# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:18:51 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 3-[[5-bromanyl-1-(3-methylsulfonylpropyl)benzimidazol-2-yl]methyl]-1-cyclopropyl-imidazo[4,5-c]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)CCCn1c(CN2C(=O)N(C3CC3)c4ccncc24)nc5cc(Br)ccc15
#
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
 5NM  5NM  3-[[5-bromanyl-1-(3-methylsulfonylpropyl)benzimidazol-2-yl]methyl]-1-cyclopropyl-imidazo[4,5-c]pyridin-2-one  ligand  53  31  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5NM
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
 5NM  C10  C   CH2   0  -0.450  -1.5008   0.2030  -1.7156
 5NM  C13  C   CH1   0  -0.109  -5.1238   0.8363   1.5509
 5NM  C15  C   CH2   0  -0.499  -6.4057   1.5995   1.4172
 5NM  C22  C   CR16  0  -0.373  -3.7576   3.6158   0.9357
 5NM  C24  C   CR16  0  -0.104  -1.7130   3.2693  -0.9013
 5NM  C26  C   CH2   0  -0.450   0.2092  -2.8149  -0.0000
 5NM  C28  C   CR16  0  -0.247   4.0581   0.2250   0.4479
 5NM  C01  C   CR5   0   0.713  -3.3876   0.1679  -0.0818
 5NM  N02  N   NR5   0  -0.601  -2.4008   0.8333  -0.7783
 5NM  N03  N   NR5   0  -0.605  -4.0595   1.1287   0.6483
 5NM  C04  C   CR5   0   0.454  -0.0671   0.3169  -1.3029
 5NM  N05  N   N     0  -0.464   0.7823   1.1146  -1.8890
 5NM  C06  C   CR56  0   0.236  -2.4491   2.1813  -0.4801
 5NM  C07  C   CR56  0   0.421  -3.4886   2.3581   0.4356
 5NM  N08  N   NR5   0  -0.540   0.4775  -0.3805  -0.2653
 5NM  C09  C   CR56  0   0.146   1.9637   0.9401  -1.2158
 5NM  C11  C   CR56  0   0.355   1.7928  -0.0010  -0.1913
 5NM  S12  S   S     0   1.195  -0.1391  -5.5062   0.2131
 5NM  C14  C   CH2   0  -0.487  -6.3478   0.1597   1.0255
 5NM  C16  C   CR16  0  -0.295   3.2027   1.5454  -1.4212
 5NM  C18  C   CR16  0  -0.299   2.8298  -0.3756   0.6537
 5NM  O19  O   OS    0  -0.687  -0.5708  -5.6159  -1.1810
 5NM  O20  O   OS    0  -0.686   1.2690  -5.7677   0.5137
 5NM  N21  N   N     0  -0.416  -1.9766   4.4882  -0.4318
 5NM  C23  C   CR6   0  -0.130   4.2276   1.1683  -0.5764
 5NM  C25  C   CH2   0  -0.341  -0.1366  -1.4255   0.5246
 5NM  C27  C   CH2   0  -0.618  -0.5488  -3.8637   0.7994
 5NM  C29  C   CH3   0  -0.787  -1.1473  -6.5787   1.2087
 5NM  BR3  BR  BR    0  -0.054   5.9358   1.9499  -0.8031
 5NM  C31  C   CR16  0  -0.086  -2.9548   4.6449   0.4528
 5NM  H1   H   HCH2  0   0.310  -1.8038  -0.8392  -1.8231
 5NM  H2   H   HCH2  0   0.315  -1.6018   0.6692  -2.6961
 5NM  H3   H   HCH1  0   0.290  -4.7972   0.5800   2.5525
 5NM  H4   H   HCH2  0   0.270  -6.9075   1.8755   2.3347
 5NM  H5   H   HCH2  0   0.268  -6.4833   2.3319   0.6239
 5NM  H6   H   HCR6  0   0.289  -4.5394   3.8060   1.6572
 5NM  H7   H   HCR6  0   0.277  -0.9037   3.1703  -1.6146
 5NM  H8   H   HCH2  0   0.269  -0.0627  -2.8827  -1.0549
