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: R9KY8

Calculation Name: 4OF0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OF0

Chain ID: A

ChEMBL ID:

UniProt ID: B1Q236

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2463983.072195
FMO2-HF: Nuclear repulsion 2373968.624835
FMO2-HF: Total energy -90014.44736
FMO2-MP2: Total energy -90275.989597


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:23:GLN)


Summations of interaction energy for fragment #1(A:23:GLN)
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.
-45.337-35.37329.854-16.16-23.658-0.014
Interaction energy analysis for fragmet #1(A:23:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.030
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].
3A25ILE00.0300.0033.808-1.1521.470-0.034-1.455-1.1330.005
4A26VAL0-0.062-0.0116.937-0.102-0.1020.0000.0000.0000.000
5A27GLU-1-0.947-0.9799.1030.2180.2180.0000.0000.0000.000
6A28ALA00.012-0.00611.6430.0190.0190.0000.0000.0000.000
7A29PRO00.0100.01412.7100.0570.0570.0000.0000.0000.000
8A30LYS10.9790.99415.905-0.149-0.1490.0000.0000.0000.000
9A31ASP-1-0.819-0.90219.349-0.137-0.1370.0000.0000.0000.000
10A32THR0-0.115-0.05922.0210.0430.0430.0000.0000.0000.000
11A33LEU0-0.019-0.01124.487-0.019-0.0190.0000.0000.0000.000
12A34ALA00.0430.01927.1930.0190.0190.0000.0000.0000.000
13A35ALA00.0020.01629.206-0.018-0.0180.0000.0000.0000.000
14A36VAL0-0.025-0.02631.9560.0090.0090.0000.0000.0000.000
15A37GLY0-0.047-0.01932.4150.0020.0020.0000.0000.0000.000
16A38GLU-1-0.925-0.95330.4250.0780.0780.0000.0000.0000.000
17A39THR0-0.021-0.02325.8120.0030.0030.0000.0000.0000.000
18A40ALA0-0.0100.00524.3040.0010.0010.0000.0000.0000.000
19A41ILE0-0.014-0.01619.9210.0290.0290.0000.0000.0000.000
20A42LEU0-0.0050.01517.920-0.020-0.0200.0000.0000.0000.000
21A43THR0-0.042-0.02816.0420.0420.0420.0000.0000.0000.000
22A44CYS00.0300.01410.2910.0890.0890.0000.0000.0000.000
23A45ARG10.9481.00410.221-0.507-0.5070.0000.0000.0000.000
24A46VAL0-0.016-0.0094.834-0.296-0.2960.0000.0000.0000.000
25A47GLU-1-0.897-0.9504.1711.6641.826-0.001-0.045-0.1160.000
26A48HIS0-0.006-0.0202.193-2.552-0.5072.381-2.201-2.225-0.016
27A49GLN0-0.003-0.0082.095-4.572-2.8707.384-4.802-4.284-0.021
28A50GLN00.011-0.0071.853-12.860-16.64112.292-3.028-5.4830.022
29A51GLY00.0390.0362.568-6.637-6.0900.933-0.124-1.3560.008
30A52PRO0-0.038-0.0084.1460.5700.7500.000-0.014-0.1660.000
31A53VAL00.0280.0046.208-0.413-0.4130.0000.0000.0000.000
32A54GLN0-0.016-0.0168.120-0.014-0.0140.0000.0000.0000.000
33A55TRP0-0.026-0.02710.761-0.218-0.2180.0000.0000.0000.000
34A56MET0-0.033-0.01010.967-0.038-0.0380.0000.0000.0000.000
35A57LYS10.8060.90515.1070.1490.1490.0000.0000.0000.000
