# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 19:22:57 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: ~{N}-[(1~{R})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-5-(4-chloranyl-3-fluoranyl-phenyl)-1~{H}-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](NC(=O)c1[nH]c(cc1)c2ccc(Cl)c(F)c2)c3sc(CO)cn3
#
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
 YBD  YBD  "~{N}-[(1~{R})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-5-(4-chloranyl-3-fluoranyl-phenyl)-1~{H}-pyrrole-2-carboxamide"
  ligand  42  26  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YBD
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
 YBD  C12   C   CH2   0  -0.296  208.5165  -29.5480  46.6275
 YBD  C11   C   CH1   0  -0.134  208.4254  -28.0596  46.2761
 YBD  C16   C   CR15  0  -0.040  205.5417  -25.9332  46.9374
 YBD  C14   C   CR5   0   0.073  207.1642  -27.4015  46.7741
 YBD  C25   C   CR6   0  -0.255  210.5380  -22.8135  39.1624
 YBD  C23   C   CR16  0  -0.348  209.1195  -24.7444  39.0197
 YBD  C24   C   CR16  0  -0.183  209.6906  -23.6319  38.4301
 YBD  C17   C   CR5   0  -0.228  205.1986  -26.6818  48.0160
 YBD  C18   C   CH2   0  -0.209  204.0876  -26.4823  48.9850
 YBD  C02   C   CR6   0   0.646  210.8107  -23.1435  40.4787
 YBD  C03   C   CR16  0  -0.487  210.2627  -24.2596  41.0734
 YBD  C04   C   CR6   0   0.097  209.3929  -25.0777  40.3496
 YBD  C05   C   CR5   0   0.356  208.7656  -26.2482  40.9480
 YBD  C06   C   CR15  0  -0.374  208.1163  -27.3099  40.3403
 YBD  C07   C   CR15  0  -0.319  207.6404  -28.1547  41.3559
 YBD  C08   C   CR5   0   0.197  208.0213  -27.6043  42.5610
 YBD  N10   N   NH1   0  -0.663  208.6237  -27.7780  44.8731
 YBD  N13   N   NH2   0  -0.797  209.7784  -30.0841  46.1532
 YBD  N15   N   N     0  -0.379  206.6491  -26.3388  46.2511
 YBD  N22   N   NR15  0  -0.705  208.7133  -26.4590  42.2914
 YBD  O19   O   OH1   0  -0.660  203.3882  -27.6953  49.1319
 YBD  O21   O   O     0  -0.471  206.7703  -28.8327  44.1165
 YBD  S20   S   S2    0   0.224  206.3183  -27.9820  48.1666
 YBD  CL26  CL  CL    0  -0.088  211.2459  -21.4079  38.4674
 YBD  H1    H   HCH2  0   0.237  208.5066  -29.6317  47.7176
 YBD  H2    H   HCH2  0   0.223  207.6312  -30.0768  46.2596
 YBD  H3    H   HCH1  0   0.296  209.2615  -27.5725  46.7863
 YBD  H4    H   HCR5  0   0.269  204.9976  -25.0582  46.6075
 YBD  H5    H   HCR6  0   0.267  208.4411  -25.3503  38.4347
 YBD  H6    H   HCR6  0   0.292  209.4667  -23.3887  37.4003
 YBD  H7    H   HCH2  0   0.229  204.4975  -26.1404  49.9431
 YBD  H8    H   HCH2  0   0.222  203.4522  -25.6722  48.6061
 YBD  H9    H   HCR6  0   0.281  210.5404  -24.4771  42.0969
 YBD  H10   H   HCR5  0   0.259  208.0123  -27.4657  39.2782
 YBD  H11   H   HCR5  0   0.259  207.1018  -29.0803  41.2300
 YBD  H12   H   HNH1  0   0.407  209.4642  -27.2827  44.6272
 YBD  H13   H   HNH2  0   0.354  209.9076  -31.0139  46.5299
 YBD  H14   H   HNH2  0   0.346  209.7444  -30.1983  45.1481
 YBD  H16   H   HNR5  0   0.421  208.9797  -25.7789  42.9871
 YBD  H17   H   HOH1  0   0.459  202.7987  -27.6099  49.8875
 YBD  C09   C   C     0   0.514  207.7441  -28.1234  43.9099
