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: 39JNL

Calculation Name: 5U50-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U50

Chain ID: C

ChEMBL ID:

UniProt ID: G9I821

Base Structure: X-ray

Registration Date: 2023-06-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1966523.211718
FMO2-HF: Nuclear repulsion 1894293.50994
FMO2-HF: Total energy -72229.701778
FMO2-MP2: Total energy -72441.020336


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(C:8:PRO)


Summations of interaction energy for fragment #1(C:8:PRO)
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.
-18.561-8.5884.198-5.473-8.7-0.035
Interaction energy analysis for fragmet #1(C:8:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / 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].
3C10ASP-1-0.876-0.9322.775-5.322-1.3310.102-1.853-2.240-0.007
4C11ARG10.9200.9772.593-4.712-3.2100.575-0.643-1.4340.002
5C12ILE0-0.001-0.0084.012-1.024-0.3810.001-0.236-0.4080.000
6C13ASN00.006-0.0045.9550.1400.1400.0000.0000.0000.000
7C14ASP-1-0.903-0.9487.6960.8220.8220.0000.0000.0000.000
8C15PHE0-0.078-0.0358.161-0.011-0.0110.0000.0000.0000.000
9C16LEU0-0.051-0.0329.782-0.065-0.0650.0000.0000.0000.000
10C17ASP-1-0.829-0.90211.936-0.035-0.0350.0000.0000.0000.000
11C18HIS0-0.091-0.06513.8390.0130.0130.0000.0000.0000.000
12C19LEU00.0490.05713.2200.0250.0250.0000.0000.0000.000
13C20ASN0-0.009-0.02816.369-0.043-0.0430.0000.0000.0000.000
14C21LEU00.0360.01418.7720.0210.0210.0000.0000.0000.000
15C22GLY0-0.040-0.00521.537-0.008-0.0080.0000.0000.0000.000
16C23GLU-1-0.977-0.97924.9320.0540.0540.0000.0000.0000.000
17C24ARG10.7760.86523.060-0.069-0.0690.0000.0000.0000.000
18C25THR0-0.012-0.01619.2470.0210.0210.0000.0000.0000.000
19C26ILE0-0.021-0.01115.746-0.025-0.0250.0000.0000.0000.000
20C27LYS10.8690.93715.7930.0620.0620.0000.0000.0000.000
21C28GLY00.015-0.00312.766-0.016-0.0160.0000.0000.0000.000
22C29CYS0-0.080-0.04011.3580.0010.0010.0000.0000.0000.000
23C30LEU0-0.0060.0016.320-0.010-0.0100.0000.0000.0000.000
24C31GLU-1-0.840-0.9119.643-0.508-0.5080.0000.0000.0000.000
25C32ALA00.006-0.0028.6100.0160.0160.0000.0000.0000.000
26C33TYR00.022-0.00110.6850.1020.1020.0000.0000.0000.000
27C34SER0-0.011-0.00613.972-0.011-0.0110.0000.0000.0000.000
28C35CYS0-0.049-0.00916.0220.0390.0390.0000.0000.0000.000
29C36LYS10.9740.99519.5690.2750.2750.0000.0000.0000.000
30C37HIS00.014-0.00422.3770.0040.0040.0000.0000.0000.000
31C38THR0-0.028-0.03225.7710.0130.0130.0000.0000.0000.000
32C39GLY00.0250.02026.626-0.009-0.0090.0000.0000.0000.000
33C40THR00.0580.01626.3140.0050.0050.0000.0000.0000.000
34C41ASP-1-0.761-0.86322.773-0.236-0.2360.0000.0000.0000.000
35C42LYS10.9350.99726.4360.1420.1420.0000.0000.0000.000
36C43ARG10.9750.98328.9020.1120.1120.0000.0000.0000.000
