# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:52:44 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](C1COC1)c2cc(Cl)c3CCN(CC4=C(OC)C=C(C)NC4=O)C(=O)c3c2Cl
#
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
 CJD  CJD  5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one  ligand  55  31  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CJD
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
 CJD  C4    C   CR66  0   0.167  -1.1133  -2.1337   0.4462
 CJD  C5    C   CR66  0   0.017  -0.6431  -0.8236   0.5751
 CJD  C6    C   CR6   0  -0.189  -1.5166   0.2490   0.3648
 CJD  C8    C   CR6   0   0.557   0.7722  -0.6236   1.0467
 CJD  C10   C   C     0  -0.283   1.2069  -2.7726  -0.0049
 CJD  C13   C   CR6   0  -0.240   3.7399  -0.3404   0.3691
 CJD  C15   C   CR16  0  -0.534   4.8039   1.8421   0.1995
 CJD  C22   C   CH3   0  -0.440   4.4124   2.1254   2.9464
 CJD  C26   C   C     0  -0.372  -4.2809   1.1703  -1.6388
 CJD  C1    C   CR6   0   0.170  -2.8629   0.0418   0.0809
 CJD  C2    C   CR16  0  -0.254  -3.3285  -1.2669   0.0361
 CJD  C3    C   CR6   0  -0.116  -2.4676  -2.3304   0.2075
 CJD  CL7   CL  CL    0  -0.103  -0.9226   1.8773   0.3821
 CJD  N9    N   NR6   0  -0.468   1.6433  -1.5956   0.7242
 CJD  C11   C   C     0  -0.516  -0.1210  -3.2508   0.5421
 CJD  C12   C   CH2   0  -0.357   3.0416  -1.4389   1.1149
 CJD  C14   C   CR6   0   0.512   4.1941   0.8146   0.9693
 CJD  C16   C   CR6   0   0.394   4.9517   1.6656  -1.1409
 CJD  N17   N   NR16  0  -0.704   4.5189   0.5191  -1.7096
 CJD  C18   C   CR6   0   0.523   3.9147  -0.5297  -1.0372
 CJD  O19   O   O     0  -0.514   3.5754  -1.5343  -1.6663
 CJD  O21   O   O2    0  -0.452   4.0641   0.9189   2.2901
 CJD  O23   O   O     0  -0.458   1.0831   0.3445   1.7203
 CJD  CL24  CL  CL    0  -0.118  -3.1127  -3.9358   0.1212
 CJD  C25   C   CH1   0  -0.012  -3.8742   1.1456  -0.1778
 CJD  C27   C   C     0  -0.126  -5.0656   2.4054  -2.0925
 CJD  O28   O   O     0  -0.511  -4.0288   2.7870  -3.0065
 CJD  C29   C   C     0  -0.128  -3.2318   1.6509  -2.6482
 CJD  O30   O   O2    0  -0.477  -5.0483   0.9382   0.5643
 CJD  C31   C   CH3   0  -0.406  -4.8884   1.1627   1.9470
 CJD  H1    H   H     0   0.249   1.1201  -2.5636  -1.0739
 CJD  H2    H   H     0   0.263   1.9609  -3.5474   0.1127
 CJD  H4    H   HCR6  0   0.290   5.1660   2.7553   0.6458
 CJD  H5    H   HCH3  0   0.269   6.4991   2.2627  -2.4867
 CJD  H6    H   HCH3  0   0.268   4.9213   2.9496  -2.8536
 CJD  H7    H   HCH3  0   0.267   5.8543   3.5671  -1.4871
 CJD  H8    H   HCH3  0   0.234   5.4781   2.3458   2.8585
 CJD  H9    H   HCH3  0   0.235   3.8376   2.9739   2.5700
 CJD  H10   H   HCH3  0   0.264   4.1722   1.9786   3.9960
 CJD  H11   H   H     0   0.278  -4.7485   0.2222  -1.9127
 CJD  H12   H   HCR6  0   0.289  -4.3789  -1.4500  -0.1492
 CJD  H13   H   H     0   0.276  -0.0134  -3.5817   1.5800
 CJD  H14   H   H     0   0.268  -0.4565  -4.1127  -0.0334
 CJD  H15   H   HCH2  0   0.262   3.5285  -2.3924   0.9130
 CJD  H16   H   HCH2  0   0.267   3.1007  -1.2748   2.1897
 CJD  H17   H   HCH1  0   0.236  -3.4381   2.1180   0.0852
 CJD  H18   H   H     0   0.222  -6.0126   2.1976  -2.5972
 CJD  H19   H   H     0   0.216  -5.2391   3.1598  -1.3184
