# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:12:57 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{4-[(3-cyano-1H-indol-5-yl)oxy]phenyl}glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)Nc1ccc(Oc2ccc3[nH]cc(C#N)c3c2)cc1
#
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
 MJP  MJP  N-{4-[(3-cyano-1H-indol-5-yl)oxy]phenyl}glycinamide  ligand  37  23  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJP
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
 MJP  N3    N  NS    0  -0.266  -3.6731  -3.6842   1.3249
 MJP  C16   C  CSP   0  -0.029  -3.9811  -2.7089   0.7888
 MJP  C14   C  CR5   0  -0.125  -4.3338  -1.5095   0.1437
 MJP  C15   C  CR15  0   0.035  -5.4809  -1.2877  -0.5871
 MJP  N2    N  NR15  0  -0.672  -5.4709  -0.0269  -1.0527
 MJP  C11   C  CR56  0   0.353  -4.3280   0.6169  -0.6496
 MJP  C10   C  CR16  0  -0.287  -3.8926   1.9152  -0.8887
 MJP  C9    C  CR16  0  -0.337  -2.6766   2.2889  -0.3520
 MJP  C12   C  CR56  0   0.121  -3.5747  -0.2920   0.1151
 MJP  C13   C  CR16  0  -0.418  -2.3537   0.1002   0.6624
 MJP  C8    C  CR6   0   0.318  -1.9251   1.3885   0.4153
 MJP  O1    O  O2    0  -0.518  -0.7488   1.8416   0.9593
 MJP  C2    C  CR6   0   0.344   0.4292   1.3048   0.5240
 MJP  C1    C  CR16  0  -0.322   0.5772   0.6749  -0.7054
 MJP  C3    C  CR16  0  -0.323   1.5304   1.4411   1.3572
 MJP  C4    C  CR16  0  -0.305   2.7736   0.9568   0.9794
 MJP  C5    C  CR6   0   0.360   2.9308   0.3101  -0.2472
 MJP  C     C  CR16  0  -0.339   1.8164   0.1822  -1.0765
 MJP  N     N  NH1   0  -0.741   4.1398  -0.2123  -0.7206
 MJP  C6    C  C     0   0.520   5.3076  -0.4158  -0.0597
 MJP  O     O  O     0  -0.467   5.5024  -0.1037   1.0995
 MJP  C7    C  CH2   0  -0.417   6.3552  -1.1154  -0.9097
 MJP  N1    N  NH2   0  -0.790   7.6390  -1.1366  -0.2491
 MJP  H15   H  HCR5  0   0.318  -6.2958  -1.9606  -0.7980
 MJP  H2    H  HNR5  0   0.430  -6.2014   0.3764  -1.6179
 MJP  H10   H  HCR6  0   0.279  -4.4757   2.6085  -1.4799
 MJP  H9    H  HCR6  0   0.274  -2.2967   3.2889  -0.5165
 MJP  H13   H  HCR6  0   0.272  -1.7612  -0.5802   1.2619
 MJP  H1    H  HCR6  0   0.280  -0.2591   0.5589  -1.3822
 MJP  H3    H  HCR6  0   0.270   1.4219   1.9374   2.3135
 MJP  H     H  HCR6  0   0.274   1.9140  -0.3114  -2.0367
 MJP  H4    H  HCR6  0   0.281   3.6062   1.0871   1.6504
 MJP  HA    H  HNH1  0   0.415   4.1109  -0.5379  -1.6756
 MJP  H71C  H  HCH2  0   0.245   5.9528  -2.1065  -1.1689
 MJP  H72C  H  HCH2  0   0.263   6.4517  -0.5773  -1.8565
 MJP  H11N  H  HNH2  0   0.347   7.6015  -1.7463   0.5572
 MJP  H12N  H  HNH2  0   0.356   8.3170  -1.5475  -0.8767

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
 MJP  N3   C16   triple    1.155  0.020  1.155
 MJP  C16  C14   single    1.407  0.020  1.407
 MJP  C14  C15   aromatic  1.378  0.020  1.378
 MJP  C14  C12   aromatic  1.435  0.020  1.435
 MJP  C15  N2    aromatic  1.344  0.020  1.344
 MJP  N2   C11   aromatic  1.372  0.020  1.372
 MJP  C11  C10   aromatic  1.390  0.020  1.390
 MJP  C11  C12   aromatic  1.407  0.020  1.407
 MJP  C10  C9    aromatic  1.381  0.020  1.381
 MJP  C9   C8    aromatic  1.402  0.020  1.402
 MJP  C12  C13   aromatic  1.394  0.020  1.394
 MJP  C13  C8    aromatic  1.380  0.020  1.380
 MJP  C8   O1    single    1.373  0.020  1.373
 MJP  O1   C2    single    1.366  0.020  1.366
 MJP  C2   C1    aromatic  1.389  0.020  1.389
 MJP  C2   C3    aromatic  1.388  0.020  1.388
 MJP  C1   C     aromatic  1.384  0.020  1.384
