# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:42:28 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-[(7S)-7-hydroxy-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-7-yl]-N-methylnaphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccc2cc(ccc2c1)[C@@]3(O)CCn4cncc34
#
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
 7D6  7D6  6-[(7S)-7-hydroxy-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-7-yl]-N-methylnaphthalene-2-carboxamide  ligand  40  23  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7D6
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
 7D6  C10   C  CR16  0  -0.299   0.6682   2.1426   0.1905
 7D6  N12   N  NH1   0  -0.643   5.8069  -1.0380  -0.3333
 7D6  C15   C  CH2   0  -0.464  -3.3535   0.8502  -1.5677
 7D6  C21   C  CR15  0  -0.275  -3.5477  -1.4074   1.3572
 7D6  C22   C  CH3   0  -0.514   7.2508  -1.0360  -0.3350
 7D6  C01   C  CR6   0  -0.036   3.6051  -0.1459   0.1004
 7D6  C02   C  CR16  0  -0.297   2.9426  -1.3915  -0.0297
 7D6  C03   C  CR16  0  -0.300   1.5789  -1.4542  -0.0837
 7D6  C04   C  CR66  0   0.148   0.7955  -0.2787  -0.0167
 7D6  C05   C  CR66  0   0.129   1.4527   0.9689   0.1190
 7D6  C06   C  CR16  0  -0.339   2.8613   1.0042   0.1847
 7D6  C07   C  CR16  0  -0.380  -0.6153  -0.3152  -0.0695
 7D6  C08   C  CR6   0   0.090  -1.3600   0.8334   0.0094
 7D6  C09   C  CR16  0  -0.296  -0.6959   2.0772   0.1380
 7D6  C11   C  C     0   0.534   5.0948  -0.0226   0.1739
 7D6  O13   O  O     0  -0.494   5.6260   0.9647   0.6688
 7D6  C14   C  CR5   0   0.045  -2.8714   0.8035  -0.0960
 7D6  C16   C  CH2   0  -0.282  -4.7116   0.1367  -1.5771
 7D6  N17   N  N     0  -0.452  -4.5536  -0.7805  -0.4634
 7D6  C18   C  CR55  0   0.373  -3.5186  -0.4713   0.3609
 7D6  C19   C  CR15  0   0.091  -5.1737  -1.8629   0.0335
 7D6  N20   N  N     0  -0.455  -4.5838  -2.2719   1.1359
 7D6  O23   O  OH1   0  -0.650  -3.4640   1.9081   0.5576
 7D6  H101  H  HCR6  0   0.257   1.1620   3.1013   0.2926
 7D6  H121  H  HNH1  0   0.411   5.3425  -1.7786  -0.8295
 7D6  H152  H  HCH2  0   0.274  -3.4093   1.8718  -1.9425
 7D6  H151  H  HCH2  0   0.271  -2.6490   0.3000  -2.1920
 7D6  H211  H  HCR5  0   0.256  -2.8839  -1.5147   2.2016
 7D6  H221  H  HCH3  0   0.238   7.6580  -0.2665  -0.9929
 7D6  H222  H  HCH3  0   0.242   7.6452  -0.8724   0.6671
 7D6  H223  H  HCH3  0   0.252   7.5949  -2.0047  -0.6850
 7D6  H021  H  HCR6  0   0.258   3.5045  -2.3162  -0.0597
 7D6  H031  H  HCR6  0   0.261   1.0844  -2.4136  -0.1730
 7D6  H061  H  HCR6  0   0.258   3.3562   1.9608   0.2981
 7D6  H071  H  HCR6  0   0.255  -1.1035  -1.2771  -0.1761
 7D6  H091  H  HCR6  0   0.259  -1.2746   2.9888   0.1981
 7D6  H161  H  HCH2  0   0.269  -5.5428   0.8176  -1.3928
 7D6  H162  H  HCH2  0   0.275  -4.9003  -0.3984  -2.5054
