# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:51:29 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R,4E)-2-[(naphthalen-2-ylcarbonyl)amino]-5-phenylpent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](C/C=C/c1ccccc1)NC(=O)c2ccc3ccccc3c2
#
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
 JZI  JZI  '(2R,4E)-2-[(naphthalen-2-ylcarbonyl)amino]-5-phenylpent-4-enoic acid'  ligand  45  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JZI
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
 JZI  C1    C  C1    0  -0.288   4.0439  -0.1866  -0.3033
 JZI  C2    C  CR6   0   0.149   4.6210   1.1562  -0.1837
 JZI  C3    C  CR16  0  -0.316   5.9115   1.2874   0.3347
 JZI  C4    C  CR16  0  -0.240   6.5037   2.5343   0.4798
 JZI  C5    C  CR16  0  -0.271   5.8148   3.6786   0.1042
 JZI  C6    C  CR16  0  -0.234   4.5301   3.5636  -0.4168
 JZI  C7    C  CR16  0  -0.327   3.9400   2.3190  -0.5595
 JZI  C8    C  CH1   0  -0.184   1.1553  -2.1305   0.1840
 JZI  C9    C  CH2   0  -0.543   2.3100  -1.9004  -0.8065
 JZI  C10   C  C     0   0.548   0.7299  -3.5929   0.1850
 JZI  O11   O  O     0  -0.428  -0.2968  -4.0060  -0.2850
 JZI  O12   O  OH1   0  -0.590   1.6507  -4.3576   0.7526
 JZI  C13   C  C1    0  -0.199   2.8220  -0.4972  -0.7379
 JZI  C14   C  CR16  0  -0.256  -6.7279   1.0624   0.6770
 JZI  C15   C  CR16  0  -0.252  -6.5714   1.9888  -0.3765
 JZI  C16   C  CR16  0  -0.308  -5.3602   2.1376  -0.9956
 JZI  C17   C  CR16  0  -0.308  -5.6683   0.3035   1.0914
 JZI  C18   C  CR66  0   0.141  -4.4036   0.4359   0.4700
 JZI  C19   C  CR66  0   0.114  -4.2472   1.3660  -0.5897
 JZI  C20   C  CR16  0  -0.300  -2.9786   1.4947  -1.2015
 JZI  C21   C  CR16  0  -0.290  -1.9224   0.7306  -0.7932
 JZI  C22   C  CR6   0  -0.043  -2.0756  -0.2050   0.2591
 JZI  C23   C  CR16  0  -0.341  -3.2927  -0.3309   0.8800
 JZI  N25   N  NH1   0  -0.658   0.0465  -1.2784  -0.1422
 JZI  O26   O  O     0  -0.477  -0.9284  -1.5170   1.8726
 JZI  H1    H  H     0   0.245   4.6999  -0.9964   0.0063
 JZI  H3    H  HCR6  0   0.253   6.4577   0.3983   0.6281
 JZI  H4    H  HCR6  0   0.257   7.5034   2.6106   0.8878
 JZI  H5    H  HCR6  0   0.257   6.2717   4.6531   0.2169
 JZI  H6    H  HCR6  0   0.258   3.9853   4.4512  -0.7121
 JZI  H7    H  HCR6  0   0.249   2.9390   2.2584  -0.9684
 JZI  H8    H  HCH1  0   0.302   1.5131  -1.8839   1.1865
 JZI  H9    H  HCH2  0   0.281   3.1141  -2.6023  -0.5841
 JZI  H9A   H  HCH2  0   0.268   1.9587  -2.1271  -1.8190
 JZI  HO12  H  HOH1  0   0.486   1.3870  -5.2895   0.7134
 JZI  H13   H  H     0   0.252   2.1366   0.2832  -1.0534
 JZI  H15   H  HCR6  0   0.263  -7.4176   2.5850  -0.6923
 JZI  H16   H  HCR6  0   0.260  -5.2413   2.8493  -1.8033
 JZI  H17   H  HCR6  0   0.260  -5.7834  -0.4068   1.9012
 JZI  H20   H  HCR6  0   0.264  -2.8498   2.2158  -1.9993
 JZI  H21   H  HCR6  0   0.256  -0.9592   0.8736  -1.2662
 JZI  H23   H  HCR6  0   0.261  -3.4159  -1.0362   1.6925
 JZI  HN25  H  HNH1  0   0.410  -0.1191  -1.0912  -1.1191
