# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:15:59 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S},6~{S})-3-[(3-bromanyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@@H]2NC(=O)[C@H](Cc3ccc(O)c(Br)c3)NC2=O)cc1
#
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
 Q47  Q47  (3~{S},6~{S})-3-[(3-bromanyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione  ligand  42  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q47
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
 Q47  C02  C   CR6   0   0.398   -6.9381  18.3759  269.2543
 Q47  C03  C   CR16  0  -0.309   -6.9434  17.2358  268.4510
 Q47  C04  C   CR16  0  -0.255   -6.5755  17.2987  267.1221
 Q47  C05  C   CR6   0   0.102   -6.1837  18.5000  266.5333
 Q47  C06  C   CH2   0  -0.510   -5.8102  18.5624  265.0813
 Q47  C07  C   CH1   0  -0.177   -6.9900  18.9210  264.1600
 Q47  C08  C   C     0   0.546   -8.0892  17.8857  264.2702
 Q47  C10  C   CH1   0  -0.174   -9.6106  19.5915  265.2856
 Q47  C11  C   CH2   0  -0.511   -9.8672  19.5375  266.8025
 Q47  C12  C   CR6   0   0.095  -10.9719  18.5783  267.1425
 Q47  C13  C   CR16  0  -0.258  -12.3055  18.9593  267.0299
 Q47  C14  C   CR16  0  -0.335  -13.3349  18.0749  267.3073
 Q47  C15  C   CR6   0   0.351  -13.0432  16.7751  267.7058
 Q47  C17  C   CR16  0  -0.292  -11.7178  16.3729  267.8196
 Q47  C18  C   CR16  0  -0.290  -10.7007  17.2708  267.5381
 Q47  C19  C   C     0   0.557   -8.5978  20.6614  264.9477
 Q47  C23  C   CR16  0  -0.255   -6.1694  19.6377  267.3288
 Q47  C24  C   CR6   0  -0.216   -6.5432  19.5770  268.6645
 Q47  N09  N   NH1   0  -0.625   -9.2664  18.2938  264.7570
 Q47  N20  N   NH1   0  -0.621   -7.4514  20.2699  264.3886
 Q47  O01  O   OH1   0  -0.593   -7.3022  18.2251  270.5325
 Q47  O16  O   OH1   0  -0.634  -14.0086  15.8710  267.9961
 Q47  O21  O   O     0  -0.516   -8.8600  21.8355  265.1756
 Q47  O22  O   O     0  -0.471   -7.8742  16.7403  263.9142
 Q47  BR1  BR  BR    0  -0.045   -6.5063  21.1566  269.7039
 Q47  H1   H   HCR6  0   0.259   -7.2318  16.2912  268.8928
 Q47  H2   H   HCR6  0   0.245   -6.5868  16.3894  266.5353
 Q47  H3   H   HCH2  0   0.275   -5.4039  17.6064  264.7505
 Q47  H4   H   HCH2  0   0.261   -5.0195  19.2980  264.9180
 Q47  H5   H   HCH1  0   0.304   -6.6299  18.8659  263.1299
 Q47  H6   H   HCH1  0   0.296  -10.5349  19.9131  264.7948
 Q47  H7   H   HCH2  0   0.269   -8.9452  19.2461  267.3077
 Q47  H8   H   HCH2  0   0.259  -10.1210  20.5420  267.1447
 Q47  H9   H   HCR6  0   0.229  -12.5568  19.9676  266.7240
 Q47  H10  H   HCR6  0   0.238  -14.3617  18.4082  267.2120
 Q47  H11  H   HCR6  0   0.247  -11.4832  15.3645  268.1343
 Q47  H12  H   HCR6  0   0.251   -9.6727  16.9453  267.6417
