# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:47:19 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-[(7R)-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
 6D7  6D7  6-[(7R)-7-hydroxy-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-7-yl]-N-methylnaphthalene-2-carboxamide  ligand  40  23  .  2022-07-23  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_6D7
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
 6D7  C11   C  CR5   0   0.046   2.8667   0.8237  -0.1202
 6D7  C13   C  CH2   0  -0.464   3.3340   0.8574  -1.5969
 6D7  C14   C  CH2   0  -0.282   4.6896   0.1390  -1.6157
 6D7  C21   C  CR16  0  -0.299  -0.6722   2.1577   0.2138
 6D7  C22   C  CR66  0   0.129  -1.4557   0.9839   0.1351
 6D7  C23   C  CR16  0  -0.339  -2.8641   1.0166   0.2102
 6D7  C10   C  CR6   0   0.089   1.3561   0.8537   0.0006
 6D7  C16   C  CR15  0   0.091   5.1673  -1.8438   0.0108
 6D7  C18   C  CR15  0  -0.274   3.5568  -1.3726   1.3477
 6D7  C19   C  CR55  0   0.371   3.5167  -0.4477   0.3413
 6D7  C20   C  CR16  0  -0.296   0.6916   2.0950   0.1484
 6D7  C01   C  CH3   0  -0.513  -7.2503  -1.0160  -0.3380
 6D7  N02   N  NH1   0  -0.642  -5.8062  -1.0112  -0.3481
 6D7  O04   O  O     0  -0.494  -5.6284   0.9506   0.7318
 6D7  C05   C  CR6   0  -0.034  -3.6063  -0.1338   0.1167
 6D7  C06   C  CR16  0  -0.296  -2.9435  -1.3771  -0.0299
 6D7  C07   C  CR16  0  -0.300  -1.5801  -1.4373  -0.0922
 6D7  C08   C  CR66  0   0.148  -0.7980  -0.2613  -0.0184
 6D7  C09   C  CR16  0  -0.380   0.6122  -0.2952  -0.0825
 6D7  O12   O  OH1   0  -0.650   3.4665   1.9333   0.5183
 6D7  N15   N  N     0  -0.452   4.5426  -0.7665  -0.4907
 6D7  N17   N  N     0  -0.455   4.5896  -2.2401   1.1243
 6D7  H132  H  HCH2  0   0.271   2.6216   0.3052  -2.2103
 6D7  H131  H  HCH2  0   0.274   3.3891   1.8759  -1.9800
 6D7  H141  H  HCH2  0   0.275   4.8638  -0.4065  -2.5408
 6D7  H142  H  HCH2  0   0.269   5.5261   0.8177  -1.4487
 6D7  H211  H  HCR6  0   0.257  -1.1664   3.1142   0.3329
 6D7  H231  H  HCR6  0   0.258  -3.3586   1.9714   0.3374
 6D7  H161  H  HCR5  0   0.280   6.0193  -2.3063  -0.4630
 6D7  H181  H  HCR5  0   0.255   2.9010  -1.4704   2.1996
 6D7  H201  H  HCR6  0   0.259   1.2697   3.0065   0.2136
 6D7  H013  H  HCH3  0   0.241  -7.6399  -0.9796   0.6792
 6D7  H011  H  HCH3  0   0.238  -7.6635  -0.1733  -0.8937
 6D7  H012  H  HCH3  0   0.251  -7.5921  -1.9359  -0.8030
 6D7  H021  H  HNH1  0   0.411  -5.3401  -1.7407  -0.8595
 6D7  H061  H  HCR6  0   0.258  -3.5057  -2.3013  -0.0665
 6D7  H071  H  HCR6  0   0.261  -1.0843  -2.3947  -0.1953
 6D7  H091  H  HCR6  0   0.255   1.1007  -1.2555  -0.2016
 6D7  H121  H  HOH1  0   0.451   3.3341   1.8523   1.4698
