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: NNKVQ

Calculation Name: 4J2P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J2P

Chain ID: A

ChEMBL ID:

UniProt ID: P09142

Base Structure: X-ray

Registration Date: 2023-09-23

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2974383.561088
FMO2-HF: Nuclear repulsion 2881858.939765
FMO2-HF: Total energy -92524.621323
FMO2-MP2: Total energy -92793.431482


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.
-8.209-3.2438.755-4.63-9.091-0.011
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 : 0.022 / q_NPA : 0.023
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].
3A3LYS10.9040.9613.133-1.7791.6400.089-1.908-1.5990.000
4A4TRP00.0170.0245.373-0.0790.064-0.001-0.008-0.1340.000
5A5ASN0-0.070-0.0517.2670.1940.1940.0000.0000.0000.000
6A6TYR00.0600.0168.0980.0240.0240.0000.0000.0000.000
7A7GLY00.0670.04813.6500.0240.0240.0000.0000.0000.000
8A8VAL0-0.026-0.00317.4280.0030.0030.0000.0000.0000.000
9A9PHE0-0.048-0.02820.760-0.001-0.0010.0000.0000.0000.000
10A10PHE00.0610.03723.8310.0120.0120.0000.0000.0000.000
11A11LEU00.0120.00127.404-0.006-0.0060.0000.0000.0000.000
12A12ASN0-0.059-0.02129.8810.0190.0190.0000.0000.0000.000
13A13PHE00.005-0.02232.7210.0070.0070.0000.0000.0000.000
14A14TYR00.0110.00635.4200.0020.0020.0000.0000.0000.000
15A15HIS10.8580.93537.6070.1090.1090.0000.0000.0000.000
16A16VAL00.0910.04632.921-0.004-0.0040.0000.0000.0000.000
17A17GLY00.0080.01835.3890.0020.0020.0000.0000.0000.000
18A18GLN0-0.038-0.03236.1980.0050.0050.0000.0000.0000.000
19A19GLN0-0.0390.00133.7080.0050.0050.0000.0000.0000.000
20A20GLU-1-0.868-0.94439.035-0.091-0.0910.0000.0000.0000.000
21A21PRO00.001-0.00738.392-0.007-0.0070.0000.0000.0000.000
22A22SER0-0.017-0.00537.816-0.007-0.0070.0000.0000.0000.000
23A23LEU00.0520.03636.645-0.004-0.0040.0000.0000.0000.000
24A24THR00.0340.01633.398-0.006-0.0060.0000.0000.0000.000
25A25MET0-0.0210.00333.261-0.013-0.0130.0000.0000.0000.000
26A26SER0-0.024-0.02333.620-0.005-0.0050.0000.0000.0000.000
27A27ASN0-0.013-0.00331.1710.0010.0010.0000.0000.0000.000
28A28ALA00.0400.01429.067-0.010-0.0100.0000.0000.0000.000
29A29LEU0-0.001-0.01728.887-0.014-0.0140.0000.0000.0000.000
30A30GLU-1-0.771-0.84628.757-0.160-0.1600.0000.0000.0000.000
31A31THR0-0.056-0.06124.059-0.005-0.0050.0000.0000.0000.000
32A32LEU0-0.040-0.02724.977-0.021-0.0210.0000.0000.0000.000
33A33ARG10.7080.79426.1420.1480.1480.0000.0000.0000.000
34A34ILE0-0.003-0.01022.485-0.004-0.0040.0000.0000.0000.000
35A35ILE0-0.084-0.03621.030-0.016-0.0160.0000.0000.0000.000
36A36ASP-1-0.970-0.97122.378-0.240-0.2400.0000.0000.0000.000