 7D6  H191  H  HCR5  0   0.280  -6.0299  -2.3211  -0.4368
 7D6  H231  H  HOH1  0   0.451  -3.3142   1.8241   1.5063

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
 7D6  C19  N20   aromatic  1.315  0.020  1.315
 7D6  C19  N17   aromatic  1.343  0.020  1.343
 7D6  N20  C21   aromatic  1.367  0.020  1.367
 7D6  N17  C16   single    1.451  0.020  1.451
 7D6  N17  C18   aromatic  1.359  0.020  1.359
 7D6  C16  C15   single    1.534  0.020  1.534
 7D6  C21  C18   aromatic  1.367  0.020  1.367
 7D6  C18  C14   single    1.501  0.020  1.501
 7D6  O23  C14   single    1.414  0.020  1.414
 7D6  C15  C14   single    1.549  0.020  1.549
 7D6  C14  C08   single    1.515  0.020  1.515
 7D6  C08  C07   aromatic  1.371  0.020  1.371
 7D6  C08  C09   aromatic  1.416  0.020  1.416
 7D6  C07  C04   aromatic  1.412  0.020  1.412
 7D6  C09  C10   aromatic  1.367  0.020  1.367
 7D6  C04  C03   aromatic  1.414  0.020  1.414
 7D6  C04  C05   aromatic  1.417  0.020  1.417
 7D6  C10  C05   aromatic  1.413  0.020  1.413
 7D6  C03  C02   aromatic  1.366  0.020  1.366
 7D6  C05  C06   aromatic  1.411  0.020  1.411
 7D6  C02  C01   aromatic  1.417  0.020  1.417
 7D6  C06  C01   aromatic  1.372  0.020  1.372
 7D6  C01  C11   single    1.497  0.020  1.497
 7D6  C11  O13   double    1.226  0.020  1.226
 7D6  C11  N12   single    1.340  0.020  1.340
 7D6  N12  C22   single    1.444  0.020  1.444
 7D6  C10  H101  single    0.930  0.020  1.080
 7D6  N12  H121  single    0.860  0.020  1.020
 7D6  C15  H152  single    0.970  0.020  1.090
 7D6  C15  H151  single    0.970  0.020  1.090
 7D6  C21  H211  single    0.930  0.020  1.080
 7D6  C22  H221  single    0.970  0.020  1.090
 7D6  C22  H222  single    0.970  0.020  1.090
 7D6  C22  H223  single    0.970  0.020  1.090
 7D6  C02  H021  single    0.930  0.020  1.080
 7D6  C03  H031  single    0.930  0.020  1.080
 7D6  C06  H061  single    0.930  0.020  1.080
 7D6  C07  H071  single    0.930  0.020  1.080
 7D6  C09  H091  single    0.930  0.020  1.080
 7D6  C16  H161  single    0.970  0.020  1.090
 7D6  C16  H162  single    0.970  0.020  1.090
 7D6  C19  H191  single    0.930  0.020  1.080
 7D6  O23  H231  single    0.850  0.020  0.980

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
 7D6  H101  C10  C09   120.06  3.000
 7D6  H101  C10  C05   119.12  3.000
 7D6  C09   C10  C05   120.81  3.000
 7D6  H121  N12  C11   119.97  3.000
 7D6  H121  N12  C22   117.55  3.000
 7D6  C11   N12  C22   122.06  3.000
 7D6  H151  C15  H152  108.01  3.000
 7D6  H151  C15  C16   109.50  3.000
 7D6  H152  C15  C16   112.87  3.000
 7D6  H151  C15  C14   109.12  3.000
 7D6  H152  C15  C14   111.77  3.000
 7D6  C16   C15  C14   105.51  3.000
 7D6  H211  C21  N20   121.98  3.000
 7D6  H211  C21  C18   128.68  3.000
