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: 7GN7K

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 OptH
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 -2138215.233065
FMO2-HF: Nuclear repulsion 2065893.001772
FMO2-HF: Total energy -72322.231293
FMO2-MP2: Total energy -72539.184603


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.
-30.126-21.1118.137-7.871-19.28-0.046
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 : -0.056 / q_NPA : -0.009
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].
3A3LEU00.0410.0123.144-1.0030.9831.814-0.895-2.904-0.009
4A4VAL00.0000.0024.309-1.165-1.2150.0310.181-0.1630.000
5A5THR00.0440.0287.851-0.156-0.1560.0000.0000.0000.000
6A6GLY00.0320.02010.3750.0460.0460.0000.0000.0000.000
7A7PHE0-0.055-0.02713.931-0.040-0.0400.0000.0000.0000.000
8A8GLU-1-0.797-0.87316.693-0.183-0.1830.0000.0000.0000.000
9A9PRO0-0.034-0.01719.0690.0210.0210.0000.0000.0000.000
10A10PHE00.0700.03522.462-0.013-0.0130.0000.0000.0000.000
11A11GLY00.001-0.00624.7400.0130.0130.0000.0000.0000.000
12A12SER0-0.034-0.02428.388-0.005-0.0050.0000.0000.0000.000
13A13LEU0-0.072-0.01626.0220.0030.0030.0000.0000.0000.000
14A14GLU-1-0.796-0.88026.768-0.055-0.0550.0000.0000.0000.000
15A15HIS0-0.046-0.05322.748-0.020-0.0200.0000.0000.0000.000
16A16ASN00.0450.04520.1000.0330.0330.0000.0000.0000.000
17A17PRO00.0350.01720.200-0.006-0.0060.0000.0000.0000.000
18A18SER0-0.016-0.03816.2300.0070.0070.0000.0000.0000.000
19A19GLN00.006-0.00215.4560.0300.0300.0000.0000.0000.000
20A20ALA00.0250.00415.979-0.009-0.0090.0000.0000.0000.000
21A21LEU0-0.0010.00214.2650.0080.0080.0000.0000.0000.000
22A22LEU0-0.023-0.01510.6110.0310.0310.0000.0000.0000.000
23A23ASP-1-0.907-0.95112.479-0.148-0.1480.0000.0000.0000.000
24A24LEU0-0.046-0.02214.9210.0010.0010.0000.0000.0000.000
25A25LEU0-0.094-0.03510.3590.0560.0560.0000.0000.0000.000
26A26PRO00.0160.01610.314-0.061-0.0610.0000.0000.0000.000
27A27SER00.0330.0008.671-0.058-0.0580.0000.0000.0000.000
28A28GLU-1-0.958-0.9876.6700.5710.5710.0000.0000.0000.000
29A29VAL00.0060.0106.826-0.186-0.1860.0000.0000.0000.000
30A30ASP-1-0.849-0.9187.3601.8331.8330.0000.0000.0000.000
31A31GLY00.0040.0148.5340.2020.2020.0000.0000.0000.000
32A32LYS10.8520.9193.486-11.411-9.9690.078-0.696-0.8240.006
33A33PRO00.0420.0102.750-2.253-0.7140.460-0.614-1.3850.000
34A34LEU00.0070.0162.477-6.233-3.2652.435-2.866-2.537-0.033
35A35ARG10.7740.8362.3301.0030.1656.403-1.945-3.620-0.005
36A36LYS10.8810.9304.0290.7060.9760.002-0.023-0.2490.001
37A37ALA0-0.0020.0037.468-0.305-0.3050.0000.0000.0000.000
38A38VAL0-0.0010.0029.3370.1420.1420.0000.0000.0000.000
39A39LEU0-0.003-0.00210.593-0.071-0.0710.0000.0000.0000.000
40A40PRO00.0380.02313.7990.0380.0380.0000.0000.0000.000
41A41VAL0-0.019-0.05517.2590.0140.0140.0000.0000.0000.000
42A42ASP-1-0.820-0.94219.276-0.202-0.2020.0000.0000.0000.000
43A43ALA00.0290.00719.464-0.019-0.0190.0000.0000.0000.000
44A44GLU-1-0.844-0.88620.409-0.170-0.1700.0000.0000.0000.000
