# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:12:21 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2NC[C@@H]3CC(=CN3C(=O)c2cc1OC)c4ccc5ccccc5c4
#
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
 PZD  PZD  (11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one  ligand  51  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PZD
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
 PZD  C1A   C  CR6   0   0.342  -5.3518   0.5153   0.1563
 PZD  C2A   C  CR6   0   0.304  -5.0267  -0.7248  -0.4386
 PZD  C3A   C  CR16  0  -0.422  -3.7112  -0.9833  -0.7376
 PZD  C4A   C  CR6   0  -0.123  -2.6842  -0.0695  -0.4450
 PZD  C5A   C  CR6   0   0.350  -2.9989   1.1508   0.1653
 PZD  C6A   C  CR16  0  -0.501  -4.3486   1.4166   0.4530
 PZD  C7A   C  C     0   0.542  -1.3352  -0.4225  -0.9334
 PZD  N1A   N  NR5   0  -0.511  -0.2911  -0.0008  -0.1788
 PZD  C8A   C  CR15  0  -0.139  -0.3974   0.5293   1.1827
 PZD  C10   C  CR15  0   0.020   1.0432  -0.1902  -0.5096
 PZD  C11   C  CR5   0  -0.057   1.8577   0.0575   0.5233
 PZD  C12   C  CH2   0  -0.520   1.0316   0.3949   1.7399
 PZD  O1A   O  O     0  -0.491  -1.1607  -1.0718  -1.9584
 PZD  C13   C  CR66  0   0.157   5.4560  -0.1795  -0.6125
 PZD  C14   C  CR66  0   0.092   6.1346  -0.2173   0.6342
 PZD  C15   C  CR16  0  -0.305   7.5450  -0.3202   0.6499
 PZD  C16   C  CR16  0  -0.263   8.2518  -0.3807  -0.5200
 PZD  C17   C  CR16  0  -0.258   7.5792  -0.3405  -1.7612
 PZD  C18   C  CR16  0  -0.314   6.2163  -0.2409  -1.8070
 PZD  C19   C  CR16  0  -0.432   4.0510  -0.0761  -0.6327
 PZD  C20   C  CR6   0   0.127   3.3124  -0.0211   0.5309
 PZD  C21   C  CR16  0  -0.325   4.0061  -0.0445   1.7695
 PZD  C22   C  CR16  0  -0.294   5.3679  -0.1436   1.8190
 PZD  O2A   O  O2    0  -0.468  -6.0659  -1.5543  -0.6720
 PZD  C23   C  CH3   0  -0.438  -5.7911  -2.7899  -1.2962
 PZD  O3A   O  O2    0  -0.457  -6.6523   0.7146   0.4042
 PZD  C24   C  CH3   0  -0.441  -7.0513   1.9455   0.9771
 PZD  C9A   C  CH2   0  -0.243  -0.8511   1.9713   1.1553
 PZD  N2A   N  NH1   0  -0.700  -2.0730   2.1590   0.3888
 PZD  H8A   H  HCR5  0   0.290  -1.1043  -0.0768   1.7513
 PZD  H24   H  HCH3  0   0.264  -8.1335   1.9049   1.0690
 PZD  H24A  H  HCH3  0   0.232  -6.6179   2.0923   1.9696
 PZD  H24B  H  HCH3  0   0.233  -6.7813   2.7940   0.3435
 PZD  H23   H  HCH3  0   0.225  -5.1172  -3.4101  -0.6981
 PZD  H23A  H  HCH3  0   0.259  -6.7431  -3.3051  -1.3985
 PZD  H23B  H  HCH3  0   0.226  -5.3540  -2.6587  -2.2903
 PZD  H3A   H  HCR6  0   0.280  -3.4330  -1.9122  -1.2164
 PZD  H6A   H  HCR6  0   0.288  -4.5918   2.3633   0.9181
 PZD  H22   H  HCR6  0   0.255   5.8742  -0.1667   2.7766
 PZD  H15   H  HCR6  0   0.255   8.0598  -0.3508   1.6028
