FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Y7ML2

Calculation Name: 2OGR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: [(4z)-4-(4-hydroxybenzylidene)-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1h-imidazol-1-yl]acetic acid | phenylalanine amide

Ligand 3-letter code: CH7 | NFA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2OGR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9U6Y4

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2857848.278599
FMO2-HF: Nuclear repulsion 2766185.155398
FMO2-HF: Total energy -91663.123201
FMO2-MP2: Total energy -91921.634197


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:6:HIS)


Summations of interaction energy for fragment #1(A:6:HIS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-15.527-6.12914.226-8.589-15.033-0.08
Interaction energy analysis for fragmet #1(A:6:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.921
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A8LEU00.0290.0162.9976.72610.8210.122-1.704-2.513-0.004
4A9LYS10.9380.9584.76625.81825.876-0.001-0.014-0.0430.000
33A38PHE00.020-0.0124.579-1.282-1.121-0.001-0.006-0.1540.000
77A84LYS10.8510.9272.43030.72931.5280.424-0.276-0.948-0.001
78A85ASN0-0.038-0.0221.907-34.599-34.12910.936-4.442-6.963-0.050
79A86SER0-0.050-0.0163.6724.1434.0490.0180.470-0.3930.000
80A87CYS0-0.0650.0092.1485.4926.0661.349-0.644-1.2790.000
81A88PRO0-0.016-0.0312.583-13.187-9.9281.380-1.970-2.669-0.025
82A89ALA00.030-0.0015.1974.4754.551-0.001-0.003-0.0710.000
5A10GLU-1-0.824-0.9257.458-25.729-25.7290.0000.0000.0000.000
6A11GLU-1-0.858-0.90110.342-17.122-17.1220.0000.0000.0000.000
7A12MET0-0.104-0.0167.650-3.667-3.6670.0000.0000.0000.000
8A13THR00.0670.04111.9061.5451.5450.0000.0000.0000.000
9A14MET0-0.045-0.01813.054-2.262-2.2620.0000.0000.0000.000
10A15LYS10.8880.95415.18117.32817.3280.0000.0000.0000.000
11A16TYR0-0.006-0.00316.096-1.082-1.0820.0000.0000.0000.000
12A17HIS0-0.040-0.03319.5920.3130.3130.0000.0000.0000.000
13A18MET0-0.023-0.00621.436-0.462-0.4620.0000.0000.0000.000
14A19GLU-1-0.840-0.88924.036-10.649-10.6490.0000.0000.0000.000
15A20GLY00.020-0.01126.728-0.356-0.3560.0000.0000.0000.000
16A21CYS-1-0.790-0.78929.361-8.504-8.5040.0000.0000.0000.000
17A22VAL00.0330.01631.688-0.230-0.2300.0000.0000.0000.000
18A23ASN0-0.050-0.04334.2790.0910.0910.0000.0000.0000.000
19A24GLY00.0340.00736.7380.2420.2420.0000.0000.0000.000
20A25HIS0-0.064-0.04235.3810.2220.2220.0000.0000.0000.000
21A26LYS10.7640.80033.9528.5158.5150.0000.0000.0000.000
22A27PHE0-0.012-0.01727.9160.1290.1290.0000.0000.0000.000
23A28VAL00.0380.02527.616-0.299-0.2990.0000.0000.0000.000