 6D7  C03   C  C     0   0.531  -5.0956  -0.0158   0.1987

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
 6D7  N17  C16   aromatic  1.316  0.020  1.316
 6D7  N17  C18   aromatic  1.367  0.020  1.367
 6D7  C16  N15   aromatic  1.343  0.020  1.343
 6D7  C18  C19   aromatic  1.367  0.020  1.367
 6D7  N15  C19   aromatic  1.359  0.020  1.359
 6D7  N15  C14   single    1.452  0.020  1.452
 6D7  C19  C11   single    1.501  0.020  1.501
 6D7  C14  C13   single    1.534  0.020  1.534
 6D7  C20  C21   aromatic  1.367  0.020  1.367
 6D7  C20  C10   aromatic  1.416  0.020  1.416
 6D7  C21  C22   aromatic  1.413  0.020  1.413
 6D7  C11  C10   single    1.516  0.020  1.516
 6D7  C11  C13   single    1.549  0.020  1.549
 6D7  C11  O12   single    1.414  0.020  1.414
 6D7  C10  C09   aromatic  1.371  0.020  1.371
 6D7  C22  C23   aromatic  1.411  0.020  1.411
 6D7  C22  C08   aromatic  1.417  0.020  1.417
 6D7  C23  C05   aromatic  1.372  0.020  1.372
 6D7  O04  C03   double    1.226  0.020  1.226
 6D7  C09  C08   aromatic  1.412  0.020  1.412
 6D7  C08  C07   aromatic  1.414  0.020  1.414
 6D7  C05  C03   single    1.496  0.020  1.496
 6D7  C05  C06   aromatic  1.417  0.020  1.417
 6D7  C03  N02   single    1.340  0.020  1.340
 6D7  C07  C06   aromatic  1.366  0.020  1.366
 6D7  N02  C01   single    1.444  0.020  1.444
 6D7  C13  H132  single    0.970  0.020  1.090
 6D7  C13  H131  single    0.970  0.020  1.090
 6D7  C14  H141  single    0.970  0.020  1.090
 6D7  C14  H142  single    0.970  0.020  1.090
 6D7  C21  H211  single    0.930  0.020  1.080
 6D7  C23  H231  single    0.930  0.020  1.080
 6D7  C16  H161  single    0.930  0.020  1.080
 6D7  C18  H181  single    0.930  0.020  1.080
 6D7  C20  H201  single    0.930  0.020  1.080
 6D7  C01  H013  single    0.970  0.020  1.090
 6D7  C01  H011  single    0.970  0.020  1.090
 6D7  C01  H012  single    0.970  0.020  1.090
 6D7  N02  H021  single    0.860  0.020  1.020
 6D7  C06  H061  single    0.930  0.020  1.080
 6D7  C07  H071  single    0.930  0.020  1.080
 6D7  C09  H091  single    0.930  0.020  1.080
 6D7  O12  H121  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
 6D7  O12   C11  C19   110.01  3.000
 6D7  O12   C11  C10   111.80  3.000
 6D7  C19   C11  C10   115.09  3.000
 6D7  O12   C11  C13   106.59  3.000
 6D7  C10   C11  C13   112.10  3.000
 6D7  C19   C11  C13   100.42  3.000
 6D7  H131  C13  H132  107.98  3.000
 6D7  H131  C13  C14   112.87  3.000
 6D7  H132  C13  C14   109.47  3.000
 6D7  H131  C13  C11   111.76  3.000
 6D7  H132  C13  C11   109.16  3.000
 6D7  C14   C13  C11   105.55  3.000
 6D7  H142  C14  H141  108.64  3.000
 6D7  H142  C14  N15   110.32  3.000
 6D7  H141  C14  N15   111.25  3.000
