# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 10:36:53 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-[4-[2-(1~{H}-indol-3-yl)ethyl]pyrimidin-2-yl]morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCO1)c2nccc(CCc3c[nH]c4ccccc34)n2
#
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
 UMT  UMT  "4-[4-[2-(1~{H}-indol-3-yl)ethyl]pyrimidin-2-yl]morpholine"
  ligand  43  23  .  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_UMT
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
 UMT  N1   N  N     0  -0.475   -9.6407  17.0029  1.8807
 UMT  C2   C  CR16  0  -0.265  -16.8290  13.0787  4.4918
 UMT  N3   N  N     0  -0.487  -11.5547  17.9515  2.9133
 UMT  C4   C  CR56  0   0.028  -16.4388  15.3541  3.8501
 UMT  N4   N  NR15  0  -0.687  -17.8990  17.0202  4.1533
 UMT  C5   C  CR5   0   0.017  -15.8608  16.5621  3.3379
 UMT  C6   C  CH2   0  -0.532  -14.5039  16.7145  2.7374
 UMT  C1   C  CR16  0  -0.282  -18.0964  13.4289  4.9873
 UMT  C10  C  CR16  0  -0.009  -10.1366  15.8017  2.1236
 UMT  C11  C  CR6   0   0.631  -10.3691  18.0446  2.3004
 UMT  C12  C  CH2   0  -0.313   -8.6728  19.5128  1.3034
 UMT  C13  C  CH2   0  -0.184   -7.8478  20.6313  1.9139
 UMT  C14  C  CH2   0  -0.184   -9.7133  21.5616  2.9328
 UMT  C15  C  CH2   0  -0.313  -10.6264  20.4871  2.3697
 UMT  C16  C  CR15  0  -0.088  -16.7890  17.5421  3.5484
 UMT  C17  C  CR56  0   0.354  -17.7177  15.6835  4.3521
 UMT  C18  C  CR16  0  -0.304  -18.5588  14.7293  4.9237
 UMT  C3   C  CR16  0  -0.374  -15.9997  14.0270  3.9252
 UMT  C8   C  CR6   0   0.302  -12.0357  16.7399  3.1500
 UMT  C9   C  CR16  0  -0.418  -11.3415  15.5951  2.7692
 UMT  N2   N  NT    0  -0.512   -9.8603  19.2860  2.1032
 UMT  O1   O  O2    0  -0.478   -8.6059  21.8046  2.0962
 UMT  H19  H  HNR5  0   0.406  -18.7215  17.5437  4.4021
 UMT  H5   H  HCH2  0   0.243  -14.3343  15.9302  1.9935
 UMT  H4   H  HCH2  0   0.250  -14.4369  17.6659  2.2049
 UMT  H1   H  HCR6  0   0.246  -18.7243  12.6639  5.4257
 UMT  H9   H  HCR6  0   0.263   -9.5409  14.9598  1.7854
 UMT  H10  H  HCH2  0   0.231   -8.9576  19.7750  0.2765
 UMT  H11  H  HCH2  0   0.268   -8.0767  18.6057  1.2609
 UMT  H13  H  HCH2  0   0.240   -7.0163  20.8771  1.2517
 UMT  H12  H  HCH2  0   0.204   -7.4288  20.2917  2.8721
 UMT  H14  H  HCH2  0   0.204   -9.3780  21.2605  3.9355
 UMT  H15  H  HCH2  0   0.240  -10.2643  22.4984  3.0286
 UMT  H16  H  HCH2  0   0.231  -11.1010  20.8436  1.4464
 UMT  H17  H  HCH2  0   0.268  -11.4158  20.2728  3.0848
 UMT  H18  H  HCR5  0   0.278  -16.7397  18.5926  3.3059
 UMT  H20  H  HCR6  0   0.255  -19.5372  14.9960  5.3034
 UMT  H3   H  HCR6  0   0.239  -15.0248  13.7463  3.5439
 UMT  H8   H  HCR6  0   0.261  -11.7252  14.6030  2.9585
 UMT  C7   C  CH2   0  -0.499  -13.3854  16.6505  3.7919
