# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 19:21:24 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-methyl-5-(2-{[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)-1H-pyrrole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(OC(F)(F)F)c(Nc3nccc(n3)c4cc(cn4C)C(N)=O)c2
#
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
 939  939  1-methyl-5-(2-{[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)-1H-pyrrole-3-carboxamide  ligand  58  34  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_939
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
 939  N1    N  N     0  -0.465   0.4744   1.4500  -0.7163
 939  C2    C  CR6   0   0.604   0.8492   0.2628  -0.2631
 939  N3    N  N     0  -0.498   2.1056  -0.1516  -0.0899
 939  C4    C  CR6   0   0.277   3.0823   0.6858  -0.4066
 939  C5    C  CR16  0  -0.403   2.7940   1.9656  -0.9017
 939  C6    C  CR16  0  -0.002   1.4623   2.2849  -1.0284
 939  N7    N  NH1   0  -0.771  -0.0869  -0.6732   0.0707
 939  C8    C  CR5   0   0.356   4.4596   0.2647  -0.2199
 939  N9    N  NR5   0  -0.480   4.8777  -1.0335  -0.0138
 939  C10   C  CR15  0  -0.033   6.2142  -1.0450   0.1339
 939  C11   C  CR5   0  -0.117   6.6962   0.2486   0.0347
 939  C12   C  CR15  0  -0.415   5.5777   1.0710  -0.1921
 939  C13   C  C     0   0.452   8.0803   0.7374   0.1395
 939  N14   N  NH2   0  -0.825   9.0385  -0.1911   0.3041
 939  O15   O  O     0  -0.493   8.3299   1.9367   0.0822
 939  C16   C  CR6   0   0.354  -1.4728  -0.6101   0.0400
 939  C17   C  CR6   0   0.200  -2.1867  -1.8163   0.0217
 939  C18   C  CR16  0  -0.282  -3.5626  -1.8213   0.0767
 939  C19   C  CR16  0  -0.389  -4.2729  -0.6314   0.1051
 939  C20   C  CR6   0   0.412  -3.5950   0.5936   0.1108
 939  C21   C  CR16  0  -0.425  -2.1927   0.5763   0.0949
 939  O22   O  O2    0  -0.527  -1.4759  -3.0166   0.0201
 939  C23   C  CT    0   1.076  -1.3120  -3.6363  -1.1579
 939  F24   F  F     0  -0.299  -0.7352  -2.8591  -2.0759
 939  F25   F  F     0  -0.277  -0.5366  -4.6892  -0.9526
 939  F26   F  F     0  -0.297  -2.4623  -4.0624  -1.6816
 939  C27   C  CH3   0  -0.507   4.0784  -2.2464  -0.0017
 939  N28   N  NT    0  -0.524  -4.2626   1.8085   0.1849
 939  C29   C  CH2   0  -0.313  -5.7059   1.7946   0.3196
 939  C30   C  CH2   0  -0.279  -6.2135   3.1483   0.7816
 939  N31   N  NT    0  -0.413  -5.7856   4.2028  -0.1114
 939  C32   C  CH2   0  -0.284  -4.3400   4.2302  -0.1689
 939  C33   C  CH2   0  -0.304  -3.7979   2.9023  -0.6574
 939  C34   C  CH3   0  -0.518  -6.3319   5.4839   0.2727
 939  H6    H  HCR6  0   0.274   1.1652   3.2569  -1.4052
 939  H7    H  HNH1  0   0.402   0.3189  -1.5476   0.3661
 939  H5    H  HCR6  0   0.272   3.5641   2.6679  -1.1821
 939  H12   H  HCR5  0   0.263   5.5899   2.1433  -0.3042
 939  H10   H  HCR5  0   0.295   6.7316  -1.9774   0.2999
 939  H271  H  HCH3  0   0.259   3.4787  -2.3207  -0.9043
 939  H272  H  HCH3  0   0.257   4.7570  -3.0940   0.0391
 939  H273  H  HCH3  0   0.261   3.4185  -2.2737   0.8600
