Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YZ3Y2

Calculation Name: 4AB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JXG8

Base Structure: X-ray

Registration Date: 2023-09-20

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2547639.574343
FMO2-HF: Nuclear repulsion 2461973.152167
FMO2-HF: Total energy -85666.422175
FMO2-MP2: Total energy -85914.202739


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:92:GLY)


Summations of interaction energy for fragment #1(A:92:GLY)
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.
-11.683-6.5986.778-6.674-5.19-0.042
Interaction energy analysis for fragmet #1(A:92:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.005
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].
3A94ALA0-0.058-0.0323.854-1.0570.091-0.008-0.556-0.5840.001
4A95GLY00.0230.0204.0900.9921.110-0.001-0.022-0.0950.000
5A96GLU-1-0.916-0.9583.985-2.627-2.4200.001-0.044-0.1640.000
6A97LEU0-0.030-0.0146.5360.3450.3450.0000.0000.0000.000
7A98ARG10.8340.9099.5861.0311.0310.0000.0000.0000.000
8A99ILE0-0.004-0.02411.6180.0690.0690.0000.0000.0000.000
9A100ALA00.0100.01814.8430.0170.0170.0000.0000.0000.000
10A101VAL0-0.005-0.01518.0770.0250.0250.0000.0000.0000.000
11A102GLU-1-0.756-0.85920.966-0.212-0.2120.0000.0000.0000.000
12A103CYS0-0.0410.00423.2890.0250.0250.0000.0000.0000.000
13A104HIS00.028-0.01724.756-0.006-0.0060.0000.0000.0000.000
14A105THR0-0.016-0.01326.144-0.002-0.0020.0000.0000.0000.000
15A107PHE00.0310.01019.639-0.001-0.0010.0000.0000.0000.000
16A108ASP-1-0.900-0.95022.424-0.072-0.0720.0000.0000.0000.000
17A109TRP00.0440.01021.1080.0050.0050.0000.0000.0000.000
18A110LEU0-0.018-0.00617.7220.0020.0020.0000.0000.0000.000
19A111MET0-0.0090.00117.389-0.012-0.0120.0000.0000.0000.000
20A112PRO0-0.019-0.01617.7720.0090.0090.0000.0000.0000.000
21A113ALA00.0190.02418.2190.0170.0170.0000.0000.0000.000
22A114MET00.005-0.00612.5480.0110.0110.0000.0000.0000.000
23A115GLY0-0.071-0.03513.3480.0210.0210.0000.0000.0000.000
24A116GLU-1-0.851-0.90015.3550.0380.0380.0000.0000.0000.000
25A117PHE00.0250.0018.9250.0500.0500.0000.0000.0000.000
26A118ARG10.9740.9858.9590.0290.0290.0000.0000.0000.000
27A119PRO0-0.037-0.0199.4620.0970.0970.0000.0000.0000.000
28A120MET0-0.0200.00011.4130.0850.0850.0000.0000.0000.000
29A121TRP0-0.040-0.0308.236-0.017-0.0170.0000.0000.0000.000
30A122PRO0-0.009-0.0086.570-0.089-0.0890.0000.0000.0000.000
31A123GLN0-0.052-0.0282.6732.4573.7550.644-0.717-1.224-0.001
32A124VAL0-0.0190.0082.788-2.652-2.2940.905-0.627-0.637-0.008
33A125GLU-1-0.894-0.9452.070-9.040-7.0675.238-4.689-2.523-0.034
34A126LEU0-0.066-0.0364.4990.0960.079-0.001-0.0190.0370.000
35A127ASP-1-0.866-0.9398.309-0.645-0.6450.0000.0000.0000.000
