Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G5361

Calculation Name: 4RZ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAV1

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102779.373421
FMO2-HF: Nuclear repulsion 2027897.735033
FMO2-HF: Total energy -74881.638388
FMO2-MP2: Total energy -75096.925681


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-27.206-27.55723.395-8.369-14.6710.009
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : 0.017
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].
3A3ASN00.0220.0222.190-4.248-2.2555.697-2.723-4.966-0.007
4A4ARG10.8940.9261.943-24.510-28.43816.961-5.313-7.7190.022
5A5THR00.033-0.0043.3450.3650.4180.0550.158-0.2650.000
6A6VAL00.0150.0326.9960.1350.1350.0000.0000.0000.000
7A7LYS10.9440.9569.508-0.355-0.3550.0000.0000.0000.000
8A8ASP-1-0.934-0.96311.2670.1410.1410.0000.0000.0000.000
9A9ALA00.0040.02911.598-0.026-0.0260.0000.0000.0000.000
10A10HIS0-0.031-0.02213.6390.0230.0230.0000.0000.0000.000
11A11SER0-0.063-0.03114.001-0.032-0.0320.0000.0000.0000.000
12A12ILE00.0330.01614.7640.0230.0230.0000.0000.0000.000
13A13HIS00.012-0.00115.886-0.035-0.0350.0000.0000.0000.000
14A14GLY0-0.0050.00517.578-0.017-0.0170.0000.0000.0000.000
15A15THR0-0.030-0.01312.577-0.035-0.0350.0000.0000.0000.000
16A16ASN00.0410.0446.2660.1510.1510.0000.0000.0000.000
17A17PRO00.1410.06910.558-0.081-0.0810.0000.0000.0000.000
18A18GLN00.023-0.0034.9790.1440.1440.0000.0000.0000.000
19A19TYR0-0.142-0.0845.697-0.272-0.2720.0000.0000.0000.000
20A20LEU00.0440.0399.8260.0240.0240.0000.0000.0000.000
21A21VAL00.0220.03010.0710.0450.0450.0000.0000.0000.000
22A22GLU-1-0.779-0.8949.856-0.915-0.9150.0000.0000.0000.000
23A23LYS10.9650.9836.0931.1051.1050.0000.0000.0000.000
24A24ILE0-0.065-0.0447.367-0.168-0.1680.0000.0000.0000.000
25A25ILE00.0390.0199.6210.0580.0580.0000.0000.0000.000
26A26ARG10.9130.9554.7801.7411.828-0.0010.000-0.0860.000
27A27THR0-0.049-0.0194.9540.1790.1790.0000.0000.0000.000
28A28ARG10.8790.9386.1430.6560.6560.0000.0000.0000.000
29A29ILE00.0100.0058.8030.1130.1130.0000.0000.0000.000
30A30TYR0-0.054-0.0382.751-0.9270.5170.683-0.491-1.635-0.006
31A31GLU-1-0.865-0.9107.128-0.225-0.2250.0000.0000.0000.000
32A32SER0-0.015-0.0159.336-0.017-0.0170.0000.0000.0000.000
33A33LYS10.8430.88312.4500.0220.0220.0000.0000.0000.000
34A34TYR00.0980.04115.0840.0200.0200.0000.0000.0000.000
35A35TRP00.012-0.0127.068-0.051-0.0510.0000.0000.0000.000
36A36LYS10.8140.88610.322-0.079-0.0790.0000.0000.0000.000
37A37GLU-1-0.832-0.90012.3430.0620.0620.0000.0000.0000.000
38A38GLU-1-0.869-0.93115.6180.0520.0520.0000.0000.0000.000
39A39CYS0-0.062-0.01212.275-0.019-0.0190.0000.0000.0000.000
40A40PHE0-0.047-0.01211.5560.0260.0260.0000.0000.0000.000
41A41GLY0-0.008-0.01411.367-0.028-0.0280.0000.0000.0000.000
