Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V2771

Calculation Name: 2EBJ-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EBJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJW4

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2137874.244558
FMO2-HF: Nuclear repulsion 2065552.77947
FMO2-HF: Total energy -72321.465088
FMO2-MP2: Total energy -72538.411009


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:1:MET )


Summations of interaction energy for fragment #1(A:1: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.
-28.501-19.5618.248-8.036-19.152-0.048
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.012
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].
3A3LEU 00.0320.0073.144-0.8811.1121.833-0.949-2.877-0.010
4A4VAL 00.0080.0074.309-1.239-1.2920.0330.179-0.1590.000
5A5THR 00.0360.0257.851-0.157-0.1570.0000.0000.0000.000
6A6GLY 00.0310.01910.3750.0360.0360.0000.0000.0000.000
7A7PHE 0-0.048-0.02413.931-0.039-0.0390.0000.0000.0000.000
8A8GLU -1-0.801-0.87516.693-0.174-0.1740.0000.0000.0000.000
9A9PRO 0-0.033-0.01619.0690.0210.0210.0000.0000.0000.000
10A10PHE 00.0720.03522.462-0.012-0.0120.0000.0000.0000.000
11A11GLY 0-0.001-0.00724.7400.0130.0130.0000.0000.0000.000
12A12SER 0-0.033-0.02428.388-0.004-0.0040.0000.0000.0000.000
13A13LEU 0-0.071-0.01526.0300.0030.0030.0000.0000.0000.000
14A14GLU -1-0.804-0.88726.769-0.053-0.0530.0000.0000.0000.000
15A15HIS 0-0.048-0.05522.747-0.019-0.0190.0000.0000.0000.000
16A16ASN 00.0480.04520.1000.0310.0310.0000.0000.0000.000
17A17PRO 00.0310.01520.200-0.005-0.0050.0000.0000.0000.000
18A18SER 0-0.018-0.03916.2290.0070.0070.0000.0000.0000.000
19A19GLN 00.0120.00115.4560.0280.0280.0000.0000.0000.000
20A20ALA 00.0210.00115.979-0.009-0.0090.0000.0000.0000.000
21A21LEU 0-0.0010.00214.2650.0070.0070.0000.0000.0000.000
22A22LEU 0-0.018-0.01210.6110.0270.0270.0000.0000.0000.000
23A23ASP -1-0.908-0.95012.479-0.143-0.1430.0000.0000.0000.000
24A24LEU 0-0.051-0.02514.9210.0020.0020.0000.0000.0000.000
25A25LEU 0-0.089-0.03210.3590.0510.0510.0000.0000.0000.000
26A26PRO 00.0120.01410.314-0.059-0.0590.0000.0000.0000.000
27A27SER 00.027-0.0038.669-0.063-0.0630.0000.0000.0000.000
28A28GLU -1-0.960-0.9886.6710.5390.5390.0000.0000.0000.000
29A29VAL 0-0.0010.0066.826-0.177-0.1770.0000.0000.0000.000
30A30ASP -1-0.814-0.8987.3611.7331.7330.0000.0000.0000.000
31A31GLY 0-0.0130.0068.5340.2050.2050.0000.0000.0000.000
32A32LYS 10.8620.9243.491-11.002-9.6100.079-0.665-0.8060.006
33A33PRO 00.0320.0042.751-2.376-0.8490.468-0.627-1.3680.000
34A34LEU 00.0150.0212.478-6.560-3.4782.398-2.925-2.555-0.034
35A35ARG 10.7700.8332.3300.8700.0286.408-1.952-3.615-0.005
36A36LYS 10.8780.9314.0290.7140.9650.003-0.023-0.2300.001
37A37ALA 0-0.0050.0027.468-0.296-0.2960.0000.0000.0000.000
38A38VAL 0-0.0010.0019.3370.1330.1330.0000.0000.0000.000
39A39LEU 0-0.006-0.00410.593-0.069-0.0690.0000.0000.0000.000
40A40PRO 00.0410.02313.7990.0360.0360.0000.0000.0000.000
41A41VAL 0-0.016-0.05317.2590.0140.0140.0000.0000.0000.000
42A42ASP -1-0.821-0.94219.276-0.193-0.1930.0000.0000.0000.000
