# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:42:20 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (4~{R},7~{a}~{R},12~{b}~{S})-7,9-dimethoxy-3-methyl-2,4,7~{a},13-tetrahydro-1~{H}-4,12-methanobenzofuro[3,2-e]isoquinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=CC=C2[C@H]3Cc4ccc(OC)c5O[C@@H]1[C@]2(CCN3C)c45
#
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
 D4R  D4R  (4~{R},7~{a}~{R},12~{b}~{S})-7,9-dimethoxy-3-methyl-2,4,7~{a},13-tetrahydro-1~{H}-4,12-methanobenzofuro[3,2-e]isoquinoline  ligand  44  23  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D4R
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
 D4R  CAV  C  CH3   0  -0.432  -11.1189   -8.7601   8.2617
 D4R  OAB  O  O2    0  -0.459  -12.3826   -9.1431   8.7667
 D4R  CAL  C  C     0   0.372  -12.4643   -9.4958  10.0588
 D4R  CAR  C  C1    0  -0.389  -11.4477   -9.5648  10.9338
 D4R  CAO  C  C1    0  -0.361  -11.6512   -9.9314  12.3305
 D4R  CAH  C  C     0   0.241  -12.8554  -10.2516  12.7986
 D4R  CAI  C  CH1   0  -0.187  -13.2532  -10.4358  14.2369
 D4R  CAN  C  CH2   0  -0.521  -14.0714   -9.1978  14.7276
 D4R  NAD  N  NT    0  -0.404  -13.9485  -11.7141  14.3623
 D4R  CAU  C  CH3   0  -0.527  -14.1570  -12.1234  15.7314
 D4R  CAQ  C  CH2   0  -0.291  -15.1727  -11.7620  13.5869
 D4R  CAM  C  CH2   0  -0.407  -14.8947  -11.4913  12.1193
 D4R  CAE  C  CT    0  -0.283  -14.0597  -10.2201  11.9123
 D4R  CAF  C  CH1   0  -0.047  -13.8613   -9.9189  10.4131
 D4R  OAA  O  O2    0  -0.493  -14.8142   -8.8754  10.0793
 D4R  CAJ  C  CR6   0   0.334  -15.1813   -8.2814  11.2420
 D4R  CAG  C  CR6   0   0.008  -14.7635   -8.9736  12.3501
 D4R  CAK  C  CR6   0   0.082  -14.8354   -8.4879  13.6391
 D4R  CAS  C  CR16  0  -0.335  -15.5058   -7.2761  13.7882
 D4R  CAT  C  CR16  0  -0.386  -16.0256   -6.5995  12.6836
 D4R  CAP  C  CR6   0   0.268  -15.8554   -7.0723  11.3782
 D4R  OAC  O  O2    0  -0.471  -16.2592   -6.4495  10.2526
 D4R  CAW  C  CH3   0  -0.435  -16.9009   -5.1974  10.3834
 D4R  H1   H  HCH3  0   0.259  -11.2614   -8.5137   7.2127
 D4R  H2   H  HCH3  0   0.229  -10.7271   -7.8846   8.7852
 D4R  H3   H  HCH3  0   0.228  -10.3903   -9.5710   8.3413
 D4R  H4   H  H     0   0.271  -10.4386   -9.3196  10.6300
 D4R  H5   H  H     0   0.242  -10.7967   -9.8780  12.9959
 D4R  H6   H  HCH1  0   0.262  -12.3537  -10.4983  14.8547
 D4R  H7   H  HCH2  0   0.261  -13.3701   -8.4851  15.1700
 D4R  H8   H  HCH2  0   0.255  -14.7359   -9.4887  15.5467
 D4R  H10  H  HCH3  0   0.233  -13.2129  -12.0957  16.2782
 D4R  H11  H  HCH3  0   0.197  -14.8819  -11.5069  16.2834
 D4R  H12  H  HCH3  0   0.237  -14.5242  -13.1509  15.7536