42A42LEU0-0.049-0.01212.926-0.017-0.0170.0000.0000.0000.000
43A43THR00.0660.03513.535-0.001-0.0010.0000.0000.0000.000
44A44ALA00.0350.00916.130-0.010-0.0100.0000.0000.0000.000
45A45GLU-1-0.889-0.95717.9390.0490.0490.0000.0000.0000.000
46A46LEU0-0.0020.00718.685-0.001-0.0010.0000.0000.0000.000
47A47VAL0-0.042-0.02416.606-0.003-0.0030.0000.0000.0000.000
48A48VAL00.0420.01219.218-0.007-0.0070.0000.0000.0000.000
49A49ASP-1-0.856-0.92722.2150.0350.0350.0000.0000.0000.000
50A50LYS10.7660.87718.677-0.050-0.0500.0000.0000.0000.000
51A51ALA0-0.024-0.02621.402-0.009-0.0090.0000.0000.0000.000
52A52MET0-0.040-0.01022.546-0.009-0.0090.0000.0000.0000.000
53A53GLU-1-0.874-0.90822.9700.0260.0260.0000.0000.0000.000
54A54LEU0-0.088-0.03220.216-0.007-0.0070.0000.0000.0000.000
55A55ARG10.9270.94624.2740.0190.0190.0000.0000.0000.000
56A56PHE0-0.067-0.05222.2920.0020.0020.0000.0000.0000.000
57A57VAL00.0390.03723.3820.0020.0020.0000.0000.0000.000
58A58GLY00.0500.01121.8250.0030.0030.0000.0000.0000.000
59A59GLY00.0560.03818.212-0.003-0.0030.0000.0000.0000.000
60A60VAL0-0.067-0.03814.6620.0040.0040.0000.0000.0000.000
61A61TYR00.0290.01217.7570.0110.0110.0000.0000.0000.000
62A62GLY00.0300.02019.495-0.006-0.0060.0000.0000.0000.000
63A63GLY00.0080.00620.354-0.017-0.0170.0000.0000.0000.000
64A64ASN0-0.001-0.00117.224-0.003-0.0030.0000.0000.0000.000
65A65ILE0-0.042-0.01913.355-0.019-0.0190.0000.0000.0000.000
66A66LYS10.9420.97214.7200.1050.1050.0000.0000.0000.000
67A67PRO00.0300.01612.3460.0000.0000.0000.0000.0000.000
68A68THR0-0.012-0.01515.3610.0310.0310.0000.0000.0000.000
69A69PRO00.0400.01316.652-0.004-0.0040.0000.0000.0000.000
70A70PHE00.0610.04217.4630.0070.0070.0000.0000.0000.000
71A71LEU00.0130.03313.994-0.005-0.0050.0000.0000.0000.000
72A72CYS0-0.078-0.03912.936-0.016-0.0160.0000.0000.0000.000
73A73LEU00.0460.02013.1100.0220.0220.0000.0000.0000.000
74A74THR00.0320.01015.1880.0000.0000.0000.0000.0000.000
75A75LEU0-0.049-0.0257.482-0.033-0.0330.0000.0000.0000.000
76A76LYS10.8520.9258.788-0.309-0.3090.0000.0000.0000.000
77A77MET00.0280.01911.692-0.005-0.0050.0000.0000.0000.000
78A78LEU0-0.024-0.00711.579-0.009-0.0090.0000.0000.0000.000
79A79GLN0-0.084-0.0375.8540.1010.1010.0000.0000.0000.000
80A80ILE0-0.008-0.0289.5100.0020.0020.0000.0000.0000.000
81A81GLN0-0.0380.00312.0710.0370.0370.0000.0000.0000.000
82A82PRO00.0070.00714.8580.0160.0160.0000.0000.0000.000
83A83GLU-1-0.835-0.90717.9610.0230.0230.0000.0000.0000.000
84A84LYS10.8270.88221.1780.0260.0260.0000.0000.0000.000
85A85ASP-1-0.896-0.95923.5280.0050.0050.0000.0000.0000.000
86A86ILE00.1090.07020.853-0.003-0.0030.0000.0000.0000.000
87A87ILE0-0.034-0.01319.506-0.006-0.0060.0000.0000.0000.000
88A88VAL0-0.056-0.03923.553-0.004-0.0040.0000.0000.0000.000