 YBD  F01   F   F     0  -0.294  211.6252  -22.3615  41.1893

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
 YBD  CL26  C25  single    1.720  0.020  1.720
 YBD  C24   C23  aromatic  1.383  0.020  1.383
 YBD  C24   C25  aromatic  1.387  0.020  1.387
 YBD  C23   C04  aromatic  1.398  0.020  1.398
 YBD  C25   C02  aromatic  1.384  0.020  1.384
 YBD  C04   C03  aromatic  1.396  0.020  1.396
 YBD  C04   C05  single    1.457  0.020  1.457
 YBD  C02   C03  aromatic  1.378  0.020  1.378
 YBD  C02   F01  single    1.334  0.020  1.334
 YBD  C06   C05  aromatic  1.385  0.020  1.385
 YBD  C06   C07  aromatic  1.404  0.020  1.404
 YBD  C05   N22  aromatic  1.361  0.020  1.361
 YBD  C07   C08  aromatic  1.379  0.020  1.379
 YBD  N22   C08  aromatic  1.365  0.020  1.365
 YBD  C08   C09  single    1.472  0.020  1.472
 YBD  C09   O21  double    1.222  0.020  1.222
 YBD  C09   N10  single    1.349  0.020  1.349
 YBD  N10   C11  single    1.445  0.020  1.445
 YBD  N15   C16  aromatic  1.365  0.020  1.365
 YBD  N15   C14  aromatic  1.292  0.020  1.292
 YBD  C12   C11  single    1.532  0.020  1.532
 YBD  C12   N13  single    1.451  0.020  1.451
 YBD  C11   C14  single    1.507  0.020  1.507
 YBD  C16   C17  aromatic  1.357  0.020  1.357
 YBD  C14   S20  aromatic  1.730  0.020  1.730
 YBD  C17   S20  aromatic  1.723  0.020  1.723
 YBD  C17   C18  single    1.488  0.020  1.488
 YBD  C18   O19  single    1.408  0.020  1.408
 YBD  C12   H1   single    0.970  0.020  1.090
 YBD  C12   H2   single    0.970  0.020  1.090
 YBD  C11   H3   single    0.970  0.020  1.090
 YBD  C16   H4   single    0.930  0.020  1.080
 YBD  C23   H5   single    0.930  0.020  1.080
 YBD  C24   H6   single    0.930  0.020  1.080
 YBD  C18   H7   single    0.970  0.020  1.090
 YBD  C18   H8   single    0.970  0.020  1.090
 YBD  C03   H9   single    0.930  0.020  1.080
 YBD  C06   H10  single    0.930  0.020  1.080
 YBD  C07   H11  single    0.930  0.020  1.080
 YBD  N10   H12  single    0.860  0.020  1.020
 YBD  N13   H13  single    0.890  0.020  1.040
 YBD  N13   H14  single    0.890  0.020  1.040
 YBD  N22   H16  single    0.860  0.020  1.020
 YBD  O19   H17  single    0.850  0.020  0.980

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
 YBD  H2    C12  H1   106.90  3.000
 YBD  H2    C12  N13  114.52  3.000
 YBD  H1    C12  N13  107.79  3.000
 YBD  H2    C12  C11  110.13  3.000
 YBD  H1    C12  C11  107.61  3.000
 YBD  N13   C12  C11  109.62  3.000
 YBD  H3    C11  N10  105.14  3.000
 YBD  H3    C11  C14  106.92  3.000
 YBD  N10   C11  C14  110.52  3.000
 YBD  H3    C11  C12  106.27  3.000
 YBD  C14   C11  C12  113.46  3.000
 YBD  N10   C11  C12  113.83  3.000
 YBD  H4    C16  N15  119.68  3.000
 YBD  H4    C16  C17  124.15  3.000
 YBD  N15   C16  C17  116.17  3.000
 YBD  S20   C14  N15  114.02  3.000
 YBD  S20   C14  C11  121.92  3.000
 YBD  N15   C14  C11  124.00  3.000
 YBD  CL26  C25  C02  119.86  3.000
 YBD  C02   C25  C24  118.80  3.000
 YBD  CL26  C25  C24  121.34  3.000
 YBD  H5    C23  C04  120.25  3.000
 YBD  H5    C23  C24  118.64  3.000
 YBD  C04   C23  C24  121.11  3.000
 YBD  H6    C24  C23  120.10  3.000
