# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:39:29 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-1-(3-cyclohexylpropanoyl)pyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H]2CCCN2C(=O)CCC3CCCCC3
#
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
 D0F  D0F  '(2~{S})-2-[[(2~{S})-1-(3-cyclohexylpropanoyl)pyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid'  ligand  61  29  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0F
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
 D0F  O22  O  O     0  -0.491   3.0850   -7.8968  25.0351
 D0F  C20  C  C     0   0.536   3.1691   -6.6836  25.1769
 D0F  C21  C  CH2   0  -0.586   2.5170   -5.7215  24.2165
 D0F  C23  C  CH2   0  -0.436   1.0894   -5.4020  24.6810
 D0F  C24  C  CH1   0  -0.225   0.2820   -4.5364  23.7127
 D0F  C29  C  CH2   0  -0.423   0.0011   -5.2400  22.3842
 D0F  C28  C  CH2   0  -0.429  -0.8693   -4.3828  21.4711
 D0F  C27  C  CH2   0  -0.428  -0.2449   -3.0115  21.2342
 D0F  C26  C  CH2   0  -0.429   0.0508   -2.3041  22.5537
 D0F  C25  C  CH2   0  -0.425   0.9178   -3.1686  23.4638
 D0F  N19  N  NT    0  -0.493   3.7975   -6.1549  26.2512
 D0F  C18  C  CH2   0  -0.288   4.0646   -4.7383  26.4991
 D0F  C17  C  CH2   0  -0.475   4.5590   -4.7330  27.9390
 D0F  C16  C  CH2   0  -0.488   5.2987   -6.0612  28.0530
 D0F  C14  C  CH1   0  -0.176   4.4531   -7.0278  27.2085
 D0F  C13  C  C     0   0.555   3.4822   -7.8213  28.0746
 D0F  O15  O  O     0  -0.492   3.8432   -8.8494  28.6271
 D0F  N5   N  NH1   0  -0.641   2.2590   -7.2922  28.2270
 D0F  C1   C  CH1   0  -0.165   1.2399   -7.8985  29.0441
 D0F  C2   C  C     0   0.549  -0.1112   -7.4726  28.5053
 D0F  O4   O  OH1   0  -0.571  -1.0384   -8.3874  28.7036
 D0F  O3   O  O     0  -0.432  -0.3083   -6.4029  27.9840
 D0F  C6   C  CH2   0  -0.528   1.3811   -7.4665  30.5213
 D0F  C7   C  CR6   0   0.134   0.3530   -8.0746  31.4319
 D0F  C12  C  CR16  0  -0.305   0.4500   -9.4114  31.8125
 D0F  C11  C  CR16  0  -0.240  -0.5057   -9.9850  32.6384
 D0F  C10  C  CR16  0  -0.270  -1.5751   -9.2262  33.0987
 D0F  C9   C  CR16  0  -0.240  -1.6794   -7.8927  32.7277
 D0F  C8   C  CR16  0  -0.305  -0.7212   -7.3236  31.8988
 D0F  H1   H  HCH2  0   0.269   2.4943   -6.2036  23.2385
 D0F  H2   H  HCH2  0   0.261   3.1010   -4.8065  24.1114
 D0F  H3   H  HCH2  0   0.230   1.1232   -4.9008  25.6542
 D0F  H4   H  HCH2  0   0.239   0.5541   -6.3419  24.8437
 D0F  H5   H  HCH1  0   0.219  -0.6882   -4.3617  24.1971
 D0F  H6   H  HCH2  0   0.224  -0.4799   -6.2048  22.5712
 D0F  H7   H  HCH2  0   0.210   0.9457   -5.4605  21.8742
 D0F  H8   H  HCH2  0   0.208  -1.8559   -4.2542  21.9302
 D0F  H9   H  HCH2  0   0.225  -1.0352   -4.8943  20.5198
 D0F  H10  H  HCH2  0   0.225  -0.9054   -2.3975  20.6165
