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: 4G86N

Calculation Name: 3PIB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: {(4z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio)propanimidoyl]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic acid | glycerol

Ligand 3-letter code: NRQ | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3PIB

Chain ID: A

ChEMBL ID:

UniProt ID: H3JQU4

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2860802.587963
FMO2-HF: Nuclear repulsion 2769576.33535
FMO2-HF: Total energy -91226.252613
FMO2-MP2: Total energy -91487.000852


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
17.34719.608-0.016-0.772-1.471-0.001
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.919
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].
3A3GLU-1-0.866-0.9283.850-46.012-44.129-0.013-0.731-1.138-0.001
4A4LEU00.004-0.0014.7516.6316.777-0.001-0.013-0.1320.000
35A35TYR0-0.010-0.0314.407-4.720-4.627-0.001-0.014-0.0780.000
80A82GLN0-0.043-0.0354.318-2.791-2.652-0.001-0.014-0.1230.000
5A5ILE0-0.046-0.0066.5924.9254.9250.0000.0000.0000.000
6A6LYS10.8930.9356.39830.14030.1400.0000.0000.0000.000
7A7GLU-1-0.855-0.9398.446-31.780-31.7800.0000.0000.0000.000
8A8ASN0-0.023-0.01410.3042.8352.8350.0000.0000.0000.000
9A9MET0-0.0110.03111.261-1.282-1.2820.0000.0000.0000.000
10A10HIS10.9020.93214.16215.92615.9260.0000.0000.0000.000
11A11MET0-0.0330.00417.276-0.838-0.8380.0000.0000.0000.000
12A12LYS10.8550.90019.49213.78813.7880.0000.0000.0000.000
13A13LEU0-0.0280.00922.298-0.460-0.4600.0000.0000.0000.000
14A14TYR0-0.025-0.03724.7080.4830.4830.0000.0000.0000.000
15A15MET00.0110.00626.958-0.294-0.2940.0000.0000.0000.000
16A16GLU-1-0.821-0.86729.383-9.177-9.1770.0000.0000.0000.000
17A17GLY00.0380.00832.117-0.282-0.2820.0000.0000.0000.000
18A18THR0-0.021-0.00134.6240.1750.1750.0000.0000.0000.000
19A19VAL0-0.0080.00136.027-0.210-0.2100.0000.0000.0000.000
20A20ASN0-0.034-0.02738.5870.0930.0930.0000.0000.0000.000
21A21ASN0-0.054-0.05041.8070.0870.0870.0000.0000.0000.000
22A22HIS0-0.0300.00240.0020.2200.2200.0000.0000.0000.000
23A23HIS00.0470.02739.198-0.396-0.3960.0000.0000.0000.000
24A24PHE0-0.008-0.01732.6990.0930.0930.0000.0000.0000.000
25A25LYS10.8470.91733.9628.3908.3900.0000.0000.0000.000
26A26CYS0-0.049-0.01830.5830.2520.2520.0000.0000.0000.000
27A27THR0-0.0120.00128.884-0.181-0.1810.0000.0000.0000.000
28A28SER0-0.011-0.05024.9830.1710.1710.0000.0000.0000.000
29A29GLU-1-0.802-0.85524.219-13.212-13.2120.0000.0000.0000.000
30A30GLY00.002-0.00421.6950.3830.3830.0000.0000.0000.000
31A31GLU-1-0.967-0.98818.404-15.051-15.0510.0000.0000.0000.000
