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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: GYYR1

Calculation Name: 4JKZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JKZ

Chain ID: A

ChEMBL ID:

UniProt ID: A0R6I8

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptH
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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1691017.730975
FMO2-HF: Nuclear repulsion 1623673.315737
FMO2-HF: Total energy -67344.415238
FMO2-MP2: Total energy -67543.45884


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:11:SER)


Summations of interaction energy for fragment #1(A:11:SER)
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.
-14.691-5.9123.343-5.162-6.9580.03
Interaction energy analysis for fragmet #1(A:11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.031
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].
3A13LYS11.0141.0062.942-9.255-5.0080.254-2.143-2.3580.010
4A14SER0-0.013-0.0152.043-4.926-2.7012.257-1.940-2.5410.019
5A15ARG10.9741.0023.990-2.388-2.0950.004-0.093-0.2040.000
6A16VAL00.0540.0246.400-0.367-0.3670.0000.0000.0000.000
7A17ALA00.0660.0417.313-0.428-0.4280.0000.0000.0000.000
8A18ILE00.0050.0127.069-0.498-0.4980.0000.0000.0000.000
9A19VAL0-0.0020.00610.328-0.251-0.2510.0000.0000.0000.000
10A20GLU-1-0.935-0.97611.9161.1121.1120.0000.0000.0000.000
11A21ALA0-0.025-0.01512.600-0.150-0.1500.0000.0000.0000.000
12A22THR0-0.024-0.02414.136-0.163-0.1630.0000.0000.0000.000
13A23ARG10.8310.88616.246-0.471-0.4710.0000.0000.0000.000
14A24ALA0-0.011-0.01017.423-0.061-0.0610.0000.0000.0000.000
15A25LEU0-0.015-0.01216.744-0.055-0.0550.0000.0000.0000.000
16A26LEU00.0210.02020.133-0.058-0.0580.0000.0000.0000.000
17A27LEU0-0.129-0.05822.263-0.052-0.0520.0000.0000.0000.000
18A28GLU-1-0.916-0.95422.0140.4540.4540.0000.0000.0000.000
19A29ARG10.8600.96023.542-0.302-0.3020.0000.0000.0000.000
20A30GLY0-0.0190.01224.994-0.028-0.0280.0000.0000.0000.000
21A31PHE00.012-0.01923.9200.0160.0160.0000.0000.0000.000
22A32ASP-1-0.937-0.97425.0340.1780.1780.0000.0000.0000.000
23A33GLY0-0.021-0.01524.898-0.006-0.0060.0000.0000.0000.000
24A34LEU00.0320.01918.8250.0350.0350.0000.0000.0000.000
25A35SER00.0270.01420.515-0.037-0.0370.0000.0000.0000.000
26A36ILE00.0540.01314.1490.0560.0560.0000.0000.0000.000
27A37GLU-1-0.852-0.93315.8390.2700.2700.0000.0000.0000.000
28A38ALA0-0.014-0.00316.8530.0540.0540.0000.0000.0000.000
29A39VAL00.0270.01613.0130.0720.0720.0000.0000.0000.000
30A40ALA0-0.023-0.01712.0940.1570.1570.0000.0000.0000.000
31A41ALA0-0.0090.00112.2520.1520.1520.0000.0000.0000.000
32A42LYS10.9180.96914.237-0.608-0.6080.0000.0000.0000.000
33A43ALA0-0.015-0.0129.1580.1080.1080.0000.0000.0000.000
34A44GLY0-0.0110.0079.1850.4170.4170.0000.0000.0000.000
35A45VAL0-0.052-0.0176.4910.0190.0190.0000.0000.0000.000
