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: 6672Z

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 OptAll
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 -2139429.491236
FMO2-HF: Nuclear repulsion 2067106.137075
FMO2-HF: Total energy -72323.354161
FMO2-MP2: Total energy -72540.140238


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.
-49.912-46.30429.041-11.318-21.3360.001
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 : -0.033 / q_NPA : 0.022
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].
3A3LEU00.0470.0213.566-0.9781.1040.954-0.632-2.404-0.004
4A4VAL0-0.021-0.0114.300-1.170-1.2350.0290.194-0.1580.000
5A5THR00.0410.0277.908-0.235-0.2350.0000.0000.0000.000
6A6GLY00.0520.02910.5340.0470.0470.0000.0000.0000.000
7A7PHE0-0.056-0.03413.836-0.042-0.0420.0000.0000.0000.000
8A8GLU-1-0.770-0.86816.638-0.177-0.1770.0000.0000.0000.000
9A9PRO0-0.034-0.01119.2180.0280.0280.0000.0000.0000.000
10A10PHE00.0360.02222.677-0.012-0.0120.0000.0000.0000.000
11A11GLY00.0140.01724.8550.0160.0160.0000.0000.0000.000
12A12SER0-0.043-0.02928.374-0.004-0.0040.0000.0000.0000.000
13A13LEU0-0.052-0.00525.8540.0050.0050.0000.0000.0000.000
14A14GLU-1-0.788-0.88326.853-0.048-0.0480.0000.0000.0000.000
15A15HIS0-0.039-0.05022.392-0.025-0.0250.0000.0000.0000.000
16A16ASN00.0330.01520.0530.0380.0380.0000.0000.0000.000
17A17PRO00.0180.01420.182-0.004-0.0040.0000.0000.0000.000
18A18SER0-0.038-0.03316.2920.0090.0090.0000.0000.0000.000
19A19GLN00.0390.01915.4070.0360.0360.0000.0000.0000.000
20A20ALA00.0350.01415.8500.0020.0020.0000.0000.0000.000
21A21LEU0-0.016-0.00214.6340.0110.0110.0000.0000.0000.000
22A22LEU0-0.026-0.01810.7170.0430.0430.0000.0000.0000.000
23A23ASP-1-0.913-0.96112.729-0.133-0.1330.0000.0000.0000.000
24A24LEU0-0.030-0.00515.213-0.006-0.0060.0000.0000.0000.000
25A25LEU0-0.055-0.01710.6500.0690.0690.0000.0000.0000.000
26A26PRO00.0170.00810.678-0.089-0.0890.0000.0000.0000.000
27A27SER00.023-0.0068.920-0.029-0.0290.0000.0000.0000.000
28A28GLU-1-0.951-0.9706.5030.3930.3930.0000.0000.0000.000
29A29VAL0-0.004-0.0076.752-0.174-0.1740.0000.0000.0000.000
30A30ASP-1-0.810-0.8897.1012.3812.3810.0000.0000.0000.000
31A31GLY00.0250.0308.3640.2480.2480.0000.0000.0000.000
32A32LYS10.8170.8831.907-29.950-34.76213.836-5.029-3.9960.058
33A33PRO00.0280.0033.222-1.975-0.9060.070-0.312-0.827-0.001
34A34LEU00.0140.0082.552-6.948-3.6021.939-2.776-2.510-0.034
35A35ARG10.7640.8382.4471.0020.6534.941-1.520-3.073-0.004
36A36LYS10.8810.9444.2650.4270.6990.002-0.077-0.1960.001
37A37ALA00.0100.0117.433-0.356-0.3560.0000.0000.0000.000
38A38VAL0-0.009-0.0099.3720.1570.1570.0000.0000.0000.000
39A39LEU00.0000.01110.414-0.094-0.0940.0000.0000.0000.000
40A40PRO00.0440.02213.8430.0420.0420.0000.0000.0000.000
41A41VAL0-0.014-0.02617.3090.0180.0180.0000.0000.0000.000
42A42ASP-1-0.801-0.89719.332-0.218-0.2180.0000.0000.0000.000
43A43ALA00.027-0.00419.472-0.018-0.0180.0000.0000.0000.000
