FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 3J6KL

Calculation Name: 2FB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q812L9

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2148101.26625
FMO2-HF: Nuclear repulsion 2069015.899714
FMO2-HF: Total energy -79085.366535
FMO2-MP2: Total energy -79315.380687


3D Structure
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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-29.041-30.19619.596-10.101-8.336-0.085
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.023
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].
3A4ALA00.0940.0323.794-1.678-0.2490.000-0.619-0.8090.004
4A5MET0-0.0190.0025.4040.0020.0020.0000.0000.0000.000
5A6HIS0-0.070-0.0494.0270.0770.200-0.001-0.013-0.1090.000
6A7GLU-1-0.768-0.8862.511-4.490-2.0920.730-1.480-1.648-0.015
7A8TRP0-0.052-0.0105.2790.1480.178-0.001-0.001-0.0270.000
8A9GLY00.0400.0138.8460.0110.0110.0000.0000.0000.000
9A10LEU00.0000.0025.7890.0370.0370.0000.0000.0000.000
10A11SER0-0.016-0.0258.6900.0090.0090.0000.0000.0000.000
11A12GLU-1-0.841-0.91510.8530.0330.0330.0000.0000.0000.000
12A13GLU-1-0.895-0.95012.7230.0440.0440.0000.0000.0000.000
13A14LEU0-0.0140.00811.3190.0000.0000.0000.0000.0000.000
14A15LYS10.7920.89814.8250.0130.0130.0000.0000.0000.000
15A16ILE0-0.009-0.00317.0300.0050.0050.0000.0000.0000.000
16A17GLN00.0350.00915.923-0.005-0.0050.0000.0000.0000.000
17A18THR0-0.031-0.02418.266-0.002-0.0020.0000.0000.0000.000
18A19LYS10.9290.96220.788-0.003-0.0030.0000.0000.0000.000
19A20GLN00.0360.02422.071-0.001-0.0010.0000.0000.0000.000
20A21MET0-0.032-0.01023.5410.0030.0030.0000.0000.0000.000
21A22ILE0-0.017-0.01124.3650.0000.0000.0000.0000.0000.000
22A23GLU-1-0.888-0.94026.7940.0040.0040.0000.0000.0000.000
23A24ILE0-0.054-0.03126.6670.0020.0020.0000.0000.0000.000
24A25ALA00.0060.00029.5650.0010.0010.0000.0000.0000.000
25A26GLU-1-0.914-0.96430.508-0.006-0.0060.0000.0000.0000.000
26A27LYS10.9290.97032.8480.0030.0030.0000.0000.0000.000
27A28GLU-1-0.814-0.89134.174-0.011-0.0110.0000.0000.0000.000
28A29LEU00.0240.01134.4880.0000.0000.0000.0000.0000.000
29A30SER0-0.110-0.05737.3580.0020.0020.0000.0000.0000.000
30A31ILE0-0.023-0.02038.6460.0010.0010.0000.0000.0000.000
31A32MET00.0070.00638.6440.0000.0000.0000.0000.0000.000
32A33ARG10.9010.94040.9090.0050.0050.0000.0000.0000.000
33A34ASN0-0.007-0.00943.2140.0010.0010.0000.0000.0000.000
34A35ALA00.0050.00544.6350.0000.0000.0000.0000.0000.000
35A36ILE0-0.036-0.01446.3360.0000.0000.0000.0000.0000.000
36A37ASP-1-0.934-0.95448.060-0.005-0.0050.0000.0000.0000.000
37A38LYS10.7810.88847.7030.0040.0040.0000.0000.0000.000
38A39GLU-1-0.901-0.95851.512-0.008-0.0080.0000.0000.0000.000
39A40ASP-1-1.021-1.00052.353-0.005-0.0050.0000.0000.0000.000
40A41GLU-1-0.880-0.93446.249-0.006-0.0060.0000.0000.0000.000
41A42CYS00.0270.01148.155-0.001-0.0010.0000.0000.0000.000
42A43ILE00.0510.01943.637-0.001-0.0010.0000.0000.0000.000
43A44LEU00.020-0.00242.989-0.001-0.0010.0000.0000.0000.000
44A45CYS0-0.097-0.04442.903-0.001-0.0010.0000.0000.0000.000
45A46LYS10.9180.94538.8700.0110.0110.0000.0000.0000.000
46A47MET0-0.045-0.01938.050-0.002-0.0020.0000.0000.0000.000
