# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:15:13 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [(2R,3R)-1-methyl-2-pyridin-3-ylpyrrolidin-3-yl]methyl 4-(ethylamino)-4-oxobutanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)CCC(=O)OC[C@@H]1CCN(C)[C@H]1c2cccnc2
#
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
 NLD  NLD  '[(2R,3R)-1-methyl-2-pyridin-3-ylpyrrolidin-3-yl]methyl 4-(ethylamino)-4-oxobutanoate'  ligand  48  23  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NLD
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
 NLD  O19   O  O     0  -0.451   1.5881  -0.3894   1.8688
 NLD  C15   C  C     0   0.610   1.5929  -0.1730   0.6828
 NLD  C16   C  CH2   0  -0.583   2.7969  -0.2646  -0.2145
 NLD  C17   C  CH2   0  -0.579   4.0854  -0.5017   0.5527
 NLD  C18   C  C     0   0.566   5.2643  -0.7000  -0.3792
 NLD  O14   O  O2    0  -0.462   0.5098   0.1722  -0.0023
 NLD  C13   C  CH2   0  -0.165  -0.7261   0.3021   0.7073
 NLD  C7    C  CH1   0  -0.299  -1.7717   0.7706  -0.2792
 NLD  C6    C  CH1   0  -0.117  -3.1617   0.8142   0.3960
 NLD  N2    N  NT    0  -0.420  -3.8055   1.9542  -0.2247
 NLD  C10   C  CH3   0  -0.525  -5.0103   2.3874   0.4401
 NLD  C9    C  CH2   0  -0.282  -2.7747   2.9713  -0.3000
 NLD  C8    C  CH2   0  -0.452  -1.5574   2.2051  -0.8048
 NLD  C2    C  CR6   0   0.042  -3.9412  -0.4599   0.2381
 NLD  C1    C  CR16  0  -0.085  -4.5164  -0.8023  -0.9839
 NLD  N1    N  N     0  -0.402  -5.1890  -1.9247  -1.1967
 NLD  C5    C  CR16  0  -0.076  -5.3203  -2.7744  -0.1818
 NLD  C4    C  CR16  0  -0.317  -4.7944  -2.5351   1.0770
 NLD  C3    C  CR16  0  -0.210  -4.0962  -1.3544   1.2871
 NLD  O20   O  O     0  -0.507   5.1515  -1.2764  -1.4540
 NLD  N21   N  NH1   0  -0.634   6.4347  -0.2368   0.0810
 NLD  C22   C  CH2   0  -0.267   7.6916  -0.3685  -0.6286
 NLD  C23   C  CH3   0  -0.691   8.8601  -0.3203   0.3388
 NLD  H161  H  HCH2  0   0.288   2.6249  -1.0721  -0.9308
 NLD  H162  H  HCH2  0   0.283   2.8588   0.6510  -0.8086
 NLD  H171  H  HCH2  0   0.262   4.2734   0.3183   1.2480
 NLD  H172  H  HCH2  0   0.281   3.9995  -1.4061   1.1621
 NLD  H131  H  HCH2  0   0.243  -1.0055  -0.6615   1.1440
 NLD  H132  H  HCH2  0   0.237  -0.6192   1.0228   1.5227
 NLD  H7    H  HCH1  0   0.264  -1.8004   0.0668  -1.1152
 NLD  H6    H  HCH1  0   0.225  -3.0203   0.9915   1.4807
 NLD  H81C  H  HCH2  0   0.242  -0.6244   2.6495  -0.4558
 NLD  H82C  H  HCH2  0   0.244  -1.5271   2.2067  -1.8942
 NLD  H101  H  HCH3  0   0.196  -4.8433   2.6740   1.4901
 NLD  H102  H  HCH3  0   0.237  -5.4286   3.2495  -0.0801
 NLD  H103  H  HCH3  0   0.237  -5.7613   1.5969   0.4237
 NLD  H91C  H  HCH2  0   0.240  -3.0780   3.7873  -0.9589
 NLD  H92C  H  HCH2  0   0.195  -2.5658   3.4103   0.6903