32A32GLY00.0570.02216.6650.7800.7800.0000.0000.0000.000
33A33LYS10.9290.97513.32417.58317.5830.0000.0000.0000.000
34A34PRO0-0.050-0.0239.3160.0910.0910.0000.0000.0000.000
36A36GLU-1-0.857-0.9349.525-19.445-19.4450.0000.0000.0000.000
37A37GLY0-0.040-0.00112.7541.1141.1140.0000.0000.0000.000
38A38THR00.0280.01613.9531.1941.1940.0000.0000.0000.000
39A39GLN00.0410.00516.509-1.440-1.4400.0000.0000.0000.000
40A40THR00.0120.00718.8360.9550.9550.0000.0000.0000.000
41A41MET0-0.0330.02121.285-0.282-0.2820.0000.0000.0000.000
42A42LYS10.9470.98024.10612.15612.1560.0000.0000.0000.000
43A43ILE00.007-0.00626.811-0.210-0.2100.0000.0000.0000.000
44A44LYS10.9590.98329.55410.15610.1560.0000.0000.0000.000
45A45VAL00.0320.00632.615-0.203-0.2030.0000.0000.0000.000
46A46VAL0-0.059-0.02833.6870.1910.1910.0000.0000.0000.000
47A47GLU-1-0.816-0.90536.267-8.012-8.0120.0000.0000.0000.000
48A48GLY00.0480.02837.963-0.159-0.1590.0000.0000.0000.000
49A49GLY00.0180.02939.781-0.027-0.0270.0000.0000.0000.000
50A50PRO0-0.016-0.03340.3590.1390.1390.0000.0000.0000.000
51A51LEU00.0190.03635.4530.0900.0900.0000.0000.0000.000
52A52PRO0-0.0030.00640.1430.0760.0760.0000.0000.0000.000
53A53PHE00.027-0.00135.3120.1360.1360.0000.0000.0000.000
54A54ALA00.0180.01037.581-0.052-0.0520.0000.0000.0000.000
55A55PHE00.025-0.01129.982-0.179-0.1790.0000.0000.0000.000
56A56ASP-1-0.769-0.86332.191-9.527-9.5270.0000.0000.0000.000
57A57ILE0-0.011-0.00331.311-0.312-0.3120.0000.0000.0000.000
58A58LEU0-0.017-0.00430.248-0.272-0.2720.0000.0000.0000.000
59A59ALA0-0.0090.00927.826-0.419-0.4190.0000.0000.0000.000
60A60THR0-0.007-0.00125.773-0.566-0.5660.0000.0000.0000.000
61A61SER0-0.024-0.01424.520-0.499-0.4990.0000.0000.0000.000
62A62PHE00.017-0.02924.046-0.268-0.2680.0000.0000.0000.000
63A63TYR0-0.044-0.02419.686-0.813-0.8130.0000.0000.0000.000
64A66SER00.0180.01817.051-0.410-0.4100.0000.0000.0000.000
65A67LYS10.8800.94514.64116.18116.1810.0000.0000.0000.000
66A68THR00.0260.01210.344-0.911-0.9110.0000.0000.0000.000
67A69PHE0-0.055-0.01710.702-2.794-2.7940.0000.0000.0000.000
68A70ILE00.0080.02111.6801.4781.4780.0000.0000.0000.000
69A71ASN0-0.016-0.00510.288-3.815-3.8150.0000.0000.0000.000
70A72HIS0-0.025-0.0288.1373.3003.3000.0000.0000.0000.000
71A73THR00.004-0.0049.229-1.795-1.7950.0000.0000.0000.000
72A74GLN00.0570.00711.471-0.373-0.3730.0000.0000.0000.000
73A75GLY00.0230.0158.9180.8830.8830.0000.0000.0000.000
74A76ILE0-0.0480.0008.892-0.817-0.8170.0000.0000.0000.000
75A77PRO0-0.071-0.0386.238-2.822-2.8220.0000.0000.0000.000
76A78ASP-1-0.733-0.8525.572-29.441-29.4410.0000.0000.0000.000
77A79PHE00.0330.0076.593-1.994-1.9940.0000.0000.0000.000
