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: 394VL

Calculation Name: 5D1Z-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1Z

Chain ID: C

ChEMBL ID:

UniProt ID: Q2FZF0

Base Structure: X-ray

Registration Date: 2023-06-26

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2118140.581781
FMO2-HF: Nuclear repulsion 2036957.02864
FMO2-HF: Total energy -81183.553141
FMO2-MP2: Total energy -81421.745717


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:2:ASP)


Summations of interaction energy for fragment #1(C:2:ASP)
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.
-45.37-38.1642.315-3.662-5.8590.03
Interaction energy analysis for fragmet #1(C:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.902 / q_NPA : -0.961
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].
3C4GLN00.0300.0323.5803.7865.8380.017-0.803-1.2670.003
4C5LEU00.003-0.0205.297-3.986-3.943-0.001-0.001-0.0400.000
5C6THR0-0.019-0.0058.5400.0180.0180.0000.0000.0000.000
6C7GLN0-0.0050.00611.692-0.154-0.1540.0000.0000.0000.000
7C8SER0-0.0480.01114.882-0.212-0.2120.0000.0000.0000.000
8C9PRO00.0680.01218.251-0.041-0.0410.0000.0000.0000.000
9C10SER00.0300.01117.2530.4000.4000.0000.0000.0000.000
10C11PHE0-0.0150.00319.0900.3140.3140.0000.0000.0000.000
11C12LEU0-0.007-0.00422.656-0.061-0.0610.0000.0000.0000.000
12C13SER0-0.017-0.02025.525-0.095-0.0950.0000.0000.0000.000
13C14ALA0-0.0120.00229.195-0.125-0.1250.0000.0000.0000.000
14C15SER0-0.0170.00031.385-0.045-0.0450.0000.0000.0000.000
15C16VAL00.008-0.01033.8590.1910.1910.0000.0000.0000.000
16C17ALA0-0.056-0.02835.249-0.228-0.2280.0000.0000.0000.000
17C18ASP-1-0.837-0.90732.4339.0089.0080.0000.0000.0000.000
18C19ARG10.9210.95929.566-9.887-9.8870.0000.0000.0000.000
19C20VAL00.0090.00825.5890.0840.0840.0000.0000.0000.000
20C21THR0-0.061-0.04923.561-0.082-0.0820.0000.0000.0000.000
21C22ILE00.0120.03418.5870.0160.0160.0000.0000.0000.000
22C23THR0-0.033-0.03517.688-0.328-0.3280.0000.0000.0000.000
23C24CYS0-0.051-0.02812.8740.1200.1200.0000.0000.0000.000
24C25ARG10.9350.98513.511-16.466-16.4660.0000.0000.0000.000
25C26ALA00.0320.0229.3421.5171.5170.0000.0000.0000.000
26C27SER00.008-0.0097.083-0.547-0.5470.0000.0000.0000.000
27C28GLN0-0.0130.0006.765-2.275-2.2750.0000.0000.0000.000
28C29ALA00.0170.01110.314-0.530-0.5300.0000.0000.0000.000
29C30VAL0-0.007-0.0089.1801.6511.6510.0000.0000.0000.000
30C31ARG10.9590.97712.006-18.784-18.7840.0000.0000.0000.000
31C32SER00.0730.02115.724-0.033-0.0330.0000.0000.0000.000
32C33SER0-0.048-0.00512.367-0.967-0.9670.0000.0000.0000.000
33C34LEU0-0.009-0.02211.7422.0502.0500.0000.0000.0000.000
34C35ALA00.0120.00913.818-1.472-1.4720.0000.0000.0000.000
