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: 89R8Y

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2966639.161666
FMO2-HF: Nuclear repulsion 2874114.817235
FMO2-HF: Total energy -92524.34443
FMO2-MP2: Total energy -92793.190641


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.
-7.313-2.6489.458-4.884-9.24-0.006
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 : 0.025 / q_NPA : 0.025
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].
3A3LYS10.8870.9523.793-1.5132.036-0.032-1.891-1.6280.005
4A4TRP0-0.0040.0105.6830.2610.2610.0000.0000.0000.000
5A5ASN0-0.077-0.0527.8880.1540.1540.0000.0000.0000.000
6A6TYR00.0580.0178.1750.0120.0120.0000.0000.0000.000
7A7GLY00.0800.06113.9640.0200.0200.0000.0000.0000.000
8A8VAL0-0.0250.00317.7180.0000.0000.0000.0000.0000.000
9A9PHE0-0.046-0.02820.8820.0000.0000.0000.0000.0000.000
10A10PHE00.0630.03823.8530.0100.0100.0000.0000.0000.000
11A11LEU00.0050.00227.375-0.005-0.0050.0000.0000.0000.000
12A12ASN0-0.080-0.03229.7320.0170.0170.0000.0000.0000.000
13A13PHE00.011-0.01332.7120.0070.0070.0000.0000.0000.000
14A14TYR00.0140.00435.3550.0010.0010.0000.0000.0000.000
15A15HIS10.8450.93337.9790.1050.1050.0000.0000.0000.000
16A16VAL00.0910.04532.973-0.002-0.0020.0000.0000.0000.000
17A17GLY00.0190.02135.4500.0030.0030.0000.0000.0000.000
18A18GLN00.0020.00336.1720.0050.0050.0000.0000.0000.000
19A19GLN0-0.052-0.01133.7510.0050.0050.0000.0000.0000.000
20A20GLU-1-0.868-0.94039.048-0.087-0.0870.0000.0000.0000.000
21A21PRO00.006-0.00638.681-0.006-0.0060.0000.0000.0000.000
22A22SER00.002-0.00238.192-0.007-0.0070.0000.0000.0000.000
23A23LEU00.0340.03336.711-0.003-0.0030.0000.0000.0000.000
24A24THR00.0330.00733.570-0.006-0.0060.0000.0000.0000.000
25A25MET0-0.0270.00233.540-0.012-0.0120.0000.0000.0000.000
26A26SER00.012-0.00733.986-0.005-0.0050.0000.0000.0000.000
27A27ASN0-0.025-0.01431.4600.0010.0010.0000.0000.0000.000
28A28ALA00.0240.01329.517-0.010-0.0100.0000.0000.0000.000
29A29LEU0-0.002-0.02429.203-0.013-0.0130.0000.0000.0000.000
30A30GLU-1-0.772-0.84928.941-0.151-0.1510.0000.0000.0000.000
31A31THR0-0.056-0.06024.347-0.004-0.0040.0000.0000.0000.000
32A32LEU0-0.038-0.02725.291-0.017-0.0170.0000.0000.0000.000
33A33ARG10.7000.80226.3880.1420.1420.0000.0000.0000.000
34A34ILE00.003-0.00122.688-0.005-0.0050.0000.0000.0000.000
35A35ILE0-0.096-0.05221.348-0.014-0.0140.0000.0000.0000.000
36A36ASP-1-0.976-0.98122.429-0.223-0.2230.0000.0000.0000.000
37A37GLU-1-0.904-0.93325.013-0.141-0.1410.0000.0000.0000.000
38A38ASP-1-0.856-0.90123.712-0.148-0.1480.0000.0000.0000.000
39A39THR0-0.129-0.07818.684-0.011-0.0110.0000.0000.0000.000
40A40SER0-0.014-0.01516.678-0.005-0.0050.0000.0000.0000.000
41A41ILE0-0.123-0.06312.770-0.063-0.0630.0000.0000.0000.000
42A42TYR0-0.061-0.04315.069-0.090-0.0900.0000.0000.0000.000
