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: 942V2

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 OptAll
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 -2131225.96291
FMO2-HF: Nuclear repulsion 2050039.468027
FMO2-HF: Total energy -81186.494883
FMO2-MP2: Total energy -81424.93869


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.
-62.009-53.9195.642-5.308-8.4250.046
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 : -0.877 / q_NPA : -0.953
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].
3C4GLN0-0.0080.0092.429-3.760-1.6931.168-1.301-1.9340.004
4C5LEU00.010-0.0045.188-3.803-3.720-0.001-0.004-0.0790.000
5C6THR0-0.0020.0048.300-0.448-0.4480.0000.0000.0000.000
6C7GLN00.023-0.01811.4371.1161.1160.0000.0000.0000.000
7C8SER0-0.053-0.01614.490-0.349-0.3490.0000.0000.0000.000
8C9PRO00.0800.03018.108-0.177-0.1770.0000.0000.0000.000
9C10SER00.0340.03216.6030.4680.4680.0000.0000.0000.000
10C11PHE0-0.022-0.01418.6770.2290.2290.0000.0000.0000.000
11C12LEU0-0.0060.00322.272-0.120-0.1200.0000.0000.0000.000
12C13SER0-0.033-0.03125.331-0.067-0.0670.0000.0000.0000.000
13C14ALA0-0.022-0.00629.024-0.159-0.1590.0000.0000.0000.000
14C15SER0-0.021-0.02630.894-0.008-0.0080.0000.0000.0000.000
15C16VAL0-0.021-0.01533.4340.1900.1900.0000.0000.0000.000
16C17ALA0-0.030-0.01234.693-0.253-0.2530.0000.0000.0000.000
17C18ASP-1-0.814-0.87431.7949.2359.2350.0000.0000.0000.000
18C19ARG10.9240.96628.347-10.189-10.1890.0000.0000.0000.000
19C20VAL00.0320.02525.1940.1380.1380.0000.0000.0000.000
20C21THR0-0.080-0.05723.596-0.061-0.0610.0000.0000.0000.000
21C22ILE0-0.0130.01618.619-0.014-0.0140.0000.0000.0000.000
22C23THR00.000-0.00617.803-0.238-0.2380.0000.0000.0000.000
23C24CYS0-0.064-0.02112.5890.2040.2040.0000.0000.0000.000
24C25ARG10.8600.91112.861-16.912-16.9120.0000.0000.0000.000
25C26ALA00.0240.0289.1711.5561.5560.0000.0000.0000.000
26C27SER00.0060.0016.791-0.479-0.4790.0000.0000.0000.000
27C28GLN00.007-0.0076.955-0.807-0.8070.0000.0000.0000.000
28C29ALA00.0080.02510.298-0.758-0.7580.0000.0000.0000.000
29C30VAL0-0.013-0.0168.8211.4151.4150.0000.0000.0000.000
30C31ARG10.9400.96611.677-20.331-20.3310.0000.0000.0000.000
31C32SER00.1080.03115.362-0.135-0.1350.0000.0000.0000.000
32C33SER0-0.051-0.00312.209-0.981-0.9810.0000.0000.0000.000
33C34LEU0-0.001-0.00411.6332.2902.2900.0000.0000.0000.000
34C35ALA0-0.019-0.00413.274-1.597-1.5970.0000.0000.0000.000
35C36TRP00.0170.00314.4961.3391.3390.0000.0000.0000.000
36C37TYR00.006-0.01313.918-1.226-1.2260.0000.0000.0000.000
37C38GLN00.0270.00618.201-0.064-0.0640.0000.0000.0000.000
