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: R8QY8

Calculation Name: 1SZI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SZI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9DBG5

Base Structure: X-ray

Registration Date: 2023-09-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1964309.687718
FMO2-HF: Nuclear repulsion 1888309.362035
FMO2-HF: Total energy -76000.325683
FMO2-MP2: Total energy -76221.925761


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:206:ASN)


Summations of interaction energy for fragment #1(A:206:ASN)
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.
-12.654-4.9851.425-3.699-5.393-0.021
Interaction energy analysis for fragmet #1(A:206:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.002
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].
3A208LEU0-0.001-0.0073.815-1.0190.666-0.014-0.777-0.8940.002
4A209PRO0-0.054-0.0146.755-0.238-0.2380.0000.0000.0000.000
5A210LEU00.005-0.0089.761-0.329-0.3290.0000.0000.0000.000
6A211THR00.0210.01510.9090.2140.2140.0000.0000.0000.000
7A212GLU-1-0.847-0.91711.713-0.604-0.6040.0000.0000.0000.000
8A213ALA00.0350.02012.602-0.165-0.1650.0000.0000.0000.000
9A214GLU-1-0.844-0.93414.0020.4790.4790.0000.0000.0000.000
10A215LEU0-0.056-0.0307.364-0.041-0.0410.0000.0000.0000.000
11A216ALA00.012-0.00211.935-0.174-0.1740.0000.0000.0000.000
12A217LEU0-0.062-0.01713.752-0.049-0.0490.0000.0000.0000.000
13A218ILE0-0.039-0.01312.0810.0370.0370.0000.0000.0000.000
14A219ALA0-0.033-0.00811.834-0.083-0.0830.0000.0000.0000.000
15A220THR0-0.097-0.05512.7140.1880.1880.0000.0000.0000.000
16A221PRO0-0.017-0.01213.055-0.206-0.2060.0000.0000.0000.000
17A222PRO00.0440.00312.1810.1220.1220.0000.0000.0000.000
18A223GLU-1-0.773-0.86514.374-0.631-0.6310.0000.0000.0000.000
19A224ASP-1-0.992-0.98917.370-0.952-0.9520.0000.0000.0000.000
20A225SER0-0.072-0.03616.4650.0030.0030.0000.0000.0000.000
21A226ASP-1-0.756-0.87417.547-0.871-0.8710.0000.0000.0000.000
22A227MET0-0.022-0.03118.661-0.084-0.0840.0000.0000.0000.000
23A228ALA0-0.035-0.00418.904-0.034-0.0340.0000.0000.0000.000
24A229SER00.0260.00214.988-0.073-0.0730.0000.0000.0000.000
25A230LEU0-0.064-0.03014.262-0.185-0.1850.0000.0000.0000.000
26A231GLN00.0400.00714.293-0.031-0.0310.0000.0000.0000.000
27A232GLN0-0.078-0.02011.8790.2020.2020.0000.0000.0000.000
28A233GLN00.0470.0159.750-0.147-0.1470.0000.0000.0000.000
29A234ARG10.8470.93410.1610.6400.6400.0000.0000.0000.000
30A235GLN0-0.012-0.01612.5630.2460.2460.0000.0000.0000.000
31A236GLU-1-0.939-0.9547.960-2.395-2.3950.0000.0000.0000.000
32A237GLN0-0.041-0.0137.027-0.152-0.1520.0000.0000.0000.000
33A238ASN0-0.053-0.0224.876-1.935-1.945-0.001-0.0040.0160.000
34A239TYR0-0.015-0.0346.6780.5330.5330.0000.0000.0000.000
35A240PHE00.0290.0046.837-0.928-0.9280.0000.0000.0000.000
36A241VAL00.0470.0218.8640.3900.3900.0000.0000.0000.000
37A242ARG10.9520.99411.2220.5470.5470.0000.0000.0000.000
38A243LEU00.0280.03010.7610.1350.1350.0000.0000.0000.000
39A244GLY0-0.016-0.04213.4930.1200.1200.0000.0000.0000.000
40A245SER0-0.067-0.03214.5660.0290.0290.0000.0000.0000.000
