# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:14:44 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [5-(6-bromo[1,2,4]triazolo[4,3-a]pyridin-3-yl)-2,4-dihydroxyphenyl](4-methylpiperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)c2cc(c(O)cc2O)c3nnc4ccc(Br)cn34
#
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
 RL3  RL3  '[5-(6-bromo[1,2,4]triazolo[4,3-a]pyridin-3-yl)-2,4-dihydroxyphenyl](4-methylpiperazin-1-yl)methanone'  ligand  45  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RL3
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
 RL3  C01  C   CR6   0   0.395  -2.3784  -1.6403   0.6384
 RL3  C02  C   CR16  0  -0.474  -1.8010  -2.8864   0.4525
 RL3  C03  C   CR6   0   0.360  -0.4836  -3.0001   0.0205
 RL3  C04  C   CR6   0  -0.100   0.2898  -1.8368  -0.1883
 RL3  C05  C   CR16  0  -0.317  -0.3346  -0.5975  -0.0366
 RL3  C06  C   CR6   0  -0.198  -1.6507  -0.4793   0.3601
 RL3  C07  C   C     0   0.510  -2.2443   0.8757   0.6072
 RL3  O08  O   O     0  -0.488  -1.9604   1.4766   1.6357
 RL3  O09  O   OH1   0  -0.626  -0.0087  -4.2308  -0.1722
 RL3  O10  O   OH1   0  -0.611  -3.6410  -1.4809   1.0554
 RL3  C11  C   CR5   0   0.514   1.6820  -1.9863  -0.5732
 RL3  N12  N   N     0  -0.595   2.7235  -1.1171  -0.3896
 RL3  C13  C   CR56  0   0.486   3.8227  -1.7643  -0.9209
 RL3  N14  N   N     0  -0.313   3.4723  -2.9467  -1.3661
 RL3  N15  N   N     0  -0.404   2.1604  -3.0682  -1.1448
 RL3  C16  C   CR16  0   0.064   2.8246   0.1015   0.2321
 RL3  C17  C   CR6   0  -0.238   4.0330   0.7076   0.2553
 RL3  C18  C   CR16  0  -0.117   5.1834   0.1053  -0.3349
 RL3  C19  C   CR16  0  -0.366   5.0798  -1.1195  -0.9065
 RL3  N20  N   NT    0  -0.434  -3.0538   1.3737  -0.3414
 RL3  N21  N   NT    0  -0.418  -5.5535   1.8697  -1.5801
 RL3  C22  C   CH3   0  -0.516  -6.9835   1.7691  -1.7630
 RL3  BR1  BR  BR    0   0.011   4.2064   2.3715   1.1024
 RL3  C24  C   CH2   0  -0.308  -3.4003   0.7179  -1.5880
 RL3  C25  C   CH2   0  -0.273  -4.9080   0.5786  -1.7095
 RL3  C26  C   CH2   0  -0.277  -5.2185   2.4878  -0.3127
 RL3  C27  C   CH2   0  -0.314  -3.7150   2.6550  -0.1739
 RL3  H1   H   HCR6  0   0.287  -2.3723  -3.7906   0.6303
 RL3  H2   H   HCR6  0   0.278   0.2016   0.3106  -0.2779
 RL3  H3   H   HOH1  0   0.478   0.8654  -4.1833  -0.6195
 RL3  H4   H   HOH1  0   0.484  -4.0715  -2.3326   1.1958
 RL3  H5   H   HCR6  0   0.333   1.9420   0.5057   0.6987
 RL3  H6   H   HCR6  0   0.304   6.1349   0.6174  -0.3111
 RL3  H7   H   HCR6  0   0.306   5.9320  -1.6187  -1.3439
 RL3  H9   H   HCH3  0   0.234  -7.4372   2.7600  -1.7160
 RL3  H10  H   HCH3  0   0.234  -7.2044   1.3465  -2.7442
 RL3  H11  H   HCH3  0   0.194  -7.4736   1.1370  -1.0066
 RL3  H12  H   HCH2  0   0.247  -3.0207   1.3206  -2.4194
 RL3  H13  H   HCH2  0   0.271  -2.9295  -0.2590  -1.6567
 RL3  H14  H   HCH2  0   0.200  -5.2662  -0.1409  -0.9541
 RL3  H15  H   HCH2  0   0.243  -5.1412   0.1609  -2.6917
 RL3  H16  H   HCH2  0   0.244  -5.6850   3.4742  -0.2608
 RL3  H17  H   HCH2  0   0.198  -5.5976   1.9043   0.5445
