# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:15:35 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-{4-[5-(phenanthren-2-yl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)Nc1ccc(cc1)n2nc(cc2c3ccc4c(ccc5ccccc45)c3)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
 M4J  M4J  N-{4-[5-(phenanthren-2-yl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}glycinamide  ligand  53  34  .  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_M4J
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
 M4J  C1   C  CR16  0  -0.241   4.6125  -5.1595  -0.7125
 M4J  C2   C  CR16  0  -0.353   3.3677  -4.5784  -0.7710
 M4J  C3   C  CR66  0   0.128   3.0426  -3.4707   0.0340
 M4J  C4   C  CR66  0   0.079   4.0331  -2.9676   0.9078
 M4J  C5   C  CR16  0  -0.306   5.3002  -3.5773   0.9529
 M4J  C6   C  CR16  0  -0.322   3.7430  -1.8405   1.7397
 M4J  O    O  O     0  -0.456   2.9453   4.1228  -1.7074
 M4J  C23  C  C     0   0.525   2.5719   4.8453  -0.8064
 M4J  C24  C  CH2   0  -0.419   3.2813   6.1334  -0.4239
 M4J  N3   N  NH2   0  -0.789   4.4435   6.3604  -1.2480
 M4J  C20  C  CR6   0   0.390   0.5696   3.5465  -0.0886
 M4J  C21  C  CR16  0  -0.353  -0.4144   3.5083   0.9043
 M4J  C22  C  CR16  0  -0.252  -1.3521   2.4950   0.9389
 M4J  C19  C  CR16  0  -0.315   0.5833   2.5439  -1.0612
 M4J  C18  C  CR16  0  -0.244  -0.3685   1.5376  -1.0299
 M4J  C17  C  CR6   0   0.275  -1.3272   1.5042  -0.0313
 M4J  N1   N  NR5   0  -0.452  -2.2887   0.4635   0.0012
 M4J  N    N  N     0  -0.274  -3.5781   0.7734   0.0128
 M4J  C16  C  CR5   0  -0.020  -4.2081  -0.3805  -0.0275
 M4J  C25  C  CT    0   1.078  -5.6922  -0.4372  -0.0169
 M4J  F1   F  F     0  -0.315  -6.1637  -1.0960  -1.0841
 M4J  F    F  F     0  -0.315  -6.1516  -1.0863   1.0622
 M4J  F2   F  F     0  -0.304  -6.2389   0.7773  -0.0178
 M4J  C14  C  CR5   0   0.439  -2.0744  -0.8800  -0.0421
 M4J  C15  C  CR15  0  -0.554  -3.3214  -1.4629  -0.0707
 M4J  C12  C  CR6   0   0.041  -0.7583  -1.5182  -0.0153
 M4J  C13  C  CR16  0  -0.348   0.2510  -1.0820   0.8164
 M4J  C8   C  CR66  0   0.111   1.5016  -1.7184   0.8370
 M4J  C9   C  CR66  0   0.119   1.7440  -2.8315   0.0015
 M4J  C10  C  CR16  0  -0.342   0.6959  -3.2683  -0.8284
 M4J  C11  C  CR16  0  -0.281  -0.5202  -2.6319  -0.8401
 M4J  C7   C  CR16  0  -0.327   2.5331  -1.2415   1.7058
 M4J  C    C  CR16  0  -0.262   5.5906  -4.6572   0.1560
 M4J  H1   H  HCR6  0   0.262   4.8356  -6.0107  -1.3423
 M4J  H2   H  HCR6  0   0.257   2.6394  -4.9932  -1.4542
 M4J  H3   H  HCR6  0   0.259   6.0472  -3.1789   1.6288
 M4J  H4   H  HCR6  0   0.259   4.5182  -1.4720   2.4002
 M4J  H5   H  HCH2  0   0.245   2.5350   6.9408  -0.4433
 M4J  H6   H  HCH2  0   0.271   3.5963   6.0467   0.6202
 M4J  H7   H  HNH2  0   0.348   4.1576   6.5892  -2.1910
 M4J  H8   H  HNH2  0   0.357   4.9321   7.1746  -0.9005
 M4J  H10  H  HNH1  0   0.418   1.2863   5.2862   0.6836
 M4J  H11  H  HCR6  0   0.280  -0.4415   4.2770   1.6670