36A58ASP-1-0.907-0.95318.890-0.308-0.3080.0000.0000.0000.000
37A59ASP-1-0.903-0.94816.011-0.654-0.6540.0000.0000.0000.000
38A60PHE00.011-0.00116.439-0.023-0.0230.0000.0000.0000.000
39A61GLY00.0160.01013.8500.0460.0460.0000.0000.0000.000
40A62LEU0-0.051-0.02714.4840.0460.0460.0000.0000.0000.000
41A63GLY00.0190.01514.9610.0550.0550.0000.0000.0000.000
42A64THR0-0.031-0.02710.5440.0290.0290.0000.0000.0000.000
43A65ASP-1-0.891-0.94613.4110.5460.5460.0000.0000.0000.000
44A66ARG10.9020.93512.738-1.060-1.0600.0000.0000.0000.000
45A67ASP-1-0.938-0.95616.5330.6540.6540.0000.0000.0000.000
46A68LYS10.8700.92718.892-0.488-0.4880.0000.0000.0000.000
47A69PRO0-0.067-0.03420.3030.0170.0170.0000.0000.0000.000
48A70LEU00.0120.02517.0600.0020.0020.0000.0000.0000.000
49A71PRO00.009-0.00118.923-0.042-0.0420.0000.0000.0000.000
50A72GLY00.0020.02020.585-0.037-0.0370.0000.0000.0000.000
51A73ASN0-0.030-0.04621.786-0.023-0.0230.0000.0000.0000.000
52A74LYS10.9760.99823.862-0.071-0.0710.0000.0000.0000.000
53A75ARG10.7580.85925.934-0.039-0.0390.0000.0000.0000.000
54A76TYR0-0.019-0.02120.663-0.003-0.0030.0000.0000.0000.000
55A77ARG10.9430.97520.714-0.321-0.3210.0000.0000.0000.000
56A78MET00.0290.03413.3540.0430.0430.0000.0000.0000.000
57A79VAL0-0.025-0.00917.4320.0430.0430.0000.0000.0000.000
58A80GLY00.0410.01116.3240.0210.0210.0000.0000.0000.000
59A81SER0-0.040-0.01616.2890.0480.0480.0000.0000.0000.000
60A82ALA00.0510.00912.8490.0670.0670.0000.0000.0000.000
61A83ALA0-0.020-0.00112.0890.2140.2140.0000.0000.0000.000
62A84ASN0-0.089-0.05312.4920.1280.1280.0000.0000.0000.000
63A85GLY00.0780.0489.5840.0010.0010.0000.0000.0000.000
64A86GLU-1-0.913-0.9559.8200.7140.7140.0000.0000.0000.000
65A87TYR0-0.024-0.0319.0860.2810.2810.0000.0000.0000.000
66A88ASN00.0680.03812.429-0.092-0.0920.0000.0000.0000.000
67A89LEU0-0.0040.01015.5640.0330.0330.0000.0000.0000.000
68A90GLU-1-0.821-0.89017.7730.1980.1980.0000.0000.0000.000
69A91ILE00.0010.01421.387-0.008-0.0080.0000.0000.0000.000
70A92SER00.018-0.02624.244-0.013-0.0130.0000.0000.0000.000
71A93ASN0-0.054-0.02527.663-0.008-0.0080.0000.0000.0000.000
72A94VAL00.0160.02027.237-0.010-0.0100.0000.0000.0000.000
73A95THR0-0.009-0.01229.461-0.010-0.0100.0000.0000.0000.000
74A96LEU00.046-0.00930.102-0.004-0.0040.0000.0000.0000.000
75A97PHE00.0030.00828.671-0.011-0.0110.0000.0000.0000.000
76A98ASP-1-0.745-0.83325.7930.0120.0120.0000.0000.0000.000
77A99ASP-1-0.874-0.93125.346-0.099-0.0990.0000.0000.0000.000
78A100ASP-1-0.782-0.89322.736-0.208-0.2080.0000.0000.0000.000
79A101ASP-1-0.926-0.95920.325-0.254-0.2540.0000.0000.0000.000
80A102PHE0-0.032-0.03617.747-0.006-0.0060.0000.0000.0000.000
81A103ALA0-0.010-0.00313.478-0.031-0.0310.0000.0000.0000.000
