# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:08:14 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-[2-[[(2R)-4-(4-hydroxyphenyl)butan-2-yl]amino]ethyl]benzene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCc1ccc(O)cc1)NCCc2ccc(O)c(O)c2
#
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
 Y00  Y00  4-[2-[[(2R)-4-(4-hydroxyphenyl)butan-2-yl]amino]ethyl]benzene-1,2-diol  ligand  45  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y00
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
 Y00  O3    O  OH1   0  -0.637   8.3328   0.7381   0.2901
 Y00  C16   C  CR6   0   0.332   6.9949   0.6169   0.1464
 Y00  C15   C  CR16  0  -0.323   6.5057   0.2181  -1.0957
 Y00  C14   C  CR16  0  -0.297   5.1405   0.0848  -1.2893
 Y00  C17   C  CR16  0  -0.369   6.0989   0.8766   1.1784
 Y00  C18   C  CR16  0  -0.306   4.7338   0.7370   0.9635
 Y00  C13   C  CR6   0   0.114   4.2249   0.3408  -0.2690
 Y00  C12   C  CH2   0  -0.493   2.7495   0.1508  -0.4863
 Y00  C11   C  CH2   0  -0.407   2.3260  -1.3098  -0.3400
 Y00  C9    C  CH1   0  -0.083   0.8442  -1.5484  -0.6255
 Y00  C10   C  CH3   0  -0.667   0.5277  -3.0445  -0.6096
 Y00  N1    N  NH1   0  -0.589   0.0349  -0.7633   0.2945
 Y00  C8    C  CH2   0  -0.243  -1.3621  -0.6354  -0.0618
 Y00  C1    C  CH2   0  -0.525  -2.0768   0.3093   0.9027
 Y00  C2    C  CR6   0   0.115  -3.5279   0.4838   0.5550
 Y00  C7    C  CR16  0  -0.391  -4.4661  -0.4687   0.9531
 Y00  C6    C  CR6   0   0.305  -5.8048  -0.3482   0.6175
 Y00  O1    O  OH1   0  -0.638  -6.6731  -1.2966   1.0332
 Y00  C5    C  CR6   0   0.236  -6.2298   0.7523  -0.1382
 Y00  O2    O  OH1   0  -0.648  -7.5537   0.8089  -0.4225
 Y00  C4    C  CR16  0  -0.358  -5.3049   1.7013  -0.5388
 Y00  C3    C  CR16  0  -0.330  -3.9633   1.5675  -0.1959
 Y00  H3    H  HOH1  0   0.472   8.5488   1.0186   1.1860
 Y00  H15   H  HCR6  0   0.258   7.1960   0.0176  -1.9062
 Y00  H17   H  HCR6  0   0.266   6.4615   1.1933   2.1501
 Y00  H14   H  HCR6  0   0.244   4.7798  -0.2251  -2.2638
 Y00  H18   H  HCR6  0   0.246   4.0528   0.9463   1.7805
 Y00  H121  H  HCH2  0   0.237   2.1831   0.7610   0.2188
 Y00  H122  H  HCH2  0   0.226   2.4767   0.5010  -1.4871
 Y00  H111  H  HCH2  0   0.224   2.9175  -1.9272  -1.0228
 Y00  H112  H  HCH2  0   0.215   2.5635  -1.6633   0.6702
 Y00  H9    H  HCH1  0   0.214   0.6340  -1.1644  -1.6313
 Y00  H101  H  HCH3  0   0.230  -0.5227  -3.2377  -0.8300
 Y00  H102  H  HCH3  0   0.224   1.1217  -3.5810  -1.3514
 Y00  H103  H  HCH3  0   0.213   0.7501  -3.4746   0.3704
 Y00  H1    H  HNH1  0   0.331   0.1109  -1.1574   1.2266
 Y00  H81C  H  HCH2  0   0.218  -1.4203  -0.2226  -1.0738
 Y00  H82C  H  HCH2  0   0.193  -1.9083  -1.5910  -0.0906
