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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: P5LZX

Calculation Name: 3VOR-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VOR

Chain ID: A

ChEMBL ID:

UniProt ID: Q59393

Base Structure: X-ray

Registration Date: 2017-11-21

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20171117
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 181
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1766427.893601
FMO2-HF: Nuclear repulsion 1699641.3706
FMO2-HF: Total energy -66786.523001
FMO2-MP2: Total energy -66980.336132


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:1:GLY)


Summations of interaction energy for fragment #1(A:1: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.
-97.983-95.6693.817-3.393-2.738-0.031
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.910
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].
3A3ASP-1-0.843-0.9083.809-46.802-46.2520.000-0.304-0.246-0.001
4A4SER0-0.070-0.0395.4648.2218.2210.0000.0000.0000.000
5A5ARG10.9610.9617.09120.10220.1020.0000.0000.0000.000
6A6THR00.0570.0299.120-1.081-1.0810.0000.0000.0000.000
7A7VAL00.0030.0144.344-0.255-0.179-0.001-0.020-0.0540.000
8A8SER00.0000.0006.5410.3320.3320.0000.0000.0000.000
9A9GLU-1-0.885-0.9407.570-20.175-20.1750.0000.0000.0000.000
10A10LEU00.0090.0139.8671.5251.5250.0000.0000.0000.000
11A11VAL0-0.013-0.0106.4681.6261.6260.0000.0000.0000.000
12A12THR00.0020.0099.7961.9721.9720.0000.0000.0000.000
13A13ASN00.0480.02711.8941.4841.4840.0000.0000.0000.000
14A14THR0-0.078-0.04712.1531.3471.3470.0000.0000.0000.000
15A15ASN0-0.024-0.02111.3151.9041.9040.0000.0000.0000.000
16A16THR00.0360.01515.3040.9210.9210.0000.0000.0000.000
17A17ILE00.0290.01617.5601.1791.1790.0000.0000.0000.000
18A18ARG10.8110.91015.85618.88918.8890.0000.0000.0000.000
19A19VAL0-0.018-0.01219.2030.8450.8450.0000.0000.0000.000
20A20ALA00.0580.03121.5560.7790.7790.0000.0000.0000.000
21A21MET0-0.023-0.00222.5310.8330.8330.0000.0000.0000.000
22A22LYS10.7990.89522.43013.72913.7290.0000.0000.0000.000
23A23ASP-1-0.875-0.93625.620-10.583-10.5830.0000.0000.0000.000
24A24ALA0-0.067-0.02927.4840.5020.5020.0000.0000.0000.000
25A25TYR00.009-0.04227.2630.2490.2490.0000.0000.0000.000
26A26GLN00.0430.03927.021-0.220-0.2200.0000.0000.0000.000
27A27ARG10.9180.94929.5709.6059.6050.0000.0000.0000.000
28A28ASP-1-0.921-0.95232.881-9.053-9.0530.0000.0000.0000.000
29A29GLY0-0.083-0.03932.5160.2600.2600.0000.0000.0000.000
30A30LYS10.8950.93331.2208.9258.9250.0000.0000.0000.000
31A31TYR0-0.0080.00026.395-0.046-0.0460.0000.0000.0000.000
32A32PRO0-0.010-0.00128.1500.2850.2850.0000.0000.0000.000
33A33ASP-1-0.865-0.91929.089-9.878-9.8780.0000.0000.0000.000
34A34TYR0-0.008-0.02124.966-0.109-0.1090.0000.0000.0000.000
35A35GLN0-0.0060.01128.4370.3570.3570.0000.0000.0000.000
36A36ALA00.0080.00127.173-0.399-0.3990.0000.0000.0000.000