 PZD  H17   H  HCR6  0   0.258   8.1509  -0.3895  -2.6789
 PZD  H18   H  HCR6  0   0.253   5.7008  -0.2081  -2.7595
 PZD  H21   H  HCR6  0   0.258   3.4465   0.0101   2.6947
 PZD  H19   H  HCR6  0   0.246   3.5564  -0.0294  -1.5963
 PZD  H10   H  HCR5  0   0.291   1.3021  -0.5043  -1.5089
 PZD  H12   H  HCH2  0   0.265   1.3586   1.3210   2.2201
 PZD  H12A  H  HCH2  0   0.273   1.0947  -0.3907   2.4971
 PZD  H9A   H  HCH2  0   0.240  -0.9808   2.3008   2.1926
 PZD  HN2A  H  HNH1  0   0.384  -2.5200   3.0286   0.6370
 PZD  H9AA  H  HCH2  0   0.233  -0.0590   2.5873   0.7196
 PZD  H16   H  HCR6  0   0.258   9.3309  -0.4581  -0.4997

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
 PZD  O3A   C1A   single    1.339  0.020  1.339
 PZD  C6A   C1A   aromatic  1.381  0.020  1.381
 PZD  C1A   C2A   aromatic  1.413  0.020  1.413
 PZD  C2A   O2A   single    1.350  0.020  1.350
 PZD  C2A   C3A   aromatic  1.374  0.020  1.374
 PZD  C4A   C3A   aromatic  1.405  0.020  1.405
 PZD  C3A   H3A   single    0.930  0.020  1.080
 PZD  C5A   C4A   aromatic  1.400  0.020  1.400
 PZD  C4A   C7A   single    1.477  0.020  1.477
 PZD  C6A   C5A   aromatic  1.405  0.020  1.405
 PZD  N2A   C5A   single    1.387  0.020  1.387
 PZD  H6A   C6A   single    0.930  0.020  1.080
 PZD  N1A   C7A   single    1.356  0.020  1.356
 PZD  C7A   O1A   double    1.226  0.020  1.226
 PZD  C8A   N1A   single    1.465  0.020  1.465
 PZD  N1A   C10   single    1.388  0.020  1.388
 PZD  C9A   C8A   single    1.512  0.020  1.512
 PZD  H8A   C8A   single    0.970  0.020  1.090
 PZD  C12   C8A   single    1.540  0.020  1.540
 PZD  C11   C10   double    1.338  0.020  1.338
 PZD  C10   H10   single    0.930  0.020  1.080
 PZD  C12   C11   single    1.509  0.020  1.509
 PZD  C11   C20   single    1.457  0.020  1.457
 PZD  H12A  C12   single    0.970  0.020  1.090
 PZD  H12   C12   single    0.970  0.020  1.090
 PZD  C18   C13   aromatic  1.417  0.020  1.417
 PZD  C19   C13   aromatic  1.409  0.020  1.409
 PZD  C13   C14   aromatic  1.420  0.020  1.420
 PZD  C14   C15   aromatic  1.414  0.020  1.414
 PZD  C14   C22   aromatic  1.413  0.020  1.413
 PZD  C16   C15   aromatic  1.368  0.020  1.368
 PZD  C15   H15   single    0.930  0.020  1.080
 PZD  C17   C16   aromatic  1.412  0.020  1.412
 PZD  C16   H16   single    0.930  0.020  1.080
 PZD  H17   C17   single    0.930  0.020  1.080
 PZD  C18   C17   aromatic  1.367  0.020  1.367
 PZD  H18   C18   single    0.930  0.020  1.080
 PZD  H19   C19   single    0.930  0.020  1.080
 PZD  C19   C20   aromatic  1.379  0.020  1.379
 PZD  C20   C21   aromatic  1.420  0.020  1.420
 PZD  C21   C22   aromatic  1.366  0.020  1.366
