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

tag_button

FMODB ID: Z7Q6N

Calculation Name: 2EMQ-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EMQ

Chain ID: B

ChEMBL ID:

UniProt ID: Q5L147

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 133
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1156903.8471
FMO2-HF: Nuclear repulsion 1102435.51028
FMO2-HF: Total energy -54468.33682
FMO2-MP2: Total energy -54622.04267


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:9:MET)


Summations of interaction energy for fragment #1(A:9:MET)
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.
16.83518.367-0.01-0.524-0.9980
Interaction energy analysis for fragmet #1(A:9:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.883 / q_NPA : 0.931
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].
3A11MET00.0430.0383.6751.0832.615-0.010-0.524-0.9980.000
4A12THR0-0.021-0.0205.6383.2983.2980.0000.0000.0000.000
5A13VAL00.0420.0139.408-0.179-0.1790.0000.0000.0000.000
6A14LYS10.9520.97412.47523.37023.3700.0000.0000.0000.000
7A15PRO0-0.027-0.0139.7011.2461.2460.0000.0000.0000.000
8A16PHE0-0.002-0.0069.3610.4400.4400.0000.0000.0000.000
9A17LEU0-0.060-0.00414.6230.9140.9140.0000.0000.0000.000
10A18ILE0-0.0020.00417.6560.3470.3470.0000.0000.0000.000
11A19PRO0-0.014-0.00721.1150.0980.0980.0000.0000.0000.000
12A20ALA00.0600.01023.2210.3530.3530.0000.0000.0000.000
13A21ASP-1-0.885-0.93826.373-11.535-11.5350.0000.0000.0000.000
14A22LYS10.8710.94323.78313.12713.1270.0000.0000.0000.000
15A23VAL0-0.071-0.02825.010-0.122-0.1220.0000.0000.0000.000
16A24ALA00.0180.01528.1700.2320.2320.0000.0000.0000.000
17A25HIS0-0.003-0.01130.921-0.206-0.2060.0000.0000.0000.000
18A26VAL00.0160.01032.9660.2840.2840.0000.0000.0000.000
19A27GLN00.0310.01435.372-0.099-0.0990.0000.0000.0000.000
20A28PRO0-0.003-0.00336.7850.1100.1100.0000.0000.0000.000
21A29GLY00.0490.02138.9070.1310.1310.0000.0000.0000.000
22A30ASN0-0.030-0.00440.024-0.006-0.0060.0000.0000.0000.000
23A31TYR00.0720.03442.545-0.033-0.0330.0000.0000.0000.000
24A32LEU00.0070.01040.873-0.214-0.2140.0000.0000.0000.000
25A33ASP-1-0.840-0.92542.564-7.158-7.1580.0000.0000.0000.000
26A34HIS00.0130.01140.441-0.114-0.1140.0000.0000.0000.000
27A35ALA00.0160.00038.289-0.183-0.1830.0000.0000.0000.000
28A36LEU00.0170.00938.570-0.240-0.2400.0000.0000.0000.000
29A37LEU0-0.0380.00040.292-0.115-0.1150.0000.0000.0000.000
30A38VAL00.018-0.00635.353-0.106-0.1060.0000.0000.0000.000
31A39LEU0-0.0120.00233.489-0.248-0.2480.0000.0000.0000.000
32A40THR0-0.048-0.02936.190-0.089-0.0890.0000.0000.0000.000
33A41LYS10.8750.93937.3747.8757.8750.0000.0000.0000.000
34A42THR0-0.033-0.02432.019-0.254-0.2540.0000.0000.0000.000
35A43GLY00.0010.01530.6290.0530.0530.0000.0000.0000.000
36A44TYR0-0.044-0.03524.691-0.715-0.7150.0000.0000.0000.000
37A45SER00.0120.00328.2100.1430.1430.0000.0000.0000.000
