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: 22RQR

Calculation Name: 2EBJ-A-Xray372

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: 2023-03-13

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

DOI:


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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2138217.243578
FMO2-HF: Nuclear repulsion 2065894.279855
FMO2-HF: Total energy -72322.963723
FMO2-MP2: Total energy -72539.808089


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.
-49.684-42.20225.312-11.542-21.2560.006
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 : -0.035 / q_NPA : 0.013
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].
3A3LEU00.0410.0203.296-1.4270.8261.176-0.916-2.513-0.008
4A4VAL0-0.003-0.0024.410-1.067-1.0480.0220.094-0.1360.000
5A5THR00.0480.0257.934-0.172-0.1720.0000.0000.0000.000
6A6GLY00.0320.02410.4320.0580.0580.0000.0000.0000.000
7A7PHE0-0.067-0.03214.041-0.045-0.0450.0000.0000.0000.000
8A8GLU-1-0.795-0.87116.802-0.203-0.2030.0000.0000.0000.000
9A9PRO0-0.020-0.00819.1620.0260.0260.0000.0000.0000.000
10A10PHE00.0490.02622.461-0.011-0.0110.0000.0000.0000.000
11A11GLY0-0.0110.00224.8370.0150.0150.0000.0000.0000.000
12A12SER0-0.014-0.01628.485-0.006-0.0060.0000.0000.0000.000
13A13LEU0-0.064-0.01325.9730.0030.0030.0000.0000.0000.000
14A14GLU-1-0.791-0.88226.872-0.066-0.0660.0000.0000.0000.000
15A15HIS0-0.049-0.05622.721-0.025-0.0250.0000.0000.0000.000
16A16ASN00.0370.02120.2030.0390.0390.0000.0000.0000.000
17A17PRO00.0470.02420.252-0.008-0.0080.0000.0000.0000.000
18A18SER0-0.030-0.02616.2780.0070.0070.0000.0000.0000.000
19A19GLN00.0170.00215.5030.0280.0280.0000.0000.0000.000
20A20ALA00.0170.00116.051-0.012-0.0120.0000.0000.0000.000
21A21LEU00.0040.00614.2350.0070.0070.0000.0000.0000.000
22A22LEU0-0.023-0.01410.6950.0310.0310.0000.0000.0000.000
23A23ASP-1-0.918-0.95812.551-0.192-0.1920.0000.0000.0000.000
24A24LEU0-0.039-0.01814.978-0.001-0.0010.0000.0000.0000.000
25A25LEU0-0.077-0.02610.4360.0620.0620.0000.0000.0000.000
26A26PRO00.0150.01410.481-0.071-0.0710.0000.0000.0000.000
27A27SER00.020-0.0058.703-0.050-0.0500.0000.0000.0000.000
28A28GLU-1-0.956-0.9846.6620.3790.3790.0000.0000.0000.000
29A29VAL00.000-0.0016.831-0.174-0.1740.0000.0000.0000.000
30A30ASP-1-0.853-0.9187.3662.1692.1690.0000.0000.0000.000
31A31GLY00.0040.0158.5310.2330.2330.0000.0000.0000.000
32A32LYS10.8210.8942.018-29.986-31.3548.977-4.063-3.5470.059
33A33PRO00.0300.0022.828-2.032-0.5990.289-0.484-1.239-0.001
34A34LEU00.0040.0122.489-6.249-3.1412.178-2.840-2.447-0.032
35A35ARG10.7760.8412.4971.1740.2776.231-1.915-3.419-0.004
36A36LYS10.8890.9424.0610.7210.9750.002-0.030-0.2270.001
37A37ALA00.0010.0017.557-0.320-0.3200.0000.0000.0000.000
38A38VAL00.0030.0019.4610.1520.1520.0000.0000.0000.000
39A39LEU0-0.0060.00210.593-0.080-0.0800.0000.0000.0000.000
40A40PRO00.0520.02613.8800.0410.0410.0000.0000.0000.000
41A41VAL0-0.012-0.02517.3260.0170.0170.0000.0000.0000.000
42A42ASP-1-0.817-0.92119.347-0.225-0.2250.0000.0000.0000.000