36A46GLY00.0510.0198.898-0.185-0.1850.0000.0000.0000.000
37A47LYS10.9720.9659.782-0.143-0.1430.0000.0000.0000.000
38A48GLN00.0410.01110.7050.0660.0660.0000.0000.0000.000
39A49THR0-0.064-0.0234.740-0.351-0.281-0.001-0.002-0.0670.000
40A50ILE00.0280.0116.790-0.076-0.0760.0000.0000.0000.000
41A51TYR00.0070.0089.272-0.067-0.0670.0000.0000.0000.000
42A52ARG10.8890.9732.7384.2595.2080.288-0.442-0.795-0.001
43A53TRP0-0.054-0.0502.394-1.072-0.0770.541-0.542-0.9930.002
44A54TRP0-0.028-0.0198.9550.0840.0840.0000.0000.0000.000
45A55PRO00.0280.01912.7170.0030.0030.0000.0000.0000.000
46A56SER00.023-0.00115.3730.0300.0300.0000.0000.0000.000
47A57ARG10.9030.94216.364-0.136-0.1360.0000.0000.0000.000
48A58HIS00.0380.02117.9100.0520.0520.0000.0000.0000.000
49A59ALA00.0220.02016.7410.0130.0130.0000.0000.0000.000
50A60LEU0-0.014-0.00612.6510.0030.0030.0000.0000.0000.000
51A61VAL0-0.015-0.02015.7710.0390.0390.0000.0000.0000.000
52A62ALA0-0.010-0.01418.8900.0120.0120.0000.0000.0000.000
53A63ASP-1-0.880-0.92514.8420.0310.0310.0000.0000.0000.000
54A64VAL00.0220.00615.6640.0170.0170.0000.0000.0000.000
55A65LEU0-0.044-0.03518.052-0.003-0.0030.0000.0000.0000.000
56A66LEU00.0110.00320.225-0.011-0.0110.0000.0000.0000.000
57A67GLU-1-0.946-0.95615.6400.3260.3260.0000.0000.0000.000
58A68ASP-1-0.862-0.90120.5500.2650.2650.0000.0000.0000.000
59A69ALA00.009-0.00123.843-0.004-0.0040.0000.0000.0000.000
60A70ASP-1-0.884-0.94126.3170.0890.0890.0000.0000.0000.000
61A71LYS10.8870.93325.872-0.195-0.1950.0000.0000.0000.000
62A72ILE0-0.097-0.03025.1500.0050.0050.0000.0000.0000.000
63A73LEU0-0.046-0.00129.175-0.005-0.0050.0000.0000.0000.000
64A74ALA0-0.028-0.01632.2250.0020.0020.0000.0000.0000.000
65A75ARG10.9610.96635.000-0.090-0.0900.0000.0000.0000.000
66A76MET0-0.0020.01938.7990.0020.0020.0000.0000.0000.000
67A77PRO0-0.067-0.02842.1950.0010.0010.0000.0000.0000.000
68A78LYS10.9670.97142.648-0.032-0.0320.0000.0000.0000.000
69A79THR0-0.056-0.05647.7460.0000.0000.0000.0000.0000.000
70A80ASP-1-0.902-0.94851.3700.0250.0250.0000.0000.0000.000
71A81ASP-1-0.821-0.90853.2650.0250.0250.0000.0000.0000.000
72A82VAL00.0690.02649.6960.0020.0020.0000.0000.0000.000
73A83THR0-0.030-0.01750.2410.0010.0010.0000.0000.0000.000
74A84ALA0-0.044-0.02150.7760.0020.0020.0000.0000.0000.000
75A85ASP-1-0.741-0.82647.3950.0360.0360.0000.0000.0000.000
76A86LEU00.0530.01145.7460.0040.0040.0000.0000.0000.000
77A87ALA0-0.020-0.00945.9570.0020.0020.0000.0000.0000.000
78A88SER0-0.025-0.00645.9120.0040.0040.0000.0000.0000.000
79A89TRP00.028-0.00138.3930.0040.0040.0000.0000.0000.000
80A90ALA00.0220.00941.6190.0040.0040.0000.0000.0000.000
81A91GLY00.0220.00142.3430.0020.0020.0000.0000.0000.000
82A92THR0-0.058-0.03839.1770.0060.0060.0000.0000.0000.000
83A93LEU00.0170.02335.6480.0080.0080.0000.0000.0000.000
84A94ALA00.0260.00537.8910.0040.0040.0000.0000.0000.000