 PZD  C21   H21   single    0.930  0.020  1.080
 PZD  C22   H22   single    0.930  0.020  1.080
 PZD  O2A   C23   single    1.411  0.020  1.411
 PZD  H23B  C23   single    0.970  0.020  1.090
 PZD  C23   H23   single    0.970  0.020  1.090
 PZD  C23   H23A  single    0.970  0.020  1.090
 PZD  C24   O3A   single    1.415  0.020  1.415
 PZD  H24A  C24   single    0.970  0.020  1.090
 PZD  C24   H24   single    0.970  0.020  1.090
 PZD  C24   H24B  single    0.970  0.020  1.090
 PZD  H9A   C9A   single    0.970  0.020  1.090
 PZD  C9A   N2A   single    1.455  0.020  1.455
 PZD  C9A   H9AA  single    0.970  0.020  1.090
 PZD  HN2A  N2A   single    0.890  0.020  1.040

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
 PZD  O3A   C1A  C6A   124.66  3.000
 PZD  C6A   C1A  C2A   119.74  3.000
 PZD  O3A   C1A  C2A   115.60  3.000
 PZD  O2A   C2A  C3A   125.73  3.000
 PZD  C3A   C2A  C1A   118.49  3.000
 PZD  O2A   C2A  C1A   115.78  3.000
 PZD  H3A   C3A  C4A   117.56  3.000
 PZD  H3A   C3A  C2A   120.29  3.000
 PZD  C4A   C3A  C2A   122.15  3.000
 PZD  C7A   C4A  C5A   123.88  3.000
 PZD  C7A   C4A  C3A   116.30  3.000
 PZD  C5A   C4A  C3A   119.55  3.000
 PZD  N2A   C5A  C6A   118.08  3.000
 PZD  N2A   C5A  C4A   123.62  3.000
 PZD  C6A   C5A  C4A   118.02  3.000
 PZD  H6A   C6A  C5A   117.98  3.000
 PZD  H6A   C6A  C1A   119.99  3.000
 PZD  C5A   C6A  C1A   122.03  3.000
 PZD  O1A   C7A  N1A   121.38  3.000
 PZD  O1A   C7A  C4A   122.20  3.000
 PZD  N1A   C7A  C4A   116.42  3.000
 PZD  C10   N1A  C8A   109.92  3.000
 PZD  C10   N1A  C7A   124.43  3.000
 PZD  C8A   N1A  C7A   125.03  3.000
 PZD  H8A   C8A  C9A   110.18  3.000
 PZD  H8A   C8A  C12   111.36  3.000
 PZD  C9A   C8A  C12   111.61  3.000
 PZD  C12   C8A  N1A   103.73  3.000
 PZD  H8A   C8A  N1A   109.29  3.000
 PZD  C9A   C8A  N1A   110.49  3.000
 PZD  H10   C10  C11   128.50  3.000
 PZD  H10   C10  N1A   119.42  3.000
 PZD  C11   C10  N1A   112.08  3.000
 PZD  C20   C11  C12   123.68  3.000
 PZD  C20   C11  C10   126.99  3.000
 PZD  C12   C11  C10   109.30  3.000
 PZD  H12A  C12  H12   106.69  3.000
 PZD  H12   C12  C11   112.33  3.000
 PZD  H12A  C12  C11   111.50  3.000
 PZD  H12   C12  C8A   111.26  3.000
 PZD  H12A  C12  C8A   111.53  3.000
 PZD  C11   C12  C8A   103.64  3.000
 PZD  C19   C13  C18   121.74  3.000
 PZD  C19   C13  C14   119.41  3.000
 PZD  C18   C13  C14   118.85  3.000
 PZD  C22   C14  C15   122.39  3.000
 PZD  C22   C14  C13   118.39  3.000
 PZD  C15   C14  C13   119.22  3.000
 PZD  H15   C15  C16   120.35  3.000
 PZD  H15   C15  C14   119.05  3.000
 PZD  C16   C15  C14   120.60  3.000
 PZD  H16   C16  C17   119.57  3.000
 PZD  H16   C16  C15   120.15  3.000
 PZD  C17   C16  C15   120.28  3.000
