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: R9J38

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2669764.077611
FMO2-HF: Nuclear repulsion 2582038.705161
FMO2-HF: Total energy -87725.372449
FMO2-MP2: Total energy -87986.198027


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.
-2.3150.3020.309-1.217-1.710.006
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 : 0.042 / q_NPA : 0.011
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].
3A41LEU00.0330.0063.8281.3622.0160.000-0.366-0.2880.001
4A42ILE00.0240.0146.6440.5860.5860.0000.0000.0000.000
5A43GLU-1-0.896-0.9433.267-0.0780.3740.030-0.128-0.355-0.001
6A44ARG10.7730.8753.101-1.570-0.0590.279-0.723-1.0670.006
7A45ILE0-0.022-0.0055.590-0.256-0.2560.0000.0000.0000.000
8A46ASN00.015-0.0148.278-0.050-0.0500.0000.0000.0000.000
9A47ASN0-0.042-0.0135.419-0.487-0.4870.0000.0000.0000.000
10A48LYS10.7690.8918.518-0.579-0.5790.0000.0000.0000.000
11A49GLY00.0510.0377.0480.0650.0650.0000.0000.0000.000
12A50THR0-0.024-0.0246.997-0.610-0.6100.0000.0000.0000.000
13A51VAL00.0130.0207.2560.2430.2430.0000.0000.0000.000
14A52THR0-0.054-0.0339.089-0.090-0.0900.0000.0000.0000.000
15A53VAL00.012-0.00311.429-0.069-0.0690.0000.0000.0000.000
16A54GLY0-0.0010.00314.9790.0100.0100.0000.0000.0000.000
17A55THR0-0.037-0.06817.5060.0100.0100.0000.0000.0000.000
18A56GLU-1-0.814-0.91221.096-0.036-0.0360.0000.0000.0000.000
19A57GLY0-0.0100.01024.2610.0020.0020.0000.0000.0000.000
20A58THR0-0.050-0.03225.5680.0030.0030.0000.0000.0000.000
21A59TYR00.0430.02328.440-0.002-0.0020.0000.0000.0000.000
22A60ALA0-0.0170.00929.9230.0040.0040.0000.0000.0000.000
23A61PRO0-0.0150.00232.110-0.004-0.0040.0000.0000.0000.000
24A62PHE00.0350.01027.7890.0070.0070.0000.0000.0000.000
25A63THR0-0.009-0.01123.6390.0100.0100.0000.0000.0000.000
26A64TYR0-0.0180.00726.495-0.008-0.0080.0000.0000.0000.000
27A65HIS10.7830.84625.170-0.030-0.0300.0000.0000.0000.000
28A66ASP-1-0.803-0.90529.2450.0540.0540.0000.0000.0000.000
29A67LYS10.8710.90431.800-0.048-0.0480.0000.0000.0000.000
30A68ASP-1-0.873-0.91031.7140.0550.0550.0000.0000.0000.000
31A69GLY0-0.005-0.00129.9510.0020.0020.0000.0000.0000.000
32A70LYS10.9140.98625.327-0.111-0.1110.0000.0000.0000.000
33A71LEU0-0.0230.01321.190-0.005-0.0050.0000.0000.0000.000
34A72THR00.014-0.03124.9360.0130.0130.0000.0000.0000.000
35A73GLY00.0220.00626.567-0.009-0.0090.0000.0000.0000.000
36A74TYR0-0.025-0.01826.7210.0100.0100.0000.0000.0000.000
37A75ASP-1-0.717-0.80823.6330.0140.0140.0000.0000.0000.000
38A76VAL0-0.0210.00621.5870.0090.0090.0000.0000.0000.000
39A77GLU-1-0.829-0.91322.0360.1250.1250.0000.0000.0000.000
40A78VAL00.0260.01422.3820.0150.0150.0000.0000.0000.000