 YBD  H6    C24  C25  119.77  3.000
 YBD  C23   C24  C25  120.13  3.000
 YBD  S20   C17  C18  121.98  3.000
 YBD  C18   C17  C16  129.24  3.000
 YBD  S20   C17  C16  108.76  3.000
 YBD  H8    C18  H7   106.73  3.000
 YBD  H8    C18  O19  112.61  3.000
 YBD  H7    C18  O19  111.29  3.000
 YBD  H8    C18  C17  107.85  3.000
 YBD  H7    C18  C17  109.38  3.000
 YBD  O19   C18  C17  108.87  3.000
 YBD  F01   C02  C03  119.18  3.000
 YBD  F01   C02  C25  119.15  3.000
 YBD  C03   C02  C25  121.67  3.000
 YBD  H9    C03  C04  122.15  3.000
 YBD  H9    C03  C02  117.95  3.000
 YBD  C04   C03  C02  119.90  3.000
 YBD  C05   C04  C03  121.74  3.000
 YBD  C05   C04  C23  119.88  3.000
 YBD  C03   C04  C23  118.38  3.000
 YBD  N22   C05  C06  107.24  3.000
 YBD  N22   C05  C04  123.13  3.000
 YBD  C06   C05  C04  129.61  3.000
 YBD  H10   C06  C07  126.35  3.000
 YBD  H10   C06  C05  126.02  3.000
 YBD  C07   C06  C05  107.62  3.000
 YBD  H11   C07  C08  125.65  3.000
 YBD  H11   C07  C06  126.97  3.000
 YBD  C08   C07  C06  107.36  3.000
 YBD  N22   C08  C09  124.92  3.000
 YBD  C09   C08  C07  127.47  3.000
 YBD  N22   C08  C07  107.61  3.000
 YBD  H12   N10  C09  119.75  3.000
 YBD  H12   N10  C11  116.61  3.000
 YBD  C09   N10  C11  123.63  3.000
 YBD  H14   N13  H13  105.68  3.000
 YBD  H14   N13  C12  109.70  3.000
 YBD  H13   N13  C12  109.21  3.000
 YBD  C14   N15  C16  111.38  3.000
 YBD  H16   N22  C08  124.29  3.000
 YBD  H16   N22  C05  124.49  3.000
 YBD  C08   N22  C05  110.14  3.000
 YBD  H17   O19  C18  108.05  3.000
 YBD  C17   S20  C14   89.67  3.000
 YBD  O21   C09  N10  123.18  3.000
 YBD  N10   C09  C08  116.18  3.000
 YBD  O21   C09  C08  120.64  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
 YBD  CONST_01  S20   C14  N15  C16     0.00   0.0  0
 YBD  CONST_02  C14   S20  C17  C16     0.00   0.0  0
 YBD  CONST_03  C17   C16  N15  C14     0.00   0.0  0
 YBD  CONST_04  C04   C23  C24  C25     0.00   0.0  0
 YBD  CONST_05  C04   C03  C02  C25     0.00   0.0  0
 YBD  CONST_06  C02   C25  C24  C23     0.00   0.0  0
 YBD  CONST_07  C02   C03  C04  C23     0.00   0.0  0
 YBD  CONST_10  C03   C04  C23  C24     0.00   0.0  0
 YBD  CONST_11  C05   C04  C23  C24   180.00   0.0  0
 YBD  CONST_12  C03   C02  C25  C24     0.00   0.0  0
 YBD  CONST_13  N15   C14  S20  C17     0.00   0.0  0
 YBD  CONST_14  C05   C04  C03  C02   180.00   0.0  0
 YBD  CONST_15  C06   C05  C04  C03   180.00   0.0  0
 YBD  CONST_17  C07   C06  C05  C04   180.00   0.0  0
 YBD  CONST_18  C08   N22  C05  C04   180.00   0.0  0
 YBD  CONST_19  C08   C07  C06  C05     0.00   0.0  0
 YBD  CONST_20  C07   C08  N22  C05     0.00   0.0  0
 YBD  CONST_21  C08   N22  C05  C06     0.00   0.0  0
 YBD  CONST_22  N22   C08  C07  C06     0.00   0.0  0
 YBD  CONST_23  N22   C05  C06  C07     0.00   0.0  0
 YBD  CONST_24  S20   C17  C16  N15     0.00   0.0  0
 YBD  CONST_25  C16   N15  C14  C11   180.00   0.0  0
 YBD  CONST_26  C17   S20  C14  C11   180.00   0.0  0
 YBD  CONST_27  C18   C17  S20  C14   180.00   0.0  0
 YBD  CONST_28  CL26  C25  C24  C23   180.00   0.0  0
 YBD  CONST_29  F01   C02  C25  C24   180.00   0.0  0
