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: 2J1GR

Calculation Name: 3E57-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E57

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1A2

Base Structure: X-ray

Registration Date: 2023-09-20

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2040238.875186
FMO2-HF: Nuclear repulsion 1968079.143972
FMO2-HF: Total energy -72159.731214
FMO2-MP2: Total energy -72373.847147


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
87.94786.53633.204-16.141-15.6490.172
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.792 / q_NPA : -0.872
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].
3A6ILE00.002-0.0142.3730.8374.3790.961-1.833-2.6690.006
4A7LEU0-0.031-0.0114.664-5.363-5.279-0.001-0.013-0.0690.000
5A8VAL0-0.030-0.0188.3300.8100.8100.0000.0000.0000.000
6A9VAL00.0310.01911.022-1.331-1.3310.0000.0000.0000.000
7A10LYS10.8270.90014.800-13.655-13.6550.0000.0000.0000.000
8A11THR00.019-0.00317.415-0.124-0.1240.0000.0000.0000.000
9A12GLU-1-0.874-0.93419.22612.19312.1930.0000.0000.0000.000
10A13ASP-1-0.825-0.91019.75113.66613.6660.0000.0000.0000.000
11A14PHE0-0.005-0.01118.874-0.281-0.2810.0000.0000.0000.000
12A15LEU0-0.011-0.00720.897-0.466-0.4660.0000.0000.0000.000
13A16LYS10.8170.90924.183-12.087-12.0870.0000.0000.0000.000
14A17GLU-1-0.855-0.89123.17911.51911.5190.0000.0000.0000.000
15A18PHE0-0.025-0.02721.197-0.262-0.2620.0000.0000.0000.000
16A19GLY00.0050.01825.544-0.289-0.2890.0000.0000.0000.000
17A20GLU-1-0.972-0.98525.59111.38711.3870.0000.0000.0000.000
18A21PHE0-0.029-0.03022.221-0.334-0.3340.0000.0000.0000.000
19A22GLU-1-0.785-0.85624.00914.05914.0590.0000.0000.0000.000
20A23GLY0-0.014-0.01423.726-0.526-0.5260.0000.0000.0000.000
21A24PHE0-0.021-0.02222.9860.5800.5800.0000.0000.0000.000
22A25MET0-0.0300.00424.320-0.825-0.8250.0000.0000.0000.000
23A26ARG10.9650.99224.930-10.540-10.5400.0000.0000.0000.000
24A27VAL00.0100.00623.030-0.291-0.2910.0000.0000.0000.000
25A28ASN0-0.045-0.04126.0110.2660.2660.0000.0000.0000.000
26A29PHE00.0530.01819.0890.2760.2760.0000.0000.0000.000
27A30GLU-1-0.932-0.96522.55011.86411.8640.0000.0000.0000.000
28A31ASP-1-0.827-0.91223.65711.71911.7190.0000.0000.0000.000
29A32PHE0-0.020-0.00416.1710.2600.2600.0000.0000.0000.000
30A33LEU0-0.005-0.01018.0920.7000.7000.0000.0000.0000.000
31A34ASN00.0070.00519.3650.6340.6340.0000.0000.0000.000
32A35PHE00.0120.01717.5480.1800.1800.0000.0000.0000.000
33A36LEU00.0040.00214.2580.4210.4210.0000.0000.0000.000
34A37ASP-1-0.788-0.88016.30616.71516.7150.0000.0000.0000.000
35A38GLN0-0.099-0.02918.240-0.246-0.2460.0000.0000.0000.000
36A39TYR0-0.079-0.08418.238-0.514-0.5140.0000.0000.0000.000
37A40GLY0-0.0120.01214.2120.4940.4940.0000.0000.0000.000
38A41PHE0-0.065-0.03812.341-0.599-0.5990.0000.0000.0000.000
39A42PHE00.0380.0236.4741.2971.2970.0000.0000.0000.000