41A79THR0-0.026-0.01917.5260.0100.0100.0000.0000.0000.000
42A80ARG10.7790.87818.627-0.096-0.0960.0000.0000.0000.000
43A81ALA00.0390.03219.9860.0270.0270.0000.0000.0000.000
44A82VAL00.0150.00717.0360.0120.0120.0000.0000.0000.000
45A83ALA0-0.060-0.03915.5750.0270.0270.0000.0000.0000.000
46A84GLU-1-0.937-0.97516.3900.2500.2500.0000.0000.0000.000
47A85LYS10.9670.99618.895-0.141-0.1410.0000.0000.0000.000
48A86LEU0-0.043-0.01213.7210.0080.0080.0000.0000.0000.000
49A87GLY00.0080.01314.0180.0840.0840.0000.0000.0000.000
50A88VAL0-0.061-0.00710.6760.1110.1110.0000.0000.0000.000
51A89LYS10.9140.96811.702-0.689-0.6890.0000.0000.0000.000
52A90VAL00.003-0.00911.9560.0680.0680.0000.0000.0000.000
53A91GLU-1-0.926-0.97811.5550.3220.3220.0000.0000.0000.000
54A92PHE00.0160.00314.158-0.029-0.0290.0000.0000.0000.000
55A93LYS10.8920.95312.367-0.062-0.0620.0000.0000.0000.000
56A94GLU-1-0.801-0.88617.3220.0180.0180.0000.0000.0000.000
57A95THR0-0.010-0.00219.757-0.014-0.0140.0000.0000.0000.000
58A96GLN00.0440.01422.3240.0070.0070.0000.0000.0000.000
59A97TRP00.0670.02724.179-0.014-0.0140.0000.0000.0000.000
60A98ASP-1-0.894-0.95724.190-0.094-0.0940.0000.0000.0000.000
61A99SER0-0.093-0.04321.932-0.016-0.0160.0000.0000.0000.000
62A100MET0-0.0300.00919.853-0.017-0.0170.0000.0000.0000.000
63A101MET00.0530.03019.090-0.022-0.0220.0000.0000.0000.000
64A102ALA0-0.020-0.00319.401-0.030-0.0300.0000.0000.0000.000
65A103GLY00.005-0.01317.469-0.035-0.0350.0000.0000.0000.000
66A104LEU00.0140.02614.102-0.047-0.0470.0000.0000.0000.000
67A105LYS10.9601.00114.6900.1640.1640.0000.0000.0000.000
68A106ALA0-0.115-0.05615.820-0.042-0.0420.0000.0000.0000.000
69A107GLY00.0240.01711.790-0.049-0.0490.0000.0000.0000.000
70A108ARG10.8890.94610.8180.1860.1860.0000.0000.0000.000
71A109PHE0-0.034-0.03011.1930.0650.0650.0000.0000.0000.000
72A110ASP-1-0.738-0.8478.082-0.379-0.3790.0000.0000.0000.000
73A111VAL0-0.017-0.00411.049-0.013-0.0130.0000.0000.0000.000
74A112VAL0-0.026-0.00514.5030.0160.0160.0000.0000.0000.000
75A113ALA00.0200.00917.9870.0050.0050.0000.0000.0000.000
76A114ASN0-0.022-0.02420.6560.0120.0120.0000.0000.0000.000
77A115GLN0-0.016-0.02524.034-0.010-0.0100.0000.0000.0000.000
78A116VAL00.0290.03222.958-0.007-0.0070.0000.0000.0000.000
79A117GLY00.0650.02225.4780.0030.0030.0000.0000.0000.000
80A118LEU0-0.086-0.04822.933-0.001-0.0010.0000.0000.0000.000
81A119THR00.0700.02726.916-0.005-0.0050.0000.0000.0000.000
82A120SER0-0.038-0.00429.705-0.002-0.0020.0000.0000.0000.000
83A121PRO00.0930.03628.868-0.009-0.0090.0000.0000.0000.000
84A122GLU-1-0.908-0.95528.458-0.115-0.1150.0000.0000.0000.000
85A123ARG10.9210.94224.7760.0940.0940.0000.0000.0000.000