 UMT  H2   H  HCR6  0   0.242  -16.5019  12.0489  4.5569
 UMT  H6   H  HCH2  0   0.251  -13.5120  17.4730  4.4978
 UMT  H7   H  HCH2  0   0.254  -13.4649  15.7165  4.3518

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
 UMT  O1   C13  single    1.409  0.020  1.409
 UMT  O1   C14  single    1.409  0.020  1.409
 UMT  C13  C12  single    1.518  0.020  1.518
 UMT  C12  N2   single    1.450  0.020  1.450
 UMT  N2   C15  single    1.449  0.020  1.449
 UMT  N2   C11  single    1.356  0.020  1.356
 UMT  C14  C15  single    1.518  0.020  1.518
 UMT  N1   C11  aromatic  1.339  0.020  1.339
 UMT  N1   C10  aromatic  1.322  0.020  1.322
 UMT  C11  N3   aromatic  1.338  0.020  1.338
 UMT  C10  C9   aromatic  1.383  0.020  1.383
 UMT  N3   C8   aromatic  1.325  0.020  1.325
 UMT  C2   C3   aromatic  1.381  0.020  1.381
 UMT  C2   C1   aromatic  1.405  0.020  1.405
 UMT  C3   C4   aromatic  1.400  0.020  1.400
 UMT  C6   C5   single    1.492  0.020  1.492
 UMT  C6   C7   single    1.539  0.020  1.539
 UMT  C9   C8   aromatic  1.392  0.020  1.392
 UMT  C8   C7   single    1.497  0.020  1.497
 UMT  C4   C5   aromatic  1.434  0.020  1.434
 UMT  C4   C17  aromatic  1.413  0.020  1.413
 UMT  C1   C18  aromatic  1.382  0.020  1.382
 UMT  C5   C16  aromatic  1.366  0.020  1.366
 UMT  C18  C17  aromatic  1.395  0.020  1.395
 UMT  C17  N4   aromatic  1.363  0.020  1.363
 UMT  C16  N4   aromatic  1.368  0.020  1.368
 UMT  C2   H2   single    0.930  0.020  1.080
 UMT  N4   H19  single    0.860  0.020  1.020
 UMT  C6   H5   single    0.970  0.020  1.090
 UMT  C6   H4   single    0.970  0.020  1.090
 UMT  C1   H1   single    0.930  0.020  1.080
 UMT  C10  H9   single    0.930  0.020  1.080
 UMT  C12  H10  single    0.970  0.020  1.090
 UMT  C12  H11  single    0.970  0.020  1.090
 UMT  C13  H13  single    0.970  0.020  1.090
 UMT  C13  H12  single    0.970  0.020  1.090
 UMT  C14  H14  single    0.970  0.020  1.090
 UMT  C14  H15  single    0.970  0.020  1.090
 UMT  C15  H16  single    0.970  0.020  1.090
 UMT  C15  H17  single    0.970  0.020  1.090
 UMT  C16  H18  single    0.930  0.020  1.080
 UMT  C18  H20  single    0.930  0.020  1.080
 UMT  C3   H3   single    0.930  0.020  1.080
 UMT  C7   H6   single    0.970  0.020  1.090
 UMT  C7   H7   single    0.970  0.020  1.090
 UMT  C9   H8   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
 UMT  C11  N1   C10  116.44  3.000
 UMT  H2   C2   C3   119.76  3.000
 UMT  H2   C2   C1   119.24  3.000
 UMT  C3   C2   C1   121.00  3.000
 UMT  C8   N3   C11  117.85  3.000
 UMT  C3   C4   C17  119.07  3.000
 UMT  C17  C4   C5   107.18  3.000
 UMT  C3   C4   C5   133.75  3.000
 UMT  H19  N4   C17  125.64  3.000
 UMT  H19  N4   C16  125.04  3.000
 UMT  C17  N4   C16  109.31  3.000
 UMT  C16  C5   C6   127.35  3.000
