# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 08:17:11 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3R)-N-(6-bromonaphthalen-2-yl)-3-hydroxy-1-propanoyl-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CC[C@@H](O)[C@H]1C(=O)Nc2ccc3cc(Br)ccc3c2
#
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
 BQD  BQD  (3R)-N-(6-bromonaphthalen-2-yl)-3-hydroxy-1-propanoyl-L-prolinamide  ligand  43  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BQD
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
 BQD  C10   C   CH2   0  -0.496   5.5204  -2.2244   0.5883
 BQD  C15   C   CR16  0  -0.431  -0.7830  -1.0478  -0.8767
 BQD  C17   C   CR16  0  -0.312  -3.1331  -1.7011  -1.2552
 BQD  C21   C   CR16  0  -0.279  -3.9879   0.5797   0.1196
 BQD  C22   C   CR66  0   0.103  -2.6035   0.3395  -0.0356
 BQD  C24   C   CR16  0  -0.303  -0.2931   0.9833   0.3292
 BQD  O01   O   O     0  -0.450   2.5387   0.7594   1.0440
 BQD  C02   C   C     0   0.567   2.5756  -0.0503   0.1437
 BQD  C03   C   CH1   0  -0.233   3.8610  -0.7472  -0.2911
 BQD  N04   N   NT    0  -0.480   5.0367  -0.0107   0.1091
 BQD  C05   C   C     0   0.571   5.2589   1.2259  -0.3770
 BQD  C06   C   CH2   0  -0.587   6.5096   1.9258   0.1063
 BQD  C07   C   CH3   0  -0.652   6.5961   3.3751  -0.3377
 BQD  O08   O   O     0  -0.504   4.4802   1.7391  -1.1700
 BQD  C09   C   CH2   0  -0.272   5.9329  -0.8025   0.9409
 BQD  C11   C   CH1   0   0.020   4.0111  -2.1149   0.4017
 BQD  O12   O   OH1   0  -0.663   3.3285  -2.0614   1.6315
 BQD  N13   N   NH1   0  -0.748   1.4968  -0.4651  -0.5699
 BQD  C14   C   CR6   0   0.393   0.1464  -0.1766  -0.3574
 BQD  C16   C   CR66  0   0.149  -2.1637  -0.8124  -0.7324
 BQD  C18   C   CR16  0  -0.231  -4.4691  -1.4606  -1.0968
 BQD  C19   C   CR6   0  -0.123  -4.8876  -0.3058  -0.4026
 BQD  BR    BR  BR    0  -0.046  -6.7393   0.0053  -0.2001
 BQD  C23   C   CR16  0  -0.303  -1.6301   1.2224   0.4820
 BQD  H102  H   HCH2  0   0.251   5.9869  -2.5236  -0.3525
 BQD  H101  H   HCH2  0   0.265   5.7980  -2.9563   1.3474
 BQD  H171  H   HCR6  0   0.267  -2.8086  -2.5878  -1.7856
 BQD  H211  H   HCR6  0   0.278  -4.3100   1.4671   0.6500
 BQD  H241  H   HCR6  0   0.282   0.4201   1.6869   0.7261
 BQD  H031  H   HCH1  0   0.298   3.8494  -0.8922  -1.3769
 BQD  H062  H   HCH2  0   0.263   6.5576   1.8589   1.1968
 BQD  H061  H   HCH2  0   0.269   7.3806   1.3708  -0.2567
 BQD  H073  H   HCH3  0   0.227   5.7583   3.9625   0.0372
 BQD  H1    H   HCH3  0   0.232   7.5128   3.8244   0.0429
 BQD  H072  H   HCH3  0   0.227   6.6094   3.4653  -1.4229
 BQD  H092  H   HCH2  0   0.244   5.7843  -0.5891   2.0029
 BQD  H091  H   HCH2  0   0.262   6.9763  -0.6073   0.7000
 BQD  H111  H   HCH1  0   0.251   3.6138  -2.9106  -0.2366
 BQD  H121  H   HOH1  0   0.461   3.3592  -2.9375   2.0291