 Q47  H13  H   HCR6  0   0.239   -5.8423  20.5811  266.9118
 Q47  H14  H   HNH1  0   0.390   -9.9975  17.5976  264.7903
 Q47  H15  H   HNH1  0   0.379   -6.8281  21.0057  264.0898
 Q47  H16  H   HOH1  0   0.455   -7.3168  19.0593  271.0133
 Q47  H17  H   HOH1  0   0.445  -14.8729  16.2876  267.9376

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
 Q47  O22  C08  double    1.219  0.020  1.219
 Q47  C07  N20  single    1.444  0.020  1.444
 Q47  C07  C08  single    1.514  0.020  1.514
 Q47  C07  C06  single    1.539  0.020  1.539
 Q47  N20  C19  single    1.334  0.020  1.334
 Q47  C08  N09  single    1.338  0.020  1.338
 Q47  O21  C19  double    1.224  0.020  1.224
 Q47  C19  C10  single    1.511  0.020  1.511
 Q47  N09  C10  single    1.443  0.020  1.443
 Q47  C10  C11  single    1.539  0.020  1.539
 Q47  C06  C05  single    1.501  0.020  1.501
 Q47  C05  C04  aromatic  1.394  0.020  1.394
 Q47  C05  C23  aromatic  1.388  0.020  1.388
 Q47  C11  C12  single    1.502  0.020  1.502
 Q47  C12  C18  aromatic  1.393  0.020  1.393
 Q47  C12  C13  aromatic  1.391  0.020  1.391
 Q47  C04  C03  aromatic  1.380  0.020  1.380
 Q47  C18  C17  aromatic  1.386  0.020  1.386
 Q47  C13  C14  aromatic  1.385  0.020  1.385
 Q47  C17  C15  aromatic  1.390  0.020  1.390
 Q47  C23  C24  aromatic  1.388  0.020  1.388
 Q47  C14  C15  aromatic  1.391  0.020  1.391
 Q47  C15  O16  single    1.354  0.020  1.354
 Q47  C03  C02  aromatic  1.395  0.020  1.395
 Q47  C24  C02  aromatic  1.395  0.020  1.395
 Q47  C24  BR1  single    1.891  0.020  1.891
 Q47  C02  O01  single    1.338  0.020  1.338
 Q47  C03  H1   single    0.930  0.020  1.080
 Q47  C04  H2   single    0.930  0.020  1.080
 Q47  C06  H3   single    0.970  0.020  1.090
 Q47  C06  H4   single    0.970  0.020  1.090
 Q47  C07  H5   single    0.970  0.020  1.090
 Q47  C10  H6   single    0.970  0.020  1.090
 Q47  C11  H7   single    0.970  0.020  1.090
 Q47  C11  H8   single    0.970  0.020  1.090
 Q47  C13  H9   single    0.930  0.020  1.080
 Q47  C14  H10  single    0.930  0.020  1.080
 Q47  C17  H11  single    0.930  0.020  1.080
 Q47  C18  H12  single    0.930  0.020  1.080
 Q47  C23  H13  single    0.930  0.020  1.080
 Q47  N09  H14  single    0.860  0.020  1.020
 Q47  N20  H15  single    0.860  0.020  1.020
 Q47  O01  H16  single    0.850  0.020  0.980
 Q47  O16  H17  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
 Q47  O01  C02  C24  125.32  3.000
 Q47  O01  C02  C03  117.20  3.000
 Q47  C24  C02  C03  117.47  3.000
 Q47  H1   C03  C04  120.26  3.000
 Q47  H1   C03  C02  118.65  3.000
 Q47  C04  C03  C02  121.08  3.000
 Q47  H2   C04  C05  119.86  3.000
 Q47  H2   C04  C03  118.75  3.000