43A43ASP-1-0.763-0.85715.437-0.688-0.6880.0000.0000.0000.000
44A44VAL0-0.040-0.01517.8680.0320.0320.0000.0000.0000.000
45A45VAL00.0260.00920.536-0.004-0.0040.0000.0000.0000.000
46A46ALA0-0.025-0.01023.2570.0030.0030.0000.0000.0000.000
47A47PHE00.0440.01224.9980.0070.0070.0000.0000.0000.000
48A48SER00.0050.01326.930-0.007-0.0070.0000.0000.0000.000
49A49GLU-1-0.861-0.95128.475-0.182-0.1820.0000.0000.0000.000
50A50HIS0-0.031-0.02328.0190.0050.0050.0000.0000.0000.000
51A51HIS0-0.036-0.01532.3490.0020.0020.0000.0000.0000.000
52A52ILE00.0120.00034.9040.0100.0100.0000.0000.0000.000
53A53ASP-1-0.805-0.89034.970-0.160-0.1600.0000.0000.0000.000
54A54LYS10.9360.98732.4300.1610.1610.0000.0000.0000.000
55A55SER0-0.070-0.02537.1890.0080.0080.0000.0000.0000.000
56A56TYR0-0.111-0.07440.0340.0080.0080.0000.0000.0000.000
57A57ASN0-0.020-0.01239.5570.0040.0040.0000.0000.0000.000
58A58ASP-1-0.899-0.94934.018-0.157-0.1570.0000.0000.0000.000
59A59GLU-1-0.911-0.94036.004-0.119-0.1190.0000.0000.0000.000
60A60THR00.013-0.00539.2060.0010.0010.0000.0000.0000.000
61A61LYS10.7770.89133.5580.1740.1740.0000.0000.0000.000
62A62LEU0-0.0100.00133.5460.0020.0020.0000.0000.0000.000
63A63ALA00.019-0.00830.115-0.001-0.0010.0000.0000.0000.000
64A64PRO00.0260.03328.972-0.001-0.0010.0000.0000.0000.000
65A65PHE0-0.033-0.03027.550-0.017-0.0170.0000.0000.0000.000
66A66VAL00.0450.01624.9820.0110.0110.0000.0000.0000.000
67A67SER0-0.043-0.01024.903-0.034-0.0340.0000.0000.0000.000
68A68LEU00.0350.02519.7580.0080.0080.0000.0000.0000.000
69A69GLY00.0540.02021.510-0.041-0.0410.0000.0000.0000.000
70A70LYS10.9280.95122.3940.4340.4340.0000.0000.0000.000
71A71GLN0-0.0160.00317.6890.0530.0530.0000.0000.0000.000
72A72ILE00.0050.00621.8920.0080.0080.0000.0000.0000.000
73A73HIS0-0.028-0.02317.554-0.044-0.0440.0000.0000.0000.000
74A74ILE0-0.018-0.01122.8740.0340.0340.0000.0000.0000.000
75A75LEU00.0030.00623.853-0.020-0.0200.0000.0000.0000.000
76A76ALA0-0.015-0.02023.2640.0200.0200.0000.0000.0000.000
77A77THR0-0.003-0.00725.4080.0050.0050.0000.0000.0000.000
78A78SER00.0580.03028.4980.0100.0100.0000.0000.0000.000
79A79PRO00.0570.02527.658-0.015-0.0150.0000.0000.0000.000
80A80GLU-1-0.860-0.94328.444-0.143-0.1430.0000.0000.0000.000
81A81THR0-0.027-0.00827.5190.0010.0010.0000.0000.0000.000
82A82VAL0-0.003-0.00123.820-0.014-0.0140.0000.0000.0000.000
83A83VAL0-0.0010.00824.974-0.012-0.0120.0000.0000.0000.000
84A84LYS10.8680.91626.9740.1560.1560.0000.0000.0000.000
85A85ALA00.0220.02023.662-0.002-0.0020.0000.0000.0000.000
86A86ALA00.0130.01322.549-0.019-0.0190.0000.0000.0000.000
87A87LYS10.8620.94023.5620.1600.1600.0000.0000.0000.000
88A88TYR0-0.011-0.01425.6950.0180.0180.0000.0000.0000.000
89A89GLY00.0240.02221.421-0.012-0.0120.0000.0000.0000.000
90A90MET0-0.053-0.01620.321-0.029-0.0290.0000.0000.0000.000