 7D6  N20   C21  C18   109.33  3.000
 7D6  H223  C22  H222  108.40  3.000
 7D6  H223  C22  H221  108.45  3.000
 7D6  H222  C22  H221  108.27  3.000
 7D6  H223  C22  N12   108.42  3.000
 7D6  H222  C22  N12   111.18  3.000
 7D6  H221  C22  N12   112.02  3.000
 7D6  C11   C01  C06   117.87  3.000
 7D6  C11   C01  C02   122.85  3.000
 7D6  C06   C01  C02   119.28  3.000
 7D6  H021  C02  C03   118.55  3.000
 7D6  H021  C02  C01   120.72  3.000
 7D6  C03   C02  C01   120.71  3.000
 7D6  H031  C03  C04   119.17  3.000
 7D6  H031  C03  C02   119.97  3.000
 7D6  C04   C03  C02   120.86  3.000
 7D6  C07   C04  C05   119.33  3.000
 7D6  C05   C04  C03   118.66  3.000
 7D6  C07   C04  C03   122.01  3.000
 7D6  C06   C05  C04   119.32  3.000
 7D6  C06   C05  C10   122.08  3.000
 7D6  C04   C05  C10   118.60  3.000
 7D6  H061  C06  C05   118.90  3.000
 7D6  H061  C06  C01   119.94  3.000
 7D6  C05   C06  C01   121.16  3.000
 7D6  H071  C07  C08   120.29  3.000
 7D6  H071  C07  C04   118.46  3.000
 7D6  C08   C07  C04   121.25  3.000
 7D6  C14   C08  C09   119.44  3.000
 7D6  C09   C08  C07   119.10  3.000
 7D6  C14   C08  C07   121.41  3.000
 7D6  H091  C09  C08   119.64  3.000
 7D6  H091  C09  C10   119.45  3.000
 7D6  C08   C09  C10   120.91  3.000
 7D6  O13   C11  C01   121.17  3.000
 7D6  O13   C11  N12   122.21  3.000
 7D6  C01   C11  N12   116.62  3.000
 7D6  O23   C14  C18   110.01  3.000
 7D6  O23   C14  C08   111.75  3.000
 7D6  C18   C14  C08   115.20  3.000
 7D6  C08   C14  C15   112.08  3.000
 7D6  O23   C14  C15   106.57  3.000
 7D6  C18   C14  C15   100.40  3.000
 7D6  H162  C16  H161  108.62  3.000
 7D6  H162  C16  N17   111.27  3.000
 7D6  H161  C16  N17   110.36  3.000
 7D6  H162  C16  C15   112.80  3.000
 7D6  H161  C16  C15   112.55  3.000
 7D6  N17   C16  C15   101.11  3.000
 7D6  C19   N17  C18   108.10  3.000
 7D6  C18   N17  C16   113.87  3.000
 7D6  C19   N17  C16   138.00  3.000
 7D6  N17   C18  C14   109.70  3.000
 7D6  C14   C18  C21   144.33  3.000
 7D6  N17   C18  C21   105.67  3.000
 7D6  H191  C19  N20   126.10  3.000
 7D6  H191  C19  N17   123.19  3.000
 7D6  N20   C19  N17   110.71  3.000
 7D6  C19   N20  C21   106.19  3.000
 7D6  H231  O23  C14   108.77  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
 7D6  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 7D6  CONST_02  C07   C04  C05  C10     0.00   0.0  0
 7D6  CONST_03  C03   C04  C05  C10   180.00   0.0  0
 7D6  CONST_04  C01   C06  C05  C10   180.00   0.0  0
 7D6  CONST_05  N17   C19  N20  C21     0.00   0.0  0
 7D6  CONST_06  C19   N17  C18  C21     0.00   0.0  0
 7D6  CONST_07  C04   C03  C02  C01     0.00   0.0  0
 7D6  CONST_08  C04   C05  C06  C01     0.00   0.0  0
 7D6  CONST_09  C07   C04  C03  C02   180.00   0.0  0
