# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 13:45:51 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 5-[(Z)-(5-chloro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-N,2,4-trimethyl-1H-pyrrole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1c(C)[nH]c(\C=C\2C(=O)Nc3ccc(Cl)cc\23)c1C
#
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
 5Z5  5Z5  5-[(Z)-(5-chloro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-N,2,4-trimethyl-1H-pyrrole-3-carboxamide  ligand  39  23  .  2022-07-23  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_5Z5
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
 5Z5  C17   C   CH3   0  -0.514   6.5224  -2.3002  -0.4308
 5Z5  N3    N   NH1   0  -0.628   5.2192  -1.6807  -0.4604
 5Z5  C16   C   C     0   0.458   4.9877  -0.4689   0.0705
 5Z5  O2    O   O     0  -0.496   5.8788   0.1866   0.6019
 5Z5  C12   C   CR5   0  -0.190   3.5946   0.0174  -0.0179
 5Z5  C11   C   CR5   0   0.041   2.4039  -0.7266   0.1044
 5Z5  C14   C   CH3   0  -0.782   2.2684  -2.1922   0.3483
 5Z5  C13   C   CR5   0   0.363   3.2390   1.3613  -0.1956
 5Z5  C15   C   CH3   0  -0.745   4.0735   2.5680  -0.4291
 5Z5  N2    N   NR15  0  -0.719   1.9075   1.4298  -0.1978
 5Z5  C10   C   CR5   0   0.331   1.3494   0.1877  -0.0097
 5Z5  C9    C   C1    0  -0.371  -0.0320  -0.0830   0.0743
 5Z5  C7    C   CR5   0  -0.072  -1.1305   0.7189  -0.0234
 5Z5  C5    C   CR56  0   0.077  -2.5074   0.2690   0.0967
 5Z5  C4    C   CR16  0  -0.341  -3.0731  -0.9739   0.3289
 5Z5  C1    C   CR6   0  -0.040  -4.4581  -1.0580   0.3888
 5Z5  CL1   CL  CL    0  -0.137  -5.1932  -2.6053   0.6790
 5Z5  C2    C   CR16  0  -0.240  -5.2730   0.0543   0.2245
 5Z5  C3    C   CR16  0  -0.301  -4.7071   1.3044  -0.0080
 5Z5  C6    C   CR56  0   0.390  -3.3310   1.3906  -0.0680
 5Z5  N1    N   NR15  0  -0.762  -2.5263   2.4950  -0.2821
 5Z5  C8    C   CR5   0   0.538  -1.2008   2.1723  -0.2679
 5Z5  O1    O   O     0  -0.495  -0.2957   2.9868  -0.4347
 5Z5  H171  H   HCH3  0   0.235   7.2542  -1.7504  -1.0252
 5Z5  H172  H   HCH3  0   0.240   6.8999  -2.3779   0.5883
 5Z5  H173  H   HCH3  0   0.249   6.4334  -3.3029  -0.8391
 5Z5  H3    H   HNH1  0   0.408   4.5016  -2.1214  -1.0096
 5Z5  H141  H   HCH3  0   0.256   2.3898  -2.7710  -0.5700
 5Z5  H142  H   HCH3  0   0.261   3.0147  -2.5473   1.0577
 5Z5  H143  H   HCH3  0   0.258   1.2902  -2.4474   0.7519
 5Z5  H151  H   HCH3  0   0.263   4.1940   2.7506  -1.4990
 5Z5  H152  H   HCH3  0   0.258   3.6080   3.4533   0.0028
 5Z5  H153  H   HCH3  0   0.267   5.0620   2.4505   0.0026
