# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 05:23:03 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N~2~-{[5-(pyridin-3-yl)thiophen-2-yl]methyl}-L-lysinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NCc1sc(cc1)c2cccnc2)C(N)=O
#
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
 RH2  RH2  N~2~-{[5-(pyridin-3-yl)thiophen-2-yl]methyl}-L-lysinamide  ligand  44  22  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RH2
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
 RH2  N01  N  NH2   0  -0.796  -3.8336   3.5431  -0.2176
 RH2  C02  C  C     0   0.502  -3.0534   2.6477   0.4010
 RH2  C03  C  CH1   0  -0.211  -3.0397   1.2474  -0.2201
 RH2  C04  C  CH2   0  -0.421  -4.0687   0.3801   0.5139
 RH2  C05  C  CH2   0  -0.416  -4.2879  -0.9724  -0.1498
 RH2  C06  C  CH2   0  -0.429  -5.2309  -1.8682   0.6419
 RH2  C07  C  CH2   0  -0.270  -5.4742  -3.2069  -0.0374
 RH2  N08  N  NH2   0  -0.801  -6.3582  -4.0456   0.7604
 RH2  N09  N  NH1   0  -0.563  -1.7406   0.6203  -0.1666
 RH2  C10  C  CH2   0  -0.326  -0.7249   1.2667  -0.9779
 RH2  C11  C  CR5   0  -0.190   0.5522   0.4895  -0.9130
 RH2  C12  C  CR15  0  -0.184   0.7913  -0.7741  -1.3680
 RH2  C13  C  CR15  0  -0.227   2.1014  -1.2300  -1.0858
 RH2  C14  C  CR5   0  -0.229   2.8571  -0.3124  -0.4055
 RH2  C15  C  CR6   0   0.053   4.2378  -0.4342   0.0478
 RH2  C16  C  CR16  0  -0.208   5.0668   0.6693   0.2473
 RH2  C17  C  CR16  0  -0.311   6.3673   0.4725   0.6776
 RH2  C18  C  CR16  0  -0.073   6.8103  -0.8245   0.8866
 RH2  N19  N  N     0  -0.394   6.0350  -1.8881   0.7038
 RH2  C20  C  CR16  0  -0.109   4.7884  -1.6934   0.3054
 RH2  S21  S  S2    0   0.230   1.9374   1.1190  -0.1149
 RH2  O22  O  O     0  -0.493  -2.4135   2.8955   1.4142
 RH2  H1   H  HNH2  0   0.407  -4.3241   3.3199  -1.0664
 RH2  H2   H  HNH2  0   0.400  -3.9502   4.4725   0.1529
 RH2  H3   H  HCH1  0   0.248  -3.3367   1.3212  -1.2728
 RH2  H4   H  HCH2  0   0.225  -3.7373   0.2412   1.5490
 RH2  H5   H  HCH2  0   0.234  -5.0194   0.9189   0.5669
 RH2  H6   H  HCH2  0   0.211  -4.6892  -0.8150  -1.1569
 RH2  H7   H  HCH2  0   0.224  -3.3252  -1.4728  -0.2778
 RH2  H8   H  HCH2  0   0.213  -4.8214  -2.0444   1.6415
 RH2  H9   H  HCH2  0   0.210  -6.1896  -1.3569   0.7865
 RH2  H10  H  HCH2  0   0.186  -5.8451  -3.0247  -1.0570
 RH2  H11  H  HCH2  0   0.210  -4.5190  -3.7278  -0.1508
 RH2  H12  H  HNH2  0   0.336  -7.2728  -3.6126   0.8062
 RH2  H13  H  HNH2  0   0.344  -6.5017  -4.9291   0.2883
 RH2  H15  H  HNH1  0   0.342  -1.4283   0.5786   0.7973
 RH2  H17  H  HCH2  0   0.253  -1.0754   1.2822  -2.0135
 RH2  H18  H  HCH2  0   0.221  -0.5338   2.3143  -0.7050
 RH2  H20  H  HCR5  0   0.262   0.0505  -1.3579  -1.8962
 RH2  H22  H  HCR5  0   0.264   2.4761  -2.1962  -1.3941
 RH2  H25  H  HCR6  0   0.269   4.7086   1.6736   0.0556
 RH2  H26  H  HCR6  0   0.276   7.0312   1.3104   0.8389
 RH2  H27  H  HCR6  0   0.268   7.8260  -1.0126   1.2148
 RH2  H28  H  HCR6  0   0.262   4.1775  -2.5826   0.1904

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
 RH2  N08  C07  single    1.456  0.020  1.456
 RH2  C07  C06  single    1.521  0.020  1.521
 RH2  C06  C05  single    1.523  0.020  1.523
 RH2  C05  C04  single    1.523  0.020  1.523
 RH2  C04  C03  single    1.533  0.020  1.533
 RH2  O22  C02  double    1.224  0.020  1.224
 RH2  C03  C02  single    1.532  0.020  1.532
 RH2  C03  N09  single    1.444  0.020  1.444