 Y00  H11C  H  HCH2  0   0.236  -1.9831  -0.0813   1.9208
 Y00  H12C  H  HCH2  0   0.238  -1.5674   1.2755   0.8904
 Y00  H7    H  HCR6  0   0.252  -4.1538  -1.3257   1.5405
 Y00  HA    H  HCR6  0   0.245  -3.2563   2.3225  -0.5174
 Y00  HB    H  HOH1  0   0.471  -7.5672  -1.0857   0.7405
 Y00  H2    H  HOH1  0   0.480  -7.7542   1.5852  -0.9562
 Y00  H4    H  HCR6  0   0.269  -5.6319   2.5580  -1.1178

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
 Y00  O3   C16   single    1.351  0.020  1.351
 Y00  C16  C15   aromatic  1.393  0.020  1.393
 Y00  C16  C17   aromatic  1.391  0.020  1.391
 Y00  C15  C14   aromatic  1.385  0.020  1.385
 Y00  C14  C13   aromatic  1.395  0.020  1.395
 Y00  C17  C18   aromatic  1.389  0.020  1.389
 Y00  C18  C13   aromatic  1.391  0.020  1.391
 Y00  C13  C12   single    1.503  0.020  1.503
 Y00  C12  C11   single    1.528  0.020  1.528
 Y00  C11  C9    single    1.528  0.020  1.528
 Y00  C9   C10   single    1.529  0.020  1.529
 Y00  C9   N1    single    1.455  0.020  1.455
 Y00  N1   C8    single    1.447  0.020  1.447
 Y00  C8   C1    single    1.528  0.020  1.528
 Y00  C1   C2    single    1.502  0.020  1.502
 Y00  C2   C7    aromatic  1.395  0.020  1.395
 Y00  C2   C3    aromatic  1.388  0.020  1.388
 Y00  C7   C6    aromatic  1.385  0.020  1.385
 Y00  C6   O1    single    1.351  0.020  1.351
 Y00  C6   C5    aromatic  1.401  0.020  1.401
 Y00  C5   O2    single    1.355  0.020  1.355
 Y00  C5   C4    aromatic  1.384  0.020  1.384
 Y00  C4   C3    aromatic  1.391  0.020  1.391
 Y00  O3   H3    single    0.850  0.020  0.980
 Y00  C15  H15   single    0.930  0.020  1.080
 Y00  C17  H17   single    0.930  0.020  1.080
 Y00  C14  H14   single    0.930  0.020  1.080
 Y00  C18  H18   single    0.930  0.020  1.080
 Y00  C12  H121  single    0.970  0.020  1.090
 Y00  C12  H122  single    0.970  0.020  1.090
 Y00  C11  H111  single    0.970  0.020  1.090
 Y00  C11  H112  single    0.970  0.020  1.090
 Y00  C9   H9    single    0.970  0.020  1.090
 Y00  C10  H101  single    0.970  0.020  1.090
 Y00  C10  H102  single    0.970  0.020  1.090
 Y00  C10  H103  single    0.970  0.020  1.090
 Y00  N1   H1    single    0.890  0.020  1.040
 Y00  C8   H81C  single    0.970  0.020  1.090
 Y00  C8   H82C  single    0.970  0.020  1.090
 Y00  C1   H11C  single    0.970  0.020  1.090
 Y00  C1   H12C  single    0.970  0.020  1.090
 Y00  C7   H7    single    0.930  0.020  1.080
 Y00  C3   HA    single    0.930  0.020  1.080
 Y00  O1   HB    single    0.850  0.020  0.980
 Y00  O2   H2    single    0.850  0.020  0.980
 Y00  C4   H4    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
 Y00  H3    O3   C16   110.31  3.000
 Y00  C17   C16  C15   119.25  3.000