 CJD  H20   H   H     0   0.209  -2.2623   1.9373  -2.2297
 CJD  H21   H   H     0   0.226  -3.0607   0.9759  -3.4905
 CJD  H22   H   HCH3  0   0.242  -5.8643   1.0466   2.4153
 CJD  H23   H   HCH3  0   0.213  -4.1976   0.4494   2.4082
 CJD  H24   H   HCH3  0   0.213  -4.5199   2.1742   2.1502
 CJD  H3    H   HNR6  0   0.412   4.6448   0.3930  -2.7055
 CJD  C20   C   CH3   0  -0.729   5.5906   2.6689  -2.0390

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
 CJD  O19   C18  double    1.233  0.020  1.233
 CJD  CL24  C3   single    1.732  0.020  1.732
 CJD  C11   C10  single    1.514  0.020  1.514
 CJD  C11   C4   single    1.497  0.020  1.497
 CJD  C10   N9   single    1.452  0.020  1.452
 CJD  C18   N17  single    1.385  0.020  1.385
 CJD  C18   C13  single    1.430  0.020  1.430
 CJD  C4    C3   aromatic  1.389  0.020  1.389
 CJD  C4    C5   aromatic  1.398  0.020  1.398
 CJD  C3    C2   aromatic  1.379  0.020  1.379
 CJD  C12   N9   single    1.460  0.020  1.460
 CJD  C12   C13  single    1.500  0.020  1.500
 CJD  N9    C8   single    1.344  0.020  1.344
 CJD  N17   C16  single    1.351  0.020  1.351
 CJD  C13   C14  double    1.379  0.020  1.379
 CJD  C8    C5   single    1.505  0.020  1.505
 CJD  C8    O23  double    1.220  0.020  1.220
 CJD  C5    C6   aromatic  1.399  0.020  1.399
 CJD  C2    C1   aromatic  1.390  0.020  1.390
 CJD  C16   C20  single    1.490  0.020  1.490
 CJD  C16   C15  double    1.360  0.020  1.360
 CJD  C14   C15  single    1.421  0.020  1.421
 CJD  C14   O21  single    1.331  0.020  1.331
 CJD  C6    C1   aromatic  1.391  0.020  1.391
 CJD  C6    CL7  single    1.733  0.020  1.733
 CJD  C1    C25  single    1.519  0.020  1.519
 CJD  O21   C22  single    1.417  0.020  1.417
 CJD  C29   C26  single    1.533  0.020  1.533
 CJD  C29   O28  single    1.433  0.020  1.433
 CJD  C26   C25  single    1.517  0.020  1.517
 CJD  C26   C27  single    1.532  0.020  1.532
 CJD  C25   O30  single    1.404  0.020  1.404
 CJD  O30   C31  single    1.410  0.020  1.410
 CJD  O28   C27  single    1.434  0.020  1.434
 CJD  C10   H1   single    0.970  0.020  1.090
 CJD  C10   H2   single    0.970  0.020  1.090
 CJD  C15   H4   single    0.930  0.020  1.080
 CJD  C20   H5   single    0.970  0.020  1.090
 CJD  C20   H6   single    0.970  0.020  1.090
 CJD  C20   H7   single    0.970  0.020  1.090
 CJD  C22   H8   single    0.970  0.020  1.090
 CJD  C22   H9   single    0.970  0.020  1.090
 CJD  C22   H10  single    0.970  0.020  1.090
 CJD  C26   H11  single    0.970  0.020  1.090
 CJD  C2    H12  single    0.930  0.020  1.080
 CJD  C11   H13  single    0.970  0.020  1.090
 CJD  C11   H14  single    0.970  0.020  1.090
 CJD  C12   H15  single    0.970  0.020  1.090
 CJD  C12   H16  single    0.970  0.020  1.090
 CJD  C25   H17  single    0.970  0.020  1.090
 CJD  C27   H18  single    0.970  0.020  1.090
 CJD  C27   H19  single    0.970  0.020  1.090
 CJD  C29   H20  single    0.970  0.020  1.090
 CJD  C29   H21  single    0.970  0.020  1.090
 CJD  C31   H22  single    0.970  0.020  1.090
 CJD  C31   H23  single    0.970  0.020  1.090
 CJD  C31   H24  single    0.970  0.020  1.090
 CJD  N17   H3   single    0.860  0.020  1.020

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
 CJD  C11   C4   C3   123.47  3.000
