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: 4J5NN

Calculation Name: 4J9J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J9J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0C6

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2740977.699579
FMO2-HF: Nuclear repulsion 2653922.309809
FMO2-HF: Total energy -87055.38977
FMO2-MP2: Total energy -87311.404971


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:0:LEU)


Summations of interaction energy for fragment #1(A:0:LEU)
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.
-19.981-10.84114.548-6.923-16.765-0.042
Interaction energy analysis for fragmet #1(A:0:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.006
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].
3A2ASP-1-0.788-0.8783.811-6.506-4.347-0.012-1.085-1.0610.006
4A3LYS10.7710.8615.8211.7111.7110.0000.0000.0000.000
5A4VAL0-0.0090.0167.599-0.122-0.1220.0000.0000.0000.000
6A5ILE0-0.0030.0069.8800.1420.1420.0000.0000.0000.000
7A6ILE0-0.040-0.02312.7790.0150.0150.0000.0000.0000.000
8A7ASN00.010-0.00515.5700.0320.0320.0000.0000.0000.000
9A8THR00.0570.01119.1660.0060.0060.0000.0000.0000.000
10A9ALA0-0.0040.00917.2680.0150.0150.0000.0000.0000.000
11A10ALA00.0200.01518.745-0.003-0.0030.0000.0000.0000.000
12A11VAL0-0.009-0.00420.3030.0180.0180.0000.0000.0000.000
13A12GLU-1-0.818-0.89823.084-0.191-0.1910.0000.0000.0000.000
14A13ASN00.0350.03520.5190.0260.0260.0000.0000.0000.000
15A14PRO00.0900.05321.215-0.038-0.0380.0000.0000.0000.000
16A15SER0-0.075-0.05621.456-0.031-0.0310.0000.0000.0000.000
17A16LEU0-0.015-0.00515.425-0.028-0.0280.0000.0000.0000.000
18A17ILE0-0.002-0.00316.571-0.076-0.0760.0000.0000.0000.000
19A18THR0-0.005-0.01016.941-0.046-0.0460.0000.0000.0000.000
20A19GLN0-0.022-0.00416.346-0.050-0.0500.0000.0000.0000.000
21A20ILE00.0230.01911.008-0.047-0.0470.0000.0000.0000.000
22A21ALA00.0080.02213.075-0.113-0.1130.0000.0000.0000.000
23A22GLN0-0.058-0.02415.2570.0240.0240.0000.0000.0000.000
24A23THR0-0.080-0.05011.3430.0770.0770.0000.0000.0000.000
25A24PHE0-0.006-0.0207.557-0.066-0.0660.0000.0000.0000.000
26A25GLY00.0400.04310.532-0.110-0.1100.0000.0000.0000.000
27A26SER00.054-0.01413.031-0.078-0.0780.0000.0000.0000.000
28A27GLN0-0.053-0.02210.1710.1720.1720.0000.0000.0000.000
29A28ALA00.0040.0089.471-0.084-0.0840.0000.0000.0000.000
30A29VAL0-0.043-0.02311.017-0.079-0.0790.0000.0000.0000.000
31A30VAL00.0170.01413.1560.1060.1060.0000.0000.0000.000
32A31VAL00.0220.00515.3080.0000.0000.0000.0000.0000.000
33A32ALA0-0.034-0.01917.4770.0330.0330.0000.0000.0000.000
34A33ILE0-0.043-0.03219.1850.0190.0190.0000.0000.0000.000
35A34ASP-1-0.861-0.92122.947-0.221-0.2210.0000.0000.0000.000
