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: JMJG9

Calculation Name: 1YZ7-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZ7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9V0E4

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1675543.528424
FMO2-HF: Nuclear repulsion 1606423.007726
FMO2-HF: Total energy -69120.520698
FMO2-MP2: Total energy -69328.651341


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:90:ACE )


Summations of interaction energy for fragment #1(A:90: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.
0.3541.4891.23-1.099-1.265-0.004
Interaction energy analysis for fragmet #1(A:90:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / 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].
3A92ALA 00.0810.0413.8560.4241.398-0.012-0.440-0.521-0.001
4A93LYS 10.9350.9436.5650.3080.3080.0000.0000.0000.000
5A94LEU 0-0.0230.0082.4900.3040.3951.243-0.655-0.680-0.003
6A95GLN 00.0640.0135.3700.2410.311-0.001-0.004-0.0640.000
7A96GLU -1-0.762-0.8457.110-0.087-0.0870.0000.0000.0000.000
8A97PHE 0-0.022-0.0158.1600.0710.0710.0000.0000.0000.000
9A98LYS 10.9010.9355.542-0.536-0.5360.0000.0000.0000.000
10A99ARG 10.7360.86010.2430.1250.1250.0000.0000.0000.000
11A100ALA 00.0620.03312.7670.0010.0010.0000.0000.0000.000
12A101GLN 0-0.031-0.02413.0200.0060.0060.0000.0000.0000.000
13A102LYS 10.8880.95614.418-0.043-0.0430.0000.0000.0000.000
14A103ALA 00.0370.01816.248-0.008-0.0080.0000.0000.0000.000
15A104GLU -1-0.888-0.94118.0990.1060.1060.0000.0000.0000.000
16A105ASN 0-0.032-0.02717.532-0.007-0.0070.0000.0000.0000.000
17A106LEU 0-0.024-0.00319.670-0.006-0.0060.0000.0000.0000.000
18A107LEU 00.0330.02222.345-0.004-0.0040.0000.0000.0000.000
19A108LYS 10.9030.95822.147-0.095-0.0950.0000.0000.0000.000
20A109LEU 00.0180.01924.753-0.004-0.0040.0000.0000.0000.000
21A110ALA 00.000-0.02826.515-0.004-0.0040.0000.0000.0000.000
22A111ALA 0-0.0050.00328.142-0.003-0.0030.0000.0000.0000.000
23A112GLU -1-0.909-0.95628.0550.0570.0570.0000.0000.0000.000
24A113LYS 10.8880.96229.227-0.033-0.0330.0000.0000.0000.000
25A114LEU 0-0.064-0.03232.443-0.002-0.0020.0000.0000.0000.000
26A115GLY 0-0.0220.00134.054-0.002-0.0020.0000.0000.0000.000
27A116LYS 10.8250.91632.780-0.017-0.0170.0000.0000.0000.000
28A117ASP -1-0.779-0.82332.1740.0320.0320.0000.0000.0000.000
29A118PHE 00.031-0.01326.4690.0000.0000.0000.0000.0000.000
30A119GLU -1-0.952-0.97128.3680.0340.0340.0000.0000.0000.000
31A120THR 0-0.093-0.11429.896-0.004-0.0040.0000.0000.0000.000
32A121ALA 00.0260.02527.738-0.004-0.0040.0000.0000.0000.000
33A122TRP 0-0.035-0.00823.924-0.004-0.0040.0000.0000.0000.000
34A123ARG 10.9370.96426.996-0.018-0.0180.0000.0000.0000.000
35A124GLU -1-0.883-0.97129.9660.0060.0060.0000.0000.0000.000
36A125VAL 0-0.0040.00425.963-0.004-0.0040.0000.0000.0000.000
37A126TRP 0-0.068-0.04318.1090.0000.0000.0000.0000.0000.000