37A37GLU-1-0.906-0.93425.158-0.145-0.1450.0000.0000.0000.000
38A38ASP-1-0.840-0.89523.791-0.154-0.1540.0000.0000.0000.000
39A39THR0-0.147-0.09818.775-0.013-0.0130.0000.0000.0000.000
40A40SER0-0.015-0.00916.510-0.004-0.0040.0000.0000.0000.000
41A41ILE0-0.125-0.06812.758-0.069-0.0690.0000.0000.0000.000
42A42TYR0-0.043-0.03314.365-0.111-0.1110.0000.0000.0000.000
43A43ASP-1-0.780-0.86214.691-0.779-0.7790.0000.0000.0000.000
44A44VAL0-0.040-0.01617.0640.0310.0310.0000.0000.0000.000
45A45VAL00.0290.01219.856-0.002-0.0020.0000.0000.0000.000
46A46ALA0-0.025-0.00822.7940.0040.0040.0000.0000.0000.000
47A47PHE00.0350.00524.7490.0120.0120.0000.0000.0000.000
48A48SER00.0020.01926.812-0.012-0.0120.0000.0000.0000.000
49A49GLU-1-0.853-0.94928.274-0.194-0.1940.0000.0000.0000.000
50A50HIS0-0.012-0.00628.2800.0060.0060.0000.0000.0000.000
51A51HIS0-0.055-0.02432.1400.0040.0040.0000.0000.0000.000
52A52ILE00.0070.00434.6440.0110.0110.0000.0000.0000.000
53A53ASP-1-0.809-0.89434.183-0.173-0.1730.0000.0000.0000.000
54A54LYS10.8640.93132.0910.1690.1690.0000.0000.0000.000
55A55SER0-0.041-0.01836.6960.0060.0060.0000.0000.0000.000
56A56TYR0-0.103-0.06939.7200.0100.0100.0000.0000.0000.000
57A57ASN0-0.026-0.00939.1890.0040.0040.0000.0000.0000.000
58A58ASP-1-0.868-0.93833.677-0.171-0.1710.0000.0000.0000.000
59A59GLU-1-0.866-0.90536.076-0.130-0.1300.0000.0000.0000.000
60A60THR0-0.014-0.02438.8300.0000.0000.0000.0000.0000.000
61A61LYS10.7850.88933.3070.1860.1860.0000.0000.0000.000
62A62LEU0-0.020-0.00933.5540.0000.0000.0000.0000.0000.000
63A63ALA00.0220.00329.965-0.001-0.0010.0000.0000.0000.000
64A64PRO00.0270.03029.049-0.001-0.0010.0000.0000.0000.000
65A65PHE0-0.038-0.03427.311-0.019-0.0190.0000.0000.0000.000
66A66VAL00.0430.01424.3060.0130.0130.0000.0000.0000.000
67A67SER0-0.045-0.01524.335-0.040-0.0400.0000.0000.0000.000
68A68LEU00.0280.02119.1970.0120.0120.0000.0000.0000.000
69A69GLY00.0610.02521.405-0.041-0.0410.0000.0000.0000.000
70A70LYS10.9030.94022.3550.4830.4830.0000.0000.0000.000
71A71GLN00.0010.01517.8190.0520.0520.0000.0000.0000.000
72A72ILE0-0.003-0.00121.9340.0100.0100.0000.0000.0000.000
73A73HIS0-0.026-0.02017.398-0.034-0.0340.0000.0000.0000.000
74A74ILE0-0.012-0.01522.6950.0360.0360.0000.0000.0000.000
75A75LEU00.0010.00623.859-0.021-0.0210.0000.0000.0000.000
76A76ALA0-0.012-0.01423.4100.0210.0210.0000.0000.0000.000
77A77THR0-0.031-0.01425.5600.0080.0080.0000.0000.0000.000
78A78SER00.027-0.01529.2120.0070.0070.0000.0000.0000.000
79A79PRO00.0770.01727.594-0.018-0.0180.0000.0000.0000.000
80A80GLU-1-0.816-0.89228.200-0.159-0.1590.0000.0000.0000.000
81A81THR0-0.0490.00027.5890.0000.0000.0000.0000.0000.000
82A82VAL00.0150.01523.669-0.015-0.0150.0000.0000.0000.000