 5NM  H9   H   HCH2  0   0.270   1.2849  -2.9843   0.0762
 5NM  H10  H   HCR6  0   0.281   4.8891  -0.0413   1.0866
 5NM  H11  H   HCH2  0   0.267  -6.3807  -0.0728  -0.0303
 5NM  H12  H   HCH2  0   0.268  -6.8148  -0.5773   1.6644
 5NM  H13  H   HCR6  0   0.282   3.3388   2.2738  -2.2094
 5NM  H14  H   HCR6  0   0.283   2.7023  -1.1036   1.4436
 5NM  H15  H   HCH2  0   0.285  -1.2143  -1.2851   0.5205
 5NM  H16  H   HCH2  0   0.288   0.1887  -1.3089   1.5594
 5NM  H17  H   HCH2  0   0.307  -0.2984  -3.8278   1.8610
 5NM  H18  H   HCH2  0   0.303  -1.6293  -3.7459   0.6938
 5NM  H19  H   HCH3  0   0.296  -0.9074  -6.4329   2.2594
 5NM  H20  H   HCH3  0   0.296  -2.1971  -6.3643   1.0231
 5NM  H21  H   HCH3  0   0.313  -0.9176  -7.6015   0.9132
 5NM  H22  H   HCR6  0   0.266  -3.1222   5.6547   0.8091
 5NM  O17  O   O     0  -0.487  -3.6132  -1.0247  -0.0989

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
 5NM  C14  C15  single    1.493  0.020  1.493
 5NM  C14  C13  single    1.494  0.020  1.494
 5NM  O17  C01  double    1.214  0.020  1.214
 5NM  C15  C13  single    1.498  0.020  1.498
 5NM  C29  S12  single    1.777  0.020  1.777
 5NM  C01  N03  single    1.381  0.020  1.381
 5NM  C01  N02  single    1.379  0.020  1.379
 5NM  C13  N03  single    1.426  0.020  1.426
 5NM  C27  S12  single    1.792  0.020  1.792
 5NM  C27  C26  single    1.521  0.020  1.521
 5NM  C10  N02  single    1.444  0.020  1.444
 5NM  C10  C04  single    1.496  0.020  1.496
 5NM  C25  C26  single    1.525  0.020  1.525
 5NM  C25  N08  single    1.447  0.020  1.447
 5NM  N03  C07  single    1.372  0.020  1.372
 5NM  N02  C06  single    1.381  0.020  1.381
 5NM  S12  O20  double    1.463  0.020  1.463
 5NM  S12  O19  double    1.464  0.020  1.464
 5NM  C04  N08  aromatic  1.364  0.020  1.364
 5NM  C04  N05  aromatic  1.304  0.020  1.304
 5NM  N08  C11  aromatic  1.371  0.020  1.371
 5NM  C07  C06  aromatic  1.397  0.020  1.397
 5NM  C07  C22  aromatic  1.380  0.020  1.380
 5NM  C06  C24  aromatic  1.379  0.020  1.379
 5NM  N05  C09  aromatic  1.371  0.020  1.371
 5NM  C11  C18  aromatic  1.389  0.020  1.389
 5NM  C11  C09  aromatic  1.402  0.020  1.402
 5NM  C22  C31  aromatic  1.392  0.020  1.392
 5NM  C18  C28  aromatic  1.383  0.020  1.383
 5NM  C09  C16  aromatic  1.394  0.020  1.394
 5NM  C24  N21  aromatic  1.333  0.020  1.333
 5NM  C31  N21  aromatic  1.328  0.020  1.328
 5NM  C28  C23  aromatic  1.403  0.020  1.403
 5NM  C16  C23  aromatic  1.381  0.020  1.381
 5NM  C23  BR3  single    1.892  0.020  1.892
 5NM  C10  H1   single    0.970  0.020  1.090
 5NM  C10  H2   single    0.970  0.020  1.090
 5NM  C13  H3   single    0.970  0.020  1.090
 5NM  C15  H4   single    0.970  0.020  1.090
 5NM  C15  H5   single    0.970  0.020  1.090
 5NM  C22  H6   single    0.930  0.020  1.080
