0.020  1.090
 JC5  C3   H4   single    0.970  0.020  1.090
 JC5  C9   H13  single    0.970  0.020  1.090
 JC5  C9   H14  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
 JC5  H11  N1   H27  105.69  3.000
 JC5  H11  N1   C6   109.26  3.000
 JC5  H27  N1   C6   109.04  3.000
 JC5  H7   C4   C2   119.02  3.000
 JC5  H7   C4   C5   119.51  3.000
 JC5  C2   C4   C5   121.46  3.000
 JC5  C7   C5   C6   120.25  3.000
 JC5  C7   C5   C4   119.05  3.000
 JC5  C6   C5   C4   120.64  3.000
 JC5  H8   C6   H9   106.33  3.000
 JC5  H8   C6   C5   109.31  3.000
 JC5  H9   C6   C5   109.01  3.000
 JC5  H8   C6   N1   107.63  3.000
 JC5  H9   C6   N1   113.78  3.000
 JC5  C5   C6   N1   110.61  3.000
 JC5  H12  C7   C8   120.58  3.000
 JC5  H12  C7   C5   118.85  3.000
 JC5  C8   C7   C5   120.57  3.000
 JC5  O1   C8   C1   115.91  3.000
 JC5  C1   C8   C7   119.67  3.000
 JC5  O1   C8   C7   124.42  3.000
 JC5  H16  C10  H15  107.35  3.000
 JC5  H16  C10  C9   109.96  3.000
 JC5  H15  C10  C9   108.87  3.000
 JC5  H16  C10  C11  109.15  3.000
 JC5  H15  C10  C11  110.76  3.000
 JC5  C9   C10  C11  110.68  3.000
 JC5  C18  C13  C14  120.85  3.000
 JC5  C18  C13  C12  108.11  3.000
 JC5  C14  C13  C12  131.03  3.000
 JC5  H22  C15  C16  119.58  3.000
 JC5  H22  C15  C14  119.81  3.000
 JC5  C16  C15  C14  120.61  3.000
 JC5  H24  C17  C18  121.11  3.000
 JC5  H24  C17  C16  120.30  3.000
 JC5  C18  C17  C16  118.59  3.000
 JC5  H6   N    H5   105.78  3.000
 JC5  H6   N    C3   109.19  3.000
 JC5  H5   N    C3   109.18  3.000
 JC5  H    C    H1   109.56  3.000
 JC5  H    C    H2   109.12  3.000
 JC5  H1   C    H2   108.43  3.000
 JC5  H    C    O    110.86  3.000
 JC5  H1   C    O    111.83  3.000
 JC5  H2   C    O    106.94  3.000
 JC5  C2   C1   O    120.73  3.000
 JC5  O    C1   C8   119.11  3.000
 JC5  C2   C1   C8   120.13  3.000
 JC5  H18  C11  H17  106.27  3.000
 JC5  H18  C11  N2   107.89  3.000
 JC5  H17  C11  N2   112.30  3.000
 JC5  H18  C11  C10  108.18  3.000
 JC5  H17  C11  C10  109.90  3.000
 JC5  N2   C11  C10  112.04  3.000
 JC5  H19  C12  H20  106.87  3.000
 JC5  H19  C12  N2   111.28  3.000
 JC5  H20  C12  N2   109.86  3.000
 JC5  H19  C12  C13  113.70  3.000
 JC5  H20  C12  C13  110.28  3.000
 JC5  N2   C12  C13  104.87  3.000
 JC5  H21  C14  C15  120.32  3.000
 JC5  H21  C14  C13  121.13  3.000
 JC5  C15  C14  C13  118.55  3.000
 JC5  H23  C16  C17  119.78  3.000
 JC5  H23  C16  C15  119.67  3.000
 JC5  C17  C16  C15  120.55  3.000
 JC5  C19  C18  C17  130.91  3.000
 JC5  C17  C18  C13  120.84  3.000
 JC5  C19  C18  C13  108.24  3.000
 JC5  H26  C19  H25  106.65  3.000
 JC5  H26  C19  N2   110.00  3.000
 JC5  H25  C19  N2   111.65  3.000
 JC5  H26  C19  C18  110.31  3.000
 JC5  H25  C19  C18  113.49  3.000
 JC5  N2   C19  C18  104.78  3.000
 JC5  C3   C2   C1   121.00  3.000
 JC5  C3   C2   C4   119.92  3.000
 JC5  C1   C2   C4   119.08  3.000
 JC5  H4   C3   H3   106.50  3.000
 JC5  H4   C3   C2   108.26  3.000
 JC5  H3   C3   C2   110.08  3.000
 JC5  H4   C3   N    113.25  3.000
 JC5  H3   C3   N    108.05  3.000
 JC5  C2   C3   N    110.61  3.000
 JC5  H14  C9   H13  107.54  3.000
 JC5  H14  C9   O1   110.49  3.000