44A44GLU-1-0.851-0.87220.903-0.175-0.1750.0000.0000.0000.000
45A45ALA00.0380.01518.067-0.025-0.0250.0000.0000.0000.000
46A46LEU0-0.024-0.00514.015-0.056-0.0560.0000.0000.0000.000
47A47GLY0-0.004-0.00314.267-0.032-0.0320.0000.0000.0000.000
48A48GLU-1-0.922-0.95914.293-0.615-0.6150.0000.0000.0000.000
49A49ALA00.0750.02512.269-0.118-0.1180.0000.0000.0000.000
50A50LEU0-0.050-0.0289.727-0.080-0.0800.0000.0000.0000.000
51A51GLU-1-0.870-0.9148.760-0.863-0.8630.0000.0000.0000.000
52A52ASP-1-0.853-0.9338.768-1.515-1.5150.0000.0000.0000.000
53A53LEU0-0.023-0.0075.426-0.387-0.3870.0000.0000.0000.000
54A54HIS0-0.031-0.0294.081-1.354-1.214-0.001-0.035-0.1050.000
55A55ARG10.8790.9375.8700.9190.9190.0000.0000.0000.000
56A56GLU-1-0.827-0.8692.520-5.513-4.5901.004-0.585-1.342-0.006
57A57GLY0-0.0230.0062.997-3.044-1.8650.233-0.693-0.720-0.007
58A58PRO0-0.019-0.0082.362-1.630-0.9264.969-2.121-3.5520.002
59A59LYS10.8360.8912.1471.4710.2391.0672.309-2.144-0.004
60A60ALA00.0470.0314.545-0.379-0.174-0.001-0.029-0.1760.000
61A61VAL0-0.013-0.0085.3370.7520.898-0.001-0.012-0.1330.000
62A62LEU0-0.011-0.0037.603-0.291-0.2910.0000.0000.0000.000
63A63HIS10.8280.8949.710-0.240-0.2400.0000.0000.0000.000
64A64LEU00.0200.01112.1870.0100.0100.0000.0000.0000.000
65A65GLY00.0540.00714.925-0.054-0.0540.0000.0000.0000.000
66A66LEU0-0.0260.00818.2120.0240.0240.0000.0000.0000.000
67A67ALA00.009-0.00521.763-0.012-0.0120.0000.0000.0000.000
68A68GLU-1-0.766-0.87124.5900.0210.0210.0000.0000.0000.000
69A69ASP-1-0.878-0.92927.6570.0480.0480.0000.0000.0000.000
70A70ARG10.7630.85923.405-0.146-0.1460.0000.0000.0000.000
71A71PRO00.014-0.00127.8140.0020.0020.0000.0000.0000.000
72A72VAL0-0.031-0.01327.2800.0050.0050.0000.0000.0000.000
73A73LEU00.0430.03020.555-0.004-0.0040.0000.0000.0000.000
74A74THR0-0.072-0.03721.910-0.009-0.0090.0000.0000.0000.000
75A75LEU00.0230.01616.8740.0150.0150.0000.0000.0000.000
76A76GLU-1-0.727-0.81919.2430.1590.1590.0000.0000.0000.000
77A77ARG10.9080.93619.368-0.233-0.2330.0000.0000.0000.000
78A78LEU0-0.0280.00220.9530.0120.0120.0000.0000.0000.000
79A79ALA00.0060.02518.724-0.001-0.0010.0000.0000.0000.000
80A80VAL00.011-0.01720.8750.0020.0020.0000.0000.0000.000
81A81ASN0-0.017-0.00722.723-0.023-0.0230.0000.0000.0000.000
82A82LEU0-0.017-0.01223.909-0.006-0.0060.0000.0000.0000.000
83A83LEU0-0.044-0.02421.5930.0040.0040.0000.0000.0000.000
84A84ASP-1-0.859-0.93425.615-0.011-0.0110.0000.0000.0000.000
85A85PHE0-0.029-0.00223.3020.0080.0080.0000.0000.0000.000
86A86PRO00.0100.01127.712-0.002-0.0020.0000.0000.0000.000
87A87ARG10.8220.89726.9610.0100.0100.0000.0000.0000.000
88A88PRO00.0450.03128.183-0.001-0.0010.0000.0000.0000.000
89A89ASP-1-0.748-0.85223.454-0.120-0.1200.0000.0000.0000.000
90A90ASN0-0.054-0.06322.3540.0200.0200.0000.0000.0000.000
91A91ARG10.7460.86321.1420.1800.1800.0000.0000.0000.000
92A92GLY0-0.0190.00126.5120.0010.0010.0000.0000.0000.000
93A93ARG10.7630.84725.9300.1530.1530.0000.0000.0000.000
94A94VAL00.025-0.00728.1220.0050.0050.0000.0000.0000.000