 M4J  H12  H  HCR6  0   0.279  -2.0955   2.4756   1.7244
 M4J  H13  H  HCR6  0   0.288   1.3155   2.5405  -1.8502
 M4J  H14  H  HCR6  0   0.280  -0.3548   0.7805  -1.8027
 M4J  H15  H  HCR5  0   0.293  -3.5468  -2.5166  -0.0840
 M4J  H16  H  HCR6  0   0.265   0.0958  -0.2430   1.4838
 M4J  H17  H  HCR6  0   0.261   0.8307  -4.1160  -1.4856
 M4J  H18  H  HCR6  0   0.263  -1.2987  -2.9842  -1.5043
 M4J  H19  H  HCR6  0   0.257   2.3263  -0.3865   2.3376
 M4J  H20  H  HCR6  0   0.261   6.5685  -5.1185   0.1961
 M4J  N2   N  NH1   0  -0.745   1.4698   4.6076  -0.0410

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
 M4J  N3   C24  single    1.443  0.020  1.443
 M4J  C24  C23  single    1.519  0.020  1.519
 M4J  C5   C    aromatic  1.373  0.020  1.373
 M4J  C5   C4   aromatic  1.407  0.020  1.407
 M4J  C6   C4   aromatic  1.431  0.020  1.431
 M4J  C6   C7   aromatic  1.350  0.020  1.350
 M4J  C    C1   aromatic  1.401  0.020  1.401
 M4J  C23  O    double    1.214  0.020  1.214
 M4J  C23  N2   single    1.363  0.020  1.363
 M4J  C4   C3   aromatic  1.413  0.020  1.413
 M4J  C7   C8   aromatic  1.431  0.020  1.431
 M4J  N2   C20  single    1.392  0.020  1.392
 M4J  C1   C2   aromatic  1.375  0.020  1.375
 M4J  C3   C2   aromatic  1.407  0.020  1.407
 M4J  C3   C9   aromatic  1.448  0.020  1.448
 M4J  C20  C21  aromatic  1.398  0.020  1.398
 M4J  C20  C19  aromatic  1.397  0.020  1.397
 M4J  C8   C9   aromatic  1.413  0.020  1.413
 M4J  C8   C13  aromatic  1.403  0.020  1.403
 M4J  C21  C22  aromatic  1.381  0.020  1.381
 M4J  C9   C10  aromatic  1.406  0.020  1.406
 M4J  C19  C18  aromatic  1.385  0.020  1.385
 M4J  C13  C12  aromatic  1.379  0.020  1.379
 M4J  C22  C17  aromatic  1.387  0.020  1.387
 M4J  C18  C17  aromatic  1.385  0.020  1.385
 M4J  C17  N1   single    1.417  0.020  1.417
 M4J  C10  C11  aromatic  1.373  0.020  1.373
 M4J  C12  C11  aromatic  1.406  0.020  1.406
 M4J  C12  C14  single    1.463  0.020  1.463
 M4J  N1   C14  aromatic  1.361  0.020  1.361
 M4J  N1   N    aromatic  1.326  0.020  1.326
 M4J  C14  C15  aromatic  1.377  0.020  1.377
 M4J  N    C16  aromatic  1.315  0.020  1.315
 M4J  C15  C16  aromatic  1.400  0.020  1.400
 M4J  C16  C25  single    1.485  0.020  1.485
 M4J  F1   C25  single    1.340  0.020  1.340
 M4J  C25  F2   single    1.332  0.020  1.332
 M4J  C25  F    single    1.340  0.020  1.340
 M4J  C1   H1   single    0.930  0.020  1.080
 M4J  C2   H2   single    0.930  0.020  1.080
 M4J  C5   H3   single    0.930  0.020  1.080
 M4J  C6   H4   single    0.930  0.020  1.080
 M4J  C24  H5   single    0.970  0.020  1.090
 M4J  C24  H6   single    0.970  0.020  1.090
 M4J  N3   H7   single    0.890  0.020  1.040
 M4J  N3   H8   single    0.890  0.020  1.040
 M4J  N2   H10  single    0.860  0.020  1.020
 M4J  C21  H11  single    0.930  0.020  1.080
 M4J  C22  H12  single    0.930  0.020  1.080
 M4J  C19  H13  single    0.930  0.020  1.080
 M4J  C18  H14  single    0.930  0.020  1.080
 M4J  C15  H15  single    0.930  0.020  1.080