 JZI  C24   C  C     0   0.555  -0.9498  -1.0568   0.7411
 JZI  H14   H  HCR6  0   0.263  -7.6923   0.9569   1.1563

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
 JZI  C1   C13   double    1.334  0.020  1.334
 JZI  C1   C2    single    1.467  0.020  1.467
 JZI  C1   H1    single    0.930  0.020  1.080
 JZI  C7   C2    aromatic  1.399  0.020  1.399
 JZI  C2   C3    aromatic  1.397  0.020  1.397
 JZI  C3   C4    aromatic  1.388  0.020  1.388
 JZI  C3   H3    single    0.930  0.020  1.080
 JZI  C5   C4    aromatic  1.388  0.020  1.388
 JZI  C4   H4    single    0.930  0.020  1.080
 JZI  C6   C5    aromatic  1.391  0.020  1.391
 JZI  C5   H5    single    0.930  0.020  1.080
 JZI  C7   C6    aromatic  1.385  0.020  1.385
 JZI  C6   H6    single    0.930  0.020  1.080
 JZI  C7   H7    single    0.930  0.020  1.080
 JZI  C10  C8    single    1.523  0.020  1.523
 JZI  N25  C8    single    1.436  0.020  1.436
 JZI  C9   C8    single    1.539  0.020  1.539
 JZI  C8   H8    single    0.970  0.020  1.090
 JZI  C9   C13   single    1.495  0.020  1.495
 JZI  C9   H9    single    0.970  0.020  1.090
 JZI  C9   H9A   single    0.970  0.020  1.090
 JZI  O11  C10   double    1.202  0.020  1.202
 JZI  C10  O12   single    1.325  0.020  1.325
 JZI  O12  HO12  single    0.850  0.020  0.980
 JZI  C13  H13   single    0.930  0.020  1.080
 JZI  C14  C17   aromatic  1.368  0.020  1.368
 JZI  C14  C15   aromatic  1.412  0.020  1.412
 JZI  C14  H14   single    0.930  0.020  1.080
 JZI  C15  C16   aromatic  1.368  0.020  1.368
 JZI  C15  H15   single    0.930  0.020  1.080
 JZI  C16  C19   aromatic  1.414  0.020  1.414
 JZI  C16  H16   single    0.930  0.020  1.080
 JZI  C17  C18   aromatic  1.415  0.020  1.415
 JZI  C17  H17   single    0.930  0.020  1.080
 JZI  C18  C23   aromatic  1.411  0.020  1.411
 JZI  C18  C19   aromatic  1.419  0.020  1.419
 JZI  C19  C20   aromatic  1.414  0.020  1.414
 JZI  C20  C21   aromatic  1.366  0.020  1.366
 JZI  C20  H20   single    0.930  0.020  1.080
 JZI  C22  C21   aromatic  1.416  0.020  1.416
 JZI  C21  H21   single    0.930  0.020  1.080
 JZI  C23  C22   aromatic  1.372  0.020  1.372
 JZI  C22  C24   single    1.492  0.020  1.492
 JZI  C23  H23   single    0.930  0.020  1.080
 JZI  N25  C24   single    1.350  0.020  1.350
 JZI  C24  O26   double    1.222  0.020  1.222
 JZI  N25  HN25  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
 JZI  H1    C1   C13  118.18  3.000
 JZI  H1    C1   C2   114.92  3.000
 JZI  C13   C1   C2   126.90  3.000
 JZI  C7    C2   C3   118.12  3.000
 JZI  C3    C2   C1   118.67  3.000
 JZI  C7    C2   C1   123.20  3.000
 JZI  H3    C3   C4   119.58  3.000
 JZI  H3    C3   C2   119.27  3.000
 JZI  C4    C3   C2   121.15  3.000
 JZI  H4    C4   C5   120.16  3.000
 JZI  H4    C4   C3   119.79  3.000
 JZI  C5    C4   C3   120.05  3.000
 JZI  H5    C5   C6   120.23  3.000
 JZI  H5    C5   C4   120.32  3.000
 JZI  C6    C5   C4   119.45  3.000
 JZI  H6    C6   C7   119.63  3.000
 JZI  H6    C6   C5   119.94  3.000
 JZI  C7    C6   C5   120.43  3.000
