# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:12:19 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N-(4-{2-[(3-chlorobenzyl)amino]ethyl}phenyl)thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CNCCc2ccc(NC(=N)c3sccc3)cc2)c1
#
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
 ARR  ARR  N-(4-{2-[(3-chlorobenzyl)amino]ethyl}phenyl)thiophene-2-carboximidamide  ligand  45  25  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ARR
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
 ARR  S     S   S2    0   0.240  -0.8913   1.4307   -6.9086
 ARR  C1    C   CR15  0  -0.458  -0.9426   1.2820   -8.6111
 ARR  C2    C   CR15  0  -0.176  -0.1427   0.2723   -9.0543
 ARR  C3    C   CR15  0  -0.206   0.5242  -0.3964   -7.9967
 ARR  C4    C   CR5   0  -0.296   0.2155   0.1152   -6.7683
 ARR  C5    C   C     0   0.420   0.7529  -0.3341   -5.4675
 ARR  N3    N   N     0  -0.637   1.9507  -0.7419   -5.3035
 ARR  N1    N   NH1   0  -0.750  -0.1595  -0.2806   -4.4494
 ARR  C6    C   CR6   0   0.355   0.0044  -0.5472   -3.0913
 ARR  C10   C   CR16  0  -0.302   1.2257  -0.8268   -2.4758
 ARR  C11   C   CR16  0  -0.300   1.2706  -1.0606   -1.1072
 ARR  C9    C   CR6   0   0.108   0.1310  -1.0343   -0.3121
 ARR  C8    C   CR16  0  -0.295  -1.0814  -0.7549   -0.9397
 ARR  C7    C   CR16  0  -0.346  -1.1489  -0.5165   -2.2997
 ARR  C12   C   CH2   0  -0.529   0.2025  -1.2546    1.1720
 ARR  C13   C   CH2   0  -0.244   0.4560   0.0471    1.9267
 ARR  N2    N   NH1   0  -0.598   0.4840  -0.1839    3.3577
 ARR  C14   C   CH2   0  -0.309   0.7295   1.0218    4.1206
 ARR  C15   C   CR6   0   0.078   0.6269   0.7766    5.6033
 ARR  C20   C   CR16  0  -0.252  -0.3899  -0.0297    6.1098
 ARR  C19   C   CR6   0  -0.019  -0.4935  -0.2215    7.4768
 ARR  C18   C   CR16  0  -0.232   0.3928   0.3674    8.3664
 ARR  C17   C   CR16  0  -0.246   1.4053   1.1658    7.8560
 ARR  C16   C   CR16  0  -0.303   1.5242   1.3665    6.4871
 ARR  CL    CL  CL    0  -0.136  -1.7660  -1.2302    8.0938
 ARR  H1    H   HCR5  0   0.305  -1.5541   1.9524   -9.1949
 ARR  H2    H   HCR5  0   0.275  -0.0362   0.0099  -10.0966
 ARR  H3    H   HCR5  0   0.278   1.1891  -1.2371   -8.1380
 ARR  HN3   H   H     0   0.346   2.4775  -0.6402   -6.1629
 ARR  HN1   H   HNH1  0   0.409  -1.1179  -0.1345   -4.7246
 ARR  H10   H   HCR6  0   0.284   2.1279  -0.8727   -3.0636
 ARR  H11   H   HCR6  0   0.244   2.2307  -1.2818   -0.6546
 ARR  H8    H   HCR6  0   0.248  -1.9943  -0.7289   -0.3556
 ARR  H7    H   HCR6  0   0.263  -2.1092  -0.3031   -2.7559
 ARR  H121  H   HCH2  0   0.240   1.0016  -1.9652    1.4029
 ARR  H122  H   HCH2  0   0.241  -0.7294  -1.6964    1.5333
 ARR  H131  H   HCH2  0   0.225  -0.3506   0.7546    1.7100
 ARR  H132  H   HCH2  0   0.197   1.3825   0.5085    1.5499
 ARR  HN2   H   HNH1  0   0.344   1.2094  -0.8598    3.5696
 ARR  H141  H   HCH2  0   0.245  -0.0269   1.7605    3.8341
 ARR  H142  H   HCH2  0   0.219   1.7018   1.4864    3.8987
 ARR  H20   H   HCR6  0   0.268  -1.0867  -0.5066    5.4333