35C36TRP00.0160.00415.1011.1501.1500.0000.0000.0000.000
36C37TYR0-0.020-0.03514.126-0.993-0.9930.0000.0000.0000.000
37C38GLN00.0270.00518.555-0.105-0.1050.0000.0000.0000.000
38C39GLN0-0.051-0.02917.9180.5480.5480.0000.0000.0000.000
39C40LYS10.9620.99020.943-11.489-11.4890.0000.0000.0000.000
40C41PRO00.021-0.01023.5510.4650.4650.0000.0000.0000.000
41C42GLY00.0010.00924.006-0.378-0.3780.0000.0000.0000.000
42C43LYS10.9270.97123.730-11.619-11.6190.0000.0000.0000.000
43C44ALA00.0440.02320.3580.5440.5440.0000.0000.0000.000
44C45PRO0-0.003-0.00716.214-0.579-0.5790.0000.0000.0000.000
45C46GLN0-0.032-0.00319.302-0.762-0.7620.0000.0000.0000.000
46C47LEU00.0110.00418.0090.3710.3710.0000.0000.0000.000
47C48LEU0-0.021-0.00520.566-0.744-0.7440.0000.0000.0000.000
48C49ILE0-0.015-0.00520.347-0.564-0.5640.0000.0000.0000.000
49C50TYR00.0560.03218.1911.2331.2330.0000.0000.0000.000
50C51SER0-0.018-0.02318.065-0.400-0.4000.0000.0000.0000.000
51C52ALA00.0010.01417.838-0.464-0.4640.0000.0000.0000.000
52C53SER0-0.042-0.03718.857-0.198-0.1980.0000.0000.0000.000
53C54THR00.0400.03522.339-0.513-0.5130.0000.0000.0000.000
54C55LEU0-0.022-0.00823.1330.5180.5180.0000.0000.0000.000
55C56GLU-1-0.902-0.94723.47612.82012.8200.0000.0000.0000.000
56C57ASN0-0.005-0.01325.559-0.241-0.2410.0000.0000.0000.000
57C58GLY0-0.031-0.01728.3030.1930.1930.0000.0000.0000.000
58C59VAL00.0000.02225.384-0.100-0.1000.0000.0000.0000.000
59C60SER0-0.014-0.00828.786-0.279-0.2790.0000.0000.0000.000
60C61SER00.0530.00129.4390.3190.3190.0000.0000.0000.000
61C62ARG10.8080.90630.729-10.106-10.1060.0000.0000.0000.000
62C63PHE00.0180.02124.9940.0810.0810.0000.0000.0000.000
63C64SER0-0.026-0.01226.014-0.192-0.1920.0000.0000.0000.000
64C65GLY00.0660.01222.1520.4200.4200.0000.0000.0000.000
65C66SER0-0.074-0.02920.383-0.281-0.2810.0000.0000.0000.000
66C67GLY0-0.0120.02519.2680.1920.1920.0000.0000.0000.000
67C68PRO00.0150.00318.392-0.538-0.5380.0000.0000.0000.000
68C69GLY0-0.019-0.03216.798-0.645-0.6450.0000.0000.0000.000
69C70THR0-0.0040.00013.7170.8730.8730.0000.0000.0000.000
70C71GLU-1-0.903-0.96214.47816.25716.2570.0000.0000.0000.000
71C72PHE00.0090.01913.610-0.802-0.8020.0000.0000.0000.000
72C73THR00.002-0.02518.0730.3810.3810.0000.0000.0000.000
73C74LEU00.0200.04520.345-0.176-0.1760.0000.0000.0000.000
74C75THR0-0.056-0.04021.935-0.383-0.3830.0000.0000.0000.000
75C76ILE00.0550.04025.0930.0450.0450.0000.0000.0000.000
76C77SER0-0.061-0.04328.009-0.195-0.1950.0000.0000.0000.000
77C78SER00.006-0.00531.517-0.209-0.2090.0000.0000.0000.000
78C79LEU0-0.0020.01528.5460.0690.0690.0000.0000.0000.000
79C80GLN00.0670.03731.980-0.397-0.3970.0000.0000.0000.000