82A105GLN00.0670.0276.920-0.025-0.0250.0000.0000.0000.000
83A106ILE0-0.037-0.0122.435-1.402-0.2643.678-1.291-3.5260.013
84A107SER0-0.031-0.0324.031-3.387-3.2150.000-0.059-0.1130.000
85A108GLU-1-0.948-0.9862.908-6.798-5.4480.079-0.705-0.724-0.008
86A109SER00.006-0.0043.7592.2112.7470.007-0.116-0.4270.000
87A110ASP-1-0.925-0.9584.969-1.238-1.223-0.0010.000-0.0140.000
88A111HIS0-0.069-0.0377.884-0.022-0.0220.0000.0000.0000.000
89A112ALA0-0.003-0.0073.175-0.779-0.0170.217-0.348-0.6310.004
90A113LYS10.9661.0023.5472.4693.2000.041-0.284-0.487-0.001
91A114ALA00.0620.0282.211-10.937-10.3302.615-1.337-1.885-0.020
92A115VAL0-0.070-0.0302.615-0.2410.8570.264-0.348-1.0140.000
93A116VAL00.0030.0034.8781.4061.484-0.001-0.003-0.0740.000
94A117SER0-0.0110.0028.5810.0310.0310.0000.0000.0000.000
95A118SER0-0.012-0.00810.862-0.042-0.0420.0000.0000.0000.000
96A119LYS10.8530.91614.4360.5660.5660.0000.0000.0000.000
97A120ALA00.0060.02117.2040.0240.0240.0000.0000.0000.000
98A121LYS10.8910.95619.6120.1440.1440.0000.0000.0000.000
99A122LEU0-0.032-0.01023.0130.0340.0340.0000.0000.0000.000
100A123THR0-0.042-0.03324.496-0.016-0.0160.0000.0000.0000.000
101A124VAL0-0.017-0.00628.2280.0180.0180.0000.0000.0000.000
102A125LEU0-0.070-0.04630.511-0.011-0.0110.0000.0000.0000.000
103A126VAL0-0.001-0.01733.8290.0080.0080.0000.0000.0000.000
104A127ARG10.8860.95237.158-0.033-0.0330.0000.0000.0000.000
105A128PRO00.0000.01039.8020.0000.0000.0000.0000.0000.000
106A129THR0-0.040-0.02243.1940.0040.0040.0000.0000.0000.000
107A130PRO00.0350.00846.391-0.002-0.0020.0000.0000.0000.000
108A131PRO0-0.0400.00148.470-0.003-0.0030.0000.0000.0000.000
109A132LYS10.9060.94950.845-0.008-0.0080.0000.0000.0000.000
110A133ILE00.0170.00554.301-0.003-0.0030.0000.0000.0000.000
111A134VAL0-0.046-0.02857.4390.0010.0010.0000.0000.0000.000
112A135LYS10.9120.96859.498-0.007-0.0070.0000.0000.0000.000
113A136SER0-0.007-0.00162.2960.0000.0000.0000.0000.0000.000
114A137HIS0-0.023-0.02960.6180.0000.0000.0000.0000.0000.000
115A138HIS0-0.0060.01164.8010.0010.0010.0000.0000.0000.000
116A139SER0-0.022-0.00466.1230.0000.0000.0000.0000.0000.000
117A140LEU00.0260.00264.723-0.001-0.0010.0000.0000.0000.000
118A141LYS10.8470.91867.867-0.004-0.0040.0000.0000.0000.000
119A142ALA00.0190.00569.753-0.001-0.0010.0000.0000.0000.000
120A143ILE0-0.0070.00171.8710.0010.0010.0000.0000.0000.000
121A144ALA0-0.0020.00572.825-0.001-0.0010.0000.0000.0000.000
122A145GLY00.0040.00272.4490.0000.0000.0000.0000.0000.000
123A146ASP-1-0.898-0.94472.776-0.009-0.0090.0000.0000.0000.000
124A147PRO0-0.043-0.03268.6310.0010.0010.0000.0000.0000.000
125A148ILE0-0.036-0.00766.1060.0000.0000.0000.0000.0000.000
126A149THR00.006-0.00862.1350.0000.0000.0000.0000.0000.000