91A91PRO00.0220.03217.3770.0120.0120.0000.0000.0000.000
92A92LEU00.016-0.00318.8170.0460.0460.0000.0000.0000.000
93A93LEU0-0.0120.00219.399-0.056-0.0560.0000.0000.0000.000
94A94PHE00.022-0.00817.3900.0390.0390.0000.0000.0000.000
95A95LYS10.8270.89221.8740.1890.1890.0000.0000.0000.000
96A96TRP00.0790.02323.1990.0010.0010.0000.0000.0000.000
97A97ASP-1-0.787-0.87724.147-0.188-0.1880.0000.0000.0000.000
98A98ASP-1-0.825-0.87525.386-0.183-0.1830.0000.0000.0000.000
99A99SER00.0580.02925.092-0.016-0.0160.0000.0000.0000.000
100A100GLN00.0980.02617.468-0.018-0.0180.0000.0000.0000.000
101A101GLN0-0.008-0.00422.042-0.021-0.0210.0000.0000.0000.000
102A102LYS10.9030.95424.1540.1760.1760.0000.0000.0000.000
103A103ARG10.8020.89920.2840.2710.2710.0000.0000.0000.000
104A104ILE00.0380.01918.777-0.019-0.0190.0000.0000.0000.000
105A105GLU-1-0.928-0.95820.931-0.134-0.1340.0000.0000.0000.000
106A106LEU0-0.061-0.02723.1760.0020.0020.0000.0000.0000.000
107A107LEU00.0020.00415.418-0.009-0.0090.0000.0000.0000.000
108A108ASN0-0.041-0.03719.660-0.001-0.0010.0000.0000.0000.000
109A109HIS00.0070.00721.1720.0110.0110.0000.0000.0000.000
110A110TYR0-0.039-0.03618.108-0.002-0.0020.0000.0000.0000.000
111A111GLN0-0.005-0.02415.429-0.041-0.0410.0000.0000.0000.000
112A112ALA0-0.0010.01419.9360.0140.0140.0000.0000.0000.000
113A113ALA0-0.045-0.02823.2060.0130.0130.0000.0000.0000.000
114A114ALA00.0390.01320.5690.0100.0100.0000.0000.0000.000
115A115ALA00.0290.02821.5360.0060.0060.0000.0000.0000.000
116A116LYS10.9260.97122.8600.1280.1280.0000.0000.0000.000
117A117PHE0-0.083-0.04325.7700.0150.0150.0000.0000.0000.000
118A118ASN0-0.053-0.02224.0330.0010.0010.0000.0000.0000.000
119A119VAL0-0.0180.00921.173-0.008-0.0080.0000.0000.0000.000
120A120ASP-1-0.844-0.92716.567-0.411-0.4110.0000.0000.0000.000
121A121ILE0-0.001-0.01116.465-0.027-0.0270.0000.0000.0000.000
122A122ALA0-0.017-0.00512.618-0.071-0.0710.0000.0000.0000.000
123A123GLY0-0.008-0.01111.267-0.117-0.1170.0000.0000.0000.000
124A124VAL0-0.0390.00012.035-0.136-0.1360.0000.0000.0000.000
125A125ARG10.8210.9018.2851.5531.5530.0000.0000.0000.000
126A126HIS00.0480.03613.0490.0500.0500.0000.0000.0000.000
127A127ARG10.7880.86414.9580.6240.6240.0000.0000.0000.000
128A128LEU00.0020.00415.7630.0660.0660.0000.0000.0000.000
129A129MET0-0.044-0.01117.739-0.021-0.0210.0000.0000.0000.000
130A130LEU0-0.001-0.00416.7200.0150.0150.0000.0000.0000.000
131A131PHE00.0190.00320.596-0.008-0.0080.0000.0000.0000.000
132A132VAL0-0.031-0.01718.498-0.006-0.0060.0000.0000.0000.000
133A133ASN0-0.058-0.04921.7020.0150.0150.0000.0000.0000.000
134A134VAL00.029-0.01220.2420.0040.0040.0000.0000.0000.000
135A135ASN00.0340.00423.5290.0170.0170.0000.0000.0000.000
136A136ASP-1-0.870-0.93425.596-0.085-0.0850.0000.0000.0000.000