43A43ALA00.0330.00419.518-0.021-0.0210.0000.0000.0000.000
44A44GLU-1-0.835-0.87820.454-0.186-0.1860.0000.0000.0000.000
45A45ALA00.0190.01618.326-0.022-0.0220.0000.0000.0000.000
46A46LEU0-0.022-0.00114.252-0.054-0.0540.0000.0000.0000.000
47A47GLY00.007-0.00714.247-0.044-0.0440.0000.0000.0000.000
48A48GLU-1-0.930-0.96113.867-0.655-0.6550.0000.0000.0000.000
49A49ALA00.0990.04312.459-0.111-0.1110.0000.0000.0000.000
50A50LEU0-0.076-0.0469.919-0.113-0.1130.0000.0000.0000.000
51A51GLU-1-0.904-0.9368.838-0.927-0.9270.0000.0000.0000.000
52A52ASP-1-0.910-0.9548.957-1.407-1.4070.0000.0000.0000.000
53A53LEU0-0.047-0.0275.508-0.409-0.4090.0000.0000.0000.000
54A54HIS0-0.028-0.0324.256-1.349-1.250-0.001-0.020-0.0780.000
55A55ARG10.9760.9945.9620.8900.8900.0000.0000.0000.000
56A56GLU-1-0.827-0.8682.587-6.086-4.8760.625-0.587-1.248-0.006
57A57GLY0-0.036-0.0053.376-2.112-1.2900.075-0.412-0.485-0.003
58A58PRO0-0.033-0.0092.619-1.912-0.8474.410-2.057-3.4180.001
59A59LYS10.8360.8912.0871.2910.4731.3301.722-2.233-0.001
60A60ALA00.0490.0254.535-0.317-0.121-0.001-0.028-0.1670.000
61A61VAL0-0.012-0.0065.6790.4550.561-0.001-0.006-0.0990.000
62A62LEU0-0.0020.0077.902-0.204-0.2040.0000.0000.0000.000
63A63HIS10.8180.8829.663-0.136-0.1360.0000.0000.0000.000
64A64LEU00.0300.01812.3660.0120.0120.0000.0000.0000.000
65A65GLY00.0650.01514.994-0.053-0.0530.0000.0000.0000.000
66A66LEU0-0.0230.00818.2840.0240.0240.0000.0000.0000.000
67A67ALA0-0.014-0.01221.794-0.009-0.0090.0000.0000.0000.000
68A68GLU-1-0.803-0.90824.6340.0000.0000.0000.0000.0000.000
69A69ASP-1-0.877-0.94227.6340.0310.0310.0000.0000.0000.000
70A70ARG10.7390.86023.398-0.113-0.1130.0000.0000.0000.000
71A71PRO00.0180.00228.065-0.001-0.0010.0000.0000.0000.000
72A72VAL0-0.028-0.01127.0840.0040.0040.0000.0000.0000.000
73A73LEU00.0600.03920.321-0.005-0.0050.0000.0000.0000.000
74A74THR0-0.055-0.02922.043-0.006-0.0060.0000.0000.0000.000
75A75LEU00.0230.01817.3750.0100.0100.0000.0000.0000.000
76A76GLU-1-0.717-0.81719.2220.1270.1270.0000.0000.0000.000
77A77ARG10.9020.93819.848-0.202-0.2020.0000.0000.0000.000
78A78LEU0-0.0130.00521.4510.0130.0130.0000.0000.0000.000
79A79ALA00.0060.03419.068-0.006-0.0060.0000.0000.0000.000
80A80VAL00.006-0.01021.2070.0010.0010.0000.0000.0000.000
81A81ASN0-0.016-0.00723.071-0.026-0.0260.0000.0000.0000.000
82A82LEU0-0.036-0.02824.198-0.003-0.0030.0000.0000.0000.000
83A83LEU0-0.049-0.01922.0520.0010.0010.0000.0000.0000.000
84A84ASP-1-0.877-0.94025.998-0.024-0.0240.0000.0000.0000.000
85A85PHE0-0.058-0.02723.3570.0060.0060.0000.0000.0000.000
86A86PRO00.0140.02427.939-0.001-0.0010.0000.0000.0000.000
87A87ARG10.8510.90427.4450.0340.0340.0000.0000.0000.000
88A88PRO00.0270.02828.466-0.002-0.0020.0000.0000.0000.000
89A89ASP-1-0.755-0.87023.600-0.139-0.1390.0000.0000.0000.000
90A90ASN0-0.031-0.04922.2500.0210.0210.0000.0000.0000.000
91A91ARG10.7730.88521.7710.2030.2030.0000.0000.0000.000
92A92GLY0-0.037-0.02226.7550.0030.0030.0000.0000.0000.000
