# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:55:20 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-[(1-methyl-1H-benzimidazol-2-yl)methyl]-6-(morpholin-4-yl)pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(CC2=NC(=CC(=O)N2)N3CCOCC3)nc4ccccc14
#
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
 VWN  VWN  2-[(1-methyl-1H-benzimidazol-2-yl)methyl]-6-(morpholin-4-yl)pyrimidin-4(3H)-one  ligand  43  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VWN
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
 VWN  C1    C  CR6   0   0.596  -2.1593  -0.0619   0.1019
 VWN  N2    N  NT    0  -0.509  -2.0209  -1.4039   0.0335
 VWN  C3    C  CH2   0  -0.323  -3.1540  -2.3056  -0.0193
 VWN  C4    C  CH2   0  -0.182  -2.8421  -3.4739  -0.9410
 VWN  O5    O  O2    0  -0.480  -1.6508  -4.1331  -0.5830
 VWN  C6    C  CH2   0  -0.189  -0.5597  -3.2412  -0.6101
 VWN  C7    C  CH2   0  -0.329  -0.7668  -2.0757   0.3375
 VWN  N8    N  N     0  -0.502  -0.9836   0.6318   0.1660
 VWN  C9    C  CR6   0   0.544  -1.0253   1.9188   0.1648
 VWN  N10   N  NR16  0  -0.698  -2.1687   2.6197   0.1191
 VWN  C11   C  CR6   0   0.530  -3.4296   2.0136   0.0933
 VWN  C12   C  CR16  0  -0.586  -3.3786   0.5962   0.0921
 VWN  O13   O  O     0  -0.511  -4.4336   2.7191   0.0788
 VWN  C14   C  CR5   0   0.469   1.4574   1.8342   0.2849
 VWN  C15   C  CH2   0  -0.681   0.2546   2.7055   0.2025
 VWN  N16   N  NR5   0  -0.518   1.8951   1.0774  -0.7582
 VWN  N17   N  N     0  -0.474   2.1995   1.7212   1.3521
 VWN  C18   C  CR56  0   0.132   3.1806   0.8215   1.0136
 VWN  C19   C  CR56  0   0.345   2.9988   0.3987  -0.3123
 VWN  C20   C  CR16  0  -0.315   3.8366  -0.5247  -0.9271
 VWN  C21   C  CR16  0  -0.277   4.8836  -1.0152  -0.1652
 VWN  C22   C  CR16  0  -0.274   5.0842  -0.5998   1.1602
 VWN  C23   C  CR16  0  -0.334   4.2424   0.3179   1.7638
 VWN  C24   C  CH3   0  -0.541   1.2808   0.9066  -2.0523
 VWN  H12   H  HCR6  0   0.269  -4.3218   0.0720   0.0819
 VWN  H31C  H  HCH2  0   0.245  -3.4007  -2.6640   0.9871
 VWN  H32C  H  HCH2  0   0.269  -4.0316  -1.8007  -0.4159
 VWN  H71C  H  HCH2  0   0.279   0.0596  -1.3765   0.2477
 VWN  H72C  H  HCH2  0   0.242  -0.7879  -2.4384   1.3724
 VWN  H41C  H  HCH2  0   0.248  -3.6524  -4.2015  -0.8890
 VWN  H42C  H  HCH2  0   0.210  -2.7826  -3.1048  -1.9743
 VWN  H61C  H  HCH2  0   0.246   0.3297  -3.7986  -0.3132
 VWN  H62C  H  HCH2  0   0.206  -0.3966  -2.8615  -1.6289
 VWN  H10   H  HNR6  0   0.425  -2.1377   3.6309   0.1214
 VWN  H151  H  HCH2  0   0.317   0.3004   3.3588  -0.6747
 VWN  H152  H  HCH2  0   0.329   0.2498   3.3617   1.0749
 VWN  H241  H  HCH3  0   0.268   2.0410   0.9360  -2.8303
 VWN  H242  H  HCH3  0   0.256   0.7469  -0.0417  -2.1060
 VWN  H243  H  HCH3  0   0.268   0.5724   1.7084  -2.2407
 VWN  H23   H  HCR6  0   0.254   4.3990   0.6344   2.7871
 VWN  H20   H  HCR6  0   0.269   3.6835  -0.8515  -1.9476