 NLD  H1    H  HCR6  0   0.255  -4.4280  -0.1209  -1.8238
 NLD  H3    H  HCR6  0   0.267  -3.6828  -1.1268   2.2629
 NLD  H5    H  HCR6  0   0.262  -5.8731  -3.6859  -0.3804
 NLD  H4    H  HCR6  0   0.270  -4.9347  -3.2523   1.8740
 NLD  H231  H  HCH3  0   0.232   8.8787   0.6180   0.8956
 NLD  H232  H  HCH3  0   0.234   8.8132  -1.1416   1.0537
 NLD  H233  H  HCH3  0   0.242   9.8004  -0.3976  -0.2055
 NLD  H221  H  HCH2  0   0.240   7.6905  -1.3153  -1.1680
 NLD  H222  H  HCH2  0   0.233   7.7911   0.4235  -1.3768
 NLD  H21   H  HNH1  0   0.398   6.4380   0.2894   0.9404

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
 NLD  O19  C15   double    1.206  0.020  1.206
 NLD  C15  C16   single    1.504  0.020  1.504
 NLD  C15  O14   single    1.327  0.020  1.327
 NLD  C16  C17   single    1.518  0.020  1.518
 NLD  C17  C18   single    1.516  0.020  1.516
 NLD  O14  C13   single    1.431  0.020  1.431
 NLD  C13  C7    single    1.512  0.020  1.512
 NLD  C7   C6    single    1.546  0.020  1.546
 NLD  C7   C8    single    1.543  0.020  1.543
 NLD  C6   N2    single    1.449  0.020  1.449
 NLD  C6   C2    single    1.502  0.020  1.502
 NLD  N2   C10   single    1.443  0.020  1.443
 NLD  N2   C9    single    1.450  0.020  1.450
 NLD  C9   C8    single    1.524  0.020  1.524
 NLD  C2   C1    aromatic  1.393  0.020  1.393
 NLD  C2   C3    aromatic  1.387  0.020  1.387
 NLD  C1   N1    aromatic  1.326  0.020  1.326
 NLD  N1   C5    aromatic  1.330  0.020  1.330
 NLD  C5   C4    aromatic  1.385  0.020  1.385
 NLD  C4   C3    aromatic  1.388  0.020  1.388
 NLD  C18  O20   double    1.225  0.020  1.225
 NLD  C18  N21   single    1.340  0.020  1.340
 NLD  N21  C22   single    1.449  0.020  1.449
 NLD  C22  C23   single    1.518  0.020  1.518
 NLD  C16  H161  single    0.970  0.020  1.090
 NLD  C16  H162  single    0.970  0.020  1.090
 NLD  C17  H171  single    0.970  0.020  1.090
 NLD  C17  H172  single    0.970  0.020  1.090
 NLD  C13  H131  single    0.970  0.020  1.090
 NLD  C13  H132  single    0.970  0.020  1.090
 NLD  C7   H7    single    0.970  0.020  1.090
 NLD  C6   H6    single    0.970  0.020  1.090
 NLD  C8   H81C  single    0.970  0.020  1.090
 NLD  C8   H82C  single    0.970  0.020  1.090
 NLD  C10  H101  single    0.970  0.020  1.090
 NLD  C10  H102  single    0.970  0.020  1.090
 NLD  C10  H103  single    0.970  0.020  1.090
 NLD  C9   H91C  single    0.970  0.020  1.090
 NLD  C9   H92C  single    0.970  0.020  1.090
 NLD  C1   H1    single    0.930  0.020  1.080
 NLD  C3   H3    single    0.930  0.020  1.080
 NLD  C5   H5    single    0.930  0.020  1.080
 NLD  C4   H4    single    0.930  0.020  1.080
 NLD  C23  H231  single    0.970  0.020  1.090
 NLD  C23  H232  single    0.970  0.020  1.090
 NLD  C23  H233  single    0.970  0.020  1.090