 UMT  C16  C5   C4   105.99  3.000
 UMT  C6   C5   C4   126.63  3.000
 UMT  H4   C6   H5   106.46  3.000
 UMT  H4   C6   C7   109.01  3.000
 UMT  H5   C6   C7   108.87  3.000
 UMT  H4   C6   C5   109.94  3.000
 UMT  H5   C6   C5   109.97  3.000
 UMT  C7   C6   C5   112.40  3.000
 UMT  H1   C1   C18  119.32  3.000
 UMT  H1   C1   C2   119.33  3.000
 UMT  C18  C1   C2   121.34  3.000
 UMT  H9   C10  C9   120.53  3.000
 UMT  H9   C10  N1   116.21  3.000
 UMT  C9   C10  N1   123.26  3.000
 UMT  N2   C11  N3   117.57  3.000
 UMT  N3   C11  N1   124.87  3.000
 UMT  N2   C11  N1   117.56  3.000
 UMT  H11  C12  H10  107.78  3.000
 UMT  H11  C12  N2   109.91  3.000
 UMT  H10  C12  N2   109.94  3.000
 UMT  H11  C12  C13  109.44  3.000
 UMT  H10  C12  C13  109.95  3.000
 UMT  N2   C12  C13  109.79  3.000
 UMT  H12  C13  H13  107.95  3.000
 UMT  H12  C13  O1   110.46  3.000
 UMT  H13  C13  O1   107.52  3.000
 UMT  H12  C13  C12  109.26  3.000
 UMT  H13  C13  C12  109.64  3.000
 UMT  O1   C13  C12  111.91  3.000
 UMT  H15  C14  H14  108.01  3.000
 UMT  H15  C14  O1   107.52  3.000
 UMT  H14  C14  O1   110.43  3.000
 UMT  H15  C14  C15  109.67  3.000
 UMT  H14  C14  C15  109.14  3.000
 UMT  O1   C14  C15  111.99  3.000
 UMT  H17  C15  H16  107.67  3.000
 UMT  H17  C15  N2   109.98  3.000
 UMT  H16  C15  N2   110.06  3.000
 UMT  H17  C15  C14  109.41  3.000
 UMT  H16  C15  C14  110.00  3.000
 UMT  N2   C15  C14  109.68  3.000
 UMT  H18  C16  C5   129.25  3.000
 UMT  H18  C16  N4   120.53  3.000
 UMT  C5   C16  N4   110.23  3.000
 UMT  C18  C17  N4   130.57  3.000
 UMT  N4   C17  C4   107.29  3.000
 UMT  C18  C17  C4   122.14  3.000
 UMT  H20  C18  C17  121.34  3.000
 UMT  H20  C18  C1   121.20  3.000
 UMT  C17  C18  C1   117.46  3.000
 UMT  H3   C3   C4   120.58  3.000
 UMT  H3   C3   C2   120.43  3.000
 UMT  C4   C3   C2   118.98  3.000
 UMT  C9   C8   C7   121.18  3.000
 UMT  C7   C8   N3   117.28  3.000
 UMT  C9   C8   N3   121.48  3.000
 UMT  H8   C9   C8   122.02  3.000
 UMT  H8   C9   C10  121.90  3.000
 UMT  C8   C9   C10  116.07  3.000
 UMT  C15  N2   C12  113.88  3.000
 UMT  C15  N2   C11  122.25  3.000
 UMT  C12  N2   C11  122.06  3.000
 UMT  C14  O1   C13  110.86  3.000
 UMT  H7   C7   H6   107.74  3.000
 UMT  H7   C7   C8   109.66  3.000
 UMT  H6   C7   C8   109.69  3.000
 UMT  H7   C7   C6   109.52  3.000
 UMT  H6   C7   C6   109.13  3.000
 UMT  C8   C7   C6   111.04  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
 UMT  CONST_01  C8   N3   C11  N1      0.00   0.0  0
 UMT  CONST_02  C8   C9   C10  N1      0.00   0.0  0
 UMT  CONST_03  C5   C4   C3   C2    180.00   0.0  0
 UMT  CONST_04  C17  C4   C3   C2      0.00   0.0  0
 UMT  CONST_05  C17  C18  C1   C2      0.00   0.0  0
 UMT  CONST_06  C10  N1   C11  N3      0.00   0.0  0