37A37PRO00.002-0.00723.4460.3320.3320.0000.0000.0000.000
38A38LEU0-0.010-0.00823.025-0.089-0.0890.0000.0000.0000.000
39A39SER0-0.0060.00526.0390.0770.0770.0000.0000.0000.000
40A40LEU0-0.063-0.01326.0620.2920.2920.0000.0000.0000.000
41A41THR00.0550.02526.871-0.315-0.3150.0000.0000.0000.000
42A42ALA00.011-0.00526.074-0.067-0.0670.0000.0000.0000.000
43A43ASP-1-0.927-0.96627.459-9.725-9.7250.0000.0000.0000.000
44A44SER00.0360.00830.806-0.040-0.0400.0000.0000.0000.000
45A45ILE0-0.0020.01924.7980.1120.1120.0000.0000.0000.000
46A46LYS10.9220.95628.88310.18110.1810.0000.0000.0000.000
47A47THR0-0.036-0.02431.4000.1850.1850.0000.0000.0000.000
48A48ASP-1-0.853-0.89631.717-9.314-9.3140.0000.0000.0000.000
49A49SER00.0120.00033.251-0.182-0.1820.0000.0000.0000.000
50A50THR0-0.051-0.04833.3560.1130.1130.0000.0000.0000.000
51A51GLY0-0.0050.00132.7210.0590.0590.0000.0000.0000.000
52A52ILE0-0.0020.01926.854-0.301-0.3010.0000.0000.0000.000
53A53ALA00.0480.02325.338-0.018-0.0180.0000.0000.0000.000
54A54VAL00.0540.01421.8000.0430.0430.0000.0000.0000.000
55A55ALA00.0260.01325.0500.0110.0110.0000.0000.0000.000
56A56GLN00.0250.04728.3720.1030.1030.0000.0000.0000.000
57A57LEU0-0.004-0.01023.8970.1680.1680.0000.0000.0000.000
58A58VAL0-0.017-0.00925.4930.0890.0890.0000.0000.0000.000
59A59GLN0-0.107-0.05727.8430.4820.4820.0000.0000.0000.000
60A60LEU0-0.073-0.03129.9620.3390.3390.0000.0000.0000.000
61A61GLY0-0.039-0.01529.5870.1240.1240.0000.0000.0000.000
62A62LYS10.7850.88826.24710.67010.6700.0000.0000.0000.000
63A63LEU00.0150.02220.592-0.526-0.5260.0000.0000.0000.000
64A64THR00.0150.00923.0760.5720.5720.0000.0000.0000.000
65A65PRO00.012-0.02322.678-0.477-0.4770.0000.0000.0000.000
66A66ASP-1-0.905-0.95919.266-16.244-16.2440.0000.0000.0000.000
67A67GLU-1-0.831-0.91118.122-16.232-16.2320.0000.0000.0000.000
68A68ALA0-0.022-0.00618.403-0.546-0.5460.0000.0000.0000.000
69A69ARG10.9190.96618.43315.59515.5950.0000.0000.0000.000
70A70ASN00.0510.03614.228-2.205-2.2050.0000.0000.0000.000
71A71GLY0-0.019-0.02614.4810.8330.8330.0000.0000.0000.000
72A72ILE0-0.073-0.0369.195-0.248-0.2480.0000.0000.0000.000
73A73SER0-0.031-0.02313.6890.5240.5240.0000.0000.0000.000
74A74GLY0-0.044-0.01816.9220.9050.9050.0000.0000.0000.000
75A75ASP-1-0.749-0.84618.778-13.430-13.4300.0000.0000.0000.000
76A76TYR0-0.051-0.04219.196-0.897-0.8970.0000.0000.0000.000
77A77ILE0-0.0060.00215.9850.1060.1060.0000.0000.0000.000
78A78GLY00.0170.02819.7130.7770.7770.0000.0000.0000.000
79A79ILE00.011-0.02620.783-0.699-0.6990.0000.0000.0000.000
80A80GLY00.0390.01123.2070.5940.5940.0000.0000.0000.000
81A81GLY00.0250.03125.465-0.266-0.2660.0000.0000.0000.000
82A82ALA0-0.013-0.00424.640-0.270-0.2700.0000.0000.0000.000
83A83ILE0-0.017-0.00126.7600.3230.3230.0000.0000.0000.000
84A84THR00.027-0.01627.308-0.293-0.2930.0000.0000.0000.000
85A85SER0-0.022-0.01629.5720.0810.0810.0000.0000.0000.000
