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: KGJ23

Calculation Name: 4YZE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YZE

Chain ID: A

ChEMBL ID:

UniProt ID: P67430

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017395.419106
FMO2-HF: Nuclear repulsion 1942336.512705
FMO2-HF: Total energy -75058.906401
FMO2-MP2: Total energy -75279.137468


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:7:HIS)


Summations of interaction energy for fragment #1(A:7:HIS)
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.
-16.546-10.5450.793-2.552-4.240.018
Interaction energy analysis for fragmet #1(A:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / 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].
3A9THR00.000-0.0052.5520.0522.4840.255-1.064-1.6220.004
4A10ARG10.9520.9852.893-11.881-9.4540.481-1.175-1.7330.013
5A11GLU-1-0.790-0.8804.260-1.361-0.9210.001-0.088-0.3520.000
6A12HIS00.0030.0166.262-0.546-0.5460.0000.0000.0000.000
7A13LEU0-0.006-0.0017.472-0.339-0.3390.0000.0000.0000.000
8A14LEU0-0.018-0.0097.102-0.381-0.3810.0000.0000.0000.000
9A15ALA00.0120.01210.154-0.273-0.2730.0000.0000.0000.000
10A16THR0-0.024-0.02112.148-0.198-0.1980.0000.0000.0000.000
11A17GLY00.006-0.01913.320-0.085-0.0850.0000.0000.0000.000
12A18GLU-1-0.846-0.90814.4950.1370.1370.0000.0000.0000.000
13A19GLN00.0210.01516.384-0.062-0.0620.0000.0000.0000.000
14A20LEU00.007-0.00717.566-0.037-0.0370.0000.0000.0000.000
15A21SER00.004-0.01618.193-0.015-0.0150.0000.0000.0000.000
16A22LEU0-0.067-0.01920.451-0.030-0.0300.0000.0000.0000.000
17A23GLN0-0.051-0.02022.366-0.005-0.0050.0000.0000.0000.000
18A24ARG10.8290.90022.981-0.243-0.2430.0000.0000.0000.000
19A25GLY00.003-0.00724.3610.0020.0020.0000.0000.0000.000
20A26PHE00.0170.00717.3340.0390.0390.0000.0000.0000.000
21A27THR0-0.047-0.03922.0750.0470.0470.0000.0000.0000.000
22A28GLY00.0010.01124.5880.0040.0040.0000.0000.0000.000
23A29MET0-0.0010.03417.0280.0110.0110.0000.0000.0000.000
24A30GLY00.0420.03021.3990.0600.0600.0000.0000.0000.000
25A31LEU00.027-0.01115.323-0.008-0.0080.0000.0000.0000.000
26A32SER00.0060.00717.6870.0480.0480.0000.0000.0000.000
27A33GLU-1-0.827-0.90619.2170.3470.3470.0000.0000.0000.000
28A34LEU00.0390.02913.062-0.039-0.0390.0000.0000.0000.000
29A35LEU0-0.031-0.02413.3410.0160.0160.0000.0000.0000.000
30A36LYS10.8940.95614.956-0.338-0.3380.0000.0000.0000.000
31A37THR0-0.051-0.05116.915-0.104-0.1040.0000.0000.0000.000
32A38ALA0-0.0060.00511.424-0.079-0.0790.0000.0000.0000.000
33A39GLU-1-0.932-0.94511.9760.0720.0720.0000.0000.0000.000
34A40VAL0-0.027-0.0099.0130.1300.1300.0000.0000.0000.000
35A41PRO00.0320.01110.696-0.036-0.0360.0000.0000.0000.000
36A42LYS11.0020.98212.368-0.525-0.5250.0000.0000.0000.000
37A43GLY00.010-0.00413.6900.1130.1130.0000.0000.0000.000
38A44SER00.0490.0208.387-0.041-0.0410.0000.0000.0000.000
39A45PHE00.0160.0128.9220.5830.5830.0000.0000.0000.000
40A46TYR0-0.043-0.03510.7100.1750.1750.0000.0000.0000.000
41A47HIS0-0.0390.0105.472-0.607-0.6070.0000.0000.0000.000