 939  H141  H  HNH2  0   0.407   8.8514  -1.1780   0.2957
 939  H142  H  HNH2  0   0.403  10.0043   0.0886   0.3489
 939  H21   H  HCR6  0   0.291  -1.6388   1.4982   0.1443
 939  H18   H  HCR6  0   0.277  -4.1014  -2.7597   0.0899
 939  H19   H  HCR6  0   0.274  -5.3512  -0.6838   0.1089
 939  H291  H  HCH2  0   0.216  -6.1996   1.5162  -0.6233
 939  H292  H  HCH2  0   0.253  -5.9959   1.0596   1.0707
 939  H331  H  HCH2  0   0.254  -2.7120   2.9579  -0.6482
 939  H332  H  HCH2  0   0.221  -4.1062   2.7420  -1.7004
 939  H301  H  HCH2  0   0.242  -7.3052   3.1159   0.8067
 939  H302  H  HCH2  0   0.194  -5.8705   3.3264   1.8162
 939  H321  H  HCH2  0   0.242  -4.0199   5.0115  -0.8622
 939  H322  H  HCH2  0   0.195  -3.8965   4.4649   0.8149
 939  H341  H  HCH3  0   0.193  -6.0199   5.8055   1.2786
 939  H342  H  HCH3  0   0.234  -6.0156   6.2514  -0.4351
 939  H343  H  HCH3  0   0.234  -7.4221   5.4445   0.2592

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
 939  N1   C2    aromatic  1.325  0.020  1.325
 939  N1   C6    aromatic  1.331  0.020  1.331
 939  C2   N3    aromatic  1.334  0.020  1.334
 939  C2   N7    single    1.365  0.020  1.365
 939  N3   C4    aromatic  1.325  0.020  1.325
 939  C4   C5    aromatic  1.402  0.020  1.402
 939  C4   C8    single    1.452  0.020  1.452
 939  C5   C6    aromatic  1.375  0.020  1.375
 939  N7   C16   single    1.388  0.020  1.388
 939  C8   N9    aromatic  1.379  0.020  1.379
 939  C8   C12   aromatic  1.379  0.020  1.379
 939  N9   C10   aromatic  1.345  0.020  1.345
 939  N9   C27   single    1.453  0.020  1.453
 939  C10  C11   aromatic  1.384  0.020  1.384
 939  C11  C12   aromatic  1.407  0.020  1.407
 939  C11  C13   single    1.472  0.020  1.472
 939  C13  N14   single    1.344  0.020  1.344
 939  C13  O15   double    1.226  0.020  1.226
 939  C16  C17   aromatic  1.402  0.020  1.402
 939  C16  C21   aromatic  1.389  0.020  1.389
 939  C17  C18   aromatic  1.377  0.020  1.377
 939  C17  O22   single    1.395  0.020  1.395
 939  C18  C19   aromatic  1.386  0.020  1.386
 939  C19  C20   aromatic  1.400  0.020  1.400
 939  C20  C21   aromatic  1.402  0.020  1.402
 939  C20  N28   single    1.388  0.020  1.388
 939  O22  C23   single    1.341  0.020  1.341
 939  C23  F24   single    1.334  0.020  1.334
 939  C23  F25   single    1.324  0.020  1.324
 939  C23  F26   single    1.334  0.020  1.334
 939  N28  C29   single    1.450  0.020  1.450
 939  N28  C33   single    1.457  0.020  1.457
 939  C29  C30   single    1.518  0.020  1.518
 939  C30  N31   single    1.447  0.020  1.447
 939  N31  C32   single    1.447  0.020  1.447
 939  N31  C34   single    1.445  0.020  1.445
 939  C32  C33   single    1.515  0.020  1.515
 939  C6   H6    single    0.930  0.020  1.080
 939  N7   H7    single    0.860  0.020  1.020
 939  C5   H5    single    0.930  0.020  1.080
 939  C12  H12   single    0.930  0.020  1.080
 939  C10  H10   single    0.930  0.020  1.080
