FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 1423Z

Calculation Name: 1B78-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B78

Chain ID: A

ChEMBL ID:

UniProt ID: Q57679

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 185
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2046175.886783
FMO2-HF: Nuclear repulsion 1973258.946891
FMO2-HF: Total energy -72916.939892
FMO2-MP2: Total energy -73134.671731


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:9:ACE )


Summations of interaction energy for fragment #1(A:9:ACE )
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.
-0.3072.2380.41-1.333-1.623-0.008
Interaction energy analysis for fragmet #1(A:9:ACE )
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 : 0.018
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].
3A11ILE 0-0.0050.0233.8221.0771.956-0.006-0.420-0.453-0.001
4A12TYR 00.0250.0046.797-0.021-0.0210.0000.0000.0000.000
5A13PHE 00.0470.00710.3130.1070.1070.0000.0000.0000.000
6A14ALA 00.0210.01913.4030.0060.0060.0000.0000.0000.000
7A15THR 00.0230.00616.6260.0410.0410.0000.0000.0000.000
8A16GLY 00.0410.02619.328-0.015-0.0150.0000.0000.0000.000
9A17ASN 0-0.030-0.02420.950-0.002-0.0020.0000.0000.0000.000
10A18PRO 00.0610.01418.607-0.020-0.0200.0000.0000.0000.000
11A19ASN 00.025-0.00318.276-0.041-0.0410.0000.0000.0000.000
12A20LYS 10.8350.93617.9050.1620.1620.0000.0000.0000.000
13A21ILE 00.0210.02512.964-0.002-0.0020.0000.0000.0000.000
14A22LYS 10.9150.96114.2750.2180.2180.0000.0000.0000.000
15A23GLU -1-0.840-0.89816.216-0.178-0.1780.0000.0000.0000.000
16A24ALA 00.0080.00212.8470.0070.0070.0000.0000.0000.000
17A25ASN 00.0750.01810.255-0.094-0.0940.0000.0000.0000.000
18A26ILE 0-0.034-0.01912.5700.0200.0200.0000.0000.0000.000
19A27ILE 0-0.060-0.03214.9250.0330.0330.0000.0000.0000.000
20A28LEU 00.0400.0139.3560.0380.0380.0000.0000.0000.000
21A29LYS 10.9081.00210.4570.1720.1720.0000.0000.0000.000
22A30ASP -1-0.892-0.94811.831-0.137-0.1370.0000.0000.0000.000
23A31LEU 0-0.031-0.0138.0610.0780.0780.0000.0000.0000.000
24A32LYS 10.9500.9597.807-0.212-0.2120.0000.0000.0000.000
25A33ASP -1-0.936-0.9484.5980.3090.3120.000-0.0200.0170.000
26A34VAL 0-0.045-0.0272.961-0.9360.5160.416-0.864-1.004-0.007
27A35GLU -1-0.911-0.9414.378-0.940-0.7290.000-0.029-0.1830.000
28A36ILE 0-0.031-0.0196.176-0.369-0.3690.0000.0000.0000.000
29A37GLU -1-0.914-0.9808.729-0.690-0.6900.0000.0000.0000.000
30A38GLN 0-0.037-0.02310.6160.0710.0710.0000.0000.0000.000
31A39ILE 00.0350.02513.348-0.010-0.0100.0000.0000.0000.000
32A40LYS 10.8940.93815.1890.2660.2660.0000.0000.0000.000
33A41ILE 00.0170.01416.1840.0180.0180.0000.0000.0000.000
34A42SER 0-0.045-0.01919.626-0.003-0.0030.0000.0000.0000.000
35A43TYR 00.0270.00020.106-0.004-0.0040.0000.0000.0000.000
36A44PRO 0-0.0030.00223.423-0.001-0.0010.0000.0000.0000.000
37A45GLU -1-0.929-0.94824.822-0.096-0.0960.0000.0000.0000.000
38A46ILE 0-0.042-0.02626.7490.0040.0040.0000.0000.0000.000