 RH2  C12  C13  aromatic  1.416  0.020  1.416
 RH2  C12  C11  aromatic  1.364  0.020  1.364
 RH2  C02  N01  single    1.339  0.020  1.339
 RH2  C13  C14  aromatic  1.370  0.020  1.370
 RH2  N09  C10  single    1.452  0.020  1.452
 RH2  C11  C10  single    1.496  0.020  1.496
 RH2  C11  S21  aromatic  1.718  0.020  1.718
 RH2  C14  C15  single    1.458  0.020  1.458
 RH2  C14  S21  aromatic  1.726  0.020  1.726
 RH2  C20  C15  aromatic  1.398  0.020  1.398
 RH2  C20  N19  aromatic  1.323  0.020  1.323
 RH2  C15  C16  aromatic  1.395  0.020  1.395
 RH2  N19  C18  aromatic  1.329  0.020  1.329
 RH2  C16  C17  aromatic  1.384  0.020  1.384
 RH2  C18  C17  aromatic  1.386  0.020  1.386
 RH2  N01  H1   single    0.860  0.020  1.020
 RH2  N01  H2   single    0.860  0.020  1.020
 RH2  C03  H3   single    0.970  0.020  1.090
 RH2  C04  H4   single    0.970  0.020  1.090
 RH2  C04  H5   single    0.970  0.020  1.090
 RH2  C05  H6   single    0.970  0.020  1.090
 RH2  C05  H7   single    0.970  0.020  1.090
 RH2  C06  H8   single    0.970  0.020  1.090
 RH2  C06  H9   single    0.970  0.020  1.090
 RH2  C07  H10  single    0.970  0.020  1.090
 RH2  C07  H11  single    0.970  0.020  1.090
 RH2  N08  H12  single    0.890  0.020  1.040
 RH2  N08  H13  single    0.890  0.020  1.040
 RH2  N09  H15  single    0.890  0.020  1.040
 RH2  C10  H17  single    0.970  0.020  1.090
 RH2  C10  H18  single    0.970  0.020  1.090
 RH2  C12  H20  single    0.930  0.020  1.080
 RH2  C13  H22  single    0.930  0.020  1.080
 RH2  C16  H25  single    0.930  0.020  1.080
 RH2  C17  H26  single    0.930  0.020  1.080
 RH2  C18  H27  single    0.930  0.020  1.080
 RH2  C20  H28  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
 RH2  H2   N01  H1   117.31  3.000
 RH2  H2   N01  C02  120.96  3.000
 RH2  H1   N01  C02  121.73  3.000
 RH2  O22  C02  C03  121.08  3.000
 RH2  C03  C02  N01  115.41  3.000
 RH2  O22  C02  N01  123.49  3.000
 RH2  H3   C03  N09  107.97  3.000
 RH2  H3   C03  C04  108.43  3.000
 RH2  N09  C03  C04  109.91  3.000
 RH2  H3   C03  C02  108.99  3.000
 RH2  N09  C03  C02  112.96  3.000
 RH2  C04  C03  C02  108.48  3.000
 RH2  H5   C04  H4   106.23  3.000
 RH2  H5   C04  C05  109.48  3.000
 RH2  H4   C04  C05  110.05  3.000
 RH2  H5   C04  C03  109.14  3.000
 RH2  H4   C04  C03  108.72  3.000
 RH2  C05  C04  C03  112.99  3.000
 RH2  H7   C05  H6   106.31  3.000
 RH2  H7   C05  C06  109.71  3.000
 RH2  H6   C05  C06  109.62  3.000
 RH2  H7   C05  C04  109.33  3.000
 RH2  H6   C05  C04  109.02  3.000
 RH2  C06  C05  C04  112.65  3.000
 RH2  H9   C06  H8   106.37  3.000
 RH2  H9   C06  C07  109.25  3.000
 RH2  H8   C06  C07  109.04  3.000
 RH2  H9   C06  C05  109.62  3.000
 RH2  H8   C06  C05  109.75  3.000
 RH2  C07  C06  C05  112.63  3.000
 RH2  H11  C07  H10  106.10  3.000
 RH2  H11  C07  N08  108.21  3.000
 RH2  H10  C07  N08  113.48  3.000
 RH2  H11  C07  C06  109.01  3.000
 RH2  H10  C07  C06  108.79  3.000
 RH2  N08  C07  C06  111.06  3.000
 RH2  H13  N08  H12  105.44  3.000
 RH2  H13  N08  C07  109.46  3.000
 RH2  H12  N08  C07  109.07  3.000
 RH2  H15  N09  C10  109.51  3.000
 RH2  H15  N09  C03  109.28  3.000
 RH2  C10  N09  C03  114.55  3.000
 RH2  H18  C10  H17  106.10  3.000
 RH2  H18  C10  C11  109.63  3.000
 RH2  H17  C10  C11  108.79  3.000
 RH2  H18  C10  N09  114.03  3.000
 RH2  H17  C10  N09  108.14  3.000
 RH2  C11  C10  N09  109.97  3.000
 RH2  S21  C11  C12  110.67  3.000
 RH2  S21  C11  C10  121.19  3.000
