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: Z7Q8N

Calculation Name: 2GEF-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2GEF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8AZM0

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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2123273.638183
FMO2-HF: Nuclear repulsion 2048289.667596
FMO2-HF: Total energy -74983.970587
FMO2-MP2: Total energy -75202.550935


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:559:ASP)


Summations of interaction energy for fragment #1(A:559:ASP)
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.
0.4522.2840.026-0.85-1.0080
Interaction energy analysis for fragmet #1(A:559:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.091 / q_NPA : -0.047
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].
3A561PRO00.0080.0013.566-0.4471.3850.026-0.850-1.0080.000
4A562ILE00.0260.0135.5241.6591.6590.0000.0000.0000.000
5A563SER0-0.0070.0047.817-0.298-0.2980.0000.0000.0000.000
6A564LEU0-0.015-0.01511.1660.3930.3930.0000.0000.0000.000
7A565LEU00.0050.00513.941-0.117-0.1170.0000.0000.0000.000
8A566GLN00.005-0.00617.4220.0140.0140.0000.0000.0000.000
9A567THR0-0.012-0.00119.1580.0180.0180.0000.0000.0000.000
10A568LEU00.0160.00720.801-0.036-0.0360.0000.0000.0000.000
11A569ALA00.0180.01524.4720.0510.0510.0000.0000.0000.000
12A570TYR0-0.036-0.02527.702-0.033-0.0330.0000.0000.0000.000
13A571LYS10.8680.95128.9980.5570.5570.0000.0000.0000.000
14A572GLN00.0360.00631.245-0.051-0.0510.0000.0000.0000.000
15A573PRO0-0.0020.00031.8440.0300.0300.0000.0000.0000.000
16A574LEU0-0.038-0.00534.4610.0240.0240.0000.0000.0000.000
17A575GLY00.0250.02737.928-0.016-0.0160.0000.0000.0000.000
18A576ARG10.8220.87339.1620.4670.4670.0000.0000.0000.000
19A577ASN0-0.052-0.03941.8970.0020.0020.0000.0000.0000.000
20A578SER0-0.040-0.03043.761-0.003-0.0030.0000.0000.0000.000
21A579ARG10.9610.97644.4410.3850.3850.0000.0000.0000.000
22A580ILE00.0210.01845.006-0.016-0.0160.0000.0000.0000.000
23A581VAL0-0.064-0.03243.9060.0120.0120.0000.0000.0000.000
24A582HIS0-0.020-0.00845.397-0.007-0.0070.0000.0000.0000.000
25A583PHE0-0.022-0.01741.734-0.009-0.0090.0000.0000.0000.000
26A584THR00.020-0.01744.6440.0080.0080.0000.0000.0000.000
27A585ASP-1-0.907-0.93940.910-0.430-0.4300.0000.0000.0000.000
28A586GLY00.0220.00137.694-0.006-0.0060.0000.0000.0000.000
29A587ALA00.0000.00133.7880.0110.0110.0000.0000.0000.000
30A588LEU00.0430.03133.509-0.029-0.0290.0000.0000.0000.000
31A589PHE0-0.003-0.01227.399-0.041-0.0410.0000.0000.0000.000
32A590PRO00.0030.02125.9400.0210.0210.0000.0000.0000.000
33A591VAL0-0.025-0.00926.007-0.116-0.1160.0000.0000.0000.000
34A592VAL0-0.014-0.02122.1330.0520.0520.0000.0000.0000.000
35A593ALA00.0160.01923.695-0.091-0.0910.0000.0000.0000.000
36A594PHE0-0.023-0.02320.5220.0770.0770.0000.0000.0000.000
37A595GLY00.0310.02223.807-0.031-0.0310.0000.0000.0000.000
38A596ASP-1-0.848-0.91525.024-0.706-0.7060.0000.0000.0000.000
39A597ASN0-0.077-0.03826.6320.0040.0040.0000.0000.0000.000
40A598HIS00.001-0.01728.1050.0610.0610.0000.0000.0000.000
41A599SER00.0040.00024.546-0.089-0.0890.0000.0000.0000.000
