# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 20:22:01 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: ~{N}-[(1~{S})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-3-methyl-5-[5-(trifluoromethyl)pyridin-2-yl]-1~{H}-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc([nH]c1C(=O)N[C@@H](CN)c2sc(CO)cn2)c3ccc(cn3)C(F)(F)F
#
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
 YB7  YB7  "~{N}-[(1~{S})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-3-methyl-5-[5-(trifluoromethyl)pyridin-2-yl]-1~{H}-pyrrole-2-carboxamide"
  ligand  47  29  .  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_YB7
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
 YB7  N1   N  NH1   0  -0.662  206.6882  -26.8917  45.7858
 YB7  C5   C  CR5   0   0.172  207.1578  -27.8284  43.6364
 YB7  C6   C  C     0   0.514  206.3662  -27.8350  44.8737
 YB7  C7   C  CR15  0  -0.418  208.1957  -28.3514  41.7231
 YB7  N3   N  NH2   0  -0.799  208.0618  -25.8516  47.9381
 YB7  N2   N  N     0  -0.375  204.0970  -25.5927  45.9601
 YB7  C1'  C  CR6   0   0.204  209.2054  -26.0051  41.3062
 YB7  C12  C  CH1   0  -0.123  205.9825  -26.7785  47.0366
 YB7  C13  C  CR5   0   0.065  204.5327  -26.4592  46.8094
 YB7  C14  C  CR15  0  -0.039  202.7361  -25.4747  46.0213
 YB7  C15  C  CR5   0  -0.260  202.1126  -26.2568  46.9408
 YB7  C16  C  CH2   0  -0.184  200.6561  -26.3553  47.2571
 YB7  C17  C  CH2   0  -0.293  206.6290  -25.6506  47.8533
 YB7  C18  C  CR16  0  -0.065  209.8499  -23.8099  41.2312
 YB7  C2'  C  CR16  0  -0.331  209.8960  -26.2895  40.1262
 YB7  C3'  C  CR16  0  -0.151  210.5795  -25.2723  39.4957
 YB7  C4'  C  CR6   0  -0.312  210.5578  -23.9964  40.0516
 YB7  C5'  C  CT    0   1.064  211.3242  -22.8784  39.4272
 YB7  C8   C  CR5   0   0.040  207.3675  -28.8661  42.7358
 YB7  C9   C  CH3   0  -0.731  206.8470  -30.2635  42.8094
 YB7  CAA  C  CR5   0   0.370  208.4564  -27.0233  42.0180
 YB7  F1   F  F     0  -0.307  211.3168  -22.9510  38.0914
 YB7  F2   F  F     0  -0.305  210.8395  -21.6786  39.7627
 YB7  F3   F  F     0  -0.312  212.6104  -22.8938  39.8064
 YB7  N7   N  NR15  0  -0.689  207.8295  -26.7342  43.1818
 YB7  N9   N  N     0  -0.448  209.1941  -24.7827  41.8395
 YB7  O6   O  O     0  -0.474  205.4559  -28.6346  45.0460
 YB7  OP3  O  OH1   0  -0.657  199.9672  -25.4845  46.4005
 YB7  S1   S  S2    0   0.231  203.2968  -27.1980  47.7632
 YB7  H1   H  HNH1  0   0.399  207.6153  -26.4855  45.7994
 YB7  H2   H  HCR5  0   0.257  208.5593  -28.8989  40.8667
 YB7  H3   H  HNH2  0   0.364  208.5085  -25.0100  48.2758
 YB7  H4   H  HNH2  0   0.353  208.2765  -26.5808  48.6068
 YB7  H6   H  HCH1  0   0.268  206.0537  -27.7115  47.6101
 YB7  H7   H  HCR5  0   0.267  202.2350  -24.7853  45.3577
