# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 07:49:57 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (4R,5R)-5-[(1S)-1-(acetylamino)-3-methylbutyl]-4-(methoxycarbonyl)-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1C[C@@H](N[C@H]1[C@H](CC(C)C)NC(C)=O)C(O)=O
#
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
 ABX  ABX  (4R,5R)-5-[(1S)-1-(acetylamino)-3-methylbutyl]-4-(methoxycarbonyl)-D-proline  ligand  45  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ABX
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
 ABX  C1    C  CH1   0  -0.383  -0.1733   1.2759  -0.6160
 ABX  C2    C  CH1   0  -0.069  -0.3595  -0.1543  -0.0735
 ABX  N1    N  NH1   0  -0.562  -1.4641  -0.6791  -0.8586
 ABX  C3    C  CH1   0  -0.227  -2.4128   0.4046  -0.9919
 ABX  C4    C  CH2   0  -0.472  -1.6290   1.7400  -0.7836
 ABX  C5    C  C     0   0.545  -3.5236   0.2788   0.0287
 ABX  O1    O  OH1   0  -0.596  -4.4668   1.1918  -0.1838
 ABX  O2    O  O     0  -0.428  -3.5628  -0.5203   0.9273
 ABX  N2    N  NH1   0  -0.638   2.0831  -0.3062   0.1591
 ABX  C6    C  C     0   0.523   2.9861   0.0839  -0.7630
 ABX  C7    C  CH3   0  -0.782   4.2203   0.7466  -0.2059
 ABX  O3    O  O     0  -0.500   2.8368  -0.0953  -1.9636
 ABX  C8    C  CH1   0  -0.081   0.8779  -1.0594  -0.1339
 ABX  C9    C  CH2   0  -0.417   0.7996  -2.2285   0.8521
 ABX  C10   C  CH1   0  -0.248  -0.3794  -3.1902   0.6983
 ABX  C11   C  CH3   0  -0.658  -0.3380  -3.9271  -0.6365
 ABX  C12   C  CH3   0  -0.651  -0.3717  -4.1888   1.8523
 ABX  C13   C  C     0   0.606   0.5957   2.1784   0.3073
 ABX  O4    O  O     0  -0.452   0.3942   2.2613   1.4951
 ABX  O5    O  O2    0  -0.450   1.5071   2.9010  -0.3294
 ABX  C14   C  CH3   0  -0.431   2.2753   3.8220   0.4450
 ABX  H1    H  HCH1  0   0.278   0.3167   1.2290  -1.5914
 ABX  H2    H  HCH1  0   0.241  -0.6880  -0.0787   0.9709
 ABX  HN1   H  HNH1  0   0.356  -1.1276  -0.9279  -1.7811
 ABX  H3    H  HCH1  0   0.302  -2.8692   0.3803  -1.9838
 ABX  H41   H  HCH2  0   0.261  -1.9688   2.2735   0.1056
 ABX  H42   H  HCH2  0   0.274  -1.7494   2.4135  -1.6296
 ABX  HO1   H  HOH1  0   0.481  -5.1590   1.1189   0.4903
 ABX  HN2   H  HNH1  0   0.398   2.3146  -0.1731   1.1313
 ABX  H71   H  HCH3  0   0.246   4.1320   1.0253   0.8427
 ABX  H72   H  HCH3  0   0.275   5.0656   0.0636  -0.3024
 ABX  H73   H  HCH3  0   0.263   4.4544   1.6371  -0.7866
 ABX  H8    H  HCH1  0   0.245   0.9857  -1.4336  -1.1553
 ABX  H91   H  HCH2  0   0.231   1.7306  -2.8014   0.7750
 ABX  H92   H  HCH2  0   0.225   0.7812  -1.8098   1.8659
 ABX  H10   H  HCH1  0   0.242  -1.3074  -2.6139   0.7443
 ABX  H111  H  HCH3  0   0.211   0.5829  -4.5092  -0.7293
 ABX  H112  H  HCH3  0   0.225  -1.1764  -4.6205  -0.7265
 ABX  H113  H  HCH3  0   0.223  -0.3877  -3.2474  -1.4876
 ABX  H121  H  HCH3  0   0.223  -0.4191  -3.6840   2.8191
 ABX  H122  H  HCH3  0   0.225  -1.2233  -4.8679   1.7891
 ABX  H123  H  HCH3  0   0.211   0.5373  -4.7956   1.8395
 ABX  H141  H  HCH3  0   0.245   1.6398   4.5605   0.9332
 ABX  H142  H  HCH3  0   0.235   2.8726   3.3101   1.1997
 ABX  H143  H  HCH3  0   0.253   2.9359   4.3231  -0.2560