89A89GLU-1-0.895-0.94726.5260.0070.0070.0000.0000.0000.000
90A90PHE0-0.040-0.04020.872-0.002-0.0020.0000.0000.0000.000
91A91ILE0-0.062-0.02625.746-0.002-0.0020.0000.0000.0000.000
92A92LYS10.9210.94328.3960.0250.0250.0000.0000.0000.000
93A93ASN00.0090.01329.343-0.001-0.0010.0000.0000.0000.000
94A94GLU-1-0.934-0.97231.254-0.014-0.0140.0000.0000.0000.000
95A95ASP-1-0.903-0.92031.960-0.004-0.0040.0000.0000.0000.000
96A96PHE0-0.023-0.02828.720-0.002-0.0020.0000.0000.0000.000
97A97LYS10.9300.96529.4870.0270.0270.0000.0000.0000.000
98A98TYR0-0.007-0.00525.441-0.005-0.0050.0000.0000.0000.000
99A99VAL00.0600.05124.748-0.006-0.0060.0000.0000.0000.000
100A100ARG10.8990.95225.2010.0230.0230.0000.0000.0000.000
101A101MET0-0.048-0.01425.532-0.007-0.0070.0000.0000.0000.000
102A102LEU0-0.0050.00318.698-0.010-0.0100.0000.0000.0000.000
103A103GLY00.0370.01021.648-0.009-0.0090.0000.0000.0000.000
104A104ALA00.0040.00123.416-0.006-0.0060.0000.0000.0000.000
105A105LEU00.0430.01118.709-0.007-0.0070.0000.0000.0000.000
106A106TYR00.0490.00815.472-0.023-0.0230.0000.0000.0000.000
107A107MET00.0200.01519.965-0.010-0.0100.0000.0000.0000.000
108A108ARG10.8340.91722.6880.1220.1220.0000.0000.0000.000
109A109LEU0-0.058-0.02916.181-0.013-0.0130.0000.0000.0000.000
110A110THR0-0.062-0.05616.794-0.013-0.0130.0000.0000.0000.000
111A111GLY00.0250.02919.4620.0100.0100.0000.0000.0000.000
112A112THR0-0.038-0.03823.100-0.008-0.0080.0000.0000.0000.000
113A113ALA00.0570.01425.658-0.001-0.0010.0000.0000.0000.000
114A114ILE00.0560.02928.1660.0010.0010.0000.0000.0000.000
115A115ASP-1-0.801-0.87926.650-0.038-0.0380.0000.0000.0000.000
116A116CYS0-0.042-0.01325.746-0.002-0.0020.0000.0000.0000.000
117A117TYR00.039-0.00928.0140.0010.0010.0000.0000.0000.000
118A118LYS10.9470.98331.4660.0270.0270.0000.0000.0000.000
119A119TYR0-0.071-0.05328.6380.0050.0050.0000.0000.0000.000
120A120LEU0-0.0060.00826.3990.0010.0010.0000.0000.0000.000
121A121GLU-1-0.750-0.83830.605-0.045-0.0450.0000.0000.0000.000
122A122PRO0-0.043-0.01833.3690.0020.0020.0000.0000.0000.000
123A123LEU0-0.009-0.00730.0210.0030.0030.0000.0000.0000.000
124A124TYR00.004-0.02634.0420.0000.0000.0000.0000.0000.000
125A125ASN0-0.090-0.04636.1320.0020.0020.0000.0000.0000.000
126A126ASP-1-0.789-0.85134.355-0.030-0.0300.0000.0000.0000.000
127A127TYR00.0500.02035.945-0.002-0.0020.0000.0000.0000.000
128A128ARG10.7430.85033.9310.0270.0270.0000.0000.0000.000
129A129LYS10.9961.00034.9190.0310.0310.0000.0000.0000.000
130A130ILE0-0.039-0.02528.6850.0040.0040.0000.0000.0000.000
131A131LYS10.8520.95328.1980.0460.0460.0000.0000.0000.000
132A132SER00.0580.02326.508-0.003-0.0030.0000.0000.0000.000
133A133GLN0-0.084-0.04622.8080.0040.0040.0000.0000.0000.000
134A134ASN00.0220.00224.054-0.019-0.0190.0000.0000.0000.000