 939  C27  H271  single    0.970  0.020  1.090
 939  C27  H272  single    0.970  0.020  1.090
 939  C27  H273  single    0.970  0.020  1.090
 939  N14  H141  single    0.860  0.020  1.020
 939  N14  H142  single    0.860  0.020  1.020
 939  C21  H21   single    0.930  0.020  1.080
 939  C18  H18   single    0.930  0.020  1.080
 939  C19  H19   single    0.930  0.020  1.080
 939  C29  H291  single    0.970  0.020  1.090
 939  C29  H292  single    0.970  0.020  1.090
 939  C33  H331  single    0.970  0.020  1.090
 939  C33  H332  single    0.970  0.020  1.090
 939  C30  H301  single    0.970  0.020  1.090
 939  C30  H302  single    0.970  0.020  1.090
 939  C32  H321  single    0.970  0.020  1.090
 939  C32  H322  single    0.970  0.020  1.090
 939  C34  H341  single    0.970  0.020  1.090
 939  C34  H342  single    0.970  0.020  1.090
 939  C34  H343  single    0.970  0.020  1.090

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
 939  C6    N1   C2    115.62  3.000
 939  N7    C2   N3    113.64  3.000
 939  N7    C2   N1    120.27  3.000
 939  N3    C2   N1    126.09  3.000
 939  C4    N3   C2    117.83  3.000
 939  C8    C4   C5    120.33  3.000
 939  C8    C4   N3    119.02  3.000
 939  C5    C4   N3    120.65  3.000
 939  H5    C5   C6    121.05  3.000
 939  H5    C5   C4    122.62  3.000
 939  C6    C5   C4    116.33  3.000
 939  H6    C6   C5    120.37  3.000
 939  H6    C6   N1    116.15  3.000
 939  C5    C6   N1    123.48  3.000
 939  H7    N7   C16   116.61  3.000
 939  H7    N7   C2    112.97  3.000
 939  C16   N7   C2    130.41  3.000
 939  C12   C8   N9    107.55  3.000
 939  C12   C8   C4    127.02  3.000
 939  N9    C8   C4    125.42  3.000
 939  C27   N9   C10   122.61  3.000
 939  C27   N9   C8    128.34  3.000
 939  C10   N9   C8    109.01  3.000
 939  H10   C10  C11   130.67  3.000
 939  H10   C10  N9    120.05  3.000
 939  C11   C10  N9    109.28  3.000
 939  C13   C11  C12   124.41  3.000
 939  C13   C11  C10   129.26  3.000
 939  C12   C11  C10   106.33  3.000
 939  H12   C12  C11   126.10  3.000
 939  H12   C12  C8    126.06  3.000
 939  C11   C12  C8    107.83  3.000
 939  O15   C13  N14   122.42  3.000
 939  O15   C13  C11   120.86  3.000
 939  N14   C13  C11   116.72  3.000
 939  H142  N14  H141  116.88  3.000
 939  H142  N14  C13   119.83  3.000
 939  H141  N14  C13   123.01  3.000
 939  C21   C16  C17   118.14  3.000
 939  C21   C16  N7    123.76  3.000
 939  C17   C16  N7    118.02  3.000
 939  O22   C17  C18   120.41  3.000
 939  O22   C17  C16   118.74  3.000
 939  C18   C17  C16   120.76  3.000
 939  H18   C18  C19   119.28  3.000
 939  H18   C18  C17   120.07  3.000
 939  C19   C18  C17   120.65  3.000
 939  H19   C19  C20   121.74  3.000
 939  H19   C19  C18   118.05  3.000
 939  C20   C19  C18   120.21  3.000
 939  N28   C20  C21   119.49  3.000
 939  N28   C20  C19   122.21  3.000
 939  C21   C20  C19   118.25  3.000
 939  H21   C21  C20   120.22  3.000
 939  H21   C21  C16   117.81  3.000
 939  C20   C21  C16   121.96  3.000