38C39GLN0-0.0050.00317.9190.7150.7150.0000.0000.0000.000
39C40LYS10.8450.91920.732-11.636-11.6360.0000.0000.0000.000
40C41PRO00.0420.00723.6200.4010.4010.0000.0000.0000.000
41C42GLY00.0260.02524.118-0.385-0.3850.0000.0000.0000.000
42C43LYS10.8500.92523.205-12.154-12.1540.0000.0000.0000.000
43C44ALA00.0630.03519.6210.5810.5810.0000.0000.0000.000
44C45PRO0-0.001-0.00915.615-0.676-0.6760.0000.0000.0000.000
45C46GLN0-0.049-0.01718.686-0.614-0.6140.0000.0000.0000.000
46C47LEU0-0.0090.00117.5720.3210.3210.0000.0000.0000.000
47C48LEU0-0.031-0.00920.018-0.764-0.7640.0000.0000.0000.000
48C49ILE00.002-0.00519.595-0.632-0.6320.0000.0000.0000.000
49C50TYR00.0470.02417.6111.2831.2830.0000.0000.0000.000
50C51SER00.023-0.00117.606-0.488-0.4880.0000.0000.0000.000
51C52ALA0-0.027-0.01216.832-0.650-0.6500.0000.0000.0000.000
52C53SER0-0.045-0.02318.184-0.554-0.5540.0000.0000.0000.000
53C54THR00.0000.01421.716-0.606-0.6060.0000.0000.0000.000
54C55LEU0-0.013-0.00122.4810.6020.6020.0000.0000.0000.000
55C56GLU-1-0.808-0.89022.76413.13013.1300.0000.0000.0000.000
56C57ASN0-0.074-0.07024.830-0.870-0.8700.0000.0000.0000.000
57C58GLY0-0.015-0.00227.8850.1410.1410.0000.0000.0000.000
58C59VAL0-0.044-0.00124.639-0.110-0.1100.0000.0000.0000.000
59C60SER00.0130.00428.038-0.341-0.3410.0000.0000.0000.000
60C61SER00.032-0.00628.8860.3450.3450.0000.0000.0000.000
61C62ARG10.7530.85729.895-10.175-10.1750.0000.0000.0000.000
62C63PHE00.0100.01924.5900.1420.1420.0000.0000.0000.000
63C64SER0-0.028-0.02325.277-0.351-0.3510.0000.0000.0000.000
64C65GLY00.0380.01921.6290.3370.3370.0000.0000.0000.000
65C66SER0-0.090-0.04919.649-0.373-0.3730.0000.0000.0000.000
66C67GLY00.0200.04118.8330.4060.4060.0000.0000.0000.000
67C68PRO0-0.005-0.00818.095-0.581-0.5810.0000.0000.0000.000
68C69GLY0-0.006-0.01816.404-0.643-0.6430.0000.0000.0000.000
69C70THR0-0.017-0.02112.8860.7900.7900.0000.0000.0000.000
70C71GLU-1-0.828-0.89613.95416.22516.2250.0000.0000.0000.000
71C72PHE0-0.0020.01013.572-0.479-0.4790.0000.0000.0000.000
72C73THR00.013-0.01017.7070.1120.1120.0000.0000.0000.000
73C74LEU00.0010.01619.9980.0330.0330.0000.0000.0000.000
74C75THR0-0.043-0.02521.712-0.405-0.4050.0000.0000.0000.000
75C76ILE00.0350.00624.5460.1730.1730.0000.0000.0000.000
76C77SER0-0.037-0.03127.660-0.214-0.2140.0000.0000.0000.000
77C78SER00.011-0.00231.155-0.341-0.3410.0000.0000.0000.000
78C79LEU0-0.0390.00128.1190.0930.0930.0000.0000.0000.000
79C80GLN00.0340.01131.401-0.448-0.4480.0000.0000.0000.000
80C81PRO00.0420.01631.6450.3370.3370.0000.0000.0000.000
81C82GLU-1-0.780-0.87930.8669.8639.8630.0000.0000.0000.000
82C83ASP-1-0.805-0.87027.63811.26111.2610.0000.0000.0000.000