137A137ASN0-0.070-0.02926.8890.0140.0140.0000.0000.0000.000
138A138PRO00.017-0.00825.484-0.007-0.0070.0000.0000.0000.000
139A139THR00.0250.00127.384-0.008-0.0080.0000.0000.0000.000
140A140GLN00.0250.01230.782-0.005-0.0050.0000.0000.0000.000
141A141ALA00.0310.03526.300-0.002-0.0020.0000.0000.0000.000
142A142LYS10.8910.93725.0330.1250.1250.0000.0000.0000.000
143A143ALA00.0030.01929.310-0.002-0.0020.0000.0000.0000.000
144A144GLU-1-0.803-0.89030.009-0.124-0.1240.0000.0000.0000.000
145A145LEU0-0.029-0.01625.967-0.003-0.0030.0000.0000.0000.000
146A146SER0-0.002-0.02930.017-0.002-0.0020.0000.0000.0000.000
147A147ILE00.0000.00132.8740.0010.0010.0000.0000.0000.000
148A148TYR0-0.041-0.01830.128-0.002-0.0020.0000.0000.0000.000
149A149LEU00.002-0.01328.943-0.002-0.0020.0000.0000.0000.000
150A150GLU-1-0.878-0.91733.417-0.088-0.0880.0000.0000.0000.000
151A151ASP-1-0.828-0.91636.989-0.096-0.0960.0000.0000.0000.000
152A152TYR0-0.015-0.01931.3450.0000.0000.0000.0000.0000.000
153A153LEU0-0.012-0.01332.428-0.002-0.0020.0000.0000.0000.000
154A154SER00.0110.00836.2830.0050.0050.0000.0000.0000.000
155A155TYR0-0.066-0.02037.9310.0010.0010.0000.0000.0000.000
156A156THR0-0.108-0.07334.822-0.002-0.0020.0000.0000.0000.000
157A157GLN0-0.046-0.00337.8920.0030.0030.0000.0000.0000.000
158A158ALA00.0240.01135.0070.0010.0010.0000.0000.0000.000
159A159GLU-1-0.824-0.90535.715-0.096-0.0960.0000.0000.0000.000
160A160THR0-0.047-0.02836.798-0.002-0.0020.0000.0000.0000.000
161A161SER0-0.064-0.04032.386-0.002-0.0020.0000.0000.0000.000
162A162ILE00.0510.02331.391-0.010-0.0100.0000.0000.0000.000
163A163ASP-1-0.885-0.94630.796-0.100-0.1000.0000.0000.0000.000
164A164GLU-1-0.926-0.97228.112-0.136-0.1360.0000.0000.0000.000
165A165ILE0-0.001-0.00427.079-0.018-0.0180.0000.0000.0000.000
166A166ILE0-0.028-0.01426.027-0.020-0.0200.0000.0000.0000.000
167A167ASN0-0.023-0.01425.144-0.012-0.0120.0000.0000.0000.000
168A168SER0-0.0150.01122.491-0.010-0.0100.0000.0000.0000.000
169A169ASN0-0.037-0.03421.516-0.055-0.0550.0000.0000.0000.000
170A170ALA00.0240.02118.9040.0100.0100.0000.0000.0000.000
171A171ALA00.0560.03220.9790.0020.0020.0000.0000.0000.000
172A172GLY00.001-0.00923.3390.0150.0150.0000.0000.0000.000
173A173ASN00.0780.07721.276-0.019-0.0190.0000.0000.0000.000
174A174PHE00.1000.02615.934-0.023-0.0230.0000.0000.0000.000
175A175ASP-1-0.797-0.90415.549-0.185-0.1850.0000.0000.0000.000
176A176THR0-0.025-0.02316.368-0.015-0.0150.0000.0000.0000.000
177A177CYS0-0.067-0.01217.839-0.018-0.0180.0000.0000.0000.000
178A178LEU0-0.010-0.01212.850-0.046-0.0460.0000.0000.0000.000
179A179HIS0-0.062-0.02013.157-0.089-0.0890.0000.0000.0000.000
180A180HIS00.0240.00814.352-0.035-0.0350.0000.0000.0000.000
181A181VAL0-0.024-0.01312.435-0.016-0.0160.0000.0000.0000.000
182A182ALA0-0.020-0.01110.169-0.071-0.0710.0000.0000.0000.000
