# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 08:25:16 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-{[(4S,5S)-5-(aminomethyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl}-N'-(4-chloro-3-fluorophenyl)ethanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)O[C@@H](CN)[C@H](CNC(=O)C(=O)Nc2ccc(Cl)c(F)c2)O1
#
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
 0M1  0M1  N-{[(4S,5S)-5-(aminomethyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl}-N'-(4-chloro-3-fluorophenyl)ethanediamide  ligand  43  24  .  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_0M1
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
 0M1  C01  C   CR6   0  -0.256   5.7695  -0.1787  -0.4991
 0M1  C02  C   CR6   0   0.654   5.0162   0.6148   0.3468
 0M1  C03  C   CR16  0  -0.488   3.6734   0.3905   0.5716
 0M1  C04  C   CR6   0   0.413   3.0558  -0.6756  -0.0802
 0M1  C05  C   CR16  0  -0.360   3.8059  -1.4853  -0.9359
 0M1  C06  C   CR16  0  -0.197   5.1492  -1.2386  -1.1427
 0M1  CL1  CL  CL    0  -0.091   7.4410   0.1607  -0.7332
 0M1  F08  F   F     0  -0.295   5.6059   1.6367   0.9688
 0M1  N09  N   NH1   0  -0.738   1.7081  -0.9926   0.0688
 0M1  C10  C   C     0   0.444   0.7647  -0.3619   0.7872
 0M1  C11  C   C     0   0.465  -0.6075  -1.0413   0.6402
 0M1  N12  N   NH1   0  -0.618  -1.5601  -0.4550   1.3565
 0M1  O13  O   O     0  -0.470  -0.7494  -2.0213  -0.0745
 0M1  O14  O   O     0  -0.442   0.9150   0.6277   1.4770
 0M1  C15  C   CH2   0  -0.328  -2.9406  -0.8770   1.3328
 0M1  C16  C   CH1   0  -0.002  -3.7406  -0.1826   0.2468
 0M1  C17  C   CH1   0   0.022  -5.2058  -0.6287   0.1917
 0M1  O18  O   O2    0  -0.516  -5.9223   0.5785   0.0018
 0M1  C19  C   CT    0   0.474  -5.0200   1.6699  -0.0525
 0M1  O20  O   O2    0  -0.506  -3.8271   1.1949   0.5279
 0M1  C21  C   CH2   0  -0.296  -5.4840  -1.6302  -0.9114
 0M1  N22  N   NH2   0  -0.802  -6.8771  -2.0378  -0.9036
 0M1  C23  C   CH3   0  -0.673  -4.7921   2.0927  -1.4995
 0M1  C24  C   CH3   0  -0.681  -5.5554   2.8078   0.7934
 0M1  H1   H   HCR6  0   0.312   3.1395   1.0447   1.2426
 0M1  H2   H   HCR6  0   0.290   3.3368  -2.3170  -1.4458
 0M1  H3   H   HCR6  0   0.296   5.7183  -1.8728  -1.8082
 0M1  H4   H   HNH1  0   0.428   1.3818  -1.8031  -0.4427
 0M1  H5   H   HNH1  0   0.418  -1.3187   0.3724   1.8808
 0M1  H6   H   HCH2  0   0.267  -2.9852  -1.9560   1.1812
 0M1  H7   H   HCH2  0   0.275  -3.3783  -0.6652   2.3089
 0M1  H8   H   HCH1  0   0.234  -3.2533  -0.3542  -0.7248
 0M1  H9   H   HCH1  0   0.225  -5.5143  -1.0704   1.1493
 0M1  H10  H   HCH2  0   0.202  -5.1431  -1.2133  -1.8710
 0M1  H11  H   HCH2  0   0.228  -4.8642  -2.5115  -0.7200
 0M1  H12  H   HNH2  0   0.343  -7.4517  -1.2699  -1.2274
 0M1  H13  H   HNH2  0   0.353  -7.0136  -2.7829  -1.5739
 0M1  H15  H   HCH3  0   0.235  -5.7295   2.4068  -1.9587
 0M1  H16  H   HCH3  0   0.232  -4.0967   2.9311  -1.5484
 0M1  H17  H   HCH3  0   0.236  -4.3833   1.2774  -2.0989
 0M1  H18  H   HCH3  0   0.241  -5.7275   2.4802   1.8190
 0M1  H19  H   HCH3  0   0.236  -4.8520   3.6403   0.8094
 0M1  H20  H   HCH3  0   0.236  -6.4962   3.1759   0.3846

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
 0M1  C24  C19  single    1.516  0.020  1.516
 0M1  O18  C19  single    1.417  0.020  1.417
 0M1  O18  C17  single    1.417  0.020  1.417
 0M1  N22  C21  single    1.452  0.020  1.452
 0M1  C23  C19  single    1.525  0.020  1.525