 CJD  C3    C4   C5   118.46  3.000
 CJD  C11   C4   C5   118.06  3.000
 CJD  C8    C5   C6   122.16  3.000
 CJD  C6    C5   C4   119.64  3.000
 CJD  C8    C5   C4   118.02  3.000
 CJD  CL7   C6   C1   118.26  3.000
 CJD  CL7   C6   C5   120.31  3.000
 CJD  C1    C6   C5   121.37  3.000
 CJD  O23   C8   N9   122.76  3.000
 CJD  O23   C8   C5   121.21  3.000
 CJD  N9    C8   C5   115.97  3.000
 CJD  H2    C10  H1   107.28  3.000
 CJD  H2    C10  C11  110.13  3.000
 CJD  H1    C10  C11  110.14  3.000
 CJD  H2    C10  N9   108.36  3.000
 CJD  H1    C10  N9   111.11  3.000
 CJD  C11   C10  N9   109.78  3.000
 CJD  C18   C13  C14  119.93  3.000
 CJD  C14   C13  C12  123.39  3.000
 CJD  C18   C13  C12  116.68  3.000
 CJD  H4    C15  C16  118.75  3.000
 CJD  H4    C15  C14  122.13  3.000
 CJD  C16   C15  C14  119.12  3.000
 CJD  H10   C22  H9   108.76  3.000
 CJD  H10   C22  H8   108.70  3.000
 CJD  H9    C22  H8   109.22  3.000
 CJD  H10   C22  O21  106.14  3.000
 CJD  H9    C22  O21  111.88  3.000
 CJD  H8    C22  O21  112.00  3.000
 CJD  H11   C26  C29  113.58  3.000
 CJD  H11   C26  C27  113.98  3.000
 CJD  C29   C26  C27   84.43  3.000
 CJD  H11   C26  C25  110.01  3.000
 CJD  C27   C26  C25  115.83  3.000
 CJD  C29   C26  C25  117.12  3.000
 CJD  C25   C1   C2   117.11  3.000
 CJD  C25   C1   C6   124.79  3.000
 CJD  C2    C1   C6   118.10  3.000
 CJD  H12   C2   C3   119.79  3.000
 CJD  H12   C2   C1   119.34  3.000
 CJD  C3    C2   C1   120.87  3.000
 CJD  CL24  C3   C2   118.43  3.000
 CJD  C2    C3   C4   121.39  3.000
 CJD  CL24  C3   C4   120.19  3.000
 CJD  C12   N9   C10  120.61  3.000
 CJD  C12   N9   C8   118.59  3.000
 CJD  C10   N9   C8   120.79  3.000
 CJD  H14   C11  H13  106.97  3.000
 CJD  H14   C11  C10  109.22  3.000
 CJD  H13   C11  C10  110.61  3.000
 CJD  H14   C11  C4   110.63  3.000
 CJD  H13   C11  C4   110.58  3.000
 CJD  C10   C11  C4   108.82  3.000
 CJD  H16   C12  H15  106.89  3.000
 CJD  H16   C12  N9   109.41  3.000
 CJD  H15   C12  N9   106.52  3.000
 CJD  H16   C12  C13  110.80  3.000
 CJD  H15   C12  C13  109.92  3.000
 CJD  N9    C12  C13  113.04  3.000
 CJD  O21   C14  C15  121.51  3.000
 CJD  O21   C14  C13  117.74  3.000
 CJD  C15   C14  C13  120.74  3.000
 CJD  N17   C16  C20  117.06  3.000
 CJD  C20   C16  C15  123.58  3.000
 CJD  N17   C16  C15  119.35  3.000
 CJD  H3    N17  C18  115.98  3.000
 CJD  H3    N17  C16  118.70  3.000
 CJD  C18   N17  C16  125.32  3.000
 CJD  O19   C18  N17  119.31  3.000
 CJD  N17   C18  C13  115.51  3.000
 CJD  O19   C18  C13  125.18  3.000
 CJD  C14   O21  C22  120.15  3.000
 CJD  H17   C25  O30  109.66  3.000
 CJD  H17   C25  C1   109.78  3.000
 CJD  O30   C25  C1   111.06  3.000
 CJD  H17   C25  C26  108.83  3.000
 CJD  O30   C25  C26  106.69  3.000
 CJD  C1    C25  C26  110.75  3.000
 CJD  H19   C27  H18  108.68  3.000
 CJD  H19   C27  O28  112.46  3.000
 CJD  H18   C27  O28  112.50  3.000
 CJD  H19   C27  C26  115.30  3.000
 CJD  H18   C27  C26  115.29  3.000
 CJD  O28   C27  C26   91.89  3.000
 CJD  C29   O28  C27   91.82  3.000
 CJD  H21   C29  H20  108.53  3.000
 CJD  H21   C29  O28  112.58  3.000
 CJD  H20   C29  O28  112.38  3.000
 CJD  H21   C29  C26  114.90  3.000
 CJD  H20   C29  C26  115.88  3.000
 CJD  O28   C29  C26   91.86  3.000
 CJD  C31   O30  C25  113.57  3.000