 RL3  H18  H   HCH2  0   0.267  -3.4700   3.0680   0.8005
 RL3  H19  H   HCH2  0   0.244  -3.3469   3.3474  -0.9371

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
 RL3  O09  C03  single    1.333  0.020  1.333
 RL3  N14  N15  aromatic  1.336  0.020  1.336
 RL3  N14  C13  aromatic  1.311  0.020  1.311
 RL3  N15  C11  aromatic  1.314  0.020  1.314
 RL3  C03  C02  aromatic  1.391  0.020  1.391
 RL3  C03  C04  aromatic  1.412  0.020  1.412
 RL3  C13  C19  aromatic  1.413  0.020  1.413
 RL3  C13  N12  aromatic  1.382  0.020  1.382
 RL3  C19  C18  aromatic  1.356  0.020  1.356
 RL3  C11  N12  aromatic  1.369  0.020  1.369
 RL3  C11  C04  single    1.452  0.020  1.452
 RL3  C02  C01  aromatic  1.386  0.020  1.386
 RL3  N12  C16  aromatic  1.372  0.020  1.372
 RL3  C04  C05  aromatic  1.396  0.020  1.396
 RL3  C18  C17  aromatic  1.426  0.020  1.426
 RL3  C16  C17  aromatic  1.352  0.020  1.352
 RL3  C17  BR1  single    1.875  0.020  1.875
 RL3  C01  O10  single    1.339  0.020  1.339
 RL3  C01  C06  aromatic  1.398  0.020  1.398
 RL3  C05  C06  aromatic  1.380  0.020  1.380
 RL3  C06  C07  single    1.500  0.020  1.500
 RL3  C24  C25  single    1.519  0.020  1.519
 RL3  C24  N20  single    1.451  0.020  1.451
 RL3  C25  N21  single    1.449  0.020  1.449
 RL3  C07  N20  single    1.343  0.020  1.343
 RL3  C07  O08  double    1.225  0.020  1.225
 RL3  N20  C27  single    1.452  0.020  1.452
 RL3  N21  C22  single    1.445  0.020  1.445
 RL3  N21  C26  single    1.449  0.020  1.449
 RL3  C27  C26  single    1.519  0.020  1.519
 RL3  C02  H1   single    0.930  0.020  1.080
 RL3  C05  H2   single    0.930  0.020  1.080
 RL3  O09  H3   single    0.850  0.020  0.980
 RL3  O10  H4   single    0.850  0.020  0.980
 RL3  C16  H5   single    0.930  0.020  1.080
 RL3  C18  H6   single    0.930  0.020  1.080
 RL3  C19  H7   single    0.930  0.020  1.080
 RL3  C22  H9   single    0.970  0.020  1.090
 RL3  C22  H10  single    0.970  0.020  1.090
 RL3  C22  H11  single    0.970  0.020  1.090
 RL3  C24  H12  single    0.970  0.020  1.090
 RL3  C24  H13  single    0.970  0.020  1.090
 RL3  C25  H14  single    0.970  0.020  1.090
 RL3  C25  H15  single    0.970  0.020  1.090
 RL3  C26  H16  single    0.970  0.020  1.090
 RL3  C26  H17  single    0.970  0.020  1.090
 RL3  C27  H18  single    0.970  0.020  1.090
 RL3  C27  H19  single    0.970  0.020  1.090

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
 RL3  O10  C01  C06  116.99  3.000
 RL3  C06  C01  C02  120.20  3.000
 RL3  O10  C01  C02  122.79  3.000
 RL3  H1   C02  C03  118.80  3.000
 RL3  H1   C02  C01  120.55  3.000
 RL3  C03  C02  C01  120.64  3.000
 RL3  O09  C03  C04  122.95  3.000
 RL3  C04  C03  C02  119.81  3.000
 RL3  O09  C03  C02  117.24  3.000
 RL3  C11  C04  C05  123.30  3.000
 RL3  C05  C04  C03  118.05  3.000
 RL3  C11  C04  C03  118.64  3.000
 RL3  H2   C05  C06  117.72  3.000
 RL3  H2   C05  C04  119.95  3.000
 RL3  C06  C05  C04  122.27  3.000
 RL3  C07  C06  C05  120.15  3.000
 RL3  C07  C06  C01  120.76  3.000