24A29ILE0-0.019-0.00825.3620.2400.2400.0000.0000.0000.000
25A30THR0-0.013-0.00124.077-0.407-0.4070.0000.0000.0000.000
26A31GLY00.0420.00722.7670.3850.3850.0000.0000.0000.000
27A32GLU-1-0.931-0.95619.791-14.243-14.2430.0000.0000.0000.000
28A33GLY00.0820.03618.7620.4650.4650.0000.0000.0000.000
29A34ILE00.0090.00116.127-0.915-0.9150.0000.0000.0000.000
30A35GLY00.0290.00514.0560.7540.7540.0000.0000.0000.000
31A36TYR0-0.057-0.05112.143-1.011-1.0110.0000.0000.0000.000
32A37PRO0-0.046-0.0237.4640.3850.3850.0000.0000.0000.000
34A39LYS10.8960.9539.62122.05322.0530.0000.0000.0000.000
35A40GLY00.0310.02512.0401.4601.4600.0000.0000.0000.000
36A41LYS10.9340.98213.51716.77816.7780.0000.0000.0000.000
37A42GLN00.024-0.00314.639-1.747-1.7470.0000.0000.0000.000
38A43THR0-0.028-0.01416.6310.7020.7020.0000.0000.0000.000
39A44ILE0-0.023-0.01018.243-0.556-0.5560.0000.0000.0000.000
40A45ASN0-0.042-0.02721.0110.8940.8940.0000.0000.0000.000
41A46LEU0-0.015-0.00322.520-0.430-0.4300.0000.0000.0000.000
42A47CYS0-0.023-0.02225.7850.6130.6130.0000.0000.0000.000
43A48VAL00.0000.00528.515-0.254-0.2540.0000.0000.0000.000
44A49ILE0-0.054-0.02928.5310.2380.2380.0000.0000.0000.000
45A50GLU-1-0.909-0.95231.884-9.155-9.1550.0000.0000.0000.000
46A51GLY00.0380.01733.049-0.200-0.2000.0000.0000.0000.000
47A52GLY0-0.0050.02135.661-0.020-0.0200.0000.0000.0000.000
48A53PRO0-0.036-0.02736.1080.1590.1590.0000.0000.0000.000
49A54LEU00.0440.02531.3860.1080.1080.0000.0000.0000.000
50A55PRO0-0.022-0.00836.0970.1150.1150.0000.0000.0000.000
51A56PHE00.020-0.00431.4660.1740.1740.0000.0000.0000.000
52A57SER0-0.026-0.03133.687-0.157-0.1570.0000.0000.0000.000
53A58GLU-1-0.795-0.90329.863-9.472-9.4720.0000.0000.0000.000
54A59ASP-1-0.791-0.84328.923-10.363-10.3630.0000.0000.0000.000
55A60ILE0-0.006-0.00728.059-0.414-0.4140.0000.0000.0000.000
56A61LEU0-0.0030.00926.504-0.336-0.3360.0000.0000.0000.000
57A62SER00.0050.00724.334-0.528-0.5280.0000.0000.0000.000
58A63ALA00.0010.00422.426-0.695-0.6950.0000.0000.0000.000
59A64GLY00.0260.00222.016-0.313-0.3130.0000.0000.0000.000
60A65PHE00.0270.00118.805-0.274-0.2740.0000.0000.0000.000
61A66TYR00.0010.00617.047-0.567-0.5670.0000.0000.0000.000
62A69ASP-1-0.725-0.84110.907-25.991-25.9910.0000.0000.0000.000
63A70ARG10.8200.88511.64219.25619.2560.0000.0000.0000.000
64A71ILE00.0050.0126.370-2.128-2.1280.0000.0000.0000.000
65A72PHE0-0.024-0.0098.400-2.332-2.3320.0000.0000.0000.000
66A73THR0-0.017-0.0109.9012.9812.9810.0000.0000.0000.000
67A74GLU-1-0.951-0.9579.822-20.953-20.9530.0000.0000.0000.000
68A75TYR00.008-0.0378.5430.7620.7620.0000.0000.0000.000