40A43ARG10.8030.8847.423-24.799-24.7990.0000.0000.0000.000
41A44GLU-1-0.811-0.8973.27131.83132.5040.029-0.402-0.300-0.003
42A45ARG10.8950.9321.693-100.138-104.47216.705-6.443-5.9280.078
43A46ASP-1-0.911-0.9604.81633.78234.039-0.001-0.011-0.2450.000
44A47GLU-1-0.957-0.9687.03319.36319.3630.0000.0000.0000.000
45A48ALA0-0.043-0.0357.897-1.820-1.8200.0000.0000.0000.000
46A49GLU-1-0.938-0.9467.90932.34032.3400.0000.0000.0000.000
47A50TYR0-0.059-0.0569.850-2.785-2.7850.0000.0000.0000.000
48A51ASP-1-0.796-0.85013.02516.55516.5550.0000.0000.0000.000
49A52GLU-1-0.810-0.89914.52816.54316.5430.0000.0000.0000.000
50A53THR0-0.065-0.04316.681-1.055-1.0550.0000.0000.0000.000
51A54THR0-0.099-0.04612.975-0.236-0.2360.0000.0000.0000.000
52A55LYS10.8330.92613.589-17.860-17.8600.0000.0000.0000.000
53A56GLN00.0410.0127.7694.0594.0590.0000.0000.0000.000
54A57VAL0-0.007-0.00610.312-1.760-1.7600.0000.0000.0000.000
55A58ILE0-0.054-0.0188.6892.9492.9490.0000.0000.0000.000
56A59PRO0-0.0190.00710.151-3.062-3.0620.0000.0000.0000.000
57A60TYR00.0270.00512.4990.7720.7720.0000.0000.0000.000
58A61VAL00.0220.00614.977-1.846-1.8460.0000.0000.0000.000
59A62VAL00.0130.01417.2900.1420.1420.0000.0000.0000.000
60A63ILE00.0110.01418.383-0.470-0.4700.0000.0000.0000.000
61A64MET0-0.027-0.01621.823-0.394-0.3940.0000.0000.0000.000
62A65ASP-1-0.835-0.90425.62611.57311.5730.0000.0000.0000.000
63A66GLY0-0.022-0.01627.720-0.324-0.3240.0000.0000.0000.000
64A67ASP-1-0.921-0.97430.6409.7089.7080.0000.0000.0000.000
65A68ARG10.8460.90529.245-10.134-10.1340.0000.0000.0000.000
66A69VAL00.001-0.00424.2090.2730.2730.0000.0000.0000.000
67A70LEU0-0.022-0.00519.950-0.338-0.3380.0000.0000.0000.000
68A71ILE0-0.022-0.00522.0090.3720.3720.0000.0000.0000.000
69A72THR00.0110.00217.651-0.463-0.4630.0000.0000.0000.000
70A73LYS10.8040.89120.748-13.011-13.0110.0000.0000.0000.000
71A74ARG11.0011.01812.212-24.155-24.1550.0000.0000.0000.000
72A87TYR0-0.052-0.06922.123-0.272-0.2720.0000.0000.0000.000
73A88SER0-0.062-0.03217.293-0.024-0.0240.0000.0000.0000.000
74A89LEU0-0.004-0.02220.045-0.313-0.3130.0000.0000.0000.000
75A90GLY0-0.017-0.00617.789-0.484-0.4840.0000.0000.0000.000
76A91ILE0-0.031-0.01012.8360.1340.1340.0000.0000.0000.000
77A92GLY00.0390.02011.913-0.642-0.6420.0000.0000.0000.000
78A93GLY00.0040.0007.8541.4191.4190.0000.0000.0000.000
79A94HIS00.012-0.0014.1824.1284.4160.001-0.058-0.2300.000
80A95VAL00.0070.0256.0490.9370.9370.0000.0000.0000.000
81A96ARG10.8100.8811.722-102.808-104.72915.510-7.381-6.2080.091
82A97GLU-1-0.790-0.8884.86022.04822.0480.0000.0000.0000.000
83A98GLY0-0.043-0.0236.366-3.151-3.1510.0000.0000.0000.000
84A99ASP-1-0.795-0.8617.52338.84338.8430.0000.0000.0000.000
85A100GLY0-0.014-0.0249.613-2.243-2.2430.0000.0000.0000.000
86A101ALA0-0.045-0.00512.1350.6140.6140.0000.0000.0000.000
87A102THR0-0.019-0.03114.865-0.325-0.3250.0000.0000.0000.000