45A45ALA00.0090.00618.306-0.020-0.0200.0000.0000.0000.000
46A46LEU0-0.0250.00014.330-0.047-0.0470.0000.0000.0000.000
47A47GLY0-0.014-0.01914.209-0.039-0.0390.0000.0000.0000.000
48A48GLU-1-0.922-0.95613.859-0.631-0.6310.0000.0000.0000.000
49A49ALA00.1220.05712.457-0.086-0.0860.0000.0000.0000.000
50A50LEU0-0.092-0.0599.792-0.092-0.0920.0000.0000.0000.000
51A51GLU-1-0.947-0.9678.822-1.007-1.0070.0000.0000.0000.000
52A52ASP-1-0.878-0.9298.999-1.129-1.1290.0000.0000.0000.000
53A53LEU0-0.068-0.0425.470-0.355-0.3550.0000.0000.0000.000
54A54HIS0-0.045-0.0454.278-1.250-1.152-0.001-0.019-0.0780.000
55A55ARG10.9670.9946.0180.7730.7730.0000.0000.0000.000
56A56GLU-1-0.836-0.8762.902-5.591-4.4640.306-0.441-0.991-0.004
57A57GLY0-0.047-0.0123.491-1.834-1.1340.045-0.342-0.403-0.002
58A58PRO0-0.084-0.0352.492-1.691-0.8875.107-2.366-3.5460.001
59A59LYS10.9130.9342.0591.168-0.1931.4592.195-2.292-0.001
60A60ALA00.0440.0214.421-0.215-0.012-0.001-0.033-0.1690.000
61A61VAL0-0.014-0.0075.5390.5610.689-0.001-0.007-0.1190.000
62A62LEU0-0.0010.0077.771-0.220-0.2200.0000.0000.0000.000
63A63HIS10.8090.8739.584-0.112-0.1120.0000.0000.0000.000
64A64LEU00.0210.01212.2660.0020.0020.0000.0000.0000.000
65A65GLY00.0640.01514.904-0.045-0.0450.0000.0000.0000.000
66A66LEU0-0.0150.00918.2050.0210.0210.0000.0000.0000.000
67A67ALA0-0.029-0.01321.718-0.008-0.0080.0000.0000.0000.000
68A68GLU-1-0.945-0.99724.546-0.003-0.0030.0000.0000.0000.000
69A69ASP-1-0.880-0.94527.5550.0260.0260.0000.0000.0000.000
70A70ARG10.7360.86023.541-0.085-0.0850.0000.0000.0000.000
71A71PRO00.0170.00327.9690.0000.0000.0000.0000.0000.000
72A72VAL0-0.023-0.00726.8840.0040.0040.0000.0000.0000.000
73A73LEU00.0600.03620.166-0.005-0.0050.0000.0000.0000.000
74A74THR0-0.064-0.03321.931-0.006-0.0060.0000.0000.0000.000
75A75LEU00.0350.02017.4980.0090.0090.0000.0000.0000.000
76A76GLU-1-0.728-0.82519.1210.1000.1000.0000.0000.0000.000
77A77ARG10.8930.93719.714-0.156-0.1560.0000.0000.0000.000
78A78LEU0-0.0110.00421.3260.0090.0090.0000.0000.0000.000
79A79ALA00.0030.03618.957-0.003-0.0030.0000.0000.0000.000
80A80VAL00.000-0.01121.1040.0000.0000.0000.0000.0000.000
81A81ASN00.0050.00822.985-0.021-0.0210.0000.0000.0000.000
82A82LEU0-0.030-0.02724.120-0.002-0.0020.0000.0000.0000.000
83A83LEU0-0.055-0.01922.1030.0010.0010.0000.0000.0000.000
84A84ASP-1-0.875-0.93125.922-0.031-0.0310.0000.0000.0000.000
85A85PHE0-0.056-0.02023.6400.0050.0050.0000.0000.0000.000
86A86PRO00.0160.02227.7920.0000.0000.0000.0000.0000.000
87A87ARG10.9100.94426.9370.0400.0400.0000.0000.0000.000
88A88PRO00.0320.02728.376-0.002-0.0020.0000.0000.0000.000
89A89ASP-1-0.752-0.85823.526-0.126-0.1260.0000.0000.0000.000
90A90ASN0-0.014-0.03222.0010.0220.0220.0000.0000.0000.000
91A91ARG10.7850.89822.2210.1770.1770.0000.0000.0000.000
92A92GLY0-0.042-0.02326.7030.0030.0030.0000.0000.0000.000
93A93ARG10.7730.84726.3560.1470.1470.0000.0000.0000.000
94A94VAL00.0190.00428.1120.0020.0020.0000.0000.0000.000
