# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:07:21 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-(carbamoylamino)-5-{4-[2-(dimethylamino)ethoxy]phenyl}thiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCOc1ccc(cc1)c2sc(NC(N)=O)c(c2)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
 YDI  YDI  2-(carbamoylamino)-5-{4-[2-(dimethylamino)ethoxy]phenyl}thiophene-3-carboxamide  ligand  44  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YDI
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
 YDI  S01   S  S2    0   0.246  -2.2443  -1.0729   0.2786
 YDI  C02   C  CR5   0   0.111  -3.6302  -0.0746   0.0419
 YDI  C03   C  CR5   0  -0.062  -3.2825   1.2469  -0.1683
 YDI  C04   C  CR15  0  -0.259  -1.8669   1.4282  -0.1388
 YDI  C05   C  CR5   0  -0.216  -1.1707   0.2852   0.0861
 YDI  N06   N  NH1   0  -0.741  -4.9038  -0.5604   0.0671
 YDI  C07   C  C     0   0.691  -5.2218  -1.8811   0.2772
 YDI  N08   N  NH2   0  -0.845  -6.5390  -2.1458   0.2794
 YDI  O09   O  O     0  -0.510  -4.3494  -2.7192   0.4617
 YDI  C10   C  C     0   0.524  -4.2946   2.2880  -0.4057
 YDI  O11   O  O     0  -0.518  -5.5025   2.0297  -0.3889
 YDI  N12   N  NH2   0  -0.819  -3.8504   3.5318  -0.6342
 YDI  C14   C  CH3   0  -0.518   8.3625  -1.1138  -0.4795
 YDI  N15   N  NT    0  -0.400   7.1079  -0.3983  -0.5599
 YDI  C16   C  CH2   0  -0.293   6.6844   0.0453   0.7517
 YDI  C17   C  CH2   0  -0.215   5.2657   0.5679   0.8012
 YDI  C19   C  CR6   0   0.113   0.2747   0.0998   0.1828
 YDI  C20   C  CR16  0  -0.302   0.8891  -1.1012  -0.1889
 YDI  C21   C  CR16  0  -0.333   2.2575  -1.2635  -0.1059
 YDI  C22   C  CR6   0   0.379   3.0692  -0.2211   0.3473
 YDI  C2    C  CH3   0  -0.526   7.1877   0.6802  -1.5202
 YDI  C23   C  CR16  0  -0.365   2.4734   0.9821   0.7222
 YDI  C24   C  CR16  0  -0.308   1.0956   1.1265   0.6446
 YDI  O1    O  O2    0  -0.463   4.3892  -0.4666   0.3906
 YDI  H06   H  HNH1  0   0.432  -5.6124   0.1565  -0.0753
 YDI  H04   H  HCR5  0   0.262  -1.3724   2.3762  -0.3022
 YDI  H081  H  HNH2  0   0.412  -7.2290  -1.4631   0.0179
 YDI  H082  H  HNH2  0   0.412  -6.8402  -3.1029   0.3407
 YDI  H121  H  HNH2  0   0.414  -2.8770   3.7648  -0.7125
 YDI  H122  H  HNH2  0   0.407  -4.5108   4.2627  -0.8413
 YDI  H141  H  HCH3  0   0.233   8.2659  -1.9686   0.1917
 YDI  H142  H  HCH3  0   0.233   8.6383  -1.4947  -1.4639
 YDI  H143  H  HCH3  0   0.191   9.1985  -0.4958  -0.1151
 YDI  H161  H  HCH2  0   0.242   6.7705  -0.7969   1.4435
 YDI  H162  H  HCH2  0   0.203   7.3326   0.8435   1.1542
 YDI  H21C  H  HCH3  0   0.236   7.5088   0.2879  -2.4857
 YDI  H22C  H  HCH3  0   0.236   6.2138   1.1455  -1.6734
 YDI  H23C  H  HCH3  0   0.191   7.8958   1.4723  -1.2282
 YDI  H171  H  HCH2  0   0.240   5.0464   0.8800   1.8281