 939  C23   O22  C17   117.44  3.000
 939  F26   C23  F25   108.18  3.000
 939  F26   C23  F24   106.79  3.000
 939  F25   C23  F24   108.47  3.000
 939  F26   C23  O22   112.78  3.000
 939  F25   C23  O22   107.63  3.000
 939  F24   C23  O22   112.84  3.000
 939  H273  C27  H272  109.28  3.000
 939  H273  C27  H271  108.80  3.000
 939  H272  C27  H271  108.83  3.000
 939  H273  C27  N9    111.23  3.000
 939  H272  C27  N9    107.94  3.000
 939  H271  C27  N9    110.74  3.000
 939  C33   N28  C29   112.25  3.000
 939  C33   N28  C20   118.22  3.000
 939  C29   N28  C20   118.39  3.000
 939  H292  C29  H291  107.48  3.000
 939  H292  C29  C30   107.62  3.000
 939  H291  C29  C30   109.66  3.000
 939  H292  C29  N28   109.59  3.000
 939  H291  C29  N28   111.69  3.000
 939  C30   C29  N28   110.66  3.000
 939  H302  C30  H301  107.07  3.000
 939  H302  C30  N31   111.65  3.000
 939  H301  C30  N31   109.36  3.000
 939  H302  C30  C29   108.97  3.000
 939  H301  C30  C29   108.35  3.000
 939  N31   C30  C29   111.30  3.000
 939  C34   N31  C32   111.82  3.000
 939  C34   N31  C30   111.74  3.000
 939  C32   N31  C30   109.50  3.000
 939  H322  C32  H321  107.20  3.000
 939  H322  C32  C33   109.26  3.000
 939  H321  C32  C33   108.50  3.000
 939  H322  C32  N31   111.71  3.000
 939  H321  C32  N31   109.35  3.000
 939  C33   C32  N31   110.71  3.000
 939  H332  C33  H331  107.19  3.000
 939  H332  C33  C32   109.47  3.000
 939  H331  C33  C32   108.04  3.000
 939  H332  C33  N28   110.46  3.000
 939  H331  C33  N28   110.62  3.000
 939  C32   C33  N28   110.95  3.000
 939  H343  C34  H342  107.88  3.000
 939  H343  C34  H341  107.76  3.000
 939  H342  C34  H341  107.76  3.000
 939  H343  C34  N31   110.04  3.000
 939  H342  C34  N31   109.98  3.000
 939  H341  C34  N31   113.25  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
 939  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 939  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 939  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 939  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 939  CONST_05  C8    C4   N3   C2    180.00   0.0  0
 939  CONST_06  C6    N1   C2   N3      0.00   0.0  0
 939  CONST_07  C6    C5   C4   N3      0.00   0.0  0
 939  CONST_10  C10   N9   C8   C4    180.00   0.0  0
 939  CONST_11  C11   C12  C8   C4    180.00   0.0  0
 939  CONST_12  N9    C8   C4   C5    180.00   0.0  0
 939  CONST_14  C8    C4   C5   C6    180.00   0.0  0
 939  CONST_15  C11   C10  N9   C8      0.00   0.0  0
 939  CONST_16  C10   C11  C12  C8      0.00   0.0  0
 939  CONST_17  C11   C12  C8   N9      0.00   0.0  0
 939  CONST_18  C12   C11  C10  N9      0.00   0.0  0
 939  CONST_19  C12   C8   N9   C10     0.00   0.0  0
 939  CONST_20  C19   C18  C17  C16     0.00   0.0  0
 939  CONST_21  C19   C20  C21  C16     0.00   0.0  0
 939  CONST_22  C20   C21  C16  C17     0.00   0.0  0
 939  CONST_23  C20   C19  C18  C17     0.00   0.0  0
 939  CONST_24  C21   C16  C17  C18     0.00   0.0  0