38A127VAL 00.0010.00224.177-0.005-0.0050.0000.0000.0000.000
39A128PRO 00.0060.00726.042-0.006-0.0060.0000.0000.0000.000
40A129LEU 00.007-0.00224.175-0.006-0.0060.0000.0000.0000.000
41A130GLU -1-0.942-0.96619.673-0.015-0.0150.0000.0000.0000.000
42A131GLU -1-0.979-0.98322.593-0.035-0.0350.0000.0000.0000.000
43A132GLU -1-0.915-0.94225.213-0.039-0.0390.0000.0000.0000.000
44A133TRP 0-0.068-0.02521.864-0.003-0.0030.0000.0000.0000.000
45A134GLY 0-0.066-0.01220.440-0.016-0.0160.0000.0000.0000.000
46A135GLU -1-0.851-0.93814.120-0.131-0.1310.0000.0000.0000.000
47A136VAL 00.0570.03018.636-0.001-0.0010.0000.0000.0000.000
48A137TYR 0-0.029-0.03115.8700.0150.0150.0000.0000.0000.000
49A138ALA 00.0280.02518.055-0.002-0.0020.0000.0000.0000.000
50A139ALA 00.0320.02819.2050.0000.0000.0000.0000.0000.000
51A140PHE 0-0.047-0.04120.4560.0060.0060.0000.0000.0000.000
52A141GLU -1-0.765-0.88716.608-0.115-0.1150.0000.0000.0000.000
53A142ASP -1-0.885-0.93021.220-0.056-0.0560.0000.0000.0000.000
54A143ALA 00.013-0.01124.2790.0040.0040.0000.0000.0000.000
55A144ALA 0-0.035-0.01523.1320.0030.0030.0000.0000.0000.000
56A145LYS 10.8610.93924.0070.0720.0720.0000.0000.0000.000
57A146ASP -1-0.939-0.96425.890-0.057-0.0570.0000.0000.0000.000
58A147GLY 0-0.0150.00028.7130.0030.0030.0000.0000.0000.000
59A148ILE 00.028-0.01128.764-0.001-0.0010.0000.0000.0000.000
60A149ASP -1-0.925-0.97330.579-0.016-0.0160.0000.0000.0000.000
61A150VAL 0-0.0580.00527.5030.0010.0010.0000.0000.0000.000
62A151LEU 00.003-0.00126.270-0.001-0.0010.0000.0000.0000.000
63A152LYS 10.9350.98130.3080.0140.0140.0000.0000.0000.000
64A153GLY 0-0.055-0.02634.072-0.003-0.0030.0000.0000.0000.000
65A154HIS 10.8160.88330.1100.0300.0300.0000.0000.0000.000
66A155VAL 00.0080.01629.0720.0020.0020.0000.0000.0000.000
67A156PRO 0-0.020-0.00432.392-0.001-0.0010.0000.0000.0000.000
68A157ASP -1-0.844-0.94334.438-0.007-0.0070.0000.0000.0000.000
69A158GLU -1-0.954-0.99635.6820.0080.0080.0000.0000.0000.000
70A159TRP 00.030-0.00129.4250.0030.0030.0000.0000.0000.000
71A160LEU 00.0010.00831.7200.0010.0010.0000.0000.0000.000
72A161PRO 0-0.025-0.01132.0460.0000.0000.0000.0000.0000.000
73A162VAL 00.0360.01930.0320.0000.0000.0000.0000.0000.000
74A163LEU 00.004-0.00826.3520.0030.0030.0000.0000.0000.000
75A164LYS 10.9480.99427.5250.0100.0100.0000.0000.0000.000
76A165GLU -1-0.945-0.96328.5990.0160.0160.0000.0000.0000.000
77A166ILE 0-0.074-0.03524.3530.0030.0030.0000.0000.0000.000
78A167ILE 0-0.015-0.01823.2770.0040.0040.0000.0000.0000.000
79A168ASP -1-0.853-0.93423.877-0.013-0.0130.0000.0000.0000.000
80A169ASN 0-0.093-0.02525.458-0.002-0.0020.0000.0000.0000.000
81A170TYR 0-0.088-0.05720.4040.0070.0070.0000.0000.0000.000
82A171VAL 0-0.080-0.02819.3430.0050.0050.0000.0000.0000.000
83A172GLU -1-0.978-0.97717.405-0.064-0.0640.0000.0000.0000.000
84A173VAL 00.0730.03020.142-0.008-0.0080.0000.0000.0000.000