 BQD  H131  H   HNH1  0   0.417   1.6691  -1.1708  -1.2713
 BQD  H181  H   HCR6  0   0.280  -5.1958  -2.1523  -1.5011
 BQD  H231  H   HCR6  0   0.264  -1.9532   2.1146   1.0038
 BQD  H151  H   HCR6  0   0.271  -0.4569  -1.9394  -1.4010

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
 BQD  O12  C11   single    1.408  0.020  1.408
 BQD  C10  C11   single    1.525  0.020  1.525
 BQD  C10  C09   single    1.522  0.020  1.522
 BQD  C11  C03   single    1.540  0.020  1.540
 BQD  C09  N04   single    1.457  0.020  1.457
 BQD  C03  C02   single    1.525  0.020  1.525
 BQD  C03  N04   single    1.444  0.020  1.444
 BQD  C24  C23   aromatic  1.367  0.020  1.367
 BQD  C24  C14   aromatic  1.418  0.020  1.418
 BQD  N13  C02   single    1.358  0.020  1.358
 BQD  N13  C14   single    1.397  0.020  1.397
 BQD  C02  O01   double    1.211  0.020  1.211
 BQD  N04  C05   single    1.347  0.020  1.347
 BQD  C23  C22   aromatic  1.412  0.020  1.412
 BQD  C14  C15   aromatic  1.376  0.020  1.376
 BQD  C22  C21   aromatic  1.414  0.020  1.414
 BQD  C22  C16   aromatic  1.416  0.020  1.416
 BQD  C15  C16   aromatic  1.408  0.020  1.408
 BQD  C21  C19   aromatic  1.366  0.020  1.366
 BQD  C16  C17   aromatic  1.415  0.020  1.415
 BQD  C19  BR    single    1.889  0.020  1.889
 BQD  C19  C18   aromatic  1.411  0.020  1.411
 BQD  C17  C18   aromatic  1.367  0.020  1.367
 BQD  C05  C06   single    1.513  0.020  1.513
 BQD  C05  O08   double    1.224  0.020  1.224
 BQD  C06  C07   single    1.518  0.020  1.518
 BQD  C10  H102  single    0.970  0.020  1.090
 BQD  C10  H101  single    0.970  0.020  1.090
 BQD  C15  H151  single    0.930  0.020  1.080
 BQD  C17  H171  single    0.930  0.020  1.080
 BQD  C21  H211  single    0.930  0.020  1.080
 BQD  C24  H241  single    0.930  0.020  1.080
 BQD  C03  H031  single    0.970  0.020  1.090
 BQD  C06  H062  single    0.970  0.020  1.090
 BQD  C06  H061  single    0.970  0.020  1.090
 BQD  C07  H073  single    0.970  0.020  1.090
 BQD  C07  H1    single    0.970  0.020  1.090
 BQD  C07  H072  single    0.970  0.020  1.090
 BQD  C09  H092  single    0.970  0.020  1.090
 BQD  C09  H091  single    0.970  0.020  1.090
 BQD  C11  H111  single    0.970  0.020  1.090
 BQD  O12  H121  single    0.850  0.020  0.980
 BQD  N13  H131  single    0.860  0.020  1.020
 BQD  C18  H181  single    0.930  0.020  1.080
 BQD  C23  H231  single    0.930  0.020  1.080

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
 BQD  H101  C10  H102  107.89  3.000
 BQD  H101  C10  C11   112.67  3.000
 BQD  H102  C10  C11   109.70  3.000
 BQD  H101  C10  C09   113.38  3.000
 BQD  H102  C10  C09   109.86  3.000
 BQD  C11   C10  C09   103.27  3.000
 BQD  H151  C15  C16   118.81  3.000
 BQD  H151  C15  C14   120.00  3.000
 BQD  C16   C15  C14   121.19  3.000
 BQD  H171  C17  C18   119.59  3.000