83A83VAL0-0.001-0.00124.816-0.015-0.0150.0000.0000.0000.000
84A84LYS10.8550.89726.9500.1750.1750.0000.0000.0000.000
85A85ALA00.0100.01623.736-0.002-0.0020.0000.0000.0000.000
86A86ALA00.0070.00322.538-0.017-0.0170.0000.0000.0000.000
87A87LYS10.8490.93123.5630.1770.1770.0000.0000.0000.000
88A88TYR00.003-0.00825.3680.0230.0230.0000.0000.0000.000
89A89GLY00.0450.03021.082-0.014-0.0140.0000.0000.0000.000
90A90MET0-0.0430.00119.970-0.038-0.0380.0000.0000.0000.000
91A91PRO00.0180.02617.5250.0140.0140.0000.0000.0000.000
92A92LEU00.0110.00218.7520.0540.0540.0000.0000.0000.000
93A93LEU00.0060.01219.373-0.066-0.0660.0000.0000.0000.000
94A94PHE00.024-0.00217.1670.0430.0430.0000.0000.0000.000
95A95LYS10.8460.90521.6580.1950.1950.0000.0000.0000.000
96A96TRP00.0980.03823.174-0.002-0.0020.0000.0000.0000.000
97A97ASP-1-0.768-0.85324.122-0.191-0.1910.0000.0000.0000.000
98A98ASP-1-0.812-0.89025.018-0.201-0.2010.0000.0000.0000.000
99A99SER00.0510.03724.916-0.014-0.0140.0000.0000.0000.000
100A100GLN00.0770.01317.180-0.025-0.0250.0000.0000.0000.000
101A101GLN00.0020.00321.479-0.026-0.0260.0000.0000.0000.000
102A102LYS10.8800.94823.7400.1880.1880.0000.0000.0000.000
103A103ARG10.7870.88319.9850.2710.2710.0000.0000.0000.000
104A104ILE00.0360.02418.463-0.025-0.0250.0000.0000.0000.000
105A105GLU-1-0.929-0.96120.589-0.137-0.1370.0000.0000.0000.000
106A106LEU0-0.056-0.02523.197-0.001-0.0010.0000.0000.0000.000
107A107LEU00.0120.01415.311-0.015-0.0150.0000.0000.0000.000
108A108ASN0-0.046-0.03719.002-0.005-0.0050.0000.0000.0000.000
109A109HIS00.0060.00420.9620.0090.0090.0000.0000.0000.000
110A110TYR0-0.022-0.03118.065-0.006-0.0060.0000.0000.0000.000
111A111GLN00.005-0.01415.255-0.048-0.0480.0000.0000.0000.000
112A112ALA00.0070.00819.7430.0110.0110.0000.0000.0000.000
113A113ALA0-0.049-0.02522.9810.0130.0130.0000.0000.0000.000
114A114ALA00.0380.01720.4180.0100.0100.0000.0000.0000.000
115A115ALA00.0210.01620.9710.0080.0080.0000.0000.0000.000
116A116LYS10.9210.96322.4780.1460.1460.0000.0000.0000.000
117A117PHE0-0.069-0.03825.4710.0170.0170.0000.0000.0000.000
118A118ASN0-0.066-0.02623.9340.0040.0040.0000.0000.0000.000
119A119VAL0-0.0240.00821.219-0.009-0.0090.0000.0000.0000.000
120A120ASP-1-0.826-0.91916.206-0.511-0.5110.0000.0000.0000.000
121A121ILE0-0.001-0.00916.168-0.017-0.0170.0000.0000.0000.000
122A122ALA0-0.027-0.01212.315-0.081-0.0810.0000.0000.0000.000
123A123GLY00.000-0.01211.147-0.147-0.1470.0000.0000.0000.000
124A124VAL0-0.0330.00512.197-0.125-0.1250.0000.0000.0000.000
125A125ARG10.8070.8868.4941.7091.7090.0000.0000.0000.000
126A126HIS00.0360.03113.1540.0510.0510.0000.0000.0000.000
127A127ARG10.7760.85514.8380.6830.6830.0000.0000.0000.000