47A48GLU-1-0.937-0.96236.028-0.030-0.0300.0000.0000.0000.000
48A49ASP-1-0.869-0.93834.388-0.023-0.0230.0000.0000.0000.000
49A50ILE0-0.014-0.01232.896-0.002-0.0020.0000.0000.0000.000
50A51HIS00.010-0.00332.527-0.004-0.0040.0000.0000.0000.000
51A52HIS00.0380.02728.031-0.006-0.0060.0000.0000.0000.000
52A53MET0-0.0280.00828.642-0.004-0.0040.0000.0000.0000.000
53A54LEU00.0190.00827.658-0.003-0.0030.0000.0000.0000.000
54A55ALA0-0.0050.00027.300-0.005-0.0050.0000.0000.0000.000
55A56ASN0-0.036-0.03924.260-0.012-0.0120.0000.0000.0000.000
56A57VAL0-0.0040.00622.957-0.006-0.0060.0000.0000.0000.000
57A58GLN0-0.046-0.01822.647-0.009-0.0090.0000.0000.0000.000
58A59THR00.0050.00120.047-0.007-0.0070.0000.0000.0000.000
59A60LEU0-0.036-0.00718.483-0.019-0.0190.0000.0000.0000.000
60A61ALA00.0570.02817.606-0.013-0.0130.0000.0000.0000.000
61A62ALA0-0.022-0.00617.936-0.007-0.0070.0000.0000.0000.000
62A63THR0-0.016-0.02413.522-0.026-0.0260.0000.0000.0000.000
63A64TYR0-0.018-0.00313.371-0.031-0.0310.0000.0000.0000.000
64A65TYR0-0.001-0.01013.376-0.011-0.0110.0000.0000.0000.000
65A66ILE0-0.0160.00411.8380.0020.0020.0000.0000.0000.000
66A67GLN0-0.007-0.0025.6930.0250.0250.0000.0000.0000.000
67A68ALA0-0.0160.0008.954-0.016-0.0160.0000.0000.0000.000
68A69TYR0-0.026-0.02410.6020.0620.0620.0000.0000.0000.000
69A70LEU00.0110.0029.4820.0540.0540.0000.0000.0000.000
70A71SER0-0.0160.0014.9380.1020.1020.0000.0000.0000.000
71A72PRO0-0.042-0.0204.0550.2260.4900.000-0.043-0.2210.000
72A73TYR0-0.040-0.0165.8000.5510.5510.0000.0000.0000.000
73A74THR0-0.062-0.0476.051-0.347-0.3470.0000.0000.0000.000
74A75GLU-1-0.818-0.8631.684-25.702-31.21118.870-7.942-5.419-0.074
75A76SER0-0.025-0.0355.1480.3310.368-0.001-0.002-0.0330.000
76A77SER00.0320.0187.8710.2050.2050.0000.0000.0000.000
77A78SER00.0560.0389.2430.1090.1090.0000.0000.0000.000
78A79PHE00.0070.00611.0690.1060.1060.0000.0000.0000.000
79A80ILE00.0460.01911.6930.0780.0780.0000.0000.0000.000
80A81THR0-0.017-0.01713.1190.0730.0730.0000.0000.0000.000
81A82THR0-0.040-0.02914.9790.0470.0470.0000.0000.0000.000
82A83ALA00.0090.00916.9920.0310.0310.0000.0000.0000.000
83A84ILE0-0.001-0.00418.0610.0310.0310.0000.0000.0000.000
84A85GLN0-0.0010.00518.0050.0240.0240.0000.0000.0000.000
85A86HIS0-0.078-0.06021.1310.0290.0290.0000.0000.0000.000
86A87LEU0-0.017-0.01121.6970.0140.0140.0000.0000.0000.000
87A88SER0-0.029-0.02223.9580.0150.0150.0000.0000.0000.000
88A89ALA0-0.019-0.01125.6520.0110.0110.0000.0000.0000.000
89A90ARG10.7570.86624.5590.1520.1520.0000.0000.0000.000
90A91LYS10.8920.95428.8230.0820.0820.0000.0000.0000.000
91A92HIS0-0.019-0.00627.181-0.002-0.0020.0000.0000.0000.000
92A93GLY00.0290.01426.897-0.007-0.0070.0000.0000.0000.000
93A94ALA0-0.025-0.01423.084-0.007-0.0070.0000.0000.0000.000
94A95LEU0-0.031-0.00923.1030.0090.0090.0000.0000.0000.000
95A96ILE0-0.009-0.00516.626-0.007-0.0070.0000.0000.0000.000
96A97VAL00.0360.02217.1280.0070.0070.0000.0000.0000.000
97A98VAL0-0.028-0.01511.616-0.042-0.0420.0000.0000.0000.000
98A99GLU-1-0.800-0.89512.885-0.074-0.0740.0000.0000.0000.000
99A100ARG10.7570.85911.667-0.034-0.0340.0000.0000.0000.000
