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: QY39Y

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2673335.699088
FMO2-HF: Nuclear repulsion 2585609.083047
FMO2-HF: Total energy -87726.616041
FMO2-MP2: Total energy -87987.459203


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.
-4.21-1.1260.261-1.57-1.7740.003
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 : 0.019 / q_NPA : 0.004
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].
3A41LEU00.016-0.0023.8281.5322.1730.001-0.359-0.2820.001
4A42ILE00.0320.0136.6440.5780.5780.0000.0000.0000.000
5A43GLU-1-0.815-0.8633.278-2.170-1.1380.076-0.556-0.552-0.003
6A44ARG10.7770.8643.374-1.709-0.2980.184-0.655-0.9400.005
7A45ILE0-0.016-0.0035.594-0.274-0.2740.0000.0000.0000.000
8A46ASN00.022-0.0018.263-0.049-0.0490.0000.0000.0000.000
9A47ASN0-0.037-0.0095.224-0.428-0.4280.0000.0000.0000.000
10A48LYS10.7470.8698.522-0.570-0.5700.0000.0000.0000.000
11A49GLY00.0730.0497.0480.0600.0600.0000.0000.0000.000
12A50THR0-0.043-0.0256.993-0.623-0.6230.0000.0000.0000.000
13A51VAL00.0090.0067.3590.3010.3010.0000.0000.0000.000
14A52THR0-0.044-0.0349.206-0.110-0.1100.0000.0000.0000.000
15A53VAL00.018-0.00611.527-0.070-0.0700.0000.0000.0000.000
16A54GLY00.0040.00815.0820.0080.0080.0000.0000.0000.000
17A55THR0-0.026-0.03117.5990.0070.0070.0000.0000.0000.000
18A56GLU-1-0.763-0.88821.191-0.019-0.0190.0000.0000.0000.000
19A57GLY0-0.0180.00724.3500.0010.0010.0000.0000.0000.000
20A58THR0-0.040-0.03825.6580.0020.0020.0000.0000.0000.000
21A59TYR00.0350.01728.567-0.004-0.0040.0000.0000.0000.000
22A60ALA0-0.0160.01230.0240.0050.0050.0000.0000.0000.000
23A61PRO0-0.028-0.00132.210-0.004-0.0040.0000.0000.0000.000
24A62PHE00.0340.00527.9120.0060.0060.0000.0000.0000.000
25A63THR0-0.023-0.03523.6710.0110.0110.0000.0000.0000.000
26A64TYR0-0.0250.00426.596-0.008-0.0080.0000.0000.0000.000
27A65HIS10.8070.87724.948-0.048-0.0480.0000.0000.0000.000
28A66ASP-1-0.812-0.91329.3330.0660.0660.0000.0000.0000.000
29A67LYS10.8290.88131.890-0.057-0.0570.0000.0000.0000.000
30A68ASP-1-0.842-0.88932.0080.0600.0600.0000.0000.0000.000
31A69GLY00.0090.00730.0240.0030.0030.0000.0000.0000.000
32A70LYS10.8450.93325.359-0.111-0.1110.0000.0000.0000.000
33A71LEU0-0.0350.00921.369-0.005-0.0050.0000.0000.0000.000
34A72THR00.007-0.04325.0300.0130.0130.0000.0000.0000.000
35A73GLY00.0360.01726.667-0.008-0.0080.0000.0000.0000.000
36A74TYR0-0.027-0.03426.8290.0110.0110.0000.0000.0000.000
37A75ASP-1-0.714-0.82523.6840.0320.0320.0000.0000.0000.000
38A76VAL0-0.0220.00621.6720.0110.0110.0000.0000.0000.000
39A77GLU-1-0.753-0.84422.1450.1420.1420.0000.0000.0000.000
40A78VAL00.0320.01722.5900.0140.0140.0000.0000.0000.000