 5NM  C24  H7   single    0.930  0.020  1.080
 5NM  C26  H8   single    0.970  0.020  1.090
 5NM  C26  H9   single    0.970  0.020  1.090
 5NM  C28  H10  single    0.930  0.020  1.080
 5NM  C14  H11  single    0.970  0.020  1.090
 5NM  C14  H12  single    0.970  0.020  1.090
 5NM  C16  H13  single    0.930  0.020  1.080
 5NM  C18  H14  single    0.930  0.020  1.080
 5NM  C25  H15  single    0.970  0.020  1.090
 5NM  C25  H16  single    0.970  0.020  1.090
 5NM  C27  H17  single    0.970  0.020  1.090
 5NM  C27  H18  single    0.970  0.020  1.090
 5NM  C29  H19  single    0.970  0.020  1.090
 5NM  C29  H20  single    0.970  0.020  1.090
 5NM  C29  H21  single    0.970  0.020  1.090
 5NM  C31  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
 5NM  H2   C10  H1   107.11  3.000
 5NM  H2   C10  C04  107.71  3.000
 5NM  H1   C10  C04  111.47  3.000
 5NM  H2   C10  N02  109.84  3.000
 5NM  H1   C10  N02  107.93  3.000
 5NM  C04  C10  N02  112.64  3.000
 5NM  H3   C13  C14  117.69  3.000
 5NM  H3   C13  N03  114.11  3.000
 5NM  C14  C13  N03  118.80  3.000
 5NM  H3   C13  C15  117.43  3.000
 5NM  N03  C13  C15  118.54  3.000
 5NM  C14  C13  C15   59.88  3.000
 5NM  H5   C15  H4   114.56  3.000
 5NM  H5   C15  C14  117.58  3.000
 5NM  H4   C15  C14  119.11  3.000
 5NM  H5   C15  C13  118.14  3.000
 5NM  H4   C15  C13  116.83  3.000
 5NM  C14  C15  C13   59.93  3.000
 5NM  H6   C22  C31  121.26  3.000
 5NM  H6   C22  C07  122.91  3.000
 5NM  C31  C22  C07  115.83  3.000
 5NM  H7   C24  N21  117.61  3.000
 5NM  H7   C24  C06  121.84  3.000
 5NM  N21  C24  C06  120.55  3.000
 5NM  H9   C26  H8   107.65  3.000
 5NM  H9   C26  C27  110.33  3.000
 5NM  H8   C26  C27  109.93  3.000
 5NM  H9   C26  C25  109.93  3.000
 5NM  H8   C26  C25  109.43  3.000
 5NM  C27  C26  C25  109.54  3.000
 5NM  H10  C28  C23  120.27  3.000
 5NM  H10  C28  C18  119.19  3.000
 5NM  C23  C28  C18  120.54  3.000
 5NM  O17  C01  N03  126.91  3.000
 5NM  N03  C01  N02  106.23  3.000
 5NM  O17  C01  N02  126.86  3.000
 5NM  C06  N02  C01  109.68  3.000
 5NM  C06  N02  C10  125.99  3.000
 5NM  C01  N02  C10  124.28  3.000
 5NM  C07  N03  C01  109.81  3.000
 5NM  C07  N03  C13  126.33  3.000
 5NM  C01  N03  C13  123.72  3.000
 5NM  N08  C04  N05  113.24  3.000
 5NM  N05  C04  C10  123.13  3.000
 5NM  N08  C04  C10  123.62  3.000
 5NM  C09  N05  C04  105.23  3.000
 5NM  C07  C06  N02  106.92  3.000
 5NM  C07  C06  C24  119.84  3.000
 5NM  N02  C06  C24  133.24  3.000
 5NM  C06  C07  N03  107.33  3.000
 5NM  C06  C07  C22  119.88  3.000
 5NM  N03  C07  C22  132.79  3.000
 5NM  C25  N08  C11  125.29  3.000
 5NM  C11  N08  C04  106.42  3.000
 5NM  C25  N08  C04  127.98  3.000
 5NM  C16  C09  C11  120.50  3.000
 5NM  C16  C09  N05  129.67  3.000
 5NM  C11  C09  N05  109.83  3.000
 5NM  C18  C11  C09  122.32  3.000