88A103PRO00.0450.01512.5181.2201.2200.0000.0000.0000.000
89A104ARG10.8320.88713.479-13.527-13.5270.0000.0000.0000.000
90A105GLU-1-0.906-0.93015.35517.37917.3790.0000.0000.0000.000
91A106ALA0-0.0060.0049.7840.6200.6200.0000.0000.0000.000
92A107PHE00.014-0.01011.1221.7931.7930.0000.0000.0000.000
93A108LEU0-0.017-0.00712.6070.4490.4490.0000.0000.0000.000
94A109LYS10.8330.91611.483-23.094-23.0940.0000.0000.0000.000
95A110GLY00.016-0.0039.2270.9650.9650.0000.0000.0000.000
96A111LEU0-0.006-0.0029.8990.8450.8450.0000.0000.0000.000
97A112GLU-1-0.876-0.92012.67720.89420.8940.0000.0000.0000.000
98A113ARG10.7140.8016.126-43.994-43.9940.0000.0000.0000.000
99A114GLU-1-0.862-0.9418.93226.67326.6730.0000.0000.0000.000
100A115VAL00.0370.0289.857-0.849-0.8490.0000.0000.0000.000
101A116ASN0-0.066-0.03813.358-1.678-1.6780.0000.0000.0000.000
102A117GLU-1-0.839-0.9007.15644.27744.2770.0000.0000.0000.000
103A118GLU-1-0.876-0.93211.70222.00322.0030.0000.0000.0000.000
104A119VAL0-0.016-0.02013.804-1.872-1.8720.0000.0000.0000.000
105A120ASP-1-0.928-0.96017.04816.20616.2060.0000.0000.0000.000
106A121VAL00.0370.00518.675-0.943-0.9430.0000.0000.0000.000
107A122SER0-0.023-0.00421.0500.1610.1610.0000.0000.0000.000
108A123LEU0-0.028-0.01418.889-0.589-0.5890.0000.0000.0000.000
109A124ARG10.7920.88323.063-10.833-10.8330.0000.0000.0000.000
110A125GLU-1-0.859-0.93024.91610.87210.8720.0000.0000.0000.000
111A126LEU00.0020.02017.6700.1080.1080.0000.0000.0000.000
112A127GLU-1-0.875-0.91922.41011.40211.4020.0000.0000.0000.000
113A128PHE00.0010.00019.4420.2930.2930.0000.0000.0000.000
114A129LEU0-0.017-0.02122.237-0.754-0.7540.0000.0000.0000.000
115A130GLY00.001-0.02622.258-0.785-0.7850.0000.0000.0000.000
116A131LEU0-0.0180.01018.7890.8400.8400.0000.0000.0000.000
117A132ILE0-0.029-0.01718.603-0.944-0.9440.0000.0000.0000.000
118A133ASN00.0190.00318.5481.8901.8900.0000.0000.0000.000
119A134SER00.0330.01419.380-0.577-0.5770.0000.0000.0000.000
120A135SER0-0.040-0.05119.5940.6970.6970.0000.0000.0000.000
121A136THR0-0.023-0.01821.5510.0350.0350.0000.0000.0000.000
122A137THR0-0.017-0.00518.1610.1320.1320.0000.0000.0000.000
123A138GLU-1-0.788-0.89816.44715.69615.6960.0000.0000.0000.000
124A139VAL00.0160.01111.9950.4340.4340.0000.0000.0000.000
125A140SER0-0.049-0.03513.9560.6120.6120.0000.0000.0000.000
126A141ARG10.7540.85816.347-15.335-15.3350.0000.0000.0000.000
127A142VAL00.0220.04211.846-0.480-0.4800.0000.0000.0000.000
128A143HIS0-0.084-0.0379.1503.3393.3390.0000.0000.0000.000
129A144LEU00.0080.01413.253-1.990-1.9900.0000.0000.0000.000
130A145GLY00.0170.01214.0661.5921.5920.0000.0000.0000.000
131A146ALA0-0.023-0.01115.498-1.496-1.4960.0000.0000.0000.000
132A147LEU0-0.0040.00316.7790.7350.7350.0000.0000.0000.000
133A148PHE00.012-0.00516.236-0.877-0.8770.0000.0000.0000.000