39A47GLN 0-0.013-0.01529.2320.0000.0000.0000.0000.0000.000
40A48GLY 00.0390.02330.8150.0040.0040.0000.0000.0000.000
41A49THR 0-0.037-0.03528.752-0.004-0.0040.0000.0000.0000.000
42A50LEU 00.018-0.00725.198-0.001-0.0010.0000.0000.0000.000
43A51GLU -1-0.794-0.87123.727-0.039-0.0390.0000.0000.0000.000
44A52GLU -1-0.825-0.88823.639-0.025-0.0250.0000.0000.0000.000
45A53VAL 00.0080.02024.203-0.001-0.0010.0000.0000.0000.000
46A54ALA 0-0.004-0.00319.964-0.008-0.0080.0000.0000.0000.000
47A55GLU -1-0.856-0.93920.039-0.015-0.0150.0000.0000.0000.000
48A56PHE 0-0.037-0.01420.9380.0020.0020.0000.0000.0000.000
49A57GLY 00.021-0.00321.287-0.001-0.0010.0000.0000.0000.000
50A58ALA 0-0.011-0.01116.324-0.012-0.0120.0000.0000.0000.000
51A59LYS 10.9220.95017.073-0.001-0.0010.0000.0000.0000.000
52A60TRP 0-0.0190.00819.2390.0060.0060.0000.0000.0000.000
53A61VAL 00.0290.00115.458-0.003-0.0030.0000.0000.0000.000
54A62TYR 0-0.0100.02311.773-0.020-0.0200.0000.0000.0000.000
55A63ASN 00.000-0.00315.8090.0240.0240.0000.0000.0000.000
56A64ILE 0-0.071-0.02818.1550.0070.0070.0000.0000.0000.000
57A65LEU 0-0.084-0.05711.566-0.007-0.0070.0000.0000.0000.000
58A66LYS 10.8950.95513.8100.0240.0240.0000.0000.0000.000
59A67LYS 10.9210.9658.4580.3630.3630.0000.0000.0000.000
60A68PRO 00.0270.0176.220-0.070-0.0700.0000.0000.0000.000
61A69VAL 0-0.044-0.0129.015-0.208-0.2080.0000.0000.0000.000
62A70ILE 0-0.010-0.00310.9300.0710.0710.0000.0000.0000.000
63A71VAL 00.0160.00713.354-0.027-0.0270.0000.0000.0000.000
64A72GLU -1-0.802-0.87016.972-0.135-0.1350.0000.0000.0000.000
65A73ASP -1-0.847-0.91519.346-0.085-0.0850.0000.0000.0000.000
66A74SER 0-0.052-0.06023.0890.0040.0040.0000.0000.0000.000
67A75GLY 0-0.0130.00325.4540.0010.0010.0000.0000.0000.000
68A76PHE 0-0.017-0.00729.2000.0000.0000.0000.0000.0000.000
69A77PHE 0-0.036-0.01229.5010.0020.0020.0000.0000.0000.000
70A78VAL 00.0670.03134.5750.0010.0010.0000.0000.0000.000
71A79GLU -1-0.857-0.90638.205-0.020-0.0200.0000.0000.0000.000
72A80ALA 0-0.0110.00640.0150.0010.0010.0000.0000.0000.000
73A81LEU 0-0.040-0.02740.7420.0010.0010.0000.0000.0000.000
74A82ASN 0-0.031-0.01440.7630.0000.0000.0000.0000.0000.000
75A83GLY 0-0.021-0.00936.5630.0000.0000.0000.0000.0000.000
76A84PHE 00.0110.01935.708-0.004-0.0040.0000.0000.0000.000
77A85PRO 0-0.005-0.01534.7110.0010.0010.0000.0000.0000.000
78A86GLY 00.0610.01832.5790.0000.0000.0000.0000.0000.000
79A87THR 00.0050.02329.120-0.004-0.0040.0000.0000.0000.000
80A88TYR 00.0350.02130.592-0.005-0.0050.0000.0000.0000.000
81A89SER 00.015-0.01630.8320.0010.0010.0000.0000.0000.000
82A90LYS 11.0021.00025.7070.1030.1030.0000.0000.0000.000
83A91PHE 00.0650.03732.4720.0010.0010.0000.0000.0000.000
84A92VAL 00.0230.01435.3880.0020.0020.0000.0000.0000.000
85A93GLN 0-0.060-0.03334.6250.0010.0010.0000.0000.0000.000
86A94GLU -1-0.951-0.98534.173-0.067-0.0670.0000.0000.0000.000
87A95THR 0-0.088-0.02238.0310.0030.0030.0000.0000.0000.000
88A96ILE 0-0.009-0.01640.7180.0020.0020.0000.0000.0000.000