42A48TYR0-0.043-0.0163.2520.4031.1050.056-0.225-0.5330.001
43A49PHE0-0.006-0.0127.776-0.021-0.0210.0000.0000.0000.000
44A50ARG10.9080.94611.623-1.333-1.3330.0000.0000.0000.000
45A51SER00.011-0.01515.005-0.142-0.1420.0000.0000.0000.000
46A52LYS10.8640.91515.478-0.501-0.5010.0000.0000.0000.000
47A53GLU-1-0.764-0.86116.9230.9780.9780.0000.0000.0000.000
48A54ALA00.0320.01914.4770.0060.0060.0000.0000.0000.000
49A55PHE0-0.023-0.01010.6710.0500.0500.0000.0000.0000.000
50A56GLY00.0630.02013.3740.0200.0200.0000.0000.0000.000
51A57VAL00.0240.02315.608-0.071-0.0710.0000.0000.0000.000
52A58ALA00.0070.00510.212-0.021-0.0210.0000.0000.0000.000
53A59MET0-0.057-0.01312.061-0.073-0.0730.0000.0000.0000.000
54A60LEU0-0.011-0.00313.274-0.179-0.1790.0000.0000.0000.000
55A61GLU-1-0.860-0.92013.6920.8680.8680.0000.0000.0000.000
56A62ARG10.8180.8929.260-0.325-0.3250.0000.0000.0000.000
57A63HIS0-0.070-0.05712.101-0.265-0.2650.0000.0000.0000.000
58A64TYR00.002-0.03515.185-0.126-0.1260.0000.0000.0000.000
59A65ALA0-0.0100.01312.257-0.090-0.0900.0000.0000.0000.000
60A66ALA00.007-0.00312.574-0.140-0.1400.0000.0000.0000.000
61A67TYR0-0.036-0.02414.111-0.090-0.0900.0000.0000.0000.000
62A68HIS00.0310.01817.153-0.005-0.0050.0000.0000.0000.000
63A69GLN00.0050.02513.8130.0470.0470.0000.0000.0000.000
64A70ARG10.9961.00515.5430.3130.3130.0000.0000.0000.000
65A71LEU0-0.032-0.00719.0060.0010.0010.0000.0000.0000.000
66A72THR00.007-0.01919.6490.0260.0260.0000.0000.0000.000
67A73GLU-1-0.925-0.96618.057-0.589-0.5890.0000.0000.0000.000
68A74LEU0-0.063-0.02521.7730.0090.0090.0000.0000.0000.000
69A75LEU0-0.001-0.01824.7030.0140.0140.0000.0000.0000.000
70A76GLN0-0.010-0.01423.549-0.003-0.0030.0000.0000.0000.000
71A77SER0-0.093-0.05824.259-0.004-0.0040.0000.0000.0000.000
72A78GLY00.0320.04726.303-0.025-0.0250.0000.0000.0000.000
73A79GLU-1-0.926-0.96927.487-0.237-0.2370.0000.0000.0000.000
74A80GLY00.0020.01330.7480.0160.0160.0000.0000.0000.000
75A81ASN0-0.041-0.03332.9300.0050.0050.0000.0000.0000.000
76A82TYR00.0530.00729.769-0.007-0.0070.0000.0000.0000.000
77A83ARG10.8520.92033.4030.0810.0810.0000.0000.0000.000
78A84ASP-1-0.841-0.92534.046-0.130-0.1300.0000.0000.0000.000
79A85ARG10.8560.95128.7930.1920.1920.0000.0000.0000.000
80A86ILE00.0200.00730.2270.0000.0000.0000.0000.0000.000
81A87LEU0-0.041-0.02531.9770.0070.0070.0000.0000.0000.000
82A88ALA00.0430.02229.7130.0030.0030.0000.0000.0000.000
83A89TYR00.0090.02525.848-0.006-0.0060.0000.0000.0000.000
84A90TYR0-0.017-0.02029.0960.0050.0050.0000.0000.0000.000
85A91GLN0-0.033-0.01531.8700.0120.0120.0000.0000.0000.000
86A92GLN00.0330.00125.0370.0030.0030.0000.0000.0000.000
87A93THR0-0.071-0.03028.2080.0030.0030.0000.0000.0000.000
88A94LEU0-0.001-0.00729.1560.0070.0070.0000.0000.0000.000
89A95ASN0-0.0190.00028.8140.0150.0150.0000.0000.0000.000
90A96GLN0-0.079-0.04123.000-0.031-0.0310.0000.0000.0000.000
91A97PHE00.0340.03727.2590.0180.0180.0000.0000.0000.000
92A98SER0-0.029-0.02529.3670.0180.0180.0000.0000.0000.000
93A99GLN0-0.009-0.00825.344-0.051-0.0510.0000.0000.0000.000