 7D6  CONST_10  C05   C04  C03  C02     0.00   0.0  0
 7D6  CONST_11  C05   C06  C01  C02     0.00   0.0  0
 7D6  CONST_12  C08   C07  C04  C03   180.00   0.0  0
 7D6  CONST_13  C06   C05  C04  C03     0.00   0.0  0
 7D6  CONST_14  C06   C01  C02  C03     0.00   0.0  0
 7D6  CONST_15  C09   C08  C07  C04     0.00   0.0  0
 7D6  CONST_16  C09   C10  C05  C04     0.00   0.0  0
 7D6  CONST_17  C08   C07  C04  C05     0.00   0.0  0
 7D6  CONST_18  C08   C09  C10  C05     0.00   0.0  0
 7D6  CONST_19  C07   C04  C05  C06   180.00   0.0  0
 7D6  CONST_20  C09   C10  C05  C06   180.00   0.0  0
 7D6  CONST_21  N20   C21  C18  N17     0.00   0.0  0
 7D6  CONST_22  N20   C19  N17  C18     0.00   0.0  0
 7D6  CONST_23  C19   N20  C21  C18     0.00   0.0  0
 7D6  CONST_24  C14   C08  C09  C10   180.00   0.0  0
 7D6  CONST_25  C14   C08  C07  C04   180.00   0.0  0
 7D6  CONST_26  C11   C01  C02  C03   180.00   0.0  0
 7D6  CONST_27  C11   C01  C06  C05   180.00   0.0  0
 7D6  CONST_28  H061  C06  C05  C10     0.00   0.0  0
 7D6  CONST_29  H191  C19  N20  C21   180.00   0.0  0
 7D6  CONST_30  H031  C03  C02  C01   180.00   0.0  0
 7D6  CONST_31  H071  C07  C04  C03     0.00   0.0  0
 7D6  CONST_32  H021  C02  C03  C04   180.00   0.0  0
 7D6  CONST_33  H101  C10  C05  C04   180.00   0.0  0
 7D6  CONST_34  H091  C09  C10  C05   180.00   0.0  0
 7D6  CONST_35  H211  C21  C18  C14     0.00   0.0  0
 7D6  CONST_36  C01   C11  N12  C22   180.00   0.0  0
 7D6  CONST_37  H121  N12  C11  C01     0.00   0.0  0
 7D6  CONST_38  O13   C11  N12  C22     0.00   0.0  0
 7D6  Var_01    C19   N17  C16  C15  -166.37  30.0  1
 7D6  Var_02    N17   C16  C15  C14   -28.20  30.0  1
 7D6  Var_03    C02   C01  C11  N12    22.20  30.0  2
 7D6  Var_04    H221  C22  N12  C11   -67.01  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
 7D6  chir_01  C14  C18  C15  C08  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
 7D6  plan-1  C10   0.020
 7D6  plan-1  C01   0.020
 7D6  plan-1  C02   0.020
 7D6  plan-1  C03   0.020
 7D6  plan-1  C04   0.020
 7D6  plan-1  C05   0.020
 7D6  plan-1  C06   0.020
 7D6  plan-1  C07   0.020
 7D6  plan-1  C08   0.020
 7D6  plan-1  C09   0.020
 7D6  plan-1  C11   0.020
 7D6  plan-1  C14   0.020
 7D6  plan-1  H101  0.020
 7D6  plan-1  H021  0.020
 7D6  plan-1  H031  0.020
 7D6  plan-1  H061  0.020
 7D6  plan-1  H071  0.020
 7D6  plan-1  H091  0.020
 7D6  plan-2  C21   0.020
 7D6  plan-2  C14   0.020
 7D6  plan-2  C16   0.020
 7D6  plan-2  N17   0.020
 7D6  plan-2  C18   0.020
 7D6  plan-2  C19   0.020
 7D6  plan-2  N20   0.020
 7D6  plan-2  H211  0.020
 7D6  plan-2  H191  0.020
 7D6  plan-3  N12   0.020
 7D6  plan-3  C22   0.020
 7D6  plan-3  C01   0.020
 7D6  plan-3  C11   0.020
 7D6  plan-3  O13   0.020
 7D6  plan-3  H121  0.020