 ARR  H18   H   HCR6  0   0.277   0.2999   0.2028    9.4313
 ARR  H17   H   HCR6  0   0.266   2.1108   1.6282    8.5338
 ARR  H16   H   HCR6  0   0.255   2.3274   1.9833    6.1027

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
 ARR  S    C1    aromatic  1.710  0.020  1.710
 ARR  S    C4    aromatic  1.725  0.020  1.725
 ARR  C1   C2    aromatic  1.362  0.020  1.362
 ARR  C1   H1    single    0.930  0.020  1.080
 ARR  C2   C3    aromatic  1.418  0.020  1.418
 ARR  C2   H2    single    0.930  0.020  1.080
 ARR  C3   C4    aromatic  1.366  0.020  1.366
 ARR  C3   H3    single    0.930  0.020  1.080
 ARR  C4   C5    single    1.477  0.020  1.477
 ARR  C5   N3    double    1.276  0.020  1.276
 ARR  C5   N1    single    1.368  0.020  1.368
 ARR  N3   HN3   single    0.890  0.020  1.040
 ARR  N1   C6    single    1.394  0.020  1.394
 ARR  N1   HN1   single    0.860  0.020  1.020
 ARR  C6   C10   aromatic  1.396  0.020  1.396
 ARR  C6   C7    aromatic  1.399  0.020  1.399
 ARR  C10  C11   aromatic  1.389  0.020  1.389
 ARR  C10  H10   single    0.930  0.020  1.080
 ARR  C11  C9    aromatic  1.390  0.020  1.390
 ARR  C11  H11   single    0.930  0.020  1.080
 ARR  C9   C8    aromatic  1.394  0.020  1.394
 ARR  C9   C12   single    1.502  0.020  1.502
 ARR  C8   C7    aromatic  1.382  0.020  1.382
 ARR  C8   H8    single    0.930  0.020  1.080
 ARR  C7   H7    single    0.930  0.020  1.080
 ARR  C12  C13   single    1.526  0.020  1.526
 ARR  C12  H121  single    0.970  0.020  1.090
 ARR  C12  H122  single    0.970  0.020  1.090
 ARR  C13  N2    single    1.450  0.020  1.450
 ARR  C13  H131  single    0.970  0.020  1.090
 ARR  C13  H132  single    0.970  0.020  1.090
 ARR  N2   C14   single    1.448  0.020  1.448
 ARR  N2   HN2   single    0.890  0.020  1.040
 ARR  C14  C15   single    1.506  0.020  1.506
 ARR  C14  H141  single    0.970  0.020  1.090
 ARR  C14  H142  single    0.970  0.020  1.090
 ARR  C15  C20   aromatic  1.393  0.020  1.393
 ARR  C15  C16   aromatic  1.391  0.020  1.391
 ARR  C20  C19   aromatic  1.384  0.020  1.384
 ARR  C20  H20   single    0.930  0.020  1.080
 ARR  C19  C18   aromatic  1.387  0.020  1.387
 ARR  C19  CL    single    1.737  0.020  1.737
 ARR  C18  C17   aromatic  1.387  0.020  1.387
 ARR  C18  H18   single    0.930  0.020  1.080
 ARR  C17  C16   aromatic  1.389  0.020  1.389
 ARR  C17  H17   single    0.930  0.020  1.080
 ARR  C16  H16   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
 ARR  C4    S    C1     91.94  3.000
 ARR  H1    C1   C2    128.12  3.000
 ARR  H1    C1   S     120.11  3.000
 ARR  C2    C1   S     111.77  3.000
 ARR  H2    C2   C3    123.98  3.000
 ARR  H2    C2   C1    123.50  3.000
 ARR  C3    C2   C1    112.53  3.000
 ARR  H3    C3   C4    123.21  3.000
 ARR  H3    C3   C2    123.95  3.000
 ARR  C4    C3   C2    112.82  3.000
 ARR  C5    C4   C3    126.56  3.000
 ARR  C5    C4   S     122.48  3.000
 ARR  C3    C4   S     110.94  3.000
 ARR  N1    C5   N3    122.88  3.000
 ARR  N1    C5   C4    113.62  3.000