36A128ILE0-0.068-0.02510.9780.0510.0510.0000.0000.0000.000
37A129VAL00.0070.00614.2190.0080.0080.0000.0000.0000.000
38A130SER0-0.053-0.06216.7260.0320.0320.0000.0000.0000.000
39A131GLY00.0130.01420.241-0.004-0.0040.0000.0000.0000.000
40A132PHE0-0.051-0.04719.4850.0060.0060.0000.0000.0000.000
41A133GLN0-0.074-0.04824.8390.0170.0170.0000.0000.0000.000
42A134ALA0-0.018-0.01126.2440.0120.0120.0000.0000.0000.000
43A135ASP-1-0.794-0.92525.590-0.205-0.2050.0000.0000.0000.000
44A136PRO0-0.019-0.00321.104-0.012-0.0120.0000.0000.0000.000
45A137VAL00.0380.02221.245-0.034-0.0340.0000.0000.0000.000
46A138GLY00.0130.00922.541-0.016-0.0160.0000.0000.0000.000
47A139LEU0-0.022-0.02518.540-0.012-0.0120.0000.0000.0000.000
48A140LEU00.0040.02917.466-0.042-0.0420.0000.0000.0000.000
49A141LEU00.0090.00618.843-0.028-0.0280.0000.0000.0000.000
50A142GLN0-0.055-0.03020.475-0.014-0.0140.0000.0000.0000.000
51A143HIS0-0.0090.00715.663-0.059-0.0590.0000.0000.0000.000
52A144ARG10.8380.92514.9060.2610.2610.0000.0000.0000.000
53A145ALA00.0150.00614.143-0.022-0.0220.0000.0000.0000.000
54A146ASP-1-0.772-0.83910.929-0.895-0.8950.0000.0000.0000.000
55A147LEU0-0.003-0.00613.9370.0510.0510.0000.0000.0000.000
56A148ALA00.0050.01116.291-0.007-0.0070.0000.0000.0000.000
57A149ILE0-0.0270.00519.3960.0210.0210.0000.0000.0000.000
58A150VAL0-0.009-0.01221.9330.0030.0030.0000.0000.0000.000
59A151SER00.0350.00225.3900.0050.0050.0000.0000.0000.000
60A152GLU-1-0.909-0.95028.654-0.101-0.1010.0000.0000.0000.000
61A153ALA0-0.0160.00028.346-0.011-0.0110.0000.0000.0000.000
62A154GLU-1-0.898-0.93329.328-0.141-0.1410.0000.0000.0000.000
63A155LYS10.9370.94729.6220.0940.0940.0000.0000.0000.000
64A156GLN00.019-0.00227.194-0.008-0.0080.0000.0000.0000.000
65A157ASN0-0.060-0.03728.2050.0000.0000.0000.0000.0000.000
66A158GLY00.0290.01524.906-0.006-0.0060.0000.0000.0000.000
67A159ILE00.0090.03322.008-0.027-0.0270.0000.0000.0000.000
68A160SER0-0.013-0.00522.0400.0180.0180.0000.0000.0000.000
69A161PHE00.0090.00622.797-0.014-0.0140.0000.0000.0000.000
70A162GLN00.0380.02120.9200.0230.0230.0000.0000.0000.000
71A163PRO00.0080.01524.508-0.006-0.0060.0000.0000.0000.000
72A164LEU0-0.030-0.00521.8550.0000.0000.0000.0000.0000.000
73A165PHE00.041-0.00425.1820.0100.0100.0000.0000.0000.000
74A166ALA0-0.0040.01129.301-0.007-0.0070.0000.0000.0000.000
75A167TYR00.0630.02029.1020.0040.0040.0000.0000.0000.000
76A168GLU-1-0.872-0.92234.357-0.050-0.0500.0000.0000.0000.000
77A169MET0-0.067-0.02934.673-0.001-0.0010.0000.0000.0000.000
78A170VAL00.0110.00837.5460.0020.0020.0000.0000.0000.000
79A171GLY00.0290.01439.885-0.003-0.0030.0000.0000.0000.000
80A172ILE0-0.032-0.02039.2080.0030.0030.0000.0000.0000.000
