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: K9613

Calculation Name: 3ZSF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZSF

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F9M1

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2680560.629238
FMO2-HF: Nuclear repulsion 2592833.48194
FMO2-HF: Total energy -87727.147298
FMO2-MP2: Total energy -87988.139306


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:39:GLY)


Summations of interaction energy for fragment #1(A:39: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.
-7.172-2.6281.181-2.668-3.058-1.7347234759768E-18
Interaction energy analysis for fragmet #1(A:39:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.013
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].
3A41LEU00.0220.0113.8391.6172.2870.006-0.381-0.2960.001
4A42ILE00.0270.0136.6050.5840.5840.0000.0000.0000.000
5A43GLU-1-0.824-0.8702.848-3.253-1.3730.472-1.216-1.136-0.010
6A44ARG10.7390.8352.919-3.751-1.7570.703-1.071-1.6260.009
7A45ILE00.0150.0145.554-0.401-0.4010.0000.0000.0000.000
8A46ASN00.0200.0118.207-0.081-0.0810.0000.0000.0000.000
9A47ASN0-0.029-0.0145.306-0.431-0.4310.0000.0000.0000.000
10A48LYS10.7540.8678.481-0.642-0.6420.0000.0000.0000.000
11A49GLY00.0430.0366.651-0.005-0.0050.0000.0000.0000.000
12A50THR0-0.057-0.0256.905-0.672-0.6720.0000.0000.0000.000
13A51VAL00.0310.0207.0950.4690.4690.0000.0000.0000.000
14A52THR0-0.023-0.0339.096-0.157-0.1570.0000.0000.0000.000
15A53VAL00.004-0.01211.440-0.068-0.0680.0000.0000.0000.000
16A54GLY00.0200.02014.9440.0030.0030.0000.0000.0000.000
17A55THR0-0.012-0.02617.5780.0070.0070.0000.0000.0000.000
18A56GLU-1-0.732-0.85921.128-0.008-0.0080.0000.0000.0000.000
19A57GLY0-0.0420.00024.405-0.001-0.0010.0000.0000.0000.000
20A58THR0-0.032-0.04225.4850.0020.0020.0000.0000.0000.000
21A59TYR00.0220.01828.222-0.004-0.0040.0000.0000.0000.000
22A60ALA0-0.0090.01029.6970.0050.0050.0000.0000.0000.000
23A61PRO0-0.0040.00731.868-0.004-0.0040.0000.0000.0000.000
24A62PHE00.012-0.00827.6100.0080.0080.0000.0000.0000.000
25A63THR0-0.035-0.04623.5460.0110.0110.0000.0000.0000.000
26A64TYR0-0.0220.00126.420-0.008-0.0080.0000.0000.0000.000
27A65HIS10.8030.87224.867-0.056-0.0560.0000.0000.0000.000
28A66ASP-1-0.805-0.90829.0740.0730.0730.0000.0000.0000.000
29A67LYS10.8020.86531.741-0.061-0.0610.0000.0000.0000.000
30A68ASP-1-0.828-0.88131.8370.0620.0620.0000.0000.0000.000
31A69GLY00.0160.01729.8990.0030.0030.0000.0000.0000.000
32A70LYS10.8440.93525.309-0.111-0.1110.0000.0000.0000.000
33A71LEU0-0.0310.00421.360-0.005-0.0050.0000.0000.0000.000
34A72THR0-0.010-0.05424.8340.0150.0150.0000.0000.0000.000
35A73GLY00.0610.02726.611-0.007-0.0070.0000.0000.0000.000