 YB7  H8   H  HCH2  0   0.228  200.4983  -26.1027  48.3136
 YB7  H9   H  HCH2  0   0.226  200.3280  -27.3963  47.1357
 YB7  H10  H  HCH2  0   0.242  206.4417  -24.7053  47.3403
 YB7  H11  H  HCH2  0   0.230  206.1165  -25.5993  48.8209
 YB7  H12  H  HCR6  0   0.281  209.8045  -22.8386  41.7102
 YB7  H13  H  HCR6  0   0.279  209.8973  -27.2875  39.7105
 YB7  H14  H  HCR6  0   0.288  211.1194  -25.4794  38.5809
 YB7  H15  H  HCH3  0   0.240  206.9905  -30.7006  43.7969
 YB7  H16  H  HCH3  0   0.241  205.7796  -30.3098  42.5911
 YB7  H17  H  HCH3  0   0.239  207.3593  -30.8955  42.0855
 YB7  H18  H  HNR5  0   0.412  207.8110  -25.8061  43.5788
 YB7  H19  H  HOH1  0   0.463  199.0354  -25.5059  46.6369

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
 YB7  F1   C5'  single    1.338  0.020  1.338
 YB7  F2   C5'  single    1.337  0.020  1.337
 YB7  C5'  F3   single    1.341  0.020  1.341
 YB7  C5'  C4'  single    1.492  0.020  1.492
 YB7  C3'  C4'  aromatic  1.392  0.020  1.392
 YB7  C3'  C2'  aromatic  1.378  0.020  1.378
 YB7  C4'  C18  aromatic  1.388  0.020  1.388
 YB7  C2'  C1'  aromatic  1.396  0.020  1.396
 YB7  C18  N9   aromatic  1.322  0.020  1.322
 YB7  C1'  N9   aromatic  1.334  0.020  1.334
 YB7  C1'  CAA  single    1.451  0.020  1.451
 YB7  CAA  C7   aromatic  1.385  0.020  1.385
 YB7  CAA  N7   aromatic  1.353  0.020  1.353
 YB7  C7   C8   aromatic  1.406  0.020  1.406
 YB7  N7   C5   aromatic  1.362  0.020  1.362
 YB7  C8   C9   single    1.493  0.020  1.493
 YB7  C8   C5   aromatic  1.390  0.020  1.390
 YB7  C5   C6   single    1.469  0.020  1.469
 YB7  C6   O6   double    1.224  0.020  1.224
 YB7  C6   N1   single    1.351  0.020  1.351
 YB7  N2   C14  aromatic  1.367  0.020  1.367
 YB7  N2   C13  aromatic  1.289  0.020  1.289
 YB7  N1   C12  single    1.441  0.020  1.441
 YB7  C14  C15  aromatic  1.359  0.020  1.359
 YB7  C13  C12  single    1.502  0.020  1.502
 YB7  C13  S1   aromatic  1.727  0.020  1.727
 YB7  OP3  C16  single    1.402  0.020  1.402
 YB7  C12  C17  single    1.535  0.020  1.535
 YB7  C15  C16  single    1.494  0.020  1.494
 YB7  C15  S1   aromatic  1.722  0.020  1.722
 YB7  N3   C17  single    1.449  0.020  1.449
 YB7  N1   H1   single    0.890  0.020  1.040
 YB7  C7   H2   single    0.930  0.020  1.080
 YB7  N3   H3   single    0.890  0.020  1.040
 YB7  N3   H4   single    0.890  0.020  1.040
 YB7  C12  H6   single    0.970  0.020  1.090
 YB7  C14  H7   single    0.930  0.020  1.080
 YB7  C16  H8   single    0.970  0.020  1.090
 YB7  C16  H9   single    0.970  0.020  1.090
 YB7  C17  H10  single    0.970  0.020  1.090
 YB7  C17  H11  single    0.970  0.020  1.090
 YB7  C18  H12  single    0.930  0.020  1.080
 YB7  C2'  H13  single    0.930  0.020  1.080