81A173CYS0-0.023-0.01942.975-0.001-0.0010.0000.0000.0000.000
82A174ALA00.0320.01746.0210.0010.0010.0000.0000.0000.000
83A175PRO00.0380.00747.3890.0000.0000.0000.0000.0000.000
84A176ASP-1-0.909-0.94350.143-0.021-0.0210.0000.0000.0000.000
85A177HIS0-0.114-0.05849.5170.0010.0010.0000.0000.0000.000
86A178PRO00.031-0.00752.0430.0010.0010.0000.0000.0000.000
87A179LEU00.0340.01548.9920.0010.0010.0000.0000.0000.000
88A180ALA00.0190.02350.570-0.001-0.0010.0000.0000.0000.000
89A181ALA0-0.034-0.00651.5210.0010.0010.0000.0000.0000.000
90A182LYS10.7940.89252.0840.0350.0350.0000.0000.0000.000
91A183ASN00.014-0.00750.978-0.001-0.0010.0000.0000.0000.000
92A184VAL00.0110.00748.456-0.001-0.0010.0000.0000.0000.000
93A185TRP0-0.060-0.03544.6020.0000.0000.0000.0000.0000.000
94A186THR00.008-0.02247.906-0.002-0.0020.0000.0000.0000.000
95A187ALA00.0580.01047.4480.0000.0000.0000.0000.0000.000
96A188GLU-1-0.781-0.89848.434-0.045-0.0450.0000.0000.0000.000
97A189ASP-1-0.806-0.85250.020-0.035-0.0350.0000.0000.0000.000
98A190PHE00.005-0.01443.6290.0000.0000.0000.0000.0000.000
99A191ILE0-0.056-0.01248.395-0.001-0.0010.0000.0000.0000.000
100A192GLY0-0.019-0.00450.773-0.001-0.0010.0000.0000.0000.000
101A193GLU-1-0.857-0.93047.845-0.037-0.0370.0000.0000.0000.000
102A194THR0-0.0200.00044.339-0.002-0.0020.0000.0000.0000.000
103A195LEU0-0.010-0.01440.7160.0010.0010.0000.0000.0000.000
104A196ILE0-0.045-0.03938.221-0.002-0.0020.0000.0000.0000.000
105A197THR0-0.009-0.00135.9190.0010.0010.0000.0000.0000.000
106A198TYR00.039-0.00130.9870.0030.0030.0000.0000.0000.000
107A199PRO0-0.066-0.02231.0800.0030.0030.0000.0000.0000.000
108A200VAL00.0370.02429.091-0.007-0.0070.0000.0000.0000.000
109A201PRO00.0160.01031.2000.0080.0080.0000.0000.0000.000
110A202ASP-1-0.761-0.89833.960-0.081-0.0810.0000.0000.0000.000
111A203GLU-1-0.896-0.92232.702-0.108-0.1080.0000.0000.0000.000
112A204MET0-0.031-0.01527.099-0.003-0.0030.0000.0000.0000.000
113A205LEU0-0.051-0.02131.7380.0020.0020.0000.0000.0000.000
114A206ASP-1-0.735-0.85534.393-0.089-0.0890.0000.0000.0000.000
115A207LEU0-0.0120.00635.9640.0030.0030.0000.0000.0000.000
116A208PRO00.010-0.01637.7530.0030.0030.0000.0000.0000.000
117A209LYS10.8640.94032.8570.1150.1150.0000.0000.0000.000
118A210LYS10.8410.90834.8960.0890.0890.0000.0000.0000.000
119A211ILE0-0.049-0.02240.3960.0040.0040.0000.0000.0000.000
120A212LEU0-0.052-0.02042.8000.0030.0030.0000.0000.0000.000
121A213ILE00.0390.02740.8630.0030.0030.0000.0000.0000.000
122A214PRO0-0.015-0.00242.8750.0020.0020.0000.0000.0000.000
123A215LYS10.8150.89845.8110.0490.0490.0000.0000.0000.000
124A216ASN0-0.057-0.03047.6060.0010.0010.0000.0000.0000.000
125A217ILE0-0.045-0.01547.0250.0020.0020.0000.0000.0000.000