85A174PRO 0-0.061-0.03519.2720.0020.0020.0000.0000.0000.000
86A175THR 00.0020.01621.4820.0070.0070.0000.0000.0000.000
87A176VAL 0-0.049-0.01022.733-0.007-0.0070.0000.0000.0000.000
88A177THR 0-0.007-0.01525.1660.0070.0070.0000.0000.0000.000
89A178ILE 0-0.051-0.02027.532-0.004-0.0040.0000.0000.0000.000
90A179ASP -1-0.948-0.97430.262-0.026-0.0260.0000.0000.0000.000
91A180ALA 0-0.054-0.02633.069-0.002-0.0020.0000.0000.0000.000
92A181GLU -1-0.924-0.97836.444-0.013-0.0130.0000.0000.0000.000
93A182PHE 00.0510.02239.801-0.001-0.0010.0000.0000.0000.000
94A183GLU -1-0.928-0.96143.442-0.013-0.0130.0000.0000.0000.000
95A184ILE 0-0.035-0.03345.834-0.001-0.0010.0000.0000.0000.000
96A185THR 00.0030.00749.1590.0010.0010.0000.0000.0000.000
97A186VAL 00.0450.01652.8070.0000.0000.0000.0000.0000.000
98A187PRO 0-0.0030.00355.5320.0010.0010.0000.0000.0000.000
99A188LYS 10.9720.97958.5040.0070.0070.0000.0000.0000.000
100A189PRO 00.0020.00658.8900.0000.0000.0000.0000.0000.000
101A190ASN 00.0160.00658.2130.0000.0000.0000.0000.0000.000
102A191GLY 00.0460.01256.0570.0000.0000.0000.0000.0000.000
103A192VAL 00.016-0.00151.2290.0000.0000.0000.0000.0000.000
104A193GLU -1-0.933-0.97551.778-0.005-0.0050.0000.0000.0000.000
105A194ILE 00.0410.02452.7470.0000.0000.0000.0000.0000.000
106A195ILE 0-0.018-0.00448.187-0.001-0.0010.0000.0000.0000.000
107A196LYS 10.9380.97747.8600.0030.0030.0000.0000.0000.000
108A197GLU -1-0.915-0.95348.152-0.008-0.0080.0000.0000.0000.000
109A198ALA 0-0.020-0.00249.539-0.001-0.0010.0000.0000.0000.000
110A199LEU 0-0.015-0.00644.012-0.001-0.0010.0000.0000.0000.000
111A200ILE 0-0.049-0.02044.523-0.001-0.0010.0000.0000.0000.000
112A201ARG 10.9420.96845.2230.0090.0090.0000.0000.0000.000
113A202ALA 00.0470.02944.184-0.001-0.0010.0000.0000.0000.000
114A203ARG 10.8590.93039.7320.0090.0090.0000.0000.0000.000
115A204ASP -1-0.879-0.94840.965-0.012-0.0120.0000.0000.0000.000
116A205ARG 10.8240.92242.3530.0160.0160.0000.0000.0000.000
117A206ALA 00.0430.00439.051-0.001-0.0010.0000.0000.0000.000
118A207ASN 00.0610.04236.984-0.003-0.0030.0000.0000.0000.000
119A208LYS 10.8800.96838.2770.0190.0190.0000.0000.0000.000
120A209GLU -1-0.928-0.96636.243-0.035-0.0350.0000.0000.0000.000
121A210LYS 10.9410.94534.7270.0280.0280.0000.0000.0000.000
122A211ASP -1-0.864-0.93630.250-0.043-0.0430.0000.0000.0000.000
123A212VAL 0-0.050-0.00331.043-0.003-0.0030.0000.0000.0000.000
124A213GLU -1-0.962-0.97430.125-0.017-0.0170.0000.0000.0000.000
125A214VAL 0-0.030-0.02433.201-0.001-0.0010.0000.0000.0000.000
126A215LYS 10.9480.96733.1680.0100.0100.0000.0000.0000.000
127A216PHE 00.0150.00636.873-0.001-0.0010.0000.0000.0000.000
128A217THR 0-0.034-0.01936.7520.0030.0030.0000.0000.0000.000
129A218TYR 00.0080.02039.487-0.001-0.0010.0000.0000.0000.000
130A219LEU 0-0.032-0.02338.5330.0010.0010.0000.0000.0000.000
131A220GLY 0-0.012-0.00142.4830.0010.0010.0000.0000.0000.000
