# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:43 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-{[(R)-{[4-(aminomethyl)phenyl]amino}{[(1R)-1-phenylethyl]amino}methyl]amino}ethane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N[C@@H](NCC(O)O)Nc1ccc(CN)cc1)c2ccccc2
#
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
 SC5  SC5  2-{[(R)-{[4-(aminomethyl)phenyl]amino}{[(1R)-1-phenylethyl]amino}methyl]amino}ethane-1,1-diol  ligand  50  24  .  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_SC5
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
 SC5  C1    C  CR16  0  -0.271   4.5538  -2.6319   1.2450
 SC5  C2    C  CR16  0  -0.242   3.9147  -2.6895   0.0121
 SC5  C3    C  CR16  0  -0.287   3.3494  -1.5470  -0.5372
 SC5  C4    C  CR6   0   0.120   3.4113  -0.3305   0.1384
 SC5  C5    C  CR16  0  -0.317   4.0465  -0.2838   1.3751
 SC5  C6    C  CR16  0  -0.241   4.6182  -1.4239   1.9260
 SC5  C7    C  CH3   0  -0.669   3.8715   1.5341  -1.4465
 SC5  C8    C  CH1   0  -0.133   2.8575   0.9356  -0.4761
 SC5  C9    C  CH2   0  -0.337  -0.5769   2.5297  -0.0618
 SC5  C10   C  CH1   0   0.234  -0.4750   3.7193   0.8847
 SC5  O1    O  OH1   0  -0.675  -1.3289   3.4622   1.9680
 SC5  O2    O  OH1   0  -0.676   0.8462   3.9073   1.2876
 SC5  N1    N  NH1   0  -0.709  -0.5455  -0.1421  -1.2741
 SC5  C11   C  CH1   0   0.204   0.4925   0.3273  -0.3739
 SC5  N2    N  NH1   0  -0.624   0.0854   1.3863   0.5371
 SC5  N3    N  NH1   0  -0.624   1.6234   0.6688  -1.1924
 SC5  C12   C  CH2   0  -0.347  -5.6372  -2.0168   0.5366
 SC5  N4    N  NH2   0  -0.791  -6.2338  -2.9312  -0.4264
 SC5  C13   C  CR16  0  -0.306  -3.1710  -1.6020   0.8803
 SC5  C14   C  CR16  0  -0.342  -1.9280  -1.1385   0.4667
 SC5  C15   C  CR6   0   0.360  -1.7684  -0.5742  -0.8024
 SC5  C16   C  CR16  0  -0.334  -2.9007  -0.4989  -1.6278
 SC5  C17   C  CR16  0  -0.274  -4.1274  -0.9717  -1.2023
 SC5  C18   C  CR6   0   0.072  -4.2938  -1.5254   0.0679
 SC5  H1    H  HCR6  0   0.253   4.9931  -3.5237   1.6730
 SC5  H2    H  HCR6  0   0.251   3.8532  -3.6290  -0.5227
 SC5  H3    H  HCR6  0   0.247   2.8434  -1.5981  -1.4930
 SC5  H5    H  HCR6  0   0.245   4.0948   0.6557   1.9146
 SC5  H6    H  HCR6  0   0.252   5.1090  -1.3683   2.8894
 SC5  H71   H  HCH3  0   0.241   4.8167   1.7275  -0.9406
 SC5  H72   H  HCH3  0   0.230   4.0610   0.8564  -2.2799
 SC5  H73   H  HCH3  0   0.234   3.5109   2.4821  -1.8518
 SC5  H8    H  HCH1  0   0.221   2.7081   1.6621   0.3346
 SC5  H91   H  HCH2  0   0.233  -0.0593   2.8023  -0.9844
 SC5  H92   H  HCH2  0   0.231  -1.6257   2.3530  -0.3280
 SC5  H10   H  HCH1  0   0.209  -0.7761   4.6365   0.3654
 SC5  HO1   H  HOH1  0   0.454  -1.3465   4.2383   2.5381
 SC5  HO2   H  HOH1  0   0.445   1.2073   3.0165   1.4221
 SC5  HN1   H  HNH1  0   0.371  -0.5945   0.3566  -2.1508
 SC5  H11   H  HCH1  0   0.253   0.7937  -0.5062   0.2660
 SC5  HN2   H  HNH1  0   0.363  -0.4789   1.0040   1.2854