85A95ALA0-0.054-0.01539.4060.0040.0040.0000.0000.0000.000
86A96ALA00.0050.00135.0140.0070.0070.0000.0000.0000.000
87A97LEU00.004-0.00533.0900.0100.0100.0000.0000.0000.000
88A98THR00.0020.00635.4430.0010.0010.0000.0000.0000.000
89A99THR00.0100.01534.3120.0070.0070.0000.0000.0000.000
90A100ARG10.9480.95132.712-0.139-0.1390.0000.0000.0000.000
91A101ARG10.9690.97925.880-0.219-0.2190.0000.0000.0000.000
92A102GLY00.0340.02729.8060.0030.0030.0000.0000.0000.000
93A103HIS00.0290.01931.444-0.003-0.0030.0000.0000.0000.000
94A104ALA0-0.024-0.01728.277-0.007-0.0070.0000.0000.0000.000
95A105MET0-0.0060.01426.3060.0030.0030.0000.0000.0000.000
96A106LEU00.0250.02327.369-0.007-0.0070.0000.0000.0000.000
97A107LYS10.9420.96629.282-0.086-0.0860.0000.0000.0000.000
98A108THR0-0.038-0.02122.794-0.004-0.0040.0000.0000.0000.000
99A109LEU00.0250.01723.899-0.010-0.0100.0000.0000.0000.000
100A110MET00.0010.01125.825-0.019-0.0190.0000.0000.0000.000
101A111ALA0-0.006-0.01525.458-0.013-0.0130.0000.0000.0000.000
102A112ALA00.009-0.00621.649-0.014-0.0140.0000.0000.0000.000
103A113SER0-0.031-0.02623.302-0.023-0.0230.0000.0000.0000.000
104A114LEU0-0.046-0.01925.668-0.014-0.0140.0000.0000.0000.000
105A115GLU-1-0.903-0.93820.914-0.047-0.0470.0000.0000.0000.000
106A116HIS0-0.036-0.02021.428-0.007-0.0070.0000.0000.0000.000
107A117GLU-1-0.880-0.93323.923-0.086-0.0860.0000.0000.0000.000
108A118ASP-1-0.861-0.93122.215-0.173-0.1730.0000.0000.0000.000
109A119THR0-0.095-0.05920.7200.0010.0010.0000.0000.0000.000
110A120ALA00.0560.01922.6300.0210.0210.0000.0000.0000.000
111A121ALA0-0.031-0.00226.0960.0150.0150.0000.0000.0000.000
112A122ARG10.9620.99318.7610.1260.1260.0000.0000.0000.000
113A123LEU0-0.003-0.00922.1250.0200.0200.0000.0000.0000.000
114A124ARG10.9580.98025.5010.0460.0460.0000.0000.0000.000
115A125GLU-1-0.920-0.96226.908-0.016-0.0160.0000.0000.0000.000
116A126GLY00.0050.00226.1220.0070.0070.0000.0000.0000.000
117A127PHE0-0.005-0.02724.2270.0130.0130.0000.0000.0000.000
118A128SER0-0.043-0.02429.4280.0000.0000.0000.0000.0000.000
119A129ARG10.9240.96530.9090.0060.0060.0000.0000.0000.000
120A130PRO00.0420.02831.1020.0000.0000.0000.0000.0000.000
121A131LEU0-0.039-0.01534.0230.0020.0020.0000.0000.0000.000
122A132ILE00.0050.00036.2510.0000.0000.0000.0000.0000.000
123A133GLU-1-0.886-0.96236.161-0.007-0.0070.0000.0000.0000.000
124A134SER00.0120.02238.3240.0000.0000.0000.0000.0000.000
125A135VAL0-0.038-0.01940.0820.0000.0000.0000.0000.0000.000
126A136ARG10.9100.93738.8890.0080.0080.0000.0000.0000.000
127A137ASP-1-0.930-0.96441.2310.0050.0050.0000.0000.0000.000
128A138ARG10.7140.84544.124-0.023-0.0230.0000.0000.0000.000
129A139LEU0-0.011-0.01746.2390.0000.0000.0000.0000.0000.000
130A140ARG10.8910.95146.1860.0040.0040.0000.0000.0000.000
131A141ASP-1-0.918-0.95047.4840.0140.0140.0000.0000.0000.000
132A142GLU-1-0.940-0.95449.9490.0160.0160.0000.0000.0000.000