128A128LEU0-0.0030.00215.2290.0670.0670.0000.0000.0000.000
129A129MET0-0.038-0.00817.698-0.017-0.0170.0000.0000.0000.000
130A130LEU0-0.006-0.00616.8420.0170.0170.0000.0000.0000.000
131A131PHE00.0210.00320.757-0.009-0.0090.0000.0000.0000.000
132A132VAL0-0.045-0.02418.781-0.007-0.0070.0000.0000.0000.000
133A133ASN0-0.048-0.05221.8130.0180.0180.0000.0000.0000.000
134A134VAL00.026-0.01120.0190.0020.0020.0000.0000.0000.000
135A135ASN00.0600.01723.3880.0160.0160.0000.0000.0000.000
136A136ASP-1-0.893-0.95125.297-0.067-0.0670.0000.0000.0000.000
137A137ASN0-0.056-0.01526.5370.0170.0170.0000.0000.0000.000
138A138PRO0-0.004-0.01425.025-0.008-0.0080.0000.0000.0000.000
139A139THR00.0300.00026.953-0.009-0.0090.0000.0000.0000.000
140A140GLN00.0180.01130.281-0.007-0.0070.0000.0000.0000.000
141A141ALA00.0220.03125.736-0.004-0.0040.0000.0000.0000.000
142A142LYS10.8470.92324.5700.1170.1170.0000.0000.0000.000
143A143ALA00.0210.03028.819-0.003-0.0030.0000.0000.0000.000
144A144GLU-1-0.800-0.88929.728-0.122-0.1220.0000.0000.0000.000
145A145LEU0-0.018-0.01025.707-0.004-0.0040.0000.0000.0000.000
146A146SER0-0.019-0.03829.717-0.003-0.0030.0000.0000.0000.000
147A147ILE00.0050.00732.5380.0000.0000.0000.0000.0000.000
148A148TYR0-0.017-0.01730.062-0.005-0.0050.0000.0000.0000.000
149A149LEU0-0.013-0.01728.787-0.004-0.0040.0000.0000.0000.000
150A150GLU-1-0.863-0.90633.211-0.087-0.0870.0000.0000.0000.000
151A151ASP-1-0.825-0.90536.967-0.100-0.1000.0000.0000.0000.000
152A152TYR0-0.003-0.01431.214-0.001-0.0010.0000.0000.0000.000
153A153LEU0-0.032-0.00632.273-0.002-0.0020.0000.0000.0000.000
154A154SER00.0160.00236.1530.0050.0050.0000.0000.0000.000
155A155TYR0-0.077-0.02337.5310.0050.0050.0000.0000.0000.000
156A156THR0-0.090-0.07434.836-0.001-0.0010.0000.0000.0000.000
157A157GLN0-0.059-0.01037.7860.0020.0020.0000.0000.0000.000
158A158ALA00.0450.02734.6500.0000.0000.0000.0000.0000.000
159A159GLU-1-0.845-0.91535.428-0.095-0.0950.0000.0000.0000.000
160A160THR0-0.036-0.02836.312-0.002-0.0020.0000.0000.0000.000
161A161SER0-0.065-0.04331.924-0.001-0.0010.0000.0000.0000.000
162A162ILE00.0270.01931.345-0.010-0.0100.0000.0000.0000.000
163A163ASP-1-0.855-0.93730.482-0.092-0.0920.0000.0000.0000.000
164A164GLU-1-0.882-0.92626.597-0.140-0.1400.0000.0000.0000.000
165A165ILE00.0110.00826.770-0.017-0.0170.0000.0000.0000.000
166A166ILE00.004-0.00525.775-0.019-0.0190.0000.0000.0000.000
167A167ASN0-0.061-0.03024.9550.0010.0010.0000.0000.0000.000
168A168SER00.004-0.00322.390-0.014-0.0140.0000.0000.0000.000
169A169ASN0-0.025-0.02921.398-0.059-0.0590.0000.0000.0000.000
170A170ALA00.0140.01918.6930.0200.0200.0000.0000.0000.000