 BQD  H171  C17  C16   119.33  3.000
 BQD  C18   C17  C16   121.08  3.000
 BQD  H211  C21  C19   121.50  3.000
 BQD  H211  C21  C22   118.97  3.000
 BQD  C19   C21  C22   119.53  3.000
 BQD  C23   C22  C16   118.34  3.000
 BQD  C16   C22  C21   119.76  3.000
 BQD  C23   C22  C21   121.90  3.000
 BQD  H241  C24  C23   119.48  3.000
 BQD  H241  C24  C14   120.48  3.000
 BQD  C23   C24  C14   120.03  3.000
 BQD  N13   C02  C03   112.33  3.000
 BQD  N13   C02  O01   124.78  3.000
 BQD  C03   C02  O01   122.88  3.000
 BQD  H031  C03  C11   109.23  3.000
 BQD  H031  C03  N04   110.54  3.000
 BQD  C11   C03  N04   104.41  3.000
 BQD  H031  C03  C02   109.51  3.000
 BQD  N04   C03  C02   111.97  3.000
 BQD  C11   C03  C02   111.07  3.000
 BQD  C09   N04  C05   127.12  3.000
 BQD  C05   N04  C03   120.17  3.000
 BQD  C09   N04  C03   112.45  3.000
 BQD  O08   C05  C06   122.62  3.000
 BQD  O08   C05  N04   120.91  3.000
 BQD  C06   C05  N04   116.48  3.000
 BQD  H061  C06  H062  105.35  3.000
 BQD  H061  C06  C07   109.98  3.000
 BQD  H062  C06  C07   110.34  3.000
 BQD  H061  C06  C05   108.50  3.000
 BQD  H062  C06  C05   109.07  3.000
 BQD  C07   C06  C05   113.29  3.000
 BQD  H072  C07  H1    107.68  3.000
 BQD  H072  C07  H073  107.91  3.000
 BQD  H1    C07  H073  107.73  3.000
 BQD  H072  C07  C06   111.79  3.000
 BQD  H1    C07  C06   109.84  3.000
 BQD  H073  C07  C06   111.73  3.000
 BQD  H091  C09  H092  108.08  3.000
 BQD  H091  C09  N04   111.46  3.000
 BQD  H092  C09  N04   111.40  3.000
 BQD  H091  C09  C10   112.09  3.000
 BQD  H092  C09  C10   111.75  3.000
 BQD  N04   C09  C10   102.05  3.000
 BQD  H111  C11  O12   111.16  3.000
 BQD  H111  C11  C03   110.35  3.000
 BQD  O12   C11  C03   108.17  3.000
 BQD  H111  C11  C10   112.24  3.000
 BQD  C03   C11  C10   102.43  3.000
 BQD  O12   C11  C10   112.08  3.000
 BQD  H121  O12  C11   108.11  3.000
 BQD  H131  N13  C14   114.51  3.000
 BQD  H131  N13  C02   116.29  3.000
 BQD  C14   N13  C02   128.66  3.000
 BQD  N13   C14  C24   122.84  3.000
 BQD  N13   C14  C15   117.70  3.000
 BQD  C24   C14  C15   119.44  3.000
 BQD  C22   C16  C17   118.67  3.000
 BQD  C17   C16  C15   121.92  3.000
 BQD  C22   C16  C15   119.40  3.000
 BQD  H181  C18  C19   120.53  3.000
 BQD  H181  C18  C17   120.06  3.000
 BQD  C19   C18  C17   119.41  3.000
 BQD  BR    C19  C18   118.58  3.000
 BQD  C18   C19  C21   121.55  3.000
 BQD  BR    C19  C21   119.87  3.000
 BQD  H231  C23  C24   119.33  3.000
 BQD  H231  C23  C22   119.08  3.000
 BQD  C24   C23  C22   121.59  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
 BQD  CONST_01  C23   C24  C14  C15     0.00   0.0  0
 BQD  CONST_02  C23   C22  C16  C15     0.00   0.0  0
 BQD  CONST_03  C21   C22  C16  C15   180.00   0.0  0
 BQD  CONST_04  C18   C17  C16  C15   180.00   0.0  0