100A101ASN0-0.063-0.03612.4070.0620.0620.0000.0000.0000.000
101A102GLU-1-0.926-0.96013.7380.0220.0220.0000.0000.0000.000
102A103THR0-0.062-0.04315.886-0.013-0.0130.0000.0000.0000.000
103A104LEU00.029-0.00117.0360.0030.0030.0000.0000.0000.000
104A105GLU-1-0.866-0.92119.868-0.060-0.0600.0000.0000.0000.000
105A106ALA0-0.025-0.01121.8840.0010.0010.0000.0000.0000.000
106A107LEU0-0.069-0.03522.2730.0040.0040.0000.0000.0000.000
107A108ILE0-0.030-0.00320.155-0.003-0.0030.0000.0000.0000.000
108A109GLN0-0.0040.00224.3120.0010.0010.0000.0000.0000.000
109A110THR0-0.027-0.02523.129-0.004-0.0040.0000.0000.0000.000
110A111GLY00.0390.04825.0850.0090.0090.0000.0000.0000.000
111A112THR0-0.054-0.03025.0540.0070.0070.0000.0000.0000.000
112A113THR0-0.012-0.02420.829-0.010-0.0100.0000.0000.0000.000
113A114LEU0-0.058-0.03319.7340.0070.0070.0000.0000.0000.000
114A115ASN0-0.062-0.03616.742-0.007-0.0070.0000.0000.0000.000
115A116ALA00.0050.01916.987-0.010-0.0100.0000.0000.0000.000
116A117HIS00.0600.02311.290-0.063-0.0630.0000.0000.0000.000
117A118LEU0-0.0030.01411.5340.0890.0890.0000.0000.0000.000
118A119THR0-0.014-0.01513.345-0.033-0.0330.0000.0000.0000.000
119A120ALA00.0630.02315.7770.0200.0200.0000.0000.0000.000
120A121PRO00.0440.01117.6510.0210.0210.0000.0000.0000.000
121A122LEU0-0.0090.00918.1370.0230.0230.0000.0000.0000.000
122A123LEU00.0280.00715.7030.0220.0220.0000.0000.0000.000
123A124GLU-1-0.786-0.87720.048-0.170-0.1700.0000.0000.0000.000
124A125SER0-0.024-0.00823.0130.0200.0200.0000.0000.0000.000
125A126ILE0-0.040-0.01820.5380.0130.0130.0000.0000.0000.000
126A127PHE00.0290.01721.1550.0110.0110.0000.0000.0000.000
127A128TYR00.0000.01326.0130.0100.0100.0000.0000.0000.000
128A129PRO00.0260.01028.8800.0030.0030.0000.0000.0000.000
129A130GLY0-0.006-0.00331.9680.0020.0020.0000.0000.0000.000
130A131ASN0-0.089-0.04427.7400.0020.0020.0000.0000.0000.000
131A132PRO00.008-0.01330.4840.0010.0010.0000.0000.0000.000
132A133LEU0-0.024-0.01524.7550.0000.0000.0000.0000.0000.000
133A134HIS0-0.036-0.01126.469-0.003-0.0030.0000.0000.0000.000
134A135ASP-1-0.953-0.96427.875-0.088-0.0880.0000.0000.0000.000
135A136GLY00.0320.01527.1240.0030.0030.0000.0000.0000.000
136A137ALA0-0.047-0.02922.198-0.007-0.0070.0000.0000.0000.000
137A138VAL0-0.0020.00217.659-0.001-0.0010.0000.0000.0000.000
138A139LEU0-0.0250.00416.3950.0060.0060.0000.0000.0000.000
139A140VAL0-0.005-0.00411.429-0.026-0.0260.0000.0000.0000.000
140A141LYS10.8900.92610.3840.1450.1450.0000.0000.0000.000
141A142ASN00.0450.0104.1120.0730.146-0.001-0.001-0.0700.000
142A143ASN00.0140.0225.1240.4600.4600.0000.0000.0000.000
143A144HIS00.000-0.0018.8430.1740.1740.0000.0000.0000.000
144A145ILE0-0.009-0.00112.2930.0300.0300.0000.0000.0000.000
145A146VAL00.0290.00914.7850.0140.0140.0000.0000.0000.000
146A147SER00.0560.02516.9360.0170.0170.0000.0000.0000.000
147A148ALA00.0130.00920.039-0.015-0.0150.0000.0000.0000.000
148A149ALA00.0330.02122.7740.0090.0090.0000.0000.0000.000
149A150ASN0-0.050-0.02621.1010.0170.0170.0000.0000.0000.000
150A151ILE00.0250.00925.1610.0030.0030.0000.0000.0000.000
151A152LEU00.0180.01422.501-0.001-0.0010.0000.0000.0000.000
152A153PRO0-0.0140.00625.6870.0040.0040.0000.0000.0000.000