 SC5  HN3   H  HNH1  0   0.355   1.4092   1.4474  -1.8060
 SC5  H121  H  HCH2  0   0.208  -5.5217  -2.4437   1.5425
 SC5  H122  H  HCH2  0   0.228  -6.3182  -1.1673   0.6477
 SC5  HN41  H  HNH2  0   0.339  -5.6796  -3.7772  -0.4739
 SC5  HN42  H  HNH2  0   0.349  -7.1482  -3.2138  -0.0968
 SC5  H13   H  HCR6  0   0.243  -3.2575  -2.0397   1.8688
 SC5  H14   H  HCR6  0   0.261  -1.0862  -1.2533   1.1375
 SC5  H16   H  HCR6  0   0.251  -2.8090  -0.0622  -2.6164
 SC5  H17   H  HCR6  0   0.242  -4.9773  -0.9038  -1.8704

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
 SC5  C1   C2    aromatic  1.390  0.020  1.390
 SC5  C1   C6    aromatic  1.388  0.020  1.388
 SC5  C1   H1    single    0.930  0.020  1.080
 SC5  C2   C3    aromatic  1.388  0.020  1.388
 SC5  C2   H2    single    0.930  0.020  1.080
 SC5  C3   C4    aromatic  1.393  0.020  1.393
 SC5  C3   H3    single    0.930  0.020  1.080
 SC5  C4   C5    aromatic  1.391  0.020  1.391
 SC5  C4   C8    single    1.512  0.020  1.512
 SC5  C5   C6    aromatic  1.389  0.020  1.389
 SC5  C5   H5    single    0.930  0.020  1.080
 SC5  C6   H6    single    0.930  0.020  1.080
 SC5  C7   C8    single    1.526  0.020  1.526
 SC5  C7   H71   single    0.970  0.020  1.090
 SC5  C7   H72   single    0.970  0.020  1.090
 SC5  C7   H73   single    0.970  0.020  1.090
 SC5  C8   N3    single    1.452  0.020  1.452
 SC5  C8   H8    single    0.970  0.020  1.090
 SC5  C9   C10   single    1.524  0.020  1.524
 SC5  C9   N2    single    1.451  0.020  1.451
 SC5  C9   H91   single    0.970  0.020  1.090
 SC5  C9   H92   single    0.970  0.020  1.090
 SC5  C10  O1    single    1.403  0.020  1.403
 SC5  C10  O2    single    1.394  0.020  1.394
 SC5  C10  H10   single    0.970  0.020  1.090
 SC5  O1   HO1   single    0.850  0.020  0.980
 SC5  O2   HO2   single    0.850  0.020  0.980
 SC5  N1   C11   single    1.452  0.020  1.452
 SC5  N1   C15   single    1.380  0.020  1.380
 SC5  N1   HN1   single    0.890  0.020  1.040
 SC5  C11  N2    single    1.455  0.020  1.455
 SC5  C11  N3    single    1.437  0.020  1.437
 SC5  C11  H11   single    0.970  0.020  1.090
 SC5  N2   HN2   single    0.890  0.020  1.040
 SC5  N3   HN3   single    0.890  0.020  1.040
 SC5  C12  N4    single    1.456  0.020  1.456
 SC5  C12  C18   single    1.505  0.020  1.505
 SC5  C12  H121  single    0.970  0.020  1.090
 SC5  C12  H122  single    0.970  0.020  1.090
 SC5  N4   HN41  single    0.890  0.020  1.040
 SC5  N4   HN42  single    0.890  0.020  1.040
 SC5  C13  C14   aromatic  1.390  0.020  1.390
 SC5  C13  C18   aromatic  1.388  0.020  1.388
 SC5  C13  H13   single    0.930  0.020  1.080
 SC5  C14  C15   aromatic  1.398  0.020  1.398
 SC5  C14  H14   single    0.930  0.020  1.080
 SC5  C15  C16   aromatic  1.403  0.020  1.403
 SC5  C16  C17   aromatic  1.382  0.020  1.382
 SC5  C16  H16   single    0.930  0.020  1.080
 SC5  C17  C18   aromatic  1.396  0.020  1.396