 YDI  H172  H  HCH2  0   0.229   5.1426   1.4481   0.1610
 YDI  H20   H  HCR6  0   0.254   0.2957  -1.9249  -0.5685
 YDI  H24   H  HCR6  0   0.257   0.6574   2.0608   0.9721
 YDI  H21   H  HCR6  0   0.265   2.7104  -2.2002  -0.4053
 YDI  H23   H  HCR6  0   0.281   3.0578   1.8134   1.0919

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
 YDI  S01  C02   aromatic  1.724  0.020  1.724
 YDI  S01  C05   aromatic  1.742  0.020  1.742
 YDI  C02  C03   aromatic  1.383  0.020  1.383
 YDI  C02  N06   single    1.363  0.020  1.363
 YDI  C03  C04   aromatic  1.428  0.020  1.428
 YDI  C03  C10   single    1.471  0.020  1.471
 YDI  C04  C05   aromatic  1.357  0.020  1.357
 YDI  C05  C19   single    1.460  0.020  1.460
 YDI  N06  C07   single    1.375  0.020  1.375
 YDI  C07  N08   single    1.344  0.020  1.344
 YDI  C07  O09   double    1.224  0.020  1.224
 YDI  C10  O11   double    1.235  0.020  1.235
 YDI  C10  N12   single    1.340  0.020  1.340
 YDI  C14  N15   single    1.446  0.020  1.446
 YDI  N15  C16   single    1.448  0.020  1.448
 YDI  N15  C2    single    1.446  0.020  1.446
 YDI  C16  C17   single    1.513  0.020  1.513
 YDI  C17  O1    single    1.417  0.020  1.417
 YDI  C19  C20   aromatic  1.399  0.020  1.399
 YDI  C19  C24   aromatic  1.393  0.020  1.393
 YDI  C20  C21   aromatic  1.380  0.020  1.380
 YDI  C21  C22   aromatic  1.397  0.020  1.397
 YDI  C22  C23   aromatic  1.394  0.020  1.394
 YDI  C22  O1    single    1.343  0.020  1.343
 YDI  C23  C24   aromatic  1.387  0.020  1.387
 YDI  N06  H06   single    0.860  0.020  1.020
 YDI  C04  H04   single    0.930  0.020  1.080
 YDI  N08  H081  single    0.860  0.020  1.020
 YDI  N08  H082  single    0.860  0.020  1.020
 YDI  N12  H121  single    0.860  0.020  1.020
 YDI  N12  H122  single    0.860  0.020  1.020
 YDI  C14  H141  single    0.970  0.020  1.090
 YDI  C14  H142  single    0.970  0.020  1.090
 YDI  C14  H143  single    0.970  0.020  1.090
 YDI  C16  H161  single    0.970  0.020  1.090
 YDI  C16  H162  single    0.970  0.020  1.090
 YDI  C2   H21C  single    0.970  0.020  1.090
 YDI  C2   H22C  single    0.970  0.020  1.090
 YDI  C2   H23C  single    0.970  0.020  1.090
 YDI  C17  H171  single    0.970  0.020  1.090
 YDI  C17  H172  single    0.970  0.020  1.090
 YDI  C20  H20   single    0.930  0.020  1.080
 YDI  C24  H24   single    0.930  0.020  1.080
 YDI  C21  H21   single    0.930  0.020  1.080
 YDI  C23  H23   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
 YDI  C05   S01  C02    91.65  3.000
 YDI  N06   C02  C03   125.33  3.000
 YDI  N06   C02  S01   122.82  3.000
 YDI  C03   C02  S01   111.85  3.000
 YDI  C10   C03  C04   126.56  3.000
 YDI  C10   C03  C02   121.87  3.000
 YDI  C04   C03  C02   111.57  3.000
 YDI  H04   C04  C05   121.92  3.000
 YDI  H04   C04  C03   124.16  3.000