 Y00  C17   C16  O3    122.83  3.000
 Y00  C15   C16  O3    117.91  3.000
 Y00  H15   C15  C14   120.37  3.000
 Y00  H15   C15  C16   119.75  3.000
 Y00  C14   C15  C16   119.88  3.000
 Y00  H14   C14  C13   119.45  3.000
 Y00  H14   C14  C15   118.74  3.000
 Y00  C13   C14  C15   121.81  3.000
 Y00  H17   C17  C18   119.78  3.000
 Y00  H17   C17  C16   120.25  3.000
 Y00  C18   C17  C16   119.97  3.000
 Y00  H18   C18  C13   119.53  3.000
 Y00  H18   C18  C17   118.78  3.000
 Y00  C13   C18  C17   121.69  3.000
 Y00  C12   C13  C18   121.54  3.000
 Y00  C12   C13  C14   121.02  3.000
 Y00  C18   C13  C14   117.41  3.000
 Y00  H122  C12  H121  106.41  3.000
 Y00  H122  C12  C11   108.92  3.000
 Y00  H121  C12  C11   109.21  3.000
 Y00  H122  C12  C13   109.65  3.000
 Y00  H121  C12  C13   110.21  3.000
 Y00  C11   C12  C13   112.28  3.000
 Y00  H112  C11  H111  106.02  3.000
 Y00  H112  C11  C9    109.38  3.000
 Y00  H111  C11  C9    108.64  3.000
 Y00  H112  C11  C12   109.66  3.000
 Y00  H111  C11  C12   109.26  3.000
 Y00  C9    C11  C12   113.60  3.000
 Y00  H9    C9   N1    106.51  3.000
 Y00  H9    C9   C10   108.20  3.000
 Y00  N1    C9   C10   113.96  3.000
 Y00  H9    C9   C11   107.61  3.000
 Y00  N1    C9   C11   109.69  3.000
 Y00  C10   C9   C11   110.59  3.000
 Y00  H103  C10  H102  107.77  3.000
 Y00  H103  C10  H101  107.90  3.000
 Y00  H102  C10  H101  107.45  3.000
 Y00  H103  C10  C9    110.62  3.000
 Y00  H102  C10  C9    111.18  3.000
 Y00  H101  C10  C9    111.75  3.000
 Y00  H1    N1   C8    109.43  3.000
 Y00  H1    N1   C9    109.24  3.000
 Y00  C8    N1   C9    115.39  3.000
 Y00  H82C  C8   H81C  106.07  3.000
 Y00  H82C  C8   C1    108.73  3.000
 Y00  H81C  C8   C1    109.01  3.000
 Y00  H82C  C8   N1    114.11  3.000
 Y00  H81C  C8   N1    108.20  3.000
 Y00  C1    C8   N1    110.54  3.000
 Y00  H12C  C1   H11C  106.63  3.000
 Y00  H12C  C1   C2    110.18  3.000
 Y00  H11C  C1   C2    109.84  3.000
 Y00  H12C  C1   C8    108.77  3.000
 Y00  H11C  C1   C8    109.06  3.000
 Y00  C2    C1   C8    112.19  3.000
 Y00  C3    C2   C7    118.45  3.000
 Y00  C3    C2   C1    121.25  3.000
 Y00  C7    C2   C1    120.28  3.000
 Y00  H7    C7   C6    118.56  3.000
 Y00  H7    C7   C2    120.02  3.000
 Y00  C6    C7   C2    121.42  3.000
 Y00  C5    C6   O1    121.49  3.000
 Y00  C5    C6   C7    119.48  3.000
 Y00  O1    C6   C7    119.03  3.000
 Y00  HB    O1   C6    110.42  3.000
 Y00  C4    C5   O2    124.29  3.000
 Y00  C4    C5   C6    119.46  3.000
 Y00  O2    C5   C6    116.25  3.000
 Y00  H2    O2   C5    110.69  3.000
 Y00  H4    C4   C3    119.90  3.000
 Y00  H4    C4   C5    119.64  3.000
 Y00  C3    C4   C5    120.47  3.000