 D0F  H11  H  HCH2  0   0.207   0.6868   -3.1277  20.6694
 D0F  H12  H  HCH2  0   0.225   0.5417   -1.3459  22.3668
 D0F  H13  H  HCH2  0   0.208  -0.8929   -2.0746  23.0609
 D0F  H14  H  HCH2  0   0.211   1.9000   -3.2983  22.9954
 D0F  H15  H  HCH2  0   0.223   1.0941   -2.6600  24.4167
 D0F  H16  H  HCH2  0   0.256   4.8336   -4.3622  25.8185
 D0F  H17  H  HCH2  0   0.260   3.1703   -4.1300  26.3670
 D0F  H18  H  HCH2  0   0.265   5.1954   -3.8748  28.1485
 D0F  H19  H  HCH2  0   0.242   3.7152   -4.6974  28.6311
 D0F  H20  H  HCH2  0   0.269   5.4292   -6.4028  29.0793
 D0F  H21  H  HCH2  0   0.262   6.2915   -5.9779  27.6084
 D0F  H22  H  HCH1  0   0.289   5.0851   -7.7616  26.7041
 D0F  H23  H  HNH1  0   0.399   2.0264   -6.4354  27.7482
 D0F  H24  H  HCH1  0   0.293   1.3306   -8.9844  28.9773
 D0F  H25  H  HOH1  0   0.487  -1.9029   -8.0648  28.4044
 D0F  H26  H  HCH2  0   0.278   2.3832   -7.7604  30.8403
 D0F  H27  H  HCH2  0   0.262   1.3366   -6.3762  30.5710
 D0F  H28  H  HCR6  0   0.249   1.2823  -10.0099  31.4592
 D0F  H29  H  HCR6  0   0.255  -0.4133  -11.0240  32.9275
 D0F  H30  H  HCR6  0   0.255  -2.3201   -9.6721  33.7450
 D0F  H31  H  HCR6  0   0.255  -2.5057   -7.2925  33.0870
 D0F  H32  H  HCR6  0   0.250  -0.8109   -6.2815  31.6138

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
 D0F  C27  C26  single    1.526  0.020  1.526
 D0F  C27  C28  single    1.525  0.020  1.525
 D0F  C26  C25  single    1.526  0.020  1.526
 D0F  C28  C29  single    1.525  0.020  1.525
 D0F  C25  C24  single    1.529  0.020  1.529
 D0F  C29  C24  single    1.529  0.020  1.529
 D0F  C24  C23  single    1.529  0.020  1.529
 D0F  C23  C21  single    1.535  0.020  1.535
 D0F  C21  C20  single    1.508  0.020  1.508
 D0F  C20  O22  double    1.224  0.020  1.224
 D0F  C20  N19  single    1.352  0.020  1.352
 D0F  N19  C14  single    1.452  0.020  1.452
 D0F  N19  C18  single    1.463  0.020  1.463
 D0F  C14  C13  single    1.524  0.020  1.524
 D0F  C14  C16  single    1.537  0.020  1.537
 D0F  C18  C17  single    1.522  0.020  1.522
 D0F  C13  O15  double    1.222  0.020  1.222
 D0F  C13  N5   single    1.341  0.020  1.341
 D0F  N5   C1   single    1.440  0.020  1.440
 D0F  C16  C17  single    1.525  0.020  1.525
 D0F  O3   C2   double    1.206  0.020  1.206
 D0F  C1   C2   single    1.516  0.020  1.516
 D0F  C1   C6   single    1.546  0.020  1.546
 D0F  C2   O4   single    1.318  0.020  1.318
 D0F  C6   C7   single    1.502  0.020  1.502
 D0F  C7   C12  aromatic  1.393  0.020  1.393
 D0F  C7   C8   aromatic  1.391  0.020  1.391
 D0F  C12  C11  aromatic  1.387  0.020  1.387
 D0F  C8   C9   aromatic  1.389  0.020  1.389
 D0F  C11  C10  aromatic  1.390  0.020  1.390
 D0F  C9   C10  aromatic  1.388  0.020  1.388