 CJD  H24   C31  H23  108.13  3.000
 CJD  H24   C31  H22  108.67  3.000
 CJD  H23   C31  H22  108.36  3.000
 CJD  H24   C31  O30  111.54  3.000
 CJD  H23   C31  O30  112.39  3.000
 CJD  H22   C31  O30  107.65  3.000
 CJD  H7    C20  H6   108.39  3.000
 CJD  H7    C20  H5   108.30  3.000
 CJD  H6    C20  H5   107.47  3.000
 CJD  H7    C20  C16  110.76  3.000
 CJD  H6    C20  C16  111.11  3.000
 CJD  H5    C20  C16  110.70  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
 CJD  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 CJD  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 CJD  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 CJD  CONST_04  C2    C1   C6   C5      0.00   0.0  0
 CJD  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 CJD  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 CJD  CONST_07  C10   N9   C8   C5      0.00   0.0  0
 CJD  CONST_08  C16   N17  C18  C13     0.00   0.0  0
 CJD  CONST_09  CL7   C6   C5   C4    180.00   0.0  0
 CJD  CONST_10  CL24  C3   C4   C5    180.00   0.0  0
 CJD  CONST_11  C25   C1   C6   C5    180.00   0.0  0
 CJD  CONST_12  CL7   C6   C5   C8      0.00   0.0  0
 CJD  CONST_13  CL24  C3   C2   C1    180.00   0.0  0
 CJD  CONST_14  CL7   C6   C1   C2    180.00   0.0  0
 CJD  CONST_15  C25   C1   C2   C3    180.00   0.0  0
 CJD  CONST_16  CL24  C3   C4   C11     0.00   0.0  0
 CJD  CONST_17  C12   N9   C8   C5    180.00   0.0  0
 CJD  CONST_18  O23   C8   N9   C10   180.00   0.0  0
 CJD  CONST_19  O19   C18  N17  C16   180.00   0.0  0
 CJD  CONST_20  H12   C2   C3   C4    180.00   0.0  0
 CJD  CONST_21  H3    N17  C18  C13   180.00   0.0  0
 CJD  CONST_22  O23   C8   N9   C12     0.00   0.0  0
 CJD  Var_01    N9    C10  C11  C4     57.19  30.0  1
 CJD  Var_02    N9    C8   C5   C4     29.97  30.0  1
 CJD  Var_03    C10   C11  C4   C5    -31.84  30.0  1
 CJD  Var_04    C11   C10  N9   C8    -42.09  30.0  1
 CJD  Var_05    C13   C12  N9   C8    -68.52  30.0  1
 CJD  Var_06    C18   C13  C12  N9    -65.88  30.0  3
 CJD  Var_07    H20   C29  O28  C27  -119.45  30.0  1
 CJD  Var_08    H18   C27  O28  C29  -118.05  30.0  1
 CJD  Var_09    H5    C20  C16  C15   116.49  30.0  3
 CJD  Var_10    H8    C22  O21  C14   -64.32  30.0  3
 CJD  Var_11    H22   C31  O30  C25   175.97  30.0  3

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
 CJD  chir_01  C26  C29  C25  C27  negativ
 CJD  chir_02  C25  O30  C26  C1   positiv

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
 CJD  plan-1  C13   0.020
 CJD  plan-1  C15   0.020
 CJD  plan-1  C12   0.020
 CJD  plan-1  C14   0.020
 CJD  plan-1  C16   0.020
 CJD  plan-1  N17   0.020
 CJD  plan-1  C18   0.020
 CJD  plan-1  O19   0.020
 CJD  plan-1  O21   0.020
 CJD  plan-1  H4    0.020
 CJD  plan-1  H3    0.020
 CJD  plan-1  C20   0.020
 CJD  plan-2  C4    0.020
 CJD  plan-2  C5    0.020
 CJD  plan-2  C6    0.020
 CJD  plan-2  C8    0.020
 CJD  plan-2  C1    0.020
 CJD  plan-2  C2    0.020
 CJD  plan-2  C3    0.020
 CJD  plan-2  CL7   0.020
 CJD  plan-2  C11   0.020
 CJD  plan-2  CL24  0.020
 CJD  plan-2  C25   0.020
 CJD  plan-2  H12   0.020
 CJD  plan-3  C5    0.020
 CJD  plan-3  C8    0.020
 CJD  plan-3  C10   0.020
 CJD  plan-3  N9    0.020
 CJD  plan-3  C12   0.020
 CJD  plan-3  O23   0.020