 VWN  H21   H  HCR6  0   0.255   5.5621  -1.7365  -0.6017
 VWN  H22   H  HCR6  0   0.252   5.9141  -1.0109   1.7201

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
 VWN  C1   N2    single    1.351  0.020  1.351
 VWN  C1   N8    single    1.367  0.020  1.367
 VWN  C1   C12   double    1.386  0.020  1.386
 VWN  N2   C3    single    1.449  0.020  1.449
 VWN  N2   C7    single    1.455  0.020  1.455
 VWN  C3   C4    single    1.520  0.020  1.520
 VWN  C4   O5    single    1.408  0.020  1.408
 VWN  O5   C6    single    1.409  0.020  1.409
 VWN  C6   C7    single    1.516  0.020  1.516
 VWN  N8   C9    double    1.288  0.020  1.288
 VWN  C9   N10   single    1.342  0.020  1.342
 VWN  C9   C15   single    1.503  0.020  1.503
 VWN  N10  C11   single    1.399  0.020  1.399
 VWN  C11  C12   single    1.418  0.020  1.418
 VWN  C11  O13   double    1.227  0.020  1.227
 VWN  C14  C15   single    1.488  0.020  1.488
 VWN  C14  N16   aromatic  1.361  0.020  1.361
 VWN  C14  N17   aromatic  1.305  0.020  1.305
 VWN  N16  C19   aromatic  1.370  0.020  1.370
 VWN  N16  C24   single    1.443  0.020  1.443
 VWN  N17  C18   aromatic  1.374  0.020  1.374
 VWN  C18  C19   aromatic  1.404  0.020  1.404
 VWN  C18  C23   aromatic  1.394  0.020  1.394
 VWN  C19  C20   aromatic  1.390  0.020  1.390
 VWN  C20  C21   aromatic  1.385  0.020  1.385
 VWN  C21  C22   aromatic  1.403  0.020  1.403
 VWN  C22  C23   aromatic  1.384  0.020  1.384
 VWN  C12  H12   single    0.930  0.020  1.080
 VWN  C3   H31C  single    0.970  0.020  1.090
 VWN  C3   H32C  single    0.970  0.020  1.090
 VWN  C7   H71C  single    0.970  0.020  1.090
 VWN  C7   H72C  single    0.970  0.020  1.090
 VWN  C4   H41C  single    0.970  0.020  1.090
 VWN  C4   H42C  single    0.970  0.020  1.090
 VWN  C6   H61C  single    0.970  0.020  1.090
 VWN  C6   H62C  single    0.970  0.020  1.090
 VWN  N10  H10   single    0.860  0.020  1.020
 VWN  C15  H151  single    0.970  0.020  1.090
 VWN  C15  H152  single    0.970  0.020  1.090
 VWN  C24  H241  single    0.970  0.020  1.090
 VWN  C24  H242  single    0.970  0.020  1.090
 VWN  C24  H243  single    0.970  0.020  1.090
 VWN  C23  H23   single    0.930  0.020  1.080
 VWN  C20  H20   single    0.930  0.020  1.080
 VWN  C21  H21   single    0.930  0.020  1.080
 VWN  C22  H22   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
 VWN  C12   C1   N8    121.09  3.000
 VWN  C12   C1   N2    124.17  3.000
 VWN  N8    C1   N2    114.74  3.000
 VWN  C7    N2   C3    113.22  3.000
 VWN  C7    N2   C1    122.44  3.000
 VWN  C3    N2   C1    122.68  3.000
 VWN  H32C  C3   H31C  107.75  3.000
 VWN  H32C  C3   C4    107.53  3.000
 VWN  H31C  C3   C4    110.58  3.000
 VWN  H32C  C3   N2    110.82  3.000
 VWN  H31C  C3   N2    110.24  3.000
 VWN  C4    C3   N2    109.87  3.000
 VWN  H42C  C4   H41C  108.02  3.000
 VWN  H42C  C4   O5    110.52  3.000