 D0F  C21  H1   single    0.970  0.020  1.090
 D0F  C21  H2   single    0.970  0.020  1.090
 D0F  C23  H3   single    0.970  0.020  1.090
 D0F  C23  H4   single    0.970  0.020  1.090
 D0F  C24  H5   single    0.970  0.020  1.090
 D0F  C29  H6   single    0.970  0.020  1.090
 D0F  C29  H7   single    0.970  0.020  1.090
 D0F  C28  H8   single    0.970  0.020  1.090
 D0F  C28  H9   single    0.970  0.020  1.090
 D0F  C27  H10  single    0.970  0.020  1.090
 D0F  C27  H11  single    0.970  0.020  1.090
 D0F  C26  H12  single    0.970  0.020  1.090
 D0F  C26  H13  single    0.970  0.020  1.090
 D0F  C25  H14  single    0.970  0.020  1.090
 D0F  C25  H15  single    0.970  0.020  1.090
 D0F  C18  H16  single    0.970  0.020  1.090
 D0F  C18  H17  single    0.970  0.020  1.090
 D0F  C17  H18  single    0.970  0.020  1.090
 D0F  C17  H19  single    0.970  0.020  1.090
 D0F  C16  H20  single    0.970  0.020  1.090
 D0F  C16  H21  single    0.970  0.020  1.090
 D0F  C14  H22  single    0.970  0.020  1.090
 D0F  N5   H23  single    0.860  0.020  1.020
 D0F  C1   H24  single    0.970  0.020  1.090
 D0F  O4   H25  single    0.850  0.020  0.980
 D0F  C6   H26  single    0.970  0.020  1.090
 D0F  C6   H27  single    0.970  0.020  1.090
 D0F  C12  H28  single    0.930  0.020  1.080
 D0F  C11  H29  single    0.930  0.020  1.080
 D0F  C10  H30  single    0.930  0.020  1.080
 D0F  C9   H31  single    0.930  0.020  1.080
 D0F  C8   H32  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
 D0F  N19  C20  C21  117.23  3.000
 D0F  N19  C20  O22  120.75  3.000
 D0F  C21  C20  O22  121.93  3.000
 D0F  H2   C21  H1   107.20  3.000
 D0F  H2   C21  C23  110.65  3.000
 D0F  H1   C21  C23  110.12  3.000
 D0F  H2   C21  C20  111.41  3.000
 D0F  H1   C21  C20  107.35  3.000
 D0F  C23  C21  C20  110.02  3.000
 D0F  H4   C23  H3   106.03  3.000
 D0F  H4   C23  C24  108.80  3.000
 D0F  H3   C23  C24  108.66  3.000
 D0F  H4   C23  C21  108.74  3.000
 D0F  H3   C23  C21  109.60  3.000
 D0F  C24  C23  C21  114.66  3.000
 D0F  H5   C24  C25  107.27  3.000
 D0F  H5   C24  C29  107.10  3.000
 D0F  C25  C24  C29  110.28  3.000
 D0F  H5   C24  C23  106.09  3.000
 D0F  C29  C24  C23  112.74  3.000
 D0F  C25  C24  C23  112.95  3.000
 D0F  H7   C29  H6   106.33  3.000
 D0F  H7   C29  C28  109.05  3.000
 D0F  H6   C29  C28  110.31  3.000
 D0F  H7   C29  C24  109.79  3.000
 D0F  H6   C29  C24  109.75  3.000
 D0F  C28  C29  C24  111.49  3.000
 D0F  H9   C28  H8   106.43  3.000
 D0F  H9   C28  C27  110.35  3.000
 D0F  H8   C28  C27  109.15  3.000
 D0F  H9   C28  C29  110.17  3.000
 D0F  H8   C28  C29  109.21  3.000
 D0F  C27  C28  C29  111.39  3.000
 D0F  H11  C27  H10  106.38  3.000
 D0F  H11  C27  C26  109.28  3.000
 D0F  H10  C27  C26  110.21  3.000