 RL3  C05  C06  C01  118.86  3.000
 RL3  N20  C07  O08  123.44  3.000
 RL3  O08  C07  C06  119.34  3.000
 RL3  N20  C07  C06  117.21  3.000
 RL3  H3   O09  C03  109.74  3.000
 RL3  H4   O10  C01  111.16  3.000
 RL3  N15  C11  N12  107.70  3.000
 RL3  N12  C11  C04  128.94  3.000
 RL3  N15  C11  C04  123.32  3.000
 RL3  C16  N12  C13  122.12  3.000
 RL3  C16  N12  C11  132.91  3.000
 RL3  C13  N12  C11  104.85  3.000
 RL3  C19  C13  N14  130.75  3.000
 RL3  C19  C13  N12  119.35  3.000
 RL3  N14  C13  N12  109.89  3.000
 RL3  N15  N14  C13  106.75  3.000
 RL3  N14  N15  C11  110.78  3.000
 RL3  H5   C16  C17  123.82  3.000
 RL3  H5   C16  N12  117.99  3.000
 RL3  C17  C16  N12  118.16  3.000
 RL3  BR1  C17  C18  119.14  3.000
 RL3  BR1  C17  C16  119.22  3.000
 RL3  C18  C17  C16  121.63  3.000
 RL3  H6   C18  C19  120.31  3.000
 RL3  H6   C18  C17  120.06  3.000
 RL3  C19  C18  C17  119.63  3.000
 RL3  H7   C19  C18  121.88  3.000
 RL3  H7   C19  C13  119.13  3.000
 RL3  C18  C19  C13  118.99  3.000
 RL3  C27  N20  C24  112.92  3.000
 RL3  C27  N20  C07  121.36  3.000
 RL3  C24  N20  C07  125.69  3.000
 RL3  C26  N21  C25  110.80  3.000
 RL3  C26  N21  C22  111.66  3.000
 RL3  C25  N21  C22  111.56  3.000
 RL3  H11  C22  H10  107.78  3.000
 RL3  H11  C22  H9   107.86  3.000
 RL3  H10  C22  H9   107.84  3.000
 RL3  H11  C22  N21  113.18  3.000
 RL3  H10  C22  N21  109.95  3.000
 RL3  H9   C22  N21  110.05  3.000
 RL3  H13  C24  H12  107.26  3.000
 RL3  H13  C24  C25  110.03  3.000
 RL3  H12  C24  C25  109.50  3.000
 RL3  H13  C24  N20  110.94  3.000
 RL3  H12  C24  N20  108.72  3.000
 RL3  C25  C24  N20  110.32  3.000
 RL3  H15  C25  H14  107.28  3.000
 RL3  H15  C25  C24  108.59  3.000
 RL3  H14  C25  C24  109.11  3.000
 RL3  H15  C25  N21  109.01  3.000
 RL3  H14  C25  N21  112.04  3.000
 RL3  C24  C25  N21  110.69  3.000
 RL3  H17  C26  H16  107.08  3.000
 RL3  H17  C26  C27  109.09  3.000
 RL3  H16  C26  C27  108.60  3.000
 RL3  H17  C26  N21  111.97  3.000
 RL3  H16  C26  N21  109.15  3.000
 RL3  C27  C26  N21  110.83  3.000
 RL3  H19  C27  H18  108.00  3.000
 RL3  H19  C27  C26  109.81  3.000
 RL3  H18  C27  C26  110.31  3.000
 RL3  H19  C27  N20  108.95  3.000
 RL3  H18  C27  N20  109.66  3.000
 RL3  C26  C27  N20  110.07  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
 RL3  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 RL3  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 RL3  CONST_03  C11  C04  C03  C02   180.00   0.0  0
 RL3  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 RL3  CONST_05  C05  C06  C01  C02     0.00   0.0  0
 RL3  CONST_06  C06  C01  C02  C03     0.00   0.0  0
 RL3  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 RL3  CONST_10  N14  N15  C11  C04   180.00   0.0  0
 RL3  CONST_11  C13  N12  C11  C04   180.00   0.0  0
 RL3  CONST_12  C16  N12  C11  C04     0.00   0.0  0
 RL3  CONST_15  C11  C04  C05  C06   180.00   0.0  0
 RL3  CONST_16  C13  N14  N15  C11     0.00   0.0  0
 RL3  CONST_17  N14  C13  N12  C11     0.00   0.0  0