 M4J  C13  H16  single    0.930  0.020  1.080
 M4J  C10  H17  single    0.930  0.020  1.080
 M4J  C11  H18  single    0.930  0.020  1.080
 M4J  C7   H19  single    0.930  0.020  1.080
 M4J  C    H20  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
 M4J  H1   C1   C    119.92  3.000
 M4J  H1   C1   C2   119.63  3.000
 M4J  C    C1   C2   120.45  3.000
 M4J  H2   C2   C3   120.52  3.000
 M4J  H2   C2   C1   118.32  3.000
 M4J  C3   C2   C1   121.16  3.000
 M4J  C9   C3   C4   119.03  3.000
 M4J  C9   C3   C2   122.81  3.000
 M4J  C4   C3   C2   118.16  3.000
 M4J  C6   C4   C5   120.36  3.000
 M4J  C6   C4   C3   119.86  3.000
 M4J  C5   C4   C3   119.78  3.000
 M4J  H3   C5   C    120.36  3.000
 M4J  H3   C5   C4   118.79  3.000
 M4J  C    C5   C4   120.84  3.000
 M4J  H4   C6   C7   120.37  3.000
 M4J  H4   C6   C4   118.53  3.000
 M4J  C7   C6   C4   121.10  3.000
 M4J  N2   C23  C24  112.59  3.000
 M4J  N2   C23  O    124.19  3.000
 M4J  C24  C23  O    123.22  3.000
 M4J  H6   C24  H5   105.70  3.000
 M4J  H6   C24  N3   109.01  3.000
 M4J  H5   C24  N3   114.90  3.000
 M4J  H6   C24  C23  107.91  3.000
 M4J  H5   C24  C23  107.52  3.000
 M4J  N3   C24  C23  111.45  3.000
 M4J  H8   N3   H7   105.95  3.000
 M4J  H8   N3   C24  108.64  3.000
 M4J  H7   N3   C24  109.91  3.000
 M4J  C19  C20  C21  118.79  3.000
 M4J  C19  C20  N2   124.36  3.000
 M4J  C21  C20  N2   116.84  3.000
 M4J  H11  C21  C22  119.08  3.000
 M4J  H11  C21  C20  119.88  3.000
 M4J  C22  C21  C20  121.04  3.000
 M4J  H12  C22  C17  120.50  3.000
 M4J  H12  C22  C21  119.87  3.000
 M4J  C17  C22  C21  119.63  3.000
 M4J  H13  C19  C18  118.79  3.000
 M4J  H13  C19  C20  121.28  3.000
 M4J  C18  C19  C20  119.92  3.000
 M4J  H14  C18  C17  120.46  3.000
 M4J  H14  C18  C19  118.91  3.000
 M4J  C17  C18  C19  120.63  3.000
 M4J  N1   C17  C18  120.26  3.000
 M4J  N1   C17  C22  119.76  3.000
 M4J  C18  C17  C22  119.98  3.000
 M4J  C14  N1   N    112.58  3.000
 M4J  N    N1   C17  119.22  3.000
 M4J  C14  N1   C17  128.12  3.000
 M4J  C16  N    N1   105.09  3.000
 M4J  C15  C16  C25  127.13  3.000
 M4J  C25  C16  N    120.79  3.000
 M4J  C15  C16  N    112.08  3.000
 M4J  F2   C25  F    107.54  3.000
 M4J  F    C25  F1   106.41  3.000
 M4J  F2   C25  F1   107.66  3.000
 M4J  F    C25  C16  111.51  3.000
 M4J  F2   C25  C16  112.05  3.000
 M4J  F1   C25  C16  111.39  3.000
 M4J  C12  C14  C15  129.09  3.000
 M4J  C15  C14  N1   106.02  3.000
 M4J  C12  C14  N1   124.86  3.000
 M4J  H15  C15  C14  127.13  3.000
 M4J  H15  C15  C16  128.60  3.000
 M4J  C14  C15  C16  104.23  3.000
 M4J  C11  C12  C13  118.72  3.000
 M4J  C11  C12  C14  119.16  3.000
 M4J  C13  C12  C14  122.11  3.000
 M4J  H16  C13  C8   118.02  3.000
 M4J  H16  C13  C12  120.79  3.000
 M4J  C8   C13  C12  121.18  3.000
 M4J  C7   C8   C9   119.88  3.000
 M4J  C9   C8   C13  120.10  3.000
 M4J  C7   C8   C13  120.02  3.000
 M4J  C10  C9   C8   117.76  3.000