78A80PHE00.0010.0129.2910.7670.7670.0000.0000.0000.000
79A81LYS10.8190.8995.75732.91432.9140.0000.0000.0000.000
81A83SER0-0.0100.0086.4471.9411.9410.0000.0000.0000.000
82A84PHE0-0.0360.0239.1742.3262.3260.0000.0000.0000.000
83A85PRO0-0.001-0.0249.382-2.846-2.8460.0000.0000.0000.000
84A86GLU-1-0.835-0.90712.215-22.499-22.4990.0000.0000.0000.000
85A87GLY00.0100.00913.4121.3531.3530.0000.0000.0000.000
86A88PHE0-0.025-0.03412.870-0.390-0.3900.0000.0000.0000.000
87A89THR0-0.0070.00316.0940.7540.7540.0000.0000.0000.000
88A90TRP0-0.062-0.02918.567-0.363-0.3630.0000.0000.0000.000
89A91GLU-1-0.769-0.84220.850-11.732-11.7320.0000.0000.0000.000
90A92ARG10.8680.91921.63012.63712.6370.0000.0000.0000.000
91A93ILE00.0190.02326.1590.2700.2700.0000.0000.0000.000
92A94THR0-0.005-0.01129.055-0.340-0.3400.0000.0000.0000.000
93A95THR0-0.016-0.00830.7830.2970.2970.0000.0000.0000.000
94A96TYR00.021-0.00632.590-0.306-0.3060.0000.0000.0000.000
95A97GLU-1-0.835-0.90936.412-7.744-7.7440.0000.0000.0000.000
96A98ASP-1-0.920-0.96639.212-7.554-7.5540.0000.0000.0000.000
97A99GLY00.0040.00040.3170.1870.1870.0000.0000.0000.000
98A100GLY0-0.0120.00238.759-0.008-0.0080.0000.0000.0000.000
99A101VAL0-0.017-0.00934.293-0.191-0.1910.0000.0000.0000.000
100A102LEU0-0.012-0.01030.1020.1240.1240.0000.0000.0000.000
101A103THR00.0040.00030.492-0.312-0.3120.0000.0000.0000.000
102A104ALA0-0.0030.00127.3180.1120.1120.0000.0000.0000.000
103A105THR0-0.036-0.01725.383-0.190-0.1900.0000.0000.0000.000
104A106GLN00.0150.01919.097-0.004-0.0040.0000.0000.0000.000
105A107ASP-1-0.831-0.89121.097-14.969-14.9690.0000.0000.0000.000
106A108THR00.006-0.00315.559-0.009-0.0090.0000.0000.0000.000
107A109SER00.0260.00816.950-0.262-0.2620.0000.0000.0000.000
108A110LEU00.003-0.00212.005-0.286-0.2860.0000.0000.0000.000
109A111GLN0-0.005-0.01416.1310.6570.6570.0000.0000.0000.000
110A112ASN00.003-0.00418.528-0.184-0.1840.0000.0000.0000.000
111A113GLY00.0160.01614.6470.1920.1920.0000.0000.0000.000
112A114CYS0-0.043-0.00815.217-0.486-0.4860.0000.0000.0000.000
113A115ILE0-0.0050.00013.012-0.222-0.2220.0000.0000.0000.000
114A116ILE0-0.018-0.00816.9011.0201.0200.0000.0000.0000.000
115A117TYR00.002-0.02216.747-0.735-0.7350.0000.0000.0000.000
116A118ASN00.008-0.00121.6200.8400.8400.0000.0000.0000.000
117A119VAL00.006-0.00524.179-0.288-0.2880.0000.0000.0000.000
118A120LYS10.8690.93026.54110.46410.4640.0000.0000.0000.000
119A121ILE0-0.005-0.01428.439-0.226-0.2260.0000.0000.0000.000
120A122ASN00.001-0.00531.6100.3990.3990.0000.0000.0000.000
121A123GLY00.0290.01934.309-0.138-0.1380.0000.0000.0000.000