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
 ABX  C1   C2    single  1.541  0.020  1.541
 ABX  C1   C4    single  1.537  0.020  1.537
 ABX  C1   C13   single  1.503  0.020  1.503
 ABX  C1   H1    single  0.970  0.020  1.090
 ABX  C2   N1    single  1.453  0.020  1.453
 ABX  C2   C8    single  1.534  0.020  1.534
 ABX  C2   H2    single  0.970  0.020  1.090
 ABX  N1   C3    single  1.446  0.020  1.446
 ABX  N1   HN1   single  0.890  0.020  1.040
 ABX  C3   C4    single  1.562  0.020  1.562
 ABX  C3   C5    single  1.514  0.020  1.514
 ABX  C3   H3    single  0.970  0.020  1.090
 ABX  C4   H41   single  0.970  0.020  1.090
 ABX  C4   H42   single  0.970  0.020  1.090
 ABX  C5   O1    single  1.330  0.020  1.330
 ABX  C5   O2    double  1.203  0.020  1.203
 ABX  O1   HO1   single  0.850  0.020  0.980
 ABX  N2   C6    single  1.348  0.020  1.348
 ABX  N2   C8    single  1.451  0.020  1.451
 ABX  N2   HN2   single  0.860  0.020  1.020
 ABX  C6   C7    single  1.508  0.020  1.508
 ABX  C6   O3    double  1.223  0.020  1.223
 ABX  C7   H71   single  0.970  0.020  1.090
 ABX  C7   H72   single  0.970  0.020  1.090
 ABX  C7   H73   single  0.970  0.020  1.090
 ABX  C8   C9    single  1.531  0.020  1.531
 ABX  C8   H8    single  0.970  0.020  1.090
 ABX  C9   C10   single  1.529  0.020  1.529
 ABX  C9   H91   single  0.970  0.020  1.090
 ABX  C9   H92   single  0.970  0.020  1.090
 ABX  C10  C11   single  1.525  0.020  1.525
 ABX  C10  C12   single  1.526  0.020  1.526
 ABX  C10  H10   single  0.970  0.020  1.090
 ABX  C11  H111  single  0.970  0.020  1.090
 ABX  C11  H112  single  0.970  0.020  1.090
 ABX  C11  H113  single  0.970  0.020  1.090
 ABX  C12  H121  single  0.970  0.020  1.090
 ABX  C12  H122  single  0.970  0.020  1.090
 ABX  C12  H123  single  0.970  0.020  1.090
 ABX  C13  O4    double  1.208  0.020  1.208
 ABX  C13  O5    single  1.326  0.020  1.326
 ABX  O5   C14   single  1.428  0.020  1.428
 ABX  C14  H141  single  0.970  0.020  1.090
 ABX  C14  H142  single  0.970  0.020  1.090
 ABX  C14  H143  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
 ABX  H1    C1   C13   110.17  3.000
 ABX  H1    C1   C4    109.89  3.000
 ABX  C13   C1   C4    111.73  3.000
 ABX  H1    C1   C2    109.19  3.000
 ABX  C13   C1   C2    113.77  3.000
 ABX  C4    C1   C2    101.78  3.000
 ABX  H2    C2   C8    108.63  3.000
 ABX  H2    C2   N1    108.15  3.000
 ABX  C8    C2   N1    112.26  3.000
 ABX  H2    C2   C1    107.89  3.000
 ABX  C8    C2   C1    115.86  3.000
 ABX  N1    C2   C1    103.70  3.000
 ABX  HN1   N1   C3    108.54  3.000
 ABX  HN1   N1   C2    109.16  3.000
 ABX  C3    N1   C2    106.13  3.000
 ABX  H3    C3   C5    107.68  3.000
 ABX  H3    C3   C4    110.47  3.000
 ABX  C5    C3   C4    110.45  3.000
 ABX  H3    C3   N1    109.95  3.000
 ABX  C5    C3   N1    110.91  3.000
 ABX  C4    C3   N1    107.40  3.000
 ABX  H42   C4   H41   107.25  3.000
 ABX  H42   C4   C3    111.71  3.000
 ABX  H41   C4   C3    111.73  3.000
 ABX  H42   C4   C1    112.12  3.000
 ABX  H41   C4   C1    110.71  3.000
 ABX  C3    C4   C1    103.39  3.000
 ABX  O2    C5   O1    123.52  3.000
 ABX  O2    C5   C3    125.64  3.000