 Y00  HA    C3   C4    119.29  3.000
 Y00  HA    C3   C2    119.99  3.000
 Y00  C4    C3   C2    120.72  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
 Y00  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 Y00  CONST_02  C13  C18  C17  C16     0.00   0.0  0
 Y00  CONST_03  C18  C17  C16  C15     0.00   0.0  0
 Y00  CONST_04  C18  C13  C14  C15     0.00   0.0  0
 Y00  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 Y00  CONST_06  C17  C18  C13  C14     0.00   0.0  0
 Y00  CONST_07  C5   C6   C7   C2      0.00   0.0  0
 Y00  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 Y00  CONST_09  C4   C3   C2   C7      0.00   0.0  0
 Y00  CONST_10  C4   C5   C6   C7      0.00   0.0  0
 Y00  CONST_11  C3   C2   C7   C6      0.00   0.0  0
 Y00  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 Y00  CONST_13  C14  C15  C16  O3    180.00   0.0  0
 Y00  CONST_14  C18  C17  C16  O3    180.00   0.0  0
 Y00  CONST_15  C12  C13  C14  C15   180.00   0.0  0
 Y00  CONST_16  C12  C13  C18  C17   180.00   0.0  0
 Y00  CONST_17  C6   C7   C2   C1    180.00   0.0  0
 Y00  CONST_18  C4   C3   C2   C1    180.00   0.0  0
 Y00  CONST_19  O1   C6   C7   C2    180.00   0.0  0
 Y00  CONST_20  O2   C5   C6   C7    180.00   0.0  0
 Y00  CONST_21  C4   C5   C6   O1    180.00   0.0  0
 Y00  CONST_22  C3   C4   C5   O2    180.00   0.0  0
 Y00  CONST_23  H14  C14  C15  C16   180.00   0.0  0
 Y00  CONST_24  H18  C18  C17  C16   180.00   0.0  0
 Y00  CONST_25  H17  C17  C16  C15   180.00   0.0  0
 Y00  CONST_26  H15  C15  C16  C17   180.00   0.0  0
 Y00  CONST_27  H4   C4   C3   C2    180.00   0.0  0
 Y00  CONST_28  HA   C3   C2   C7    180.00   0.0  0
 Y00  CONST_29  H7   C7   C6   C5    180.00   0.0  0
 Y00  Var_01    C11  C12  C13  C14    81.38  30.0  2
 Y00  Var_02    C7   C2   C1   C8     81.52  30.0  2
 Y00  Var_03    C9   C11  C12  C13  -177.03  30.0  3
 Y00  Var_04    C2   C1   C8   N1    179.22  30.0  3
 Y00  Var_05    C1   C8   N1   C9   -174.84  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
 Y00  chir_01  C9  C11  C10  N1  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
 Y00  plan-1  O3   0.020
 Y00  plan-1  C16  0.020
 Y00  plan-1  C15  0.020
 Y00  plan-1  C14  0.020
 Y00  plan-1  C17  0.020
 Y00  plan-1  C18  0.020
 Y00  plan-1  C13  0.020
 Y00  plan-1  C12  0.020
 Y00  plan-1  H15  0.020
 Y00  plan-1  H17  0.020
 Y00  plan-1  H14  0.020
 Y00  plan-1  H18  0.020
 Y00  plan-2  C1   0.020
 Y00  plan-2  C2   0.020
 Y00  plan-2  C7   0.020
 Y00  plan-2  C6   0.020
 Y00  plan-2  O1   0.020
 Y00  plan-2  C5   0.020
 Y00  plan-2  O2   0.020
 Y00  plan-2  C4   0.020
 Y00  plan-2  C3   0.020
 Y00  plan-2  H7   0.020
 Y00  plan-2  HA   0.020
 Y00  plan-2  H4   0.020