95A95LEU0-0.054-0.01725.0500.0010.0010.0000.0000.0000.000
96A96GLU-1-0.888-0.94529.123-0.037-0.0370.0000.0000.0000.000
97A97ASP-1-0.883-0.93630.979-0.034-0.0340.0000.0000.0000.000
98A98LEU0-0.039-0.01127.660-0.005-0.0050.0000.0000.0000.000
99A99PRO0-0.022-0.02026.4100.0040.0040.0000.0000.0000.000
100A100ILE0-0.0360.00019.514-0.013-0.0130.0000.0000.0000.000
101A101VAL0-0.027-0.02519.751-0.024-0.0240.0000.0000.0000.000
102A102PRO00.0190.01422.9010.0180.0180.0000.0000.0000.000
103A103GLY00.0020.00425.929-0.006-0.0060.0000.0000.0000.000
104A104GLY00.0030.02123.7330.0060.0060.0000.0000.0000.000
105A105PRO0-0.002-0.01122.8030.0060.0060.0000.0000.0000.000
106A106LEU00.0450.03224.672-0.003-0.0030.0000.0000.0000.000
107A107ALA00.001-0.01124.147-0.002-0.0020.0000.0000.0000.000
108A108LEU0-0.0210.01418.6180.0010.0010.0000.0000.0000.000
109A109PRO00.0030.00020.8530.0030.0030.0000.0000.0000.000
110A110ALA00.003-0.00617.5990.0040.0040.0000.0000.0000.000
111A111ARG10.8510.94512.904-0.196-0.1960.0000.0000.0000.000
112A112PHE00.059-0.00212.8070.0650.0650.0000.0000.0000.000
113A113PRO00.0450.05014.854-0.085-0.0850.0000.0000.0000.000
114A114VAL00.000-0.02017.907-0.013-0.0130.0000.0000.0000.000
115A115LYS10.9250.94920.499-0.208-0.2080.0000.0000.0000.000
116A116PRO00.0470.02119.450-0.018-0.0180.0000.0000.0000.000
117A117VAL00.0890.07116.478-0.007-0.0070.0000.0000.0000.000
118A118LEU0-0.049-0.02219.589-0.028-0.0280.0000.0000.0000.000
119A119ALA0-0.035-0.02122.984-0.021-0.0210.0000.0000.0000.000
120A120ARG11.0051.01318.984-0.383-0.3830.0000.0000.0000.000
121A121TRP0-0.040-0.04418.078-0.031-0.0310.0000.0000.0000.000
122A122ARG10.9450.97422.811-0.187-0.1870.0000.0000.0000.000
123A123GLU-1-0.902-0.93924.1020.2770.2770.0000.0000.0000.000
124A124ALA0-0.095-0.03422.692-0.008-0.0080.0000.0000.0000.000
125A125GLY00.0100.00424.801-0.012-0.0120.0000.0000.0000.000
126A126ILE0-0.052-0.02821.885-0.014-0.0140.0000.0000.0000.000
127A127PRO0-0.031-0.01925.7340.0090.0090.0000.0000.0000.000
128A128GLY00.0580.02524.9550.0060.0060.0000.0000.0000.000
129A129ARG10.8820.94425.166-0.114-0.1140.0000.0000.0000.000
130A130PRO00.0060.01024.0460.0060.0060.0000.0000.0000.000
131A131SER0-0.072-0.06523.454-0.023-0.0230.0000.0000.0000.000
132A132LEU0-0.007-0.02224.2740.0140.0140.0000.0000.0000.000
133A133SER00.0480.02825.365-0.009-0.0090.0000.0000.0000.000
134A134ALA00.0310.03620.8270.0050.0050.0000.0000.0000.000
135A135GLY0-0.001-0.00722.765-0.010-0.0100.0000.0000.0000.000
136A136SER0-0.028-0.02624.3530.0080.0080.0000.0000.0000.000
137A137TYR00.019-0.01523.225-0.010-0.0100.0000.0000.0000.000
138A138LEU00.0320.04018.5810.0030.0030.0000.0000.0000.000
139A139CYS0-0.0420.00317.862-0.001-0.0010.0000.0000.0000.000
140A140ASN00.003-0.00717.5960.0300.0300.0000.0000.0000.000
141A141GLN00.0390.02118.0400.0210.0210.0000.0000.0000.000
142A142ALA00.0170.00613.536-0.018-0.0180.0000.0000.0000.000
143A143PHE0-0.041-0.03114.0260.0070.0070.0000.0000.0000.000