36A74TYR0-0.034-0.03226.4030.0120.0120.0000.0000.0000.000
37A75ASP-1-0.701-0.81523.2810.0520.0520.0000.0000.0000.000
38A76VAL0-0.0100.02421.8120.0150.0150.0000.0000.0000.000
39A77GLU-1-0.726-0.83121.7710.1540.1540.0000.0000.0000.000
40A78VAL00.0120.01022.1370.0150.0150.0000.0000.0000.000
41A79THR0-0.031-0.03017.2690.0140.0140.0000.0000.0000.000
42A80ARG10.7350.84418.277-0.125-0.1250.0000.0000.0000.000
43A81ALA00.0390.03019.4580.0290.0290.0000.0000.0000.000
44A82VAL00.002-0.00316.6720.0130.0130.0000.0000.0000.000
45A83ALA0-0.029-0.01915.2560.0290.0290.0000.0000.0000.000
46A84GLU-1-0.917-0.96715.9990.2640.2640.0000.0000.0000.000
47A85LYS10.8200.90718.485-0.139-0.1390.0000.0000.0000.000
48A86LEU0-0.037-0.01413.3780.0040.0040.0000.0000.0000.000
49A87GLY00.0170.02414.0520.0770.0770.0000.0000.0000.000
50A88VAL0-0.074-0.02710.5950.1260.1260.0000.0000.0000.000
51A89LYS10.8930.93310.948-0.820-0.8200.0000.0000.0000.000
52A90VAL00.009-0.00511.6450.1070.1070.0000.0000.0000.000
53A91GLU-1-0.851-0.90311.9240.3750.3750.0000.0000.0000.000
54A92PHE00.0190.00114.105-0.018-0.0180.0000.0000.0000.000
55A93LYS10.8190.90112.576-0.182-0.1820.0000.0000.0000.000
56A94GLU-1-0.775-0.87617.1970.0500.0500.0000.0000.0000.000
57A95THR0-0.036-0.01919.986-0.015-0.0150.0000.0000.0000.000
58A96GLN00.0430.02322.4800.0060.0060.0000.0000.0000.000
59A97TRP00.0300.00224.174-0.010-0.0100.0000.0000.0000.000
60A98ASP-1-0.887-0.94324.037-0.057-0.0570.0000.0000.0000.000
61A99SER0-0.028-0.02322.269-0.018-0.0180.0000.0000.0000.000
62A100MET0-0.0550.00719.917-0.010-0.0100.0000.0000.0000.000
63A101MET00.0190.00719.171-0.014-0.0140.0000.0000.0000.000
64A102ALA0-0.008-0.01319.813-0.025-0.0250.0000.0000.0000.000
65A103GLY0-0.031-0.02317.588-0.027-0.0270.0000.0000.0000.000
66A104LEU00.0070.01614.029-0.036-0.0360.0000.0000.0000.000
67A105LYS10.9640.99614.7960.1480.1480.0000.0000.0000.000
68A106ALA0-0.081-0.03215.943-0.031-0.0310.0000.0000.0000.000
69A107GLY00.0090.00711.763-0.037-0.0370.0000.0000.0000.000
70A108ARG10.8890.95010.7790.1300.1300.0000.0000.0000.000
71A109PHE0-0.011-0.01610.9890.0650.0650.0000.0000.0000.000
72A110ASP-1-0.785-0.8387.6470.0540.0540.0000.0000.0000.000
73A111VAL0-0.022-0.00710.714-0.039-0.0390.0000.0000.0000.000
74A112VAL0-0.031-0.00814.3340.0050.0050.0000.0000.0000.000
75A113ALA00.0360.01817.9410.0040.0040.0000.0000.0000.000
76A114ASN0-0.020-0.03420.6140.0130.0130.0000.0000.0000.000
77A115GLN0-0.007-0.02323.961-0.016-0.0160.0000.0000.0000.000
78A116VAL00.0200.02322.876-0.007-0.0070.0000.0000.0000.000
79A117GLY00.0680.02825.3210.0000.0000.0000.0000.0000.000
80A118LEU0-0.044-0.01922.478-0.001-0.0010.0000.0000.0000.000
81A119THR00.0520.03026.492-0.006-0.0060.0000.0000.0000.000