41A246LEU00.0100.0319.7390.0610.0610.0000.0000.0000.000
42A247SER00.0090.00414.2830.0030.0030.0000.0000.0000.000
43A248GLU-1-0.892-0.95914.8180.3970.3970.0000.0000.0000.000
44A249ARG10.9890.99613.765-0.879-0.8790.0000.0000.0000.000
45A250LEU00.0670.0289.6980.1570.1570.0000.0000.0000.000
46A251ARG10.8920.96010.334-0.079-0.0790.0000.0000.0000.000
47A252ASN00.017-0.00611.539-0.116-0.1160.0000.0000.0000.000
48A253HIS00.0020.0175.883-0.742-0.7420.0000.0000.0000.000
49A254ALA00.015-0.0136.7320.2290.2290.0000.0000.0000.000
50A255TYR0-0.035-0.0157.785-0.253-0.2530.0000.0000.0000.000
51A256GLU-1-0.897-0.94910.3340.6850.6850.0000.0000.0000.000
52A257HIS0-0.047-0.0162.875-2.220-1.2830.127-0.392-0.673-0.002
53A258SER0-0.040-0.0637.356-0.627-0.6270.0000.0000.0000.000
54A259LEU00.0090.0118.516-0.224-0.2240.0000.0000.0000.000
55A260GLY00.0540.02810.142-0.081-0.0810.0000.0000.0000.000
56A261LYS10.8860.9455.1753.4603.4600.0000.0000.0000.000
57A262LEU00.0280.0129.772-0.078-0.0780.0000.0000.0000.000
58A263GLN00.0150.02212.999-0.048-0.0480.0000.0000.0000.000
59A264ASN00.006-0.00210.2400.0890.0890.0000.0000.0000.000
60A265ALA0-0.045-0.00812.795-0.010-0.0100.0000.0000.0000.000
61A266ARG10.9870.99814.4440.2400.2400.0000.0000.0000.000
62A267GLN0-0.066-0.04017.1110.0310.0310.0000.0000.0000.000
63A268LYS10.9620.97812.6930.8090.8090.0000.0000.0000.000
64A269ALA00.024-0.03218.323-0.025-0.0250.0000.0000.0000.000
65A270GLN0-0.051-0.03220.1570.0390.0390.0000.0000.0000.000
66A271GLU-1-0.856-0.92120.788-0.236-0.2360.0000.0000.0000.000
67A272THR00.0410.02321.7480.0100.0100.0000.0000.0000.000
68A273LEU0-0.018-0.00324.2570.0250.0250.0000.0000.0000.000
69A274GLN00.004-0.01325.7270.0240.0240.0000.0000.0000.000
70A275GLN0-0.0060.00424.6290.0040.0040.0000.0000.0000.000
71A276LEU00.0230.01427.6640.0190.0190.0000.0000.0000.000
72A277THR0-0.001-0.00430.3760.0190.0190.0000.0000.0000.000
73A278SER0-0.045-0.02031.6180.0200.0200.0000.0000.0000.000
74A279VAL00.001-0.00232.1310.0120.0120.0000.0000.0000.000
75A280LEU0-0.0050.00734.5210.0100.0100.0000.0000.0000.000
76A281GLY00.0310.01736.3190.0100.0100.0000.0000.0000.000
77A282LEU0-0.027-0.01036.3590.0100.0100.0000.0000.0000.000
78A283MET0-0.014-0.00936.7190.0060.0060.0000.0000.0000.000
79A284GLU-1-0.844-0.90240.539-0.120-0.1200.0000.0000.0000.000
80A285SER0-0.058-0.04542.2260.0080.0080.0000.0000.0000.000
81A286VAL0-0.041-0.02243.0880.0060.0060.0000.0000.0000.000
82A287LYS10.8760.96344.6120.1260.1260.0000.0000.0000.000
83A288GLN0-0.070-0.01746.4060.0060.0060.0000.0000.0000.000
84A321ALA00.009-0.00447.3040.0020.0020.0000.0000.0000.000
85A322LYS10.9340.95846.7670.0860.0860.0000.0000.0000.000
86A323PRO00.0180.01347.126-0.002-0.0020.0000.0000.0000.000
87A324GLU-1-0.835-0.93646.007-0.133-0.1330.0000.0000.0000.000
88A325GLN00.0190.00442.9420.0010.0010.0000.0000.0000.000
89A326VAL0-0.031-0.00841.807-0.010-0.0100.0000.0000.0000.000
90A327GLU-1-0.812-0.91140.729-0.149-0.1490.0000.0000.0000.000
91A328ALA00.0720.03040.016-0.011-0.0110.0000.0000.0000.000
92A329ARG10.9230.97537.1370.1410.1410.0000.0000.0000.000