 YB7  C3'  H14  single    0.930  0.020  1.080
 YB7  C9   H15  single    0.970  0.020  1.090
 YB7  C9   H16  single    0.970  0.020  1.090
 YB7  C9   H17  single    0.970  0.020  1.090
 YB7  N7   H18  single    0.860  0.020  1.020
 YB7  OP3  H19  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
 YB7  H1   N1   C12  113.92  3.000
 YB7  H1   N1   C6   120.50  3.000
 YB7  C12  N1   C6   121.61  3.000
 YB7  N7   C5   C8   108.01  3.000
 YB7  C8   C5   C6   128.59  3.000
 YB7  N7   C5   C6   123.41  3.000
 YB7  O6   C6   C5   121.50  3.000
 YB7  O6   C6   N1   122.58  3.000
 YB7  C5   C6   N1   115.91  3.000
 YB7  H2   C7   CAA  126.28  3.000
 YB7  H2   C7   C8   125.75  3.000
 YB7  CAA  C7   C8   107.97  3.000
 YB7  H4   N3   H3   106.58  3.000
 YB7  H4   N3   C17  110.38  3.000
 YB7  H3   N3   C17  109.93  3.000
 YB7  C14  N2   C13  111.40  3.000
 YB7  N9   C1'  CAA  116.28  3.000
 YB7  CAA  C1'  C2'  121.80  3.000
 YB7  N9   C1'  C2'  121.93  3.000
 YB7  H6   C12  C17  108.61  3.000
 YB7  H6   C12  C13  108.81  3.000
 YB7  C17  C12  C13  109.32  3.000
 YB7  H6   C12  N1   110.80  3.000
 YB7  C17  C12  N1   108.26  3.000
 YB7  C13  C12  N1   111.00  3.000
 YB7  S1   C13  C12  121.09  3.000
 YB7  S1   C13  N2   114.17  3.000
 YB7  C12  C13  N2   124.67  3.000
 YB7  H7   C14  C15  124.77  3.000
 YB7  H7   C14  N2   119.29  3.000
 YB7  C15  C14  N2   115.93  3.000
 YB7  S1   C15  C16  122.24  3.000
 YB7  S1   C15  C14  108.80  3.000
 YB7  C16  C15  C14  128.96  3.000
 YB7  H9   C16  H8   106.36  3.000
 YB7  H9   C16  OP3  111.99  3.000
 YB7  H8   C16  OP3  111.98  3.000
 YB7  H9   C16  C15  109.29  3.000
 YB7  H8   C16  C15  109.19  3.000
 YB7  OP3  C16  C15  107.98  3.000
 YB7  H11  C17  H10  107.10  3.000
 YB7  H11  C17  C12  107.88  3.000
 YB7  H10  C17  C12  108.29  3.000
 YB7  H11  C17  N3   114.65  3.000
 YB7  H10  C17  N3   108.50  3.000
 YB7  C12  C17  N3   110.22  3.000
 YB7  H12  C18  N9   115.81  3.000
 YB7  H12  C18  C4'  121.15  3.000
 YB7  N9   C18  C4'  123.04  3.000
 YB7  H13  C2'  C3'  120.32  3.000
 YB7  H13  C2'  C1'  120.90  3.000
 YB7  C3'  C2'  C1'  118.78  3.000
 YB7  H14  C3'  C4'  121.38  3.000
 YB7  H14  C3'  C2'  119.53  3.000
 YB7  C4'  C3'  C2'  119.09  3.000
 YB7  C5'  C4'  C3'  120.77  3.000
 YB7  C3'  C4'  C18  118.07  3.000
 YB7  C5'  C4'  C18  121.11  3.000
 YB7  F3   C5'  F2   106.69  3.000
 YB7  F3   C5'  F1   106.68  3.000
 YB7  F2   C5'  F1   107.29  3.000
 YB7  F3   C5'  C4'  111.45  3.000
 YB7  F2   C5'  C4'  112.41  3.000
 YB7  F1   C5'  C4'  111.98  3.000
 YB7  C9   C8   C7   125.70  3.000
 YB7  C9   C8   C5   127.90  3.000
 YB7  C7   C8   C5   106.40  3.000
 YB7  H17  C9   H16  107.62  3.000
 YB7  H17  C9   H15  107.93  3.000