41A79THR0-0.037-0.02217.6440.0110.0110.0000.0000.0000.000
42A80ARG10.7440.84018.714-0.114-0.1140.0000.0000.0000.000
43A81ALA00.0440.03419.9860.0260.0260.0000.0000.0000.000
44A82VAL00.0100.00417.1020.0090.0090.0000.0000.0000.000
45A83ALA0-0.061-0.03915.6080.0250.0250.0000.0000.0000.000
46A84GLU-1-0.935-0.97316.3900.2470.2470.0000.0000.0000.000
47A85LYS10.8420.92418.895-0.133-0.1330.0000.0000.0000.000
48A86LEU0-0.051-0.01513.7530.0060.0060.0000.0000.0000.000
49A87GLY00.0160.01814.0220.0800.0800.0000.0000.0000.000
50A88VAL0-0.075-0.01810.8080.1090.1090.0000.0000.0000.000
51A89LYS10.8960.93411.473-0.801-0.8010.0000.0000.0000.000
52A90VAL00.000-0.00912.0150.0830.0830.0000.0000.0000.000
53A91GLU-1-0.864-0.92212.0250.4110.4110.0000.0000.0000.000
54A92PHE00.017-0.00114.250-0.022-0.0220.0000.0000.0000.000
55A93LYS10.8550.93212.455-0.168-0.1680.0000.0000.0000.000
56A94GLU-1-0.782-0.87917.3990.0420.0420.0000.0000.0000.000
57A95THR0-0.032-0.01819.915-0.014-0.0140.0000.0000.0000.000
58A96GLN00.0480.02822.3970.0090.0090.0000.0000.0000.000
59A97TRP00.0290.01024.254-0.012-0.0120.0000.0000.0000.000
60A98ASP-1-0.894-0.95724.269-0.071-0.0710.0000.0000.0000.000
61A99SER0-0.061-0.03421.961-0.018-0.0180.0000.0000.0000.000
62A100MET0-0.0650.00520.015-0.014-0.0140.0000.0000.0000.000
63A101MET00.0790.03719.167-0.017-0.0170.0000.0000.0000.000
64A102ALA0-0.017-0.00719.472-0.028-0.0280.0000.0000.0000.000
65A103GLY00.014-0.00817.522-0.033-0.0330.0000.0000.0000.000
66A104LEU0-0.0100.01814.162-0.040-0.0400.0000.0000.0000.000
67A105LYS10.9620.99614.7580.1680.1680.0000.0000.0000.000
68A106ALA0-0.121-0.05915.862-0.043-0.0430.0000.0000.0000.000
69A107GLY00.0190.01311.834-0.047-0.0470.0000.0000.0000.000
70A108ARG10.8910.94710.8670.1550.1550.0000.0000.0000.000
71A109PHE0-0.021-0.02011.2560.0660.0660.0000.0000.0000.000
72A110ASP-1-0.765-0.8348.010-0.198-0.1980.0000.0000.0000.000
73A111VAL00.0040.00011.149-0.025-0.0250.0000.0000.0000.000
74A112VAL0-0.033-0.00214.6090.0200.0200.0000.0000.0000.000
75A113ALA00.0160.00518.0900.0020.0020.0000.0000.0000.000
76A114ASN0-0.016-0.04020.7640.0140.0140.0000.0000.0000.000
77A115GLN0-0.006-0.00224.139-0.014-0.0140.0000.0000.0000.000
78A116VAL00.0310.03723.154-0.007-0.0070.0000.0000.0000.000
79A117GLY00.0800.02825.5850.0030.0030.0000.0000.0000.000
80A118LEU0-0.069-0.02723.081-0.001-0.0010.0000.0000.0000.000
81A119THR00.0780.03827.013-0.005-0.0050.0000.0000.0000.000
82A120SER0-0.0100.00729.499-0.003-0.0030.0000.0000.0000.000
83A121PRO00.0880.03928.868-0.008-0.0080.0000.0000.0000.000
84A122GLU-1-0.824-0.89228.487-0.101-0.1010.0000.0000.0000.000