126A218ASN00.0290.01744.283-0.005-0.0050.0000.0000.0000.000
127A219PRO00.0270.03744.3400.0010.0010.0000.0000.0000.000
128A220PRO00.0140.00745.172-0.003-0.0030.0000.0000.0000.000
129A221ARG10.8190.89340.1600.0680.0680.0000.0000.0000.000
130A222ARG10.9320.96440.6740.0500.0500.0000.0000.0000.000
131A223HIS0-0.013-0.01135.727-0.001-0.0010.0000.0000.0000.000
132A224SER0-0.030-0.02534.6090.0040.0040.0000.0000.0000.000
133A225GLU-1-0.765-0.88429.181-0.112-0.1120.0000.0000.0000.000
134A226LEU0-0.037-0.01029.043-0.002-0.0020.0000.0000.0000.000
135A227THR00.1280.05230.5270.0020.0020.0000.0000.0000.000
136A228ILE00.0380.02032.4410.0040.0040.0000.0000.0000.000
137A229ALA0-0.0110.00134.7610.0040.0040.0000.0000.0000.000
138A230ILE00.0100.00934.3160.0030.0030.0000.0000.0000.000
139A231ILE00.0150.00936.1660.0030.0030.0000.0000.0000.000
140A232GLN00.0230.01439.1620.0040.0040.0000.0000.0000.000
141A233LEU0-0.034-0.00139.4120.0030.0030.0000.0000.0000.000
142A234VAL0-0.0030.00841.1010.0020.0020.0000.0000.0000.000
143A235ALA00.0290.01143.2730.0020.0020.0000.0000.0000.000
144A236SER0-0.062-0.02344.9160.0030.0030.0000.0000.0000.000
145A237ARG10.8770.93047.0730.0280.0280.0000.0000.0000.000
146A238ARG10.8170.90844.7890.0320.0320.0000.0000.0000.000
147A239GLY00.0410.02244.913-0.002-0.0020.0000.0000.0000.000
148A240ILE00.0000.01344.1940.0020.0020.0000.0000.0000.000
149A241ALA00.0110.00638.736-0.003-0.0030.0000.0000.0000.000
150A242ALA00.0040.00938.6590.0030.0030.0000.0000.0000.000
151A243LEU0-0.023-0.01533.695-0.004-0.0040.0000.0000.0000.000
152A244PRO00.0740.03631.4570.0030.0030.0000.0000.0000.000
153A245TYR0-0.027-0.01434.6280.0040.0040.0000.0000.0000.000
154A246TRP00.0240.00428.4290.0050.0050.0000.0000.0000.000
155A247THR0-0.012-0.00631.2560.0030.0030.0000.0000.0000.000
156A248VAL0-0.004-0.01333.3890.0040.0040.0000.0000.0000.000
157A249MET00.0180.02736.1510.0030.0030.0000.0000.0000.000
158A250PRO00.0500.02034.1170.0030.0030.0000.0000.0000.000
159A251TYR0-0.024-0.03133.2950.0050.0050.0000.0000.0000.000
160A252LEU0-0.043-0.00339.6370.0010.0010.0000.0000.0000.000
161A253GLU-1-0.900-0.95338.976-0.016-0.0160.0000.0000.0000.000
162A254LYS10.8030.90737.8500.0210.0210.0000.0000.0000.000
163A255GLY00.0140.02243.3320.0010.0010.0000.0000.0000.000
164A256TYR0-0.053-0.02539.699-0.001-0.0010.0000.0000.0000.000
165A257VAL00.001-0.00641.156-0.001-0.0010.0000.0000.0000.000
166A258VAL0-0.0160.00144.4540.0020.0020.0000.0000.0000.000
167A259HIS00.0390.00642.298-0.004-0.0040.0000.0000.0000.000
168A260ARG10.8260.90944.2140.0330.0330.0000.0000.0000.000
169A261GLN00.0000.01144.172-0.001-0.0010.0000.0000.0000.000
170A262ILE00.0010.00340.8160.0010.0010.0000.0000.0000.000