83C84VAL0-0.0200.01626.4450.5630.5630.0000.0000.0000.000
84C85GLY00.0390.00623.5980.0370.0370.0000.0000.0000.000
85C86THR0-0.053-0.01617.489-0.433-0.4330.0000.0000.0000.000
86C87TYR0-0.002-0.00518.9340.1880.1880.0000.0000.0000.000
87C88TYR0-0.020-0.01813.4010.4970.4970.0000.0000.0000.000
88C90GLN00.0170.0129.421-0.837-0.8370.0000.0000.0000.000
89C91GLN00.0150.0014.478-7.728-7.662-0.001-0.003-0.0620.000
90C92LEU0-0.015-0.0208.1782.3632.3630.0000.0000.0000.000
91C93ASN0-0.016-0.0028.636-4.173-4.1730.0000.0000.0000.000
92C94THR0-0.009-0.0114.697-2.386-2.332-0.001-0.003-0.0510.000
93C95TYR0-0.0180.0185.7113.2083.2080.0000.0000.0000.000
94C96PRO00.0540.0232.725-8.232-4.6212.842-2.530-3.9230.030
95C97PHE0-0.006-0.0074.1091.9072.1000.000-0.045-0.1470.000
96C98THR0-0.008-0.0062.556-8.164-6.1701.636-1.420-2.2100.012
97C99PHE00.036-0.0015.509-6.583-6.561-0.001-0.002-0.0190.000
98C100GLY00.0180.0187.3982.8142.8140.0000.0000.0000.000
99C101PRO0-0.056-0.0349.949-0.405-0.4050.0000.0000.0000.000
100C102GLY0-0.0040.00511.944-1.117-1.1170.0000.0000.0000.000
101C103THR0-0.051-0.04415.125-0.033-0.0330.0000.0000.0000.000
102C104LYS10.8300.89518.520-13.470-13.4700.0000.0000.0000.000
103C105VAL0-0.004-0.00821.467-0.218-0.2180.0000.0000.0000.000
104C106GLU-1-0.811-0.83924.87210.02210.0220.0000.0000.0000.000
105C107ILE00.011-0.00428.265-0.046-0.0460.0000.0000.0000.000
106C108LYS10.9710.99231.373-9.241-9.2410.0000.0000.0000.000
107C109ARG10.8560.91033.773-8.252-8.2520.0000.0000.0000.000
108C110THR00.0160.00137.4100.0290.0290.0000.0000.0000.000
109C111VAL0-0.0010.01040.1940.1220.1220.0000.0000.0000.000
110C112ALA0-0.025-0.00540.845-0.176-0.1760.0000.0000.0000.000
111C113ALA00.0420.01741.7250.1640.1640.0000.0000.0000.000
112C114PRO0-0.0130.01041.440-0.002-0.0020.0000.0000.0000.000
113C115SER00.013-0.01043.228-0.129-0.1290.0000.0000.0000.000
114C116VAL00.0050.01144.4780.1110.1110.0000.0000.0000.000
115C117PHE0-0.029-0.01045.274-0.234-0.2340.0000.0000.0000.000
116C118ILE00.006-0.00445.5630.1630.1630.0000.0000.0000.000
117C119PHE0-0.011-0.00644.614-0.123-0.1230.0000.0000.0000.000
118C120PRO00.0080.01047.2550.1180.1180.0000.0000.0000.000
119C121PRO00.002-0.00447.9620.0740.0740.0000.0000.0000.000
120C122SER00.0020.01548.739-0.119-0.1190.0000.0000.0000.000
121C123ASP-1-0.897-0.94350.5735.8995.8990.0000.0000.0000.000
122C124GLU-1-0.944-0.97948.8476.3736.3730.0000.0000.0000.000
123C125GLN0-0.146-0.09247.5520.1550.1550.0000.0000.0000.000
124C126LEU00.0320.03640.9330.0800.0800.0000.0000.0000.000
125C127LYS10.9630.98642.505-7.237-7.2370.0000.0000.0000.000