37C44LEU00.0550.02826.8790.0060.0060.0000.0000.0000.000
38C45SER00.025-0.00826.907-0.001-0.0010.0000.0000.0000.000
39C46ILE0-0.060-0.02828.9340.0050.0050.0000.0000.0000.000
40C47SER00.0280.01332.4920.0080.0080.0000.0000.0000.000
41C48LEU00.0030.00227.3740.0050.0050.0000.0000.0000.000
42C49GLU-1-0.942-0.97231.117-0.135-0.1350.0000.0000.0000.000
43C50HIS0-0.086-0.05032.6630.0110.0110.0000.0000.0000.000
44C51GLU-1-0.848-0.88033.431-0.106-0.1060.0000.0000.0000.000
45C52ILE0-0.041-0.03633.255-0.001-0.0010.0000.0000.0000.000
46C71LEU0-0.0080.01029.5090.0040.0040.0000.0000.0000.000
47C72LEU0-0.0270.00125.252-0.007-0.0070.0000.0000.0000.000
48C73SER00.0110.00629.1690.0110.0110.0000.0000.0000.000
49C74ARG10.9900.96630.0570.0840.0840.0000.0000.0000.000
50C75SER00.0040.01228.4930.0000.0000.0000.0000.0000.000
51C76SER00.037-0.00425.729-0.005-0.0050.0000.0000.0000.000
52C77ARG10.8820.95326.6800.1240.1240.0000.0000.0000.000
53C78LYS10.8990.92926.1430.1640.1640.0000.0000.0000.000
54C79ALA00.0450.02222.604-0.009-0.0090.0000.0000.0000.000
55C80LEU00.0100.01723.494-0.015-0.0150.0000.0000.0000.000
56C81ILE0-0.017-0.00225.025-0.005-0.0050.0000.0000.0000.000
57C82TYR00.022-0.01120.738-0.005-0.0050.0000.0000.0000.000
58C83LEU00.0140.03519.652-0.019-0.0190.0000.0000.0000.000
59C84VAL00.0630.02221.804-0.005-0.0050.0000.0000.0000.000
60C85LEU0-0.062-0.02322.2190.0010.0010.0000.0000.0000.000
61C86THR0-0.052-0.04416.869-0.020-0.0200.0000.0000.0000.000
62C87LEU00.0390.02719.903-0.008-0.0080.0000.0000.0000.000
63C88TYR0-0.019-0.00622.1090.0070.0070.0000.0000.0000.000
64C89HIS10.7490.85719.4030.2700.2700.0000.0000.0000.000
65C90MET0-0.0310.01616.0680.0060.0060.0000.0000.0000.000
66C91TYR00.016-0.00320.2350.0150.0150.0000.0000.0000.000
67C92PRO0-0.008-0.00123.2290.0040.0040.0000.0000.0000.000
68C93ASP-1-0.937-0.97026.026-0.105-0.1050.0000.0000.0000.000
69C94TYR0-0.082-0.06927.6850.0130.0130.0000.0000.0000.000
70C95ASP-1-0.878-0.92529.436-0.101-0.1010.0000.0000.0000.000
71C96PHE0-0.045-0.02725.0360.0020.0020.0000.0000.0000.000
72C97SER0-0.029-0.03329.7480.0050.0050.0000.0000.0000.000
73C98ALA00.0260.00430.039-0.006-0.0060.0000.0000.0000.000
74C99VAL0-0.008-0.00431.109-0.003-0.0030.0000.0000.0000.000
75C100LYS10.8910.95630.2490.1060.1060.0000.0000.0000.000
76C101ALA00.0190.01926.979-0.003-0.0030.0000.0000.0000.000
77C102HIS0-0.040-0.02627.988-0.011-0.0110.0000.0000.0000.000
78C103GLN0-0.043-0.02930.2480.0060.0060.0000.0000.0000.000
79C104PHE00.0240.01027.4580.0010.0010.0000.0000.0000.000
80C105PHE0-0.027-0.00621.214-0.008-0.0080.0000.0000.0000.000
81C106THR00.006-0.00424.4940.0140.0140.0000.0000.0000.000
82C107GLU-1-0.918-0.94723.191-0.189-0.1890.0000.0000.0000.000
83C108GLU-1-0.836-0.86620.378-0.134-0.1340.0000.0000.0000.000
