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: 3ZM6L

Calculation Name: 4JG2-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4JG2

Chain ID: A

ChEMBL ID:

UniProt ID: Q73EI2

Base Structure: X-ray

Registration Date: 2025-10-04

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1812910.461185
FMO2-HF: Nuclear repulsion 1742970.14289
FMO2-HF: Total energy -69940.318295
FMO2-MP2: Total energy -70147.479416


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:-11:LYS)


Summations of interaction energy for fragment #1(A:-11:LYS)
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.
-154.079-142.76839.487-23.752-27.045-0.266
Interaction energy analysis for fragmet #1(A:-11:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.694 / q_NPA : 1.851
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].
3A-9THR00.0400.0183.6733.7184.7700.001-0.306-0.7460.000
4A-8GLU-1-0.751-0.8261.704-198.275-198.48419.602-10.612-8.782-0.129
5A-7ASN00.0480.0174.6311.3781.486-0.001-0.011-0.0970.000
6A-6LEU00.0380.0084.424-6.329-6.249-0.001-0.004-0.0740.000
9A-3GLN0-0.056-0.0242.323-31.171-28.9301.853-2.026-2.068-0.021
10A-2SER0-0.026-0.0471.929-7.184-4.6629.159-5.949-5.731-0.065
11A-1ASN00.006-0.0013.950-9.067-8.4750.000-0.198-0.394-0.001
12A0ALA00.0130.0214.7627.6797.813-0.001-0.023-0.1100.000
13A4GLN00.029-0.0052.317-44.212-40.2746.819-4.432-6.325-0.044
14A5ASN0-0.029-0.0132.18011.70912.3132.047-0.309-2.342-0.006
15A6ARG10.9160.9363.54249.39449.5200.0100.119-0.2560.000
17A8LYS10.9030.9644.75476.57276.695-0.001-0.001-0.1200.000
7A-5TYR00.0060.0146.051-1.930-1.9300.0000.0000.0000.000
8A-4PHE0-0.034-0.0187.4162.6662.6660.0000.0000.0000.000
16A7THR00.0470.0297.1493.8813.8810.0000.0000.0000.000
18A9VAL00.0140.0126.976-2.961-2.9610.0000.0000.0000.000
19A10VAL0-0.038-0.0277.6760.6790.6790.0000.0000.0000.000
20A11THR00.0410.01910.419-0.652-0.6520.0000.0000.0000.000
21A12SER00.0320.00114.019-0.333-0.3330.0000.0000.0000.000
22A13VAL00.003-0.00515.4430.7450.7450.0000.0000.0000.000
23A14ASN0-0.022-0.00718.0892.0492.0490.0000.0000.0000.000
24A15THR0-0.040-0.00317.7050.7060.7060.0000.0000.0000.000
25A16ARG10.8750.93520.27721.07721.0770.0000.0000.0000.000
26A17LEU0-0.0180.00020.134-0.604-0.6040.0000.0000.0000.000
27A18SER00.0570.03223.7481.1791.1790.0000.0000.0000.000
28A19TYR00.007-0.00925.616-0.760-0.7600.0000.0000.0000.000
29A20PHE0-0.030-0.01322.110-0.831-0.8310.0000.0000.0000.000
30A21HIS00.0120.00824.8310.8850.8850.0000.0000.0000.000
31A22GLY00.0430.01022.283-0.725-0.7250.0000.0000.0000.000
32A23TRP0-0.018-0.02822.743-0.932-0.9320.0000.0000.0000.000
33A24GLU-1-0.848-0.90325.358-19.403-19.4030.0000.0000.0000.000
34A25PRO0-0.058-0.01525.059-0.427-0.4270.0000.0000.0000.000
35A26VAL00.0760.02726.5150.6730.6730.0000.0000.0000.000
36A27SER00.0020.00028.109-0.530-0.5300.0000.0000.0000.000
37A28ILE0-0.020-0.01926.7680.0670.0670.0000.0000.0000.000
38A29ASN0-0.025-0.02230.702-0.250-0.2500.0000.0000.0000.000