 PZD  H17   C17  C18   120.09  3.000
 PZD  C18   C17  C16   120.41  3.000
 PZD  H17   C17  C16   119.49  3.000
 PZD  H18   C18  C17   120.39  3.000
 PZD  H18   C18  C13   118.97  3.000
 PZD  C17   C18  C13   120.64  3.000
 PZD  H19   C19  C20   120.26  3.000
 PZD  C20   C19  C13   121.66  3.000
 PZD  H19   C19  C13   118.09  3.000
 PZD  C21   C20  C19   118.28  3.000
 PZD  C21   C20  C11   119.56  3.000
 PZD  C19   C20  C11   122.17  3.000
 PZD  H21   C21  C22   119.20  3.000
 PZD  H21   C21  C20   119.48  3.000
 PZD  C22   C21  C20   121.31  3.000
 PZD  H22   C22  C21   119.96  3.000
 PZD  H22   C22  C14   119.10  3.000
 PZD  C21   C22  C14   120.94  3.000
 PZD  C23   O2A  C2A   117.68  3.000
 PZD  H23B  C23  H23A  108.74  3.000
 PZD  H23A  C23  H23   108.79  3.000
 PZD  H23B  C23  H23   108.59  3.000
 PZD  H23A  C23  O2A   106.62  3.000
 PZD  H23   C23  O2A   111.99  3.000
 PZD  H23B  C23  O2A   112.01  3.000
 PZD  C24   O3A  C1A   118.58  3.000
 PZD  H24B  C24  H24A  108.92  3.000
 PZD  H24B  C24  H24   108.91  3.000
 PZD  H24A  C24  H24   108.85  3.000
 PZD  H24B  C24  O3A   111.77  3.000
 PZD  H24   C24  O3A   106.41  3.000
 PZD  H24A  C24  O3A   111.88  3.000
 PZD  H9AA  C9A  H9A   107.06  3.000
 PZD  H9AA  C9A  N2A   109.01  3.000
 PZD  H9A   C9A  N2A   111.13  3.000
 PZD  H9AA  C9A  C8A   109.09  3.000
 PZD  N2A   C9A  C8A   112.62  3.000
 PZD  H9A   C9A  C8A   107.76  3.000
 PZD  HN2A  N2A  C9A   110.72  3.000
 PZD  HN2A  N2A  C5A   111.74  3.000
 PZD  C9A   N2A  C5A   123.50  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
 PZD  CONST_01  C4A   C5A  C6A  C1A     0.00   0.0  0
 PZD  CONST_02  C4A   C3A  C2A  C1A     0.00   0.0  0
 PZD  CONST_03  C5A   C6A  C1A  C2A     0.00   0.0  0
 PZD  CONST_04  C5A   C4A  C3A  C2A     0.00   0.0  0
 PZD  CONST_05  C6A   C1A  C2A  C3A     0.00   0.0  0
 PZD  CONST_06  C6A   C5A  C4A  C3A     0.00   0.0  0
 PZD  CONST_07  C16   C17  C18  C13     0.00   0.0  0
 PZD  CONST_08  C21   C20  C19  C13     0.00   0.0  0
 PZD  CONST_09  C16   C15  C14  C13     0.00   0.0  0
 PZD  CONST_10  C21   C22  C14  C13     0.00   0.0  0
 PZD  CONST_11  C17   C18  C13  C14     0.00   0.0  0
 PZD  CONST_12  C20   C19  C13  C14     0.00   0.0  0
 PZD  CONST_13  C17   C16  C15  C14     0.00   0.0  0
 PZD  CONST_14  C20   C21  C22  C14     0.00   0.0  0
 PZD  CONST_15  C18   C13  C14  C15     0.00   0.0  0
 PZD  CONST_16  C19   C13  C14  C15   180.00   0.0  0
 PZD  CONST_17  C21   C22  C14  C15   180.00   0.0  0
 PZD  CONST_18  C18   C17  C16  C15     0.00   0.0  0
 PZD  CONST_19  C22   C14  C15  C16   180.00   0.0  0
 PZD  CONST_20  C19   C13  C18  C17   180.00   0.0  0
 PZD  CONST_21  C20   C19  C13  C18   180.00   0.0  0