36A35ALA00.003-0.01725.1200.0030.0030.0000.0000.0000.000
37A36LYS10.9190.96128.7830.1290.1290.0000.0000.0000.000
38A37ARG10.7590.83132.1970.1170.1170.0000.0000.0000.000
39A38VAL0-0.069-0.05234.9690.0060.0060.0000.0000.0000.000
40A39ASP-1-0.916-0.95437.653-0.092-0.0920.0000.0000.0000.000
41A40GLY0-0.0070.00340.5700.0000.0000.0000.0000.0000.000
42A41GLU-1-0.875-0.93237.144-0.131-0.1310.0000.0000.0000.000
43A42PHE0-0.025-0.00932.3160.0000.0000.0000.0000.0000.000
44A43MET0-0.0220.02032.386-0.006-0.0060.0000.0000.0000.000
45A44ALA00.0650.03027.035-0.003-0.0030.0000.0000.0000.000
46A45PHE0-0.051-0.01527.2600.0170.0170.0000.0000.0000.000
47A46THR00.0710.03523.780-0.012-0.0120.0000.0000.0000.000
48A47TYR0-0.114-0.09623.2480.0210.0210.0000.0000.0000.000
49A48SER00.0300.00921.8560.0200.0200.0000.0000.0000.000
50A49GLY00.0610.03123.9690.0160.0160.0000.0000.0000.000
51A50LYS10.8020.90527.1460.1320.1320.0000.0000.0000.000
52A51LYS10.9020.96327.4960.1850.1850.0000.0000.0000.000
53A52ASN00.0290.01029.219-0.020-0.0200.0000.0000.0000.000
54A53THR0-0.038-0.03927.3070.0040.0040.0000.0000.0000.000
55A54GLY00.0190.01630.4470.0010.0010.0000.0000.0000.000
56A55ILE0-0.029-0.01328.5070.0020.0020.0000.0000.0000.000
57A56LEU00.0400.01631.585-0.003-0.0030.0000.0000.0000.000
58A57LEU0-0.016-0.02027.865-0.013-0.0130.0000.0000.0000.000
59A58ARG10.8960.91329.8030.1380.1380.0000.0000.0000.000
60A59ASP-1-0.808-0.88331.116-0.175-0.1750.0000.0000.0000.000
61A60TRP00.0200.00422.474-0.012-0.0120.0000.0000.0000.000
62A61VAL00.0300.01325.889-0.024-0.0240.0000.0000.0000.000
63A62VAL00.0220.01526.043-0.020-0.0200.0000.0000.0000.000
64A63GLU-1-0.807-0.88425.789-0.276-0.2760.0000.0000.0000.000
65A64VAL0-0.011-0.02321.600-0.023-0.0230.0000.0000.0000.000
66A65GLU-1-0.723-0.83722.006-0.327-0.3270.0000.0000.0000.000
67A66LYS10.7660.87623.4070.2570.2570.0000.0000.0000.000
68A67ARG10.7750.88421.6390.2960.2960.0000.0000.0000.000
69A68GLY00.0440.03120.075-0.026-0.0260.0000.0000.0000.000
70A69ALA0-0.026-0.01117.850-0.073-0.0730.0000.0000.0000.000
71A70GLY00.0240.02016.3490.0340.0340.0000.0000.0000.000
72A71GLU-1-0.796-0.89115.423-0.608-0.6080.0000.0000.0000.000
73A72ILE0-0.0020.00318.575-0.026-0.0260.0000.0000.0000.000
74A73LEU0-0.042-0.00816.9210.0170.0170.0000.0000.0000.000
75A74LEU00.0170.02320.1740.0140.0140.0000.0000.0000.000
76A75ALA00.009-0.00223.1810.0110.0110.0000.0000.0000.000
77A76SER0-0.044-0.02925.1640.0060.0060.0000.0000.0000.000
78A85GLY0-0.016-0.02931.8280.0000.0000.0000.0000.0000.000
79A86TYR00.0330.00925.1870.0050.0050.0000.0000.0000.000
80A87ASP-1-0.716-0.81030.424-0.124-0.1240.0000.0000.0000.000