94A100HIS00.0220.00025.7840.0290.0290.0000.0000.0000.000
95A101GLY00.0180.02730.7400.0090.0090.0000.0000.0000.000
96A102THR0-0.041-0.01129.0760.0180.0180.0000.0000.0000.000
97A103ILE00.002-0.02129.732-0.013-0.0130.0000.0000.0000.000
98A104SER0-0.0150.00724.8720.0090.0090.0000.0000.0000.000
99A105GLY0-0.0080.00026.5100.0020.0020.0000.0000.0000.000
100A106CYS00.0400.01824.375-0.009-0.0090.0000.0000.0000.000
101A107LEU00.0430.02318.5960.0200.0200.0000.0000.0000.000
102A108THR00.0760.03822.8120.0390.0390.0000.0000.0000.000
103A109VAL00.0320.01724.7590.0160.0160.0000.0000.0000.000
104A110LYS10.8010.93924.960-0.250-0.2500.0000.0000.0000.000
105A111LEU00.033-0.00720.9500.0140.0140.0000.0000.0000.000
106A112SER0-0.013-0.01825.4540.0140.0140.0000.0000.0000.000
107A113ALA0-0.040-0.01728.5930.0090.0090.0000.0000.0000.000
108A114GLU-1-0.755-0.87225.4200.3630.3630.0000.0000.0000.000
109A115VAL0-0.021-0.00326.4480.0240.0240.0000.0000.0000.000
110A116SER0-0.052-0.02128.1630.0110.0110.0000.0000.0000.000
111A117ASP-1-0.943-0.95828.9730.3120.3120.0000.0000.0000.000
112A118LEU0-0.038-0.03222.6640.0440.0440.0000.0000.0000.000
113A119SER0-0.033-0.02721.170-0.029-0.0290.0000.0000.0000.000
114A120GLU-1-0.730-0.83624.2630.4020.4020.0000.0000.0000.000
115A121ASP-1-0.909-0.95219.9090.7240.7240.0000.0000.0000.000
116A122MET0-0.032-0.01018.8430.0300.0300.0000.0000.0000.000
117A123ARG10.8090.85921.255-0.392-0.3920.0000.0000.0000.000
118A124SER0-0.015-0.00522.900-0.045-0.0450.0000.0000.0000.000
119A125ALA0-0.025-0.01818.727-0.029-0.0290.0000.0000.0000.000
120A126MET0-0.019-0.01020.722-0.035-0.0350.0000.0000.0000.000
121A127ASP-1-0.858-0.88123.0180.2320.2320.0000.0000.0000.000
122A128LYS10.8590.90317.972-0.647-0.6470.0000.0000.0000.000
123A129GLY00.0140.00520.647-0.035-0.0350.0000.0000.0000.000
124A130ALA0-0.014-0.01121.532-0.053-0.0530.0000.0000.0000.000
125A131ARG10.8830.92324.674-0.318-0.3180.0000.0000.0000.000
126A132GLY00.0210.02222.016-0.025-0.0250.0000.0000.0000.000
127A133VAL00.003-0.00522.860-0.039-0.0390.0000.0000.0000.000
128A134ILE0-0.0050.00224.633-0.026-0.0260.0000.0000.0000.000
129A135ALA00.003-0.00325.408-0.017-0.0170.0000.0000.0000.000
130A136LEU0-0.0060.00221.427-0.016-0.0160.0000.0000.0000.000
131A137LEU0-0.005-0.00826.086-0.018-0.0180.0000.0000.0000.000
132A138SER00.007-0.00529.251-0.004-0.0040.0000.0000.0000.000
133A139GLN0-0.037-0.01828.0610.0080.0080.0000.0000.0000.000
134A140ALA0-0.0030.00629.262-0.010-0.0100.0000.0000.0000.000
135A141LEU0-0.041-0.02330.978-0.005-0.0050.0000.0000.0000.000
136A142GLU-1-0.848-0.94033.706-0.009-0.0090.0000.0000.0000.000
137A143ASN00.0280.01429.9900.0080.0080.0000.0000.0000.000
138A144GLY00.008-0.00934.206-0.006-0.0060.0000.0000.0000.000
139A145ARG10.8190.89936.3770.0090.0090.0000.0000.0000.000
140A146GLU-1-0.967-0.97536.425-0.042-0.0420.0000.0000.0000.000
141A147ASN0-0.0290.00536.1740.0020.0020.0000.0000.0000.000
142A148HIS0-0.032-0.01839.006-0.003-0.0030.0000.0000.0000.000
143A149SER0-0.028-0.03837.433-0.006-0.0060.0000.0000.0000.000