127A150GLN0-0.069-0.03760.8360.0030.0030.0000.0000.0000.000
128A151SER00.0370.02057.474-0.001-0.0010.0000.0000.0000.000
129A152CYS0-0.074-0.01253.3510.0000.0000.0000.0000.0000.000
130A153LEU0-0.0150.00051.967-0.003-0.0030.0000.0000.0000.000
131A154SER00.0070.00646.8550.0030.0030.0000.0000.0000.000
132A155ARG10.9060.93246.8490.0140.0140.0000.0000.0000.000
133A156LYS10.9540.97842.5770.0150.0150.0000.0000.0000.000
134A157GLY00.0700.05341.0220.0050.0050.0000.0000.0000.000
135A158LYS10.8960.98632.5960.0510.0510.0000.0000.0000.000
136A159PRO00.0640.01135.5540.0050.0050.0000.0000.0000.000
137A160PRO00.0530.02638.2150.0070.0070.0000.0000.0000.000
138A161PRO00.0010.01541.9750.0010.0010.0000.0000.0000.000
139A162THR0-0.0190.00643.355-0.004-0.0040.0000.0000.0000.000
140A163ILE00.024-0.00345.5530.0050.0050.0000.0000.0000.000
141A164GLY0-0.024-0.01249.252-0.003-0.0030.0000.0000.0000.000
142A165TRP0-0.003-0.01652.0170.0030.0030.0000.0000.0000.000
143A166ALA00.006-0.00455.549-0.001-0.0010.0000.0000.0000.000
144A167ILE00.0190.02857.5630.0000.0000.0000.0000.0000.000
145A168ALA00.0230.01958.4030.0010.0010.0000.0000.0000.000
146A169SER00.0050.00160.541-0.001-0.0010.0000.0000.0000.000
147A170ASP-1-0.805-0.89258.0570.0210.0210.0000.0000.0000.000
148A171GLU-1-0.918-0.97458.9750.0190.0190.0000.0000.0000.000
149A172HIS0-0.014-0.01254.761-0.001-0.0010.0000.0000.0000.000
150A173GLY0-0.019-0.00754.3940.0010.0010.0000.0000.0000.000
151A174LYS10.8780.93151.180-0.030-0.0300.0000.0000.0000.000
152A175HIS0-0.014-0.00955.7230.0000.0000.0000.0000.0000.000
153A176ILE00.0050.00054.065-0.002-0.0020.0000.0000.0000.000
154A177VAL0-0.018-0.02258.3440.0000.0000.0000.0000.0000.000
155A178SER00.032-0.01160.395-0.001-0.0010.0000.0000.0000.000
156A179TRP0-0.0190.00951.6930.0000.0000.0000.0000.0000.000
157A180LEU00.0240.01857.171-0.001-0.0010.0000.0000.0000.000
158A181GLY00.0290.02456.415-0.001-0.0010.0000.0000.0000.000
159A182GLU-1-0.886-0.94752.720-0.017-0.0170.0000.0000.0000.000
160A183SER0-0.033-0.02651.971-0.001-0.0010.0000.0000.0000.000
161A184ARG10.9740.98851.079-0.001-0.0010.0000.0000.0000.000
162A185SER0-0.079-0.03449.5610.0010.0010.0000.0000.0000.000
163A186LYS10.9230.96946.8010.0170.0170.0000.0000.0000.000
164A187PHE0-0.050-0.01346.2350.0030.0030.0000.0000.0000.000
165A195GLU-1-0.912-0.97956.8690.0020.0020.0000.0000.0000.000
166A196ILE0-0.016-0.00358.8610.0000.0000.0000.0000.0000.000
167A197SER0-0.032-0.00762.4020.0000.0000.0000.0000.0000.000
168A198GLN0-0.021-0.01363.498-0.001-0.0010.0000.0000.0000.000
169A199GLU-1-0.876-0.93965.689-0.005-0.0050.0000.0000.0000.000
170A200THR0-0.012-0.01362.6140.0000.0000.0000.0000.0000.000
171A201VAL00.0360.02463.1180.0000.0000.0000.0000.0000.000
