# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:30:53 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[3-[[[(2S)-pyrrolidin-2-yl]methylamino]methyl]phenyl]thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=C(Nc1cccc(CNC[C@@H]2CCCN2)c1)c3sccc3
#
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
 H49  H49  N-[3-[[[(2S)-pyrrolidin-2-yl]methylamino]methyl]phenyl]thiophene-2-carboximidamide  ligand  44  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H49
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
 H49  C22   C  CH2   0  -0.450  -6.0839  -1.6769  -0.9179
 H49  C21   C  CH2   0  -0.467  -6.6974  -2.4368   0.2738
 H49  C20   C  CH2   0  -0.322  -5.7478  -2.1200   1.4513
 H49  N19   N  NH1   0  -0.585  -4.9764  -0.9422   1.0714
 H49  C18   C  CH1   0  -0.121  -4.7640  -1.1132  -0.3648
 H49  C17   C  CH2   0  -0.264  -4.3120   0.1717  -1.0275
 H49  N16   N  NH1   0  -0.597  -3.0253   0.6064  -0.5225
 H49  C15   C  CH2   0  -0.307  -2.6309   1.8984  -1.0415
 H49  C12   C  CR6   0   0.095  -1.2606   2.3119  -0.5717
 H49  C13   C  CR16  0  -0.415  -0.2374   1.3803  -0.4771
 H49  C11   C  CR16  0  -0.335  -0.9934   3.6424  -0.2582
 H49  C10   C  CR16  0  -0.232   0.2840   4.0139   0.1311
 H49  C09   C  CR16  0  -0.334   1.3140   3.0876   0.2186
 H49  C08   C  CR6   0   0.403   1.0535   1.7499  -0.0869
 H49  N07   N  NH1   0  -0.755   1.9952   0.7254  -0.0080
 H49  C06   C  C     0   0.419   3.3525   0.7973   0.1606
 H49  N14   N  N     0  -0.634   3.9898   1.9016   0.1884
 H49  C05   C  CR5   0  -0.296   3.9995  -0.5230   0.2990
 H49  S01   S  S2    0   0.241   3.2521  -1.8335   1.1358
 H49  C02   C  CR15  0  -0.458   4.5963  -2.8529   0.8590
 H49  C03   C  CR15  0  -0.175   5.5773  -2.2167   0.1599
 H49  C04   C  CR15  0  -0.207   5.2366  -0.8782  -0.1593
 H49  H221  H  HCH2  0   0.234  -5.9256  -2.3112  -1.7908
 H49  H222  H  HCH2  0   0.222  -6.7345  -0.8553  -1.2313
 H49  H211  H  HCH2  0   0.230  -7.7090  -2.0870   0.4820
 H49  H212  H  HCH2  0   0.231  -6.7623  -3.5098   0.0907
 H49  H18   H  HCH1  0   0.225  -3.9754  -1.8656  -0.4907
 H49  H201  H  HCH2  0   0.236  -6.2698  -1.9511   2.3933
 H49  H202  H  HCH2  0   0.222  -5.0575  -2.9535   1.6078
 H49  H19   H  HNH1  0   0.335  -5.5670  -0.1251   1.2004
 H49  H171  H  HCH2  0   0.230  -4.2276   0.0064  -2.1061
 H49  H172  H  HCH2  0   0.186  -5.1017   0.9328  -0.8943
 H49  H16   H  HNH1  0   0.343  -3.0719   0.6524   0.4887
 H49  H151  H  HCH2  0   0.239  -2.6228   1.8318  -2.1352
 H49  H152  H  HCH2  0   0.213  -3.3496   2.6965  -0.7991
 H49  H13   H  HCR6  0   0.256  -0.4500   0.3416  -0.7052
 H49  H11   H  HCR6  0   0.245  -1.7819   4.3827  -0.3162
 H49  H10   H  HCR6  0   0.252   0.4912   5.0482   0.3749
 H49  H09   H  HCR6  0   0.282   2.3026   3.3984   0.5127