 SC5  C17  H17   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
 SC5  H1    C1   C6    120.28  3.000
 SC5  H1    C1   C2    120.21  3.000
 SC5  C6    C1   C2    119.51  3.000
 SC5  H2    C2   C3    119.71  3.000
 SC5  H2    C2   C1    120.01  3.000
 SC5  C3    C2   C1    120.28  3.000
 SC5  H3    C3   C4    119.35  3.000
 SC5  H3    C3   C2    120.06  3.000
 SC5  C4    C3   C2    120.59  3.000
 SC5  C8    C4   C5    120.02  3.000
 SC5  C8    C4   C3    121.18  3.000
 SC5  C5    C4   C3    118.74  3.000
 SC5  H5    C5   C6    119.69  3.000
 SC5  H5    C5   C4    119.46  3.000
 SC5  C6    C5   C4    120.85  3.000
 SC5  H6    C6   C5    119.82  3.000
 SC5  H6    C6   C1    120.15  3.000
 SC5  C5    C6   C1    120.03  3.000
 SC5  H73   C7   H72   108.25  3.000
 SC5  H73   C7   H71   107.74  3.000
 SC5  H72   C7   H71   108.32  3.000
 SC5  H73   C7   C8    110.92  3.000
 SC5  H72   C7   C8    110.96  3.000
 SC5  H71   C7   C8    110.55  3.000
 SC5  H8    C8   N3    111.72  3.000
 SC5  H8    C8   C7    107.47  3.000
 SC5  N3    C8   C7    108.86  3.000
 SC5  H8    C8   C4    107.66  3.000
 SC5  N3    C8   C4    110.98  3.000
 SC5  C7    C8   C4    110.08  3.000
 SC5  H92   C9   H91   106.76  3.000
 SC5  H92   C9   N2    114.20  3.000
 SC5  H91   C9   N2    109.21  3.000
 SC5  H92   C9   C10   109.92  3.000
 SC5  H91   C9   C10   107.35  3.000
 SC5  N2    C9   C10   109.17  3.000
 SC5  H10   C10  O2    106.52  3.000
 SC5  H10   C10  O1    110.60  3.000
 SC5  O2    C10  O1    112.23  3.000
 SC5  H10   C10  C9    109.91  3.000
 SC5  O2    C10  C9    110.38  3.000
 SC5  O1    C10  C9    107.21  3.000
 SC5  HO1   O1   C10   108.69  3.000
 SC5  HO2   O2   C10   105.60  3.000
 SC5  HN1   N1   C15   114.10  3.000
 SC5  HN1   N1   C11   114.41  3.000
 SC5  C15   N1   C11   121.52  3.000
 SC5  H11   C11  N3    107.32  3.000
 SC5  H11   C11  N2    105.40  3.000
 SC5  N3    C11  N2    113.81  3.000
 SC5  H11   C11  N1    108.27  3.000
 SC5  N3    C11  N1    106.63  3.000
 SC5  N2    C11  N1    115.05  3.000
 SC5  HN2   N2   C11   110.12  3.000
 SC5  HN2   N2   C9    110.39  3.000
 SC5  C11   N2   C9    116.28  3.000
 SC5  HN3   N3   C11   111.15  3.000
 SC5  HN3   N3   C8    109.69  3.000
 SC5  C11   N3   C8    115.57  3.000
 SC5  H122  C12  H121  105.91  3.000
 SC5  H122  C12  C18   109.48  3.000
 SC5  H121  C12  C18   108.54  3.000
 SC5  H122  C12  N4    107.44  3.000
 SC5  H121  C12  N4    113.86  3.000
 SC5  C18   C12  N4    111.40  3.000
 SC5  HN42  N4   HN41  106.05  3.000
 SC5  HN42  N4   C12   109.28  3.000
 SC5  HN41  N4   C12   109.37  3.000
 SC5  H13   C13  C18   119.42  3.000
 SC5  H13   C13  C14   118.51  3.000
 SC5  C18   C13  C14   122.07  3.000
 SC5  H14   C14  C15   121.10  3.000
 SC5  H14   C14  C13   118.41  3.000
 SC5  C15   C14  C13   120.46  3.000
 SC5  C16   C15  C14   117.61  3.000
 SC5  C16   C15  N1    119.82  3.000
 SC5  C14   C15  N1    122.54  3.000
 SC5  H16   C16  C17   119.58  3.000
 SC5  H16   C16  C15   119.30  3.000