89A97GLY 00.0320.03239.2010.0010.0010.0000.0000.0000.000
90A98ASN 0-0.010-0.03537.5990.0010.0010.0000.0000.0000.000
91A99GLU -1-0.874-0.93840.685-0.035-0.0350.0000.0000.0000.000
92A100GLY 00.0200.01743.4460.0020.0020.0000.0000.0000.000
93A101ILE 0-0.058-0.02739.0470.0020.0020.0000.0000.0000.000
94A102LEU 00.002-0.00242.4690.0020.0020.0000.0000.0000.000
95A103LYS 10.9160.98145.0590.0260.0260.0000.0000.0000.000
96A104LEU 0-0.047-0.03342.9930.0020.0020.0000.0000.0000.000
97A105LEU 0-0.046-0.03641.8920.0020.0020.0000.0000.0000.000
98A106GLU -1-0.863-0.93646.303-0.024-0.0240.0000.0000.0000.000
99A107GLY 0-0.031-0.01049.7610.0010.0010.0000.0000.0000.000
100A108LYS 10.8630.93546.5110.0220.0220.0000.0000.0000.000
101A109ASP -1-0.879-0.94148.403-0.017-0.0170.0000.0000.0000.000
102A110ASN 0-0.091-0.05742.474-0.001-0.0010.0000.0000.0000.000
103A111ARG 10.9090.94343.1840.0270.0270.0000.0000.0000.000
104A112ASN 00.0340.03039.035-0.004-0.0040.0000.0000.0000.000
105A113ALA 00.001-0.00936.1820.0000.0000.0000.0000.0000.000
106A114TYR 0-0.066-0.03030.3850.0020.0020.0000.0000.0000.000
107A115PHE 00.0410.04528.353-0.002-0.0020.0000.0000.0000.000
108A116LYS 10.8370.89325.8310.0400.0400.0000.0000.0000.000
109A117THR 0-0.001-0.01720.477-0.004-0.0040.0000.0000.0000.000
110A118VAL 0-0.035-0.02620.9340.0090.0090.0000.0000.0000.000
111A119ILE 00.0110.01214.557-0.009-0.0090.0000.0000.0000.000
112A120GLY 00.001-0.01617.2580.0240.0240.0000.0000.0000.000
113A121TYR 0-0.064-0.0588.522-0.033-0.0330.0000.0000.0000.000
114A122CYS 0-0.016-0.01312.7330.0380.0380.0000.0000.0000.000
115A123ASP -1-0.732-0.83210.2470.1850.1850.0000.0000.0000.000
116A124GLU -1-0.847-0.9369.2670.2870.2870.0000.0000.0000.000
117A125ASN 0-0.068-0.03012.545-0.036-0.0360.0000.0000.0000.000
118A126GLY 0-0.0140.00715.293-0.016-0.0160.0000.0000.0000.000
119A127VAL 0-0.015-0.02715.186-0.003-0.0030.0000.0000.0000.000
120A128ARG 10.8920.96413.892-0.078-0.0780.0000.0000.0000.000
121A129LEU 0-0.0020.00516.502-0.024-0.0240.0000.0000.0000.000
122A130PHE 00.0090.01213.8590.0130.0130.0000.0000.0000.000
123A131LYS 10.8790.90518.4470.0100.0100.0000.0000.0000.000
124A132GLY 00.0510.03221.5780.0040.0040.0000.0000.0000.000
125A133ILE 0-0.099-0.06123.178-0.002-0.0020.0000.0000.0000.000
126A134VAL 00.0370.03926.9160.0010.0010.0000.0000.0000.000
127A135LYS 10.9580.95629.5250.0250.0250.0000.0000.0000.000
128A136GLY 00.0650.02633.162-0.001-0.0010.0000.0000.0000.000
129A137ARG 10.9520.99236.0640.0320.0320.0000.0000.0000.000
130A138VAL 0-0.027-0.02138.735-0.003-0.0030.0000.0000.0000.000
131A139SER 0-0.040-0.03640.5240.0020.0020.0000.0000.0000.000
132A140GLU -1-0.897-0.96842.719-0.025-0.0250.0000.0000.0000.000
133A141GLU -1-0.911-0.95444.923-0.030-0.0300.0000.0000.0000.000
134A142ILE 0-0.0350.02541.496-0.002-0.0020.0000.0000.0000.000
135A143ARG 10.8280.94540.3440.0390.0390.0000.0000.0000.000
136A144SER 0-0.004-0.02738.820-0.004-0.0040.0000.0000.0000.000
137A145LYS 10.9400.96938.1720.0480.0480.0000.0000.0000.000