82A120SER0-0.0020.01829.112-0.003-0.0030.0000.0000.0000.000
83A121PRO00.1030.03328.311-0.007-0.0070.0000.0000.0000.000
84A122GLU-1-0.823-0.88427.822-0.088-0.0880.0000.0000.0000.000
85A123ARG10.8060.87224.5380.0700.0700.0000.0000.0000.000
86A124GLN0-0.004-0.00323.619-0.013-0.0130.0000.0000.0000.000
87A125ALA0-0.0120.00323.875-0.008-0.0080.0000.0000.0000.000
88A126THR0-0.083-0.05221.361-0.014-0.0140.0000.0000.0000.000
89A127PHE0-0.031-0.01218.184-0.025-0.0250.0000.0000.0000.000
90A128ASP-1-0.825-0.89717.786-0.147-0.1470.0000.0000.0000.000
91A129LYS10.8060.88119.1760.0220.0220.0000.0000.0000.000
92A130SER0-0.039-0.02019.266-0.002-0.0020.0000.0000.0000.000
93A131GLU-1-0.810-0.90520.8230.0220.0220.0000.0000.0000.000
94A132PRO0-0.053-0.01423.5360.0090.0090.0000.0000.0000.000
95A133TYR0-0.003-0.03321.6880.0060.0060.0000.0000.0000.000
96A134SER0-0.0100.00926.1640.0060.0060.0000.0000.0000.000
97A135TRP00.0180.01329.504-0.008-0.0080.0000.0000.0000.000
98A136SER00.002-0.01032.3410.0040.0040.0000.0000.0000.000
99A137GLY00.032-0.00334.951-0.003-0.0030.0000.0000.0000.000
100A138ALA0-0.0100.00937.9330.0010.0010.0000.0000.0000.000
101A139VAL00.0010.00741.2640.0010.0010.0000.0000.0000.000
102A140LEU0-0.025-0.00643.882-0.002-0.0020.0000.0000.0000.000
103A141VAL00.0090.00646.0260.0020.0020.0000.0000.0000.000
104A142ALA00.0380.01348.879-0.002-0.0020.0000.0000.0000.000
105A143HIS00.017-0.00152.5430.0020.0020.0000.0000.0000.000
106A144ASN00.0430.00653.2900.0000.0000.0000.0000.0000.000
107A145ASP-1-0.811-0.88055.7680.0080.0080.0000.0000.0000.000
108A146SER0-0.0010.01955.6790.0000.0000.0000.0000.0000.000
109A147ASN00.0350.01756.8060.0010.0010.0000.0000.0000.000
110A148ILE00.0140.01453.3020.0000.0000.0000.0000.0000.000
111A149LYS10.8130.89352.720-0.005-0.0050.0000.0000.0000.000
112A150SER0-0.029-0.03750.7090.0000.0000.0000.0000.0000.000
113A151ILE00.0430.01447.4010.0000.0000.0000.0000.0000.000
114A152ALA00.0070.01051.303-0.001-0.0010.0000.0000.0000.000
115A153ASP-1-0.827-0.89254.8310.0040.0040.0000.0000.0000.000
116A154ILE00.0380.01351.2700.0000.0000.0000.0000.0000.000
117A155LYS10.8850.95755.4220.0040.0040.0000.0000.0000.000
118A156GLY0-0.008-0.01257.6400.0000.0000.0000.0000.0000.000
119A157VAL0-0.029-0.00457.1430.0000.0000.0000.0000.0000.000
120A158LYS10.8940.94857.010-0.001-0.0010.0000.0000.0000.000
121A159THR00.0070.00051.2010.0010.0010.0000.0000.0000.000
122A160ALA00.0210.02251.975-0.001-0.0010.0000.0000.0000.000
123A161GLN0-0.0100.00447.2390.0010.0010.0000.0000.0000.000
124A162SER00.0670.05846.077-0.001-0.0010.0000.0000.0000.000
125A163LEU00.004-0.01547.672-0.001-0.0010.0000.0000.0000.000
126A164THR0-0.0040.00245.8720.0000.0000.0000.0000.0000.000
127A165SER0-0.0070.00243.298-0.001-0.0010.0000.0000.0000.000