 D4R  H13  H  HCH2  0   0.204  -15.9368  -11.0627  13.9668
 D4R  H14  H  HCH2  0   0.246  -15.6054  -12.7603  13.6890
 D4R  H15  H  HCH2  0   0.243  -15.8369  -11.4117  11.5710
 D4R  H16  H  HCH2  0   0.242  -14.3406  -12.3315  11.6912
 D4R  H17  H  HCH1  0   0.276  -14.1299  -10.7818   9.7954
 D4R  H18  H  HCR6  0   0.248  -15.6104   -6.8244  14.7674
 D4R  H19  H  HCR6  0   0.279  -16.5337   -5.6600  12.8560
 D4R  H20  H  HCH3  0   0.258  -17.1311   -4.8600   9.3758
 D4R  H21  H  HCH3  0   0.227  -17.8328   -5.2721  10.9502
 D4R  H22  H  HCH3  0   0.227  -16.2562   -4.4560  10.8634

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
 D4R  CAV  OAB  single    1.414  0.020  1.414
 D4R  OAB  CAL  single    1.342  0.020  1.342
 D4R  CAL  CAF  single    1.502  0.020  1.502
 D4R  CAL  CAR  double    1.343  0.020  1.343
 D4R  OAA  CAF  single    1.452  0.020  1.452
 D4R  OAA  CAJ  single    1.356  0.020  1.356
 D4R  OAC  CAW  single    1.413  0.020  1.413
 D4R  OAC  CAP  single    1.348  0.020  1.348
 D4R  CAF  CAE  single    1.542  0.020  1.542
 D4R  CAR  CAO  single    1.458  0.020  1.458
 D4R  CAJ  CAP  aromatic  1.391  0.020  1.391
 D4R  CAJ  CAG  aromatic  1.372  0.020  1.372
 D4R  CAP  CAT  aromatic  1.399  0.020  1.399
 D4R  CAE  CAM  single    1.535  0.020  1.535
 D4R  CAE  CAG  single    1.497  0.020  1.497
 D4R  CAE  CAH  single    1.496  0.020  1.496
 D4R  CAM  CAQ  single    1.518  0.020  1.518
 D4R  CAG  CAK  aromatic  1.379  0.020  1.379
 D4R  CAO  CAH  double    1.331  0.020  1.331
 D4R  CAT  CAS  aromatic  1.396  0.020  1.396
 D4R  CAH  CAI  single    1.504  0.020  1.504
 D4R  CAQ  NAD  single    1.450  0.020  1.450
 D4R  CAK  CAS  aromatic  1.393  0.020  1.393
 D4R  CAK  CAN  single    1.508  0.020  1.508
 D4R  CAI  NAD  single    1.461  0.020  1.461
 D4R  CAI  CAN  single    1.563  0.020  1.563
 D4R  NAD  CAU  single    1.444  0.020  1.444
 D4R  CAV  H1   single    0.970  0.020  1.090
 D4R  CAV  H2   single    0.970  0.020  1.090
 D4R  CAV  H3   single    0.970  0.020  1.090
 D4R  CAR  H4   single    0.930  0.020  1.080
 D4R  CAO  H5   single    0.930  0.020  1.080
 D4R  CAI  H6   single    0.970  0.020  1.090
 D4R  CAN  H7   single    0.970  0.020  1.090
 D4R  CAN  H8   single    0.970  0.020  1.090
 D4R  CAU  H10  single    0.970  0.020  1.090
 D4R  CAU  H11  single    0.970  0.020  1.090
 D4R  CAU  H12  single    0.970  0.020  1.090
 D4R  CAQ  H13  single    0.970  0.020  1.090
 D4R  CAQ  H14  single    0.970  0.020  1.090
 D4R  CAM  H15  single    0.970  0.020  1.090
 D4R  CAM  H16  single    0.970  0.020  1.090
 D4R  CAF  H17  single    0.970  0.020  1.090