42A600THR0-0.003-0.00626.3870.0640.0640.0000.0000.0000.000
43A601SER0-0.045-0.06726.638-0.087-0.0870.0000.0000.0000.000
44A602GLU-1-0.836-0.91128.703-0.609-0.6090.0000.0000.0000.000
45A603LEU00.0230.01630.054-0.060-0.0600.0000.0000.0000.000
46A604TYR00.0450.02130.8960.0160.0160.0000.0000.0000.000
47A605ILE00.0170.01932.853-0.014-0.0140.0000.0000.0000.000
48A606ALA0-0.034-0.01732.201-0.015-0.0150.0000.0000.0000.000
49A607VAL00.0550.01734.3140.0240.0240.0000.0000.0000.000
50A608ARG10.8360.91637.2280.4460.4460.0000.0000.0000.000
51A609GLY00.0280.01438.4090.0310.0310.0000.0000.0000.000
52A610ASP-1-0.974-0.99739.039-0.493-0.4930.0000.0000.0000.000
53A611HIS10.9090.94239.6060.4930.4930.0000.0000.0000.000
54A612ARG10.9660.96038.4980.5210.5210.0000.0000.0000.000
55A613ASP-1-0.907-0.94640.933-0.415-0.4150.0000.0000.0000.000
56A614LEU0-0.004-0.00341.3430.0110.0110.0000.0000.0000.000
57A615MET0-0.0350.02035.283-0.002-0.0020.0000.0000.0000.000
58A616SER00.0340.01937.5870.0350.0350.0000.0000.0000.000
59A617PRO0-0.028-0.04038.557-0.019-0.0190.0000.0000.0000.000
60A618ASP-1-0.880-0.93035.918-0.522-0.5220.0000.0000.0000.000
61A619VAL00.0020.00432.688-0.040-0.0400.0000.0000.0000.000
62A620ARG10.8670.92434.8060.4250.4250.0000.0000.0000.000
63A621ASP-1-0.911-0.94135.862-0.533-0.5330.0000.0000.0000.000
64A622SER0-0.055-0.02829.954-0.029-0.0290.0000.0000.0000.000
65A623TYR0-0.016-0.02831.2100.0300.0300.0000.0000.0000.000
66A624ALA00.0120.04526.354-0.041-0.0410.0000.0000.0000.000
67A625LEU0-0.016-0.02627.3870.0630.0630.0000.0000.0000.000
68A626THR00.0330.01226.840-0.095-0.0950.0000.0000.0000.000
69A627GLY00.0630.03026.668-0.020-0.0200.0000.0000.0000.000
70A628ASP-1-0.884-0.94727.436-0.694-0.6940.0000.0000.0000.000
71A629ASP-1-0.873-0.93330.135-0.754-0.7540.0000.0000.0000.000
72A630HIS10.8760.94731.6810.6390.6390.0000.0000.0000.000
73A631LYS10.9130.96331.5820.5810.5810.0000.0000.0000.000
74A632VAL00.0200.01229.3670.0310.0310.0000.0000.0000.000
75A633TRP00.015-0.01431.368-0.045-0.0450.0000.0000.0000.000
76A634GLY00.0900.02632.4430.0130.0130.0000.0000.0000.000
77A635ALA0-0.062-0.01427.360-0.033-0.0330.0000.0000.0000.000
78A636THR00.000-0.01424.9030.0180.0180.0000.0000.0000.000
79A637HIS-1-0.924-0.96820.732-1.500-1.5000.0000.0000.0000.000
80A651LYS21.5981.82422.3802.2422.2420.0000.0000.0000.000
81A652PHE00.0720.02122.248-0.155-0.1550.0000.0000.0000.000
82A653ASN00.0030.01120.7540.1590.1590.0000.0000.0000.000
83A654VAL00.0280.01223.4630.0820.0820.0000.0000.0000.000
84A655LYS10.8910.94526.6490.9220.9220.0000.0000.0000.000
85A656THR00.0350.00230.1380.0080.0080.0000.0000.0000.000
86A657ARG10.8740.92333.2260.5730.5730.0000.0000.0000.000
87A658THR0-0.045-0.03435.3830.0460.0460.0000.0000.0000.000
88A659ASP-1-0.812-0.87834.997-0.637-0.6370.0000.0000.0000.000
89A660LEU0-0.0140.00132.4120.0190.0190.0000.0000.0000.000
90A661THR0-0.036-0.01335.139-0.005-0.0050.0000.0000.0000.000
91A662ILE0-0.049-0.01529.537-0.003-0.0030.0000.0000.0000.000
92A663LEU0-0.010-0.00233.7930.0060.0060.0000.0000.0000.000
93A664PRO00.0090.02434.050-0.012-0.0120.0000.0000.0000.000
94A665VAL0-0.010-0.01735.3440.0340.0340.0000.0000.0000.000