135A135ARG10.9210.96119.6010.1940.1940.0000.0000.0000.000
136A136ASN00.000-0.02422.904-0.011-0.0110.0000.0000.0000.000
137A137GLY0-0.052-0.03224.2120.0030.0030.0000.0000.0000.000
138A138GLU-1-0.885-0.92625.081-0.063-0.0630.0000.0000.0000.000
139A139PHE0-0.042-0.04225.658-0.003-0.0030.0000.0000.0000.000
140A140GLU-1-0.830-0.89129.423-0.080-0.0800.0000.0000.0000.000
141A141LEU0-0.085-0.06330.9180.0020.0020.0000.0000.0000.000
142A142MET00.0190.03828.927-0.003-0.0030.0000.0000.0000.000
143A143HIS00.018-0.00533.2840.0040.0040.0000.0000.0000.000
144A144VAL0-0.052-0.03831.200-0.004-0.0040.0000.0000.0000.000
145A145ASP-1-0.833-0.92831.592-0.051-0.0510.0000.0000.0000.000
146A146GLU-1-0.820-0.90332.781-0.061-0.0610.0000.0000.0000.000
147A147PHE0-0.013-0.01623.241-0.008-0.0080.0000.0000.0000.000
148A148ILE0-0.025-0.02328.189-0.007-0.0070.0000.0000.0000.000
149A149ASP-1-0.805-0.87829.797-0.071-0.0710.0000.0000.0000.000
150A150GLU-1-0.934-0.96027.105-0.106-0.1060.0000.0000.0000.000
151A151LEU0-0.088-0.04623.556-0.010-0.0100.0000.0000.0000.000
152A152LEU0-0.038-0.01726.490-0.007-0.0070.0000.0000.0000.000
153A153HIS0-0.091-0.03929.1510.0010.0010.0000.0000.0000.000
154A154SER0-0.0100.00226.6190.0010.0010.0000.0000.0000.000
155A155GLU-1-0.959-0.97824.255-0.149-0.1490.0000.0000.0000.000
156A156ARG10.8850.93419.3070.2160.2160.0000.0000.0000.000
157A157VAL00.1030.06321.1240.0110.0110.0000.0000.0000.000
158A158CYS0-0.041-0.01119.286-0.011-0.0110.0000.0000.0000.000
159A159ASP-1-0.893-0.95617.508-0.219-0.2190.0000.0000.0000.000
160A160ILE0-0.033-0.01415.178-0.048-0.0480.0000.0000.0000.000
161A161ILE0-0.043-0.02517.0760.0270.0270.0000.0000.0000.000
162A162LEU00.0180.02018.227-0.018-0.0180.0000.0000.0000.000
163A163PRO0-0.0110.00318.3100.0020.0020.0000.0000.0000.000
164A164ARG10.9470.96620.8970.1400.1400.0000.0000.0000.000
165A165LEU00.0280.03424.3200.0010.0010.0000.0000.0000.000
166A166GLN00.0010.01226.974-0.001-0.0010.0000.0000.0000.000
167A167LYS10.9740.98530.2650.0870.0870.0000.0000.0000.000
168A168ARG10.8050.84433.3690.0440.0440.0000.0000.0000.000
169A169TYR00.0630.02435.3910.0000.0000.0000.0000.0000.000
170A170VAL0-0.0060.00534.8380.0020.0020.0000.0000.0000.000
171A171LEU0-0.029-0.02031.5130.0020.0020.0000.0000.0000.000
172A172GLU-1-0.874-0.92435.834-0.037-0.0370.0000.0000.0000.000
173A173GLU-1-0.941-0.97539.333-0.036-0.0360.0000.0000.0000.000
174A174ALA0-0.080-0.02836.7610.0020.0020.0000.0000.0000.000
175A175GLU-1-0.950-0.97138.453-0.017-0.0170.0000.0000.0000.000
176A176GLN0-0.077-0.04433.620-0.002-0.0020.0000.0000.0000.000
177A177LEU0-0.070-0.04133.845-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.910-0.94537.679-0.021-0.0210.0000.0000.0000.000
179A179PRO0-0.0090.01440.558-0.001-0.0010.0000.0000.0000.000