 PZD  CONST_22  C22   C14  C13  C18   180.00   0.0  0
 PZD  CONST_23  C22   C14  C13  C19     0.00   0.0  0
 PZD  CONST_24  C22   C21  C20  C19     0.00   0.0  0
 PZD  CONST_25  C13   C19  C20  C11   180.00   0.0  0
 PZD  CONST_26  C22   C21  C20  C11   180.00   0.0  0
 PZD  CONST_27  C8A   N1A  C7A  C4A     0.00   0.0  0
 PZD  CONST_28  C10   N1A  C7A  C4A   180.00   0.0  0
 PZD  CONST_29  O3A   C1A  C2A  C3A   180.00   0.0  0
 PZD  CONST_30  O2A   C2A  C3A  C4A   180.00   0.0  0
 PZD  CONST_31  O3A   C1A  C6A  C5A   180.00   0.0  0
 PZD  CONST_32  O2A   C2A  C1A  C6A   180.00   0.0  0
 PZD  CONST_33  O1A   C7A  N1A  C8A   180.00   0.0  0
 PZD  CONST_34  O1A   C7A  N1A  C10     0.00   0.0  0
 PZD  CONST_35  H3A   C3A  C2A  C1A   180.00   0.0  0
 PZD  CONST_36  H6A   C6A  C1A  C2A   180.00   0.0  0
 PZD  CONST_37  H19   C19  C20  C11     0.00   0.0  0
 PZD  CONST_38  H21   C21  C20  C11     0.00   0.0  0
 PZD  CONST_39  H17   C17  C18  C13   180.00   0.0  0
 PZD  CONST_40  H15   C15  C14  C13   180.00   0.0  0
 PZD  CONST_41  H22   C22  C14  C13   180.00   0.0  0
 PZD  CONST_42  H18   C18  C13  C14   180.00   0.0  0
 PZD  CONST_43  H16   C16  C15  C14   180.00   0.0  0
 PZD  Var_01    N1A   C7A  C4A  C3A  -148.41  30.0  1
 PZD  Var_02    C9A   N2A  C5A  C4A   -57.10  30.0  1
 PZD  Var_03    C8A   C9A  N2A  C5A    24.15  30.0  1
 PZD  Var_04    C11   C10  N1A  C7A  -166.55  30.0  1
 PZD  Var_05    C12   C11  C10  N1A     2.99  30.0  1
 PZD  Var_06    C10   C11  C12  C8A    -9.03  30.0  1
 PZD  Var_07    C19   C20  C11  C10    15.07  30.0  2
 PZD  Var_08    H24A  C24  O3A  C1A   -62.57  30.0  3
 PZD  Var_09    H23B  C23  O2A  C2A   -60.98  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
 PZD  chir_01  C8A  N1A  C9A  C12  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
 PZD  plan-1  C11  0.020
 PZD  plan-1  C13  0.020
 PZD  plan-1  C14  0.020
 PZD  plan-1  C15  0.020
 PZD  plan-1  C16  0.020
 PZD  plan-1  C17  0.020
 PZD  plan-1  C18  0.020
 PZD  plan-1  C19  0.020
 PZD  plan-1  C20  0.020
 PZD  plan-1  C21  0.020
 PZD  plan-1  C22  0.020
 PZD  plan-1  H22  0.020
 PZD  plan-1  H15  0.020
 PZD  plan-1  H17  0.020
 PZD  plan-1  H18  0.020
 PZD  plan-1  H21  0.020
 PZD  plan-1  H19  0.020
 PZD  plan-1  H16  0.020
 PZD  plan-2  C1A  0.020
 PZD  plan-2  C2A  0.020
 PZD  plan-2  C3A  0.020
 PZD  plan-2  C4A  0.020
 PZD  plan-2  C5A  0.020
 PZD  plan-2  C6A  0.020
 PZD  plan-2  C7A  0.020
 PZD  plan-2  O2A  0.020
 PZD  plan-2  O3A  0.020
 PZD  plan-2  N2A  0.020
 PZD  plan-2  H3A  0.020
 PZD  plan-2  H6A  0.020
 PZD  plan-3  C4A  0.020
 PZD  plan-3  C7A  0.020
 PZD  plan-3  N1A  0.020
 PZD  plan-3  C8A  0.020
 PZD  plan-3  C10  0.020
 PZD  plan-3  O1A  0.020