126C128SER00.0370.00645.4480.0040.0040.0000.0000.0000.000
127C129GLY0-0.011-0.02145.427-0.136-0.1360.0000.0000.0000.000
128C130THR00.002-0.00641.2740.0550.0550.0000.0000.0000.000
129C131ALA00.0390.04044.6840.0420.0420.0000.0000.0000.000
130C132SER0-0.027-0.02643.0640.0680.0680.0000.0000.0000.000
131C133VAL0-0.0050.01644.695-0.090-0.0900.0000.0000.0000.000
132C134VAL00.0250.01741.2220.1530.1530.0000.0000.0000.000
133C135CYS0-0.042-0.01942.112-0.072-0.0720.0000.0000.0000.000
134C136LEU0-0.0140.01039.6890.2290.2290.0000.0000.0000.000
135C137LEU00.012-0.00139.417-0.239-0.2390.0000.0000.0000.000
136C138ASN00.001-0.01239.5190.2890.2890.0000.0000.0000.000
137C139ASN00.0100.02238.4810.3710.3710.0000.0000.0000.000
138C140PHE0-0.050-0.00736.330-0.215-0.2150.0000.0000.0000.000
139C141TYR00.041-0.01032.8860.1710.1710.0000.0000.0000.000
140C142PRO00.0110.00335.047-0.289-0.2890.0000.0000.0000.000
141C143ARG10.9420.98127.627-10.998-10.9980.0000.0000.0000.000
142C144GLU-1-0.891-0.94534.0719.2669.2660.0000.0000.0000.000
143C145ALA0-0.053-0.01535.765-0.299-0.2990.0000.0000.0000.000
144C146LYS10.9270.95137.642-7.919-7.9190.0000.0000.0000.000
145C147VAL00.0380.01839.767-0.224-0.2240.0000.0000.0000.000
146C148GLN0-0.025-0.00841.7490.1290.1290.0000.0000.0000.000
147C149TRP00.0260.00141.317-0.278-0.2780.0000.0000.0000.000
148C150LYS10.8140.89445.689-6.345-6.3450.0000.0000.0000.000
149C151VAL00.0270.01949.3470.0090.0090.0000.0000.0000.000
150C152ASP-1-0.798-0.88751.9925.6095.6090.0000.0000.0000.000
151C153ASN0-0.026-0.01853.2820.0150.0150.0000.0000.0000.000
152C154ALA00.0250.02751.9060.0240.0240.0000.0000.0000.000
153C155LEU00.008-0.01246.5400.0580.0580.0000.0000.0000.000
154C156GLN00.0300.01845.2800.0000.0000.0000.0000.0000.000
155C157SER0-0.043-0.03042.5530.1340.1340.0000.0000.0000.000
156C158GLY00.0450.03139.981-0.026-0.0260.0000.0000.0000.000
157C159ASN0-0.049-0.01640.1650.1350.1350.0000.0000.0000.000
158C160SER00.0350.01139.815-0.133-0.1330.0000.0000.0000.000
159C161GLN0-0.061-0.01934.1800.2780.2780.0000.0000.0000.000
160C162GLU-1-0.876-0.92334.5838.4088.4080.0000.0000.0000.000
161C163SER0-0.012-0.00231.1330.4180.4180.0000.0000.0000.000
162C164VAL00.0030.00130.302-0.318-0.3180.0000.0000.0000.000
163C165THR00.0070.00430.1500.2950.2950.0000.0000.0000.000
164C166GLU-1-0.833-0.89724.86812.69512.6950.0000.0000.0000.000
165C167GLN0-0.013-0.00428.693-0.041-0.0410.0000.0000.0000.000
166C168ASP-1-0.760-0.86730.3399.2299.2290.0000.0000.0000.000
167C169SER0-0.043-0.03230.3180.1680.1680.0000.0000.0000.000
168C170LYS10.8290.89332.422-8.529-8.5290.0000.0000.0000.000