 YB7  H16  C9   H15  107.06  3.000
 YB7  H17  C9   C8   110.27  3.000
 YB7  H16  C9   C8   111.78  3.000
 YB7  H15  C9   C8   111.98  3.000
 YB7  N7   CAA  C1'  120.74  3.000
 YB7  N7   CAA  C7   107.50  3.000
 YB7  C1'  CAA  C7   131.74  3.000
 YB7  H18  N7   CAA  122.89  3.000
 YB7  H18  N7   C5   126.74  3.000
 YB7  CAA  N7   C5   110.12  3.000
 YB7  C18  N9   C1'  119.10  3.000
 YB7  H19  OP3  C16  108.18  3.000
 YB7  C15  S1   C13   89.69  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
 YB7  CONST_01  C1'  CAA  N7   C5    180.00   0.0  0
 YB7  CONST_02  C7   CAA  N7   C5      0.00   0.0  0
 YB7  CONST_03  CAA  C7   C8   C5      0.00   0.0  0
 YB7  CONST_04  C2'  C1'  CAA  C7      0.00   0.0  0
 YB7  CONST_05  N9   C1'  CAA  C7    180.00   0.0  0
 YB7  CONST_06  N7   C5   C8   C7      0.00   0.0  0
 YB7  CONST_07  S1   C15  C14  N2      0.00   0.0  0
 YB7  CONST_08  C15  S1   C13  N2      0.00   0.0  0
 YB7  CONST_09  C4'  C3'  C2'  C1'     0.00   0.0  0
 YB7  CONST_10  C4'  C18  N9   C1'     0.00   0.0  0
 YB7  CONST_11  C8   C7   CAA  C1'   180.00   0.0  0
 YB7  CONST_12  C15  C14  N2   C13     0.00   0.0  0
 YB7  CONST_13  C14  C15  S1   C13     0.00   0.0  0
 YB7  CONST_14  S1   C13  N2   C14     0.00   0.0  0
 YB7  CONST_15  C2'  C3'  C4'  C18     0.00   0.0  0
 YB7  CONST_16  C2'  C1'  N9   C18     0.00   0.0  0
 YB7  CONST_17  CAA  C1'  N9   C18   180.00   0.0  0
 YB7  CONST_18  N7   CAA  C1'  C2'   180.00   0.0  0
 YB7  CONST_19  N9   C18  C4'  C3'     0.00   0.0  0
 YB7  CONST_20  N9   C1'  C2'  C3'     0.00   0.0  0
 YB7  CONST_21  CAA  C1'  C2'  C3'   180.00   0.0  0
 YB7  CONST_22  N7   CAA  C7   C8      0.00   0.0  0
 YB7  CONST_23  CAA  N7   C5   C8      0.00   0.0  0
 YB7  CONST_24  N9   C1'  CAA  N7      0.00   0.0  0
 YB7  CONST_25  CAA  N7   C5   C6    180.00   0.0  0
 YB7  CONST_26  C7   C8   C5   C6    180.00   0.0  0
 YB7  CONST_27  C16  C15  C14  N2    180.00   0.0  0
 YB7  CONST_28  C14  N2   C13  C12   180.00   0.0  0
 YB7  CONST_29  C15  S1   C13  C12   180.00   0.0  0
 YB7  CONST_30  C16  C15  S1   C13   180.00   0.0  0
 YB7  CONST_31  C5'  C4'  C3'  C2'   180.00   0.0  0
 YB7  CONST_32  N9   C18  C4'  C5'   180.00   0.0  0
 YB7  CONST_33  CAA  C7   C8   C9    180.00   0.0  0
 YB7  CONST_34  N7   C5   C8   C9    180.00   0.0  0
 YB7  CONST_35  H2   C7   C8   C5    180.00   0.0  0
 YB7  CONST_36  H18  N7   CAA  C7    180.00   0.0  0
 YB7  CONST_37  H14  C3'  C2'  C1'   180.00   0.0  0
 YB7  CONST_38  H12  C18  N9   C1'   180.00   0.0  0
 YB7  CONST_39  H2   C7   CAA  C1'     0.00   0.0  0
 YB7  CONST_40  H18  N7   CAA  C1'     0.00   0.0  0
 YB7  CONST_41  H7   C14  N2   C13   180.00   0.0  0
 YB7  CONST_42  H14  C3'  C4'  C18   180.00   0.0  0