 UMT  CONST_07  C10  C9   C8   N3      0.00   0.0  0
 UMT  CONST_08  C1   C2   C3   C4      0.00   0.0  0
 UMT  CONST_09  N4   C16  C5   C4      0.00   0.0  0
 UMT  CONST_10  C1   C18  C17  C4      0.00   0.0  0
 UMT  CONST_11  C16  N4   C17  C4      0.00   0.0  0
 UMT  CONST_12  C3   C4   C17  N4    180.00   0.0  0
 UMT  CONST_13  C5   C4   C17  N4      0.00   0.0  0
 UMT  CONST_14  C1   C18  C17  N4    180.00   0.0  0
 UMT  CONST_15  C18  C17  C4   C5    180.00   0.0  0
 UMT  CONST_16  C17  N4   C16  C5      0.00   0.0  0
 UMT  CONST_17  C9   C10  N1   C11     0.00   0.0  0
 UMT  CONST_18  C9   C8   N3   C11     0.00   0.0  0
 UMT  CONST_19  C3   C4   C5   C16   180.00   0.0  0
 UMT  CONST_20  C17  C4   C5   C16     0.00   0.0  0
 UMT  CONST_21  C18  C17  N4   C16   180.00   0.0  0
 UMT  CONST_22  C3   C2   C1   C18     0.00   0.0  0
 UMT  CONST_23  C3   C4   C17  C18     0.00   0.0  0
 UMT  CONST_24  N2   C11  N1   C10   180.00   0.0  0
 UMT  CONST_25  N2   C11  N3   C8    180.00   0.0  0
 UMT  CONST_26  C6   C5   C16  N4    180.00   0.0  0
 UMT  CONST_27  C3   C4   C5   C6      0.00   0.0  0
 UMT  CONST_28  C17  C4   C5   C6    180.00   0.0  0
 UMT  CONST_29  C7   C8   C9   C10   180.00   0.0  0
 UMT  CONST_30  C7   C8   N3   C11   180.00   0.0  0
 UMT  CONST_31  H8   C9   C10  N1    180.00   0.0  0
 UMT  CONST_32  H20  C18  C1   C2    180.00   0.0  0
 UMT  CONST_33  H8   C9   C8   N3    180.00   0.0  0
 UMT  CONST_34  H2   C2   C3   C4    180.00   0.0  0
 UMT  CONST_35  H18  C16  C5   C4    180.00   0.0  0
 UMT  CONST_36  H20  C18  C17  C4    180.00   0.0  0
 UMT  CONST_37  H19  N4   C17  C4    180.00   0.0  0
 UMT  CONST_38  H20  C18  C17  N4      0.00   0.0  0
 UMT  CONST_39  H3   C3   C4   C5      0.00   0.0  0
 UMT  CONST_40  H19  N4   C16  C5    180.00   0.0  0
 UMT  CONST_41  H3   C3   C2   C1    180.00   0.0  0
 UMT  CONST_42  H9   C10  N1   C11   180.00   0.0  0
 UMT  CONST_43  H3   C3   C4   C17   180.00   0.0  0
 UMT  CONST_44  H1   C1   C18  C17   180.00   0.0  0
 UMT  CONST_45  H18  C16  N4   C17   180.00   0.0  0
 UMT  CONST_46  H2   C2   C1   C18   180.00   0.0  0
 UMT  CONST_47  H19  N4   C17  C18     0.00   0.0  0
 UMT  CONST_48  H1   C1   C2   C3    180.00   0.0  0
 UMT  CONST_49  H9   C10  C9   C8    180.00   0.0  0
 UMT  Var_01    C12  N2   C11  N1      8.73  30.0  1
 UMT  Var_02    C15  N2   C11  N1    172.48  30.0  1
 UMT  Var_03    C12  N2   C11  N3   -171.99  30.0  1
 UMT  Var_04    C15  N2   C11  N3     -8.25  30.0  1
 UMT  Var_05    C13  C12  N2   C11  -143.40  30.0  1
 UMT  Var_06    C14  C15  N2   C11   143.47  30.0  1
 UMT  Var_07    C14  O1   C13  C12    58.86  30.0  1
 UMT  Var_08    C14  C15  N2   C12   -51.57  30.0  1
 UMT  Var_09    C15  C14  O1   C13   -58.93  30.0  1
 UMT  Var_10    C15  N2   C12  C13    51.60  30.0  1