 BQD  CONST_05  C23   C22  C16  C17   180.00   0.0  0
 BQD  CONST_06  C21   C22  C16  C17     0.00   0.0  0
 BQD  CONST_07  C14   C15  C16  C17   180.00   0.0  0
 BQD  CONST_08  C21   C19  C18  C17     0.00   0.0  0
 BQD  CONST_09  C24   C23  C22  C21   180.00   0.0  0
 BQD  CONST_10  C14   C24  C23  C22     0.00   0.0  0
 BQD  CONST_11  C18   C19  C21  C22     0.00   0.0  0
 BQD  CONST_12  C14   C15  C16  C22     0.00   0.0  0
 BQD  CONST_13  C18   C17  C16  C22     0.00   0.0  0
 BQD  CONST_14  C16   C22  C23  C24     0.00   0.0  0
 BQD  CONST_15  C16   C15  C14  C24     0.00   0.0  0
 BQD  CONST_16  C19   C21  C22  C16     0.00   0.0  0
 BQD  CONST_17  C19   C18  C17  C16     0.00   0.0  0
 BQD  CONST_18  C23   C22  C21  C19   180.00   0.0  0
 BQD  CONST_19  BR    C19  C18  C17   180.00   0.0  0
 BQD  CONST_20  BR    C19  C21  C22   180.00   0.0  0
 BQD  CONST_21  C23   C24  C14  N13   180.00   0.0  0
 BQD  CONST_22  C16   C15  C14  N13   180.00   0.0  0
 BQD  CONST_23  H241  C24  C14  C15   180.00   0.0  0
 BQD  CONST_24  H171  C17  C16  C15     0.00   0.0  0
 BQD  CONST_25  H151  C15  C16  C17     0.00   0.0  0
 BQD  CONST_26  H231  C23  C22  C21     0.00   0.0  0
 BQD  CONST_27  H181  C18  C19  C21   180.00   0.0  0
 BQD  CONST_28  H211  C21  C22  C16   180.00   0.0  0
 BQD  CONST_29  C14   N13  C02  C03   180.00   0.0  0
 BQD  CONST_30  C06   C05  N04  C03   180.00   0.0  0
 BQD  CONST_31  O08   C05  N04  C03     0.00   0.0  0
 BQD  CONST_32  C09   N04  C05  C06     0.00   0.0  0
 BQD  CONST_33  C09   N04  C05  O08   180.00   0.0  0
 BQD  CONST_36  H131  N13  C14  C15     0.00   0.0  0
 BQD  CONST_37  C14   N13  C02  O01     0.00   0.0  0
 BQD  Var_01    C03   N04  C09  C10    21.45  30.0  1
 BQD  Var_02    C11   C10  C09  N04   -36.43  30.0  1
 BQD  Var_03    C07   C06  C05  N04  -172.37  30.0  3
 BQD  Var_04    H073  C07  C06  C05    60.30  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
 BQD  chir_01  C03  C11  C02  N04  negativ
 BQD  chir_02  C11  O12  C03  C10  negativ

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
 BQD  plan-1  C15   0.020
 BQD  plan-1  C17   0.020
 BQD  plan-1  C21   0.020
 BQD  plan-1  C22   0.020
 BQD  plan-1  C24   0.020
 BQD  plan-1  N13   0.020
 BQD  plan-1  C14   0.020
 BQD  plan-1  C16   0.020
 BQD  plan-1  C18   0.020
 BQD  plan-1  C19   0.020
 BQD  plan-1  BR    0.020
 BQD  plan-1  C23   0.020
 BQD  plan-1  H171  0.020
 BQD  plan-1  H211  0.020
 BQD  plan-1  H241  0.020
 BQD  plan-1  H181  0.020
 BQD  plan-1  H231  0.020
 BQD  plan-1  H151  0.020
 BQD  plan-2  C03   0.020
 BQD  plan-2  N04   0.020
 BQD  plan-2  C05   0.020
 BQD  plan-2  C06   0.020
 BQD  plan-2  O08   0.020
 BQD  plan-2  C09   0.020
 BQD  plan-3  O01   0.020
 BQD  plan-3  C02   0.020
 BQD  plan-3  C03   0.020
 BQD  plan-3  N13   0.020
 BQD  plan-3  C14   0.020
 BQD  plan-3  H131  0.020