 5Z5  H2    H   HNR5  0   0.433   1.3282   2.2630  -0.3255
 5Z5  H9    H   H     0   0.260  -0.2485  -1.1315   0.2502
 5Z5  H4    H   HCR6  0   0.272  -2.4615  -1.8573   0.4618
 5Z5  HA    H   HCR6  0   0.280  -6.3483  -0.0460   0.2761
 5Z5  HB    H   HCR6  0   0.278  -5.3380   2.1735  -0.1363
 5Z5  H1    H   HNR5  0   0.415  -2.8629   3.4339  -0.4317

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
 5Z5  C17  N3    single    1.443  0.020  1.443
 5Z5  C17  H171  single    0.970  0.020  1.090
 5Z5  C17  H172  single    0.970  0.020  1.090
 5Z5  C17  H173  single    0.970  0.020  1.090
 5Z5  N3   C16   single    1.343  0.020  1.343
 5Z5  N3   H3    single    0.860  0.020  1.020
 5Z5  C16  O2    double    1.227  0.020  1.227
 5Z5  C16  C12   single    1.478  0.020  1.478
 5Z5  C12  C11   aromatic  1.409  0.020  1.409
 5Z5  C12  C13   aromatic  1.401  0.020  1.401
 5Z5  C11  C14   single    1.492  0.020  1.492
 5Z5  C11  C10   aromatic  1.400  0.020  1.400
 5Z5  C14  H141  single    0.970  0.020  1.090
 5Z5  C14  H142  single    0.970  0.020  1.090
 5Z5  C14  H143  single    0.970  0.020  1.090
 5Z5  C13  C15   single    1.486  0.020  1.486
 5Z5  C13  N2    aromatic  1.333  0.020  1.333
 5Z5  C15  H151  single    0.970  0.020  1.090
 5Z5  C15  H152  single    0.970  0.020  1.090
 5Z5  C15  H153  single    0.970  0.020  1.090
 5Z5  N2   C10   aromatic  1.375  0.020  1.375
 5Z5  N2   H2    single    0.860  0.020  1.020
 5Z5  C10  C9    single    1.410  0.020  1.410
 5Z5  C9   C7    double    1.364  0.020  1.364
 5Z5  C9   H9    single    0.930  0.020  1.080
 5Z5  C7   C5    single    1.454  0.020  1.454
 5Z5  C7   C8    single    1.476  0.020  1.476
 5Z5  C5   C4    aromatic  1.385  0.020  1.385
 5Z5  C5   C6    aromatic  1.401  0.020  1.401
 5Z5  C4   C1    aromatic  1.389  0.020  1.389
 5Z5  C4   H4    single    0.930  0.020  1.080
 5Z5  C1   CL1   single    1.737  0.020  1.737
 5Z5  C1   C2    aromatic  1.389  0.020  1.389
 5Z5  C2   C3    aromatic  1.392  0.020  1.392
 5Z5  C2   HA    single    0.930  0.020  1.080
 5Z5  C3   C6    aromatic  1.380  0.020  1.380
 5Z5  C3   HB    single    0.930  0.020  1.080
 5Z5  C6   N1    single    1.383  0.020  1.383
 5Z5  N1   C8    single    1.364  0.020  1.364
 5Z5  N1   H1    single    0.860  0.020  1.020
 5Z5  C8   O1    double    1.229  0.020  1.229

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
 5Z5  H173  C17  H172  108.31  3.000
 5Z5  H173  C17  H171  108.38  3.000
 5Z5  H172  C17  H171  108.24  3.000
 5Z5  H173  C17  N3    108.33  3.000
 5Z5  H172  C17  N3    111.27  3.000
 5Z5  H171  C17  N3    112.21  3.000