85A123ARG10.8190.87024.8510.0840.0840.0000.0000.0000.000
86A124GLN0-0.011-0.00424.129-0.015-0.0150.0000.0000.0000.000
87A125ALA0-0.0010.01223.957-0.010-0.0100.0000.0000.0000.000
88A126THR0-0.067-0.04021.487-0.015-0.0150.0000.0000.0000.000
89A127PHE0-0.044-0.02718.217-0.025-0.0250.0000.0000.0000.000
90A128ASP-1-0.785-0.86718.127-0.174-0.1740.0000.0000.0000.000
91A129LYS10.7760.86819.6950.0400.0400.0000.0000.0000.000
92A130SER0-0.017-0.01119.4740.0000.0000.0000.0000.0000.000
93A131GLU-1-0.834-0.91821.1490.0050.0050.0000.0000.0000.000
94A132PRO0-0.074-0.03323.7570.0080.0080.0000.0000.0000.000
95A133TYR0-0.009-0.03422.0320.0060.0060.0000.0000.0000.000
96A134SER00.0100.01226.6240.0070.0070.0000.0000.0000.000
97A135TRP0-0.0060.01529.811-0.009-0.0090.0000.0000.0000.000
98A136SER0-0.007-0.01832.7800.0040.0040.0000.0000.0000.000
99A137GLY00.0550.02035.199-0.004-0.0040.0000.0000.0000.000
100A138ALA0-0.0380.00138.2600.0020.0020.0000.0000.0000.000
101A139VAL0-0.0030.00341.5470.0010.0010.0000.0000.0000.000
102A140LEU0-0.020-0.00944.113-0.001-0.0010.0000.0000.0000.000
103A141VAL0-0.013-0.00246.3830.0020.0020.0000.0000.0000.000
104A142ALA00.0550.02649.173-0.001-0.0010.0000.0000.0000.000
105A143HIS00.012-0.00652.7330.0020.0020.0000.0000.0000.000
106A144ASN00.0700.01453.3660.0000.0000.0000.0000.0000.000
107A145ASP-1-0.830-0.87555.6770.0050.0050.0000.0000.0000.000
108A146SER00.0040.01755.881-0.001-0.0010.0000.0000.0000.000
109A147ASN00.0170.00057.2970.0000.0000.0000.0000.0000.000
110A148ILE00.0150.01153.6390.0000.0000.0000.0000.0000.000
111A149LYS10.8440.92053.220-0.001-0.0010.0000.0000.0000.000
112A150SER0-0.028-0.03251.1970.0000.0000.0000.0000.0000.000
113A151ILE00.0430.01447.5950.0000.0000.0000.0000.0000.000
114A152ALA00.0120.00651.484-0.001-0.0010.0000.0000.0000.000
115A153ASP-1-0.852-0.91554.927-0.001-0.0010.0000.0000.0000.000
116A154ILE00.0490.01851.4080.0000.0000.0000.0000.0000.000
117A155LYS10.9300.98755.7710.0090.0090.0000.0000.0000.000
118A156GLY0-0.030-0.02757.5380.0010.0010.0000.0000.0000.000
119A157VAL0-0.047-0.00457.1160.0000.0000.0000.0000.0000.000
120A158LYS10.8920.95357.4320.0030.0030.0000.0000.0000.000
121A159THR00.0230.00051.7350.0010.0010.0000.0000.0000.000
122A160ALA00.0190.02252.017-0.001-0.0010.0000.0000.0000.000
123A161GLN0-0.0100.00547.1680.0010.0010.0000.0000.0000.000
124A162SER00.0500.05046.348-0.001-0.0010.0000.0000.0000.000
125A163LEU00.028-0.00748.055-0.001-0.0010.0000.0000.0000.000
126A164THR0-0.020-0.00246.149-0.001-0.0010.0000.0000.0000.000
127A165SER0-0.0210.00443.503-0.001-0.0010.0000.0000.0000.000
128A166ASN00.0570.00039.4890.0010.0010.0000.0000.0000.000
129A167TYR00.028-0.00239.0460.0000.0000.0000.0000.0000.000