 VWN  H41C  C4   O5    107.71  3.000
 VWN  H42C  C4   C3    108.85  3.000
 VWN  H41C  C4   C3    109.35  3.000
 VWN  O5    C4   C3    112.29  3.000
 VWN  C6    O5   C4    110.72  3.000
 VWN  H62C  C6   H61C  107.92  3.000
 VWN  H62C  C6   C7    109.50  3.000
 VWN  H61C  C6   C7    109.51  3.000
 VWN  H62C  C6   O5    110.56  3.000
 VWN  H61C  C6   O5    107.61  3.000
 VWN  C7    C6   O5    111.63  3.000
 VWN  H72C  C7   H71C  107.79  3.000
 VWN  H72C  C7   C6    109.76  3.000
 VWN  H71C  C7   C6    109.83  3.000
 VWN  H72C  C7   N2    109.47  3.000
 VWN  H71C  C7   N2    109.96  3.000
 VWN  C6    C7   N2    110.00  3.000
 VWN  C9    N8   C1    118.65  3.000
 VWN  C15   C9   N10   116.94  3.000
 VWN  C15   C9   N8    119.71  3.000
 VWN  N10   C9   N8    123.35  3.000
 VWN  H10   N10  C11   117.43  3.000
 VWN  H10   N10  C9    119.73  3.000
 VWN  C11   N10  C9    122.83  3.000
 VWN  O13   C11  C12   127.15  3.000
 VWN  O13   C11  N10   119.24  3.000
 VWN  C12   C11  N10   113.61  3.000
 VWN  H12   C12  C11   117.00  3.000
 VWN  H12   C12  C1    122.58  3.000
 VWN  C11   C12  C1    120.41  3.000
 VWN  N17   C14  N16   113.32  3.000
 VWN  N17   C14  C15   123.78  3.000
 VWN  N16   C14  C15   122.90  3.000
 VWN  H152  C15  H151  106.37  3.000
 VWN  H152  C15  C14   108.14  3.000
 VWN  H151  C15  C14   111.11  3.000
 VWN  H152  C15  C9    109.32  3.000
 VWN  H151  C15  C9    109.14  3.000
 VWN  C14   C15  C9    112.54  3.000
 VWN  C24   N16  C19   125.19  3.000
 VWN  C24   N16  C14   128.06  3.000
 VWN  C19   N16  C14   106.56  3.000
 VWN  C18   N17  C14   105.16  3.000
 VWN  C23   C18  C19   119.88  3.000
 VWN  C23   C18  N17   130.39  3.000
 VWN  C19   C18  N17   109.73  3.000
 VWN  C20   C19  C18   122.67  3.000
 VWN  C20   C19  N16   132.11  3.000
 VWN  C18   C19  N16   105.23  3.000
 VWN  H20   C20  C21   121.25  3.000
 VWN  H20   C20  C19   122.16  3.000
 VWN  C21   C20  C19   116.59  3.000
 VWN  H21   C21  C22   119.25  3.000
 VWN  H21   C21  C20   119.23  3.000
 VWN  C22   C21  C20   121.53  3.000
 VWN  H22   C22  C23   119.51  3.000
 VWN  H22   C22  C21   119.07  3.000
 VWN  C23   C22  C21   121.42  3.000
 VWN  H23   C23  C22   121.22  3.000
 VWN  H23   C23  C18   120.87  3.000
 VWN  C22   C23  C18   117.91  3.000
 VWN  H243  C24  H242  108.32  3.000
 VWN  H243  C24  H241  108.16  3.000
 VWN  H242  C24  H241  109.31  3.000
 VWN  H243  C24  N16   110.23  3.000
 VWN  H242  C24  N16   110.85  3.000
 VWN  H241  C24  N16   109.92  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
 VWN  CONST_01  C18   C19  N16  C14     0.00   0.0  0
 VWN  CONST_02  C20   C19  N16  C14   180.00   0.0  0
 VWN  CONST_03  C19   C18  N17  C14     0.00   0.0  0
 VWN  CONST_04  C23   C18  N17  C14   180.00   0.0  0
 VWN  CONST_05  C18   N17  C14  N16     0.00   0.0  0
 VWN  CONST_06  N17   C18  C19  N16     0.00   0.0  0
 VWN  CONST_07  C23   C18  C19  N16   180.00   0.0  0