84C109SER00.008-0.02120.652-0.012-0.0120.0000.0000.0000.000
85C110TRP00.0770.01910.834-0.013-0.0130.0000.0000.0000.000
86C111ASN0-0.005-0.01017.3630.0070.0070.0000.0000.0000.000
87C112THR0-0.050-0.00819.8100.0140.0140.0000.0000.0000.000
88C113PHE00.0500.02812.2340.0030.0030.0000.0000.0000.000
89C114LYS10.8040.89215.5350.0730.0730.0000.0000.0000.000
90C115GLN00.0150.00216.9540.0140.0140.0000.0000.0000.000
91C116ILE00.0190.03018.5360.0170.0170.0000.0000.0000.000
92C117PHE00.0170.00211.7920.0050.0050.0000.0000.0000.000
93C118GLU-1-0.820-0.90516.708-0.018-0.0180.0000.0000.0000.000
94C119THR0-0.057-0.03918.4540.0190.0190.0000.0000.0000.000
95C120TYR0-0.033-0.02019.6400.0090.0090.0000.0000.0000.000
96C121MET0-0.0300.00013.7510.0140.0140.0000.0000.0000.000
97C122PHE00.0290.02316.0820.0270.0270.0000.0000.0000.000
98C123GLU-1-0.806-0.89317.8460.1010.1010.0000.0000.0000.000
99C124ALA00.0360.02213.9620.0260.0260.0000.0000.0000.000
100C125SER0-0.011-0.02412.9820.0480.0480.0000.0000.0000.000
101C126LYS10.7800.89014.058-0.148-0.1480.0000.0000.0000.000
102C127GLU-1-0.814-0.90315.3390.2500.2500.0000.0000.0000.000
103C128TRP0-0.033-0.0224.8820.1420.1420.0000.0000.0000.000
104C129SER0-0.126-0.06212.4220.0800.0800.0000.0000.0000.000
105C130GLU-1-0.862-0.91714.2560.2370.2370.0000.0000.0000.000
106C131THR0-0.064-0.01311.8710.0030.0030.0000.0000.0000.000
107C132TYR0-0.039-0.0318.6710.3880.3880.0000.0000.0000.000
108C133GLY0-0.0120.00010.753-0.099-0.0990.0000.0000.0000.000
109C134GLY00.0270.00812.648-0.024-0.0240.0000.0000.0000.000
110C135SER0-0.099-0.06312.013-0.060-0.0600.0000.0000.0000.000
111C136SER0-0.049-0.03011.963-0.059-0.0590.0000.0000.0000.000
112C137LEU00.0760.0468.0770.0240.0240.0000.0000.0000.000
113C138LEU00.0040.0117.987-0.065-0.0650.0000.0000.0000.000
114C139GLU-1-0.770-0.8818.5680.2150.2150.0000.0000.0000.000
115C140THR0-0.031-0.0214.086-0.217-0.085-0.001-0.014-0.1170.000
116C141LEU00.0590.0303.924-0.621-0.3560.002-0.095-0.1730.000
117C142TYR0-0.032-0.0155.896-0.205-0.2050.0000.0000.0000.000
118C143LYS10.8860.9333.6851.0461.3560.002-0.055-0.2570.000
119C144ALA0-0.0050.0012.266-0.775-0.6071.471-0.498-1.1410.000
120C145LEU0-0.009-0.0183.776-0.279-0.2340.0140.059-0.1190.000
121C146ASP-1-0.903-0.9487.226-0.556-0.5560.0000.0000.0000.000
122C147GLU-1-0.910-0.9412.455-9.623-6.7062.032-2.138-2.811-0.030
123C148VAL0-0.051-0.0135.1960.1710.1710.0000.0000.0000.000
124C149VAL0-0.092-0.0767.8300.2460.2460.0000.0000.0000.000
125C150LYS10.9050.93910.7450.3770.3770.0000.0000.0000.000
126C151LEU00.1150.04610.5090.0700.0700.0000.0000.0000.000
127C152PRO0-0.034-0.00613.7710.0440.0440.0000.0000.0000.000
128C153GLU-1-0.930-0.95216.342-0.265-0.2650.0000.0000.0000.000
129C154CYS0-0.129-0.05914.399-0.022-0.0220.0000.0000.0000.000