38A46ALA0-0.027-0.02229.0130.2950.2950.0000.0000.0000.000
39A47ILE00.0170.01829.841-0.315-0.3150.0000.0000.0000.000
40A48PRO0-0.023-0.01028.0120.1040.1040.0000.0000.0000.000
41A49VAL00.0020.00330.1050.2810.2810.0000.0000.0000.000
42A50LEU0-0.0010.00129.392-0.247-0.2470.0000.0000.0000.000
43A51ASP-1-0.740-0.84533.387-9.138-9.1380.0000.0000.0000.000
44A52THR00.006-0.01235.279-0.122-0.1220.0000.0000.0000.000
45A53SER0-0.076-0.04434.8550.1370.1370.0000.0000.0000.000
46A54TYR00.001-0.01228.616-0.388-0.3880.0000.0000.0000.000
47A55LYS10.9110.96830.07910.10210.1020.0000.0000.0000.000
48A56LEU0-0.0110.00226.4070.2810.2810.0000.0000.0000.000
49A57HIS0-0.019-0.03430.280-0.050-0.0500.0000.0000.0000.000
50A58GLY00.0250.00030.4290.1150.1150.0000.0000.0000.000
51A59LEU0-0.074-0.02126.123-0.222-0.2220.0000.0000.0000.000
52A60ILE00.0620.02930.7340.2280.2280.0000.0000.0000.000
53A61SER00.032-0.03332.286-0.223-0.2230.0000.0000.0000.000
54A62MET00.0530.02134.2320.2350.2350.0000.0000.0000.000
55A63THR00.008-0.00534.7900.2200.2200.0000.0000.0000.000
56A64MET0-0.0310.03431.4710.1220.1220.0000.0000.0000.000
57A65MET0-0.0150.01337.2970.1960.1960.0000.0000.0000.000
58A66MET0-0.021-0.01040.2080.2500.2500.0000.0000.0000.000
59A67ASP-1-0.907-0.95739.407-7.713-7.7130.0000.0000.0000.000
60A68ALA00.0270.01841.4110.1790.1790.0000.0000.0000.000
61A69ILE0-0.061-0.02043.1080.1780.1780.0000.0000.0000.000
62A70LEU0-0.0050.00142.7310.1620.1620.0000.0000.0000.000
63A71GLY00.0370.03046.6060.0100.0100.0000.0000.0000.000
64A72LEU0-0.059-0.04550.183-0.013-0.0130.0000.0000.0000.000
65A73GLU-1-0.946-0.96652.143-5.486-5.4860.0000.0000.0000.000
66A74ARG10.7880.86452.4776.0156.0150.0000.0000.0000.000
67A75ILE00.0080.01446.606-0.075-0.0750.0000.0000.0000.000
68A76GLU-1-0.909-0.94849.058-6.151-6.1510.0000.0000.0000.000
69A77PHE00.003-0.01946.227-0.089-0.0890.0000.0000.0000.000
70A78GLU-1-0.731-0.83349.289-6.212-6.2120.0000.0000.0000.000
71A79ARG10.8300.88946.6116.6696.6690.0000.0000.0000.000
72A80LEU0-0.031-0.02444.019-0.130-0.1300.0000.0000.0000.000
73A81GLU-1-0.906-0.95046.746-6.288-6.2880.0000.0000.0000.000
74A82THR0-0.068-0.02449.2490.1110.1110.0000.0000.0000.000
75A83MET0-0.0260.00244.0860.0070.0070.0000.0000.0000.000
76A84LYS10.8600.92843.1436.8066.8060.0000.0000.0000.000
77A85VAL00.008-0.01437.121-0.104-0.1040.0000.0000.0000.000
78A86GLU-1-0.957-1.01038.368-7.974-7.9740.0000.0000.0000.000
79A87GLU-1-0.876-0.92639.450-7.147-7.1470.0000.0000.0000.000
80A88VAL0-0.010-0.00738.4710.0190.0190.0000.0000.0000.000
81A89MET0-0.076-0.00834.336-0.228-0.2280.0000.0000.0000.000
82A90ASN00.003-0.00629.0050.2230.2230.0000.0000.0000.000
83A91ARG11.0010.98631.2918.5918.5910.0000.0000.0000.000
84A92ASN0-0.039-0.00527.538-0.205-0.2050.0000.0000.0000.000
85A93ILE0-0.0180.00326.045-0.127-0.1270.0000.0000.0000.000
86A94PRO0-0.010-0.00120.664-0.198-0.1980.0000.0000.0000.000