 D0F  H11  C27  C28  109.43  3.000
 D0F  H10  C27  C28  110.21  3.000
 D0F  C26  C27  C28  111.21  3.000
 D0F  H13  C26  H12  106.40  3.000
 D0F  H13  C26  C25  109.39  3.000
 D0F  H12  C26  C25  110.09  3.000
 D0F  H13  C26  C27  109.30  3.000
 D0F  H12  C26  C27  110.22  3.000
 D0F  C25  C26  C27  111.30  3.000
 D0F  H15  C25  H14  106.42  3.000
 D0F  H15  C25  C26  110.34  3.000
 D0F  H14  C25  C26  108.75  3.000
 D0F  H15  C25  C24  109.94  3.000
 D0F  H14  C25  C24  109.66  3.000
 D0F  C26  C25  C24  111.58  3.000
 D0F  C14  N19  C18  112.84  3.000
 D0F  C18  N19  C20  126.73  3.000
 D0F  C14  N19  C20  119.91  3.000
 D0F  H17  C18  H16  108.05  3.000
 D0F  H17  C18  C17  112.28  3.000
 D0F  H16  C18  C17  111.04  3.000
 D0F  H17  C18  N19  111.73  3.000
 D0F  H16  C18  N19  110.86  3.000
 D0F  C17  C18  N19  102.88  3.000
 D0F  H19  C17  H18  107.70  3.000
 D0F  H19  C17  C16  110.85  3.000
 D0F  H18  C17  C16  112.88  3.000
 D0F  H19  C17  C18  110.40  3.000
 D0F  H18  C17  C18  112.00  3.000
 D0F  C16  C17  C18  103.02  3.000
 D0F  H21  C16  H20  107.39  3.000
 D0F  H21  C16  C14  108.95  3.000
 D0F  H20  C16  C14  112.73  3.000
 D0F  H21  C16  C17  110.15  3.000
 D0F  H20  C16  C17  113.68  3.000
 D0F  C14  C16  C17  103.88  3.000
 D0F  H22  C14  C13  106.34  3.000
 D0F  H22  C14  C16  110.98  3.000
 D0F  C13  C14  C16  111.44  3.000
 D0F  H22  C14  N19  111.15  3.000
 D0F  C16  C14  N19  103.45  3.000
 D0F  C13  C14  N19  113.58  3.000
 D0F  N5   C13  O15  123.37  3.000
 D0F  N5   C13  C14  116.11  3.000
 D0F  O15  C13  C14  120.46  3.000
 D0F  H23  N5   C1   117.63  3.000
 D0F  H23  N5   C13  119.44  3.000
 D0F  C1   N5   C13  122.93  3.000
 D0F  H24  C1   C6   109.20  3.000
 D0F  H24  C1   C2   109.38  3.000
 D0F  C6   C1   C2   110.04  3.000
 D0F  H24  C1   N5   108.98  3.000
 D0F  C6   C1   N5   111.10  3.000
 D0F  C2   C1   N5   108.11  3.000
 D0F  O3   C2   O4   124.46  3.000
 D0F  O4   C2   C1   112.26  3.000
 D0F  O3   C2   C1   123.27  3.000
 D0F  H25  O4   C2   110.48  3.000
 D0F  H27  C6   H26  107.03  3.000
 D0F  H27  C6   C7   110.41  3.000
 D0F  H26  C6   C7   110.00  3.000
 D0F  H27  C6   C1   108.59  3.000
 D0F  H26  C6   C1   106.72  3.000
 D0F  C7   C6   C1   113.81  3.000
 D0F  C8   C7   C12  118.68  3.000
 D0F  C8   C7   C6   120.88  3.000
 D0F  C12  C7   C6   120.43  3.000
 D0F  H28  C12  C11  119.65  3.000
 D0F  H28  C12  C7   119.60  3.000
 D0F  C11  C12  C7   120.75  3.000
 D0F  H29  C11  C10  120.09  3.000
 D0F  H29  C11  C12  119.80  3.000
 D0F  C10  C11  C12  120.11  3.000
 D0F  H30  C10  C9   120.24  3.000
 D0F  H30  C10  C11  120.16  3.000
 D0F  C9   C10  C11  119.60  3.000
 D0F  H31  C9   C8   119.83  3.000
 D0F  H31  C9   C10  120.09  3.000
 D0F  C8   C9   C10  120.08  3.000