 JZI  H7    C7   C6   118.89  3.000
 JZI  H7    C7   C2   120.32  3.000
 JZI  C6    C7   C2   120.79  3.000
 JZI  H8    C8   N25  109.11  3.000
 JZI  H8    C8   C10  107.91  3.000
 JZI  N25   C8   C10  110.75  3.000
 JZI  H8    C8   C9   108.13  3.000
 JZI  N25   C8   C9   110.15  3.000
 JZI  C10   C8   C9   110.71  3.000
 JZI  H9A   C9   H9   106.97  3.000
 JZI  H9A   C9   C13  110.27  3.000
 JZI  H9    C9   C13  110.01  3.000
 JZI  H9A   C9   C8   108.86  3.000
 JZI  H9    C9   C8   109.02  3.000
 JZI  C13   C9   C8   111.58  3.000
 JZI  O12   C10  O11  124.25  3.000
 JZI  O12   C10  C8   111.12  3.000
 JZI  O11   C10  C8   124.62  3.000
 JZI  HO12  O12  C10  110.40  3.000
 JZI  H13   C13  C9   116.44  3.000
 JZI  H13   C13  C1   120.38  3.000
 JZI  C9    C13  C1   123.18  3.000
 JZI  H14   C14  C17  120.14  3.000
 JZI  H14   C14  C15  119.57  3.000
 JZI  C17   C14  C15  120.29  3.000
 JZI  H15   C15  C16  120.01  3.000
 JZI  H15   C15  C14  119.51  3.000
 JZI  C16   C15  C14  120.48  3.000
 JZI  H16   C16  C19  119.10  3.000
 JZI  H16   C16  C15  120.40  3.000
 JZI  C19   C16  C15  120.50  3.000
 JZI  H17   C17  C18  118.98  3.000
 JZI  H17   C17  C14  120.53  3.000
 JZI  C18   C17  C14  120.49  3.000
 JZI  C23   C18  C19  119.13  3.000
 JZI  C19   C18  C17  119.19  3.000
 JZI  C23   C18  C17  121.68  3.000
 JZI  C20   C19  C18  118.79  3.000
 JZI  C20   C19  C16  122.16  3.000
 JZI  C18   C19  C16  119.05  3.000
 JZI  H20   C20  C21  120.05  3.000
 JZI  H20   C20  C19  119.06  3.000
 JZI  C21   C20  C19  120.89  3.000
 JZI  H21   C21  C22  120.53  3.000
 JZI  H21   C21  C20  118.91  3.000
 JZI  C22   C21  C20  120.53  3.000
 JZI  C24   C22  C23  118.08  3.000
 JZI  C24   C22  C21  122.39  3.000
 JZI  C23   C22  C21  119.52  3.000
 JZI  H23   C23  C22  120.02  3.000
 JZI  H23   C23  C18  118.85  3.000
 JZI  C22   C23  C18  121.13  3.000
 JZI  HN25  N25  C24  118.84  3.000
 JZI  HN25  N25  C8   117.20  3.000
 JZI  C24   N25  C8   121.24  3.000
 JZI  O26   C24  N25  122.10  3.000
 JZI  O26   C24  C22  121.85  3.000
 JZI  N25   C24  C22  116.06  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
 JZI  CONST_01  C5    C6   C7   C2      0.00   0.0  0
 JZI  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 JZI  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 JZI  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 JZI  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 JZI  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 JZI  CONST_07  C23   C18  C17  C14   180.00   0.0  0
 JZI  CONST_08  C19   C18  C17  C14     0.00   0.0  0
 JZI  CONST_09  C19   C16  C15  C14     0.00   0.0  0
 JZI  CONST_10  C18   C17  C14  C15     0.00   0.0  0
 JZI  CONST_11  C18   C19  C16  C15     0.00   0.0  0
 JZI  CONST_12  C20   C19  C16  C15   180.00   0.0  0
 JZI  CONST_13  C17   C14  C15  C16     0.00   0.0  0
 JZI  CONST_14  C17   C18  C19  C16     0.00   0.0  0
 JZI  CONST_15  C23   C18  C19  C16   180.00   0.0  0
 JZI  CONST_16  C21   C20  C19  C16   180.00   0.0  0