183A183GLU-1-0.847-0.92711.650-0.165-0.1650.0000.0000.0000.000
184A184MET0-0.052-0.01614.2590.0220.0220.0000.0000.0000.000
185A185ALA0-0.006-0.00610.7950.0020.0020.0000.0000.0000.000
186A186GLN00.0090.01610.2240.0040.0040.0000.0000.0000.000
187A187GLY0-0.017-0.00912.1450.0660.0660.0000.0000.0000.000
188A188LEU0-0.056-0.02914.6710.0400.0400.0000.0000.0000.000
189A189ASN0-0.023-0.02311.782-0.032-0.0320.0000.0000.0000.000
190A190ASN0-0.012-0.0077.578-0.154-0.1540.0000.0000.0000.000
191A191LYS10.8360.9218.5910.4850.4850.0000.0000.0000.000
192A192VAL0-0.030-0.00511.1280.0550.0550.0000.0000.0000.000
193A193ASP-1-0.759-0.83810.820-1.568-1.5680.0000.0000.0000.000
194A194PHE00.003-0.01210.0680.1150.1150.0000.0000.0000.000
195A195LEU0-0.043-0.01215.065-0.012-0.0120.0000.0000.0000.000
196A196PHE00.0230.00213.8750.0130.0130.0000.0000.0000.000
197A197CYS0-0.0460.00019.5750.0200.0200.0000.0000.0000.000
198A198PHE00.0870.01318.3080.0060.0060.0000.0000.0000.000
199A199GLU-1-0.744-0.86624.204-0.180-0.1800.0000.0000.0000.000
200A200SER0-0.050-0.00826.6520.0150.0150.0000.0000.0000.000
201A201MET0-0.0360.01024.8540.0020.0020.0000.0000.0000.000
202A202LYS10.8490.90928.6770.1060.1060.0000.0000.0000.000
203A203ASP-1-0.891-0.92030.555-0.101-0.1010.0000.0000.0000.000
204A204GLN00.053-0.00529.436-0.016-0.0160.0000.0000.0000.000
205A205GLU-1-0.781-0.87428.632-0.120-0.1200.0000.0000.0000.000
206A206ASN0-0.024-0.00927.084-0.004-0.0040.0000.0000.0000.000
207A207LYS10.7920.89424.8390.1640.1640.0000.0000.0000.000
208A208LYS10.9100.94523.6880.1020.1020.0000.0000.0000.000
209A209SER0-0.024-0.01923.170-0.009-0.0090.0000.0000.0000.000
210A210LEU0-0.034-0.01019.224-0.009-0.0090.0000.0000.0000.000
211A211MET0-0.0250.00119.194-0.022-0.0220.0000.0000.0000.000
212A212ILE00.0640.03318.511-0.032-0.0320.0000.0000.0000.000
213A213ASN0-0.039-0.01918.0820.0010.0010.0000.0000.0000.000
214A214PHE0-0.015-0.01111.743-0.011-0.0110.0000.0000.0000.000
215A215ASP-1-0.753-0.87213.634-0.388-0.3880.0000.0000.0000.000
216A216LYS10.9750.98113.8370.1110.1110.0000.0000.0000.000
217A217ARG10.8120.91310.7170.3050.3050.0000.0000.0000.000
218A218VAL00.0150.0118.998-0.041-0.0410.0000.0000.0000.000
219A219ILE00.0010.0059.036-0.043-0.0430.0000.0000.0000.000
220A220ASN0-0.061-0.04910.5350.1400.1400.0000.0000.0000.000
221A221TYR00.0580.0402.592-1.687-0.9761.680-0.587-1.803-0.008
222A222ARG10.9020.9405.9541.4831.4830.0000.0000.0000.000
223A223LYS10.9690.9967.0610.0960.0960.0000.0000.0000.000
224A224GLU-1-0.917-0.9536.7320.9230.9230.0000.0000.0000.000
225A225HIS10.7870.8822.758-3.269-3.3474.544-1.649-2.8170.001
226A226ASN0-0.031-0.0064.5280.0690.4020.011-0.103-0.2410.000
227A227LEU0-0.024-0.0112.200-2.127-1.9773.255-0.654-2.751-0.004
228A228ASN0-0.020-0.0085.995-0.038-0.0380.0000.0000.0000.000