 ARR  N3    C5   C4    123.50  3.000
 ARR  HN3   N3   C5    110.31  3.000
 ARR  HN1   N1   C6    113.94  3.000
 ARR  HN1   N1   C5    115.89  3.000
 ARR  C6    N1   C5    129.73  3.000
 ARR  C7    C6   C10   118.43  3.000
 ARR  C7    C6   N1    116.75  3.000
 ARR  C10   C6   N1    124.81  3.000
 ARR  H10   C10  C11   120.20  3.000
 ARR  H10   C10  C6    120.03  3.000
 ARR  C11   C10  C6    119.76  3.000
 ARR  H11   C11  C9    119.42  3.000
 ARR  H11   C11  C10   118.31  3.000
 ARR  C9    C11  C10   122.27  3.000
 ARR  C12   C9   C8    121.05  3.000
 ARR  C12   C9   C11   121.57  3.000
 ARR  C8    C9   C11   117.36  3.000
 ARR  H8    C8   C7    119.00  3.000
 ARR  H8    C8   C9    119.66  3.000
 ARR  C7    C8   C9    121.34  3.000
 ARR  H7    C7   C8    119.41  3.000
 ARR  H7    C7   C6    119.76  3.000
 ARR  C8    C7   C6    120.84  3.000
 ARR  H122  C12  H121  106.89  3.000
 ARR  H122  C12  C13   108.85  3.000
 ARR  H121  C12  C13   109.17  3.000
 ARR  H122  C12  C9    110.21  3.000
 ARR  H121  C12  C9    109.79  3.000
 ARR  C13   C12  C9    111.81  3.000
 ARR  H132  C13  H131  106.34  3.000
 ARR  H132  C13  N2    112.85  3.000
 ARR  H131  C13  N2    108.22  3.000
 ARR  H132  C13  C12   109.14  3.000
 ARR  H131  C13  C12   109.33  3.000
 ARR  N2    C13  C12   110.82  3.000
 ARR  HN2   N2   C14   108.89  3.000
 ARR  HN2   N2   C13   109.05  3.000
 ARR  C14   N2   C13   113.00  3.000
 ARR  H142  C14  H141  105.83  3.000
 ARR  H142  C14  C15   109.11  3.000
 ARR  H141  C14  C15   108.67  3.000
 ARR  H142  C14  N2    113.28  3.000
 ARR  H141  C14  N2    107.86  3.000
 ARR  C15   C14  N2    111.81  3.000
 ARR  C16   C15  C20   119.03  3.000
 ARR  C16   C15  C14   120.84  3.000
 ARR  C20   C15  C14   120.12  3.000
 ARR  H20   C20  C19   120.55  3.000
 ARR  H20   C20  C15   119.86  3.000
 ARR  C19   C20  C15   119.60  3.000
 ARR  CL    C19  C18   119.13  3.000
 ARR  CL    C19  C20   119.08  3.000
 ARR  C18   C19  C20   121.79  3.000
 ARR  H18   C18  C17   120.84  3.000
 ARR  H18   C18  C19   120.80  3.000
 ARR  C17   C18  C19   118.35  3.000
 ARR  H17   C17  C16   119.99  3.000
 ARR  H17   C17  C18   119.44  3.000
 ARR  C16   C17  C18   120.56  3.000
 ARR  H16   C16  C17   119.71  3.000
 ARR  H16   C16  C15   119.62  3.000
 ARR  C17   C16  C15   120.66  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
 ARR  CONST_01  C3   C2   C1   S       0.00   0.0  0
 ARR  CONST_02  C2   C3   C4   S       0.00   0.0  0
 ARR  CONST_03  C3   C4   S    C1      0.00   0.0  0
 ARR  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 ARR  CONST_05  C4   S    C1   C2      0.00   0.0  0
 ARR  CONST_06  C9   C11  C10  C6      0.00   0.0  0
 ARR  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 ARR  CONST_08  C8   C7   C6   C10     0.00   0.0  0
 ARR  CONST_09  C8   C9   C11  C10     0.00   0.0  0
 ARR  CONST_10  C7   C6   C10  C11     0.00   0.0  0
 ARR  CONST_11  C7   C8   C9   C11     0.00   0.0  0
 ARR  CONST_12  C18  C19  C20  C15     0.00   0.0  0