93A330ALA0-0.006-0.00236.060-0.013-0.0130.0000.0000.0000.000
94A331LEU00.0460.02735.308-0.016-0.0160.0000.0000.0000.000
95A332SER0-0.095-0.06234.541-0.020-0.0200.0000.0000.0000.000
96A333MET00.0510.03231.210-0.015-0.0150.0000.0000.0000.000
97A334PHE0-0.035-0.02630.798-0.020-0.0200.0000.0000.0000.000
98A335ARG10.8840.93930.6280.2330.2330.0000.0000.0000.000
99A336ASP-1-0.850-0.91927.716-0.374-0.3740.0000.0000.0000.000
100A337ILE0-0.028-0.00626.225-0.036-0.0360.0000.0000.0000.000
101A338THR0-0.015-0.01125.569-0.033-0.0330.0000.0000.0000.000
102A339GLN0-0.004-0.00324.507-0.046-0.0460.0000.0000.0000.000
103A340GLN00.0080.00422.047-0.027-0.0270.0000.0000.0000.000
104A341LEU00.0190.00020.980-0.073-0.0730.0000.0000.0000.000
105A342GLN00.023-0.00221.767-0.028-0.0280.0000.0000.0000.000
106A343SER0-0.018-0.00118.298-0.055-0.0550.0000.0000.0000.000
107A344MET0-0.0630.01617.286-0.115-0.1150.0000.0000.0000.000
108A345CYS0-0.045-0.01217.482-0.043-0.0430.0000.0000.0000.000
109A346VAL0-0.005-0.00717.156-0.025-0.0250.0000.0000.0000.000
110A347ALA00.0000.01113.522-0.087-0.0870.0000.0000.0000.000
111A348LEU00.0330.00214.627-0.076-0.0760.0000.0000.0000.000
112A349GLY0-0.025-0.02315.9780.0250.0250.0000.0000.0000.000
113A350ALA00.0050.00113.5820.0410.0410.0000.0000.0000.000
114A351SER0-0.055-0.01811.595-0.123-0.1230.0000.0000.0000.000
115A352ILE00.0030.02213.0300.1060.1060.0000.0000.0000.000
116A353GLN00.0590.02114.7840.0670.0670.0000.0000.0000.000
117A354GLY00.0110.00715.576-0.038-0.0380.0000.0000.0000.000
118A355LEU0-0.046-0.01416.4890.0930.0930.0000.0000.0000.000
119A356PRO00.0020.00119.349-0.012-0.0120.0000.0000.0000.000
120A357SER00.0830.02723.106-0.019-0.0190.0000.0000.0000.000
121A358HIS00.0340.02525.322-0.020-0.0200.0000.0000.0000.000
122A359VAL0-0.012-0.00420.9670.0040.0040.0000.0000.0000.000
123A360ARG10.7850.84619.5360.6180.6180.0000.0000.0000.000
124A361GLU-1-0.914-0.95123.126-0.310-0.3100.0000.0000.0000.000
125A362GLN00.0530.03025.926-0.004-0.0040.0000.0000.0000.000
126A363ALA00.0220.01221.753-0.002-0.0020.0000.0000.0000.000
127A364GLN0-0.042-0.02623.5170.0080.0080.0000.0000.0000.000
128A365GLN00.0310.00925.2820.0050.0050.0000.0000.0000.000
129A366ALA00.0610.04925.5120.0100.0100.0000.0000.0000.000
130A367ARG10.9450.97520.2290.7300.7300.0000.0000.0000.000
131A368SER0-0.012-0.02025.252-0.009-0.0090.0000.0000.0000.000
132A369GLN0-0.0020.01128.5080.0200.0200.0000.0000.0000.000
133A370VAL0-0.004-0.00625.7000.0190.0190.0000.0000.0000.000
134A371ASN00.0110.00326.180-0.005-0.0050.0000.0000.0000.000
135A372ASP-1-0.883-0.93429.249-0.290-0.2900.0000.0000.0000.000
136A373LEU0-0.067-0.03130.0250.0230.0230.0000.0000.0000.000
137A374GLN0-0.046-0.02228.3780.0460.0460.0000.0000.0000.000
138A375ALA00.0150.00631.7500.0130.0130.0000.0000.0000.000
139A376THR0-0.0170.00034.3300.0190.0190.0000.0000.0000.000
140A377PHE00.043-0.00334.4570.0140.0140.0000.0000.0000.000
141A378SER0-0.093-0.02235.2410.0060.0060.0000.0000.0000.000
142A379GLY0-0.004-0.00836.8120.0050.0050.0000.0000.0000.000
143A380ILE0-0.071-0.01238.3250.0120.0120.0000.0000.0000.000