80C81PRO00.017-0.00832.0250.3250.3250.0000.0000.0000.000
81C82GLU-1-0.967-0.96731.2559.7369.7360.0000.0000.0000.000
82C83ASP-1-0.813-0.91827.90511.08011.0800.0000.0000.0000.000
83C84VAL0-0.0030.04126.4990.6130.6130.0000.0000.0000.000
84C85GLY0-0.0070.00423.9690.1420.1420.0000.0000.0000.000
85C86THR0-0.042-0.01917.613-0.339-0.3390.0000.0000.0000.000
86C87TYR0-0.033-0.03819.2090.0570.0570.0000.0000.0000.000
87C88TYR0-0.021-0.00213.5310.5200.5200.0000.0000.0000.000
88C90GLN00.0290.03110.180-0.447-0.4470.0000.0000.0000.000
89C91GLN00.0470.0284.974-6.812-6.8120.0000.0000.0000.000
90C92LEU0-0.041-0.0348.6642.2792.2790.0000.0000.0000.000
91C93ASN0-0.029-0.0048.949-3.141-3.1410.0000.0000.0000.000
92C94THR0-0.041-0.0306.188-0.334-0.3340.0000.0000.0000.000
93C95TYR0-0.0060.0175.9721.8981.8980.0000.0000.0000.000
94C96PRO00.0560.0332.514-6.646-3.0342.139-2.230-3.5210.023
95C97PHE0-0.005-0.0114.4782.0982.213-0.001-0.012-0.1020.000
96C98THR0-0.007-0.0113.115-6.388-5.0040.161-0.616-0.9290.004
97C99PHE00.025-0.0056.218-5.908-5.9080.0000.0000.0000.000
98C100GLY00.0160.0117.8822.4062.4060.0000.0000.0000.000
99C101PRO0-0.038-0.02510.476-0.149-0.1490.0000.0000.0000.000
100C102GLY00.019-0.00512.289-0.662-0.6620.0000.0000.0000.000
101C103THR0-0.027-0.01715.617-0.116-0.1160.0000.0000.0000.000
102C104LYS10.8620.92118.852-13.625-13.6250.0000.0000.0000.000
103C105VAL0-0.006-0.00821.813-0.270-0.2700.0000.0000.0000.000
104C106GLU-1-0.830-0.88825.00510.13010.1300.0000.0000.0000.000
105C107ILE00.0230.01028.279-0.085-0.0850.0000.0000.0000.000
106C108LYS10.9730.99731.549-8.927-8.9270.0000.0000.0000.000
107C109ARG10.8610.91334.232-8.235-8.2350.0000.0000.0000.000
108C110THR00.015-0.00637.8290.0460.0460.0000.0000.0000.000
109C111VAL0-0.0230.00040.3910.1150.1150.0000.0000.0000.000
110C112ALA00.0030.01741.328-0.198-0.1980.0000.0000.0000.000
111C113ALA00.0300.00842.1330.1430.1430.0000.0000.0000.000
112C114PRO0-0.0080.01441.3500.0290.0290.0000.0000.0000.000
113C115SER0-0.024-0.02443.271-0.151-0.1510.0000.0000.0000.000
114C116VAL00.0100.00244.5260.1170.1170.0000.0000.0000.000
115C117PHE0-0.021-0.01045.353-0.208-0.2080.0000.0000.0000.000
116C118ILE0-0.0040.00945.5280.1740.1740.0000.0000.0000.000
117C119PHE0-0.007-0.01444.061-0.143-0.1430.0000.0000.0000.000
118C120PRO00.001-0.00447.2900.0980.0980.0000.0000.0000.000
119C121PRO0-0.031-0.01647.9310.0660.0660.0000.0000.0000.000
120C122SER0-0.0260.00448.508-0.112-0.1120.0000.0000.0000.000
121C123ASP-1-0.880-0.94250.1095.9395.9390.0000.0000.0000.000
122C124GLU-1-0.967-0.98148.8716.4206.4200.0000.0000.0000.000
123C125GLN0-0.186-0.10446.5360.1990.1990.0000.0000.0000.000