 Q47  C05  C04  C03  121.39  3.000
 Q47  C23  C05  C06  121.19  3.000
 Q47  C23  C05  C04  117.84  3.000
 Q47  C06  C05  C04  120.97  3.000
 Q47  H4   C06  H3   105.99  3.000
 Q47  H4   C06  C07  107.97  3.000
 Q47  H3   C06  C07  107.96  3.000
 Q47  H4   C06  C05  110.66  3.000
 Q47  H3   C06  C05  110.48  3.000
 Q47  C07  C06  C05  113.46  3.000
 Q47  H5   C07  N20  107.56  3.000
 Q47  H5   C07  C08  105.87  3.000
 Q47  N20  C07  C08  113.28  3.000
 Q47  H5   C07  C06  107.46  3.000
 Q47  C08  C07  C06  110.71  3.000
 Q47  N20  C07  C06  111.58  3.000
 Q47  O22  C08  N09  123.25  3.000
 Q47  N09  C08  C07  117.18  3.000
 Q47  O22  C08  C07  119.56  3.000
 Q47  H6   C10  N09  107.54  3.000
 Q47  H6   C10  C19  104.93  3.000
 Q47  N09  C10  C19  113.26  3.000
 Q47  H6   C10  C11  108.14  3.000
 Q47  N09  C10  C11  111.67  3.000
 Q47  C19  C10  C11  110.90  3.000
 Q47  H8   C11  H7   107.29  3.000
 Q47  H8   C11  C12  110.23  3.000
 Q47  H7   C11  C12  110.26  3.000
 Q47  H8   C11  C10  108.39  3.000
 Q47  H7   C11  C10  108.95  3.000
 Q47  C12  C11  C10  111.60  3.000
 Q47  C18  C12  C13  117.82  3.000
 Q47  C13  C12  C11  120.78  3.000
 Q47  C18  C12  C11  121.37  3.000
 Q47  H9   C13  C14  118.58  3.000
 Q47  H9   C13  C12  120.01  3.000
 Q47  C14  C13  C12  121.41  3.000
 Q47  H10  C14  C15  120.76  3.000
 Q47  H10  C14  C13  119.35  3.000
 Q47  C15  C14  C13  119.89  3.000
 Q47  O16  C15  C17  117.98  3.000
 Q47  O16  C15  C14  122.41  3.000
 Q47  C17  C15  C14  119.60  3.000
 Q47  H11  C17  C18  120.25  3.000
 Q47  H11  C17  C15  120.02  3.000
 Q47  C18  C17  C15  119.73  3.000
 Q47  H12  C18  C17  118.84  3.000
 Q47  H12  C18  C12  119.61  3.000
 Q47  C17  C18  C12  121.54  3.000
 Q47  O21  C19  N20  122.91  3.000
 Q47  O21  C19  C10  119.58  3.000
 Q47  N20  C19  C10  117.50  3.000
 Q47  H13  C23  C24  119.35  3.000
 Q47  H13  C23  C05  119.79  3.000
 Q47  C24  C23  C05  120.85  3.000
 Q47  BR1  C24  C23  119.14  3.000
 Q47  BR1  C24  C02  119.49  3.000
 Q47  C23  C24  C02  121.37  3.000
 Q47  H14  N09  C10  115.79  3.000
 Q47  H14  N09  C08  116.02  3.000
 Q47  C10  N09  C08  128.14  3.000
 Q47  H15  N20  C19  116.15  3.000
 Q47  H15  N20  C07  115.89  3.000
 Q47  C19  N20  C07  127.96  3.000
 Q47  H16  O01  C02  112.55  3.000
 Q47  H17  O16  C15  109.79  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
 Q47  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 Q47  CONST_02  C05  C23  C24  C02    0.00   0.0  0
 Q47  CONST_03  C23  C05  C04  C03    0.00   0.0  0
 Q47  CONST_04  C23  C24  C02  C03    0.00   0.0  0
 Q47  CONST_05  C24  C23  C05  C04    0.00   0.0  0
 Q47  CONST_06  C24  C02  C03  C04    0.00   0.0  0