39A30GLY00.0970.06433.8280.2320.2320.0000.0000.0000.000
40A31GLY0-0.043-0.01130.029-0.075-0.0750.0000.0000.0000.000
41A32ALA0-0.032-0.02627.257-0.068-0.0680.0000.0000.0000.000
42A33GLU-1-0.891-0.93627.222-20.735-20.7350.0000.0000.0000.000
43A34LYS10.8000.88622.09722.78322.7830.0000.0000.0000.000
44A35TYR00.0950.07320.9100.5750.5750.0000.0000.0000.000
45A36SER0-0.050-0.05221.638-0.640-0.6400.0000.0000.0000.000
46A37VAL00.0330.01420.1120.2670.2670.0000.0000.0000.000
47A38SER0-0.033-0.01121.760-0.724-0.7240.0000.0000.0000.000
48A39VAL0-0.026-0.01417.7050.3320.3320.0000.0000.0000.000
49A40LEU00.0280.01621.081-0.220-0.2200.0000.0000.0000.000
50A41ILE0-0.008-0.01717.358-0.918-0.9180.0000.0000.0000.000
51A42PRO00.0610.03520.5880.6530.6530.0000.0000.0000.000
52A43LYS10.8120.88221.55720.30020.3000.0000.0000.0000.000
53A44THR0-0.003-0.00622.796-0.239-0.2390.0000.0000.0000.000
54A45ASP-1-0.785-0.84116.448-34.100-34.1000.0000.0000.0000.000
55A46LYS10.9090.92017.73824.56424.5640.0000.0000.0000.000
56A47GLU-1-0.934-0.94210.932-43.480-43.4800.0000.0000.0000.000
57A48THR0-0.008-0.04213.117-3.011-3.0110.0000.0000.0000.000
58A49ILE0-0.023-0.00714.246-0.870-0.8700.0000.0000.0000.000
59A50ASN0-0.016-0.01114.3760.9490.9490.0000.0000.0000.000
60A51ALA00.0050.0149.948-0.956-0.9560.0000.0000.0000.000
61A52ILE00.0150.00111.493-1.396-1.3960.0000.0000.0000.000
62A53ASN0-0.011-0.00513.7970.6840.6840.0000.0000.0000.000
63A54ALA00.0060.00411.3910.5910.5910.0000.0000.0000.000
64A55ALA00.0120.01810.294-0.680-0.6800.0000.0000.0000.000
65A56VAL0-0.031-0.02311.7280.5870.5870.0000.0000.0000.000
66A57ASP-1-0.813-0.89215.326-30.042-30.0420.0000.0000.0000.000
67A58ALA0-0.025-0.00710.7070.6630.6630.0000.0000.0000.000
68A59ALA00.0280.02012.8090.2540.2540.0000.0000.0000.000
69A60ILE0-0.052-0.02814.0141.7141.7140.0000.0000.0000.000
70A61GLU-1-0.846-0.91514.643-35.095-35.0950.0000.0000.0000.000
71A62GLU-1-0.903-0.9569.566-52.016-52.0160.0000.0000.0000.000
72A63GLY0-0.016-0.00714.2350.9000.9000.0000.0000.0000.000
73A64ILE0-0.068-0.03617.4981.1311.1310.0000.0000.0000.000
74A65ALA0-0.014-0.00615.0541.0441.0440.0000.0000.0000.000
75A66LYS10.9030.97716.01131.95531.9550.0000.0000.0000.000
76A67PHE0-0.013-0.02717.6870.7320.7320.0000.0000.0000.000
77A68GLY00.0360.04220.9571.2661.2660.0000.0000.0000.000
78A69GLY00.0120.00222.870-0.036-0.0360.0000.0000.0000.000
79A70LYS10.9050.94324.65020.93120.9310.0000.0000.0000.000
80A71LYS10.9630.97718.99929.66429.6640.0000.0000.0000.000
81A72PRO0-0.0020.00522.0611.1961.1960.0000.0000.0000.000
82A73ASN00.0250.01124.642-0.867-0.8670.0000.0000.0000.000
83A74LYS10.8980.90819.35829.10029.1000.0000.0000.0000.000
84A75ALA00.0420.02624.865-0.174-0.1740.0000.0000.0000.000
85A76ALA0-0.042-0.01227.7190.6370.6370.0000.0000.0000.000
86A77ILE0-0.067-0.03922.2220.0030.0030.0000.0000.0000.000
87A78LYS10.9840.99524.11523.07923.0790.0000.0000.0000.000
88A79LEU00.0320.01020.964-1.218-1.2180.0000.0000.0000.000