 0M1  C19  O20  single    1.409  0.020  1.409
 0M1  C17  C21  single    1.516  0.020  1.516
 0M1  C17  C16  single    1.533  0.020  1.533
 0M1  O20  C16  single    1.409  0.020  1.409
 0M1  C16  C15  single    1.517  0.020  1.517
 0M1  C15  N12  single    1.444  0.020  1.444
 0M1  N12  C11  single    1.328  0.020  1.328
 0M1  C11  O13  double    1.221  0.020  1.221
 0M1  C11  C10  single    1.538  0.020  1.538
 0M1  O14  C10  double    1.216  0.020  1.216
 0M1  C10  N09  single    1.343  0.020  1.343
 0M1  N09  C04  single    1.393  0.020  1.393
 0M1  C03  C04  aromatic  1.394  0.020  1.394
 0M1  C03  C02  aromatic  1.380  0.020  1.380
 0M1  C04  C05  aromatic  1.397  0.020  1.397
 0M1  F08  C02  single    1.334  0.020  1.334
 0M1  C02  C01  aromatic  1.383  0.020  1.383
 0M1  C05  C06  aromatic  1.381  0.020  1.381
 0M1  C01  C06  aromatic  1.386  0.020  1.386
 0M1  C01  CL1  single    1.722  0.020  1.722
 0M1  C03  H1   single    0.930  0.020  1.080
 0M1  C05  H2   single    0.930  0.020  1.080
 0M1  C06  H3   single    0.930  0.020  1.080
 0M1  N09  H4   single    0.860  0.020  1.020
 0M1  N12  H5   single    0.860  0.020  1.020
 0M1  C15  H6   single    0.970  0.020  1.090
 0M1  C15  H7   single    0.970  0.020  1.090
 0M1  C16  H8   single    0.970  0.020  1.090
 0M1  C17  H9   single    0.970  0.020  1.090
 0M1  C21  H10  single    0.970  0.020  1.090
 0M1  C21  H11  single    0.970  0.020  1.090
 0M1  N22  H12  single    0.890  0.020  1.040
 0M1  N22  H13  single    0.890  0.020  1.040
 0M1  C23  H15  single    0.970  0.020  1.090
 0M1  C23  H16  single    0.970  0.020  1.090
 0M1  C23  H17  single    0.970  0.020  1.090
 0M1  C24  H18  single    0.970  0.020  1.090
 0M1  C24  H19  single    0.970  0.020  1.090
 0M1  C24  H20  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
 0M1  CL1  C01  C06  121.46  3.000
 0M1  CL1  C01  C02  119.93  3.000
 0M1  C06  C01  C02  118.61  3.000
 0M1  F08  C02  C03  118.61  3.000
 0M1  F08  C02  C01  118.95  3.000
 0M1  C03  C02  C01  122.44  3.000
 0M1  H1   C03  C04  122.38  3.000
 0M1  H1   C03  C02  118.98  3.000
 0M1  C04  C03  C02  118.64  3.000
 0M1  N09  C04  C05  116.96  3.000
 0M1  C05  C04  C03  119.47  3.000
 0M1  N09  C04  C03  123.57  3.000
 0M1  H2   C05  C06  119.22  3.000
 0M1  H2   C05  C04  120.09  3.000
 0M1  C06  C05  C04  120.69  3.000
 0M1  H3   C06  C05  119.94  3.000
 0M1  H3   C06  C01  119.92  3.000
 0M1  C05  C06  C01  120.14  3.000
 0M1  H4   N09  C10  114.82  3.000
 0M1  H4   N09  C04  116.11  3.000
 0M1  C10  N09  C04  129.06  3.000
 0M1  O14  C10  C11  121.61  3.000
 0M1  O14  C10  N09  126.79  3.000
 0M1  C11  C10  N09  111.60  3.000
 0M1  O13  C11  N12  125.91  3.000
 0M1  O13  C11  C10  120.93  3.000
 0M1  N12  C11  C10  113.16  3.000
 0M1  H5   N12  C15  118.49  3.000
 0M1  H5   N12  C11  118.08  3.000
 0M1  C15  N12  C11  123.22  3.000
 0M1  H7   C15  H6   107.47  3.000
 0M1  H7   C15  C16  109.89  3.000
 0M1  H6   C15  C16  109.37  3.000
 0M1  H7   C15  N12  108.21  3.000
 0M1  H6   C15  N12  109.31  3.000
 0M1  C16  C15  N12  112.47  3.000
 0M1  H8   C16  O20  110.85  3.000
 0M1  H8   C16  C17  110.25  3.000
 0M1  O20  C16  C17  103.48  3.000
 0M1  H8   C16  C15  109.10  3.000
 0M1  O20  C16  C15  109.70  3.000
 0M1  C17  C16  C15  113.37  3.000
 0M1  H9   C17  C21  108.49  3.000
 0M1  H9   C17  O18  108.51  3.000
 0M1  C21  C17  O18  111.88  3.000
 0M1  H9   C17  C16  110.74  3.000
 0M1  C21  C17  C16  113.20  3.000