 MJP  C3   C4    aromatic  1.387  0.020  1.387
 MJP  C4   C5    aromatic  1.396  0.020  1.396
 MJP  C5   C     aromatic  1.395  0.020  1.395
 MJP  C5   N     single    1.399  0.020  1.399
 MJP  N    C6    single    1.357  0.020  1.357
 MJP  C6   O     double    1.216  0.020  1.216
 MJP  C6   C7    single    1.520  0.020  1.520
 MJP  C7   N1    single    1.444  0.020  1.444
 MJP  C15  H15   single    0.930  0.020  1.080
 MJP  N2   H2    single    0.860  0.020  1.020
 MJP  C10  H10   single    0.930  0.020  1.080
 MJP  C9   H9    single    0.930  0.020  1.080
 MJP  C13  H13   single    0.930  0.020  1.080
 MJP  C1   H1    single    0.930  0.020  1.080
 MJP  C3   H3    single    0.930  0.020  1.080
 MJP  C    H     single    0.930  0.020  1.080
 MJP  C4   H4    single    0.930  0.020  1.080
 MJP  N    HA    single    0.860  0.020  1.020
 MJP  C7   H71C  single    0.970  0.020  1.090
 MJP  C7   H72C  single    0.970  0.020  1.090
 MJP  N1   H11N  single    0.890  0.020  1.040
 MJP  N1   H12N  single    0.890  0.020  1.040

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
 MJP  C14   C16  N3    180.00  3.000
 MJP  C12   C14  C15   107.04  3.000
 MJP  C12   C14  C16   126.86  3.000
 MJP  C15   C14  C16   126.09  3.000
 MJP  H15   C15  N2    121.57  3.000
 MJP  H15   C15  C14   129.25  3.000
 MJP  N2    C15  C14   109.18  3.000
 MJP  H2    N2   C11   125.49  3.000
 MJP  H2    N2   C15   124.36  3.000
 MJP  C11   N2   C15   110.15  3.000
 MJP  C12   C11  C10   121.96  3.000
 MJP  C12   C11  N2    107.61  3.000
 MJP  C10   C11  N2    130.43  3.000
 MJP  H10   C10  C9    120.91  3.000
 MJP  H10   C10  C11   121.58  3.000
 MJP  C9    C10  C11   117.50  3.000
 MJP  H9    C9   C8    119.25  3.000
 MJP  H9    C9   C10   120.01  3.000
 MJP  C8    C9   C10   120.74  3.000
 MJP  C13   C12  C11   120.04  3.000
 MJP  C13   C12  C14   133.94  3.000
 MJP  C11   C12  C14   106.01  3.000
 MJP  H13   C13  C8    121.04  3.000
 MJP  H13   C13  C12   121.30  3.000
 MJP  C8    C13  C12   117.66  3.000
 MJP  O1    C8   C13   120.21  3.000
 MJP  O1    C8   C9    117.66  3.000
 MJP  C13   C8   C9    122.09  3.000
 MJP  C2    O1   C8    118.89  3.000
 MJP  C3    C2   C1    119.43  3.000
 MJP  C3    C2   O1    117.04  3.000
 MJP  C1    C2   O1    123.51  3.000
 MJP  H1    C1   C     119.08  3.000
 MJP  H1    C1   C2    121.32  3.000
 MJP  C     C1   C2    119.60  3.000
 MJP  H3    C3   C4    119.37  3.000
 MJP  H3    C3   C2    119.72  3.000
 MJP  C4    C3   C2    120.91  3.000
 MJP  H4    C4   C5    121.09  3.000
 MJP  H4    C4   C3    118.75  3.000
 MJP  C5    C4   C3    120.15  3.000
 MJP  N     C5   C     117.05  3.000
 MJP  N     C5   C4    124.59  3.000
 MJP  C     C5   C4    118.36  3.000
 MJP  H     C    C5    119.76  3.000
 MJP  H     C    C1    118.69  3.000
 MJP  C5    C    C1    121.54  3.000
 MJP  HA    N    C6    115.91  3.000
 MJP  HA    N    C5    114.56  3.000
 MJP  C6    N    C5    129.39  3.000
 MJP  C7    C6   O     122.74  3.000
 MJP  C7    C6   N     112.94  3.000
 MJP  O     C6   N     124.30  3.000
 MJP  H72C  C7   H71C  105.76  3.000
 MJP  H72C  C7   N1    108.96  3.000
 MJP  H71C  C7   N1    114.80  3.000
 MJP  H72C  C7   C6    108.58  3.000
 MJP  H71C  C7   C6    107.11  3.000
 MJP  N1    C7   C6    111.33  3.000
 MJP  H12N  N1   H11N  105.94  3.000
 MJP  H12N  N1   C7    108.55  3.000
 MJP  H11N  N1   C7    109.91  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
 MJP  CONST_01  C11   N2   C15  C14    0.00   0.0  0