169C171ASP-1-0.806-0.90236.1868.0838.0830.0000.0000.0000.000
170C172SER0-0.035-0.00733.876-0.060-0.0600.0000.0000.0000.000
171C173THR0-0.046-0.03834.9070.0470.0470.0000.0000.0000.000
172C174TYR0-0.070-0.06929.5920.4330.4330.0000.0000.0000.000
173C175SER00.0370.01334.494-0.254-0.2540.0000.0000.0000.000
174C176LEU0-0.042-0.01534.6690.3070.3070.0000.0000.0000.000
175C177SER0-0.013-0.00136.004-0.371-0.3710.0000.0000.0000.000
176C178SER00.039-0.01136.5820.1960.1960.0000.0000.0000.000
177C179THR00.0110.00138.328-0.238-0.2380.0000.0000.0000.000
178C180LEU0-0.0240.00040.0740.1250.1250.0000.0000.0000.000
179C181THR0-0.033-0.02640.396-0.025-0.0250.0000.0000.0000.000
180C182LEU00.0230.01243.4160.0030.0030.0000.0000.0000.000
181C183SER0-0.008-0.02646.672-0.009-0.0090.0000.0000.0000.000
182C184LYS10.8750.90948.554-5.968-5.9680.0000.0000.0000.000
183C185ALA0-0.029-0.01451.424-0.127-0.1270.0000.0000.0000.000
184C186ASP-1-0.828-0.88249.4996.3406.3400.0000.0000.0000.000
185C187TYR00.0290.00550.395-0.097-0.0970.0000.0000.0000.000
186C188GLU-1-0.789-0.87852.3045.6105.6100.0000.0000.0000.000
187C189LYS10.8860.96155.530-5.637-5.6370.0000.0000.0000.000
188C190HIS0-0.060-0.03054.425-0.065-0.0650.0000.0000.0000.000
189C191LYS10.8540.91356.552-5.406-5.4060.0000.0000.0000.000
190C192VAL0-0.0050.00255.464-0.014-0.0140.0000.0000.0000.000
191C193TYR00.006-0.01349.9400.1070.1070.0000.0000.0000.000
192C194ALA0-0.002-0.01450.392-0.049-0.0490.0000.0000.0000.000
193C196GLU-1-0.838-0.90347.1616.3966.3960.0000.0000.0000.000
194C197VAL00.013-0.00842.7820.1940.1940.0000.0000.0000.000
195C198THR0-0.024-0.01443.317-0.201-0.2010.0000.0000.0000.000
196C199HIS00.029-0.00938.707-0.017-0.0170.0000.0000.0000.000
197C200GLN00.0400.01138.482-0.035-0.0350.0000.0000.0000.000
198C201GLY0-0.0090.00142.712-0.107-0.1070.0000.0000.0000.000
199C202LEU0-0.065-0.03044.766-0.139-0.1390.0000.0000.0000.000
200C203SER00.0100.00847.3560.0500.0500.0000.0000.0000.000
201C204SER0-0.015-0.02049.970-0.152-0.1520.0000.0000.0000.000
202C205PRO0-0.017-0.00247.9040.0420.0420.0000.0000.0000.000
203C206VAL00.0130.03447.215-0.155-0.1550.0000.0000.0000.000
204C207THR00.028-0.00748.5790.1350.1350.0000.0000.0000.000
205C208LYS10.8550.93648.783-6.500-6.5000.0000.0000.0000.000
206C209SER00.010-0.00750.1410.0990.0990.0000.0000.0000.000
207C210PHE0-0.0310.00149.623-0.039-0.0390.0000.0000.0000.000
208C211ASN0-0.021-0.03854.5890.1190.1190.0000.0000.0000.000
209C212ARG10.8230.91855.151-5.567-5.5670.0000.0000.0000.000
210C213GLY00.0390.01957.915-0.087-0.0870.0000.0000.0000.000
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