 0M1  O18  C17  C16  103.91  3.000
 0M1  C19  O18  C17  109.84  3.000
 0M1  C24  C19  C23  111.98  3.000
 0M1  C23  C19  O20  110.97  3.000
 0M1  C24  C19  O20  108.80  3.000
 0M1  O20  C19  O18  105.28  3.000
 0M1  C23  C19  O18  110.19  3.000
 0M1  C24  C19  O18  109.39  3.000
 0M1  C19  O20  C16  107.43  3.000
 0M1  H11  C21  H10  106.40  3.000
 0M1  H11  C21  N22  108.45  3.000
 0M1  H10  C21  N22  114.10  3.000
 0M1  H11  C21  C17  107.51  3.000
 0M1  H10  C21  C17  109.12  3.000
 0M1  N22  C21  C17  110.96  3.000
 0M1  H13  N22  H12  105.68  3.000
 0M1  H13  N22  C21  109.44  3.000
 0M1  H12  N22  C21  109.27  3.000
 0M1  H17  C23  H16  108.11  3.000
 0M1  H17  C23  H15  107.82  3.000
 0M1  H16  C23  H15  107.94  3.000
 0M1  H17  C23  C19  111.72  3.000
 0M1  H16  C23  C19  110.56  3.000
 0M1  H15  C23  C19  110.56  3.000
 0M1  H20  C24  H19  107.73  3.000
 0M1  H20  C24  H18  108.55  3.000
 0M1  H19  C24  H18  108.52  3.000
 0M1  H20  C24  C19  110.44  3.000
 0M1  H19  C24  C19  110.72  3.000
 0M1  H18  C24  C19  110.80  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
 0M1  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 0M1  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 0M1  CONST_03  C05  C04  C03  C02    0.00   0.0  0
 0M1  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 0M1  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 0M1  CONST_06  C06  C01  C02  C03    0.00   0.0  0
 0M1  CONST_07  N09  C04  C03  C02  180.00   0.0  0
 0M1  CONST_08  CL1  C01  C02  C03  180.00   0.0  0
 0M1  CONST_09  F08  C02  C03  C04  180.00   0.0  0
 0M1  CONST_10  CL1  C01  C06  C05  180.00   0.0  0
 0M1  CONST_11  N09  C04  C05  C06  180.00   0.0  0
 0M1  CONST_12  F08  C02  C01  C06  180.00   0.0  0
 0M1  CONST_13  H1   C03  C02  C01  180.00   0.0  0
 0M1  CONST_14  H2   C05  C06  C01  180.00   0.0  0
 0M1  CONST_15  H3   C06  C01  C02  180.00   0.0  0
 0M1  CONST_16  C10  N09  C04  C03    0.00   0.0  0
 0M1  CONST_17  C10  N09  C04  C05  180.00   0.0  0
 0M1  CONST_18  H4   N09  C04  C03  180.00   0.0  0
 0M1  CONST_19  C11  C10  N09  C04  180.00   0.0  0
 0M1  CONST_20  O14  C10  N09  C04    0.00   0.0  0
 0M1  CONST_21  N12  C11  C10  N09  180.00   0.0  0
 0M1  CONST_22  C15  N12  C11  C10  180.00   0.0  0
 0M1  CONST_23  O14  C10  C11  N12    0.00   0.0  0
 0M1  CONST_24  C15  N12  C11  O13    0.00   0.0  0
 0M1  CONST_25  H5   N12  C11  C10    0.00   0.0  0
 0M1  Var_01    O18  C19  O20  C16   31.43  30.0  1
 0M1  Var_02    O20  C19  O18  C17  -18.57  30.0  1
 0M1  Var_03    H18  C24  C19  O18   56.56  30.0  3
 0M1  Var_04    H15  C23  C19  O18   60.65  30.0  3
 0M1  Var_05    C16  C15  N12  C11  -88.87  30.0  1
 0M1  Var_06    H12  N22  C21  C17   71.32  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
 0M1  chir_01  C16  C17  O20  C15  negativ
 0M1  chir_02  C17  O18  C16  C21  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
 0M1  plan-1  C01  0.020
 0M1  plan-1  C02  0.020
 0M1  plan-1  C03  0.020
 0M1  plan-1  C04  0.020
 0M1  plan-1  C05  0.020
 0M1  plan-1  C06  0.020
 0M1  plan-1  CL1  0.020
 0M1  plan-1  F08  0.020
 0M1  plan-1  N09  0.020
 0M1  plan-1  H1   0.020
 0M1  plan-1  H2   0.020
 0M1  plan-1  H3   0.020
 0M1  plan-2  C04  0.020
 0M1  plan-2  N09  0.020
 0M1  plan-2  C10  0.020
 0M1  plan-2  C11  0.020
 0M1  plan-2  N12  0.020
 0M1  plan-2  O13  0.020
 0M1  plan-2  O14  0.020
 0M1  plan-2  C15  0.020
 0M1  plan-2  H4   0.020
 0M1  plan-2  H5   0.020