130A168GLY00.0270.03044.9020.0010.0010.0000.0000.0000.000
131A169GLU-1-0.956-0.97945.730-0.019-0.0190.0000.0000.0000.000
132A170LYS11.0171.00740.6700.0160.0160.0000.0000.0000.000
133A171ALA00.0210.00847.2790.0010.0010.0000.0000.0000.000
134A172LYS10.9350.96850.3920.0160.0160.0000.0000.0000.000
135A173ALA0-0.0100.00749.4400.0000.0000.0000.0000.0000.000
136A174ALA0-0.024-0.00750.8070.0000.0000.0000.0000.0000.000
137A175GLY0-0.032-0.03152.6570.0010.0010.0000.0000.0000.000
138A176ALA00.0050.02853.8090.0010.0010.0000.0000.0000.000
139A177GLN00.0220.01355.7290.0000.0000.0000.0000.0000.000
140A178LEU0-0.034-0.01451.8340.0010.0010.0000.0000.0000.000
141A179VAL0-0.032-0.02054.5490.0000.0000.0000.0000.0000.000
142A180PRO0-0.014-0.01152.9910.0000.0000.0000.0000.0000.000
143A181VAL0-0.017-0.00949.4630.0010.0010.0000.0000.0000.000
144A182ASP-1-0.832-0.91747.790-0.007-0.0070.0000.0000.0000.000
145A183GLY0-0.023-0.02345.490-0.001-0.0010.0000.0000.0000.000
146A184LEU00.0110.01642.3800.0000.0000.0000.0000.0000.000
147A185ALA00.0690.04945.6490.0000.0000.0000.0000.0000.000
148A186GLN00.022-0.00147.5370.0000.0000.0000.0000.0000.000
149A187SER0-0.070-0.04248.0940.0000.0000.0000.0000.0000.000
150A188LEU00.018-0.00546.6800.0000.0000.0000.0000.0000.000
151A189THR00.0490.03250.8630.0000.0000.0000.0000.0000.000
152A190LEU0-0.040-0.02453.4550.0000.0000.0000.0000.0000.000
153A191ILE0-0.052-0.02051.4230.0000.0000.0000.0000.0000.000
154A192GLU-1-0.933-0.96852.1060.0080.0080.0000.0000.0000.000
155A193GLN0-0.067-0.04356.346-0.001-0.0010.0000.0000.0000.000
156A194LYS10.8540.92158.583-0.004-0.0040.0000.0000.0000.000
157A195ARG10.9040.96358.9590.0000.0000.0000.0000.0000.000
158A196ALA0-0.045-0.03155.435-0.001-0.0010.0000.0000.0000.000
159A197ASP-1-0.883-0.94056.9440.0010.0010.0000.0000.0000.000
160A198ALA0-0.038-0.02852.4150.0010.0010.0000.0000.0000.000
161A199THR0-0.019-0.01847.899-0.001-0.0010.0000.0000.0000.000
162A200LEU0-0.0010.00346.0670.0010.0010.0000.0000.0000.000
163A201ASN00.004-0.01541.883-0.001-0.0010.0000.0000.0000.000
164A202ASP-1-0.780-0.86936.790-0.001-0.0010.0000.0000.0000.000
165A203GLU-1-0.768-0.87137.8230.0140.0140.0000.0000.0000.000
166A204LEU0-0.0030.00132.8110.0030.0030.0000.0000.0000.000
167A205ALA00.0140.00036.8770.0030.0030.0000.0000.0000.000
168A206VAL0-0.004-0.01238.4570.0020.0020.0000.0000.0000.000
169A207LEU0-0.020-0.00838.1210.0010.0010.0000.0000.0000.000
170A208ASP-1-0.795-0.88436.7320.0240.0240.0000.0000.0000.000
171A209TYR00.0180.00238.9070.0010.0010.0000.0000.0000.000
172A210LEU0-0.010-0.01842.2050.0010.0010.0000.0000.0000.000
173A211LYS10.8450.95337.290-0.037-0.0370.0000.0000.0000.000