95A95LEU0-0.050-0.00824.774-0.003-0.0030.0000.0000.0000.000
96A96GLU-1-0.892-0.95028.953-0.025-0.0250.0000.0000.0000.000
97A97ASP-1-0.908-0.95530.887-0.014-0.0140.0000.0000.0000.000
98A98LEU0-0.031-0.00427.324-0.005-0.0050.0000.0000.0000.000
99A99PRO0-0.024-0.02726.1150.0060.0060.0000.0000.0000.000
100A100ILE0-0.049-0.00519.212-0.015-0.0150.0000.0000.0000.000
101A101VAL0-0.009-0.01319.709-0.027-0.0270.0000.0000.0000.000
102A102PRO00.0210.01622.8210.0210.0210.0000.0000.0000.000
103A103GLY00.0010.00825.906-0.007-0.0070.0000.0000.0000.000
104A104GLY0-0.0030.01223.4620.0070.0070.0000.0000.0000.000
105A105PRO00.013-0.00122.6650.0050.0050.0000.0000.0000.000
106A106LEU00.0450.03224.294-0.001-0.0010.0000.0000.0000.000
107A107ALA0-0.007-0.00623.801-0.001-0.0010.0000.0000.0000.000
108A108LEU0-0.0040.01518.397-0.002-0.0020.0000.0000.0000.000
109A109PRO00.0080.00220.5120.0040.0040.0000.0000.0000.000
110A110ALA00.011-0.00717.3300.0090.0090.0000.0000.0000.000
111A111ARG10.8020.92412.750-0.319-0.3190.0000.0000.0000.000
112A112PHE00.0680.00312.6940.1050.1050.0000.0000.0000.000
113A113PRO00.0420.04314.860-0.115-0.1150.0000.0000.0000.000
114A114VAL0-0.020-0.02317.826-0.031-0.0310.0000.0000.0000.000
115A115LYS10.9220.95220.152-0.299-0.2990.0000.0000.0000.000
116A116PRO00.0550.01919.369-0.029-0.0290.0000.0000.0000.000
117A117VAL00.0680.05816.357-0.022-0.0220.0000.0000.0000.000
118A118LEU0-0.026-0.01019.546-0.039-0.0390.0000.0000.0000.000
119A119ALA0-0.046-0.02323.013-0.032-0.0320.0000.0000.0000.000
120A120ARG10.8690.92918.269-0.543-0.5430.0000.0000.0000.000
121A121TRP0-0.033-0.03718.375-0.042-0.0420.0000.0000.0000.000
122A122ARG10.9440.96822.829-0.253-0.2530.0000.0000.0000.000
123A123GLU-1-0.873-0.92123.1840.3790.3790.0000.0000.0000.000
124A124ALA0-0.0240.00322.581-0.018-0.0180.0000.0000.0000.000
125A125GLY00.0160.01524.684-0.018-0.0180.0000.0000.0000.000
126A126ILE0-0.057-0.02521.798-0.017-0.0170.0000.0000.0000.000
127A127PRO0-0.020-0.01625.7910.0110.0110.0000.0000.0000.000
128A128GLY00.0550.01825.1040.0060.0060.0000.0000.0000.000
129A129ARG10.8430.92325.417-0.168-0.1680.0000.0000.0000.000
130A130PRO00.0370.01623.9380.0140.0140.0000.0000.0000.000
131A131SER0-0.082-0.06423.377-0.034-0.0340.0000.0000.0000.000
132A132LEU0-0.003-0.01224.1020.0230.0230.0000.0000.0000.000
133A133SER00.0630.02924.734-0.015-0.0150.0000.0000.0000.000
134A134ALA00.0020.01920.2040.0030.0030.0000.0000.0000.000
135A135GLY00.0050.00222.248-0.015-0.0150.0000.0000.0000.000
136A136SER0-0.024-0.02524.2180.0110.0110.0000.0000.0000.000
137A137TYR00.029-0.00922.880-0.013-0.0130.0000.0000.0000.000
138A138LEU00.0270.01318.8980.0120.0120.0000.0000.0000.000
139A139CYS0-0.047-0.01517.711-0.008-0.0080.0000.0000.0000.000
140A140ASN00.0270.00717.3360.0440.0440.0000.0000.0000.000
141A141GLN00.0060.00217.8240.0230.0230.0000.0000.0000.000
142A142ALA00.0340.00913.301-0.020-0.0200.0000.0000.0000.000
143A143PHE0-0.072-0.02513.4140.0210.0210.0000.0000.0000.000