95A666ALA0-0.071-0.02236.678-0.018-0.0180.0000.0000.0000.000
96A667ASP-1-0.861-0.94339.213-0.385-0.3850.0000.0000.0000.000
97A668VAL0-0.064-0.03538.836-0.010-0.0100.0000.0000.0000.000
98A669PHE0-0.0010.00741.9270.0080.0080.0000.0000.0000.000
99A670TRP0-0.007-0.02038.8340.0030.0030.0000.0000.0000.000
100A671ARG10.7980.87945.7870.3190.3190.0000.0000.0000.000
101A672ALA0-0.004-0.01648.216-0.007-0.0070.0000.0000.0000.000
102A673ASP-1-0.854-0.88849.393-0.302-0.3020.0000.0000.0000.000
103A674GLY00.0240.01045.657-0.006-0.0060.0000.0000.0000.000
104A675SER0-0.045-0.04444.328-0.023-0.0230.0000.0000.0000.000
105A676ALA00.0300.00042.9900.0060.0060.0000.0000.0000.000
106A677ASP-1-0.858-0.89445.125-0.318-0.3180.0000.0000.0000.000
107A678VAL0-0.016-0.01140.069-0.006-0.0060.0000.0000.0000.000
108A679ASP-1-0.820-0.88442.475-0.377-0.3770.0000.0000.0000.000
109A680VAL0-0.009-0.00639.600-0.028-0.0280.0000.0000.0000.000
110A681VAL0-0.009-0.01037.8150.0240.0240.0000.0000.0000.000
111A682TRP0-0.061-0.03838.356-0.017-0.0170.0000.0000.0000.000
112A683ASN00.026-0.01932.2350.0270.0270.0000.0000.0000.000
113A684ASP-1-0.855-0.90735.562-0.486-0.4860.0000.0000.0000.000
114A685MET0-0.035-0.00628.684-0.008-0.0080.0000.0000.0000.000
115A686PRO0-0.008-0.00527.2890.0190.0190.0000.0000.0000.000
116A687ALA00.0230.00929.203-0.006-0.0060.0000.0000.0000.000
117A688VAL0-0.0060.00825.488-0.068-0.0680.0000.0000.0000.000
118A689ALA00.0340.02921.649-0.013-0.0130.0000.0000.0000.000
119A690GLY00.0010.00220.085-0.055-0.0550.0000.0000.0000.000
120A691GLN00.0300.00220.1040.1770.1770.0000.0000.0000.000
121A692SER00.0040.01620.6970.1020.1020.0000.0000.0000.000
122A693SER00.1140.06022.4090.0420.0420.0000.0000.0000.000
123A694SER0-0.045-0.04923.7140.0900.0900.0000.0000.0000.000
124A695ILE00.0400.03025.0290.0580.0580.0000.0000.0000.000
125A696ALA00.0550.03828.0760.0600.0600.0000.0000.0000.000
126A697LEU0-0.040-0.02227.4520.0500.0500.0000.0000.0000.000
127A698ALA00.0350.01429.7810.0480.0480.0000.0000.0000.000
128A699LEU00.0370.05131.5820.0480.0480.0000.0000.0000.000
129A700ALA00.0310.02833.9100.0440.0440.0000.0000.0000.000
130A701SER0-0.097-0.05734.1230.0340.0340.0000.0000.0000.000
131A702SER0-0.082-0.05935.2380.0270.0270.0000.0000.0000.000
132A703LEU00.0550.04936.5110.0240.0240.0000.0000.0000.000
133A704PRO0-0.055-0.02039.631-0.006-0.0060.0000.0000.0000.000
134A705PHE00.0760.03139.3910.0210.0210.0000.0000.0000.000
135A706VAL0-0.008-0.00139.274-0.029-0.0290.0000.0000.0000.000
136A707PRO00.0140.00736.2120.0140.0140.0000.0000.0000.000
137A708LYS10.9020.98037.9200.3230.3230.0000.0000.0000.000
138A709ALA0-0.004-0.02033.3930.0040.0040.0000.0000.0000.000
139A710ALA0-0.0290.00230.863-0.013-0.0130.0000.0000.0000.000
140A711TYR00.033-0.00628.807-0.034-0.0340.0000.0000.0000.000
141A712THR0-0.055-0.05023.291-0.081-0.0810.0000.0000.0000.000
142A713GLY00.0670.02621.5510.0090.0090.0000.0000.0000.000
143A714CYS0-0.096-0.03217.9820.0710.0710.0000.0000.0000.000
144A715LEU00.0420.01520.9610.0630.0630.0000.0000.0000.000
145A716SER0-0.041-0.01719.372-0.082-0.0820.0000.0000.0000.000
146A717GLY0-0.003-0.00921.5000.0840.0840.0000.0000.0000.000