69A76PRO00.0030.02610.625-0.988-0.9880.0000.0000.0000.000
70A77GLN0-0.022-0.0409.865-1.807-1.8070.0000.0000.0000.000
71A78ASP-1-0.897-0.93910.290-19.545-19.5450.0000.0000.0000.000
72A79ILE0-0.025-0.00511.3270.6950.6950.0000.0000.0000.000
73A80VAL0-0.049-0.0316.432-2.391-2.3910.0000.0000.0000.000
74A81ASP-1-0.730-0.8595.172-34.942-34.9420.0000.0000.0000.000
75A82TYR0-0.022-0.0445.325-5.858-5.8580.0000.0000.0000.000
76A83PHE00.0160.0197.138-1.054-1.0540.0000.0000.0000.000
83A90GLY00.0230.0186.6002.8052.8050.0000.0000.0000.000
84A91TYR0-0.066-0.0767.8451.1891.1890.0000.0000.0000.000
85A92THR0-0.016-0.00310.7471.1881.1880.0000.0000.0000.000
86A93TRP0-0.041-0.02414.412-0.270-0.2700.0000.0000.0000.000
87A94GLY00.0510.04016.8080.4320.4320.0000.0000.0000.000
88A95ARG10.8200.92018.18214.60714.6070.0000.0000.0000.000
89A96SER0-0.024-0.00922.7460.4510.4510.0000.0000.0000.000
90A97PHE0-0.006-0.02023.678-0.321-0.3210.0000.0000.0000.000
91A98LEU00.0160.00728.5520.3240.3240.0000.0000.0000.000
92A99PHE00.0460.00330.462-0.200-0.2000.0000.0000.0000.000
93A100GLU-1-0.848-0.92034.158-8.078-8.0780.0000.0000.0000.000
94A101ASP-1-0.855-0.92137.172-8.035-8.0350.0000.0000.0000.000
95A102GLY0-0.0010.00338.1060.1690.1690.0000.0000.0000.000
96A103ALA0-0.0200.01035.587-0.007-0.0070.0000.0000.0000.000
97A104VAL00.001-0.00532.116-0.215-0.2150.0000.0000.0000.000
98A105CYS0-0.055-0.00128.9320.1270.1270.0000.0000.0000.000
99A106ILE0-0.025-0.01525.607-0.179-0.1790.0000.0000.0000.000
100A107CYS0-0.0340.01821.7210.1840.1840.0000.0000.0000.000
101A108ASN0-0.035-0.01120.782-0.646-0.6460.0000.0000.0000.000
102A109VAL00.0100.00816.1340.2630.2630.0000.0000.0000.000
103A110ASP-1-0.893-0.92814.616-19.763-19.7630.0000.0000.0000.000
104A111ILE00.0170.00910.1090.2960.2960.0000.0000.0000.000
105A112THR00.0060.0079.818-1.239-1.2390.0000.0000.0000.000
106A113VAL0-0.0030.0045.8180.8360.8360.0000.0000.0000.000
107A114SER0-0.033-0.0188.885-0.686-0.6860.0000.0000.0000.000
108A115VAL00.009-0.0186.4920.1410.1410.0000.0000.0000.000
109A116LYS10.9170.9569.39219.77019.7700.0000.0000.0000.000
110A117GLU-1-0.764-0.84913.004-17.187-17.1870.0000.0000.0000.000
111A118ASN0-0.053-0.03110.087-1.878-1.8780.0000.0000.0000.000
112A119CYS0-0.0200.01811.8380.7920.7920.0000.0000.0000.000
113A120ILE0-0.012-0.0148.286-1.268-1.2680.0000.0000.0000.000
114A121TYR0-0.016-0.04111.5372.2202.2200.0000.0000.0000.000
115A122HIS10.8050.88412.47319.63919.6390.0000.0000.0000.000
116A123LYS10.9670.98315.85915.77015.7700.0000.0000.0000.000
117A124SER00.008-0.02018.842-0.541-0.5410.0000.0000.0000.000
118A125ILE0-0.021-0.00321.0550.4340.4340.0000.0000.0000.000