144A144TYR00.032-0.01814.9060.0130.0130.0000.0000.0000.000
145A145LEU00.0310.01114.223-0.002-0.0020.0000.0000.0000.000
146A146SER0-0.011-0.00410.697-0.062-0.0620.0000.0000.0000.000
147A147LEU0-0.046-0.01712.1360.0200.0200.0000.0000.0000.000
148A148TYR0-0.018-0.00314.8310.0060.0060.0000.0000.0000.000
149A149ARG10.8030.89612.1260.4290.4290.0000.0000.0000.000
150A150LEU0-0.0260.0047.525-0.050-0.0500.0000.0000.0000.000
151A151PRO00.0200.02310.6710.0560.0560.0000.0000.0000.000
152A152GLU-1-0.829-0.92313.0170.4040.4040.0000.0000.0000.000
153A153GLU-1-0.943-0.98411.9160.4230.4230.0000.0000.0000.000
154A154VAL0-0.052-0.0108.0620.2520.2520.0000.0000.0000.000
155A155PRO0-0.003-0.0108.819-0.140-0.1400.0000.0000.0000.000
156A156VAL00.0100.0009.8870.1260.1260.0000.0000.0000.000
157A157GLY0-0.019-0.00611.949-0.087-0.0870.0000.0000.0000.000
158A158PHE00.009-0.00413.1190.0170.0170.0000.0000.0000.000
159A159LEU0-0.024-0.00415.319-0.007-0.0070.0000.0000.0000.000
160A160HIS0-0.048-0.02917.231-0.036-0.0360.0000.0000.0000.000
161A161LEU00.0020.00917.3810.0150.0150.0000.0000.0000.000
162A162PRO00.0070.00321.211-0.021-0.0210.0000.0000.0000.000
163A163PRO00.0320.02623.818-0.003-0.0030.0000.0000.0000.000
164A164ASP-1-0.730-0.83923.9320.0590.0590.0000.0000.0000.000
165A165GLU-1-0.777-0.90025.8750.0770.0770.0000.0000.0000.000
166A166THR0-0.025-0.01925.293-0.010-0.0100.0000.0000.0000.000
167A167LEU0-0.017-0.01525.630-0.008-0.0080.0000.0000.0000.000
168A168ALA0-0.056-0.01729.267-0.004-0.0040.0000.0000.0000.000
169A169LEU0-0.026-0.01830.936-0.003-0.0030.0000.0000.0000.000
170A170LYS10.7920.90431.7930.0200.0200.0000.0000.0000.000
171A171ARG10.9380.95633.472-0.030-0.0300.0000.0000.0000.000
172A172PRO00.0190.01934.0540.0060.0060.0000.0000.0000.000
173A173ARG10.7840.87229.815-0.037-0.0370.0000.0000.0000.000
174A174PRO00.012-0.00331.6760.0030.0030.0000.0000.0000.000
175A175TYR0-0.024-0.00327.956-0.005-0.0050.0000.0000.0000.000
176A176VAL0-0.018-0.00624.4500.0080.0080.0000.0000.0000.000
177A177PRO00.0330.01325.1880.0000.0000.0000.0000.0000.000
178A178LEU00.0350.00919.9510.0260.0260.0000.0000.0000.000
179A179GLU-1-0.853-0.92120.3800.1610.1610.0000.0000.0000.000
180A180VAL0-0.050-0.02920.8460.0340.0340.0000.0000.0000.000
181A181GLN0-0.053-0.04119.8830.0440.0440.0000.0000.0000.000
182A182ALA00.0730.03616.6350.0480.0480.0000.0000.0000.000
183A183ARG10.8590.92716.342-0.207-0.2070.0000.0000.0000.000
184A184ALA00.0060.00017.8550.0520.0520.0000.0000.0000.000
185A185VAL00.0110.00612.8120.0650.0650.0000.0000.0000.000
186A186ARG10.8770.91412.858-0.471-0.4710.0000.0000.0000.000
187A187LEU0-0.036-0.02113.4040.0980.0980.0000.0000.0000.000
188A188ALA0-0.045-0.03014.7640.0570.0570.0000.0000.0000.000
189A189LEU00.003-0.0028.6510.0850.0850.0000.0000.0000.000
190A190GLU-1-0.807-0.86810.4030.8400.8400.0000.0000.0000.000
191A191HIS0-0.085-0.04112.365-0.107-0.1070.0000.0000.0000.000
192A192LEU0-0.074-0.0408.6420.2110.2110.0000.0000.0000.000