147A718THR00.0240.00625.121-0.027-0.0270.0000.0000.0000.000
148A719ASN0-0.0100.00722.0390.0820.0820.0000.0000.0000.000
149A720VAL00.0220.00922.127-0.118-0.1180.0000.0000.0000.000
150A721GLN0-0.039-0.02516.656-0.041-0.0410.0000.0000.0000.000
151A722PRO00.0010.00515.6560.0430.0430.0000.0000.0000.000
152A723VAL0-0.0120.00116.495-0.354-0.3540.0000.0000.0000.000
153A724GLN00.0220.00213.5230.0880.0880.0000.0000.0000.000
154A725PHE00.040-0.00216.8260.1360.1360.0000.0000.0000.000
155A726GLY00.0900.04520.4260.1000.1000.0000.0000.0000.000
156A727ASN0-0.014-0.02122.6050.1160.1160.0000.0000.0000.000
157A728LEU0-0.011-0.00123.3520.0730.0730.0000.0000.0000.000
158A729LYS10.8490.94021.4481.3531.3530.0000.0000.0000.000
159A730ALA00.0500.02926.1590.0500.0500.0000.0000.0000.000
160A731ARG10.8640.94428.1670.6310.6310.0000.0000.0000.000
161A732ALA00.0000.00929.8700.0460.0460.0000.0000.0000.000
162A733ALA00.0250.01430.9510.0320.0320.0000.0000.0000.000
163A734HIS10.8250.88131.2110.5720.5720.0000.0000.0000.000
164A735LYS10.8930.96434.3760.5080.5080.0000.0000.0000.000
165A736ILE00.0090.01036.3380.0210.0210.0000.0000.0000.000
166A737GLY0-0.0050.00437.9350.0080.0080.0000.0000.0000.000
167A738LEU0-0.0050.01034.9860.0050.0050.0000.0000.0000.000
168A739PRO0-0.0070.00032.524-0.020-0.0200.0000.0000.0000.000
169A740LEU0-0.046-0.03625.328-0.038-0.0380.0000.0000.0000.000
170A741VAL0-0.017-0.00628.7170.0120.0120.0000.0000.0000.000
171A742GLY00.0310.02325.659-0.055-0.0550.0000.0000.0000.000
172A743MET0-0.042-0.00819.7940.0080.0080.0000.0000.0000.000
173A744THR0-0.044-0.03519.817-0.115-0.1150.0000.0000.0000.000
174A745GLN0-0.086-0.07413.638-0.112-0.1120.0000.0000.0000.000
175A746ASP-1-0.838-0.90816.505-1.181-1.1810.0000.0000.0000.000
176A747GLY0-0.0120.00718.7640.1320.1320.0000.0000.0000.000
177A748GLY0-0.020-0.01221.6290.0910.0910.0000.0000.0000.000
178A749GLU-1-0.820-0.88123.014-0.949-0.9490.0000.0000.0000.000
179A750ASP-1-0.760-0.84826.152-0.533-0.5330.0000.0000.0000.000
180A751THR0-0.044-0.02929.0030.0570.0570.0000.0000.0000.000
181A752ARG10.8690.92919.1950.9360.9360.0000.0000.0000.000
182A753ILE00.0090.01026.0950.0460.0460.0000.0000.0000.000
183A754CYS0-0.004-0.02323.717-0.093-0.0930.0000.0000.0000.000
184A755THR0-0.036-0.02724.438-0.075-0.0750.0000.0000.0000.000
185A756LEU0-0.007-0.02027.1290.0010.0010.0000.0000.0000.000
186A757ASP-1-0.880-0.93629.300-0.564-0.5640.0000.0000.0000.000
187A758ASP-1-0.814-0.88929.279-0.564-0.5640.0000.0000.0000.000
188A759ALA0-0.057-0.03829.4590.0120.0120.0000.0000.0000.000
189A760ALA0-0.030-0.01931.5350.0140.0140.0000.0000.0000.000
190A761ASP-1-0.892-0.93634.925-0.408-0.4080.0000.0000.0000.000
191A762HIS00.0600.03033.216-0.006-0.0060.0000.0000.0000.000
192A763ALA0-0.013-0.01135.1300.0150.0150.0000.0000.0000.000
193A764PHE0-0.0150.00036.5870.0230.0230.0000.0000.0000.000
194A765ASP-1-0.872-0.93737.727-0.369-0.3690.0000.0000.0000.000
195A766SER0-0.123-0.07337.3060.0140.0140.0000.0000.0000.000
196A767MET0-0.054-0.01839.3870.0000.0000.0000.0000.0000.000
197A768GLU-1-0.976-0.97942.871-0.254-0.2540.0000.0000.0000.000
198A769SER-1-0.981-0.98044.146-0.292-0.2920.0000.0000.0000.000