81A88THR00.0530.00831.839-0.009-0.0090.0000.0000.0000.000
82A89GLU-1-0.853-0.90833.410-0.113-0.1130.0000.0000.0000.000
83A90MET0-0.0220.00929.513-0.008-0.0080.0000.0000.0000.000
84A91ILE0-0.020-0.01228.235-0.009-0.0090.0000.0000.0000.000
85A92ARG10.9470.97730.6030.1120.1120.0000.0000.0000.000
86A93PHE0-0.037-0.01132.426-0.002-0.0020.0000.0000.0000.000
87A94VAL00.008-0.01427.196-0.003-0.0030.0000.0000.0000.000
88A95ARG10.7880.87925.4500.2430.2430.0000.0000.0000.000
89A96PRO0-0.0200.00230.016-0.009-0.0090.0000.0000.0000.000
90A97LEU0-0.062-0.02430.4990.0010.0010.0000.0000.0000.000
91A98THR0-0.048-0.03525.625-0.019-0.0190.0000.0000.0000.000
92A99THR0-0.018-0.00325.9370.0060.0060.0000.0000.0000.000
93A100LEU0-0.038-0.00220.837-0.008-0.0080.0000.0000.0000.000
94A101PRO00.0050.00718.6940.0300.0300.0000.0000.0000.000
95A102ILE0-0.019-0.00621.262-0.023-0.0230.0000.0000.0000.000
96A103ILE0-0.015-0.01017.0520.0220.0220.0000.0000.0000.000
97A104ALA00.0280.01521.6430.0030.0030.0000.0000.0000.000
98A105SER0-0.019-0.03321.7410.0020.0020.0000.0000.0000.000
99A106GLY0-0.0080.00722.3810.0180.0180.0000.0000.0000.000
100A107GLY0-0.014-0.00824.3610.0030.0030.0000.0000.0000.000
101A108ALA0-0.054-0.01726.5520.0150.0150.0000.0000.0000.000
102A109GLY00.0470.00427.263-0.002-0.0020.0000.0000.0000.000
103A110LYS10.8000.88929.3670.0640.0640.0000.0000.0000.000
104A111MET00.0900.04228.985-0.009-0.0090.0000.0000.0000.000
105A112GLU-1-0.830-0.90231.990-0.064-0.0640.0000.0000.0000.000
106A113HIS00.0000.00331.515-0.004-0.0040.0000.0000.0000.000
107A114PHE00.018-0.01726.280-0.008-0.0080.0000.0000.0000.000
108A115LEU00.0000.00329.642-0.011-0.0110.0000.0000.0000.000
109A116GLU-1-0.873-0.93932.032-0.106-0.1060.0000.0000.0000.000
110A117ALA0-0.048-0.01527.892-0.006-0.0060.0000.0000.0000.000
111A118PHE0-0.017-0.02024.172-0.008-0.0080.0000.0000.0000.000
112A119LEU0-0.0470.00129.126-0.003-0.0030.0000.0000.0000.000
113A120ALA0-0.068-0.03331.3860.0010.0010.0000.0000.0000.000
114A121GLY00.028-0.00329.8050.0000.0000.0000.0000.0000.000
115A122ALA0-0.058-0.00925.353-0.016-0.0160.0000.0000.0000.000
116A123ASP-1-0.778-0.87322.207-0.274-0.2740.0000.0000.0000.000
117A124LYS10.7660.85715.7480.5530.5530.0000.0000.0000.000
118A125VAL0-0.0170.00521.8200.0110.0110.0000.0000.0000.000
119A126SER0-0.0090.00318.037-0.012-0.0120.0000.0000.0000.000
120A127ILE0-0.007-0.00120.1250.0270.0270.0000.0000.0000.000
121A128ASN00.0470.00418.5820.0120.0120.0000.0000.0000.000
122A129THR00.0480.00520.4660.0180.0180.0000.0000.0000.000
123A130ALA00.0200.01323.4510.0130.0130.0000.0000.0000.000
124A131ALA00.0120.00820.9160.0060.0060.0000.0000.0000.000