86A86SER00.0030.00432.698-0.069-0.0690.0000.0000.0000.000
87A87GLY00.0450.01834.4230.2130.2130.0000.0000.0000.000
88A88SER0-0.039-0.00233.4590.3160.3160.0000.0000.0000.000
89A89THR00.0220.00735.070-0.129-0.1290.0000.0000.0000.000
90A90ILE0-0.028-0.01433.4620.0570.0570.0000.0000.0000.000
91A91ASN0-0.030-0.02329.374-0.218-0.2180.0000.0000.0000.000
92A92LYS10.8930.93530.2099.3329.3320.0000.0000.0000.000
93A93GLY00.0410.02425.881-0.150-0.1500.0000.0000.0000.000
94A94PHE0-0.021-0.01220.1830.2500.2500.0000.0000.0000.000
95A95ALA00.015-0.00621.173-0.531-0.5310.0000.0000.0000.000
96A96MET0-0.0110.00916.7750.1010.1010.0000.0000.0000.000
97A97GLU-1-0.834-0.92917.828-15.300-15.3000.0000.0000.0000.000
98A98LEU0-0.040-0.02111.881-0.053-0.0530.0000.0000.0000.000
99A99ASN00.002-0.02215.060-1.422-1.4220.0000.0000.0000.000
100A100GLY00.0230.01215.104-0.772-0.7720.0000.0000.0000.000
101A101LEU0-0.048-0.01010.672-1.194-1.1940.0000.0000.0000.000
102A102SER00.0840.02910.3370.3380.3380.0000.0000.0000.000
103A103GLN00.0530.01610.696-2.115-2.1150.0000.0000.0000.000
104A104GLU-1-0.949-0.9706.960-31.677-31.6770.0000.0000.0000.000
105A105GLN00.0270.0096.051-4.672-4.6720.0000.0000.0000.000
106170CYS0-0.057-0.0106.806-4.446-4.4460.0000.0000.0000.000
107A107ARG10.9210.9536.57524.95224.9520.0000.0000.0000.000
108A108SER0-0.026-0.0112.240-15.490-14.6853.794-2.652-1.948-0.026
109A109ILE00.0370.0163.883-6.762-6.585-0.001-0.065-0.111-0.001
110A110LEU00.0090.0046.5470.7880.7880.0000.0000.0000.000
111A111GLY0-0.023-0.0134.4692.4842.498-0.001-0.005-0.0070.000
112A112GLN0-0.089-0.0403.172-0.2580.4340.026-0.347-0.372-0.003
113A113VAL00.0120.0015.5284.3544.3540.0000.0000.0000.000
114A114GLY00.0130.0188.7913.1693.1690.0000.0000.0000.000
115A115ASP-1-0.806-0.91710.848-20.907-20.9070.0000.0000.0000.000
116A116ASN0-0.036-0.00610.9402.6572.6570.0000.0000.0000.000
117A117TRP00.0190.01713.0882.0422.0420.0000.0000.0000.000
118A118GLU-1-0.754-0.86516.235-13.700-13.7000.0000.0000.0000.000
119A119TYR00.000-0.00218.7780.6440.6440.0000.0000.0000.000
120A120VAL0-0.005-0.00513.221-0.801-0.8010.0000.0000.0000.000
121A121ALA0-0.0060.00516.5130.5440.5440.0000.0000.0000.000
122A122VAL0-0.022-0.01413.996-1.074-1.0740.0000.0000.0000.000
123A123GLY00.0060.00116.7351.0471.0470.0000.0000.0000.000
124A124THR0-0.012-0.01917.621-0.801-0.8010.0000.0000.0000.000
125A125SER00.0090.02619.1700.7340.7340.0000.0000.0000.000
126A126PRO00.0330.01118.549-1.191-1.1910.0000.0000.0000.000
127A127SER00.024-0.01617.982-0.186-0.1860.0000.0000.0000.000
128A128GLY0-0.0150.00119.9650.5290.5290.0000.0000.0000.000
129A129SER0-0.072-0.03622.1600.7370.7370.0000.0000.0000.000
130A130TYR0-0.032-0.03718.901-0.918-0.9180.0000.0000.0000.000
131A131ASP-1-0.833-0.93522.825-12.237-12.2370.0000.0000.0000.000
132A132ALA0-0.041-0.01722.0770.4880.4880.0000.0000.0000.000
133A133LEU0-0.058-0.03021.8990.4560.4560.0000.0000.0000.000