 H49  H141  H  H     0   0.346   4.9699   1.7369   0.3851
 H49  H142  H  HNH1  0   0.409   1.6326  -0.1827  -0.2530
 H49  H04   H  HCR5  0   0.278   5.8744  -0.2126  -0.7247
 H49  H02   H  HCR5  0   0.305   4.5956  -3.8646   1.2344
 H49  H03   H  HCR5  0   0.275   6.5084  -2.6858  -0.1226

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
 H49  C22  C21   single    1.541  0.020  1.541
 H49  C22  C18   single    1.538  0.020  1.538
 H49  C21  C20   single    1.545  0.020  1.545
 H49  C20  N19   single    1.458  0.020  1.458
 H49  N19  C18   single    1.462  0.020  1.462
 H49  C18  C17   single    1.515  0.020  1.515
 H49  C17  N16   single    1.449  0.020  1.449
 H49  N16  C15   single    1.447  0.020  1.447
 H49  C15  C12   single    1.506  0.020  1.506
 H49  C12  C13   aromatic  1.387  0.020  1.387
 H49  C12  C11   aromatic  1.393  0.020  1.393
 H49  C13  C08   aromatic  1.398  0.020  1.398
 H49  C11  C10   aromatic  1.386  0.020  1.386
 H49  C10  C09   aromatic  1.388  0.020  1.388
 H49  C09  C08   aromatic  1.397  0.020  1.397
 H49  C08  N07   single    1.394  0.020  1.394
 H49  N07  C06   single    1.370  0.020  1.370
 H49  C06  N14   double    1.275  0.020  1.275
 H49  C06  C05   single    1.477  0.020  1.477
 H49  C05  S01   aromatic  1.725  0.020  1.725
 H49  C05  C04   aromatic  1.366  0.020  1.366
 H49  S01  C02   aromatic  1.710  0.020  1.710
 H49  C02  C03   aromatic  1.362  0.020  1.362
 H49  C03  C04   aromatic  1.418  0.020  1.418
 H49  C22  H221  single    0.970  0.020  1.090
 H49  C22  H222  single    0.970  0.020  1.090
 H49  C21  H211  single    0.970  0.020  1.090
 H49  C21  H212  single    0.970  0.020  1.090
 H49  C18  H18   single    0.970  0.020  1.090
 H49  C20  H201  single    0.970  0.020  1.090
 H49  C20  H202  single    0.970  0.020  1.090
 H49  N19  H19   single    0.890  0.020  1.040
 H49  C17  H171  single    0.970  0.020  1.090
 H49  C17  H172  single    0.970  0.020  1.090
 H49  N16  H16   single    0.890  0.020  1.040
 H49  C15  H151  single    0.970  0.020  1.090
 H49  C15  H152  single    0.970  0.020  1.090
 H49  C13  H13   single    0.930  0.020  1.080
 H49  C11  H11   single    0.930  0.020  1.080
 H49  C10  H10   single    0.930  0.020  1.080
 H49  C09  H09   single    0.930  0.020  1.080
 H49  N14  H141  single    0.890  0.020  1.040
 H49  N07  H142  single    0.860  0.020  1.020
 H49  C04  H04   single    0.930  0.020  1.080
 H49  C02  H02   single    0.930  0.020  1.080
 H49  C03  H03   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
 H49  H222  C22  H221  107.08  3.000
 H49  H222  C22  C18   109.77  3.000
 H49  H221  C22  C18   112.11  3.000
 H49  H222  C22  C21   110.81  3.000
 H49  H221  C22  C21   112.95  3.000
 H49  C18   C22  C21   104.14  3.000
 H49  H212  C21  H211  107.00  3.000