125A132VAL00.0080.00321.0020.0130.0130.0000.0000.0000.000
126A133GLU-1-0.814-0.88323.0070.0120.0120.0000.0000.0000.000
127A134ASN00.0020.01525.8910.0070.0070.0000.0000.0000.000
128A135PRO00.0900.04223.050-0.014-0.0140.0000.0000.0000.000
129A136SER0-0.056-0.03524.251-0.009-0.0090.0000.0000.0000.000
130A137LEU0-0.010-0.00725.541-0.009-0.0090.0000.0000.0000.000
131A138ILE00.0010.00819.790-0.014-0.0140.0000.0000.0000.000
132A139THR0-0.001-0.00923.435-0.009-0.0090.0000.0000.0000.000
133A140GLN0-0.045-0.01725.422-0.009-0.0090.0000.0000.0000.000
134A141ILE00.0100.01424.328-0.003-0.0030.0000.0000.0000.000
135A142ALA00.0010.01322.349-0.010-0.0100.0000.0000.0000.000
136A143GLN0-0.046-0.01623.9410.0020.0020.0000.0000.0000.000
137A144THR0-0.084-0.05027.2010.0060.0060.0000.0000.0000.000
138A145PHE0-0.005-0.01825.6450.0010.0010.0000.0000.0000.000
139A146GLY00.0420.04423.403-0.017-0.0170.0000.0000.0000.000
140A147SER00.045-0.00618.5820.0000.0000.0000.0000.0000.000
141A148GLN0-0.037-0.01717.585-0.013-0.0130.0000.0000.0000.000
142A149ALA00.0000.00918.630-0.042-0.0420.0000.0000.0000.000
143A150VAL0-0.023-0.01719.6110.0110.0110.0000.0000.0000.000
144A151VAL00.0230.02015.150-0.028-0.0280.0000.0000.0000.000
145A152VAL00.012-0.00315.9220.0430.0430.0000.0000.0000.000
146A153ALA0-0.0170.00214.672-0.037-0.0370.0000.0000.0000.000
147A154ILE0-0.020-0.01412.5590.0600.0600.0000.0000.0000.000
148A155VAL0-0.012-0.01713.222-0.015-0.0150.0000.0000.0000.000
149A156ALA00.0380.02412.6650.0220.0220.0000.0000.0000.000
150A157LYS10.9250.95114.449-0.131-0.1310.0000.0000.0000.000
151A158ARG10.7410.8089.677-0.464-0.4640.0000.0000.0000.000
152A159VAL0-0.058-0.04716.165-0.045-0.0450.0000.0000.0000.000
153A160ASP-1-0.901-0.94219.6770.1860.1860.0000.0000.0000.000
154A161GLY0-0.032-0.00817.6990.0060.0060.0000.0000.0000.000
155A162GLU-1-0.923-0.95715.8610.3600.3600.0000.0000.0000.000
156A163PHE0-0.018-0.0149.867-0.045-0.0450.0000.0000.0000.000
157A164MET00.0190.02614.524-0.009-0.0090.0000.0000.0000.000
158A165VAL00.0290.01115.806-0.013-0.0130.0000.0000.0000.000
159A166PHE0-0.027-0.00917.729-0.014-0.0140.0000.0000.0000.000
160A167THR00.0240.00619.319-0.018-0.0180.0000.0000.0000.000
161A168TYR0-0.115-0.08422.012-0.001-0.0010.0000.0000.0000.000
162A169SER0-0.004-0.01421.4690.0010.0010.0000.0000.0000.000
163A170GLY00.0300.00920.069-0.001-0.0010.0000.0000.0000.000
164A171LYS10.8820.94920.6890.0430.0430.0000.0000.0000.000
165A172LYS10.9000.95823.981-0.014-0.0140.0000.0000.0000.000
166A173ASN00.0550.02822.2850.0040.0040.0000.0000.0000.000
167A174THR0-0.051-0.04820.939-0.001-0.0010.0000.0000.0000.000
168A175GLY00.0220.02222.720-0.004-0.0040.0000.0000.0000.000