 D4R  CAS  H18  single    0.930  0.020  1.080
 D4R  CAT  H19  single    0.930  0.020  1.080
 D4R  CAW  H20  single    0.970  0.020  1.090
 D4R  CAW  H21  single    0.970  0.020  1.090
 D4R  CAW  H22  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
 D4R  H3   CAV  H2   108.70  3.000
 D4R  H3   CAV  H1   109.02  3.000
 D4R  H2   CAV  H1   109.14  3.000
 D4R  H3   CAV  OAB  111.64  3.000
 D4R  H2   CAV  OAB  111.49  3.000
 D4R  H1   CAV  OAB  106.79  3.000
 D4R  CAL  OAB  CAV  118.01  3.000
 D4R  CAF  CAL  CAR  122.40  3.000
 D4R  CAR  CAL  OAB  126.50  3.000
 D4R  CAF  CAL  OAB  110.96  3.000
 D4R  H4   CAR  CAO  117.13  3.000
 D4R  H4   CAR  CAL  120.76  3.000
 D4R  CAO  CAR  CAL  122.09  3.000
 D4R  H5   CAO  CAH  120.60  3.000
 D4R  H5   CAO  CAR  117.74  3.000
 D4R  CAH  CAO  CAR  121.57  3.000
 D4R  CAE  CAH  CAI  110.88  3.000
 D4R  CAI  CAH  CAO  127.24  3.000
 D4R  CAE  CAH  CAO  121.00  3.000
 D4R  H6   CAI  NAD  107.05  3.000
 D4R  H6   CAI  CAN  107.37  3.000
 D4R  NAD  CAI  CAN  114.65  3.000
 D4R  H6   CAI  CAH  109.27  3.000
 D4R  CAN  CAI  CAH  109.99  3.000
 D4R  NAD  CAI  CAH  108.38  3.000
 D4R  H8   CAN  H7   105.07  3.000
 D4R  H8   CAN  CAK  110.97  3.000
 D4R  H7   CAN  CAK  108.07  3.000
 D4R  H8   CAN  CAI  110.02  3.000
 D4R  H7   CAN  CAI  107.92  3.000
 D4R  CAK  CAN  CAI  114.30  3.000
 D4R  CAQ  NAD  CAU  112.07  3.000
 D4R  CAU  NAD  CAI  113.47  3.000
 D4R  CAQ  NAD  CAI  112.64  3.000
 D4R  H12  CAU  H11  107.20  3.000
 D4R  H12  CAU  H10  107.75  3.000
 D4R  H11  CAU  H10  107.72  3.000
 D4R  H12  CAU  NAD  109.56  3.000
 D4R  H11  CAU  NAD  114.33  3.000
 D4R  H10  CAU  NAD  110.05  3.000
 D4R  H14  CAQ  H13  105.82  3.000
 D4R  H14  CAQ  CAM  109.01  3.000
 D4R  H13  CAQ  CAM  110.29  3.000
 D4R  H14  CAQ  NAD  108.33  3.000
 D4R  H13  CAQ  NAD  112.32  3.000
 D4R  CAM  CAQ  NAD  110.89  3.000
 D4R  H16  CAM  H15  107.23  3.000
 D4R  H16  CAM  CAE  107.93  3.000
 D4R  H15  CAM  CAE  109.94  3.000
 D4R  H16  CAM  CAQ  109.53  3.000
 D4R  H15  CAM  CAQ  109.88  3.000
 D4R  CAE  CAM  CAQ  112.19  3.000
 D4R  CAG  CAE  CAF  100.50  3.000
 D4R  CAG  CAE  CAM  113.23  3.000
 D4R  CAF  CAE  CAM  111.28  3.000
 D4R  CAG  CAE  CAH  102.88  3.000
 D4R  CAM  CAE  CAH  109.92  3.000
 D4R  CAF  CAE  CAH  118.47  3.000
 D4R  H17  CAF  OAA  106.01  3.000
 D4R  H17  CAF  CAE  111.29  3.000
 D4R  OAA  CAF  CAE  106.23  3.000
 D4R  H17  CAF  CAL  108.49  3.000
 D4R  CAE  CAF  CAL  113.83  3.000
 D4R  OAA  CAF  CAL  110.71  3.000
 D4R  CAJ  OAA  CAF  107.18  3.000
 D4R  CAP  CAJ  CAG  120.47  3.000
 D4R  CAG  CAJ  OAA  112.90  3.000
 D4R  CAP  CAJ  OAA  126.57  3.000
