# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 22:04:12 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R)-2-phenyl-N-pyridin-4-ylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C(=O)Nc1ccncc1)c2ccccc2
#
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
 1CM  1CM  (2R)-2-phenyl-N-pyridin-4-ylbutanamide  ligand  34  18  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1CM
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
 1CM  O23   O  O     0  -0.447  -0.4147   1.1640  -1.6113
 1CM  C22   C  C     0   0.583  -0.1636   0.9942  -0.4357
 1CM  C31   C  CH1   0  -0.487   1.1911   1.3239   0.1766
 1CM  C36   C  CH2   0  -0.408   1.8648   2.4948  -0.5411
 1CM  C35   C  CH3   0  -0.666   3.1884   2.8803   0.1030
 1CM  C33   C  CR16  0  -0.321   2.4191  -0.5371   1.3594
 1CM  C32   C  CR6   0   0.158   2.0259   0.0598   0.1659
 1CM  C41   C  CR16  0  -0.239   3.1688  -1.6918  -1.0430
 1CM  C42   C  CR16  0  -0.268   3.5588  -2.2799   0.1544
 1CM  N21   N  NH1   0  -0.740  -1.0431   0.4526   0.4558
 1CM  C14   C  CR6   0   0.465  -2.3195  -0.0417   0.2353
 1CM  C15   C  CR16  0  -0.419  -3.0499  -0.4586   1.3511
 1CM  C11   C  CR16  0  -0.240   3.1815  -1.6987   1.3563
 1CM  C16   C  CR16  0  -0.062  -4.3208  -0.9679   1.1735
 1CM  N11   N  N     0  -0.417  -4.9110  -1.0923  -0.0118
 1CM  C12   C  CR16  0  -0.070  -4.2098  -0.6946  -1.0659
 1CM  C10   C  CR16  0  -0.288   2.4084  -0.5319  -1.0372
 1CM  C13   C  CR16  0  -0.375  -2.9289  -0.1670  -1.0136
 1CM  H31   H  HCH1  0   0.282   1.0387   1.6150   1.2216
 1CM  H361  H  HCH2  0   0.241   1.1874   3.3519  -0.5225
 1CM  H362  H  HCH2  0   0.232   2.0220   2.2495  -1.5930
 1CM  H351  H  HCH3  0   0.236   3.6196   3.7463  -0.3991
 1CM  H352  H  HCH3  0   0.221   3.0596   3.1376   1.1560
 1CM  H353  H  HCH3  0   0.227   3.9154   2.0696   0.0467
 1CM  H33   H  HCR6  0   0.254   2.1335  -0.0879   2.3034
 1CM  H41   H  HCR6  0   0.257   3.4545  -2.1398  -1.9860
 1CM  H42   H  HCR6  0   0.257   4.1533  -3.1842   0.1485
 1CM  H21   H  HNH1  0   0.418  -0.7353   0.4144   1.4164
 1CM  H15   H  HCR6  0   0.284  -2.6336  -0.3833   2.3479
 1CM  H11   H  HCR6  0   0.257   3.4777  -2.1479   2.2953
 1CM  H16   H  HCR6  0   0.267  -4.8904  -1.2899   2.0382
 1CM  H12   H  HCR6  0   0.265  -4.6902  -0.7997  -2.0327
 1CM  H10   H  HCR6  0   0.254   2.1112  -0.0884  -1.9794
 1CM  H13   H  HCR6  0   0.289  -2.4404   0.1257  -1.9269

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
 1CM  O23  C22   double    1.214  0.020  1.214
 1CM  C22  C31   single    1.523  0.020  1.523
 1CM  C22  N21   single    1.364  0.020  1.364
 1CM  C31  C36   single    1.530  0.020  1.530
 1CM  C31  C32   single    1.515  0.020  1.515
 1CM  C31  H31   single    0.970  0.020  1.090
 1CM  C36  C35   single    1.522  0.020  1.522
 1CM  C36  H361  single    0.970  0.020  1.090
 1CM  C36  H362  single    0.970  0.020  1.090
 1CM  C35  H351  single    0.970  0.020  1.090