 5Z5  H3    N3   C16   119.24  3.000
 5Z5  H3    N3   C17   117.88  3.000
 5Z5  C16   N3   C17   122.33  3.000
 5Z5  C12   C16  O2    122.31  3.000
 5Z5  C12   C16  N3    115.82  3.000
 5Z5  O2    C16  N3    121.87  3.000
 5Z5  C13   C12  C11   107.63  3.000
 5Z5  C13   C12  C16   124.21  3.000
 5Z5  C11   C12  C16   128.12  3.000
 5Z5  C10   C11  C14   125.89  3.000
 5Z5  C10   C11  C12   106.53  3.000
 5Z5  C14   C11  C12   127.56  3.000
 5Z5  H143  C14  H142  107.33  3.000
 5Z5  H143  C14  H141  106.71  3.000
 5Z5  H142  C14  H141  107.38  3.000
 5Z5  H143  C14  C11   111.87  3.000
 5Z5  H142  C14  C11   111.38  3.000
 5Z5  H141  C14  C11   111.90  3.000
 5Z5  N2    C13  C15   121.27  3.000
 5Z5  N2    C13  C12   107.63  3.000
 5Z5  C15   C13  C12   131.02  3.000
 5Z5  H153  C15  H152  108.63  3.000
 5Z5  H153  C15  H151  107.90  3.000
 5Z5  H152  C15  H151  107.43  3.000
 5Z5  H153  C15  C13   111.18  3.000
 5Z5  H152  C15  C13   110.96  3.000
 5Z5  H151  C15  C13   110.60  3.000
 5Z5  H2    N2   C10   121.55  3.000
 5Z5  H2    N2   C13   127.42  3.000
 5Z5  C10   N2   C13   111.03  3.000
 5Z5  C9    C10  N2    125.40  3.000
 5Z5  C9    C10  C11   127.41  3.000
 5Z5  N2    C10  C11   107.18  3.000
 5Z5  H9    C9   C7    114.78  3.000
 5Z5  H9    C9   C10   112.99  3.000
 5Z5  C7    C9   C10   132.22  3.000
 5Z5  C8    C7   C5    105.87  3.000
 5Z5  C8    C7   C9    129.02  3.000
 5Z5  C5    C7   C9    125.11  3.000
 5Z5  C6    C5   C4    119.86  3.000
 5Z5  C6    C5   C7    107.41  3.000
 5Z5  C4    C5   C7    132.72  3.000
 5Z5  H4    C4   C1    120.57  3.000
 5Z5  H4    C4   C5    121.47  3.000
 5Z5  C1    C4   C5    117.96  3.000
 5Z5  C2    C1   CL1   119.00  3.000
 5Z5  C2    C1   C4    122.11  3.000
 5Z5  CL1   C1   C4    118.89  3.000
 5Z5  HA    C2   C3    119.72  3.000
 5Z5  HA    C2   C1    120.24  3.000
 5Z5  C3    C2   C1    120.04  3.000
 5Z5  HB    C3   C6    121.75  3.000
 5Z5  HB    C3   C2    120.29  3.000
 5Z5  C6    C3   C2    117.96  3.000
 5Z5  N1    C6   C3    129.55  3.000
 5Z5  N1    C6   C5    108.38  3.000
 5Z5  C3    C6   C5    122.06  3.000
 5Z5  H1    N1   C8    123.09  3.000
 5Z5  H1    N1   C6    124.89  3.000
 5Z5  C8    N1   C6    112.02  3.000
 5Z5  O1    C8   N1    123.88  3.000
 5Z5  O1    C8   C7    129.80  3.000
 5Z5  N1    C8   C7    106.32  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
 5Z5  CONST_01  N2    C10  C11  C12     0.00   0.0  0
 5Z5  CONST_02  C10   N2   C13  C12     0.00   0.0  0
 5Z5  CONST_03  N2    C13  C12  C11     0.00   0.0  0
 5Z5  CONST_04  C13   N2   C10  C11     0.00   0.0  0