119A126PHE00.0460.00024.301-0.216-0.2160.0000.0000.0000.000
120A127ASN0-0.029-0.01326.4780.6040.6040.0000.0000.0000.000
121A128GLY00.0430.00429.893-0.212-0.2120.0000.0000.0000.000
122A129MET0-0.016-0.00932.3390.2060.2060.0000.0000.0000.000
123A130ASN00.0630.01336.0260.0010.0010.0000.0000.0000.000
124A131PHE00.0190.02532.3320.0370.0370.0000.0000.0000.000
125A132PRO00.0520.03038.4730.1420.1420.0000.0000.0000.000
126A133ALA00.0130.00541.841-0.091-0.0910.0000.0000.0000.000
127A134ASP-1-0.895-0.96744.028-6.679-6.6790.0000.0000.0000.000
128A135GLY00.0490.03641.1330.0290.0290.0000.0000.0000.000
129A136PRO0-0.001-0.00337.770-0.004-0.0040.0000.0000.0000.000
130A137VAL00.0140.00834.606-0.070-0.0700.0000.0000.0000.000
131A138MET0-0.0060.00337.032-0.187-0.1870.0000.0000.0000.000
132A139LYS10.8720.94839.7156.9076.9070.0000.0000.0000.000
133A140LYS10.8580.94237.4288.1908.1900.0000.0000.0000.000
134A141MET00.0310.01838.781-0.014-0.0140.0000.0000.0000.000
135A142THR0-0.034-0.01933.8210.0800.0800.0000.0000.0000.000
136A143THR0-0.076-0.04334.2850.0810.0810.0000.0000.0000.000
137A144ASN00.0720.02829.329-0.553-0.5530.0000.0000.0000.000
138A145TRP0-0.013-0.01326.4630.2430.2430.0000.0000.0000.000
139A146GLU-1-0.819-0.88328.282-9.495-9.4950.0000.0000.0000.000
140A147ALA0-0.061-0.02925.300-0.396-0.3960.0000.0000.0000.000
141A148SER00.013-0.00823.4320.1610.1610.0000.0000.0000.000
142A149CYS0-0.025-0.02221.816-0.715-0.7150.0000.0000.0000.000
143A150GLU-1-0.769-0.83918.075-15.735-15.7350.0000.0000.0000.000
144A151LYS10.8840.95019.47011.89111.8910.0000.0000.0000.000
145A152ILE0-0.0010.00714.135-0.006-0.0060.0000.0000.0000.000
146A153MET00.006-0.01017.5960.4070.4070.0000.0000.0000.000
147A154PRO00.0150.02314.893-0.194-0.1940.0000.0000.0000.000
148A155VAL00.0280.00816.5901.0301.0300.0000.0000.0000.000
149A156PRO00.017-0.00716.643-0.366-0.3660.0000.0000.0000.000
150A157LYS10.9450.96717.48311.55911.5590.0000.0000.0000.000
151A158GLN0-0.009-0.00718.5230.6130.6130.0000.0000.0000.000
152A159GLY00.0240.02614.348-0.318-0.3180.0000.0000.0000.000
153A160ILE0-0.050-0.00713.677-1.333-1.3330.0000.0000.0000.000
154A161LEU00.0140.00312.1020.2590.2590.0000.0000.0000.000
155A162LYS10.9360.97015.74113.15813.1580.0000.0000.0000.000
156A163GLY00.0170.01218.294-0.588-0.5880.0000.0000.0000.000
157A164ASP-1-0.897-0.93019.516-11.244-11.2440.0000.0000.0000.000
158A165VAL00.0530.00722.247-0.265-0.2650.0000.0000.0000.000
159A166SER00.0500.04424.4770.3250.3250.0000.0000.0000.000
160A167MET0-0.0630.00124.357-0.122-0.1220.0000.0000.0000.000
161A168TYR00.0340.00127.9670.4760.4760.0000.0000.0000.000
162A169LEU0-0.030-0.00630.010-0.287-0.2870.0000.0000.0000.000