43A43ALA 00.0190.00419.464-0.018-0.0180.0000.0000.0000.000
44A44GLU -1-0.836-0.88320.409-0.163-0.1630.0000.0000.0000.000
45A45ALA 00.0100.00618.306-0.020-0.0200.0000.0000.0000.000
46A46LEU 0-0.0260.00014.330-0.045-0.0450.0000.0000.0000.000
47A47GLY 0-0.011-0.01714.209-0.039-0.0390.0000.0000.0000.000
48A48GLU -1-0.926-0.95813.859-0.603-0.6030.0000.0000.0000.000
49A49ALA 00.1230.05712.457-0.084-0.0840.0000.0000.0000.000
50A50LEU 0-0.093-0.0589.792-0.087-0.0870.0000.0000.0000.000
51A51GLU -1-0.948-0.9678.822-0.973-0.9730.0000.0000.0000.000
52A52ASP -1-0.880-0.9308.999-1.084-1.0840.0000.0000.0000.000
53A53LEU 0-0.067-0.0425.469-0.349-0.3490.0000.0000.0000.000
54A54HIS 0-0.043-0.0434.278-1.215-1.1220.000-0.020-0.0720.000
55A55ARG 10.9650.9936.0180.7290.7290.0000.0000.0000.000
56A56GLU -1-0.837-0.8772.902-5.321-4.2090.308-0.431-0.989-0.004
57A57GLY 0-0.052-0.0143.491-1.807-1.1090.046-0.343-0.401-0.002
58A58PRO 0-0.084-0.0362.492-1.748-0.9665.167-2.414-3.5340.001
59A59LYS 10.9120.9342.0531.238-0.1781.5052.175-2.264-0.001
60A60ALA 00.0670.0354.415-0.1650.0310.000-0.033-0.1640.000
61A61VAL 0-0.024-0.0125.5390.5450.6710.000-0.008-0.1180.000
62A62LEU 00.0090.0127.771-0.225-0.2250.0000.0000.0000.000
63A63HIS 10.8020.8699.585-0.112-0.1120.0000.0000.0000.000
64A64LEU 00.0260.01412.266-0.004-0.0040.0000.0000.0000.000
65A65GLY 00.0630.01014.904-0.044-0.0440.0000.0000.0000.000
66A66LEU 0-0.0260.00618.2050.0190.0190.0000.0000.0000.000
67A67ALA 0-0.030-0.01421.718-0.008-0.0080.0000.0000.0000.000
68A68GLU -1-0.945-0.99624.546-0.003-0.0030.0000.0000.0000.000
69A69ASP -1-0.884-0.94727.5550.0230.0230.0000.0000.0000.000
70A70ARG 10.7360.86023.541-0.079-0.0790.0000.0000.0000.000
71A71PRO 00.0150.00327.9690.0000.0000.0000.0000.0000.000
72A72VAL 0-0.026-0.00826.8840.0040.0040.0000.0000.0000.000
73A73LEU 00.0610.03720.166-0.005-0.0050.0000.0000.0000.000
74A74THR 0-0.062-0.03221.931-0.006-0.0060.0000.0000.0000.000
75A75LEU 00.0390.02317.4980.0080.0080.0000.0000.0000.000
76A76GLU -1-0.734-0.82719.1210.0920.0920.0000.0000.0000.000
77A77ARG 10.9010.94019.714-0.145-0.1450.0000.0000.0000.000
78A78LEU 0-0.0150.00321.3260.0070.0070.0000.0000.0000.000
79A79ALA 00.0050.03718.957-0.004-0.0040.0000.0000.0000.000
80A80VAL 0-0.001-0.01321.104-0.001-0.0010.0000.0000.0000.000
81A81ASN 00.0050.00922.985-0.021-0.0210.0000.0000.0000.000
82A82LEU 0-0.034-0.02824.121-0.002-0.0020.0000.0000.0000.000
83A83LEU 0-0.060-0.02122.1030.0010.0010.0000.0000.0000.000
84A84ASP -1-0.870-0.93125.922-0.030-0.0300.0000.0000.0000.000
85A85PHE 0-0.056-0.02023.6400.0050.0050.0000.0000.0000.000
86A86PRO 00.0150.02127.7920.0000.0000.0000.0000.0000.000
87A87ARG 10.9090.94426.9360.0390.0390.0000.0000.0000.000
88A88PRO 00.0330.02428.376-0.002-0.0020.0000.0000.0000.000
89A89ASP -1-0.753-0.85723.526-0.120-0.1200.0000.0000.0000.000
90A90ASN 0-0.014-0.03022.0010.0200.0200.0000.0000.0000.000
91A91ARG 10.7840.89722.2210.1680.1680.0000.0000.0000.000
92A92GLY 0-0.044-0.02426.7030.0030.0030.0000.0000.0000.000