128A166ASN00.046-0.00139.9650.0010.0010.0000.0000.0000.000
129A167TYR00.0390.02038.9270.0000.0000.0000.0000.0000.000
130A168GLY00.0110.01544.8580.0010.0010.0000.0000.0000.000
131A169GLU-1-0.965-0.98745.272-0.013-0.0130.0000.0000.0000.000
132A170LYS10.9710.97941.3950.0080.0080.0000.0000.0000.000
133A171ALA00.0020.01147.0320.0010.0010.0000.0000.0000.000
134A172LYS10.9470.97150.1690.0120.0120.0000.0000.0000.000
135A173ALA0-0.0120.00048.8990.0000.0000.0000.0000.0000.000
136A174ALA00.0030.00550.4430.0000.0000.0000.0000.0000.000
137A175GLY0-0.041-0.01752.0750.0010.0010.0000.0000.0000.000
138A176ALA00.0010.01453.6200.0010.0010.0000.0000.0000.000
139A177GLN0-0.008-0.00255.5920.0000.0000.0000.0000.0000.000
140A178LEU0-0.012-0.01051.6990.0010.0010.0000.0000.0000.000
141A179VAL0-0.005-0.00354.2940.0000.0000.0000.0000.0000.000
142A180PRO0-0.020-0.01152.9390.0000.0000.0000.0000.0000.000
143A181VAL0-0.007-0.01049.5360.0010.0010.0000.0000.0000.000
144A182ASP-1-0.839-0.90647.417-0.002-0.0020.0000.0000.0000.000
145A183GLY0-0.018-0.02545.256-0.001-0.0010.0000.0000.0000.000
146A184LEU00.0010.01242.3600.0000.0000.0000.0000.0000.000
147A185ALA00.0770.05245.5710.0000.0000.0000.0000.0000.000
148A186GLN00.0020.00047.4350.0000.0000.0000.0000.0000.000
149A187SER0-0.056-0.04248.0500.0000.0000.0000.0000.0000.000
150A188LEU00.0240.00646.5860.0000.0000.0000.0000.0000.000
151A189THR00.0600.02750.7440.0000.0000.0000.0000.0000.000
152A190LEU0-0.040-0.03253.3350.0000.0000.0000.0000.0000.000
153A191ILE0-0.058-0.01551.3910.0000.0000.0000.0000.0000.000
154A192GLU-1-0.913-0.96351.9990.0120.0120.0000.0000.0000.000
155A193GLN0-0.062-0.03956.198-0.001-0.0010.0000.0000.0000.000
156A194LYS10.8100.91258.523-0.007-0.0070.0000.0000.0000.000
157A195ARG10.8970.96058.455-0.003-0.0030.0000.0000.0000.000
158A196ALA0-0.067-0.03555.383-0.001-0.0010.0000.0000.0000.000
159A197ASP-1-0.871-0.93956.6910.0050.0050.0000.0000.0000.000
160A198ALA0-0.027-0.03052.0340.0010.0010.0000.0000.0000.000
161A199THR00.008-0.00747.643-0.001-0.0010.0000.0000.0000.000
162A200LEU0-0.0170.00145.9410.0010.0010.0000.0000.0000.000
163A201ASN0-0.006-0.02041.8840.0000.0000.0000.0000.0000.000
164A202ASP-1-0.753-0.85036.5740.0090.0090.0000.0000.0000.000
165A203GLU-1-0.794-0.88137.6270.0220.0220.0000.0000.0000.000
166A204LEU00.0120.00232.6590.0030.0030.0000.0000.0000.000
167A205ALA00.0100.00336.6620.0030.0030.0000.0000.0000.000
168A206VAL0-0.014-0.01038.4050.0010.0010.0000.0000.0000.000
169A207LEU0-0.017-0.00637.9580.0010.0010.0000.0000.0000.000
170A208ASP-1-0.793-0.88236.4620.0310.0310.0000.0000.0000.000
171A209TYR00.0270.00738.6560.0010.0010.0000.0000.0000.000
172A210LEU00.009-0.00842.0300.0000.0000.0000.0000.0000.000