163A170LEU00.0260.01431.9140.3280.3280.0000.0000.0000.000
164A171LEU00.000-0.00134.391-0.109-0.1090.0000.0000.0000.000
165A172LYS10.8290.88437.7068.2768.2760.0000.0000.0000.000
166A173ASP-1-0.895-0.93440.129-7.398-7.3980.0000.0000.0000.000
167A174GLY0-0.0210.00039.4550.1280.1280.0000.0000.0000.000
168A175GLY0-0.0150.00139.510-0.045-0.0450.0000.0000.0000.000
169A176ARG10.7700.84733.8708.5668.5660.0000.0000.0000.000
170A177TYR0-0.025-0.02234.3450.0580.0580.0000.0000.0000.000
171A178ARG10.8970.93432.0768.8228.8220.0000.0000.0000.000
172A179CYS0-0.061-0.02529.3570.0030.0030.0000.0000.0000.000
173A180GLN0-0.064-0.03326.948-0.073-0.0730.0000.0000.0000.000
174A181PHE0-0.013-0.02022.755-0.066-0.0660.0000.0000.0000.000
175A182ASP-1-0.843-0.90924.119-11.735-11.7350.0000.0000.0000.000
176A183THR0-0.024-0.00918.550-0.003-0.0030.0000.0000.0000.000
177A184VAL0-0.037-0.02018.569-0.009-0.0090.0000.0000.0000.000
178A185TYR0-0.015-0.05013.700-0.494-0.4940.0000.0000.0000.000
179A186LYS10.9430.96714.19017.90017.9000.0000.0000.0000.000
180A187ALA00.0400.0139.356-0.353-0.3530.0000.0000.0000.000
181A188LYS10.7860.87810.26523.78823.7880.0000.0000.0000.000
182A189SER0-0.032-0.0049.1651.0561.0560.0000.0000.0000.000
183A190VAL0-0.006-0.01011.165-0.356-0.3560.0000.0000.0000.000
184A191PRO00.0020.0188.561-1.530-1.5300.0000.0000.0000.000
185A192SER0-0.003-0.0166.3911.5831.5830.0000.0000.0000.000
186A193LYS10.9490.9676.75230.87530.8750.0000.0000.0000.000
187A194MET0-0.0170.0088.833-1.958-1.9580.0000.0000.0000.000
188A195PRO0-0.0190.00410.1100.0970.0970.0000.0000.0000.000
189A196GLU-1-0.827-0.91311.982-14.615-14.6150.0000.0000.0000.000
190A197TRP0-0.022-0.01515.203-0.584-0.5840.0000.0000.0000.000
191A198HIS0-0.0100.00112.893-0.778-0.7780.0000.0000.0000.000
192A199PHE00.016-0.00417.5810.6360.6360.0000.0000.0000.000
193A200ILE00.0060.00513.255-1.004-1.0040.0000.0000.0000.000
194A201GLN0-0.0090.00417.1011.0241.0240.0000.0000.0000.000
195A202HIS10.8140.87317.15314.80814.8080.0000.0000.0000.000
196A203LYS10.9710.98320.42112.07412.0740.0000.0000.0000.000
197A204LEU0-0.0020.01021.777-0.495-0.4950.0000.0000.0000.000
198A205LEU0-0.042-0.02323.3580.5400.5400.0000.0000.0000.000
199A206ARG10.8630.90725.3349.4119.4110.0000.0000.0000.000
200A207GLU-1-0.874-0.91128.001-10.086-10.0860.0000.0000.0000.000
201A208ASP-1-0.809-0.88829.740-9.416-9.4160.0000.0000.0000.000
202A209ARG10.7450.84328.33610.39210.3920.0000.0000.0000.000
203A210SER00.014-0.01132.502-0.013-0.0130.0000.0000.0000.000
204A211ASP-1-0.803-0.88235.033-8.572-8.5720.0000.0000.0000.000
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