93A93ARG 10.7720.84726.3550.1410.1410.0000.0000.0000.000
94A94VAL 00.0210.00528.1120.0020.0020.0000.0000.0000.000
95A95LEU 0-0.054-0.01625.0500.0010.0010.0000.0000.0000.000
96A96GLU -1-0.888-0.94529.123-0.036-0.0360.0000.0000.0000.000
97A97ASP -1-0.885-0.93730.979-0.033-0.0330.0000.0000.0000.000
98A98LEU 0-0.039-0.01227.660-0.005-0.0050.0000.0000.0000.000
99A99PRO 0-0.023-0.02026.4100.0040.0040.0000.0000.0000.000
100A100ILE 0-0.0330.00119.514-0.013-0.0130.0000.0000.0000.000
101A101VAL 0-0.025-0.02519.751-0.023-0.0230.0000.0000.0000.000
102A102PRO 00.0140.01322.9010.0180.0180.0000.0000.0000.000
103A103GLY 00.0020.00425.929-0.005-0.0050.0000.0000.0000.000
104A104GLY 00.0030.02123.7330.0050.0050.0000.0000.0000.000
105A105PRO 00.000-0.01022.8030.0070.0070.0000.0000.0000.000
106A106LEU 00.0410.03024.672-0.003-0.0030.0000.0000.0000.000
107A107ALA 00.003-0.00924.147-0.001-0.0010.0000.0000.0000.000
108A108LEU 0-0.0200.01318.6180.0010.0010.0000.0000.0000.000
109A109PRO 00.001-0.00120.8530.0040.0040.0000.0000.0000.000
110A110ALA 00.001-0.00717.5990.0030.0030.0000.0000.0000.000
111A111ARG 10.8420.94212.904-0.172-0.1720.0000.0000.0000.000
112A112PHE 00.0720.00512.8060.0540.0540.0000.0000.0000.000
113A113PRO 00.0550.05414.845-0.085-0.0850.0000.0000.0000.000
114A114VAL 0-0.010-0.02417.898-0.015-0.0150.0000.0000.0000.000
115A115LYS 10.9190.94520.491-0.195-0.1950.0000.0000.0000.000
116A116PRO 00.0470.02119.450-0.018-0.0180.0000.0000.0000.000
117A117VAL 00.0980.07716.478-0.008-0.0080.0000.0000.0000.000
118A118LEU 0-0.055-0.02619.590-0.028-0.0280.0000.0000.0000.000
119A119ALA 0-0.037-0.02322.984-0.020-0.0200.0000.0000.0000.000
120A120ARG 11.0111.01618.985-0.363-0.3630.0000.0000.0000.000
121A121TRP 0-0.041-0.04518.078-0.031-0.0310.0000.0000.0000.000
122A122ARG 10.9400.97222.812-0.177-0.1770.0000.0000.0000.000
123A123GLU -1-0.904-0.93924.1020.2620.2620.0000.0000.0000.000
124A124ALA 0-0.093-0.03322.693-0.007-0.0070.0000.0000.0000.000
125A125GLY 00.0090.00324.802-0.013-0.0130.0000.0000.0000.000
126A126ILE 0-0.054-0.02921.887-0.014-0.0140.0000.0000.0000.000
127A127PRO 0-0.034-0.02125.7350.0080.0080.0000.0000.0000.000
128A128GLY 00.0630.02824.9550.0060.0060.0000.0000.0000.000
129A129ARG 10.8780.94125.167-0.106-0.1060.0000.0000.0000.000
130A130PRO 00.0070.01124.0460.0060.0060.0000.0000.0000.000
131A131SER 0-0.072-0.06623.454-0.022-0.0220.0000.0000.0000.000
132A132LEU 0-0.008-0.02224.2740.0120.0120.0000.0000.0000.000
133A133SER 00.0440.02625.365-0.009-0.0090.0000.0000.0000.000
134A134ALA 00.0330.03620.8260.0050.0050.0000.0000.0000.000
135A135GLY 0-0.001-0.00722.765-0.010-0.0100.0000.0000.0000.000
136A136SER 0-0.024-0.02424.3530.0070.0070.0000.0000.0000.000
137A137TYR 00.013-0.01823.220-0.010-0.0100.0000.0000.0000.000
138A138LEU 00.0290.03918.5820.0020.0020.0000.0000.0000.000
139A139CYS 0-0.0450.00217.863-0.006-0.0060.0000.0000.0000.000
140A140ASN 00.0090.00017.5960.0280.0280.0000.0000.0000.000
141A141GLN 00.0400.02118.0400.0190.0190.0000.0000.0000.000
142A142ALA 00.0180.00613.536-0.018-0.0180.0000.0000.0000.000