 JC5  H13  C9   O1   110.25  3.000
 JC5  H14  C9   C10  110.06  3.000
 JC5  H13  C9   C10  110.44  3.000
 JC5  O1   C9   C10  108.07  3.000
 JC5  C19  N2   C12  104.96  3.000
 JC5  C19  N2   C11  111.67  3.000
 JC5  C12  N2   C11  111.95  3.000
 JC5  C9   O1   C8   118.82  3.000
 JC5  C1   O    C    114.81  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
 JC5  CONST_01  C8   C7   C5   C4      0.00   0.0  0
 JC5  CONST_02  C8   C1   C2   C4      0.00   0.0  0
 JC5  CONST_03  C1   C8   C7   C5      0.00   0.0  0
 JC5  CONST_04  C1   C2   C4   C5      0.00   0.0  0
 JC5  CONST_05  C2   C4   C5   C7      0.00   0.0  0
 JC5  CONST_06  C2   C1   C8   C7      0.00   0.0  0
 JC5  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 JC5  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 JC5  CONST_09  C18  C13  C14  C15     0.00   0.0  0
 JC5  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 JC5  CONST_11  C14  C13  C18  C17     0.00   0.0  0
 JC5  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 JC5  CONST_13  O    C1   C2   C4    180.00   0.0  0
 JC5  CONST_14  O1   C8   C7   C5    180.00   0.0  0
 JC5  CONST_15  C3   C2   C4   C5    180.00   0.0  0
 JC5  CONST_16  C8   C7   C5   C6    180.00   0.0  0
 JC5  CONST_17  C2   C4   C5   C6    180.00   0.0  0
 JC5  CONST_18  O    C1   C8   C7    180.00   0.0  0
 JC5  CONST_19  C3   C2   C1   C8    180.00   0.0  0
 JC5  CONST_20  O1   C8   C1   C2    180.00   0.0  0
 JC5  CONST_21  H12  C7   C5   C4    180.00   0.0  0
 JC5  CONST_22  H7   C4   C5   C7    180.00   0.0  0
 JC5  CONST_23  H22  C15  C14  C13   180.00   0.0  0
 JC5  CONST_24  H24  C17  C18  C13   180.00   0.0  0
 JC5  CONST_25  H21  C14  C13  C12     0.00   0.0  0
 JC5  CONST_26  H23  C16  C15  C14   180.00   0.0  0
 JC5  Var_01    C19  N2   C12  C13    29.00  30.0  1
 JC5  Var_02    N2   C19  C18  C13    18.19  30.0  1
 JC5  Var_03    C18  C19  N2   C12   -29.03  30.0  1
 JC5  Var_04    N2   C12  C13  C14   162.99  30.0  1
 JC5  Var_05    C7   C5   C6   N1    108.12  30.0  2
 JC5  Var_06    N    C3   C2   C4    -95.58  30.0  2
 JC5  Var_07    C12  N2   C11  C10  -165.04  30.0  2
 JC5  Var_08    C2   C1   O    C     -97.56  30.0  2
 JC5  Var_09    C10  C9   O1   C8   -176.30  30.0  3
 JC5  Var_10    N2   C11  C10  C9   -176.91  30.0  3
 JC5  Var_11    H27  N1   C6   C5    178.07  30.0  3
 JC5  Var_12    H2   C    O    C1    179.70  30.0  3
 JC5  Var_13    H5   N    C3   C2     68.03  30.0  3
 JC5  Var_14    O1   C9   C10  C11  -176.75  30.0  1

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
 JC5  plan-1  C4   0.020
 JC5  plan-1  C5   0.020
 JC5  plan-1  C6   0.020
 JC5  plan-1  C7   0.020
 JC5  plan-1  C8   0.020
 JC5  plan-1  C1   0.020
 JC5  plan-1  C2   0.020
 JC5  plan-1  C3   0.020
 JC5  plan-1  O1   0.020
 JC5  plan-1  H7   0.020
 JC5  plan-1  H12  0.020
 JC5  plan-1  O    0.020
 JC5  plan-2  C13  0.020
 JC5  plan-2  C15  0.020
 JC5  plan-2  C17  0.020
 JC5  plan-2  C12  0.020
 JC5  plan-2  C14  0.020
 JC5  plan-2  C16  0.020
 JC5  plan-2  C18  0.020
 JC5  plan-2  C19  0.020
 JC5  plan-2  H24  0.020
 JC5  plan-2  H21  0.020
 JC5  plan-2  H23  0.020
 JC5  plan-2  H22  0.020