 NLD  C22  H221  single    0.970  0.020  1.090
 NLD  C22  H222  single    0.970  0.020  1.090
 NLD  N21  H21   single    0.860  0.020  1.020

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
 NLD  O14   C15  C16   111.17  3.000
 NLD  O14   C15  O19   123.45  3.000
 NLD  C16   C15  O19   125.38  3.000
 NLD  H162  C16  H161  105.76  3.000
 NLD  H162  C16  C17   110.94  3.000
 NLD  H161  C16  C17   110.45  3.000
 NLD  H162  C16  C15   108.57  3.000
 NLD  H161  C16  C15   108.05  3.000
 NLD  C17   C16  C15   112.79  3.000
 NLD  H172  C17  H171  106.24  3.000
 NLD  H172  C17  C18   107.18  3.000
 NLD  H171  C17  C18   110.86  3.000
 NLD  H172  C17  C16   110.12  3.000
 NLD  H171  C17  C16   110.53  3.000
 NLD  C18   C17  C16   111.71  3.000
 NLD  N21   C18  O20   122.98  3.000
 NLD  N21   C18  C17   115.02  3.000
 NLD  O20   C18  C17   121.97  3.000
 NLD  C13   O14  C15   118.19  3.000
 NLD  H132  C13  H131  107.92  3.000
 NLD  H132  C13  C7    110.48  3.000
 NLD  H131  C13  C7    110.89  3.000
 NLD  H132  C13  O14   110.19  3.000
 NLD  H131  C13  O14   109.79  3.000
 NLD  C7    C13  O14   107.57  3.000
 NLD  H7    C7   C8    109.98  3.000
 NLD  H7    C7   C6    109.18  3.000
 NLD  C8    C7   C6    104.33  3.000
 NLD  H7    C7   C13   108.52  3.000
 NLD  C8    C7   C13   114.48  3.000
 NLD  C6    C7   C13   110.22  3.000
 NLD  H6    C6   C2    107.75  3.000
 NLD  H6    C6   N2    110.50  3.000
 NLD  C2    C6   N2    113.07  3.000
 NLD  H6    C6   C7    108.50  3.000
 NLD  C2    C6   C7    113.38  3.000
 NLD  N2    C6   C7    103.57  3.000
 NLD  C9    N2   C10   114.02  3.000
 NLD  C9    N2   C6    104.97  3.000
 NLD  C10   N2   C6    114.20  3.000
 NLD  H103  C10  H102  107.56  3.000
 NLD  H103  C10  H101  107.91  3.000
 NLD  H102  C10  H101  107.90  3.000
 NLD  H103  C10  N2    110.52  3.000
 NLD  H102  C10  N2    109.75  3.000
 NLD  H101  C10  N2    113.01  3.000
 NLD  H92C  C9   H91C  107.27  3.000
 NLD  H92C  C9   C8    110.25  3.000
 NLD  H91C  C9   C8    113.43  3.000
 NLD  H92C  C9   N2    111.54  3.000
 NLD  H91C  C9   N2    110.98  3.000
 NLD  C8    C9   N2    103.44  3.000
 NLD  H82C  C8   H81C  107.18  3.000
 NLD  H82C  C8   C9    110.64  3.000
 NLD  H81C  C8   C9    111.86  3.000
 NLD  H82C  C8   C7    110.23  3.000
 NLD  H81C  C8   C7    112.87  3.000
 NLD  C9    C8   C7    104.10  3.000
 NLD  C3    C2   C1    117.30  3.000
 NLD  C3    C2   C6    121.70  3.000
 NLD  C1    C2   C6    120.99  3.000
 NLD  H1    C1   N1    116.66  3.000
 NLD  H1    C1   C2    119.40  3.000
 NLD  N1    C1   C2    123.94  3.000
 NLD  C5    N1   C1    117.94  3.000
 NLD  H5    C5   C4    120.35  3.000
 NLD  H5    C5   N1    116.59  3.000
 NLD  C4    C5   N1    123.06  3.000
 NLD  H4    C4   C3    121.20  3.000