130C155GLU-1-0.770-0.82617.029-0.196-0.1960.0000.0000.0000.000
131C156ILE00.000-0.00916.417-0.037-0.0370.0000.0000.0000.000
132C157TYR0-0.038-0.04618.3870.0350.0350.0000.0000.0000.000
133C158SER0-0.006-0.02119.042-0.024-0.0240.0000.0000.0000.000
134C159TYR0-0.072-0.06221.2380.0050.0050.0000.0000.0000.000
135C160ASN0-0.035-0.02223.0360.0030.0030.0000.0000.0000.000
136C161PRO0-0.012-0.00225.3870.0060.0060.0000.0000.0000.000
137C162ASP-1-0.857-0.92928.465-0.078-0.0780.0000.0000.0000.000
138C163SER0-0.069-0.04131.8240.0040.0040.0000.0000.0000.000
139C164ASP-1-0.862-0.94131.267-0.058-0.0580.0000.0000.0000.000
140C165SER0-0.083-0.04231.5150.0010.0010.0000.0000.0000.000
141C166ASP-1-0.811-0.85826.998-0.131-0.1310.0000.0000.0000.000
142C167PRO00.0550.05324.8590.0020.0020.0000.0000.0000.000
143C168PHE0-0.122-0.05921.062-0.008-0.0080.0000.0000.0000.000
144C169LEU00.0440.00622.661-0.005-0.0050.0000.0000.0000.000
145C170GLU-1-0.761-0.88525.063-0.014-0.0140.0000.0000.0000.000
146C171LYS10.8230.89927.1260.0100.0100.0000.0000.0000.000
147C172GLY0-0.0120.00628.8790.0020.0020.0000.0000.0000.000
148C173ALA0-0.022-0.01725.5950.0060.0060.0000.0000.0000.000
149C174ILE0-0.031-0.00525.064-0.001-0.0010.0000.0000.0000.000
150C175TRP00.0480.00618.640-0.006-0.0060.0000.0000.0000.000
151C176SER0-0.022-0.01421.423-0.003-0.0030.0000.0000.0000.000
152C177PHE00.0470.03818.7070.0020.0020.0000.0000.0000.000
153C178ASN0-0.003-0.00717.635-0.044-0.0440.0000.0000.0000.000
154C179PHE00.0400.01615.5530.0180.0180.0000.0000.0000.000
155C180PHE0-0.008-0.01015.358-0.053-0.0530.0000.0000.0000.000
156C181PHE00.0200.01312.3750.0310.0310.0000.0000.0000.000
157C182TYR0-0.025-0.01314.178-0.042-0.0420.0000.0000.0000.000
158C183ASN00.1000.04915.6230.0430.0430.0000.0000.0000.000
159C184ARG10.8380.90317.3100.2110.2110.0000.0000.0000.000
160C185LYS10.9290.94820.3180.2210.2210.0000.0000.0000.000
161C186LEU0-0.0100.00313.7160.0060.0060.0000.0000.0000.000
162C187LYS10.8500.94017.2930.2500.2500.0000.0000.0000.000
163C188ARG10.9400.97311.6580.6730.6730.0000.0000.0000.000
164C189VAL00.0130.00114.9240.0310.0310.0000.0000.0000.000
165C190VAL0-0.0030.0078.876-0.048-0.0480.0000.0000.0000.000
166C191SER00.0070.01312.0650.0970.0970.0000.0000.0000.000
167C192PHE00.006-0.01111.265-0.102-0.1020.0000.0000.0000.000
168C193ARG10.8730.94212.9940.2810.2810.0000.0000.0000.000
169C194PHE00.0430.00814.343-0.006-0.0060.0000.0000.0000.000
170C195SER0-0.009-0.01316.412-0.002-0.0020.0000.0000.0000.000
171C196CYS0-0.0450.00218.9620.0190.0190.0000.0000.0000.000
172C197LEU00.004-0.00121.594-0.010-0.0100.0000.0000.0000.000
173C198SER00.0380.01224.0430.0160.0160.0000.0000.0000.000
174C199ASN00.0540.02124.976-0.009-0.0090.0000.0000.0000.000
175C200LEU0-0.036-0.00527.8760.0000.0000.0000.0000.0000.000