174A212LYS10.7890.88236.602-0.021-0.0210.0000.0000.0000.000
175A213ASN0-0.080-0.03142.8460.0000.0000.0000.0000.0000.000
176A214PRO00.0540.02745.877-0.001-0.0010.0000.0000.0000.000
177A215ASN0-0.062-0.04248.0380.0000.0000.0000.0000.0000.000
178A216ALA0-0.0190.00348.626-0.001-0.0010.0000.0000.0000.000
179A217GLY00.0740.04350.747-0.001-0.0010.0000.0000.0000.000
180A218VAL0-0.051-0.03149.508-0.001-0.0010.0000.0000.0000.000
181A219LYS10.8240.91249.159-0.006-0.0060.0000.0000.0000.000
182A220ILE00.0200.00543.429-0.001-0.0010.0000.0000.0000.000
183A221VAL0-0.048-0.03147.8030.0010.0010.0000.0000.0000.000
184A222TRP00.0300.01245.2940.0000.0000.0000.0000.0000.000
185A223SER0-0.046-0.02942.4390.0010.0010.0000.0000.0000.000
186A224ALA00.0140.01241.2080.0000.0000.0000.0000.0000.000
187A225PRO00.0300.01841.7610.0020.0020.0000.0000.0000.000
188A226ALA00.0300.00237.751-0.001-0.0010.0000.0000.0000.000
189A227ASP-1-0.916-0.94937.350-0.011-0.0110.0000.0000.0000.000
190A228GLU-1-0.969-0.98938.485-0.013-0.0130.0000.0000.0000.000
191A229LYS10.7610.89035.706-0.007-0.0070.0000.0000.0000.000
192A230VAL0-0.028-0.02431.099-0.004-0.0040.0000.0000.0000.000
193A231GLY00.0470.01629.9160.0050.0050.0000.0000.0000.000
194A232SER0-0.036-0.04826.496-0.012-0.0120.0000.0000.0000.000
195A233GLY00.0330.01223.6050.0100.0100.0000.0000.0000.000
196A234LEU0-0.0220.00317.437-0.007-0.0070.0000.0000.0000.000
197A235ILE0-0.0020.01619.127-0.015-0.0150.0000.0000.0000.000
198A236VAL00.013-0.00413.9730.0070.0070.0000.0000.0000.000
199A237ASN00.018-0.01812.7550.0680.0680.0000.0000.0000.000
200A238LYS10.8270.91115.3390.1660.1660.0000.0000.0000.000
201A239GLY00.0110.01314.694-0.063-0.0630.0000.0000.0000.000
202A240ASN0-0.031-0.02310.587-0.206-0.2060.0000.0000.0000.000
203A241ASP-1-0.867-0.93813.161-0.159-0.1590.0000.0000.0000.000
204A242GLU-1-0.895-0.96111.633-0.152-0.1520.0000.0000.0000.000
205A243ALA0-0.017-0.01310.8530.0700.0700.0000.0000.0000.000
206A244VAL00.0240.02112.7390.0670.0670.0000.0000.0000.000
207A245ALA00.0240.03316.3030.0360.0360.0000.0000.0000.000
208A246LYS10.9350.98112.717-0.173-0.1730.0000.0000.0000.000
209A247PHE00.0340.01212.5810.0240.0240.0000.0000.0000.000
210A248SER00.033-0.00217.4260.0040.0040.0000.0000.0000.000
211A249THR0-0.065-0.04119.2640.0010.0010.0000.0000.0000.000
212A250ALA00.0270.01118.4460.0030.0030.0000.0000.0000.000
213A251ILE0-0.028-0.01020.4950.0000.0000.0000.0000.0000.000
214A252ASN00.007-0.01323.045-0.004-0.0040.0000.0000.0000.000
215A253GLU-1-0.864-0.92421.6640.1460.1460.0000.0000.0000.000
216A254LEU0-0.031-0.00822.299-0.004-0.0040.0000.0000.0000.000
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