86A124GLN0-0.0060.00624.121-0.016-0.0160.0000.0000.0000.000
87A125ALA0-0.0140.00523.957-0.009-0.0090.0000.0000.0000.000
88A126THR0-0.071-0.04021.484-0.015-0.0150.0000.0000.0000.000
89A127PHE0-0.053-0.02718.185-0.027-0.0270.0000.0000.0000.000
90A128ASP-1-0.801-0.89918.094-0.181-0.1810.0000.0000.0000.000
91A129LYS10.8370.90719.6950.0480.0480.0000.0000.0000.000
92A130SER0-0.035-0.01619.4270.0010.0010.0000.0000.0000.000
93A131GLU-1-0.883-0.95321.149-0.005-0.0050.0000.0000.0000.000
94A132PRO0-0.078-0.04223.7560.0060.0060.0000.0000.0000.000
95A133TYR0-0.041-0.06022.0040.0070.0070.0000.0000.0000.000
96A134SER0-0.048-0.02726.6030.0060.0060.0000.0000.0000.000
97A135TRP00.0280.01729.695-0.010-0.0100.0000.0000.0000.000
98A136SER00.0190.00332.6650.0050.0050.0000.0000.0000.000
99A137GLY00.0540.02135.087-0.004-0.0040.0000.0000.0000.000
100A138ALA0-0.045-0.00338.1490.0020.0020.0000.0000.0000.000
101A139VAL00.0040.00941.5770.0020.0020.0000.0000.0000.000
102A140LEU0-0.019-0.01144.001-0.002-0.0020.0000.0000.0000.000
103A141VAL0-0.018-0.00346.3770.0020.0020.0000.0000.0000.000
104A142ALA00.0580.02749.061-0.001-0.0010.0000.0000.0000.000
105A143HIS0-0.004-0.00352.6210.0010.0010.0000.0000.0000.000
106A144ASN00.0250.01253.3370.0000.0000.0000.0000.0000.000
107A145ASP-1-0.898-0.95455.5640.0030.0030.0000.0000.0000.000
108A146SER0-0.0060.01455.757-0.001-0.0010.0000.0000.0000.000
109A147ASN0-0.016-0.01457.1830.0000.0000.0000.0000.0000.000
110A148ILE00.0050.00253.8610.0000.0000.0000.0000.0000.000
111A149LYS10.8890.93153.1060.0000.0000.0000.0000.0000.000
112A150SER0-0.031-0.01251.0810.0000.0000.0000.0000.0000.000
113A151ILE00.0460.01647.5500.0000.0000.0000.0000.0000.000
114A152ALA00.0040.00051.375-0.001-0.0010.0000.0000.0000.000
115A153ASP-1-0.817-0.90354.841-0.003-0.0030.0000.0000.0000.000
116A154ILE00.022-0.00351.5130.0000.0000.0000.0000.0000.000
117A155LYS10.9460.99255.6630.0120.0120.0000.0000.0000.000
118A156GLY0-0.043-0.03457.4320.0010.0010.0000.0000.0000.000
119A157VAL0-0.0410.00956.8580.0000.0000.0000.0000.0000.000
120A158LYS10.8940.95557.3260.0060.0060.0000.0000.0000.000
121A159THR00.0400.01051.6750.0010.0010.0000.0000.0000.000
122A160ALA00.0210.01951.846-0.001-0.0010.0000.0000.0000.000
123A161GLN0-0.0100.01946.9940.0010.0010.0000.0000.0000.000
124A162SER00.0480.04846.264-0.001-0.0010.0000.0000.0000.000
125A163LEU00.030-0.01547.959-0.001-0.0010.0000.0000.0000.000
126A164THR0-0.024-0.00646.2630.0000.0000.0000.0000.0000.000
127A165SER0-0.0190.01943.402-0.002-0.0020.0000.0000.0000.000
128A166ASN00.0760.00538.8380.0000.0000.0000.0000.0000.000
129A167TYR00.029-0.00138.8040.0000.0000.0000.0000.0000.000