93A93ARG10.7720.84726.3350.1620.1620.0000.0000.0000.000
94A94VAL00.0180.00228.1840.0030.0030.0000.0000.0000.000
95A95LEU0-0.051-0.01425.0510.0010.0010.0000.0000.0000.000
96A96GLU-1-0.890-0.94629.189-0.036-0.0360.0000.0000.0000.000
97A97ASP-1-0.887-0.93831.000-0.025-0.0250.0000.0000.0000.000
98A98LEU0-0.029-0.00427.549-0.006-0.0060.0000.0000.0000.000
99A99PRO0-0.016-0.01626.2740.0060.0060.0000.0000.0000.000
100A100ILE0-0.048-0.00719.573-0.015-0.0150.0000.0000.0000.000
101A101VAL0-0.014-0.01719.743-0.026-0.0260.0000.0000.0000.000
102A102PRO00.0250.01722.9360.0210.0210.0000.0000.0000.000
103A103GLY0-0.0020.00525.950-0.006-0.0060.0000.0000.0000.000
104A104GLY0-0.0060.01223.7750.0080.0080.0000.0000.0000.000
105A105PRO00.006-0.00622.9090.0050.0050.0000.0000.0000.000
106A106LEU00.0470.03424.736-0.003-0.0030.0000.0000.0000.000
107A107ALA0-0.002-0.01124.227-0.003-0.0030.0000.0000.0000.000
108A108LEU0-0.0040.02318.6790.0030.0030.0000.0000.0000.000
109A109PRO0-0.001-0.00321.0830.0010.0010.0000.0000.0000.000
110A110ALA0-0.003-0.00917.8080.0080.0080.0000.0000.0000.000
111A111ARG10.8420.94313.271-0.285-0.2850.0000.0000.0000.000
112A112PHE00.0660.00013.0210.0880.0880.0000.0000.0000.000
113A113PRO00.0490.04715.092-0.108-0.1080.0000.0000.0000.000
114A114VAL0-0.010-0.01918.129-0.021-0.0210.0000.0000.0000.000
115A115LYS10.9260.95120.514-0.261-0.2610.0000.0000.0000.000
116A116PRO00.0550.02419.448-0.024-0.0240.0000.0000.0000.000
117A117VAL00.0810.06616.418-0.011-0.0110.0000.0000.0000.000
118A118LEU0-0.050-0.01919.604-0.037-0.0370.0000.0000.0000.000
119A119ALA0-0.043-0.02722.999-0.027-0.0270.0000.0000.0000.000
120A120ARG10.9450.96818.932-0.458-0.4580.0000.0000.0000.000
121A121TRP0-0.025-0.03418.263-0.040-0.0400.0000.0000.0000.000
122A122ARG10.9500.97422.826-0.226-0.2260.0000.0000.0000.000
123A123GLU-1-0.860-0.89823.7420.3360.3360.0000.0000.0000.000
124A124ALA0-0.060-0.01622.730-0.013-0.0130.0000.0000.0000.000
125A125GLY00.0130.00924.815-0.016-0.0160.0000.0000.0000.000
126A126ILE0-0.060-0.03321.810-0.017-0.0170.0000.0000.0000.000
127A127PRO0-0.025-0.01525.7500.0120.0120.0000.0000.0000.000
128A128GLY00.0530.02425.1190.0070.0070.0000.0000.0000.000
129A129ARG10.8680.93425.292-0.140-0.1400.0000.0000.0000.000
130A130PRO00.0230.01724.1820.0080.0080.0000.0000.0000.000
131A131SER0-0.087-0.07223.597-0.029-0.0290.0000.0000.0000.000
132A132LEU0-0.003-0.02024.4030.0170.0170.0000.0000.0000.000
133A133SER00.0480.02625.481-0.010-0.0100.0000.0000.0000.000
134A134ALA00.0250.03320.9210.0050.0050.0000.0000.0000.000
135A135GLY00.003-0.00622.886-0.013-0.0130.0000.0000.0000.000
136A136SER0-0.015-0.01424.4620.0110.0110.0000.0000.0000.000
137A137TYR00.019-0.01123.364-0.011-0.0110.0000.0000.0000.000
138A138LEU00.0290.01118.7660.0040.0040.0000.0000.0000.000
139A139CYS0-0.057-0.00917.991-0.010-0.0100.0000.0000.0000.000
140A140ASN00.000-0.00517.7070.0350.0350.0000.0000.0000.000
141A141GLN00.0370.02118.2140.0210.0210.0000.0000.0000.000
142A142ALA00.0250.01013.644-0.018-0.0180.0000.0000.0000.000