 6D7  H142  C14  C13   112.62  3.000
 6D7  H141  C14  C13   112.74  3.000
 6D7  N15   C14  C13   101.13  3.000
 6D7  H211  C21  C20   120.06  3.000
 6D7  H211  C21  C22   119.12  3.000
 6D7  C20   C21  C22   120.82  3.000
 6D7  C08   C22  C23   119.32  3.000
 6D7  C08   C22  C21   118.60  3.000
 6D7  C23   C22  C21   122.08  3.000
 6D7  H231  C23  C05   120.02  3.000
 6D7  H231  C23  C22   118.86  3.000
 6D7  C05   C23  C22   121.13  3.000
 6D7  C09   C10  C20   119.10  3.000
 6D7  C09   C10  C11   121.28  3.000
 6D7  C20   C10  C11   119.57  3.000
 6D7  H161  C16  N17   126.11  3.000
 6D7  H161  C16  N15   123.18  3.000
 6D7  N17   C16  N15   110.71  3.000
 6D7  H181  C18  N17   122.04  3.000
 6D7  H181  C18  C19   128.62  3.000
 6D7  N17   C18  C19   109.33  3.000
 6D7  N15   C19  C18   105.65  3.000
 6D7  N15   C19  C11   109.72  3.000
 6D7  C18   C19  C11   144.30  3.000
 6D7  H201  C20  C10   119.63  3.000
 6D7  H201  C20  C21   119.47  3.000
 6D7  C10   C20  C21   120.90  3.000
 6D7  H012  C01  H011  108.48  3.000
 6D7  H012  C01  H013  108.38  3.000
 6D7  H011  C01  H013  108.32  3.000
 6D7  H012  C01  N02   108.33  3.000
 6D7  H011  C01  N02   111.88  3.000
 6D7  H013  C01  N02   111.34  3.000
 6D7  H021  N02  C03   120.06  3.000
 6D7  H021  N02  C01   117.69  3.000
 6D7  C03   N02  C01   122.01  3.000
 6D7  C06   C05  C03   122.72  3.000
 6D7  C06   C05  C23   119.33  3.000
 6D7  C03   C05  C23   117.94  3.000
 6D7  H061  C06  C07   118.63  3.000
 6D7  H061  C06  C05   120.66  3.000
 6D7  C07   C06  C05   120.69  3.000
 6D7  H071  C07  C08   119.13  3.000
 6D7  H071  C07  C06   120.01  3.000
 6D7  C08   C07  C06   120.85  3.000
 6D7  C09   C08  C07   122.00  3.000
 6D7  C07   C08  C22   118.68  3.000
 6D7  C09   C08  C22   119.32  3.000
 6D7  H091  C09  C08   118.44  3.000
 6D7  H091  C09  C10   120.30  3.000
 6D7  C08   C09  C10   121.26  3.000
 6D7  H121  O12  C11   108.76  3.000
 6D7  C19   N15  C16   108.11  3.000
 6D7  C19   N15  C14   113.87  3.000
 6D7  C16   N15  C14   137.99  3.000
 6D7  C18   N17  C16   106.20  3.000
 6D7  C05   C03  O04   121.24  3.000
 6D7  C05   C03  N02   116.55  3.000
 6D7  O04   C03  N02   122.20  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
 6D7  CONST_01  C09   C10  C20  C21    0.00   0.0  0
 6D7  CONST_02  C05   C23  C22  C21  180.00   0.0  0
 6D7  CONST_03  C09   C08  C22  C21    0.00   0.0  0
 6D7  CONST_04  C07   C08  C22  C21  180.00   0.0  0
 6D7  CONST_05  C10   C20  C21  C22    0.00   0.0  0
 6D7  CONST_06  C06   C05  C23  C22    0.00   0.0  0
 6D7  CONST_07  C10   C09  C08  C22    0.00   0.0  0
 6D7  CONST_08  C06   C07  C08  C22    0.00   0.0  0
 6D7  CONST_09  C20   C21  C22  C23  180.00   0.0  0