130A168GLY00.0220.02544.8000.0010.0010.0000.0000.0000.000
131A169GLU-1-0.958-0.97645.661-0.024-0.0240.0000.0000.0000.000
132A170LYS10.9990.99840.4670.0220.0220.0000.0000.0000.000
133A171ALA00.0320.01347.1780.0010.0010.0000.0000.0000.000
134A172LYS10.9270.96350.2890.0210.0210.0000.0000.0000.000
135A173ALA0-0.0090.01049.3590.0010.0010.0000.0000.0000.000
136A174ALA0-0.024-0.00950.7350.0000.0000.0000.0000.0000.000
137A175GLY0-0.036-0.02952.5540.0010.0010.0000.0000.0000.000
138A176ALA00.0090.03253.6970.0010.0010.0000.0000.0000.000
139A177GLN00.009-0.00755.625-0.001-0.0010.0000.0000.0000.000
140A178LEU0-0.035-0.01351.3990.0010.0010.0000.0000.0000.000
141A179VAL0-0.036-0.02254.4320.0000.0000.0000.0000.0000.000
142A180PRO0-0.016-0.01552.8970.0000.0000.0000.0000.0000.000
143A181VAL0-0.033-0.01049.2800.0010.0010.0000.0000.0000.000
144A182ASP-1-0.843-0.94047.623-0.014-0.0140.0000.0000.0000.000
145A183GLY0-0.044-0.03245.392-0.001-0.0010.0000.0000.0000.000
146A184LEU00.0070.01342.2610.0010.0010.0000.0000.0000.000
147A185ALA00.0770.05945.5460.0010.0010.0000.0000.0000.000
148A186GLN00.0660.03047.4360.0000.0000.0000.0000.0000.000
149A187SER0-0.072-0.04548.0120.0000.0000.0000.0000.0000.000
150A188LEU00.0450.00446.6310.0000.0000.0000.0000.0000.000
151A189THR00.0390.02950.7570.0010.0010.0000.0000.0000.000
152A190LEU0-0.042-0.02953.3510.0000.0000.0000.0000.0000.000
153A191ILE0-0.035-0.00951.3270.0000.0000.0000.0000.0000.000
154A192GLU-1-0.953-0.97152.0610.0040.0040.0000.0000.0000.000
155A193GLN0-0.081-0.05156.238-0.001-0.0010.0000.0000.0000.000
156A194LYS10.8950.96158.472-0.001-0.0010.0000.0000.0000.000
157A195ARG10.9080.96158.8130.0040.0040.0000.0000.0000.000
158A196ALA0-0.051-0.03455.287-0.001-0.0010.0000.0000.0000.000
159A197ASP-1-0.877-0.93356.835-0.002-0.0020.0000.0000.0000.000
160A198ALA0-0.038-0.02552.2910.0010.0010.0000.0000.0000.000
161A199THR0-0.042-0.04447.780-0.001-0.0010.0000.0000.0000.000
162A200LEU00.0170.00945.9280.0010.0010.0000.0000.0000.000
163A201ASN0-0.011-0.01541.551-0.002-0.0020.0000.0000.0000.000
164A202ASP-1-0.794-0.89136.657-0.010-0.0100.0000.0000.0000.000
165A203GLU-1-0.842-0.93337.5740.0070.0070.0000.0000.0000.000
166A204LEU00.0040.00232.6530.0030.0030.0000.0000.0000.000
167A205ALA00.0240.01636.7650.0030.0030.0000.0000.0000.000
168A206VAL0-0.018-0.02038.3490.0020.0020.0000.0000.0000.000
169A207LEU0-0.024-0.00937.9750.0020.0020.0000.0000.0000.000
170A208ASP-1-0.815-0.90236.7650.0150.0150.0000.0000.0000.000
171A209TYR0-0.009-0.00838.7980.0010.0010.0000.0000.0000.000
172A210LEU0-0.018-0.02642.0980.0010.0010.0000.0000.0000.000
173A211LYS10.9070.97837.451-0.031-0.0310.0000.0000.0000.000