138A146GLY 0-0.022-0.00137.254-0.001-0.0010.0000.0000.0000.000
139A147TYR 0-0.023-0.01432.732-0.003-0.0030.0000.0000.0000.000
140A148GLY 0-0.009-0.00731.779-0.004-0.0040.0000.0000.0000.000
141A149PHE 0-0.096-0.03926.845-0.004-0.0040.0000.0000.0000.000
142A150ALA 00.0440.00932.1620.0020.0020.0000.0000.0000.000
143A151TYR 00.029-0.01032.9340.0030.0030.0000.0000.0000.000
144A152ASP -1-0.817-0.90231.019-0.073-0.0730.0000.0000.0000.000
145A153SER 0-0.036-0.02834.2380.0030.0030.0000.0000.0000.000
146A154ILE 00.0190.01937.4240.0030.0030.0000.0000.0000.000
147A155PHE 0-0.0250.00732.1650.0020.0020.0000.0000.0000.000
148A156ILE 00.0050.00435.972-0.003-0.0030.0000.0000.0000.000
149A157PRO 0-0.059-0.01432.5530.0020.0020.0000.0000.0000.000
150A158GLU -1-0.934-1.00331.173-0.037-0.0370.0000.0000.0000.000
151A159GLU -1-0.943-0.96235.370-0.021-0.0210.0000.0000.0000.000
152A160GLU -1-0.825-0.88235.103-0.042-0.0420.0000.0000.0000.000
153A161GLU -1-0.890-0.94437.999-0.025-0.0250.0000.0000.0000.000
154A162ARG 10.7340.84935.6040.0460.0460.0000.0000.0000.000
155A163THR 00.013-0.02737.171-0.001-0.0010.0000.0000.0000.000
156A164PHE 00.0530.01129.418-0.003-0.0030.0000.0000.0000.000
157A165ALA 0-0.042-0.01333.441-0.004-0.0040.0000.0000.0000.000
158A166GLU -1-0.870-0.93535.445-0.042-0.0420.0000.0000.0000.000
159A167MET 0-0.068-0.01832.2580.0010.0010.0000.0000.0000.000
160A168THR 00.019-0.00331.540-0.006-0.0060.0000.0000.0000.000
161A169THR 00.001-0.01325.4040.0010.0010.0000.0000.0000.000
162A170GLU -1-0.857-0.94726.857-0.096-0.0960.0000.0000.0000.000
163A171GLU -1-0.836-0.88027.931-0.054-0.0540.0000.0000.0000.000
164A172LYS 10.8720.95028.1510.0830.0830.0000.0000.0000.000
165A173SER 0-0.108-0.07523.833-0.002-0.0020.0000.0000.0000.000
166A174GLN 0-0.012-0.02522.886-0.005-0.0050.0000.0000.0000.000
167A175ILE 00.0660.03925.0850.0020.0020.0000.0000.0000.000
168A176SER 00.0110.02723.9940.0020.0020.0000.0000.0000.000
169A177HIS 00.0550.02524.2090.0010.0010.0000.0000.0000.000
170A178ARG 10.8230.88419.5740.1530.1530.0000.0000.0000.000
171A179LYS 10.8540.93319.4370.0820.0820.0000.0000.0000.000
172A180LYS 10.9620.96919.4620.0410.0410.0000.0000.0000.000
173A181ALA 00.0100.01019.3170.0080.0080.0000.0000.0000.000
174A182PHE 00.022-0.00913.656-0.002-0.0020.0000.0000.0000.000
175A183GLU -1-0.820-0.89614.868-0.091-0.0910.0000.0000.0000.000
176A184GLU -1-0.949-0.95616.4540.0080.0080.0000.0000.0000.000
177A185PHE 0-0.035-0.0259.5700.0160.0160.0000.0000.0000.000
178A186LYS 10.9170.95111.5460.1090.1090.0000.0000.0000.000
179A187LYS 10.8800.95212.3410.0270.0270.0000.0000.0000.000
180A188PHE 0-0.001-0.0059.8860.0500.0500.0000.0000.0000.000
181A189LEU 0-0.059-0.0436.8120.0460.0460.0000.0000.0000.000
182A190LEU 0-0.009-0.0209.4040.0940.0940.0000.0000.0000.000
183A191ASP -1-0.954-0.96411.5260.1470.1470.0000.0000.0000.000
184A192ARG 10.7630.8906.142-0.517-0.5170.0000.0000.0000.000
185A193ILE -1-0.969-0.96610.8310.5840.5840.0000.0000.0000.000