 ABX  O1    C5   C3    110.84  3.000
 ABX  HO1   O1   C5    110.11  3.000
 ABX  HN2   N2   C8    116.99  3.000
 ABX  HN2   N2   C6    117.88  3.000
 ABX  C8    N2   C6    124.64  3.000
 ABX  O3    C6   C7    121.81  3.000
 ABX  O3    C6   N2    123.18  3.000
 ABX  C7    C6   N2    115.01  3.000
 ABX  H73   C7   H72   107.36  3.000
 ABX  H73   C7   H71   108.78  3.000
 ABX  H72   C7   H71   107.96  3.000
 ABX  H73   C7   C6    109.78  3.000
 ABX  H72   C7   C6    109.06  3.000
 ABX  H71   C7   C6    113.71  3.000
 ABX  H8    C8   C9    110.20  3.000
 ABX  H8    C8   N2    106.52  3.000
 ABX  C9    C8   N2    107.98  3.000
 ABX  H8    C8   C2    108.55  3.000
 ABX  C9    C8   C2    112.57  3.000
 ABX  N2    C8   C2    110.84  3.000
 ABX  H92   C9   H91   106.19  3.000
 ABX  H92   C9   C10   108.67  3.000
 ABX  H91   C9   C10   108.61  3.000
 ABX  H92   C9   C8    107.73  3.000
 ABX  H91   C9   C8    108.08  3.000
 ABX  C10   C9   C8    117.05  3.000
 ABX  H10   C10  C12   108.50  3.000
 ABX  H10   C10  C11   108.33  3.000
 ABX  C12   C10  C11   110.21  3.000
 ABX  H10   C10  C9    108.59  3.000
 ABX  C12   C10  C9    109.36  3.000
 ABX  C11   C10  C9    111.77  3.000
 ABX  H113  C11  H112  107.25  3.000
 ABX  H113  C11  H111  107.70  3.000
 ABX  H112  C11  H111  107.56  3.000
 ABX  H113  C11  C10   112.37  3.000
 ABX  H112  C11  C10   110.98  3.000
 ABX  H111  C11  C10   110.75  3.000
 ABX  H123  C12  H122  107.63  3.000
 ABX  H123  C12  H121  107.65  3.000
 ABX  H122  C12  H121  107.78  3.000
 ABX  H123  C12  C10   111.01  3.000
 ABX  H122  C12  C10   111.07  3.000
 ABX  H121  C12  C10   111.52  3.000
 ABX  O5    C13  O4    123.34  3.000
 ABX  O5    C13  C1    112.58  3.000
 ABX  O4    C13  C1    124.07  3.000
 ABX  C14   O5   C13   117.45  3.000
 ABX  H143  C14  H142  109.29  3.000
 ABX  H143  C14  H141  109.35  3.000
 ABX  H142  C14  H141  109.12  3.000
 ABX  H143  C14  O5    105.96  3.000
 ABX  H142  C14  O5    111.56  3.000
 ABX  H141  C14  O5    111.49  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
 ABX  CONST_01  HO1   O1   C5   C3   180.00   0.0  0
 ABX  CONST_02  C8    N2   C6   C7   180.00   0.0  0
 ABX  CONST_03  C8    N2   C6   O3     0.00   0.0  0
 ABX  CONST_04  HN2   N2   C6   C7     0.00   0.0  0
 ABX  Var_01    C11   C10  C9   C8    63.84  30.0  3
 ABX  Var_02    H71   C7   C6   N2   -12.84  30.0  3
 ABX  Var_03    H111  C11  C10  C9    59.75  30.0  3
 ABX  Var_04    H121  C12  C10  C9    57.77  30.0  3
 ABX  Var_05    H141  C14  O5   C13  -59.78  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
 ABX  chir_01  C1  C2  C4  C13  negativ
 ABX  chir_02  C2  N1  C1  C8   positiv
 ABX  chir_03  C3  N1  C4  C5   positiv
 ABX  chir_04  C8  N2  C9  C2   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
 ABX  plan-1  N2   0.020
 ABX  plan-1  C6   0.020
 ABX  plan-1  C7   0.020
 ABX  plan-1  O3   0.020
 ABX  plan-1  C8   0.020
 ABX  plan-1  HN2  0.020
 ABX  plan-2  C3   0.020
 ABX  plan-2  C5   0.020
 ABX  plan-2  O1   0.020
 ABX  plan-2  O2   0.020
 ABX  plan-2  HO1  0.020
 ABX  plan-3  C1   0.020
 ABX  plan-3  C13  0.020
 ABX  plan-3  O4   0.020
 ABX  plan-3  O5   0.020