133A143ASP-1-0.959-0.97452.281-0.001-0.0010.0000.0000.0000.000
134A144ILE0-0.055-0.00350.563-0.001-0.0010.0000.0000.0000.000
135A145ASP-1-0.815-0.90550.835-0.009-0.0090.0000.0000.0000.000
136A146ALA0-0.001-0.03646.6090.0010.0010.0000.0000.0000.000
137A147ASP-1-0.884-0.93246.851-0.018-0.0180.0000.0000.0000.000
138A148HIS0-0.053-0.05248.1140.0010.0010.0000.0000.0000.000
139A149ALA00.0080.01046.5460.0020.0020.0000.0000.0000.000
140A150GLN0-0.042-0.02640.1540.0010.0010.0000.0000.0000.000
141A151ALA00.0240.02344.0040.0020.0020.0000.0000.0000.000
142A152ALA00.0030.00346.2090.0020.0020.0000.0000.0000.000
143A153ALA00.003-0.00941.7720.0040.0040.0000.0000.0000.000
144A154ASP-1-0.877-0.93141.185-0.005-0.0050.0000.0000.0000.000
145A155ALA0-0.031-0.01242.0500.0020.0020.0000.0000.0000.000
146A156LEU0-0.0170.00143.4660.0030.0030.0000.0000.0000.000
147A157LEU0-0.002-0.00535.8610.0050.0050.0000.0000.0000.000
148A158GLY00.0170.00539.5680.0030.0030.0000.0000.0000.000
149A159ALA0-0.026-0.01540.6730.0020.0020.0000.0000.0000.000
150A160VAL0-0.013-0.00638.5540.0030.0030.0000.0000.0000.000
151A161VAL00.012-0.00234.7610.0040.0040.0000.0000.0000.000
152A162ASN00.0250.01237.2180.0000.0000.0000.0000.0000.000
153A163ALA00.0120.02239.1530.0010.0010.0000.0000.0000.000
154A164VAL0-0.020-0.00935.6500.0030.0030.0000.0000.0000.000
155A165LEU0-0.055-0.03932.5430.0050.0050.0000.0000.0000.000
156A166SER0-0.053-0.01436.280-0.002-0.0020.0000.0000.0000.000
157A167GLU-1-0.813-0.87039.4940.0350.0350.0000.0000.0000.000
158A168GLY0-0.0250.00337.4690.0040.0040.0000.0000.0000.000
159A169ARG10.8100.87435.629-0.089-0.0890.0000.0000.0000.000
160A170SER00.0370.02839.3470.0030.0030.0000.0000.0000.000
161A171TYR00.0170.02641.127-0.002-0.0020.0000.0000.0000.000
162A172SER00.0380.01242.7260.0040.0040.0000.0000.0000.000
163A173ARG10.9500.97542.761-0.066-0.0660.0000.0000.0000.000
164A174GLN00.0760.02945.262-0.002-0.0020.0000.0000.0000.000
165A175ARG10.8150.87345.790-0.036-0.0360.0000.0000.0000.000
166A176ALA00.0280.03043.921-0.003-0.0030.0000.0000.0000.000
167A177GLU-1-0.941-0.98045.8430.0420.0420.0000.0000.0000.000
168A178THR0-0.041-0.02648.444-0.003-0.0030.0000.0000.0000.000
169A179SER0-0.019-0.01747.078-0.003-0.0030.0000.0000.0000.000
170A180ALA00.0190.01147.087-0.002-0.0020.0000.0000.0000.000
171A181ARG10.9660.97748.765-0.034-0.0340.0000.0000.0000.000
172A182ILE0-0.039-0.01252.064-0.002-0.0020.0000.0000.0000.000
173A183ILE0-0.0020.00347.044-0.002-0.0020.0000.0000.0000.000
174A184VAL00.0260.01450.174-0.002-0.0020.0000.0000.0000.000
175A185ALA0-0.051-0.02552.436-0.001-0.0010.0000.0000.0000.000
176A186GLY0-0.047-0.02554.509-0.001-0.0010.0000.0000.0000.000
177A187LEU0-0.0020.00150.220-0.002-0.0020.0000.0000.0000.000
178A188ARG10.9060.96254.903-0.013-0.0130.0000.0000.0000.000
179A189PRO00.0200.02857.1360.0000.0000.0000.0000.0000.000