171A171ALA00.0360.02920.610-0.001-0.0010.0000.0000.0000.000
172A172GLY00.026-0.00722.8930.0160.0160.0000.0000.0000.000
173A173ASN00.0670.07021.223-0.011-0.0110.0000.0000.0000.000
174A174PHE00.1020.02915.793-0.020-0.0200.0000.0000.0000.000
175A175ASP-1-0.783-0.87415.271-0.134-0.1340.0000.0000.0000.000
176A176THR0-0.016-0.01816.139-0.010-0.0100.0000.0000.0000.000
177A177CYS0-0.056-0.01117.817-0.013-0.0130.0000.0000.0000.000
178A178LEU0-0.033-0.02112.537-0.046-0.0460.0000.0000.0000.000
179A179HIS0-0.062-0.02312.793-0.087-0.0870.0000.0000.0000.000
180A180HIS00.0260.00813.980-0.035-0.0350.0000.0000.0000.000
181A181VAL0-0.021-0.01412.356-0.020-0.0200.0000.0000.0000.000
182A182ALA0-0.0050.0009.827-0.088-0.0880.0000.0000.0000.000
183A183GLU-1-0.854-0.92511.286-0.093-0.0930.0000.0000.0000.000
184A184MET0-0.058-0.02013.9840.0160.0160.0000.0000.0000.000
185A185ALA0-0.007-0.00710.479-0.003-0.0030.0000.0000.0000.000
186A186GLN00.0110.01210.0760.0320.0320.0000.0000.0000.000
187A187GLY0-0.004-0.00411.8750.0690.0690.0000.0000.0000.000
188A188LEU0-0.061-0.03114.6130.0350.0350.0000.0000.0000.000
189A189ASN0-0.018-0.01511.710-0.052-0.0520.0000.0000.0000.000
190A190ASN0-0.012-0.0097.426-0.173-0.1730.0000.0000.0000.000
191A191LYS10.8030.9068.7840.4870.4870.0000.0000.0000.000
192A192VAL0-0.025-0.00111.0410.0390.0390.0000.0000.0000.000
193A193ASP-1-0.745-0.82110.186-1.782-1.7820.0000.0000.0000.000
194A194PHE0-0.001-0.0179.8310.1420.1420.0000.0000.0000.000
195A195LEU0-0.036-0.01414.876-0.015-0.0150.0000.0000.0000.000
196A196PHE00.0230.00614.0300.0170.0170.0000.0000.0000.000
197A197CYS0-0.040-0.00219.6930.0190.0190.0000.0000.0000.000
198A198PHE00.0990.01918.4680.0070.0070.0000.0000.0000.000
199A199GLU-1-0.755-0.86024.372-0.188-0.1880.0000.0000.0000.000
200A200SER0-0.032-0.00126.5080.0160.0160.0000.0000.0000.000
201A201MET0-0.0480.01024.6780.0040.0040.0000.0000.0000.000
202A202LYS10.8320.90228.5770.1060.1060.0000.0000.0000.000
203A203ASP-1-0.840-0.88730.238-0.098-0.0980.0000.0000.0000.000
204A204GLN00.043-0.00529.105-0.019-0.0190.0000.0000.0000.000
205A205GLU-1-0.766-0.86428.230-0.126-0.1260.0000.0000.0000.000
206A206ASN0-0.066-0.03826.598-0.005-0.0050.0000.0000.0000.000
207A207LYS10.7880.88724.6910.1730.1730.0000.0000.0000.000
208A208LYS10.8650.92423.4090.1060.1060.0000.0000.0000.000
209A209SER0-0.031-0.02822.922-0.009-0.0090.0000.0000.0000.000
210A210LEU0-0.042-0.01718.765-0.008-0.0080.0000.0000.0000.000
211A211MET0-0.0110.00918.815-0.022-0.0220.0000.0000.0000.000
212A212ILE00.0540.02818.249-0.036-0.0360.0000.0000.0000.000
213A213ASN0-0.043-0.02917.9130.0040.0040.0000.0000.0000.000
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