 UMT  Var_11    O1   C13  C12  N2    -54.38  30.0  1
 UMT  Var_12    O1   C14  C15  N2     54.43  30.0  1
 UMT  Var_13    H10  C12  N2   C11    95.51  30.0  1
 UMT  Var_14    H11  C12  N2   C11   -22.97  30.0  1
 UMT  Var_15    H16  C15  N2   C11   -95.38  30.0  1
 UMT  Var_16    H17  C15  N2   C11    23.09  30.0  1
 UMT  Var_17    H16  C15  N2   C12    69.59  30.0  1
 UMT  Var_18    H17  C15  N2   C12  -171.95  30.0  1
 UMT  Var_19    H14  C14  O1   C13    62.92  30.0  1
 UMT  Var_20    H15  C14  O1   C13  -179.47  30.0  1
 UMT  Var_21    H13  C13  O1   C14   179.31  30.0  1
 UMT  Var_22    H12  C13  O1   C14   -63.12  30.0  1
 UMT  Var_23    H10  C12  N2   C15   -69.49  30.0  1
 UMT  Var_24    H11  C12  N2   C15   172.04  30.0  1
 UMT  Var_25    H13  C13  C12  N2   -173.60  30.0  1
 UMT  Var_26    H12  C13  C12  N2     68.28  30.0  1
 UMT  Var_27    H14  C14  C15  N2    -68.16  30.0  1
 UMT  Var_28    H15  C14  C15  N2    173.71  30.0  1
 UMT  Var_29    H10  C12  C13  O1     66.70  30.0  1
 UMT  Var_30    H11  C12  C13  O1   -175.10  30.0  1
 UMT  Var_31    H16  C15  C14  O1    -66.76  30.0  1
 UMT  Var_32    H17  C15  C14  O1    175.15  30.0  1
 UMT  Var_33    C6   C7   C8   N3     85.78  30.0  2
 UMT  Var_34    C7   C6   C5   C4    -73.22  30.0  2
 UMT  Var_35    C8   C7   C6   C5    177.25  30.0  3
 UMT  Var_36    C9   C8   C7   C6    -91.68  30.0  2
 UMT  Var_37    C7   C6   C5   C16   104.73  30.0  2
 UMT  Var_38    H6   C7   C8   N3    -34.93  30.0  2
 UMT  Var_39    H7   C7   C8   N3   -153.06  30.0  2
 UMT  Var_40    H5   C6   C5   C4     48.25  30.0  2
 UMT  Var_41    H4   C6   C5   C4    165.16  30.0  2
 UMT  Var_42    H5   C6   C5   C16  -133.80  30.0  2
 UMT  Var_43    H4   C6   C5   C16   -16.89  30.0  2
 UMT  Var_44    H6   C7   C8   C9    147.62  30.0  2
 UMT  Var_45    H7   C7   C8   C9     29.49  30.0  2
 UMT  Var_46    H6   C7   C6   C5    -61.72  30.0  3
 UMT  Var_47    H7   C7   C6   C5     55.99  30.0  3
 UMT  Var_48    H5   C6   C7   C8     55.16  30.0  1
 UMT  Var_49    H4   C6   C7   C8    -60.60  30.0  1

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
 UMT  plan-1  N1   0.020
 UMT  plan-1  N3   0.020
 UMT  plan-1  C10  0.020
 UMT  plan-1  C11  0.020
 UMT  plan-1  C8   0.020
 UMT  plan-1  C9   0.020
 UMT  plan-1  N2   0.020
 UMT  plan-1  H9   0.020
 UMT  plan-1  H8   0.020
 UMT  plan-1  C7   0.020
 UMT  plan-2  C2   0.020
 UMT  plan-2  C4   0.020
 UMT  plan-2  N4   0.020
 UMT  plan-2  C5   0.020
 UMT  plan-2  C6   0.020
 UMT  plan-2  C1   0.020
 UMT  plan-2  C16  0.020
 UMT  plan-2  C17  0.020
 UMT  plan-2  C18  0.020
 UMT  plan-2  C3   0.020
 UMT  plan-2  H19  0.020
 UMT  plan-2  H1   0.020
 UMT  plan-2  H18  0.020
 UMT  plan-2  H20  0.020
 UMT  plan-2  H3   0.020
 UMT  plan-2  H2   0.020