172A202ILE00.0190.01563.644-0.001-0.0010.0000.0000.0000.000
173A203ALA00.007-0.02161.0250.0010.0010.0000.0000.0000.000
174A204HIS0-0.0090.00057.6070.0000.0000.0000.0000.0000.000
175A205VAL00.002-0.00154.0420.0010.0010.0000.0000.0000.000
176A206ASN00.0090.00655.670-0.004-0.0040.0000.0000.0000.000
177A207GLU-1-0.918-0.97248.314-0.026-0.0260.0000.0000.0000.000
178A208THR0-0.049-0.01251.121-0.003-0.0030.0000.0000.0000.000
179A209THR00.0340.00244.6290.0030.0030.0000.0000.0000.000
180A210GLN0-0.0170.00047.428-0.003-0.0030.0000.0000.0000.000
181A211VAL0-0.0070.00341.7230.0020.0020.0000.0000.0000.000
182A212GLU-1-0.882-0.96441.194-0.024-0.0240.0000.0000.0000.000
183A222SER00.030-0.00132.184-0.002-0.0020.0000.0000.0000.000
184A223SER0-0.0180.00034.1580.0050.0050.0000.0000.0000.000
185A224ILE0-0.023-0.00537.6740.0020.0020.0000.0000.0000.000
186A225TYR00.0270.00638.758-0.003-0.0030.0000.0000.0000.000
187A226SER0-0.083-0.03343.1730.0060.0060.0000.0000.0000.000
188A227ILE00.0220.01646.507-0.004-0.0040.0000.0000.0000.000
189A228MET00.0100.01048.6990.0050.0050.0000.0000.0000.000
190A229SER00.0110.01452.162-0.002-0.0020.0000.0000.0000.000
191A230ASN00.022-0.01453.8640.0040.0040.0000.0000.0000.000
192A231LEU00.0180.03657.549-0.002-0.0020.0000.0000.0000.000
193A232SER00.001-0.01159.4300.0010.0010.0000.0000.0000.000
194A233PHE00.002-0.01762.7970.0000.0000.0000.0000.0000.000
195A234ILE00.0270.03064.7680.0000.0000.0000.0000.0000.000
196A235PRO0-0.0400.00267.6520.0010.0010.0000.0000.0000.000
197A236ARG10.8180.86865.045-0.001-0.0010.0000.0000.0000.000
198A237PRO00.0320.00270.7660.0010.0010.0000.0000.0000.000
199A238GLU-1-0.861-0.92769.3350.0020.0020.0000.0000.0000.000
200A239ASP-1-0.792-0.86766.5840.0020.0020.0000.0000.0000.000
201A240ASP-1-0.830-0.92268.1110.0060.0060.0000.0000.0000.000
202A241HIS0-0.095-0.04269.1760.0020.0020.0000.0000.0000.000
203A242LYS10.8700.95064.516-0.006-0.0060.0000.0000.0000.000
204A243TYR0-0.012-0.01961.148-0.001-0.0010.0000.0000.0000.000
205A244LEU00.0000.02159.9720.0000.0000.0000.0000.0000.000
206A245ILE0-0.020-0.02254.7870.0010.0010.0000.0000.0000.000
207A247ILE00.002-0.01249.2110.0030.0030.0000.0000.0000.000
208A248SER00.0240.00446.303-0.004-0.0040.0000.0000.0000.000
209A249GLN00.0390.01943.4790.0090.0090.0000.0000.0000.000
210A250HIS00.0340.01137.8360.0010.0010.0000.0000.0000.000
211A251MET00.0250.01635.1360.0050.0050.0000.0000.0000.000
212A252THR00.006-0.02836.0210.0070.0070.0000.0000.0000.000
213A253PHE0-0.078-0.04437.5210.0080.0080.0000.0000.0000.000
214A254PRO00.0840.03936.024-0.004-0.0040.0000.0000.0000.000
215A255ASN0-0.043-0.02539.0340.0010.0010.0000.0000.0000.000
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