 1CM  C35  H352  single    0.970  0.020  1.090
 1CM  C35  H353  single    0.970  0.020  1.090
 1CM  C33  C32   aromatic  1.391  0.020  1.391
 1CM  C33  C11   aromatic  1.389  0.020  1.389
 1CM  C33  H33   single    0.930  0.020  1.080
 1CM  C32  C10   aromatic  1.394  0.020  1.394
 1CM  C41  C42   aromatic  1.390  0.020  1.390
 1CM  C41  C10   aromatic  1.387  0.020  1.387
 1CM  C41  H41   single    0.930  0.020  1.080
 1CM  C42  C11   aromatic  1.387  0.020  1.387
 1CM  C42  H42   single    0.930  0.020  1.080
 1CM  N21  C14   single    1.386  0.020  1.386
 1CM  N21  H21   single    0.860  0.020  1.020
 1CM  C14  C15   aromatic  1.397  0.020  1.397
 1CM  C14  C13   aromatic  1.395  0.020  1.395
 1CM  C15  C16   aromatic  1.381  0.020  1.381
 1CM  C15  H15   single    0.930  0.020  1.080
 1CM  C11  H11   single    0.930  0.020  1.080
 1CM  C16  N11   aromatic  1.330  0.020  1.330
 1CM  C16  H16   single    0.930  0.020  1.080
 1CM  N11  C12   aromatic  1.327  0.020  1.327
 1CM  C12  C13   aromatic  1.386  0.020  1.386
 1CM  C12  H12   single    0.930  0.020  1.080
 1CM  C10  H10   single    0.930  0.020  1.080
 1CM  C13  H13   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
 1CM  N21   C22  C31   113.37  3.000
 1CM  N21   C22  O23   123.71  3.000
 1CM  C31   C22  O23   122.89  3.000
 1CM  H31   C31  C32   107.76  3.000
 1CM  H31   C31  C36   107.79  3.000
 1CM  C32   C31  C36   113.12  3.000
 1CM  H31   C31  C22   108.50  3.000
 1CM  C32   C31  C22   107.86  3.000
 1CM  C36   C31  C22   111.65  3.000
 1CM  H362  C36  H361  106.38  3.000
 1CM  H362  C36  C35   109.86  3.000
 1CM  H361  C36  C35   109.47  3.000
 1CM  H362  C36  C31   110.10  3.000
 1CM  H361  C36  C31   108.62  3.000
 1CM  C35   C36  C31   112.23  3.000
 1CM  H353  C35  H352  107.69  3.000
 1CM  H353  C35  H351  107.65  3.000
 1CM  H352  C35  H351  107.69  3.000
 1CM  H353  C35  C36   111.69  3.000
 1CM  H352  C35  C36   111.43  3.000
 1CM  H351  C35  C36   110.51  3.000
 1CM  H33   C33  C11   119.55  3.000
 1CM  H33   C33  C32   119.67  3.000
 1CM  C11   C33  C32   120.79  3.000
 1CM  C10   C32  C33   118.73  3.000
 1CM  C10   C32  C31   120.76  3.000
 1CM  C33   C32  C31   120.51  3.000
 1CM  H41   C41  C10   119.63  3.000
 1CM  H41   C41  C42   120.09  3.000
 1CM  C10   C41  C42   120.27  3.000
 1CM  H42   C42  C11   120.28  3.000
 1CM  H42   C42  C41   120.20  3.000
 1CM  C11   C42  C41   119.52  3.000
 1CM  H21   N21  C14   114.74  3.000
 1CM  H21   N21  C22   116.12  3.000
 1CM  C14   N21  C22   129.13  3.000
 1CM  C13   C14  C15   117.36  3.000
 1CM  C13   C14  N21   125.20  3.000
 1CM  C15   C14  N21   117.43  3.000
 1CM  H15   C15  C16   119.86  3.000
 1CM  H15   C15  C14   120.89  3.000
 1CM  C16   C15  C14   119.25  3.000
 1CM  H11   C11  C42   120.22  3.000
 1CM  H11   C11  C33   119.68  3.000
 1CM  C42   C11  C33   120.10  3.000
 1CM  H16   C16  N11   116.74  3.000
 1CM  H16   C16  C15   119.37  3.000
 1CM  N11   C16  C15   123.89  3.000