 5Z5  CONST_05  C10   C11  C12  C13     0.00   0.0  0
 5Z5  CONST_06  C2    C1   C4   C5      0.00   0.0  0
 5Z5  CONST_07  C2    C3   C6   C5      0.00   0.0  0
 5Z5  CONST_08  C3    C6   C5   C4      0.00   0.0  0
 5Z5  CONST_09  C3    C2   C1   C4      0.00   0.0  0
 5Z5  CONST_10  C6    C5   C4   C1      0.00   0.0  0
 5Z5  CONST_11  C6    C3   C2   C1      0.00   0.0  0
 5Z5  CONST_12  C6    N1   C8   C7      0.00   0.0  0
 5Z5  CONST_13  C10   C11  C12  C16   180.00   0.0  0
 5Z5  CONST_14  N2    C13  C12  C16   180.00   0.0  0
 5Z5  CONST_15  C9    C10  C11  C12   180.00   0.0  0
 5Z5  CONST_16  C15   C13  C12  C11   180.00   0.0  0
 5Z5  CONST_17  C13   C12  C11  C14   180.00   0.0  0
 5Z5  CONST_18  N2    C10  C11  C14   180.00   0.0  0
 5Z5  CONST_19  C9    C10  N2   C13   180.00   0.0  0
 5Z5  CONST_20  C10   N2   C13  C15   180.00   0.0  0
 5Z5  CONST_21  CL1   C1   C4   C5    180.00   0.0  0
 5Z5  CONST_22  C3    C2   C1   CL1   180.00   0.0  0
 5Z5  CONST_23  O1    C8   N1   C6    180.00   0.0  0
 5Z5  CONST_24  H2    N2   C13  C12   180.00   0.0  0
 5Z5  CONST_25  H4    C4   C5   C7      0.00   0.0  0
 5Z5  CONST_26  HB    C3   C6   C5    180.00   0.0  0
 5Z5  CONST_27  HA    C2   C1   C4    180.00   0.0  0
 5Z5  CONST_28  H1    N1   C8   C7    180.00   0.0  0
 5Z5  CONST_29  C12   C16  N3   C17   180.00   0.0  0
 5Z5  CONST_30  H3    N3   C16  C12     0.00   0.0  0
 5Z5  CONST_31  O2    C16  N3   C17     0.00   0.0  0
 5Z5  Var_01    C7    C9   C10  C11  -179.84  30.0  2
 5Z5  Var_02    C5    C7   C9   C10  -179.66  30.0  2
 5Z5  Var_03    C11   C12  C16  N3     37.03  30.0  2
 5Z5  Var_04    H141  C14  C11  C12   -81.04  30.0  2
 5Z5  Var_05    H151  C15  C13  C12    92.09  30.0  2
 5Z5  Var_06    H171  C17  N3   C16   -65.39  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
 5Z5  plan-1  C16  0.020
 5Z5  plan-1  C12  0.020
 5Z5  plan-1  C11  0.020
 5Z5  plan-1  C14  0.020
 5Z5  plan-1  C13  0.020
 5Z5  plan-1  C15  0.020
 5Z5  plan-1  N2   0.020
 5Z5  plan-1  C10  0.020
 5Z5  plan-1  C9   0.020
 5Z5  plan-1  H2   0.020
 5Z5  plan-2  C9   0.020
 5Z5  plan-2  C7   0.020
 5Z5  plan-2  C5   0.020
 5Z5  plan-2  C4   0.020
 5Z5  plan-2  C1   0.020
 5Z5  plan-2  CL1  0.020
 5Z5  plan-2  C2   0.020
 5Z5  plan-2  C3   0.020
 5Z5  plan-2  C6   0.020
 5Z5  plan-2  N1   0.020
 5Z5  plan-2  C8   0.020
 5Z5  plan-2  O1   0.020
 5Z5  plan-2  H4   0.020
 5Z5  plan-2  HA   0.020
 5Z5  plan-2  HB   0.020
 5Z5  plan-2  H1   0.020
 5Z5  plan-3  C17  0.020
 5Z5  plan-3  N3   0.020
 5Z5  plan-3  C16  0.020
 5Z5  plan-3  O2   0.020
 5Z5  plan-3  C12  0.020
 5Z5  plan-3  H3   0.020