 M4J  C10  C9   C3   123.00  3.000
 M4J  C8   C9   C3   119.24  3.000
 M4J  H17  C10  C11  117.96  3.000
 M4J  H17  C10  C9   120.62  3.000
 M4J  C11  C10  C9   121.42  3.000
 M4J  H18  C11  C10  119.45  3.000
 M4J  H18  C11  C12  119.73  3.000
 M4J  C10  C11  C12  120.82  3.000
 M4J  H19  C7   C8   118.67  3.000
 M4J  H19  C7   C6   120.44  3.000
 M4J  C8   C7   C6   120.89  3.000
 M4J  H20  C    C5   120.32  3.000
 M4J  H20  C    C1   120.07  3.000
 M4J  C5   C    C1   119.61  3.000
 M4J  H10  N2   C20  114.79  3.000
 M4J  H10  N2   C23  115.65  3.000
 M4J  C20  N2   C23  129.54  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
 M4J  CONST_01  C4   C5   C    C1     0.00   0.0  0
 M4J  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 M4J  CONST_03  C9   C3   C2   C1   180.00   0.0  0
 M4J  CONST_04  C5   C    C1   C2     0.00   0.0  0
 M4J  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 M4J  CONST_06  C6   C4   C3   C2   180.00   0.0  0
 M4J  CONST_07  C8   C9   C3   C2   180.00   0.0  0
 M4J  CONST_08  C10  C9   C3   C2     0.00   0.0  0
 M4J  CONST_09  C    C5   C4   C3     0.00   0.0  0
 M4J  CONST_10  C7   C6   C4   C3     0.00   0.0  0
 M4J  CONST_11  C    C1   C2   C3     0.00   0.0  0
 M4J  CONST_12  C7   C8   C9   C3     0.00   0.0  0
 M4J  CONST_13  C13  C8   C9   C3   180.00   0.0  0
 M4J  CONST_14  C11  C10  C9   C3   180.00   0.0  0
 M4J  CONST_15  C8   C7   C6   C4     0.00   0.0  0
 M4J  CONST_16  C8   C9   C3   C4     0.00   0.0  0
 M4J  CONST_17  C10  C9   C3   C4   180.00   0.0  0
 M4J  CONST_18  C7   C6   C4   C5   180.00   0.0  0
 M4J  CONST_19  C9   C3   C4   C5   180.00   0.0  0
 M4J  CONST_20  C    C5   C4   C6   180.00   0.0  0
 M4J  CONST_21  C9   C3   C4   C6     0.00   0.0  0
 M4J  CONST_22  C9   C8   C7   C6     0.00   0.0  0
 M4J  CONST_23  C13  C8   C7   C6   180.00   0.0  0
 M4J  CONST_24  C17  C22  C21  C20    0.00   0.0  0
 M4J  CONST_25  C17  C18  C19  C20    0.00   0.0  0
 M4J  CONST_26  C18  C19  C20  C21    0.00   0.0  0
 M4J  CONST_27  C18  C17  C22  C21    0.00   0.0  0
 M4J  CONST_28  N1   C17  C22  C21  180.00   0.0  0
 M4J  CONST_29  C19  C20  C21  C22    0.00   0.0  0
 M4J  CONST_30  C19  C18  C17  C22    0.00   0.0  0
 M4J  CONST_33  N1   C17  C18  C19  180.00   0.0  0
 M4J  CONST_36  C12  C14  N1   C17    0.00   0.0  0
 M4J  CONST_37  C15  C14  N1   C17  180.00   0.0  0
 M4J  CONST_38  C16  N    N1   C17  180.00   0.0  0
 M4J  CONST_41  C16  C15  C14  N1     0.00   0.0  0
 M4J  CONST_42  C15  C16  N    N1     0.00   0.0  0
 M4J  CONST_43  C12  C14  N1   N    180.00   0.0  0
 M4J  CONST_44  C15  C14  N1   N      0.00   0.0  0
 M4J  CONST_45  C14  C15  C16  N      0.00   0.0  0
 M4J  CONST_46  C14  N1   N    C16    0.00   0.0  0
 M4J  CONST_47  C12  C14  C15  C16  180.00   0.0  0
 M4J  CONST_48  C8   C13  C12  C14  180.00   0.0  0
 M4J  CONST_49  C10  C11  C12  C14  180.00   0.0  0
 M4J  CONST_52  C7   C8   C13  C12  180.00   0.0  0
 M4J  CONST_53  C9   C8   C13  C12    0.00   0.0  0