 RL3  CONST_18  C19  C13  N12  C11   180.00   0.0  0
 RL3  CONST_19  C17  C16  N12  C11   180.00   0.0  0
 RL3  CONST_20  N15  N14  C13  N12     0.00   0.0  0
 RL3  CONST_21  C18  C19  C13  N12     0.00   0.0  0
 RL3  CONST_22  N14  N15  C11  N12     0.00   0.0  0
 RL3  CONST_23  C18  C17  C16  N12     0.00   0.0  0
 RL3  CONST_24  C17  C18  C19  C13     0.00   0.0  0
 RL3  CONST_25  N15  C11  N12  C13     0.00   0.0  0
 RL3  CONST_26  C17  C16  N12  C13     0.00   0.0  0
 RL3  CONST_27  C18  C19  C13  N14   180.00   0.0  0
 RL3  CONST_28  C16  N12  C13  N14   180.00   0.0  0
 RL3  CONST_29  C19  C13  N14  N15   180.00   0.0  0
 RL3  CONST_30  C16  N12  C11  N15   180.00   0.0  0
 RL3  CONST_31  C19  C13  N12  C16     0.00   0.0  0
 RL3  CONST_32  C19  C18  C17  C16     0.00   0.0  0
 RL3  CONST_33  O09  C03  C02  C01   180.00   0.0  0
 RL3  CONST_34  C07  C06  C01  C02   180.00   0.0  0
 RL3  CONST_35  O10  C01  C02  C03   180.00   0.0  0
 RL3  CONST_36  C07  C06  C05  C04   180.00   0.0  0
 RL3  CONST_37  O09  C03  C04  C05   180.00   0.0  0
 RL3  CONST_38  O10  C01  C06  C05   180.00   0.0  0
 RL3  CONST_39  C11  C04  C03  O09     0.00   0.0  0
 RL3  CONST_40  BR1  C17  C16  N12   180.00   0.0  0
 RL3  CONST_41  BR1  C17  C18  C19   180.00   0.0  0
 RL3  CONST_42  C24  N20  C07  C06     0.00   0.0  0
 RL3  CONST_43  C27  N20  C07  C06   180.00   0.0  0
 RL3  CONST_44  H2   C05  C06  C01   180.00   0.0  0
 RL3  CONST_45  H1   C02  C03  C04   180.00   0.0  0
 RL3  CONST_46  H5   C16  N12  C11     0.00   0.0  0
 RL3  CONST_47  H7   C19  C13  N12   180.00   0.0  0
 RL3  CONST_48  H6   C18  C19  C13   180.00   0.0  0
 RL3  CONST_49  C24  N20  C07  O08   180.00   0.0  0
 RL3  CONST_50  C27  N20  C07  O08     0.00   0.0  0
 RL3  Var_01    N21  C25  C24  N20    55.59  30.0  1
 RL3  Var_02    N21  C26  C27  N20   -55.74  30.0  1
 RL3  Var_03    C26  N21  C25  C24   -57.96  30.0  1
 RL3  Var_04    C26  C27  N20  C24    54.82  30.0  1
 RL3  Var_05    C27  N20  C24  C25   -54.85  30.0  1
 RL3  Var_06    C27  C26  N21  C25    58.16  30.0  1
 RL3  Var_07    N20  C07  C06  C01   -82.56  30.0  2
 RL3  Var_08    H9   C22  N21  C25  -176.86  30.0  3

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
 RL3  plan-1  C01  0.020
 RL3  plan-1  C02  0.020
 RL3  plan-1  C03  0.020
 RL3  plan-1  C04  0.020
 RL3  plan-1  C05  0.020
 RL3  plan-1  C06  0.020
 RL3  plan-1  C07  0.020
 RL3  plan-1  O09  0.020
 RL3  plan-1  O10  0.020
 RL3  plan-1  C11  0.020
 RL3  plan-1  H1   0.020
 RL3  plan-1  H2   0.020
 RL3  plan-2  C04  0.020
 RL3  plan-2  C11  0.020
 RL3  plan-2  N12  0.020
 RL3  plan-2  C13  0.020
 RL3  plan-2  N14  0.020
 RL3  plan-2  N15  0.020
 RL3  plan-2  C16  0.020
 RL3  plan-2  C17  0.020
 RL3  plan-2  C18  0.020
 RL3  plan-2  C19  0.020
 RL3  plan-2  BR1  0.020
 RL3  plan-2  H5   0.020
 RL3  plan-2  H6   0.020
 RL3  plan-2  H7   0.020
 RL3  plan-3  C06  0.020
 RL3  plan-3  C07  0.020
 RL3  plan-3  O08  0.020
 RL3  plan-3  N20  0.020
 RL3  plan-3  C24  0.020
 RL3  plan-3  C27  0.020