 6D7  CONST_10  C09   C08  C22  C23  180.00   0.0  0
 6D7  CONST_11  C07   C08  C22  C23    0.00   0.0  0
 6D7  CONST_12  C07   C06  C05  C23    0.00   0.0  0
 6D7  CONST_13  C07   C08  C09  C10  180.00   0.0  0
 6D7  CONST_14  C19   C18  N17  C16    0.00   0.0  0
 6D7  CONST_15  C18   C19  N15  C16    0.00   0.0  0
 6D7  CONST_16  N15   C16  N17  C18    0.00   0.0  0
 6D7  CONST_17  N17   C16  N15  C19    0.00   0.0  0
 6D7  CONST_18  C08   C22  C21  C20    0.00   0.0  0
 6D7  CONST_19  C08   C09  C10  C20    0.00   0.0  0
 6D7  CONST_20  C08   C22  C23  C05    0.00   0.0  0
 6D7  CONST_21  C08   C07  C06  C05    0.00   0.0  0
 6D7  CONST_22  C09   C08  C07  C06  180.00   0.0  0
 6D7  CONST_23  N17   C18  C19  N15    0.00   0.0  0
 6D7  CONST_24  C21   C20  C10  C11  180.00   0.0  0
 6D7  CONST_25  C08   C09  C10  C11  180.00   0.0  0
 6D7  CONST_26  C03   C05  C23  C22  180.00   0.0  0
 6D7  CONST_27  C07   C06  C05  C03  180.00   0.0  0
 6D7  CONST_28  H181  C18  C19  C11    0.00   0.0  0
 6D7  CONST_29  H201  C20  C10  C11    0.00   0.0  0
 6D7  CONST_30  H091  C09  C10  C11    0.00   0.0  0
 6D7  CONST_31  H161  C16  N15  C14    0.00   0.0  0
 6D7  CONST_32  H231  C23  C22  C21    0.00   0.0  0
 6D7  CONST_33  H071  C07  C08  C22  180.00   0.0  0
 6D7  CONST_34  H211  C21  C22  C23    0.00   0.0  0
 6D7  CONST_35  H061  C06  C05  C23  180.00   0.0  0
 6D7  CONST_36  C05   C03  N02  C01  180.00   0.0  0
 6D7  CONST_37  H021  N02  C03  C05    0.00   0.0  0
 6D7  CONST_38  O04   C03  N02  C01    0.00   0.0  0
 6D7  Var_01    N15   C14  C13  C11   28.01  30.0  1
 6D7  Var_02    C16   N15  C14  C13  166.57  30.0  1
 6D7  Var_03    O04   C03  C05  C23  -22.33  30.0  2
 6D7  Var_04    H013  C01  N02  C03  -58.81  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
 6D7  chir_01  C11  C10  C13  C19  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
 6D7  plan-1  C11   0.020
 6D7  plan-1  C21   0.020
 6D7  plan-1  C22   0.020
 6D7  plan-1  C23   0.020
 6D7  plan-1  C10   0.020
 6D7  plan-1  C20   0.020
 6D7  plan-1  C05   0.020
 6D7  plan-1  C06   0.020
 6D7  plan-1  C07   0.020
 6D7  plan-1  C08   0.020
 6D7  plan-1  C09   0.020
 6D7  plan-1  H211  0.020
 6D7  plan-1  H231  0.020
 6D7  plan-1  H201  0.020
 6D7  plan-1  H061  0.020
 6D7  plan-1  H071  0.020
 6D7  plan-1  H091  0.020
 6D7  plan-1  C03   0.020
 6D7  plan-2  C11   0.020
 6D7  plan-2  C14   0.020
 6D7  plan-2  C16   0.020
 6D7  plan-2  C18   0.020
 6D7  plan-2  C19   0.020
 6D7  plan-2  N15   0.020
 6D7  plan-2  N17   0.020
 6D7  plan-2  H161  0.020
 6D7  plan-2  H181  0.020
 6D7  plan-3  C01   0.020
 6D7  plan-3  N02   0.020
 6D7  plan-3  O04   0.020
 6D7  plan-3  C05   0.020
 6D7  plan-3  H021  0.020
 6D7  plan-3  C03   0.020