 D0F  H32  C8   C9   119.59  3.000
 D0F  H32  C8   C7   119.64  3.000
 D0F  C9   C8   C7   120.78  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
 D0F  CONST_01  C10  C11  C12  C7      0.00   0.0  0
 D0F  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 D0F  CONST_03  C9   C8   C7   C12     0.00   0.0  0
 D0F  CONST_04  C9   C10  C11  C12     0.00   0.0  0
 D0F  CONST_05  C8   C7   C12  C11     0.00   0.0  0
 D0F  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 D0F  CONST_07  C11  C12  C7   C6    180.00   0.0  0
 D0F  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 D0F  CONST_09  H29  C11  C12  C7    180.00   0.0  0
 D0F  CONST_10  H31  C9   C8   C7    180.00   0.0  0
 D0F  CONST_11  H32  C8   C7   C12   180.00   0.0  0
 D0F  CONST_12  H30  C10  C11  C12   180.00   0.0  0
 D0F  CONST_13  H28  C12  C11  C10   180.00   0.0  0
 D0F  CONST_14  C14  N19  C20  O22     0.00   0.0  0
 D0F  CONST_15  C18  N19  C20  O22   180.00   0.0  0
 D0F  CONST_16  C14  N19  C20  C21   180.00   0.0  0
 D0F  CONST_17  C18  N19  C20  C21     0.00   0.0  0
 D0F  CONST_18  C1   N5   C13  C14   180.00   0.0  0
 D0F  CONST_19  H23  N5   C13  C14     0.00   0.0  0
 D0F  CONST_20  C1   N5   C13  O15     0.00   0.0  0
 D0F  CONST_21  H25  O4   C2   C1    180.00   0.0  0
 D0F  Var_01    C27  C26  C25  C24   -55.71  30.0  1
 D0F  Var_02    C27  C28  C29  C24    55.76  30.0  1
 D0F  Var_03    C26  C27  C28  C29   -54.86  30.0  1
 D0F  Var_04    C25  C26  C27  C28    54.78  30.0  1
 D0F  Var_05    C16  C17  C18  N19    33.42  30.0  1
 D0F  Var_06    C14  C16  C17  C18   -37.08  30.0  1
 D0F  Var_07    C14  N19  C18  C17   -17.97  30.0  1
 D0F  Var_08    C12  C7   C6   C1     74.92  30.0  2
 D0F  Var_09    C24  C23  C21  C20  -174.54  30.0  2
 D0F  Var_10    N19  C20  C21  C23   -86.83  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
 D0F  chir_01  C24  C25  C29  C23  negativ
 D0F  chir_02  C14  N19  C13  C16  positiv
 D0F  chir_03  C1   N5   C2   C6   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
 D0F  plan-1  O22  0.020
 D0F  plan-1  C20  0.020
 D0F  plan-1  C21  0.020
 D0F  plan-1  N19  0.020
 D0F  plan-1  C18  0.020
 D0F  plan-1  C14  0.020
 D0F  plan-2  C6   0.020
 D0F  plan-2  C7   0.020
 D0F  plan-2  C12  0.020
 D0F  plan-2  C11  0.020
 D0F  plan-2  C10  0.020
 D0F  plan-2  C9   0.020
 D0F  plan-2  C8   0.020
 D0F  plan-2  H28  0.020
 D0F  plan-2  H29  0.020
 D0F  plan-2  H30  0.020
 D0F  plan-2  H31  0.020
 D0F  plan-2  H32  0.020
 D0F  plan-3  C14  0.020
 D0F  plan-3  C13  0.020
 D0F  plan-3  O15  0.020
 D0F  plan-3  N5   0.020
 D0F  plan-3  C1   0.020
 D0F  plan-3  H23  0.020
 D0F  plan-4  C1   0.020
 D0F  plan-4  C2   0.020
 D0F  plan-4  O4   0.020
 D0F  plan-4  O3   0.020
 D0F  plan-4  H25  0.020