143A143PHE0-0.049-0.03514.1170.0100.0100.0000.0000.0000.000
144A144TYR00.030-0.02215.5190.0150.0150.0000.0000.0000.000
145A145LEU00.0290.01514.440-0.002-0.0020.0000.0000.0000.000
146A146SER0-0.0020.00910.881-0.054-0.0540.0000.0000.0000.000
147A147LEU0-0.0260.00312.4360.0200.0200.0000.0000.0000.000
148A148TYR0-0.032-0.02015.0310.0070.0070.0000.0000.0000.000
149A149ARG10.8390.92212.6920.4380.4380.0000.0000.0000.000
150A150LEU0-0.037-0.0028.209-0.036-0.0360.0000.0000.0000.000
151A151PRO00.0290.02311.0270.0500.0500.0000.0000.0000.000
152A152GLU-1-0.841-0.93213.3290.3790.3790.0000.0000.0000.000
153A153GLU-1-0.949-0.98211.7770.4170.4170.0000.0000.0000.000
154A154VAL0-0.056-0.0168.2250.2440.2440.0000.0000.0000.000
155A155PRO0-0.013-0.0098.817-0.133-0.1330.0000.0000.0000.000
156A156VAL00.0170.00010.2680.0680.0680.0000.0000.0000.000
157A157GLY0-0.0090.00212.193-0.064-0.0640.0000.0000.0000.000
158A158PHE00.009-0.01113.3860.0020.0020.0000.0000.0000.000
159A159LEU0-0.036-0.01315.7620.0020.0020.0000.0000.0000.000
160A160HIS0-0.047-0.03917.433-0.037-0.0370.0000.0000.0000.000
161A161LEU0-0.006-0.00617.4010.0190.0190.0000.0000.0000.000
162A162PRO0-0.0020.01521.360-0.019-0.0190.0000.0000.0000.000
163A163PRO00.0320.01424.167-0.005-0.0050.0000.0000.0000.000
164A164ASP-1-0.715-0.85723.3830.0290.0290.0000.0000.0000.000
165A165GLU-1-0.794-0.91425.5350.0470.0470.0000.0000.0000.000
166A166THR00.0030.01425.389-0.008-0.0080.0000.0000.0000.000
167A167LEU0-0.042-0.02025.734-0.006-0.0060.0000.0000.0000.000
168A168ALA0-0.045-0.01529.307-0.003-0.0030.0000.0000.0000.000
169A169LEU0-0.026-0.01030.562-0.001-0.0010.0000.0000.0000.000
170A170LYS10.7900.90331.4750.0370.0370.0000.0000.0000.000
171A171ARG10.9450.95933.625-0.010-0.0100.0000.0000.0000.000
172A172PRO00.0210.02034.1780.0050.0050.0000.0000.0000.000
173A173ARG10.8060.89629.979-0.014-0.0140.0000.0000.0000.000
174A174PRO00.007-0.00731.6740.0030.0030.0000.0000.0000.000
175A175TYR0-0.015-0.00328.059-0.003-0.0030.0000.0000.0000.000
176A176VAL0-0.028-0.00824.5160.0090.0090.0000.0000.0000.000
177A177PRO00.0360.01725.284-0.003-0.0030.0000.0000.0000.000
178A178LEU00.0520.01019.7340.0240.0240.0000.0000.0000.000
179A179GLU-1-0.865-0.92820.3650.1170.1170.0000.0000.0000.000
180A180VAL0-0.053-0.02820.8190.0300.0300.0000.0000.0000.000
181A181GLN0-0.044-0.03819.8400.0390.0390.0000.0000.0000.000
182A182ALA00.0760.03216.5740.0420.0420.0000.0000.0000.000
183A183ARG10.8800.94316.186-0.190-0.1900.0000.0000.0000.000
184A184ALA0-0.005-0.00717.5580.0530.0530.0000.0000.0000.000
185A185VAL00.0140.00612.6010.0610.0610.0000.0000.0000.000
186A186ARG10.8630.91812.792-0.416-0.4160.0000.0000.0000.000
187A187LEU0-0.024-0.01213.1970.0930.0930.0000.0000.0000.000
188A188ALA0-0.042-0.02314.6540.0660.0660.0000.0000.0000.000
189A189LEU0-0.004-0.0118.4900.0880.0880.0000.0000.0000.000
190A190GLU-1-0.813-0.88510.1620.8360.8360.0000.0000.0000.000
191A191HIS0-0.139-0.06712.153-0.028-0.0280.0000.0000.0000.000
192A192LEU0-0.038-0.0069.0910.0200.0200.0000.0000.0000.000