169A176ILE0-0.027-0.00519.1770.0120.0120.0000.0000.0000.000
170A177LEU00.0680.02517.0310.0080.0080.0000.0000.0000.000
171A178LEU0-0.021-0.02810.295-0.027-0.0270.0000.0000.0000.000
172A179ARG10.8720.90012.894-0.390-0.3900.0000.0000.0000.000
173A180ASP-1-0.794-0.87513.9210.2900.2900.0000.0000.0000.000
174A181TRP00.0220.00915.951-0.030-0.0300.0000.0000.0000.000
175A182VAL00.0180.00910.331-0.053-0.0530.0000.0000.0000.000
176A183VAL00.0210.01313.627-0.044-0.0440.0000.0000.0000.000
177A184GLU-1-0.853-0.90515.5570.0410.0410.0000.0000.0000.000
178A185VAL0-0.017-0.02015.099-0.033-0.0330.0000.0000.0000.000
179A186GLU-1-0.758-0.85413.2070.0410.0410.0000.0000.0000.000
180A187LYS10.8970.95116.793-0.167-0.1670.0000.0000.0000.000
181A188ARG10.7610.87320.107-0.048-0.0480.0000.0000.0000.000
182A189GLY00.0630.04119.813-0.007-0.0070.0000.0000.0000.000
183A190ALA0-0.044-0.02916.476-0.028-0.0280.0000.0000.0000.000
184A191GLY00.0300.02315.9520.0140.0140.0000.0000.0000.000
185A192GLU-1-0.803-0.88912.429-0.890-0.8900.0000.0000.0000.000
186A193ILE00.0200.01710.3110.1330.1330.0000.0000.0000.000
187A194LEU0-0.028-0.00110.767-0.178-0.1780.0000.0000.0000.000
188A195LEU00.0280.0196.6810.1440.1440.0000.0000.0000.000
189A196THR0-0.024-0.0279.797-0.110-0.1100.0000.0000.0000.000
190A197SER00.0240.00410.0370.0480.0480.0000.0000.0000.000
191A198ILE0-0.070-0.02712.260-0.055-0.0550.0000.0000.0000.000
192A199ASP-1-0.804-0.88213.0310.2170.2170.0000.0000.0000.000
193A200ARG10.9770.98413.040-0.057-0.0570.0000.0000.0000.000
194A201VAL0-0.046-0.04213.434-0.010-0.0100.0000.0000.0000.000
195A202GLY00.0810.0399.9070.0780.0780.0000.0000.0000.000
196A203THR00.0040.03410.527-0.072-0.0720.0000.0000.0000.000
197A204LYS10.8090.86411.2800.2380.2380.0000.0000.0000.000
198A205SER0-0.029-0.00311.780-0.068-0.0680.0000.0000.0000.000
199A206GLY0-0.081-0.04210.241-0.088-0.0880.0000.0000.0000.000
200A207TYR00.0090.0006.1670.0410.0410.0000.0000.0000.000
201A208ASP-1-0.701-0.7977.2530.6530.6530.0000.0000.0000.000
202A209THR00.0260.0083.296-0.0560.3310.025-0.100-0.3120.000
203A210GLU-1-0.917-0.9423.6721.1361.5890.012-0.198-0.267-0.001
204A211MET0-0.0100.0136.1860.2300.2300.0000.0000.0000.000
205A212ILE00.0070.0032.182-0.629-0.8193.450-0.623-2.6370.003
206A213ARG10.9350.9692.248-3.272-1.9483.629-1.847-3.1070.000
207A214PHE0-0.045-0.0102.9051.215-0.5380.1131.910-0.2700.000
208A215VAL00.013-0.0146.146-0.142-0.1420.0000.0000.0000.000
209A216ARG10.7960.8792.573-0.5431.2331.322-0.828-2.2700.000
210A217PRO0-0.0170.0044.782-0.546-0.455-0.001-0.010-0.0790.000
211A218LEU0-0.084-0.0337.623-0.341-0.3410.0000.0000.0000.000
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