144A144TYR00.034-0.02115.4250.0070.0070.0000.0000.0000.000
145A145LEU00.0270.01314.381-0.005-0.0050.0000.0000.0000.000
146A146SER00.0150.01910.812-0.040-0.0400.0000.0000.0000.000
147A147LEU0-0.0310.00312.3650.0090.0090.0000.0000.0000.000
148A148TYR0-0.015-0.00614.9570.0120.0120.0000.0000.0000.000
149A149ARG10.8920.95212.7260.3630.3630.0000.0000.0000.000
150A150LEU0-0.0320.0028.124-0.031-0.0310.0000.0000.0000.000
151A151PRO00.0160.01011.0050.0480.0480.0000.0000.0000.000
152A152GLU-1-0.882-0.94813.2400.2930.2930.0000.0000.0000.000
153A153GLU-1-0.932-0.97811.7190.2610.2610.0000.0000.0000.000
154A154VAL0-0.050-0.0108.1990.1710.1710.0000.0000.0000.000
155A155PRO0-0.014-0.0128.640-0.088-0.0880.0000.0000.0000.000
156A156VAL00.0270.00810.1330.0640.0640.0000.0000.0000.000
157A157GLY0-0.010-0.00212.059-0.055-0.0550.0000.0000.0000.000
158A158PHE00.024-0.00513.2610.0110.0110.0000.0000.0000.000
159A159LEU0-0.033-0.01315.6810.0000.0000.0000.0000.0000.000
160A160HIS0-0.069-0.05017.316-0.029-0.0290.0000.0000.0000.000
161A161LEU0-0.022-0.01117.2890.0160.0160.0000.0000.0000.000
162A162PRO0-0.0030.01321.268-0.016-0.0160.0000.0000.0000.000
163A163PRO00.0360.01024.042-0.003-0.0030.0000.0000.0000.000
164A164ASP-1-0.722-0.86423.4220.0300.0300.0000.0000.0000.000
165A165GLU-1-0.807-0.92225.6350.0400.0400.0000.0000.0000.000
166A166THR00.0190.02325.533-0.007-0.0070.0000.0000.0000.000
167A167LEU0-0.044-0.01425.751-0.005-0.0050.0000.0000.0000.000
168A168ALA0-0.051-0.02229.205-0.003-0.0030.0000.0000.0000.000
169A169LEU0-0.028-0.00930.473-0.001-0.0010.0000.0000.0000.000
170A170LYS10.8100.91031.2010.0300.0300.0000.0000.0000.000
171A171ARG10.9370.95633.220-0.006-0.0060.0000.0000.0000.000
172A172PRO00.0170.01934.0660.0040.0040.0000.0000.0000.000
173A173ARG10.9100.95630.147-0.013-0.0130.0000.0000.0000.000
174A174PRO00.001-0.00531.6600.0030.0030.0000.0000.0000.000
175A175TYR0-0.0060.00028.007-0.003-0.0030.0000.0000.0000.000
176A176VAL0-0.025-0.00724.5280.0070.0070.0000.0000.0000.000
177A177PRO00.0330.01525.158-0.003-0.0030.0000.0000.0000.000
178A178LEU00.0660.02219.5610.0200.0200.0000.0000.0000.000
179A179GLU-1-0.858-0.92820.2540.1070.1070.0000.0000.0000.000
180A180VAL0-0.059-0.02720.6980.0260.0260.0000.0000.0000.000
181A181GLN0-0.034-0.03319.7360.0370.0370.0000.0000.0000.000
182A182ALA00.0830.03616.4260.0350.0350.0000.0000.0000.000
183A183ARG10.8820.95516.053-0.180-0.1800.0000.0000.0000.000
184A184ALA00.004-0.00617.5250.0450.0450.0000.0000.0000.000
185A185VAL00.0320.01512.4680.0490.0490.0000.0000.0000.000
186A186ARG10.9300.97312.688-0.337-0.3370.0000.0000.0000.000
187A187LEU0-0.038-0.02613.1830.0770.0770.0000.0000.0000.000
188A188ALA0-0.027-0.01214.4430.0480.0480.0000.0000.0000.000
189A189LEU0-0.015-0.0168.5730.0610.0610.0000.0000.0000.000
190A190GLU-1-0.896-0.94410.1490.7340.7340.0000.0000.0000.000
191A191HIS0-0.135-0.06012.142-0.024-0.0240.0000.0000.0000.000
192A192LEU0-0.023-0.0038.801-0.103-0.1030.0000.0000.0000.000