 ARR  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 ARR  CONST_14  C17  C16  C15  C20     0.00   0.0  0
 ARR  CONST_15  C17  C18  C19  C20     0.00   0.0  0
 ARR  CONST_16  C16  C15  C20  C19     0.00   0.0  0
 ARR  CONST_17  C16  C17  C18  C19     0.00   0.0  0
 ARR  CONST_18  C5   C4   S    C1    180.00   0.0  0
 ARR  CONST_19  C5   C4   C3   C2    180.00   0.0  0
 ARR  CONST_20  C11  C10  C6   N1    180.00   0.0  0
 ARR  CONST_21  C8   C7   C6   N1    180.00   0.0  0
 ARR  CONST_22  C12  C9   C11  C10   180.00   0.0  0
 ARR  CONST_23  C12  C9   C8   C7    180.00   0.0  0
 ARR  CONST_24  C19  C20  C15  C14   180.00   0.0  0
 ARR  CONST_25  C17  C16  C15  C14   180.00   0.0  0
 ARR  CONST_26  CL   C19  C20  C15   180.00   0.0  0
 ARR  CONST_27  CL   C19  C18  C17   180.00   0.0  0
 ARR  CONST_28  H2   C2   C1   S     180.00   0.0  0
 ARR  CONST_29  H3   C3   C4   S     180.00   0.0  0
 ARR  CONST_30  H1   C1   C2   C3    180.00   0.0  0
 ARR  CONST_31  H11  C11  C10  C6    180.00   0.0  0
 ARR  CONST_32  H8   C8   C7   C6    180.00   0.0  0
 ARR  CONST_33  H7   C7   C6   C10   180.00   0.0  0
 ARR  CONST_34  H10  C10  C11  C9    180.00   0.0  0
 ARR  CONST_35  H17  C17  C16  C15   180.00   0.0  0
 ARR  CONST_36  H16  C16  C15  C20   180.00   0.0  0
 ARR  CONST_37  H18  C18  C19  C20   180.00   0.0  0
 ARR  CONST_38  H20  C20  C19  C18   180.00   0.0  0
 ARR  CONST_39  C6   N1   C5   C4    180.00   0.0  0
 ARR  CONST_40  C10  C6   N1   C5      0.00   0.0  0
 ARR  CONST_41  C7   C6   N1   C5    180.00   0.0  0
 ARR  CONST_42  HN1  N1   C6   C10   180.00   0.0  0
 ARR  CONST_43  C6   N1   C5   N3      0.00   0.0  0
 ARR  CONST_44  HN3  N3   C5   C4      0.00   0.0  0
 ARR  Var_01    N3   C5   C4   S    -142.79  30.0  2
 ARR  Var_02    C13  C12  C9   C11    87.71  30.0  2
 ARR  Var_03    C20  C15  C14  N2    -41.58  30.0  2
 ARR  Var_04    N2   C13  C12  C9    178.41  30.0  3
 ARR  Var_05    C15  C14  N2   C13   174.73  30.0  3
 ARR  Var_06    C14  N2   C13  C12   179.68  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
 ARR  plan-1  S    0.020
 ARR  plan-1  C1   0.020
 ARR  plan-1  C2   0.020
 ARR  plan-1  C3   0.020
 ARR  plan-1  C4   0.020
 ARR  plan-1  C5   0.020
 ARR  plan-1  H1   0.020
 ARR  plan-1  H2   0.020
 ARR  plan-1  H3   0.020
 ARR  plan-2  N1   0.020
 ARR  plan-2  C6   0.020
 ARR  plan-2  C10  0.020
 ARR  plan-2  C11  0.020
 ARR  plan-2  C9   0.020
 ARR  plan-2  C8   0.020
 ARR  plan-2  C7   0.020
 ARR  plan-2  C12  0.020
 ARR  plan-2  H10  0.020
 ARR  plan-2  H11  0.020
 ARR  plan-2  H8   0.020
 ARR  plan-2  H7   0.020
 ARR  plan-3  C14  0.020
 ARR  plan-3  C15  0.020
 ARR  plan-3  C20  0.020
 ARR  plan-3  C19  0.020
 ARR  plan-3  C18  0.020
 ARR  plan-3  C17  0.020
 ARR  plan-3  C16  0.020
 ARR  plan-3  CL   0.020
 ARR  plan-3  H20  0.020
 ARR  plan-3  H18  0.020
 ARR  plan-3  H17  0.020
 ARR  plan-3  H16  0.020
 ARR  plan-4  C4   0.020
 ARR  plan-4  C5   0.020
 ARR  plan-4  N3   0.020
 ARR  plan-4  N1   0.020
 ARR  plan-4  C6   0.020
 ARR  plan-4  HN3  0.020
 ARR  plan-4  HN1  0.020