 JZI  CONST_17  C22   C23  C18  C17   180.00   0.0  0
 JZI  CONST_18  C20   C19  C18  C17   180.00   0.0  0
 JZI  CONST_19  C21   C22  C23  C18     0.00   0.0  0
 JZI  CONST_20  C21   C20  C19  C18     0.00   0.0  0
 JZI  CONST_21  C22   C23  C18  C19     0.00   0.0  0
 JZI  CONST_22  C22   C21  C20  C19     0.00   0.0  0
 JZI  CONST_23  C23   C18  C19  C20     0.00   0.0  0
 JZI  CONST_24  C23   C22  C21  C20     0.00   0.0  0
 JZI  CONST_25  C6    C7   C2   C1    180.00   0.0  0
 JZI  CONST_26  C4    C3   C2   C1    180.00   0.0  0
 JZI  CONST_27  C24   C22  C23  C18   180.00   0.0  0
 JZI  CONST_28  C24   C22  C21  C20   180.00   0.0  0
 JZI  CONST_29  H6    C6   C7   C2    180.00   0.0  0
 JZI  CONST_30  H4    C4   C3   C2    180.00   0.0  0
 JZI  CONST_31  H7    C7   C2   C3    180.00   0.0  0
 JZI  CONST_32  H5    C5   C4   C3    180.00   0.0  0
 JZI  CONST_33  H3    C3   C4   C5    180.00   0.0  0
 JZI  CONST_34  H16   C16  C15  C14   180.00   0.0  0
 JZI  CONST_35  H17   C17  C14  C15   180.00   0.0  0
 JZI  CONST_36  H14   C14  C15  C16   180.00   0.0  0
 JZI  CONST_37  H20   C20  C19  C16     0.00   0.0  0
 JZI  CONST_38  H15   C15  C14  C17   180.00   0.0  0
 JZI  CONST_39  H23   C23  C18  C17     0.00   0.0  0
 JZI  CONST_40  H21   C21  C20  C19   180.00   0.0  0
 JZI  CONST_41  C22   C24  N25  C8    180.00   0.0  0
 JZI  CONST_43  O26   C24  N25  C8      0.00   0.0  0
 JZI  CONST_44  HO12  O12  C10  C8    180.00   0.0  0
 JZI  Var_01    C13   C1   C2   C3    178.02  30.0  2
 JZI  Var_02    N25   C24  C22  C21   -24.02  30.0  2
 JZI  Var_03    C9    C13  C1   C2   -179.05   0.0  2
 JZI  Var_04    C8    C9   C13  C1    113.59  30.0  1

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
 JZI  chir_01  C8  C10  N25  C9  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
 JZI  plan-1  C1    0.020
 JZI  plan-1  C2    0.020
 JZI  plan-1  C3    0.020
 JZI  plan-1  C4    0.020
 JZI  plan-1  C5    0.020
 JZI  plan-1  C6    0.020
 JZI  plan-1  C7    0.020
 JZI  plan-1  H3    0.020
 JZI  plan-1  H4    0.020
 JZI  plan-1  H5    0.020
 JZI  plan-1  H6    0.020
 JZI  plan-1  H7    0.020
 JZI  plan-2  C14   0.020
 JZI  plan-2  C15   0.020
 JZI  plan-2  C16   0.020
 JZI  plan-2  C17   0.020
 JZI  plan-2  C18   0.020
 JZI  plan-2  C19   0.020
 JZI  plan-2  C20   0.020
 JZI  plan-2  C21   0.020
 JZI  plan-2  C22   0.020
 JZI  plan-2  C23   0.020
 JZI  plan-2  H15   0.020
 JZI  plan-2  H16   0.020
 JZI  plan-2  H17   0.020
 JZI  plan-2  H20   0.020
 JZI  plan-2  H21   0.020
 JZI  plan-2  H23   0.020
 JZI  plan-2  C24   0.020
 JZI  plan-2  H14   0.020
 JZI  plan-3  C8    0.020
 JZI  plan-3  C22   0.020
 JZI  plan-3  N25   0.020
 JZI  plan-3  O26   0.020
 JZI  plan-3  HN25  0.020
 JZI  plan-3  C24   0.020
 JZI  plan-4  C8    0.020
 JZI  plan-4  C10   0.020
 JZI  plan-4  O11   0.020
 JZI  plan-4  O12   0.020
 JZI  plan-4  HO12  0.020
 JZI  plan-5  C1    0.020
 JZI  plan-5  C2    0.020
 JZI  plan-5  C9    0.020
 JZI  plan-5  C13   0.020
 JZI  plan-5  H1    0.020
 JZI  plan-5  H13   0.020