132A221ALA 0-0.046-0.00546.227-0.001-0.0010.0000.0000.0000.000
133A222PRO 00.019-0.00647.8720.0010.0010.0000.0000.0000.000
134A223ARG 10.9570.97939.8270.0090.0090.0000.0000.0000.000
135A224TYR 0-0.028-0.01642.4760.0020.0020.0000.0000.0000.000
136A225ARG 10.8430.89131.0540.0170.0170.0000.0000.0000.000
137A226ILE 0-0.030-0.01336.7650.0020.0020.0000.0000.0000.000
138A227ASP -1-0.806-0.87132.036-0.020-0.0200.0000.0000.0000.000
139A228ILE 00.018-0.00532.2980.0020.0020.0000.0000.0000.000
140A229THR 00.0250.02427.338-0.004-0.0040.0000.0000.0000.000
141A230ALA 00.0220.01028.4480.0030.0030.0000.0000.0000.000
142A231PRO 00.0590.02826.579-0.004-0.0040.0000.0000.0000.000
143A232ASP -1-0.862-0.92925.445-0.080-0.0800.0000.0000.0000.000
144A233TYR 00.009-0.02523.4470.0080.0080.0000.0000.0000.000
145A234TYR 0-0.074-0.03428.8130.0040.0040.0000.0000.0000.000
146A235LYS 10.9440.97131.1170.0470.0470.0000.0000.0000.000
147A236ALA 00.0300.00630.4240.0050.0050.0000.0000.0000.000
148A237GLU -1-0.828-0.90432.427-0.043-0.0430.0000.0000.0000.000
149A238GLU -1-0.851-0.90034.684-0.039-0.0390.0000.0000.0000.000
150A239VAL 0-0.037-0.00634.7430.0040.0040.0000.0000.0000.000
151A240LEU 0-0.028-0.02535.9960.0040.0040.0000.0000.0000.000
152A241GLU -1-0.916-0.94838.051-0.028-0.0280.0000.0000.0000.000
153A242SER 00.0040.00940.4170.0030.0030.0000.0000.0000.000
154A243ILE 0-0.024-0.02438.6720.0030.0030.0000.0000.0000.000
155A244ALA 0-0.029-0.02942.0700.0020.0020.0000.0000.0000.000
156A245GLU -1-0.907-0.95643.722-0.025-0.0250.0000.0000.0000.000
157A246GLU -1-0.962-0.98645.878-0.016-0.0160.0000.0000.0000.000
158A247ILE 00.004-0.00443.7720.0020.0020.0000.0000.0000.000
159A248LEU 0-0.028-0.02246.3850.0020.0020.0000.0000.0000.000
160A249ARG 10.9390.98548.8120.0200.0200.0000.0000.0000.000
161A250VAL 00.0280.00850.5710.0010.0010.0000.0000.0000.000
162A251ILE 0-0.040-0.00649.9690.0010.0010.0000.0000.0000.000
163A252LYS 10.9010.95451.3470.0170.0170.0000.0000.0000.000
164A253GLU -1-0.956-0.95055.271-0.013-0.0130.0000.0000.0000.000
165A254ALA 0-0.093-0.04456.0070.0010.0010.0000.0000.0000.000
166A255GLY 0-0.029-0.02357.8540.0010.0010.0000.0000.0000.000
167A256GLY 0-0.043-0.02955.1100.0000.0000.0000.0000.0000.000
168A257GLU -1-0.966-0.98952.257-0.014-0.0140.0000.0000.0000.000
169A258ALA 0-0.024-0.00947.8480.0010.0010.0000.0000.0000.000
170A259THR 00.0390.01245.680-0.001-0.0010.0000.0000.0000.000
171A260LEU 00.0090.01939.6030.0010.0010.0000.0000.0000.000
172A261LEU 0-0.0190.00141.133-0.001-0.0010.0000.0000.0000.000
173A262ARG 10.8620.89533.3180.0400.0400.0000.0000.0000.000
174A263LYS 10.9400.96733.0800.0230.0230.0000.0000.0000.000
175A264GLU -1-0.864-0.92934.082-0.041-0.0410.0000.0000.0000.000
176A265LYS 10.9320.95228.9100.0390.0390.0000.0000.0000.000
177A266ARG 10.9090.93926.3350.0610.0610.0000.0000.0000.000
178A267NME 00.0410.05932.085-0.001-0.0010.0000.0000.0000.000