 5NM  C09  C11  N08  105.27  3.000
 5NM  C18  C11  N08  132.41  3.000
 5NM  C29  S12  C27  103.90  3.000
 5NM  C27  S12  O20  108.46  3.000
 5NM  C29  S12  O20  108.84  3.000
 5NM  O20  S12  O19  117.78  3.000
 5NM  C27  S12  O19  108.24  3.000
 5NM  C29  S12  O19  108.73  3.000
 5NM  H12  C14  H11  114.65  3.000
 5NM  H12  C14  C15  119.04  3.000
 5NM  H11  C14  C15  117.53  3.000
 5NM  H12  C14  C13  117.04  3.000
 5NM  H11  C14  C13  117.75  3.000
 5NM  C15  C14  C13   60.19  3.000
 5NM  H13  C16  C23  122.43  3.000
 5NM  H13  C16  C09  120.76  3.000
 5NM  C23  C16  C09  116.81  3.000
 5NM  H14  C18  C11  122.52  3.000
 5NM  H14  C18  C28  120.38  3.000
 5NM  C11  C18  C28  117.09  3.000
 5NM  C31  N21  C24  119.23  3.000
 5NM  BR3  C23  C16  118.95  3.000
 5NM  BR3  C23  C28  118.32  3.000
 5NM  C16  C23  C28  122.74  3.000
 5NM  H16  C25  H15  106.59  3.000
 5NM  H16  C25  N08  108.31  3.000
 5NM  H15  C25  N08  108.99  3.000
 5NM  H16  C25  C26  110.86  3.000
 5NM  H15  C25  C26  109.95  3.000
 5NM  N08  C25  C26  111.96  3.000
 5NM  H18  C27  H17  108.51  3.000
 5NM  H18  C27  S12  107.07  3.000
 5NM  H17  C27  S12  107.22  3.000
 5NM  H18  C27  C26  111.59  3.000
 5NM  H17  C27  C26  111.97  3.000
 5NM  S12  C27  C26  110.26  3.000
 5NM  H21  C29  H20  110.03  3.000
 5NM  H21  C29  H19  109.97  3.000
 5NM  H20  C29  H19  110.58  3.000
 5NM  H21  C29  S12  107.17  3.000
 5NM  H20  C29  S12  109.45  3.000
 5NM  H19  C29  S12  109.58  3.000
 5NM  H22  C31  N21  116.27  3.000
 5NM  H22  C31  C22  119.06  3.000
 5NM  N21  C31  C22  124.67  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
 5NM  CONST_01  C24  C06  C07  C22     0.00   0.0  0
 5NM  CONST_02  C24  N21  C31  C22     0.00   0.0  0
 5NM  CONST_03  N08  C11  C18  C28   180.00   0.0  0
 5NM  CONST_04  C09  C11  C18  C28     0.00   0.0  0
 5NM  CONST_05  C09  C16  C23  C28     0.00   0.0  0
 5NM  CONST_06  C18  C11  N08  C04   180.00   0.0  0
 5NM  CONST_07  C09  C11  N08  C04     0.00   0.0  0
 5NM  CONST_08  C11  C09  N05  C04     0.00   0.0  0
 5NM  CONST_09  C16  C09  N05  C04   180.00   0.0  0
 5NM  CONST_10  C11  N08  C04  N05     0.00   0.0  0
 5NM  CONST_11  N08  C11  C09  N05     0.00   0.0  0
 5NM  CONST_12  C18  C11  C09  N05   180.00   0.0  0
 5NM  CONST_13  C23  C16  C09  N05   180.00   0.0  0
 5NM  CONST_14  C31  C22  C07  C06     0.00   0.0  0
 5NM  CONST_15  C31  N21  C24  C06     0.00   0.0  0
 5NM  CONST_16  N21  C24  C06  C07     0.00   0.0  0
 5NM  CONST_17  N21  C31  C22  C07     0.00   0.0  0
 5NM  CONST_18  C09  N05  C04  N08     0.00   0.0  0
 5NM  CONST_19  C16  C09  C11  N08   180.00   0.0  0
 5NM  CONST_20  C23  C28  C18  C11     0.00   0.0  0
 5NM  CONST_21  C23  C16  C09  C11     0.00   0.0  0
 5NM  CONST_22  C18  C11  C09  C16     0.00   0.0  0
 5NM  CONST_23  C18  C28  C23  C16     0.00   0.0  0