122A124VAL00.002-0.00736.0690.2280.2280.0000.0000.0000.000
123A125ASN00.0260.00139.159-0.011-0.0110.0000.0000.0000.000
124A126PHE00.0500.04035.4680.0480.0480.0000.0000.0000.000
125A127PRO00.0410.03741.5710.1540.1540.0000.0000.0000.000
126A128SER00.002-0.01844.941-0.051-0.0510.0000.0000.0000.000
127A129ASN0-0.014-0.01947.141-0.037-0.0370.0000.0000.0000.000
128A130GLY00.0440.03444.1830.0460.0460.0000.0000.0000.000
129A131SER0-0.004-0.01241.0790.0630.0630.0000.0000.0000.000
130A132VAL00.0510.03737.693-0.039-0.0390.0000.0000.0000.000
131A133MET0-0.0090.00240.189-0.138-0.1380.0000.0000.0000.000
132A134GLN0-0.011-0.00943.1800.0830.0830.0000.0000.0000.000
133A135LYS10.8300.91740.9357.6937.6930.0000.0000.0000.000
134A136LYS10.9180.97342.1236.7286.7280.0000.0000.0000.000
135A137THR0-0.046-0.03836.8190.0790.0790.0000.0000.0000.000
136A138LEU0-0.020-0.00936.9990.0780.0780.0000.0000.0000.000
137A139GLY00.0230.02432.818-0.169-0.1690.0000.0000.0000.000
138A140TRP0-0.023-0.03029.0610.2350.2350.0000.0000.0000.000
139A141GLU-1-0.801-0.87730.207-9.471-9.4710.0000.0000.0000.000
140A142ALA0-0.053-0.02525.460-0.304-0.3040.0000.0000.0000.000
141A143ASN0-0.005-0.01123.6790.3220.3220.0000.0000.0000.000
142A144THR00.009-0.00721.676-0.368-0.3680.0000.0000.0000.000
143A145GLU-1-0.840-0.87818.873-14.925-14.9250.0000.0000.0000.000
144A146MET00.0070.00020.262-0.404-0.4040.0000.0000.0000.000
145A147LEU0-0.032-0.02315.7630.3400.3400.0000.0000.0000.000
146A148TYR00.0240.01117.286-0.081-0.0810.0000.0000.0000.000
147A149PRO0-0.005-0.00315.3540.2270.2270.0000.0000.0000.000
148A150ALA00.0190.00817.8640.7050.7050.0000.0000.0000.000
149A151ASP-1-0.822-0.88720.474-11.930-11.9300.0000.0000.0000.000
150A152GLY0-0.008-0.00119.9450.0630.0630.0000.0000.0000.000
151A153GLY0-0.024-0.01316.675-0.571-0.5710.0000.0000.0000.000
152A154LEU0-0.049-0.00713.164-0.006-0.0060.0000.0000.0000.000
153A155ARG10.7630.86116.74012.54612.5460.0000.0000.0000.000
154A156GLY00.0410.01519.087-0.595-0.5950.0000.0000.0000.000
155A157HIS0-0.035-0.02020.7930.4520.4520.0000.0000.0000.000
156A158SER00.0480.01723.448-0.521-0.5210.0000.0000.0000.000
157A159GLN00.0020.00325.5390.5660.5660.0000.0000.0000.000
158A160MET0-0.040-0.01526.675-0.384-0.3840.0000.0000.0000.000
159A161ALA00.0340.02230.0910.2920.2920.0000.0000.0000.000
160A162LEU0-0.027-0.01032.691-0.210-0.2100.0000.0000.0000.000
161A163LYS10.8670.93732.2139.8189.8180.0000.0000.0000.000
162A164LEU0-0.007-0.00736.8090.0290.0290.0000.0000.0000.000
163A165VAL0-0.007-0.01540.4430.0350.0350.0000.0000.0000.000
164A166GLY0-0.022-0.01143.2320.1080.1080.0000.0000.0000.000
165A167GLY0-0.026-0.00641.4400.0880.0880.0000.0000.0000.000