 1CM  C12   N11  C16   116.45  3.000
 1CM  H12   C12  C13   118.67  3.000
 1CM  H12   C12  N11   116.42  3.000
 1CM  C13   C12  N11   124.91  3.000
 1CM  H10   C10  C41   119.29  3.000
 1CM  H10   C10  C32   120.11  3.000
 1CM  C41   C10  C32   120.59  3.000
 1CM  H13   C13  C12   119.40  3.000
 1CM  H13   C13  C14   122.47  3.000
 1CM  C12   C13  C14   118.13  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
 1CM  CONST_01  C41   C10  C32  C33     0.00   0.0  0
 1CM  CONST_02  C41   C42  C11  C33     0.00   0.0  0
 1CM  CONST_03  C42   C11  C33  C32     0.00   0.0  0
 1CM  CONST_04  C42   C41  C10  C32     0.00   0.0  0
 1CM  CONST_05  N11   C16  C15  C14     0.00   0.0  0
 1CM  CONST_06  N11   C12  C13  C14     0.00   0.0  0
 1CM  CONST_07  C12   C13  C14  C15     0.00   0.0  0
 1CM  CONST_08  C12   N11  C16  C15     0.00   0.0  0
 1CM  CONST_09  C10   C32  C33  C11     0.00   0.0  0
 1CM  CONST_10  C10   C41  C42  C11     0.00   0.0  0
 1CM  CONST_11  C13   C14  C15  C16     0.00   0.0  0
 1CM  CONST_12  C13   C12  N11  C16     0.00   0.0  0
 1CM  CONST_13  C11   C33  C32  C31   180.00   0.0  0
 1CM  CONST_14  C41   C10  C32  C31   180.00   0.0  0
 1CM  CONST_15  C16   C15  C14  N21   180.00   0.0  0
 1CM  CONST_16  C12   C13  C14  N21   180.00   0.0  0
 1CM  CONST_17  H10   C10  C32  C33   180.00   0.0  0
 1CM  CONST_18  H42   C42  C11  C33   180.00   0.0  0
 1CM  CONST_19  H11   C11  C33  C32   180.00   0.0  0
 1CM  CONST_20  H41   C41  C10  C32   180.00   0.0  0
 1CM  CONST_21  H33   C33  C11  C42   180.00   0.0  0
 1CM  CONST_22  H16   C16  C15  C14   180.00   0.0  0
 1CM  CONST_23  H12   C12  C13  C14   180.00   0.0  0
 1CM  CONST_24  H13   C13  C14  C15   180.00   0.0  0
 1CM  CONST_25  H15   C15  C16  N11   180.00   0.0  0
 1CM  CONST_26  C15   C14  N21  C22   180.00   0.0  0
 1CM  CONST_27  C13   C14  N21  C22     0.00   0.0  0
 1CM  CONST_28  H21   N21  C14  C15     0.00   0.0  0
 1CM  CONST_29  C14   N21  C22  O23     0.00   0.0  0
 1CM  CONST_30  C14   N21  C22  C31   180.00   0.0  0
 1CM  Var_01    H351  C35  C36  C31  -177.23  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
 1CM  chir_01  C31  C22  C36  C32  positiv

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
 1CM  plan-1  C31  0.020
 1CM  plan-1  C33  0.020
 1CM  plan-1  C32  0.020
 1CM  plan-1  C41  0.020
 1CM  plan-1  C42  0.020
 1CM  plan-1  C11  0.020
 1CM  plan-1  C10  0.020
 1CM  plan-1  H33  0.020
 1CM  plan-1  H41  0.020
 1CM  plan-1  H42  0.020
 1CM  plan-1  H11  0.020
 1CM  plan-1  H10  0.020
 1CM  plan-2  N21  0.020
 1CM  plan-2  C14  0.020
 1CM  plan-2  C15  0.020
 1CM  plan-2  C16  0.020
 1CM  plan-2  N11  0.020
 1CM  plan-2  C12  0.020
 1CM  plan-2  C13  0.020
 1CM  plan-2  H15  0.020
 1CM  plan-2  H16  0.020
 1CM  plan-2  H12  0.020
 1CM  plan-2  H13  0.020
 1CM  plan-3  O23  0.020
 1CM  plan-3  C22  0.020
 1CM  plan-3  C31  0.020
 1CM  plan-3  N21  0.020
 1CM  plan-3  C14  0.020
 1CM  plan-3  H21  0.020