144A150LEU0-0.098-0.04735.702-0.002-0.0020.0000.0000.0000.000
145A151THR0-0.034-0.00540.2980.0060.0060.0000.0000.0000.000
146A152PHE00.0310.00837.683-0.001-0.0010.0000.0000.0000.000
147A153SER00.0030.00942.4100.0020.0020.0000.0000.0000.000
148A154GLY00.0530.02242.1010.0030.0030.0000.0000.0000.000
149A155GLU-1-0.829-0.90238.4520.0450.0450.0000.0000.0000.000
150A156PRO00.0460.02634.7750.0030.0030.0000.0000.0000.000
151A157LEU00.0500.03931.640-0.001-0.0010.0000.0000.0000.000
152A158GLN0-0.050-0.04234.4220.0020.0020.0000.0000.0000.000
153A159GLN00.0030.00636.8090.0010.0010.0000.0000.0000.000
154A160ALA00.0180.00231.292-0.004-0.0040.0000.0000.0000.000
155A161GLN0-0.030-0.01832.3870.0130.0130.0000.0000.0000.000
156A162VAL00.0000.01233.5420.0060.0060.0000.0000.0000.000
157A163LEU00.0410.03333.075-0.001-0.0010.0000.0000.0000.000
158A164TYR00.0350.01725.4470.0060.0060.0000.0000.0000.000
159A165ALA00.006-0.00731.3670.0050.0050.0000.0000.0000.000
160A166LEU0-0.016-0.00833.9070.0020.0020.0000.0000.0000.000
161A167TRP00.010-0.00925.5800.0140.0140.0000.0000.0000.000
162A168LEU0-0.0020.00829.446-0.001-0.0010.0000.0000.0000.000
163A169GLY00.0070.00031.7110.0040.0040.0000.0000.0000.000
164A170ALA00.0170.01334.752-0.001-0.0010.0000.0000.0000.000
165A171ASN00.007-0.01930.014-0.012-0.0120.0000.0000.0000.000
166A172LEU0-0.044-0.01032.3340.0010.0010.0000.0000.0000.000
167A173GLN00.0170.00934.1610.0050.0050.0000.0000.0000.000
168A174ALA00.0270.02934.409-0.003-0.0030.0000.0000.0000.000
169A175LYS10.9390.96529.533-0.115-0.1150.0000.0000.0000.000
170A176ILE0-0.076-0.04134.517-0.001-0.0010.0000.0000.0000.000
171A177SER0-0.048-0.03537.343-0.004-0.0040.0000.0000.0000.000
172A178ARG10.9020.95236.398-0.024-0.0240.0000.0000.0000.000
173A179SER00.0530.04238.127-0.012-0.0120.0000.0000.0000.000
174A180PHE00.0110.00435.8680.0070.0070.0000.0000.0000.000
175A181GLU-1-0.838-0.91937.466-0.012-0.0120.0000.0000.0000.000
176A182PRO00.0290.01837.560-0.001-0.0010.0000.0000.0000.000
177A183LEU0-0.035-0.01732.6470.0010.0010.0000.0000.0000.000
178A184GLU-1-0.909-0.96236.280-0.069-0.0690.0000.0000.0000.000
179A185ASN0-0.088-0.04338.756-0.003-0.0030.0000.0000.0000.000
180A186ALA00.0110.00636.4640.0010.0010.0000.0000.0000.000
181A187LEU0-0.017-0.01135.224-0.001-0.0010.0000.0000.0000.000
182A188ALA0-0.018-0.01737.537-0.004-0.0040.0000.0000.0000.000
183A189HIS00.0340.01940.302-0.003-0.0030.0000.0000.0000.000
184A190VAL00.024-0.00335.5970.0020.0020.0000.0000.0000.000
185A191LYS10.8900.95738.3580.0840.0840.0000.0000.0000.000
186A192ASN0-0.0210.00040.602-0.005-0.0050.0000.0000.0000.000
187A193ILE0-0.043-0.01040.3960.0030.0030.0000.0000.0000.000
188A194ILE0-0.0200.00036.8310.0030.0030.0000.0000.0000.000
189A195ALA00.0380.04240.087-0.010-0.0100.0000.0000.0000.000
190A196THR00.0500.00941.990-0.003-0.0030.0000.0000.0000.000
191A197PRO0-0.039-0.01342.4830.0060.0060.0000.0000.0000.000
192A198ALA0-0.019-0.00945.672-0.003-0.0030.0000.0000.0000.000
193A199VAL00.0280.03547.3040.0000.0000.0000.0000.0000.000