173A211LYS10.8120.93436.884-0.044-0.0440.0000.0000.0000.000
174A212LYS10.7680.86936.627-0.028-0.0280.0000.0000.0000.000
175A213ASN0-0.080-0.02442.832-0.001-0.0010.0000.0000.0000.000
176A214PRO00.0470.01845.702-0.001-0.0010.0000.0000.0000.000
177A215ASN0-0.026-0.02248.0060.0010.0010.0000.0000.0000.000
178A216ALA00.0020.00248.817-0.001-0.0010.0000.0000.0000.000
179A217GLY00.0350.02750.904-0.001-0.0010.0000.0000.0000.000
180A218VAL0-0.059-0.02349.206-0.001-0.0010.0000.0000.0000.000
181A219LYS10.8130.89949.238-0.010-0.0100.0000.0000.0000.000
182A220ILE00.007-0.00243.329-0.001-0.0010.0000.0000.0000.000
183A221VAL0-0.050-0.02947.7320.0010.0010.0000.0000.0000.000
184A222TRP00.0230.00844.548-0.001-0.0010.0000.0000.0000.000
185A223SER0-0.044-0.03742.2860.0020.0020.0000.0000.0000.000
186A224ALA00.0220.02340.4780.0000.0000.0000.0000.0000.000
187A225PRO00.0060.01241.2500.0020.0020.0000.0000.0000.000
188A226ALA00.0380.00437.277-0.001-0.0010.0000.0000.0000.000
189A227ASP-1-0.902-0.94636.739-0.002-0.0020.0000.0000.0000.000
190A228GLU-1-0.913-0.96938.238-0.007-0.0070.0000.0000.0000.000
191A229LYS10.7390.88035.401-0.017-0.0170.0000.0000.0000.000
192A230VAL0-0.017-0.01431.029-0.004-0.0040.0000.0000.0000.000
193A231GLY00.0510.02129.6460.0050.0050.0000.0000.0000.000
194A232SER0-0.040-0.03026.347-0.011-0.0110.0000.0000.0000.000
195A233GLY00.0300.01023.2850.0100.0100.0000.0000.0000.000
196A234LEU0-0.0100.01017.135-0.008-0.0080.0000.0000.0000.000
197A235ILE0-0.036-0.01318.714-0.016-0.0160.0000.0000.0000.000
198A236VAL00.0300.00313.6490.0100.0100.0000.0000.0000.000
199A237ASN00.012-0.01912.8190.0530.0530.0000.0000.0000.000
200A238LYS10.8370.91214.7220.1350.1350.0000.0000.0000.000
201A239GLY00.0180.02414.137-0.061-0.0610.0000.0000.0000.000
202A240ASN0-0.030-0.03110.164-0.190-0.1900.0000.0000.0000.000
203A241ASP-1-0.857-0.92512.645-0.131-0.1310.0000.0000.0000.000
204A242GLU-1-0.886-0.95511.617-0.077-0.0770.0000.0000.0000.000
205A243ALA0-0.013-0.00510.5900.0750.0750.0000.0000.0000.000
206A244VAL00.0100.01212.5880.0550.0550.0000.0000.0000.000
207A245ALA00.0320.03216.2090.0290.0290.0000.0000.0000.000
208A246LYS10.9040.96412.353-0.204-0.2040.0000.0000.0000.000
209A247PHE00.0400.00312.4480.0240.0240.0000.0000.0000.000
210A248SER00.013-0.01517.099-0.001-0.0010.0000.0000.0000.000
211A249THR0-0.049-0.01618.973-0.006-0.0060.0000.0000.0000.000
212A250ALA00.0380.02418.403-0.002-0.0020.0000.0000.0000.000
213A251ILE0-0.027-0.01520.401-0.003-0.0030.0000.0000.0000.000
214A252ASN0-0.015-0.02522.890-0.010-0.0100.0000.0000.0000.000
215A253GLU-1-0.862-0.91921.8710.1580.1580.0000.0000.0000.000
216A254LEU0-0.029-0.00522.168-0.007-0.0070.0000.0000.0000.000
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