134A134SER0-0.045-0.01925.2210.5830.5830.0000.0000.0000.000
135A135ALA0-0.0200.00727.3860.4450.4450.0000.0000.0000.000
136A136GLY0-0.017-0.00828.5740.4190.4190.0000.0000.0000.000
137A137ALA0-0.038-0.00527.893-0.419-0.4190.0000.0000.0000.000
138A138VAL00.0250.00922.5470.0630.0630.0000.0000.0000.000
139A139ASN00.0320.01025.9520.1240.1240.0000.0000.0000.000
140A140MET0-0.017-0.00222.249-0.200-0.2000.0000.0000.0000.000
141A141LEU00.003-0.00224.546-0.310-0.3100.0000.0000.0000.000
142A142ALA0-0.0190.01324.8930.3070.3070.0000.0000.0000.000
143A143ALA00.007-0.00224.818-0.420-0.4200.0000.0000.0000.000
144A144THR0-0.0160.00020.7310.1040.1040.0000.0000.0000.000
145A145ASP-1-0.798-0.89721.326-13.668-13.6680.0000.0000.0000.000
146A146ASN0-0.090-0.07118.916-1.180-1.1800.0000.0000.0000.000
147A147THR0-0.021-0.00217.613-0.678-0.6780.0000.0000.0000.000
148A148THR00.0220.04117.662-0.844-0.8440.0000.0000.0000.000
149A149ILE00.0110.01218.675-0.688-0.6880.0000.0000.0000.000
150A150LEU0-0.0040.00113.7250.0640.0640.0000.0000.0000.000
151A151ARG10.8200.90514.69918.87718.8770.0000.0000.0000.000
152A152SER00.016-0.00618.4190.1550.1550.0000.0000.0000.000
153A153LEU0-0.037-0.01521.7590.0030.0030.0000.0000.0000.000
154A154ALA0-0.0290.00624.8090.5690.5690.0000.0000.0000.000
155A155ALA00.015-0.00425.807-0.249-0.2490.0000.0000.0000.000
156A156ASN0-0.060-0.04224.902-0.182-0.1820.0000.0000.0000.000
157A157GLY00.0770.05522.432-0.396-0.3960.0000.0000.0000.000
158A158GLN0-0.072-0.04719.488-1.103-1.1030.0000.0000.0000.000
159A159VAL00.0020.00116.448-0.164-0.1640.0000.0000.0000.000
160A160SER00.0050.00614.456-0.271-0.2710.0000.0000.0000.000
161A161LEU0-0.014-0.02611.2880.4550.4550.0000.0000.0000.000
162A162THR00.0290.01210.062-2.296-2.2960.0000.0000.0000.000
163A163ALA00.0540.0218.265-0.494-0.4940.0000.0000.0000.000
164A164GLU-1-0.890-0.9619.357-23.538-23.5380.0000.0000.0000.000
165A165LYS10.8350.93212.81519.95819.9580.0000.0000.0000.000
166A166ILE00.0130.0187.5411.0651.0650.0000.0000.0000.000
167A167LEU0-0.029-0.01210.0110.1370.1370.0000.0000.0000.000
168A168LYS10.8850.95312.24917.96017.9600.0000.0000.0000.000
169A169THR00.0400.00312.4030.9190.9190.0000.0000.0000.000
170A171THR0-0.007-0.01213.038-0.650-0.6500.0000.0000.0000.000
171A172ALA00.0360.04115.4900.9400.9400.0000.0000.0000.000
172A173THR0-0.023-0.03015.659-1.148-1.1480.0000.0000.0000.000
173A174VAL00.0020.01416.189-0.725-0.7250.0000.0000.0000.000
174A175ASN0-0.048-0.03613.4030.9790.9790.0000.0000.0000.000
175A176SER00.0210.02714.905-0.204-0.2040.0000.0000.0000.000
176A177ILE00.0140.00810.377-0.218-0.2180.0000.0000.0000.000
177A178THR0-0.015-0.00114.8300.7890.7890.0000.0000.0000.000
178A179LEU0-0.021-0.00212.850-0.405-0.4050.0000.0000.0000.000
179A180ALA00.0290.00216.9460.7860.7860.0000.0000.0000.000
180A181SER0-0.089-0.07419.717-0.708-0.7080.0000.0000.0000.000
181A182ARG00.0880.08221.693-0.261-0.2610.0000.0000.0000.000