 MJP  CONST_02  N2    C11  C12  C14    0.00   0.0  0
 MJP  CONST_03  C10   C11  C12  C14  180.00   0.0  0
 MJP  CONST_04  C8    C13  C12  C14  180.00   0.0  0
 MJP  CONST_05  C11   C12  C14  C15    0.00   0.0  0
 MJP  CONST_06  C13   C12  C14  C15  180.00   0.0  0
 MJP  CONST_07  C10   C11  N2   C15  180.00   0.0  0
 MJP  CONST_08  C12   C11  N2   C15    0.00   0.0  0
 MJP  CONST_09  C12   C14  C15  N2     0.00   0.0  0
 MJP  CONST_10  C9    C10  C11  N2   180.00   0.0  0
 MJP  CONST_11  C13   C12  C11  N2   180.00   0.0  0
 MJP  CONST_12  C8    C9   C10  C11    0.00   0.0  0
 MJP  CONST_13  C8    C13  C12  C11    0.00   0.0  0
 MJP  CONST_14  C13   C12  C11  C10    0.00   0.0  0
 MJP  CONST_15  C13   C8   C9   C10    0.00   0.0  0
 MJP  CONST_16  C12   C11  C10  C9     0.00   0.0  0
 MJP  CONST_17  C12   C13  C8   C9     0.00   0.0  0
 MJP  CONST_18  C5    C    C1   C2     0.00   0.0  0
 MJP  CONST_19  C5    C4   C3   C2     0.00   0.0  0
 MJP  CONST_20  C4    C3   C2   C1     0.00   0.0  0
 MJP  CONST_21  C4    C5   C    C1     0.00   0.0  0
 MJP  CONST_22  C     C1   C2   C3     0.00   0.0  0
 MJP  CONST_23  C     C5   C4   C3     0.00   0.0  0
 MJP  CONST_24  N2    C15  C14  C16  180.00   0.0  0
 MJP  CONST_25  C11   C12  C14  C16  180.00   0.0  0
 MJP  CONST_26  C13   C12  C14  C16    0.00   0.0  0
 MJP  CONST_27  O1    C8   C9   C10  180.00   0.0  0
 MJP  CONST_28  O1    C8   C13  C12  180.00   0.0  0
 MJP  CONST_29  C     C1   C2   O1   180.00   0.0  0
 MJP  CONST_30  C4    C3   C2   O1   180.00   0.0  0
 MJP  CONST_31  N     C5   C    C1   180.00   0.0  0
 MJP  CONST_32  N     C5   C4   C3   180.00   0.0  0
 MJP  CONST_33  H2    N2   C15  C14  180.00   0.0  0
 MJP  CONST_34  H13   C13  C12  C14    0.00   0.0  0
 MJP  CONST_35  H10   C10  C11  N2     0.00   0.0  0
 MJP  CONST_36  H15   C15  N2   C11  180.00   0.0  0
 MJP  CONST_37  H9    C9   C10  C11  180.00   0.0  0
 MJP  CONST_38  H     C    C1   C2   180.00   0.0  0
 MJP  CONST_39  H4    C4   C3   C2   180.00   0.0  0
 MJP  CONST_40  H3    C3   C2   C1   180.00   0.0  0
 MJP  CONST_41  H1    C1   C2   C3   180.00   0.0  0
 MJP  CONST_42  C6    N    C5   C4     0.00   0.0  0
 MJP  CONST_43  C6    N    C5   C    180.00   0.0  0
 MJP  CONST_44  HA    N    C5   C4   180.00   0.0  0
 MJP  CONST_45  O     C6   N    C5     0.00   0.0  0
 MJP  CONST_46  C7    C6   N    C5   180.00   0.0  0
 MJP  Var_01    C1    C2   O1   C8    22.26  30.0  2
 MJP  Var_02    N1    C7   C6   N    171.42  30.0  3
 MJP  Var_03    H11N  N1   C7   C6    68.72  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
 MJP  plan-1  O1   0.020
 MJP  plan-1  C2   0.020
 MJP  plan-1  C1   0.020
 MJP  plan-1  C3   0.020
 MJP  plan-1  C4   0.020
 MJP  plan-1  C5   0.020
 MJP  plan-1  C    0.020
 MJP  plan-1  N    0.020
 MJP  plan-1  H1   0.020
 MJP  plan-1  H3   0.020
 MJP  plan-1  H    0.020
 MJP  plan-1  H4   0.020
 MJP  plan-2  N3   0.020
 MJP  plan-2  C16  0.020
 MJP  plan-2  C14  0.020
 MJP  plan-2  C15  0.020
 MJP  plan-2  N2   0.020
 MJP  plan-2  C11  0.020
 MJP  plan-2  C10  0.020
 MJP  plan-2  C9   0.020
 MJP  plan-2  C12  0.020
 MJP  plan-2  C13  0.020
 MJP  plan-2  C8   0.020
 MJP  plan-2  O1   0.020
 MJP  plan-2  H15  0.020
 MJP  plan-2  H2   0.020
 MJP  plan-2  H10  0.020
 MJP  plan-2  H9   0.020
 MJP  plan-2  H13  0.020
 MJP  plan-3  C5   0.020
 MJP  plan-3  N    0.020
 MJP  plan-3  C6   0.020
 MJP  plan-3  O    0.020
 MJP  plan-3  C7   0.020
 MJP  plan-3  HA   0.020