 RH2  C12  C11  C10  128.04  3.000
 RH2  H20  C12  C13  123.90  3.000
 RH2  H20  C12  C11  122.89  3.000
 RH2  C13  C12  C11  113.21  3.000
 RH2  H22  C13  C14  123.31  3.000
 RH2  H22  C13  C12  123.48  3.000
 RH2  C14  C13  C12  113.19  3.000
 RH2  S21  C14  C15  121.43  3.000
 RH2  S21  C14  C13  110.20  3.000
 RH2  C15  C14  C13  128.37  3.000
 RH2  C20  C15  C16  116.88  3.000
 RH2  C16  C15  C14  122.76  3.000
 RH2  C20  C15  C14  120.35  3.000
 RH2  H25  C16  C17  119.84  3.000
 RH2  H25  C16  C15  120.77  3.000
 RH2  C17  C16  C15  119.38  3.000
 RH2  H26  C17  C18  120.41  3.000
 RH2  H26  C17  C16  120.88  3.000
 RH2  C18  C17  C16  118.70  3.000
 RH2  H27  C18  N19  116.71  3.000
 RH2  H27  C18  C17  120.50  3.000
 RH2  N19  C18  C17  122.79  3.000
 RH2  C20  N19  C18  118.25  3.000
 RH2  H28  C20  N19  116.22  3.000
 RH2  H28  C20  C15  119.80  3.000
 RH2  N19  C20  C15  123.98  3.000
 RH2  C14  S21  C11   92.72  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
 RH2  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 RH2  CONST_02  C13  C14  S21  C11     0.00   0.0  0
 RH2  CONST_03  C15  C14  S21  C11   180.00   0.0  0
 RH2  CONST_04  C15  C14  C13  C12   180.00   0.0  0
 RH2  CONST_05  S21  C14  C13  C12     0.00   0.0  0
 RH2  CONST_06  C14  S21  C11  C12     0.00   0.0  0
 RH2  CONST_07  S21  C11  C12  C13     0.00   0.0  0
 RH2  CONST_10  N19  C20  C15  C14   180.00   0.0  0
 RH2  CONST_11  C17  C16  C15  C14   180.00   0.0  0
 RH2  CONST_12  C18  N19  C20  C15     0.00   0.0  0
 RH2  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 RH2  CONST_15  N19  C20  C15  C16     0.00   0.0  0
 RH2  CONST_16  N19  C18  C17  C16     0.00   0.0  0
 RH2  CONST_17  C20  C15  C16  C17     0.00   0.0  0
 RH2  CONST_18  C20  N19  C18  C17     0.00   0.0  0
 RH2  CONST_20  C13  C12  C11  C10   180.00   0.0  0
 RH2  CONST_21  C14  S21  C11  C10   180.00   0.0  0
 RH2  CONST_22  H22  C13  C12  C11   180.00   0.0  0
 RH2  CONST_23  H20  C12  C13  C14   180.00   0.0  0
 RH2  CONST_24  H28  C20  C15  C14     0.00   0.0  0
 RH2  CONST_25  H25  C16  C15  C14     0.00   0.0  0
 RH2  CONST_26  H26  C17  C16  C15   180.00   0.0  0
 RH2  CONST_27  H27  C18  C17  C16   180.00   0.0  0
 RH2  CONST_28  H1   N01  C02  C03     0.00   0.0  0
 RH2  CONST_29  H2   N01  C02  C03   180.00   0.0  0
 RH2  Var_01    C12  C11  C10  N09    64.91  30.0  2
 RH2  Var_02    C11  C10  N09  C03  -176.58  30.0  3
 RH2  Var_03    C06  C05  C04  C03   175.66  30.0  1
 RH2  Var_04    C07  C06  C05  C04   178.70  30.0  1
 RH2  Var_05    N08  C07  C06  C05   178.87  30.0  1
 RH2  Var_06    H12  N08  C07  C06    65.25  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
 RH2  chir_01  C03  C04  C02  N09  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
 RH2  plan-1  C10  0.020
 RH2  plan-1  C11  0.020
 RH2  plan-1  C12  0.020
 RH2  plan-1  C13  0.020
 RH2  plan-1  C14  0.020
 RH2  plan-1  C15  0.020
 RH2  plan-1  S21  0.020
 RH2  plan-1  H20  0.020
 RH2  plan-1  H22  0.020
 RH2  plan-2  C14  0.020
 RH2  plan-2  C15  0.020
 RH2  plan-2  C16  0.020
 RH2  plan-2  C17  0.020
 RH2  plan-2  C18  0.020
 RH2  plan-2  N19  0.020
 RH2  plan-2  C20  0.020
 RH2  plan-2  H25  0.020
 RH2  plan-2  H26  0.020
 RH2  plan-2  H27  0.020
 RH2  plan-2  H28  0.020
 RH2  plan-3  N01  0.020
 RH2  plan-3  C02  0.020
 RH2  plan-3  C03  0.020
 RH2  plan-3  O22  0.020
 RH2  plan-3  H1   0.020
 RH2  plan-3  H2   0.020