 VWN  CONST_08  C21   C20  C19  N16   180.00   0.0  0
 VWN  CONST_09  C19   N16  C14  N17     0.00   0.0  0
 VWN  CONST_10  C20   C19  C18  N17   180.00   0.0  0
 VWN  CONST_11  C22   C23  C18  N17   180.00   0.0  0
 VWN  CONST_12  C21   C20  C19  C18     0.00   0.0  0
 VWN  CONST_13  C21   C22  C23  C18     0.00   0.0  0
 VWN  CONST_14  C22   C23  C18  C19     0.00   0.0  0
 VWN  CONST_15  C22   C21  C20  C19     0.00   0.0  0
 VWN  CONST_16  C23   C18  C19  C20     0.00   0.0  0
 VWN  CONST_17  C23   C22  C21  C20     0.00   0.0  0
 VWN  CONST_18  N10   C9   N8   C1      0.00   0.0  0
 VWN  CONST_19  C9    N8   C1   N2    180.00   0.0  0
 VWN  CONST_20  N8    C1   N2   C3    180.00   0.0  0
 VWN  CONST_21  C12   C1   N2   C3      0.00   0.0  0
 VWN  CONST_22  N8    C1   N2   C7      0.00   0.0  0
 VWN  CONST_23  C12   C1   N2   C7    180.00   0.0  0
 VWN  CONST_24  C11   N10  C9   N8      0.00   0.0  0
 VWN  CONST_25  C12   C1   N8   C9      0.00   0.0  0
 VWN  CONST_26  C12   C11  N10  C9      0.00   0.0  0
 VWN  CONST_27  C19   N16  C14  C15   180.00   0.0  0
 VWN  CONST_28  C18   N17  C14  C15   180.00   0.0  0
 VWN  CONST_29  C24   N16  C14  N17   180.00   0.0  0
 VWN  CONST_30  C24   N16  C19  C18   180.00   0.0  0
 VWN  CONST_31  C24   N16  C19  C20     0.00   0.0  0
 VWN  CONST_32  C15   C9   N8   C1    180.00   0.0  0
 VWN  CONST_33  O13   C11  N10  C9    180.00   0.0  0
 VWN  CONST_34  C15   C9   N10  C11   180.00   0.0  0
 VWN  CONST_35  H20   C20  C19  N16     0.00   0.0  0
 VWN  CONST_36  H23   C23  C18  N17     0.00   0.0  0
 VWN  CONST_37  H22   C22  C23  C18   180.00   0.0  0
 VWN  CONST_38  H21   C21  C20  C19   180.00   0.0  0
 VWN  CONST_39  H10   N10  C9   N8    180.00   0.0  0
 VWN  Var_01    C4    C3   N2   C1    142.93  30.0  1
 VWN  Var_02    C6    C7   N2   C1   -142.10  30.0  1
 VWN  Var_03    O5    C4   C3   N2     54.25  30.0  1
 VWN  Var_04    O5    C6   C7   N2    -55.31  30.0  1
 VWN  Var_05    C7    C6   O5   C4     59.06  30.0  1
 VWN  Var_06    C14   C15  C9   N8     -1.96  30.0  3
 VWN  Var_07    N16   C14  C15  C9     71.61  30.0  1
 VWN  Var_08    H241  C24  N16  C14   137.71  30.0  2

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
 VWN  plan-1  C14  0.020
 VWN  plan-1  C15  0.020
 VWN  plan-1  N16  0.020
 VWN  plan-1  N17  0.020
 VWN  plan-1  C18  0.020
 VWN  plan-1  C19  0.020
 VWN  plan-1  C20  0.020
 VWN  plan-1  C21  0.020
 VWN  plan-1  C22  0.020
 VWN  plan-1  C23  0.020
 VWN  plan-1  C24  0.020
 VWN  plan-1  H23  0.020
 VWN  plan-1  H20  0.020
 VWN  plan-1  H21  0.020
 VWN  plan-1  H22  0.020
 VWN  plan-2  C1   0.020
 VWN  plan-2  N2   0.020
 VWN  plan-2  C3   0.020
 VWN  plan-2  C7   0.020
 VWN  plan-2  N8   0.020
 VWN  plan-2  C9   0.020
 VWN  plan-2  N10  0.020
 VWN  plan-2  C11  0.020
 VWN  plan-2  C12  0.020
 VWN  plan-2  O13  0.020
 VWN  plan-2  C15  0.020
 VWN  plan-2  H12  0.020
 VWN  plan-2  H10  0.020