171A263THR0-0.001-0.01844.307-0.001-0.0010.0000.0000.0000.000
172A264ALA0-0.033-0.02546.9270.0010.0010.0000.0000.0000.000
173A265ASP-1-0.907-0.95145.515-0.045-0.0450.0000.0000.0000.000
174A266GLY0-0.0010.02043.413-0.001-0.0010.0000.0000.0000.000
175A267LEU0-0.032-0.01737.609-0.002-0.0020.0000.0000.0000.000
176A268GLN00.0320.02835.688-0.003-0.0030.0000.0000.0000.000
177A269SER0-0.032-0.03631.985-0.002-0.0020.0000.0000.0000.000
178A270LYS10.8860.92831.6310.0830.0830.0000.0000.0000.000
179A271LEU00.0310.01925.699-0.007-0.0070.0000.0000.0000.000
180A272TYR00.021-0.00525.4650.0100.0100.0000.0000.0000.000
181A273ALA00.0160.01919.913-0.008-0.0080.0000.0000.0000.000
182A274ALA0-0.016-0.01521.1890.0100.0100.0000.0000.0000.000
183A275ILE00.0400.01317.125-0.030-0.0300.0000.0000.0000.000
184A276ARG10.8360.90713.7740.5840.5840.0000.0000.0000.000
185A277THR0-0.046-0.04619.482-0.001-0.0010.0000.0000.0000.000
186A278GLU-1-0.878-0.95217.582-0.381-0.3810.0000.0000.0000.000
187A279ASP-1-0.790-0.87114.961-0.588-0.5880.0000.0000.0000.000
188A280THR0-0.049-0.02916.842-0.001-0.0010.0000.0000.0000.000
189A281ASP-1-0.886-0.93718.504-0.182-0.1820.0000.0000.0000.000
190A282LYS10.8060.90311.3150.7060.7060.0000.0000.0000.000
191A283SER00.018-0.00313.9380.0150.0150.0000.0000.0000.000
192A284TYR00.016-0.0089.2410.0610.0610.0000.0000.0000.000
193A285LEU00.0240.03012.3250.0200.0200.0000.0000.0000.000
194A286ASN0-0.011-0.01314.4890.0530.0530.0000.0000.0000.000
195A287ASN0-0.028-0.01714.6960.0320.0320.0000.0000.0000.000
196A288PHE00.0570.02313.9730.0240.0240.0000.0000.0000.000
197A289CYS0-0.033-0.01515.9180.0190.0190.0000.0000.0000.000
198A290GLN0-0.083-0.04719.0760.0070.0070.0000.0000.0000.000
199A291ILE00.0350.04015.5590.0130.0130.0000.0000.0000.000
200A292ILE0-0.009-0.00718.4390.0140.0140.0000.0000.0000.000
201A293ARG10.8090.89321.2520.1330.1330.0000.0000.0000.000
202A294GLU-1-0.894-0.93922.565-0.030-0.0300.0000.0000.0000.000
203A295ARG10.8590.91220.0420.0260.0260.0000.0000.0000.000
204A296GLY00.0280.01324.2170.0050.0050.0000.0000.0000.000
205A297PHE0-0.040-0.03626.5680.0040.0040.0000.0000.0000.000
206A298ALA0-0.053-0.00527.3800.0050.0050.0000.0000.0000.000
207A299ASP-1-0.974-0.97627.237-0.025-0.0250.0000.0000.0000.000
208A300LEU0-0.045-0.01927.408-0.001-0.0010.0000.0000.0000.000
209A301PRO0-0.022-0.00931.1000.0000.0000.0000.0000.0000.000
210A302GLY00.001-0.02234.754-0.003-0.0030.0000.0000.0000.000
211A303LEU0-0.0420.00129.011-0.004-0.0040.0000.0000.0000.000
212A304SER0-0.041-0.02333.3940.0040.0040.0000.0000.0000.000
213A305GLU-1-0.914-0.96131.803-0.058-0.0580.0000.0000.0000.000
214A306LEU0-0.082-0.02829.5090.0020.0020.0000.0000.0000.000
215A307GLU-1-0.977-0.98431.446-0.072-0.0720.0000.0000.0000.000