124C126LEU00.1680.10441.1640.0860.0860.0000.0000.0000.000
125C127LYS10.9390.95941.570-7.335-7.3350.0000.0000.0000.000
126C128SER00.054-0.00445.013-0.030-0.0300.0000.0000.0000.000
127C129GLY00.007-0.12144.850-0.129-0.1290.0000.0000.0000.000
128C130THR0-0.0600.07541.2510.1050.1050.0000.0000.0000.000
129C131ALA00.0460.02944.6580.0480.0480.0000.0000.0000.000
130C132SER0-0.0420.00242.3950.1230.1230.0000.0000.0000.000
131C133VAL00.0260.02244.405-0.104-0.1040.0000.0000.0000.000
132C134VAL00.0200.01840.7920.1010.1010.0000.0000.0000.000
133C135CYS0-0.051-0.03641.800-0.084-0.0840.0000.0000.0000.000
134C136LEU00.0040.01839.6820.2120.2120.0000.0000.0000.000
135C137LEU0-0.011-0.01539.380-0.216-0.2160.0000.0000.0000.000
136C138ASN00.012-0.00639.5240.2950.2950.0000.0000.0000.000
137C139ASN00.0620.05439.1900.3140.3140.0000.0000.0000.000
138C140PHE0-0.0480.00336.137-0.188-0.1880.0000.0000.0000.000
139C141TYR00.0370.02532.7770.1620.1620.0000.0000.0000.000
140C142PRO00.012-0.00235.318-0.274-0.2740.0000.0000.0000.000
141C143ARG10.9920.98326.775-11.066-11.0660.0000.0000.0000.000
142C144GLU-1-0.918-0.95533.8999.2169.2160.0000.0000.0000.000
143C145ALA0-0.0120.00035.640-0.304-0.3040.0000.0000.0000.000
144C146LYS10.9470.97037.405-7.915-7.9150.0000.0000.0000.000
145C147VAL00.0300.01539.624-0.221-0.2210.0000.0000.0000.000
146C148GLN0-0.015-0.00541.3560.1510.1510.0000.0000.0000.000
147C149TRP00.018-0.00841.251-0.250-0.2500.0000.0000.0000.000
148C150LYS10.8560.91745.647-6.457-6.4570.0000.0000.0000.000
149C151VAL00.0320.02649.2930.0080.0080.0000.0000.0000.000
150C152ASP-1-0.877-0.94751.8675.6765.6760.0000.0000.0000.000
151C153ASN0-0.063-0.03453.4790.0120.0120.0000.0000.0000.000
152C154ALA00.0190.01851.696-0.015-0.0150.0000.0000.0000.000
153C155LEU0-0.006-0.02145.3240.0610.0610.0000.0000.0000.000
154C156GLN00.0340.02944.812-0.085-0.0850.0000.0000.0000.000
155C157SER0-0.015-0.02841.9800.1750.1750.0000.0000.0000.000
156C158GLY00.0120.01039.315-0.056-0.0560.0000.0000.0000.000
157C159ASN0-0.0220.00139.6270.0080.0080.0000.0000.0000.000
158C160SER00.0310.01338.809-0.116-0.1160.0000.0000.0000.000
159C161GLN0-0.064-0.01733.1750.0490.0490.0000.0000.0000.000
160C162GLU-1-0.940-0.97033.5058.8398.8390.0000.0000.0000.000
161C163SER0-0.023-0.01631.5350.4060.4060.0000.0000.0000.000
162C164VAL0-0.0080.00529.976-0.286-0.2860.0000.0000.0000.000
163C165THR00.0090.00930.1430.2790.2790.0000.0000.0000.000
164C166GLU-1-0.901-0.96325.16212.59112.5910.0000.0000.0000.000
165C167GLN0-0.036-0.02928.845-0.011-0.0110.0000.0000.0000.000
166C168ASP-1-0.847-0.92430.6079.2419.2410.0000.0000.0000.000
167C169SER0-0.041-0.04030.6360.1510.1510.0000.0000.0000.000