174A212LYS10.8130.89736.119-0.014-0.0140.0000.0000.0000.000
175A213ASN0-0.063-0.01542.7400.0000.0000.0000.0000.0000.000
176A214PRO00.0490.02945.926-0.001-0.0010.0000.0000.0000.000
177A215ASN0-0.053-0.04147.9290.0010.0010.0000.0000.0000.000
178A216ALA0-0.021-0.00148.572-0.001-0.0010.0000.0000.0000.000
179A217GLY00.0710.03350.638-0.001-0.0010.0000.0000.0000.000
180A218VAL0-0.039-0.02549.195-0.001-0.0010.0000.0000.0000.000
181A219LYS10.9270.95849.019-0.004-0.0040.0000.0000.0000.000
182A220ILE00.0200.01043.327-0.001-0.0010.0000.0000.0000.000
183A221VAL0-0.052-0.03147.6890.0010.0010.0000.0000.0000.000
184A222TRP00.0270.01145.1140.0000.0000.0000.0000.0000.000
185A223SER0-0.037-0.02542.3520.0010.0010.0000.0000.0000.000
186A224ALA00.0200.01441.0640.0000.0000.0000.0000.0000.000
187A225PRO00.0260.02041.7290.0020.0020.0000.0000.0000.000
188A226ALA00.008-0.01637.701-0.002-0.0020.0000.0000.0000.000
189A227ASP-1-0.896-0.94537.349-0.017-0.0170.0000.0000.0000.000
190A228GLU-1-0.991-1.00038.485-0.018-0.0180.0000.0000.0000.000
191A229LYS10.7990.91735.591-0.002-0.0020.0000.0000.0000.000
192A230VAL0-0.011-0.01231.044-0.005-0.0050.0000.0000.0000.000
193A231GLY00.0190.00429.9140.0040.0040.0000.0000.0000.000
194A232SER0-0.033-0.03226.387-0.012-0.0120.0000.0000.0000.000
195A233GLY00.0290.01423.5540.0120.0120.0000.0000.0000.000
196A234LEU0-0.0220.00317.326-0.008-0.0080.0000.0000.0000.000
197A235ILE0-0.0030.01619.021-0.013-0.0130.0000.0000.0000.000
198A236VAL00.0360.00714.084-0.001-0.0010.0000.0000.0000.000
199A237ASN0-0.006-0.03912.9410.0700.0700.0000.0000.0000.000
200A238LYS10.8830.95415.3390.1820.1820.0000.0000.0000.000
201A239GLY00.0120.01114.692-0.067-0.0670.0000.0000.0000.000
202A240ASN0-0.028-0.01510.444-0.211-0.2110.0000.0000.0000.000
203A241ASP-1-0.856-0.93213.161-0.148-0.1480.0000.0000.0000.000
204A242GLU-1-0.919-0.96511.772-0.125-0.1250.0000.0000.0000.000
205A243ALA0-0.014-0.01710.8690.0710.0710.0000.0000.0000.000
206A244VAL00.0320.01612.7390.0670.0670.0000.0000.0000.000
207A245ALA00.0160.02316.3030.0360.0360.0000.0000.0000.000
208A246LYS10.9340.97312.571-0.181-0.1810.0000.0000.0000.000
209A247PHE00.0310.01312.7500.0220.0220.0000.0000.0000.000
210A248SER00.0460.02017.4250.0060.0060.0000.0000.0000.000
211A249THR0-0.073-0.03119.2080.0020.0020.0000.0000.0000.000
212A250ALA00.0270.01618.4390.0040.0040.0000.0000.0000.000
213A251ILE0-0.023-0.01120.4930.0010.0010.0000.0000.0000.000
214A252ASN00.011-0.00823.043-0.004-0.0040.0000.0000.0000.000
215A253GLU-1-0.935-0.97321.2230.1510.1510.0000.0000.0000.000
216A254LEU0-0.032-0.01022.378-0.003-0.0030.0000.0000.0000.000
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