89A80PRO0-0.021-0.01017.9341.0381.0380.0000.0000.0000.000
90A81LEU0-0.014-0.00118.4630.0880.0880.0000.0000.0000.000
91A82ARG10.7740.87720.94523.58623.5860.0000.0000.0000.000
92A83ASP-1-0.794-0.89724.451-21.659-21.6590.0000.0000.0000.000
93A84GLY00.007-0.00626.7940.5690.5690.0000.0000.0000.000
94A85ASP-1-0.765-0.86328.418-19.323-19.3230.0000.0000.0000.000
95A86VAL0-0.012-0.01030.6360.6380.6380.0000.0000.0000.000
96A87GLU-1-0.835-0.88527.590-21.393-21.3930.0000.0000.0000.000
97A88ARG10.8470.91929.28119.84219.8420.0000.0000.0000.000
98A89ASP-1-0.867-0.91732.740-16.446-16.4460.0000.0000.0000.000
99A90ASP-1-0.887-0.94432.194-18.062-18.0620.0000.0000.0000.000
100A91GLU-1-0.869-0.96032.832-17.397-17.3970.0000.0000.0000.000
101A92ALA0-0.081-0.03329.965-0.315-0.3150.0000.0000.0000.000
102A93TYR0-0.047-0.04227.092-1.130-1.1300.0000.0000.0000.000
103A94LYS10.9360.98428.70617.20817.2080.0000.0000.0000.000
104A95GLY00.0030.00728.775-0.334-0.3340.0000.0000.0000.000
105A96HIS0-0.084-0.05423.993-1.561-1.5610.0000.0000.0000.000
106A97TYR00.0040.00321.5620.6600.6600.0000.0000.0000.000
107A98PHE0-0.014-0.01322.139-0.354-0.3540.0000.0000.0000.000
108A99VAL00.0160.01217.451-0.333-0.3330.0000.0000.0000.000
109A100ASN0-0.022-0.00420.8530.5480.5480.0000.0000.0000.000
110A101ALA00.0160.02217.554-0.456-0.4560.0000.0000.0000.000
111A102ASN0-0.028-0.03418.7921.3611.3610.0000.0000.0000.000
112A103SER00.0520.03617.102-1.509-1.5090.0000.0000.0000.000
113A104LYS10.9520.97419.05625.04425.0440.0000.0000.0000.000
114A105THR0-0.0120.00616.5531.0401.0400.0000.0000.0000.000
115A106PRO00.0440.02919.095-0.481-0.4810.0000.0000.0000.000
116A107PRO0-0.0390.00016.466-1.538-1.5380.0000.0000.0000.000
117A108GLN00.012-0.01413.471-0.585-0.5850.0000.0000.0000.000
118A109ILE0-0.0060.01016.730-1.507-1.5070.0000.0000.0000.000
119A110VAL00.000-0.00115.5380.7140.7140.0000.0000.0000.000
120A111ASP-1-0.688-0.82818.932-27.710-27.7100.0000.0000.0000.000
121A112LYS10.8830.93218.48425.16825.1680.0000.0000.0000.000
122A113ALA0-0.049-0.01318.893-0.838-0.8380.0000.0000.0000.000
123A114VAL0-0.049-0.02613.676-1.002-1.0020.0000.0000.0000.000
124A115ARG10.8890.92916.99125.43025.4300.0000.0000.0000.000
125A116PRO00.004-0.01219.548-0.002-0.0020.0000.0000.0000.000
126A117ILE0-0.033-0.00521.2670.8650.8650.0000.0000.0000.000
127A118LEU0-0.010-0.01123.8670.0520.0520.0000.0000.0000.000
128A119ASP-1-0.817-0.89327.266-18.631-18.6310.0000.0000.0000.000
129A120ARG10.8780.90027.73719.98219.9820.0000.0000.0000.000
130A121ASN0-0.021-0.01728.567-0.199-0.1990.0000.0000.0000.000
131A122GLU-1-0.891-0.93326.155-21.433-21.4330.0000.0000.0000.000
132A123VAL0-0.060-0.03822.325-0.831-0.8310.0000.0000.0000.000
133A124TYR00.028-0.01725.5410.2940.2940.0000.0000.0000.000
134A125SER00.0240.00626.615-1.026-1.0260.0000.0000.0000.000
135A126GLY00.0530.03727.1420.8040.8040.0000.0000.0000.000
136A127CYS0-0.0630.01424.587-0.401-0.4010.0000.0000.0000.000
137A128TYR00.017-0.00822.930-0.185-0.1850.0000.0000.0000.000