143A143PHE 0-0.039-0.02914.0260.0060.0060.0000.0000.0000.000
144A144TYR 00.034-0.02215.4250.0050.0050.0000.0000.0000.000
145A145LEU 00.0220.01114.381-0.007-0.0070.0000.0000.0000.000
146A146SER 00.0160.02010.812-0.039-0.0390.0000.0000.0000.000
147A147LEU 0-0.0330.00412.3650.0070.0070.0000.0000.0000.000
148A148TYR 0-0.013-0.00614.9570.0090.0090.0000.0000.0000.000
149A149ARG 10.8890.95012.7260.3550.3550.0000.0000.0000.000
150A150LEU 0-0.0320.0028.124-0.033-0.0330.0000.0000.0000.000
151A151PRO 00.0150.00911.0050.0490.0490.0000.0000.0000.000
152A152GLU -1-0.886-0.95013.2360.2680.2680.0000.0000.0000.000
153A153GLU -1-0.934-0.97911.7100.2340.2340.0000.0000.0000.000
154A154VAL 0-0.049-0.0098.1970.1520.1520.0000.0000.0000.000
155A155PRO 00.004-0.0018.632-0.091-0.0910.0000.0000.0000.000
156A156VAL 00.0210.00510.1330.0520.0520.0000.0000.0000.000
157A157GLY 0-0.007-0.00112.058-0.054-0.0540.0000.0000.0000.000
158A158PHE 00.009-0.01413.2610.0080.0080.0000.0000.0000.000
159A159LEU 0-0.020-0.00815.679-0.002-0.0020.0000.0000.0000.000
160A160HIS 0-0.071-0.05117.316-0.029-0.0290.0000.0000.0000.000
161A161LEU 0-0.018-0.01017.2900.0140.0140.0000.0000.0000.000
162A162PRO 0-0.0070.01121.268-0.016-0.0160.0000.0000.0000.000
163A163PRO 00.0340.00924.042-0.003-0.0030.0000.0000.0000.000
164A164ASP -1-0.722-0.86223.4220.0280.0280.0000.0000.0000.000
165A165GLU -1-0.804-0.92125.6350.0370.0370.0000.0000.0000.000
166A166THR 00.0170.02325.521-0.007-0.0070.0000.0000.0000.000
167A167LEU 0-0.047-0.01525.751-0.005-0.0050.0000.0000.0000.000
168A168ALA 0-0.045-0.01929.205-0.003-0.0030.0000.0000.0000.000
169A169LEU 0-0.031-0.01030.473-0.001-0.0010.0000.0000.0000.000
170A170LYS 10.8110.91531.1980.0290.0290.0000.0000.0000.000
171A171ARG 10.9370.95533.220-0.005-0.0050.0000.0000.0000.000
172A172PRO 00.0160.01934.0660.0040.0040.0000.0000.0000.000
173A173ARG 10.9110.95630.148-0.012-0.0120.0000.0000.0000.000
174A174PRO 0-0.002-0.00731.6600.0030.0030.0000.0000.0000.000
175A175TYR 0-0.0040.00228.007-0.003-0.0030.0000.0000.0000.000
176A176VAL 0-0.024-0.00724.5280.0070.0070.0000.0000.0000.000
177A177PRO 00.0300.01325.158-0.004-0.0040.0000.0000.0000.000
178A178LEU 00.0700.02419.5610.0190.0190.0000.0000.0000.000
179A179GLU -1-0.860-0.92920.2540.1000.1000.0000.0000.0000.000
180A180VAL 0-0.062-0.02820.6980.0250.0250.0000.0000.0000.000
181A181GLN 0-0.040-0.03619.7360.0350.0350.0000.0000.0000.000
182A182ALA 00.0860.03716.4260.0330.0330.0000.0000.0000.000
183A183ARG 10.8830.95616.053-0.170-0.1700.0000.0000.0000.000
184A184ALA 00.004-0.00617.5250.0420.0420.0000.0000.0000.000
185A185VAL 00.0300.01412.4680.0450.0450.0000.0000.0000.000
186A186ARG 10.9220.97012.689-0.318-0.3180.0000.0000.0000.000
187A187LEU 0-0.041-0.02813.1830.0700.0700.0000.0000.0000.000
188A188ALA 0-0.039-0.01914.4350.0450.0450.0000.0000.0000.000
189A189LEU 0-0.016-0.0198.5740.0490.0490.0000.0000.0000.000
190A190GLU -1-0.900-0.94510.1490.6760.6760.0000.0000.0000.000
191A191HIS 0-0.166-0.07912.142-0.036-0.0360.0000.0000.0000.000
192A192LEU -1-0.933-0.9588.7931.4731.4730.0000.0000.0000.000