134A149LEU0-0.0040.00820.2530.1840.1840.0000.0000.0000.000
135A150GLY00.035-0.00121.095-0.143-0.1430.0000.0000.0000.000
136A151ARG10.8430.92222.033-11.573-11.5730.0000.0000.0000.000
137A152GLY00.030-0.01024.6270.1060.1060.0000.0000.0000.000
138A153LYS10.8940.97725.439-11.013-11.0130.0000.0000.0000.000
139A154PHE00.0390.00620.8300.4960.4960.0000.0000.0000.000
140A155PHE0-0.090-0.04723.299-0.907-0.9070.0000.0000.0000.000
141A156SER0-0.023-0.01422.258-0.305-0.3050.0000.0000.0000.000
142A157VAL00.0370.02818.6560.4720.4720.0000.0000.0000.000
143A158LYS10.7850.89815.424-19.975-19.9750.0000.0000.0000.000
144A159GLU-1-0.898-0.95513.81621.76221.7620.0000.0000.0000.000
145A160LYS10.8150.87917.428-14.228-14.2280.0000.0000.0000.000
146A161ASP-1-0.853-0.91019.08514.53614.5360.0000.0000.0000.000
147A162LEU0-0.071-0.01112.8850.2950.2950.0000.0000.0000.000
148A163PHE00.005-0.01312.833-0.025-0.0250.0000.0000.0000.000
149A164GLU-1-0.855-0.89518.80212.54712.5470.0000.0000.0000.000
150A165TRP0-0.001-0.03021.4730.4690.4690.0000.0000.0000.000
151A166GLU-1-0.832-0.87723.35111.20311.2030.0000.0000.0000.000
152A167LEU00.0010.00825.3340.3670.3670.0000.0000.0000.000
153A168ILE0-0.0030.01627.508-0.578-0.5780.0000.0000.0000.000
154A169LYS10.8300.92029.688-8.668-8.6680.0000.0000.0000.000
155A170LEU00.0810.03229.1140.0420.0420.0000.0000.0000.000
156A171GLU-1-0.850-0.91632.2008.7218.7210.0000.0000.0000.000
157A172GLU-1-0.866-0.94432.2369.8689.8680.0000.0000.0000.000
158A173LEU0-0.006-0.00226.7980.1680.1680.0000.0000.0000.000
159A174GLU-1-0.907-0.94830.5169.7999.7990.0000.0000.0000.000
160A175LYS10.8630.93532.645-9.872-9.8720.0000.0000.0000.000
161A176PHE00.021-0.00228.141-0.011-0.0110.0000.0000.0000.000
162A177SER0-0.0040.00627.4760.3410.3410.0000.0000.0000.000
163A178GLY0-0.017-0.01128.3690.1600.1600.0000.0000.0000.000
164A179VAL0-0.069-0.03627.435-0.073-0.0730.0000.0000.0000.000
165A180MET0-0.0610.00223.8660.4510.4510.0000.0000.0000.000
166A181GLU-1-0.851-0.94322.22012.40612.4060.0000.0000.0000.000
167A182GLY0-0.005-0.00720.1300.6410.6410.0000.0000.0000.000
168A183TRP00.0330.01413.955-0.501-0.5010.0000.0000.0000.000
169A184SER00.0340.03819.434-0.348-0.3480.0000.0000.0000.000
170A185LYS10.9460.97821.476-12.122-12.1220.0000.0000.0000.000
171A186ILE0-0.0130.00521.690-0.546-0.5460.0000.0000.0000.000
172A187SER00.018-0.01521.086-0.283-0.2830.0000.0000.0000.000
173A188ALA00.0060.00123.652-0.376-0.3760.0000.0000.0000.000
174A189ALA0-0.0130.00226.555-0.447-0.4470.0000.0000.0000.000
175A190VAL0-0.019-0.00825.421-0.456-0.4560.0000.0000.0000.000
176A191LEU00.021-0.00524.142-0.369-0.3690.0000.0000.0000.000
177A192LEU0-0.027-0.01328.130-0.327-0.3270.0000.0000.0000.000
178A193ASN0-0.053-0.02131.317-0.499-0.4990.0000.0000.0000.000
179A194LEU0-0.070-0.02727.785-0.280-0.2800.0000.0000.0000.000
180A195PHE0-0.047-0.00828.942-0.324-0.3240.0000.0000.0000.000