144A381HIS0-0.006-0.02639.886-0.010-0.0100.0000.0000.0000.000
145A382SER00.0140.01242.2660.0060.0060.0000.0000.0000.000
146A383PHE00.0220.00540.831-0.004-0.0040.0000.0000.0000.000
147A384GLN0-0.011-0.02344.3570.0070.0070.0000.0000.0000.000
148A385ASP-1-0.804-0.89943.334-0.157-0.1570.0000.0000.0000.000
149A386LEU0-0.042-0.00139.809-0.005-0.0050.0000.0000.0000.000
150A387SER0-0.017-0.01843.3340.0090.0090.0000.0000.0000.000
151A388ALA00.0610.01744.002-0.004-0.0040.0000.0000.0000.000
152A389GLY00.0170.00743.798-0.002-0.0020.0000.0000.0000.000
153A390VAL00.0140.01039.625-0.006-0.0060.0000.0000.0000.000
154A391LEU00.0180.01439.291-0.012-0.0120.0000.0000.0000.000
155A392ALA00.0020.00438.907-0.004-0.0040.0000.0000.0000.000
156A393GLN00.0180.00537.313-0.010-0.0100.0000.0000.0000.000
157A394THR00.005-0.00634.286-0.018-0.0180.0000.0000.0000.000
158A395ARG10.8500.91234.0070.1290.1290.0000.0000.0000.000
159A396GLU-1-0.818-0.88533.824-0.196-0.1960.0000.0000.0000.000
160A397ARG10.8570.91831.7140.2380.2380.0000.0000.0000.000
161A398ILE0-0.028-0.00729.300-0.019-0.0190.0000.0000.0000.000
162A399ALA0-0.017-0.00829.083-0.011-0.0110.0000.0000.0000.000
163A400ARG10.8870.92229.4740.2210.2210.0000.0000.0000.000
164A401ALA0-0.022-0.00725.560-0.017-0.0170.0000.0000.0000.000
165A402ARG10.8950.93925.0760.1910.1910.0000.0000.0000.000
166A403GLU-1-0.929-0.95225.293-0.203-0.2030.0000.0000.0000.000
167A404ALA00.0650.03824.5710.0000.0000.0000.0000.0000.000
168A405LEU0-0.065-0.03819.243-0.023-0.0230.0000.0000.0000.000
169A406ASP-1-0.871-0.94021.314-0.213-0.2130.0000.0000.0000.000
170A407ASN0-0.013-0.00222.863-0.003-0.0030.0000.0000.0000.000
171A408THR0-0.020-0.02218.221-0.005-0.0050.0000.0000.0000.000
172A409VAL0-0.046-0.03817.1950.0030.0030.0000.0000.0000.000
173A410GLU-1-0.906-0.95518.942-0.072-0.0720.0000.0000.0000.000
174A411TYR00.0010.01519.9140.0260.0260.0000.0000.0000.000
175A412VAL0-0.051-0.02014.6300.0340.0340.0000.0000.0000.000
176A413ALA0-0.020-0.00217.3490.0560.0560.0000.0000.0000.000
177A414GLN0-0.034-0.00318.3090.0510.0510.0000.0000.0000.000
178A415ASN0-0.078-0.04919.2990.0180.0180.0000.0000.0000.000
179A416THR00.0150.01415.4620.0200.0200.0000.0000.0000.000
180A417PRO0-0.007-0.00615.763-0.001-0.0010.0000.0000.0000.000
181A418ALA00.0900.04416.201-0.047-0.0470.0000.0000.0000.000
182A419MET0-0.004-0.00216.662-0.026-0.0260.0000.0000.0000.000
183A420TRP0-0.049-0.03312.204-0.006-0.0060.0000.0000.0000.000
184A421LEU0-0.023-0.00311.7730.0670.0670.0000.0000.0000.000
185A422VAL00.0060.0186.894-0.212-0.2120.0000.0000.0000.000
186A423GLY00.0240.0275.3590.1080.1080.0000.0000.0000.000
187A424PRO0-0.091-0.0513.3280.1430.7120.007-0.125-0.4510.000
188A425PHE0-0.019-0.0312.559-7.993-4.9121.274-1.780-2.575-0.022
189A426ALA00.0670.0313.542-0.3461.0380.033-0.613-0.8030.001
190A427PRO00.0210.0265.2621.2821.305-0.001-0.008-0.0130.000
191A428GLY0-0.050-0.0517.1760.8670.8670.0000.0000.0000.000
192A429ILE0-0.023-0.0108.279-0.015-0.0150.0000.0000.0000.000
193A430THR0-0.029-0.01211.991-0.190-0.1900.0000.0000.0000.000
194A431GLU-1-0.927-0.95314.0030.2560.2560.0000.0000.0000.000