 NLD  H4    C4   C5    120.40  3.000
 NLD  C3    C4   C5    118.40  3.000
 NLD  H3    C3   C4    120.45  3.000
 NLD  H3    C3   C2    120.18  3.000
 NLD  C4    C3   C2    119.36  3.000
 NLD  H21   N21  C22   117.52  3.000
 NLD  H21   N21  C18   118.43  3.000
 NLD  C22   N21  C18   123.91  3.000
 NLD  H222  C22  H221  106.89  3.000
 NLD  H222  C22  C23   110.05  3.000
 NLD  H221  C22  C23   110.11  3.000
 NLD  H222  C22  N21   110.37  3.000
 NLD  H221  C22  N21   108.68  3.000
 NLD  C23   C22  N21   110.65  3.000
 NLD  H233  C23  H232  108.15  3.000
 NLD  H233  C23  H231  107.54  3.000
 NLD  H232  C23  H231  108.30  3.000
 NLD  H233  C23  C22   110.11  3.000
 NLD  H232  C23  C22   111.16  3.000
 NLD  H231  C23  C22   111.45  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
 NLD  CONST_01  C5    N1   C1   C2      0.00   0.0  0
 NLD  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 NLD  CONST_03  C4    C3   C2   C1      0.00   0.0  0
 NLD  CONST_04  C4    C5   N1   C1      0.00   0.0  0
 NLD  CONST_05  C3    C2   C1   N1      0.00   0.0  0
 NLD  CONST_06  C3    C4   C5   N1      0.00   0.0  0
 NLD  CONST_07  N1    C1   C2   C6    180.00   0.0  0
 NLD  CONST_08  C4    C3   C2   C6    180.00   0.0  0
 NLD  CONST_09  H1    C1   C2   C6      0.00   0.0  0
 NLD  CONST_10  H3    C3   C2   C6      0.00   0.0  0
 NLD  CONST_11  H4    C4   C3   C2    180.00   0.0  0
 NLD  CONST_12  H5    C5   N1   C1    180.00   0.0  0
 NLD  CONST_13  C22   N21  C18  C17   180.00   0.0  0
 NLD  CONST_14  C22   N21  C18  O20     0.00   0.0  0
 NLD  CONST_15  H21   N21  C18  C17     0.00   0.0  0
 NLD  Var_01    N2    C9   C8   C7    -28.98  30.0  1
 NLD  Var_02    C8    C9   N2   C6     44.65  30.0  1
 NLD  Var_03    H101  C10  N2   C6     59.08  30.0  3
 NLD  Var_04    C7    C13  O14  C15   177.02  30.0  3
 NLD  Var_05    C17   C16  C15  O19    -7.02  30.0  3
 NLD  Var_06    C18   C17  C16  C15   175.46  30.0  3
 NLD  Var_07    O20   C18  C17  C16   -35.22  30.0  3
 NLD  Var_08    C23   C22  N21  C18  -155.28  30.0  3
 NLD  Var_09    H231  C23  C22  N21   -59.49  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
 NLD  chir_01  C7  C13  C6  C8  negativ
 NLD  chir_02  C6  N2   C2  C7  negativ

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
 NLD  plan-1  C6   0.020
 NLD  plan-1  C2   0.020
 NLD  plan-1  C1   0.020
 NLD  plan-1  N1   0.020
 NLD  plan-1  C5   0.020
 NLD  plan-1  C4   0.020
 NLD  plan-1  C3   0.020
 NLD  plan-1  H1   0.020
 NLD  plan-1  H3   0.020
 NLD  plan-1  H5   0.020
 NLD  plan-1  H4   0.020
 NLD  plan-2  C17  0.020
 NLD  plan-2  C18  0.020
 NLD  plan-2  O20  0.020
 NLD  plan-2  N21  0.020
 NLD  plan-2  C22  0.020
 NLD  plan-2  H21  0.020
 NLD  plan-3  O19  0.020
 NLD  plan-3  C15  0.020
 NLD  plan-3  C16  0.020
 NLD  plan-3  O14  0.020