166A168GLY00.0030.01341.542-0.034-0.0340.0000.0000.0000.000
167A169TYR0-0.069-0.07235.222-0.115-0.1150.0000.0000.0000.000
168A170LEU0-0.0220.00337.5720.2010.2010.0000.0000.0000.000
169A171HIS0-0.001-0.00933.116-0.238-0.2380.0000.0000.0000.000
170A172CYS0-0.024-0.00831.1690.0140.0140.0000.0000.0000.000
171A173SER0-0.0020.00529.895-0.208-0.2080.0000.0000.0000.000
172A174PHE00.0250.00023.2650.1200.1200.0000.0000.0000.000
173A175LYS10.9360.98525.61110.15810.1580.0000.0000.0000.000
174A176THR00.0120.00521.1390.2240.2240.0000.0000.0000.000
175A177THR0-0.0190.00420.330-0.003-0.0030.0000.0000.0000.000
176A178TYR0-0.001-0.02516.0780.0010.0010.0000.0000.0000.000
177A179ARG10.8170.86317.15712.65412.6540.0000.0000.0000.000
178A180SER00.027-0.00812.122-0.067-0.0670.0000.0000.0000.000
179A181LYS10.8440.90714.72416.70916.7090.0000.0000.0000.000
180A182LYS10.7980.9038.96128.53028.5300.0000.0000.0000.000
181A183PRO00.009-0.00114.0190.6260.6260.0000.0000.0000.000
182A184ALA00.019-0.00813.783-0.975-0.9750.0000.0000.0000.000
183A185LYS10.9240.96413.57114.66414.6640.0000.0000.0000.000
184A186ASN0-0.0210.00111.094-0.057-0.0570.0000.0000.0000.000
185A187LEU00.0190.0078.326-2.072-2.0720.0000.0000.0000.000
186A188LYS10.9630.9966.34230.83330.8330.0000.0000.0000.000
187A189MET00.0260.0068.174-1.541-1.5410.0000.0000.0000.000
188A190PRO0-0.0150.00110.060-0.013-0.0130.0000.0000.0000.000
189A191GLY00.0480.01811.6451.1391.1390.0000.0000.0000.000
190A192PHE0-0.019-0.01615.136-0.310-0.3100.0000.0000.0000.000
191A193HIS0-0.063-0.03713.883-0.855-0.8550.0000.0000.0000.000
192A194PHE00.0210.00917.0440.7780.7780.0000.0000.0000.000
193A195VAL0-0.009-0.01314.902-1.236-1.2360.0000.0000.0000.000
194A196ASP-1-0.819-0.87517.656-12.917-12.9170.0000.0000.0000.000
195A197HIS10.7690.84918.38214.24114.2410.0000.0000.0000.000
196A198ARG10.9440.97221.23212.26012.2600.0000.0000.0000.000
197A199LEU0-0.0090.01122.944-0.450-0.4500.0000.0000.0000.000
198A200GLU-1-0.881-0.95124.754-11.011-11.0110.0000.0000.0000.000
199A201ARG10.7890.85827.1168.9908.9900.0000.0000.0000.000
200A202ILE0-0.001-0.00426.5930.2130.2130.0000.0000.0000.000
201A203LYS10.8280.89930.28810.20010.2000.0000.0000.0000.000
202A204GLU-1-0.843-0.92832.677-8.453-8.4530.0000.0000.0000.000
203A205ALA00.0260.01835.4560.0850.0850.0000.0000.0000.000
204A206ASP-1-0.864-0.92738.034-8.008-8.0080.0000.0000.0000.000
205A207LYS10.8960.95640.5917.0807.0800.0000.0000.0000.000
206A208GLU-1-0.779-0.88436.045-8.588-8.5880.0000.0000.0000.000
207A209THR0-0.052-0.02735.964-0.213-0.2130.0000.0000.0000.000
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