 Q47  CONST_07  C15  C17  C18  C12    0.00   0.0  0
 Q47  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 Q47  CONST_09  C17  C18  C12  C13    0.00   0.0  0
 Q47  CONST_10  C17  C15  C14  C13    0.00   0.0  0
 Q47  CONST_11  C18  C12  C13  C14    0.00   0.0  0
 Q47  CONST_12  C18  C17  C15  C14    0.00   0.0  0
 Q47  CONST_13  C10  C19  N20  C07    0.00   0.0  0
 Q47  CONST_14  C10  N09  C08  C07    0.00   0.0  0
 Q47  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 Q47  CONST_16  BR1  C24  C02  C03  180.00   0.0  0
 Q47  CONST_17  O01  C02  C03  C04  180.00   0.0  0
 Q47  CONST_18  BR1  C24  C23  C05  180.00   0.0  0
 Q47  CONST_19  C24  C23  C05  C06  180.00   0.0  0
 Q47  CONST_20  C17  C18  C12  C11  180.00   0.0  0
 Q47  CONST_21  C14  C13  C12  C11  180.00   0.0  0
 Q47  CONST_22  O16  C15  C14  C13  180.00   0.0  0
 Q47  CONST_23  O16  C15  C17  C18  180.00   0.0  0
 Q47  CONST_24  O01  C02  C24  C23  180.00   0.0  0
 Q47  CONST_25  O21  C19  N20  C07  180.00   0.0  0
 Q47  CONST_26  O22  C08  N09  C10  180.00   0.0  0
 Q47  CONST_27  H2   C04  C03  C02  180.00   0.0  0
 Q47  CONST_28  H13  C23  C24  C02  180.00   0.0  0
 Q47  CONST_29  H1   C03  C04  C05  180.00   0.0  0
 Q47  CONST_30  H11  C17  C18  C12  180.00   0.0  0
 Q47  CONST_31  H10  C14  C13  C12  180.00   0.0  0
 Q47  CONST_32  H12  C18  C12  C13  180.00   0.0  0
 Q47  CONST_33  H9   C13  C14  C15  180.00   0.0  0
 Q47  CONST_34  H14  N09  C08  C07  180.00   0.0  0
 Q47  CONST_35  H15  N20  C19  C10  180.00   0.0  0
 Q47  Var_01    C07  C06  C05  C04   92.43  30.0  2
 Q47  Var_02    C18  C12  C11  C10   96.42  30.0  2

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
 Q47  chir_01  C07  N20  C08  C06  positiv
 Q47  chir_02  C10  N09  C11  C19  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
 Q47  plan-1  C02  0.020
 Q47  plan-1  C03  0.020
 Q47  plan-1  C04  0.020
 Q47  plan-1  C05  0.020
 Q47  plan-1  C06  0.020
 Q47  plan-1  C23  0.020
 Q47  plan-1  C24  0.020
 Q47  plan-1  O01  0.020
 Q47  plan-1  BR1  0.020
 Q47  plan-1  H1   0.020
 Q47  plan-1  H2   0.020
 Q47  plan-1  H13  0.020
 Q47  plan-2  C11  0.020
 Q47  plan-2  C12  0.020
 Q47  plan-2  C13  0.020
 Q47  plan-2  C14  0.020
 Q47  plan-2  C15  0.020
 Q47  plan-2  C17  0.020
 Q47  plan-2  C18  0.020
 Q47  plan-2  O16  0.020
 Q47  plan-2  H9   0.020
 Q47  plan-2  H10  0.020
 Q47  plan-2  H11  0.020
 Q47  plan-2  H12  0.020
 Q47  plan-3  C07  0.020
 Q47  plan-3  C10  0.020
 Q47  plan-3  C19  0.020
 Q47  plan-3  N20  0.020
 Q47  plan-3  O21  0.020
 Q47  plan-3  H15  0.020
 Q47  plan-4  C07  0.020
 Q47  plan-4  C08  0.020
 Q47  plan-4  C10  0.020
 Q47  plan-4  N09  0.020
 Q47  plan-4  O22  0.020
 Q47  plan-4  H14  0.020