 H49  H212  C21  C20   111.48  3.000
 H49  H211  C21  C20   111.03  3.000
 H49  H212  C21  C22   112.28  3.000
 H49  H211  C21  C22   111.03  3.000
 H49  C20   C21  C22   104.10  3.000
 H49  H202  C20  H201  107.26  3.000
 H49  H202  C20  N19   108.60  3.000
 H49  H201  C20  N19   110.68  3.000
 H49  H202  C20  C21   109.92  3.000
 H49  H201  C20  C21   113.33  3.000
 H49  N19   C20  C21   106.98  3.000
 H49  H19   N19  C18   107.65  3.000
 H49  H19   N19  C20   107.99  3.000
 H49  C18   N19  C20   103.79  3.000
 H49  H18   C18  C17   108.48  3.000
 H49  H18   C18  N19   107.30  3.000
 H49  C17   C18  N19   111.96  3.000
 H49  H18   C18  C22   108.91  3.000
 H49  C17   C18  C22   114.18  3.000
 H49  N19   C18  C22   105.75  3.000
 H49  H172  C17  H171  106.14  3.000
 H49  H172  C17  N16   112.71  3.000
 H49  H171  C17  N16   108.68  3.000
 H49  H172  C17  C18   108.56  3.000
 H49  H171  C17  C18   109.03  3.000
 H49  N16   C17  C18   111.53  3.000
 H49  H16   N16  C15   109.26  3.000
 H49  H16   N16  C17   108.70  3.000
 H49  C15   N16  C17   112.64  3.000
 H49  H152  C15  H151  105.58  3.000
 H49  H152  C15  C12   109.03  3.000
 H49  H151  C15  C12   108.74  3.000
 H49  H152  C15  N16   112.98  3.000
 H49  H151  C15  N16   107.80  3.000
 H49  C12   C15  N16   112.41  3.000
 H49  C11   C12  C13   118.99  3.000
 H49  C11   C12  C15   120.46  3.000
 H49  C13   C12  C15   120.53  3.000
 H49  H13   C13  C08   119.53  3.000
 H49  H13   C13  C12   118.97  3.000
 H49  C08   C13  C12   121.50  3.000
 H49  H11   C11  C10   120.18  3.000
 H49  H11   C11  C12   120.08  3.000
 H49  C10   C11  C12   119.74  3.000
 H49  H10   C10  C09   118.77  3.000
 H49  H10   C10  C11   119.71  3.000
 H49  C09   C10  C11   121.52  3.000
 H49  H09   C09  C08   120.48  3.000
 H49  H09   C09  C10   120.38  3.000
 H49  C08   C09  C10   119.14  3.000
 H49  N07   C08  C09   124.44  3.000
 H49  N07   C08  C13   116.44  3.000
 H49  C09   C08  C13   119.11  3.000
 H49  H142  N07  C06   115.70  3.000
 H49  H142  N07  C08   113.91  3.000
 H49  C06   N07  C08   129.64  3.000
 H49  C05   C06  N14   123.59  3.000
 H49  C05   C06  N07   113.50  3.000
 H49  N14   C06  N07   122.92  3.000
 H49  H141  N14  C06   110.30  3.000
 H49  C04   C05  S01   110.95  3.000
 H49  C04   C05  C06   126.70  3.000
 H49  S01   C05  C06   122.33  3.000
 H49  C02   S01  C05    91.93  3.000
 H49  H02   C02  C03   128.08  3.000
 H49  H02   C02  S01   120.15  3.000
 H49  C03   C02  S01   111.77  3.000
 H49  H03   C03  C04   123.94  3.000
 H49  H03   C03  C02   123.51  3.000
 H49  C04   C03  C02   112.54  3.000
 H49  H04   C04  C03   123.85  3.000
 H49  H04   C04  C05   123.33  3.000
 H49  C03   C04  C05   112.80  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
 H49  CONST_01  C09   C08  C13  C12     0.00   0.0  0