 YB7  CONST_43  H12  C18  C4'  C3'   180.00   0.0  0
 YB7  CONST_44  H13  C2'  C3'  C4'   180.00   0.0  0
 YB7  CONST_45  H18  N7   C5   C8    180.00   0.0  0
 YB7  CONST_46  H13  C2'  C1'  CAA     0.00   0.0  0
 YB7  CONST_47  H2   C7   CAA  N7    180.00   0.0  0
 YB7  CONST_48  H13  C2'  C1'  N9    180.00   0.0  0
 YB7  CONST_49  H7   C14  C15  S1    180.00   0.0  0
 YB7  CONST_50  C12  N1   C6   C5    180.00   0.0  0
 YB7  CONST_52  O6   C6   N1   C12     0.00   0.0  0
 YB7  Var_01    N7   C5   C6   N1    -22.49  30.0  2
 YB7  Var_02    C8   C5   C6   N1    157.63  30.0  2
 YB7  Var_03    OP3  C16  C15  C14     0.99  30.0  2
 YB7  Var_04    F1   C5'  C4'  C18  -146.17  30.0  3
 YB7  Var_05    F2   C5'  C4'  C18   -25.29  30.0  3
 YB7  Var_06    F3   C5'  C4'  C18    94.42  30.0  3
 YB7  Var_07    F1   C5'  C4'  C3'    36.57  30.0  3
 YB7  Var_08    F2   C5'  C4'  C3'   157.44  30.0  3
 YB7  Var_09    F3   C5'  C4'  C3'   -82.84  30.0  3
 YB7  Var_10    O6   C6   C5   C8    -23.72  30.0  2
 YB7  Var_11    O6   C6   C5   N7    156.16  30.0  2
 YB7  Var_12    S1   C15  C16  OP3  -178.93  30.0  2
 YB7  Var_13    H15  C9   C8   C5    -47.13  30.0  2
 YB7  Var_14    H16  C9   C8   C5     73.01  30.0  2
 YB7  Var_15    H17  C9   C8   C5   -167.32  30.0  2
 YB7  Var_16    H15  C9   C8   C7    132.00  30.0  2
 YB7  Var_17    H16  C9   C8   C7   -107.87  30.0  2
 YB7  Var_18    H17  C9   C8   C7     11.80  30.0  2
 YB7  Var_19    H8   C16  C15  C14  -120.99  30.0  2
 YB7  Var_20    H9   C16  C15  C14   123.04  30.0  2
 YB7  Var_21    H8   C16  C15  S1     59.08  30.0  2
 YB7  Var_22    H9   C16  C15  S1    -56.88  30.0  2
 YB7  Var_23    H3   N3   C17  C12   166.44  30.0  3
 YB7  Var_24    H4   N3   C17  C12   -76.27  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
 YB7  chir_01  C12  N1  C13  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
 YB7  plan-1  N2   0.020
 YB7  plan-1  C12  0.020
 YB7  plan-1  C13  0.020
 YB7  plan-1  C14  0.020
 YB7  plan-1  C15  0.020
 YB7  plan-1  C16  0.020
 YB7  plan-1  S1   0.020
 YB7  plan-1  H7   0.020
 YB7  plan-2  C5   0.020
 YB7  plan-2  C6   0.020
 YB7  plan-2  C7   0.020
 YB7  plan-2  C1'  0.020
 YB7  plan-2  C8   0.020
 YB7  plan-2  C9   0.020
 YB7  plan-2  CAA  0.020
 YB7  plan-2  N7   0.020
 YB7  plan-2  H2   0.020
 YB7  plan-2  H18  0.020
 YB7  plan-3  C1'  0.020
 YB7  plan-3  C18  0.020
 YB7  plan-3  C2'  0.020
 YB7  plan-3  C3'  0.020
 YB7  plan-3  C4'  0.020
 YB7  plan-3  C5'  0.020
 YB7  plan-3  CAA  0.020
 YB7  plan-3  N9   0.020
 YB7  plan-3  H12  0.020
 YB7  plan-3  H13  0.020
 YB7  plan-3  H14  0.020
 YB7  plan-4  N1   0.020
 YB7  plan-4  C5   0.020
 YB7  plan-4  C6   0.020
 YB7  plan-4  C12  0.020
 YB7  plan-4  O6   0.020
 YB7  plan-4  H1   0.020