138A129ALA00.0550.00519.531-0.035-0.0350.0000.0000.0000.000
139A130ARG10.8170.92110.65843.72443.7240.0000.0000.0000.000
140A131VAL00.0560.02014.9300.3860.3860.0000.0000.0000.000
141A132SER0-0.031-0.0179.733-4.255-4.2550.0000.0000.0000.000
142A133LEU0-0.017-0.00610.9262.5492.5490.0000.0000.0000.000
143A134ASN00.0130.0038.551-9.552-9.5520.0000.0000.0000.000
144A135PHE00.0170.00811.1733.9213.9210.0000.0000.0000.000
145A136TYR00.011-0.01012.363-2.214-2.2140.0000.0000.0000.000
146A137ALA00.0390.02414.8961.9111.9110.0000.0000.0000.000
147A138PHE0-0.067-0.02917.974-0.024-0.0240.0000.0000.0000.000
148A139ASN0-0.005-0.02121.0531.0141.0140.0000.0000.0000.000
149A140SER00.0200.01624.762-0.159-0.1590.0000.0000.0000.000
150A141ASN00.0290.00626.8580.5090.5090.0000.0000.0000.000
151A142GLY00.0600.03829.9000.1460.1460.0000.0000.0000.000
152A143ASN0-0.068-0.02326.9320.0510.0510.0000.0000.0000.000
153A144LYS11.0010.99324.96120.06320.0630.0000.0000.0000.000
154A145GLY00.0100.01522.5660.6250.6250.0000.0000.0000.000
155A146VAL0-0.042-0.01216.514-0.818-0.8180.0000.0000.0000.000
156A147ALA0-0.0220.00218.2251.2121.2120.0000.0000.0000.000
157A148CYS0-0.023-0.02415.630-1.907-1.9070.0000.0000.0000.000
158A149GLY00.0380.02814.5741.6301.6300.0000.0000.0000.000
159A150LEU0-0.034-0.02314.125-2.275-2.2750.0000.0000.0000.000
160A151GLY00.0120.00712.358-0.412-0.4120.0000.0000.0000.000
161A152ASN0-0.017-0.01811.5423.5643.5640.0000.0000.0000.000
162A153ILE00.0260.01514.169-1.179-1.1790.0000.0000.0000.000
163A154GLN0-0.050-0.02915.367-0.873-0.8730.0000.0000.0000.000
164A155LYS10.8310.91817.33523.01723.0170.0000.0000.0000.000
165A156ILE0-0.090-0.04717.512-0.485-0.4850.0000.0000.0000.000
166A157ARG10.9250.96221.47223.56323.5630.0000.0000.0000.000
167A158ASP-1-0.732-0.83825.251-21.720-21.7200.0000.0000.0000.000
168A159GLY0-0.046-0.04028.206-0.331-0.3310.0000.0000.0000.000
169A160GLU-1-0.882-0.92229.746-17.359-17.3590.0000.0000.0000.000
170A161PRO00.0250.01231.363-0.627-0.6270.0000.0000.0000.000
171A162LEU0-0.061-0.03128.6250.2730.2730.0000.0000.0000.000
172A163GLY00.0280.01632.343-0.088-0.0880.0000.0000.0000.000
173A164GLY00.0030.00132.498-0.621-0.6210.0000.0000.0000.000
174A165ARG10.9330.96027.32920.93020.9300.0000.0000.0000.000
175A166THR0-0.005-0.00334.5700.0160.0160.0000.0000.0000.000
176A167ASN0-0.006-0.01434.1490.5090.5090.0000.0000.0000.000
177A168ALA00.0650.04237.5660.0190.0190.0000.0000.0000.000
178A169ALA0-0.011-0.00740.6470.2580.2580.0000.0000.0000.000
179A170ASP-1-0.958-0.97736.323-16.581-16.5810.0000.0000.0000.000
180A171ASP-1-0.974-0.96938.575-15.994-15.9940.0000.0000.0000.000
181A172PHE0-0.092-0.05240.9070.3070.3070.0000.0000.0000.000
182A173THR0-0.015-0.01044.591-0.142-0.1420.0000.0000.0000.000
183A174THR0-0.074-0.06147.263-0.074-0.0740.0000.0000.0000.000
184A175ILE0-0.066-0.02850.550-0.042-0.0420.0000.0000.0000.000
185A176GLU-2-1.830-1.88552.990-22.506-22.5060.0000.0000.0000.000