 H49  CONST_02  C09   C10  C11  C12     0.00   0.0  0
 H49  CONST_03  C10   C11  C12  C13     0.00   0.0  0
 H49  CONST_04  C10   C09  C08  C13     0.00   0.0  0
 H49  CONST_05  C08   C13  C12  C11     0.00   0.0  0
 H49  CONST_06  C08   C09  C10  C11     0.00   0.0  0
 H49  CONST_07  C03   C02  S01  C05     0.00   0.0  0
 H49  CONST_08  C02   C03  C04  C05     0.00   0.0  0
 H49  CONST_09  C03   C04  C05  S01     0.00   0.0  0
 H49  CONST_10  C04   C03  C02  S01     0.00   0.0  0
 H49  CONST_11  C04   C05  S01  C02     0.00   0.0  0
 H49  CONST_12  C08   C13  C12  C15   180.00   0.0  0
 H49  CONST_13  C10   C11  C12  C15   180.00   0.0  0
 H49  CONST_14  N07   C08  C13  C12   180.00   0.0  0
 H49  CONST_15  N07   C08  C09  C10   180.00   0.0  0
 H49  CONST_16  C02   S01  C05  C06   180.00   0.0  0
 H49  CONST_17  C03   C04  C05  C06   180.00   0.0  0
 H49  CONST_18  H10   C10  C11  C12   180.00   0.0  0
 H49  CONST_19  H11   C11  C12  C13   180.00   0.0  0
 H49  CONST_20  H09   C09  C08  C13   180.00   0.0  0
 H49  CONST_21  H13   C13  C12  C11   180.00   0.0  0
 H49  CONST_22  H02   C02  S01  C05   180.00   0.0  0
 H49  CONST_23  H03   C03  C04  C05   180.00   0.0  0
 H49  CONST_24  H04   C04  C05  S01   180.00   0.0  0
 H49  CONST_25  C06   N07  C08  C13   180.00   0.0  0
 H49  CONST_26  C06   N07  C08  C09     0.00   0.0  0
 H49  CONST_27  C05   C06  N07  C08   180.00   0.0  0
 H49  CONST_28  H142  N07  C08  C13     0.00   0.0  0
 H49  CONST_29  N14   C06  N07  C08     0.00   0.0  0
 H49  CONST_30  H141  N14  C06  C05     0.00   0.0  0
 H49  Var_01    N19   C20  C21  C22    18.12  30.0  1
 H49  Var_02    C18   N19  C20  C21   -35.85  30.0  1
 H49  Var_03    C18   C22  C21  C20     5.70  30.0  1
 H49  Var_04    C13   C12  C15  N16    39.26  30.0  2
 H49  Var_05    S01   C05  C06  N07   -36.52  30.0  2
 H49  Var_06    C15   N16  C17  C18  -174.29  30.0  3
 H49  Var_07    C12   C15  N16  C17  -176.93  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
 H49  chir_01  C18  C22  N19  C17  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
 H49  plan-1  C06   0.020
 H49  plan-1  C05   0.020
 H49  plan-1  S01   0.020
 H49  plan-1  C02   0.020
 H49  plan-1  C03   0.020
 H49  plan-1  C04   0.020
 H49  plan-1  H04   0.020
 H49  plan-1  H02   0.020
 H49  plan-1  H03   0.020
 H49  plan-2  C15   0.020
 H49  plan-2  C12   0.020
 H49  plan-2  C13   0.020
 H49  plan-2  C11   0.020
 H49  plan-2  C10   0.020
 H49  plan-2  C09   0.020
 H49  plan-2  C08   0.020
 H49  plan-2  N07   0.020
 H49  plan-2  H13   0.020
 H49  plan-2  H11   0.020
 H49  plan-2  H10   0.020
 H49  plan-2  H09   0.020
 H49  plan-3  C08   0.020
 H49  plan-3  N07   0.020
 H49  plan-3  C06   0.020
 H49  plan-3  N14   0.020
 H49  plan-3  C05   0.020
 H49  plan-3  H141  0.020
 H49  plan-3  H142  0.020