 YDI  C05   C04  C03   113.90  3.000
 YDI  C19   C05  C04   128.72  3.000
 YDI  C19   C05  S01   120.25  3.000
 YDI  C04   C05  S01   111.03  3.000
 YDI  H06   N06  C07   122.48  3.000
 YDI  H06   N06  C02   113.37  3.000
 YDI  C07   N06  C02   124.14  3.000
 YDI  O09   C07  N08   124.32  3.000
 YDI  O09   C07  N06   121.07  3.000
 YDI  N08   C07  N06   114.60  3.000
 YDI  H082  N08  H081  117.18  3.000
 YDI  H082  N08  C07   118.78  3.000
 YDI  H081  N08  C07   122.60  3.000
 YDI  N12   C10  O11   121.36  3.000
 YDI  N12   C10  C03   117.14  3.000
 YDI  O11   C10  C03   121.50  3.000
 YDI  H122  N12  H121  116.84  3.000
 YDI  H122  N12  C10   119.43  3.000
 YDI  H121  N12  C10   123.37  3.000
 YDI  H143  C14  H142  107.61  3.000
 YDI  H143  C14  H141  107.64  3.000
 YDI  H142  C14  H141  107.69  3.000
 YDI  H143  C14  N15   113.53  3.000
 YDI  H142  C14  N15   109.99  3.000
 YDI  H141  C14  N15   110.17  3.000
 YDI  C2    N15  C16   112.90  3.000
 YDI  C2    N15  C14   110.97  3.000
 YDI  C16   N15  C14   110.79  3.000
 YDI  H162  C16  H161  106.26  3.000
 YDI  H162  C16  C17   106.79  3.000
 YDI  H161  C16  C17   108.61  3.000
 YDI  H162  C16  N15   112.33  3.000
 YDI  H161  C16  N15   108.31  3.000
 YDI  C17   C16  N15   114.19  3.000
 YDI  H172  C17  H171  107.25  3.000
 YDI  H172  C17  O1    110.36  3.000
 YDI  H171  C17  O1    110.85  3.000
 YDI  H172  C17  C16   111.34  3.000
 YDI  H171  C17  C16   108.47  3.000
 YDI  O1    C17  C16   108.57  3.000
 YDI  C24   C19  C20   117.50  3.000
 YDI  C24   C19  C05   120.77  3.000
 YDI  C20   C19  C05   121.73  3.000
 YDI  H20   C20  C21   118.32  3.000
 YDI  H20   C20  C19   120.33  3.000
 YDI  C21   C20  C19   121.34  3.000
 YDI  H21   C21  C22   119.49  3.000
 YDI  H21   C21  C20   119.98  3.000
 YDI  C22   C21  C20   120.53  3.000
 YDI  O1    C22  C23   124.69  3.000
 YDI  O1    C22  C21   116.43  3.000
 YDI  C23   C22  C21   118.88  3.000
 YDI  H23C  C2   H22C  107.73  3.000
 YDI  H23C  C2   H21C  107.70  3.000
 YDI  H22C  C2   H21C  106.99  3.000
 YDI  H23C  C2   N15   113.31  3.000
 YDI  H22C  C2   N15   111.24  3.000
 YDI  H21C  C2   N15   109.62  3.000
 YDI  H23   C23  C24   118.41  3.000
 YDI  H23   C23  C22   121.63  3.000
 YDI  C24   C23  C22   119.95  3.000
 YDI  H24   C24  C23   118.35  3.000
 YDI  H24   C24  C19   119.84  3.000
 YDI  C23   C24  C19   121.80  3.000
 YDI  C22   O1   C17   118.93  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
 YDI  CONST_01  C04   C03  C02  S01     0.00   0.0  0
 YDI  CONST_02  C03   C04  C05  S01     0.00   0.0  0
 YDI  CONST_05  C04   C05  S01  C02     0.00   0.0  0
 YDI  CONST_06  C19   C05  S01  C02   180.00   0.0  0
 YDI  CONST_07  C05   C04  C03  C02     0.00   0.0  0
 YDI  CONST_08  C05   S01  C02  C03     0.00   0.0  0
 YDI  CONST_09  C19   C05  C04  C03   180.00   0.0  0