 YBD  CONST_30  N15   C16  C17  C18   180.00   0.0  0
 YBD  CONST_31  CL26  C25  C02  C03   180.00   0.0  0
 YBD  CONST_32  F01   C02  C03  C04   180.00   0.0  0
 YBD  CONST_33  C09   C08  N22  C05   180.00   0.0  0
 YBD  CONST_34  C09   C08  C07  C06   180.00   0.0  0
 YBD  CONST_35  H4    C16  N15  C14   180.00   0.0  0
 YBD  CONST_36  H5    C23  C24  C25   180.00   0.0  0
 YBD  CONST_37  H9    C03  C02  C25   180.00   0.0  0
 YBD  CONST_38  H9    C03  C04  C23   180.00   0.0  0
 YBD  CONST_39  H6    C24  C25  C02   180.00   0.0  0
 YBD  CONST_40  H5    C23  C04  C03   180.00   0.0  0
 YBD  CONST_41  H6    C24  C23  C04   180.00   0.0  0
 YBD  CONST_42  H10   C06  C05  C04     0.00   0.0  0
 YBD  CONST_43  H16   N22  C05  C04     0.00   0.0  0
 YBD  CONST_44  H5    C23  C04  C05     0.00   0.0  0
 YBD  CONST_45  H9    C03  C04  C05     0.00   0.0  0
 YBD  CONST_46  H11   C07  C06  C05   180.00   0.0  0
 YBD  CONST_47  H16   N22  C05  C06   180.00   0.0  0
 YBD  CONST_48  H16   N22  C08  C07   180.00   0.0  0
 YBD  CONST_49  H10   C06  C07  C08   180.00   0.0  0
 YBD  CONST_50  H10   C06  C05  N22   180.00   0.0  0
 YBD  CONST_51  H11   C07  C08  N22   180.00   0.0  0
 YBD  CONST_52  H4    C16  C17  S20   180.00   0.0  0
 YBD  CONST_53  C08   C09  N10  C11   180.00   0.0  0
 YBD  CONST_54  H12   N10  C09  C08     0.00   0.0  0
 YBD  CONST_55  O21   C09  N10  C11     0.00   0.0  0
 YBD  CONST_56  H12   N10  C09  O21   180.00   0.0  0
 YBD  Var_01    O19   C18  C17  C16   130.84  30.0  2
 YBD  Var_02    O21   C09  C08  C07   -25.92  30.0  2
 YBD  Var_03    N10   C09  C08  C07   153.60  30.0  2
 YBD  Var_04    N22   C08  C09  N10   -26.79  30.0  2
 YBD  Var_05    O21   C09  C08  N22   153.69  30.0  2
 YBD  Var_06    S20   C17  C18  O19   -50.74  30.0  3
 YBD  Var_07    H7    C18  C17  C16  -107.36  30.0  2
 YBD  Var_08    H8    C18  C17  C16     8.36  30.0  2
 YBD  Var_09    H7    C18  C17  S20    71.06  30.0  2
 YBD  Var_10    H8    C18  C17  S20  -173.22  30.0  2
 YBD  Var_11    H13   N13  C12  C11   169.86  30.0  3
 YBD  Var_12    H14   N13  C12  C11   -74.75  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
 YBD  chir_01  C11  N10  C12  C14  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
 YBD  plan-1  C04   0.020
 YBD  plan-1  C05   0.020
 YBD  plan-1  C06   0.020
 YBD  plan-1  C07   0.020
 YBD  plan-1  C08   0.020
 YBD  plan-1  N22   0.020
 YBD  plan-1  H10   0.020
 YBD  plan-1  H11   0.020
 YBD  plan-1  H16   0.020
 YBD  plan-1  C09   0.020
 YBD  plan-2  C11   0.020
 YBD  plan-2  C16   0.020
 YBD  plan-2  C14   0.020
 YBD  plan-2  C17   0.020
 YBD  plan-2  C18   0.020
 YBD  plan-2  N15   0.020
 YBD  plan-2  S20   0.020
 YBD  plan-2  H4    0.020
 YBD  plan-3  C25   0.020
 YBD  plan-3  C23   0.020
 YBD  plan-3  C24   0.020
 YBD  plan-3  C02   0.020
 YBD  plan-3  C03   0.020
 YBD  plan-3  C04   0.020
 YBD  plan-3  C05   0.020
 YBD  plan-3  CL26  0.020
 YBD  plan-3  H5    0.020
 YBD  plan-3  H6    0.020
 YBD  plan-3  H9    0.020
 YBD  plan-3  F01   0.020
 YBD  plan-4  C11   0.020
 YBD  plan-4  C08   0.020
 YBD  plan-4  N10   0.020
 YBD  plan-4  O21   0.020
 YBD  plan-4  H12   0.020
 YBD  plan-4  C09   0.020