 939  CONST_25  C21   C20  C19  C18     0.00   0.0  0
 939  CONST_26  N28   C20  C21  C16   180.00   0.0  0
 939  CONST_27  N28   C20  C19  C18   180.00   0.0  0
 939  CONST_28  N7    C2   N3   C4    180.00   0.0  0
 939  CONST_29  C27   N9   C8   C4      0.00   0.0  0
 939  CONST_30  N7    C2   N1   C6    180.00   0.0  0
 939  CONST_31  C18   C17  C16  N7    180.00   0.0  0
 939  CONST_32  C20   C21  C16  N7    180.00   0.0  0
 939  CONST_33  C13   C11  C12  C8    180.00   0.0  0
 939  CONST_34  C13   C11  C10  N9    180.00   0.0  0
 939  CONST_35  C27   N9   C10  C11   180.00   0.0  0
 939  CONST_36  C27   N9   C8   C12   180.00   0.0  0
 939  CONST_37  O22   C17  C18  C19   180.00   0.0  0
 939  CONST_38  O22   C17  C16  C21   180.00   0.0  0
 939  CONST_39  H5    C5   C6   N1    180.00   0.0  0
 939  CONST_40  H6    C6   N1   C2    180.00   0.0  0
 939  CONST_41  H12   C12  C8   C4      0.00   0.0  0
 939  CONST_42  H10   C10  N9   C8    180.00   0.0  0
 939  CONST_43  H18   C18  C17  C16   180.00   0.0  0
 939  CONST_44  H21   C21  C16  C17   180.00   0.0  0
 939  CONST_45  H19   C19  C18  C17   180.00   0.0  0
 939  CONST_46  H141  N14  C13  C11     0.00   0.0  0
 939  CONST_47  H142  N14  C13  C11   180.00   0.0  0
 939  Var_01    C29   N28  C20  C19     2.76  30.0  2
 939  Var_02    C30   C29  N28  C20   163.65  30.0  1
 939  Var_03    C32   C33  N28  C20  -163.05  30.0  1
 939  Var_04    N31   C30  C29  N28    56.03  30.0  1
 939  Var_05    N31   C32  C33  N28   -56.49  30.0  1
 939  Var_06    C32   N31  C30  C29   -59.13  30.0  1
 939  Var_07    C33   C32  N31  C30    59.16  30.0  1
 939  Var_08    C16   N7   C2   N1     -0.98  30.0  2
 939  Var_09    C17   C16  N7   C2    159.95  30.0  2
 939  Var_10    N14   C13  C11  C10     2.87  30.0  2
 939  Var_11    H271  C27  N9   C8     52.48  30.0  2
 939  Var_12    H341  C34  N31  C30    61.03  30.0  3
 939  Var_13    F24   C23  O22  C17    55.86  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
 939  plan-1  C4    0.020
 939  plan-1  C8    0.020
 939  plan-1  N9    0.020
 939  plan-1  C10   0.020
 939  plan-1  C11   0.020
 939  plan-1  C12   0.020
 939  plan-1  C13   0.020
 939  plan-1  C27   0.020
 939  plan-1  H12   0.020
 939  plan-1  H10   0.020
 939  plan-2  N1    0.020
 939  plan-2  C2    0.020
 939  plan-2  N3    0.020
 939  plan-2  C4    0.020
 939  plan-2  C5    0.020
 939  plan-2  C6    0.020
 939  plan-2  N7    0.020
 939  plan-2  C8    0.020
 939  plan-2  H6    0.020
 939  plan-2  H5    0.020
 939  plan-3  N7    0.020
 939  plan-3  C16   0.020
 939  plan-3  C17   0.020
 939  plan-3  C18   0.020
 939  plan-3  C19   0.020
 939  plan-3  C20   0.020
 939  plan-3  C21   0.020
 939  plan-3  O22   0.020
 939  plan-3  N28   0.020
 939  plan-3  H21   0.020
 939  plan-3  H18   0.020
 939  plan-3  H19   0.020
 939  plan-4  C11   0.020
 939  plan-4  C13   0.020
 939  plan-4  N14   0.020
 939  plan-4  O15   0.020
 939  plan-4  H141  0.020
 939  plan-4  H142  0.020