153A154LEU0-0.008-0.00928.252-0.002-0.0020.0000.0000.0000.000
154A155THR0-0.014-0.04329.7680.0050.0050.0000.0000.0000.000
155A156LYS10.9120.94231.4290.0370.0370.0000.0000.0000.000
156A157SER0-0.0260.00232.6420.0030.0030.0000.0000.0000.000
157A158THR00.005-0.02834.557-0.002-0.0020.0000.0000.0000.000
158A159GLU-1-0.930-0.93634.572-0.021-0.0210.0000.0000.0000.000
159A160VAL0-0.066-0.02431.941-0.001-0.0010.0000.0000.0000.000
160A161ASP-1-0.859-0.93133.128-0.043-0.0430.0000.0000.0000.000
161A162PRO0-0.027-0.03834.963-0.002-0.0020.0000.0000.0000.000
162A163GLU-1-0.939-0.95536.459-0.040-0.0400.0000.0000.0000.000
163A164LEU0-0.079-0.01730.575-0.005-0.0050.0000.0000.0000.000
164A165GLY00.0710.03033.1500.0020.0020.0000.0000.0000.000
165A166THR0-0.009-0.03232.030-0.002-0.0020.0000.0000.0000.000
166A167ARG10.8760.90827.1100.0960.0960.0000.0000.0000.000
167A168HIS00.0540.02027.273-0.005-0.0050.0000.0000.0000.000
168A169ARG10.9430.96227.7780.0480.0480.0000.0000.0000.000
169A170ALA00.0130.01426.9430.0050.0050.0000.0000.0000.000
170A171ALA00.0170.01723.4780.0000.0000.0000.0000.0000.000
171A172ILE00.0100.00224.0250.0030.0030.0000.0000.0000.000
172A173GLY00.0190.00926.0190.0060.0060.0000.0000.0000.000
173A174LEU00.009-0.00720.3620.0050.0050.0000.0000.0000.000
174A175SER0-0.035-0.01621.7730.0080.0080.0000.0000.0000.000
175A176GLU-1-0.829-0.88022.742-0.026-0.0260.0000.0000.0000.000
176A177LYS10.7620.87924.7700.0360.0360.0000.0000.0000.000
177A178SER00.0200.02319.780-0.002-0.0020.0000.0000.0000.000
178A179ASP-1-0.774-0.88115.3330.0470.0470.0000.0000.0000.000
179A180ALA0-0.0030.01216.3040.0000.0000.0000.0000.0000.000
180A181LEU00.0050.01314.4000.0060.0060.0000.0000.0000.000
181A182ILE0-0.061-0.02816.904-0.025-0.0250.0000.0000.0000.000
182A183LEU00.0010.00815.7530.0130.0130.0000.0000.0000.000
183A184VAL0-0.015-0.01919.9130.0010.0010.0000.0000.0000.000
184A185VAL00.0010.01422.874-0.001-0.0010.0000.0000.0000.000
185A186SER00.0120.00625.3400.0040.0040.0000.0000.0000.000
186A187GLU-1-0.788-0.88829.093-0.086-0.0860.0000.0000.0000.000
187A188GLU-1-0.954-0.95131.334-0.059-0.0590.0000.0000.0000.000
188A189THR0-0.006-0.02631.5680.0010.0010.0000.0000.0000.000
189A190GLY00.0190.01628.4860.0010.0010.0000.0000.0000.000
190A191ARG10.9410.99526.9360.0570.0570.0000.0000.0000.000
191A192THR00.0030.00722.147-0.004-0.0040.0000.0000.0000.000
192A193SER0-0.037-0.03423.2680.0090.0090.0000.0000.0000.000
193A194PHE00.0170.00618.881-0.018-0.0180.0000.0000.0000.000
194A195ALA0-0.0070.01020.8740.0120.0120.0000.0000.0000.000
195A196LEU00.022-0.00917.035-0.009-0.0090.0000.0000.0000.000
196A197ASN00.0210.00720.4900.0070.0070.0000.0000.0000.000
197A198GLY00.0100.00622.6360.0040.0040.0000.0000.0000.000
198A199ILE0-0.040-0.00324.2920.0000.0000.0000.0000.0000.000
199A200LEU0-0.002-0.00523.748-0.008-0.0080.0000.0000.0000.000
200A201TYR00.0010.00121.8930.0070.0070.0000.0000.0000.000
201A202THR0-0.035-0.02623.260-0.010-0.0100.0000.0000.0000.000
202A203ILE0-0.0010.00219.0260.0010.0010.0000.0000.0000.000
203A204SER00.0500.02122.1600.0030.0030.0000.0000.0000.000
204A205LEU00.0130.01516.835-0.001-0.0010.0000.0000.0000.000