 5NM  CONST_24  N02  C01  N03  C13   180.00   0.0  0
 5NM  CONST_25  C06  C07  N03  C13   180.00   0.0  0
 5NM  CONST_26  C06  C07  N03  C01     0.00   0.0  0
 5NM  CONST_27  C07  C06  N02  C01     0.00   0.0  0
 5NM  CONST_28  C07  N03  C01  N02     0.00   0.0  0
 5NM  CONST_29  N03  C07  C06  N02     0.00   0.0  0
 5NM  CONST_30  C06  N02  C01  N03     0.00   0.0  0
 5NM  CONST_31  C11  N08  C04  C10   180.00   0.0  0
 5NM  CONST_32  C09  N05  C04  C10   180.00   0.0  0
 5NM  CONST_33  C25  N08  C04  N05   180.00   0.0  0
 5NM  CONST_34  C25  N08  C11  C09   180.00   0.0  0
 5NM  CONST_35  BR3  C23  C16  C09   180.00   0.0  0
 5NM  CONST_36  C25  N08  C11  C18     0.00   0.0  0
 5NM  CONST_37  BR3  C23  C28  C18   180.00   0.0  0
 5NM  CONST_38  N03  C01  N02  C10   180.00   0.0  0
 5NM  CONST_39  C07  C06  N02  C10   180.00   0.0  0
 5NM  CONST_40  O17  C01  N03  C13     0.00   0.0  0
 5NM  CONST_41  O17  C01  N02  C06   180.00   0.0  0
 5NM  CONST_42  O17  C01  N03  C07   180.00   0.0  0
 5NM  CONST_43  H22  C31  N21  C24   180.00   0.0  0
 5NM  CONST_44  H13  C16  C23  C28   180.00   0.0  0
 5NM  CONST_45  H7   C24  C06  N02     0.00   0.0  0
 5NM  CONST_46  H6   C22  C07  N03     0.00   0.0  0
 5NM  CONST_47  H14  C18  C11  N08     0.00   0.0  0
 5NM  CONST_48  H10  C28  C18  C11   180.00   0.0  0
 5NM  CONST_49  O17  C01  N02  C10     0.00   0.0  0
 5NM  Var_01    N03  C13  C14  C15  -108.14  30.0  1
 5NM  Var_02    C01  N03  C13  C15  -128.85  30.0  3
 5NM  Var_03    C04  C10  N02  C01  -118.71  30.0  2
 5NM  Var_04    N08  C04  C10  N02    72.21  30.0  2
 5NM  Var_05    H4   C15  C14  C13  -105.93  30.0  1
 5NM  Var_06    C04  N08  C25  C26    95.07  30.0  2
 5NM  Var_07    C27  C26  C25  N08  -175.59  30.0  3
 5NM  Var_08    C29  S12  C27  C26  -178.04  30.0  3
 5NM  Var_09    C25  C26  C27  S12  -179.23  30.0  3
 5NM  Var_10    H19  C29  S12  O19  -174.25  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5NM  chir_01  C13  C14  C15  N03  both

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
 5NM  plan-1  C10  0.020
 5NM  plan-1  C13  0.020
 5NM  plan-1  C22  0.020
 5NM  plan-1  C24  0.020
 5NM  plan-1  C01  0.020
 5NM  plan-1  N02  0.020
 5NM  plan-1  N03  0.020
 5NM  plan-1  C06  0.020
 5NM  plan-1  C07  0.020
 5NM  plan-1  N21  0.020
 5NM  plan-1  C31  0.020
 5NM  plan-1  H6   0.020
 5NM  plan-1  H7   0.020
 5NM  plan-1  H22  0.020
 5NM  plan-1  O17  0.020
 5NM  plan-2  C10  0.020
 5NM  plan-2  C28  0.020
 5NM  plan-2  C04  0.020
 5NM  plan-2  N05  0.020
 5NM  plan-2  N08  0.020
 5NM  plan-2  C09  0.020
 5NM  plan-2  C11  0.020
 5NM  plan-2  C16  0.020
 5NM  plan-2  C18  0.020
 5NM  plan-2  C23  0.020
 5NM  plan-2  C25  0.020
 5NM  plan-2  BR3  0.020
 5NM  plan-2  H10  0.020
 5NM  plan-2  H13  0.020
 5NM  plan-2  H14  0.020