 M4J  CONST_54  C9   C10  C11  C12    0.00   0.0  0
 M4J  CONST_55  C10  C9   C8   C13    0.00   0.0  0
 M4J  CONST_56  C10  C11  C12  C13    0.00   0.0  0
 M4J  CONST_57  C11  C10  C9   C8     0.00   0.0  0
 M4J  CONST_58  C11  C12  C13  C8     0.00   0.0  0
 M4J  CONST_59  C7   C8   C9   C10  180.00   0.0  0
 M4J  CONST_60  C22  C21  C20  N2   180.00   0.0  0
 M4J  CONST_61  C18  C19  C20  N2   180.00   0.0  0
 M4J  CONST_62  C25  C16  N    N1   180.00   0.0  0
 M4J  CONST_63  C14  C15  C16  C25  180.00   0.0  0
 M4J  CONST_64  H3   C5   C    C1   180.00   0.0  0
 M4J  CONST_65  H20  C    C1   C2   180.00   0.0  0
 M4J  CONST_66  H4   C6   C4   C3   180.00   0.0  0
 M4J  CONST_67  H1   C1   C2   C3   180.00   0.0  0
 M4J  CONST_68  H17  C10  C9   C3     0.00   0.0  0
 M4J  CONST_69  H19  C7   C6   C4   180.00   0.0  0
 M4J  CONST_70  H2   C2   C3   C4   180.00   0.0  0
 M4J  CONST_71  H12  C22  C21  C20  180.00   0.0  0
 M4J  CONST_72  H14  C18  C19  C20  180.00   0.0  0
 M4J  CONST_73  H13  C19  C20  C21  180.00   0.0  0
 M4J  CONST_74  H11  C21  C20  C19  180.00   0.0  0
 M4J  CONST_75  H15  C15  C14  N1   180.00   0.0  0
 M4J  CONST_76  H16  C13  C12  C14    0.00   0.0  0
 M4J  CONST_77  H18  C11  C12  C14    0.00   0.0  0
 M4J  CONST_78  C21  C20  N2   C23  180.00   0.0  0
 M4J  CONST_79  C19  C20  N2   C23    0.00   0.0  0
 M4J  CONST_80  H10  N2   C20  C21    0.00   0.0  0
 M4J  CONST_81  C20  N2   C23  O      0.00   0.0  0
 M4J  CONST_82  C20  N2   C23  C24  180.00   0.0  0
 M4J  Var_01    F1   C25  C16  N    123.17  30.0  2
 M4J  Var_02    N3   C24  C23  O     -0.86  30.0  3
 M4J  Var_03    H7   N3   C24  C23   70.00  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
 M4J  plan-1  C17  0.020
 M4J  plan-1  N1   0.020
 M4J  plan-1  N    0.020
 M4J  plan-1  C16  0.020
 M4J  plan-1  C25  0.020
 M4J  plan-1  C14  0.020
 M4J  plan-1  C15  0.020
 M4J  plan-1  C12  0.020
 M4J  plan-1  H15  0.020
 M4J  plan-2  C20  0.020
 M4J  plan-2  C21  0.020
 M4J  plan-2  C22  0.020
 M4J  plan-2  C19  0.020
 M4J  plan-2  C18  0.020
 M4J  plan-2  C17  0.020
 M4J  plan-2  N1   0.020
 M4J  plan-2  H11  0.020
 M4J  plan-2  H12  0.020
 M4J  plan-2  H13  0.020
 M4J  plan-2  H14  0.020
 M4J  plan-2  N2   0.020
 M4J  plan-3  C1   0.020
 M4J  plan-3  C2   0.020
 M4J  plan-3  C3   0.020
 M4J  plan-3  C4   0.020
 M4J  plan-3  C5   0.020
 M4J  plan-3  C6   0.020
 M4J  plan-3  C14  0.020
 M4J  plan-3  C12  0.020
 M4J  plan-3  C13  0.020
 M4J  plan-3  C8   0.020
 M4J  plan-3  C9   0.020
 M4J  plan-3  C10  0.020
 M4J  plan-3  C11  0.020
 M4J  plan-3  C7   0.020
 M4J  plan-3  C    0.020
 M4J  plan-3  H1   0.020
 M4J  plan-3  H2   0.020
 M4J  plan-3  H3   0.020
 M4J  plan-3  H4   0.020
 M4J  plan-3  H16  0.020
 M4J  plan-3  H17  0.020
 M4J  plan-3  H18  0.020
 M4J  plan-3  H19  0.020
 M4J  plan-3  H20  0.020
 M4J  plan-4  O    0.020
 M4J  plan-4  C23  0.020
 M4J  plan-4  C24  0.020
 M4J  plan-4  C20  0.020
 M4J  plan-4  H10  0.020
 M4J  plan-4  N2   0.020