87A95ARG10.8270.89321.33912.04712.0470.0000.0000.0000.000
88A96LEU0-0.069-0.03615.287-0.856-0.8560.0000.0000.0000.000
89A97ARG10.9840.98716.30118.39618.3960.0000.0000.0000.000
90A98LEU00.033-0.00316.035-1.341-1.3410.0000.0000.0000.000
91A99ASP-1-0.917-0.95413.191-21.320-21.3200.0000.0000.0000.000
92A100ASP-1-0.739-0.84312.274-21.426-21.4260.0000.0000.0000.000
93A101SER00.002-0.0117.651-3.188-3.1880.0000.0000.0000.000
94A102LEU00.0280.0037.0972.0832.0830.0000.0000.0000.000
95A103MET0-0.009-0.0035.6771.6031.6030.0000.0000.0000.000
96A104LYS10.8610.9388.36821.39721.3970.0000.0000.0000.000
97A105ALA00.0240.01611.7781.7251.7250.0000.0000.0000.000
98A106VAL00.018-0.00810.1811.5491.5490.0000.0000.0000.000
99A107GLY00.0270.01612.1931.3491.3490.0000.0000.0000.000
100A108LEU0-0.006-0.00213.9101.3991.3990.0000.0000.0000.000
101A109ILE0-0.0020.00715.0831.1241.1240.0000.0000.0000.000
102A110VAL00.0120.02515.4530.5860.5860.0000.0000.0000.000
103A111ASN00.0100.01518.1630.5690.5690.0000.0000.0000.000
104A112HIS0-0.047-0.02420.3081.2061.2060.0000.0000.0000.000
105A113PRO00.0080.00020.929-0.639-0.6390.0000.0000.0000.000
106A114PHE0-0.024-0.02721.046-0.598-0.5980.0000.0000.0000.000
107A115VAL00.0060.01118.6370.3670.3670.0000.0000.0000.000
108A116CYS0-0.0020.01121.061-0.277-0.2770.0000.0000.0000.000
109A117VAL0-0.025-0.01618.184-0.602-0.6020.0000.0000.0000.000
110A118GLU-1-0.822-0.89620.951-12.101-12.1010.0000.0000.0000.000
111A119ASN0-0.055-0.04820.907-0.821-0.8210.0000.0000.0000.000
112A120ASP-1-0.880-0.95319.801-15.862-15.8620.0000.0000.0000.000
113A121ASP-1-0.913-0.93422.658-12.095-12.0950.0000.0000.0000.000
114A122GLY0-0.028-0.01925.2350.5930.5930.0000.0000.0000.000
115A123TYR0-0.052-0.02226.2150.5950.5950.0000.0000.0000.000
116A124PHE00.004-0.00825.179-0.696-0.6960.0000.0000.0000.000
117A125ALA00.0370.01221.8150.2310.2310.0000.0000.0000.000
118A126GLY00.0250.00222.608-0.046-0.0460.0000.0000.0000.000
119A127ILE0-0.050-0.01521.545-0.071-0.0710.0000.0000.0000.000
120A128PHE00.0240.02312.914-0.565-0.5650.0000.0000.0000.000
121A129THR00.032-0.00517.9540.6040.6040.0000.0000.0000.000
122A130ARG10.8930.93217.71313.28413.2840.0000.0000.0000.000
123A131ARG10.9560.98718.43812.82712.8270.0000.0000.0000.000
124A132GLU-1-0.781-0.89216.760-15.884-15.8840.0000.0000.0000.000
125A133VAL00.0150.01212.958-0.993-0.9930.0000.0000.0000.000
126A134LEU00.003-0.00414.489-0.749-0.7490.0000.0000.0000.000
127A135LYS10.8160.90717.21315.73915.7390.0000.0000.0000.000
128A136GLN0-0.034-0.02610.3841.7331.7330.0000.0000.0000.000
129A137LEU00.006-0.00313.276-0.515-0.5150.0000.0000.0000.000
130A138ASN0-0.027-0.02314.1910.4740.4740.0000.0000.0000.000
131A139LYS10.9160.96914.14021.09021.0900.0000.0000.0000.000
132A140GLN0-0.096-0.0389.533-2.065-2.0650.0000.0000.0000.000
133A141LEU-1-0.924-0.93613.734-17.204-17.2040.0000.0000.0000.000