168C170LYS10.9210.96032.782-8.613-8.6130.0000.0000.0000.000
169C171ASP-1-0.853-0.91036.5208.0598.0590.0000.0000.0000.000
170C172SER0-0.030-0.01734.116-0.074-0.0740.0000.0000.0000.000
171C173THR0-0.038-0.01135.1450.0420.0420.0000.0000.0000.000
172C174TYR0-0.059-0.04529.7760.3900.3900.0000.0000.0000.000
173C175SER00.012-0.03034.546-0.288-0.2880.0000.0000.0000.000
174C176LEU0-0.037-0.02134.7130.3000.3000.0000.0000.0000.000
175C177SER00.0060.00635.825-0.356-0.3560.0000.0000.0000.000
176C178SER00.0460.02436.3720.1980.1980.0000.0000.0000.000
177C179THR00.0280.01238.247-0.278-0.2780.0000.0000.0000.000
178C180LEU00.0020.00739.5470.1630.1630.0000.0000.0000.000
179C181THR0-0.038-0.02639.873-0.082-0.0820.0000.0000.0000.000
180C182LEU00.0270.00742.686-0.011-0.0110.0000.0000.0000.000
181C183SER00.0420.04145.957-0.028-0.0280.0000.0000.0000.000
182C184LYS10.9720.97347.887-5.986-5.9860.0000.0000.0000.000
183C185ALA0-0.047-0.02151.034-0.115-0.1150.0000.0000.0000.000
184C186ASP-1-0.892-0.94649.2496.3196.3190.0000.0000.0000.000
185C187TYR0-0.014-0.00550.079-0.055-0.0550.0000.0000.0000.000
186C188GLU-1-0.923-0.98151.9535.6735.6730.0000.0000.0000.000
187C189LYS10.8750.95355.202-5.647-5.6470.0000.0000.0000.000
188C190HIS00.0170.01254.186-0.041-0.0410.0000.0000.0000.000
189C191LYS10.8850.95755.937-5.321-5.3210.0000.0000.0000.000
190C192VAL0-0.001-0.00354.9500.0090.0090.0000.0000.0000.000
191C193TYR00.0200.00749.5920.0970.0970.0000.0000.0000.000
192C194ALA0-0.010-0.00750.4380.0000.0000.0000.0000.0000.000
193C196GLU-1-0.903-0.95447.1046.5036.5030.0000.0000.0000.000
194C197VAL00.0320.02142.4710.1950.1950.0000.0000.0000.000
195C198THR0-0.043-0.02642.880-0.181-0.1810.0000.0000.0000.000
196C199HIS00.009-0.02638.736-0.014-0.0140.0000.0000.0000.000
197C200GLN00.0350.01438.6820.0190.0190.0000.0000.0000.000
198C201GLY00.0100.00742.972-0.124-0.1240.0000.0000.0000.000
199C202LEU0-0.061-0.02844.851-0.125-0.1250.0000.0000.0000.000
200C203SER00.0000.00647.3660.0450.0450.0000.0000.0000.000
201C204SER0-0.007-0.01150.133-0.120-0.1200.0000.0000.0000.000
202C205PRO00.0050.01447.9440.0320.0320.0000.0000.0000.000
203C206VAL00.0040.02247.333-0.152-0.1520.0000.0000.0000.000
204C207THR00.010-0.01348.3560.1500.1500.0000.0000.0000.000
205C208LYS10.9160.96748.820-6.479-6.4790.0000.0000.0000.000
206C209SER0-0.054-0.04150.2420.0520.0520.0000.0000.0000.000
207C210PHE00.0520.04549.532-0.053-0.0530.0000.0000.0000.000
208C211ASN00.043-0.00554.6260.0800.0800.0000.0000.0000.000
209C212ARG10.9600.97655.933-5.496-5.4960.0000.0000.0000.000
210C213GLY00.0150.02157.715-0.082-0.0820.0000.0000.0000.000
211C214GLU-1-0.979-0.96858.6155.1605.1600.0000.0000.0000.000