 D4R  CAK  CAG  CAJ  124.14  3.000
 D4R  CAK  CAG  CAE  126.23  3.000
 D4R  CAJ  CAG  CAE  109.10  3.000
 D4R  CAS  CAK  CAG  115.56  3.000
 D4R  CAS  CAK  CAN  125.19  3.000
 D4R  CAG  CAK  CAN  118.85  3.000
 D4R  H18  CAS  CAT  118.51  3.000
 D4R  H18  CAS  CAK  120.39  3.000
 D4R  CAT  CAS  CAK  121.08  3.000
 D4R  H19  CAT  CAP  119.96  3.000
 D4R  H19  CAT  CAS  118.01  3.000
 D4R  CAP  CAT  CAS  121.97  3.000
 D4R  OAC  CAP  CAT  125.91  3.000
 D4R  CAT  CAP  CAJ  116.37  3.000
 D4R  OAC  CAP  CAJ  117.70  3.000
 D4R  CAW  OAC  CAP  117.91  3.000
 D4R  H22  CAW  H21  108.74  3.000
 D4R  H22  CAW  H20  108.74  3.000
 D4R  H21  CAW  H20  108.74  3.000
 D4R  H22  CAW  OAC  111.95  3.000
 D4R  H21  CAW  OAC  111.99  3.000
 D4R  H20  CAW  OAC  106.58  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
 D4R  CONST_01  CAS  CAT  CAP  CAJ     0.00   0.0  0
 D4R  CONST_02  CAS  CAK  CAG  CAJ     0.00   0.0  0
 D4R  CONST_03  CAT  CAP  CAJ  CAG     0.00   0.0  0
 D4R  CONST_04  CAT  CAS  CAK  CAG     0.00   0.0  0
 D4R  CONST_05  CAP  CAJ  CAG  CAK     0.00   0.0  0
 D4R  CONST_06  CAP  CAT  CAS  CAK     0.00   0.0  0
 D4R  CONST_07  OAC  CAP  CAJ  OAA     0.00   0.0  0
 D4R  CONST_08  OAC  CAP  CAJ  CAG   180.00   0.0  0
 D4R  CONST_09  OAC  CAP  CAT  CAS   180.00   0.0  0
 D4R  CONST_10  H18  CAS  CAK  CAN     0.00   0.0  0
 D4R  CONST_11  H19  CAT  CAP  CAJ   180.00   0.0  0
 D4R  Var_01    CAE  CAH  CAO  CAR    -1.32   0.0  0
 D4R  Var_02    CAH  CAO  CAR  CAL     1.85  30.0  1
 D4R  Var_03    CAF  CAL  CAR  CAO    -6.16  30.0  1
 D4R  Var_04    CAM  CAQ  NAD  CAI    57.49  30.0  3
 D4R  Var_05    CAG  CAK  CAN  CAI     0.49  30.0  1
 D4R  Var_06    CAE  CAM  CAQ  NAD   -50.59  30.0  3
 D4R  Var_07    CAP  CAJ  OAA  CAF   165.92  30.0  1
 D4R  Var_08    H5   CAO  CAH  CAI     6.74   0.0  0
 D4R  Var_09    H10  CAU  NAD  CAI   -52.24  30.0  3
 D4R  Var_10    H1   CAV  OAB  CAL  -179.91  30.0  3
 D4R  Var_11    H20  CAW  OAC  CAP   179.18  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
 D4R  chir_01  CAI  CAH  NAD  CAN  positiv
 D4R  chir_02  CAE  CAF  CAG  CAH  positiv
 D4R  chir_03  CAF  OAA  CAE  CAL  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
 D4R  plan-1  CAR  0.020
 D4R  plan-1  CAO  0.020
 D4R  plan-1  CAH  0.020
 D4R  plan-1  CAI  0.020
 D4R  plan-1  CAE  0.020
 D4R  plan-1  H5   0.020
 D4R  plan-2  CAN  0.020
 D4R  plan-2  CAE  0.020
 D4R  plan-2  OAA  0.020
 D4R  plan-2  CAJ  0.020
 D4R  plan-2  CAG  0.020
 D4R  plan-2  CAK  0.020
 D4R  plan-2  CAS  0.020
 D4R  plan-2  CAT  0.020
 D4R  plan-2  CAP  0.020
 D4R  plan-2  OAC  0.020
 D4R  plan-2  H18  0.020
 D4R  plan-2  H19  0.020