 YDI  CONST_12  C21   C20  C19  C05   180.00   0.0  0
 YDI  CONST_13  C23   C24  C19  C05   180.00   0.0  0
 YDI  CONST_14  C22   C21  C20  C19     0.00   0.0  0
 YDI  CONST_15  C22   C23  C24  C19     0.00   0.0  0
 YDI  CONST_16  C23   C24  C19  C20     0.00   0.0  0
 YDI  CONST_17  C23   C22  C21  C20     0.00   0.0  0
 YDI  CONST_18  C24   C19  C20  C21     0.00   0.0  0
 YDI  CONST_19  C24   C23  C22  C21     0.00   0.0  0
 YDI  CONST_20  C10   C03  C02  S01   180.00   0.0  0
 YDI  CONST_21  N06   C02  C03  C04   180.00   0.0  0
 YDI  CONST_22  N06   C02  S01  C05   180.00   0.0  0
 YDI  CONST_23  C10   C03  C04  C05   180.00   0.0  0
 YDI  CONST_24  O1    C22  C21  C20   180.00   0.0  0
 YDI  CONST_25  O1    C22  C23  C24   180.00   0.0  0
 YDI  CONST_26  H04   C04  C05  S01   180.00   0.0  0
 YDI  CONST_27  H20   C20  C19  C05     0.00   0.0  0
 YDI  CONST_28  H24   C24  C19  C05     0.00   0.0  0
 YDI  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 YDI  CONST_30  H23   C23  C24  C19   180.00   0.0  0
 YDI  CONST_31  N12   C10  C03  C02   180.00   0.0  0
 YDI  CONST_32  C07   N06  C02  S01     0.00   0.0  0
 YDI  CONST_33  C07   N06  C02  C03   180.00   0.0  0
 YDI  CONST_34  H06   N06  C02  S01   180.00   0.0  0
 YDI  CONST_35  O09   C07  N06  C02     0.00   0.0  0
 YDI  CONST_36  N08   C07  N06  C02   180.00   0.0  0
 YDI  CONST_37  H121  N12  C10  C03     0.00   0.0  0
 YDI  CONST_38  H122  N12  C10  C03   180.00   0.0  0
 YDI  CONST_39  H081  N08  C07  O09   180.00   0.0  0
 YDI  CONST_40  H082  N08  C07  O09     0.00   0.0  0
 YDI  Var_01    C21   C22  O1   C17   178.00  30.0  2
 YDI  Var_02    H171  C17  O1   C22    61.46  30.0  1
 YDI  Var_03    C17   C16  N15  C14  -168.98  30.0  3
 YDI  Var_04    O1    C17  C16  N15    59.73  30.0  3
 YDI  Var_05    H21C  C2   N15  C14    55.01  30.0  3
 YDI  Var_06    H141  C14  N15  C16    57.96  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
 YDI  plan-1  C05   0.020
 YDI  plan-1  C19   0.020
 YDI  plan-1  C20   0.020
 YDI  plan-1  C21   0.020
 YDI  plan-1  C22   0.020
 YDI  plan-1  C23   0.020
 YDI  plan-1  C24   0.020
 YDI  plan-1  O1    0.020
 YDI  plan-1  H20   0.020
 YDI  plan-1  H24   0.020
 YDI  plan-1  H21   0.020
 YDI  plan-1  H23   0.020
 YDI  plan-2  C02   0.020
 YDI  plan-2  N06   0.020
 YDI  plan-2  C07   0.020
 YDI  plan-2  N08   0.020
 YDI  plan-2  O09   0.020
 YDI  plan-2  H06   0.020
 YDI  plan-2  H081  0.020
 YDI  plan-2  H082  0.020
 YDI  plan-3  S01   0.020
 YDI  plan-3  C02   0.020
 YDI  plan-3  C03   0.020
 YDI  plan-3  C04   0.020
 YDI  plan-3  C05   0.020
 YDI  plan-3  N06   0.020
 YDI  plan-3  C10   0.020
 YDI  plan-3  O11   0.020
 YDI  plan-3  N12   0.020
 YDI  plan-3  C19   0.020
 YDI  plan-3  H04   0.020
 YDI  plan-3  H121  0.020
 YDI  plan-3  H122  0.020