 SC5  C17   C16  C15   121.12  3.000
 SC5  H17   C17  C18   119.52  3.000
 SC5  H17   C17  C16   119.02  3.000
 SC5  C18   C17  C16   121.46  3.000
 SC5  C17   C18  C13   117.27  3.000
 SC5  C17   C18  C12   121.29  3.000
 SC5  C13   C18  C12   121.45  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
 SC5  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 SC5  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 SC5  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 SC5  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 SC5  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 SC5  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 SC5  CONST_07  C16   C15  C14  C13     0.00   0.0  0
 SC5  CONST_08  C16   C17  C18  C13     0.00   0.0  0
 SC5  CONST_09  C17   C18  C13  C14     0.00   0.0  0
 SC5  CONST_10  C17   C16  C15  C14     0.00   0.0  0
 SC5  CONST_11  C18   C13  C14  C15     0.00   0.0  0
 SC5  CONST_12  C18   C17  C16  C15     0.00   0.0  0
 SC5  CONST_13  C8    C4   C3   C2    180.00   0.0  0
 SC5  CONST_14  C8    C4   C5   C6    180.00   0.0  0
 SC5  CONST_15  C13   C14  C15  N1    180.00   0.0  0
 SC5  CONST_16  C17   C16  C15  N1    180.00   0.0  0
 SC5  CONST_17  C14   C13  C18  C12   180.00   0.0  0
 SC5  CONST_18  C16   C17  C18  C12   180.00   0.0  0
 SC5  CONST_19  H3    C3   C2   C1    180.00   0.0  0
 SC5  CONST_20  H5    C5   C6   C1    180.00   0.0  0
 SC5  CONST_21  H6    C6   C1   C2    180.00   0.0  0
 SC5  CONST_22  H1    C1   C2   C3    180.00   0.0  0
 SC5  CONST_23  H2    C2   C3   C4    180.00   0.0  0
 SC5  CONST_24  H17   C17  C18  C13   180.00   0.0  0
 SC5  CONST_25  H16   C16  C15  C14   180.00   0.0  0
 SC5  CONST_26  H13   C13  C14  C15   180.00   0.0  0
 SC5  CONST_27  H14   C14  C15  C16   180.00   0.0  0
 SC5  CONST_30  HN1   N1   C15  C14   180.00   0.0  0
 SC5  Var_01    C13   C18  C12  N4   -128.42  30.0  2
 SC5  Var_02    HN41  N4   C12  C18    66.42  30.0  3
 SC5  Var_03    C11   N2   C9   C10  -159.47  30.0  3
 SC5  Var_04    N2    C9   C10  O1    -71.75  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
 SC5  chir_01  C8   C4  C7  N3  negativ
 SC5  chir_02  C11  N1  N2  N3  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
 SC5  plan-1  C1   0.020
 SC5  plan-1  C2   0.020
 SC5  plan-1  C3   0.020
 SC5  plan-1  C4   0.020
 SC5  plan-1  C5   0.020
 SC5  plan-1  C6   0.020
 SC5  plan-1  C8   0.020
 SC5  plan-1  H1   0.020
 SC5  plan-1  H2   0.020
 SC5  plan-1  H3   0.020
 SC5  plan-1  H5   0.020
 SC5  plan-1  H6   0.020
 SC5  plan-2  N1   0.020
 SC5  plan-2  C12  0.020
 SC5  plan-2  C13  0.020
 SC5  plan-2  C14  0.020
 SC5  plan-2  C15  0.020
 SC5  plan-2  C16  0.020
 SC5  plan-2  C17  0.020
 SC5  plan-2  C18  0.020
 SC5  plan-2  H13  0.020
 SC5  plan-2  H14  0.020
 SC5  plan-2  H16  0.020
 SC5  plan-2  H17  0.020
 SC5  plan-3  N1   0.020
 SC5  plan-3  C11  0.020
 SC5  plan-3  C15  0.020
 SC5  plan-3  HN1  0.020

