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: 22Y9R

Calculation Name: 1VJN-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1VJN

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9WY50

Base Structure: X-ray

Registration Date: 2023-06-20

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2389103.929585
FMO2-HF: Nuclear repulsion 2310070.913229
FMO2-HF: Total energy -79033.016356
FMO2-MP2: Total energy -79265.280222


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-27.698-17.40912.625-8.899-14.013-0.054
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.021
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].
3A2LYS10.9290.9762.816-2.3771.1010.174-1.394-2.2580.008
4A3ILE0-0.0080.0064.5170.7630.8740.000-0.021-0.0890.000
5A4THR0-0.006-0.0028.233-0.501-0.5010.0000.0000.0000.000
6A5TRP0-0.052-0.01310.3630.2090.2090.0000.0000.0000.000
7A6PHE00.030-0.01412.873-0.049-0.0490.0000.0000.0000.000
8A7GLY00.0490.01516.6670.0510.0510.0000.0000.0000.000
9A8HIS10.7880.88419.6040.3100.3100.0000.0000.0000.000
10A9ALA00.0740.04619.935-0.027-0.0270.0000.0000.0000.000
11A10CYS0-0.0310.03317.6190.0020.0020.0000.0000.0000.000
12A11PHE00.024-0.00512.828-0.079-0.0790.0000.0000.0000.000
13A12ALA0-0.0060.00310.6670.1070.1070.0000.0000.0000.000
14A13LEU0-0.026-0.0188.806-0.258-0.2580.0000.0000.0000.000
15A14GLU-1-0.939-0.9755.124-0.471-0.4710.0000.0000.0000.000
16A15MET00.0440.0225.4580.6420.705-0.001-0.011-0.0510.000
17A16GLU-1-0.841-0.9235.4990.4860.4860.0000.0000.0000.000
18A17GLY0-0.072-0.0286.909-0.168-0.1680.0000.0000.0000.000
19A18LYS10.8240.9218.734-1.084-1.0840.0000.0000.0000.000
20A19THR00.0230.0079.1470.1060.1060.0000.0000.0000.000
21A20ILE0-0.013-0.00911.057-0.042-0.0420.0000.0000.0000.000
22A21VAL00.008-0.00912.651-0.090-0.0900.0000.0000.0000.000
23A22THR00.0130.00215.2520.0250.0250.0000.0000.0000.000
24A23ASP-1-0.802-0.87717.617-0.217-0.2170.0000.0000.0000.000
25A24PRO0-0.017-0.01719.483-0.031-0.0310.0000.0000.0000.000
26A25PHE0-0.057-0.02520.3140.0220.0220.0000.0000.0000.000
27A26ASP-1-0.805-0.93123.346-0.167-0.1670.0000.0000.0000.000
28A27GLU-1-0.830-0.87925.892-0.261-0.2610.0000.0000.0000.000
29A28SER0-0.083-0.05927.5740.0160.0160.0000.0000.0000.000
30A29VAL0-0.042-0.03629.444-0.006-0.0060.0000.0000.0000.000
31A30GLY0-0.008-0.00427.6200.0050.0050.0000.0000.0000.000
32A31TYR0-0.031-0.01421.333-0.030-0.0300.0000.0000.0000.000
33A32PRO0-0.028-0.00820.7630.0140.0140.0000.0000.0000.000
34A33ILE00.0150.00420.612-0.026-0.0260.0000.0000.0000.000
35A34PRO00.0370.02416.807-0.032-0.0320.0000.0000.0000.000
36A35ASN0-0.041-0.01116.8390.0900.0900.0000.0000.0000.000
37A36VAL00.023-0.00512.376-0.050-0.0500.0000.0000.0000.000
38A37THR0-0.043-0.02613.8950.0110.0110.0000.0000.0000.000
39A38ALA00.0060.00513.5730.0480.0480.0000.0000.0000.000
40A39ASP-1-0.830-0.90613.3150.4100.4100.0000.0000.0000.000
41A40VAL0-0.031-0.02515.612-0.013-0.0130.0000.0000.0000.000
42A41VAL00.0060.01616.414-0.032-0.0320.0000.0000.0000.000
43A42THR00.002-0.00618.1970.0170.0170.0000.0000.0000.000
44A43GLU-1-0.830-0.92220.429-0.151-0.1510.0000.0000.0000.000
45A44SER0-0.031-0.03023.2230.0230.0230.0000.0000.0000.000
46A45HIS10.8700.93324.7520.1570.1570.0000.0000.0000.000
47A46GLN0-0.007-0.01527.6070.0020.0020.0000.0000.0000.000
48A47HIS00.009-0.02825.731-0.007-0.0070.0000.0000.0000.000
49A48PHE0-0.035-0.00926.6100.0040.0040.0000.0000.0000.000
50A49ASP-1-0.779-0.88230.699-0.094-0.0940.0000.0000.0000.000
51A50HIS0-0.111-0.05631.5700.0070.0070.0000.0000.0000.000
52A51ASN0-0.037-0.02326.932-0.007-0.0070.0000.0000.0000.000
53A52ALA00.1000.04924.324-0.003-0.0030.0000.0000.0000.000
54A53HIS0-0.0360.00122.214-0.002-0.0020.0000.0000.0000.000
55A54HIS10.8380.91823.2990.1240.1240.0000.0000.0000.000
56A55LEU0-0.013-0.00523.2470.0100.0100.0000.0000.0000.000
57A56VAL0-0.0150.02117.473-0.024-0.0240.0000.0000.0000.000
58A57LYS10.9450.97118.1060.1860.1860.0000.0000.0000.000
59A58GLY00.0450.02618.1040.0080.0080.0000.0000.0000.000
60A59ASN0-0.071-0.02719.172-0.036-0.0360.0000.0000.0000.000
61A60PHE0-0.0050.00418.5300.0280.0280.0000.0000.0000.000
62A61ARG10.8990.96019.971-0.076-0.0760.0000.0000.0000.000
63A62VAL00.0420.01620.715-0.006-0.0060.0000.0000.0000.000
64A63ILE0-0.064-0.03919.6750.0160.0160.0000.0000.0000.000
65A64ASP-1-0.843-0.92023.359-0.041-0.0410.0000.0000.0000.000
66A65ARG10.9210.94225.7010.0050.0050.0000.0000.0000.000
67A66PRO00.0410.03525.0050.0040.0040.0000.0000.0000.000
68A67GLY00.0010.01024.4740.0090.0090.0000.0000.0000.000
69A68ALA0-0.014-0.00621.350-0.007-0.0070.0000.0000.0000.000
70A69TYR0-0.046-0.04319.7670.0130.0130.0000.0000.0000.000
71A70THR0-0.036-0.01916.5500.0110.0110.0000.0000.0000.000
72A71VAL0-0.0150.00016.423-0.003-0.0030.0000.0000.0000.000
73A72ASN0-0.018-0.02114.839-0.012-0.0120.0000.0000.0000.000
74A73GLY00.0290.01413.0070.0720.0720.0000.0000.0000.000
75A74VAL00.0550.05310.0770.0070.0070.0000.0000.0000.000
76A75LYS10.8980.95412.633-0.205-0.2050.0000.0000.0000.000
77A76ILE00.0300.00414.368-0.037-0.0370.0000.0000.0000.000
78A77LYS10.8690.94516.885-0.012-0.0120.0000.0000.0000.000
79A78GLY00.0210.01919.494-0.025-0.0250.0000.0000.0000.000
80A79VAL00.000-0.00322.0520.0140.0140.0000.0000.0000.000
81A80GLU-1-0.875-0.94424.402-0.048-0.0480.0000.0000.0000.000
82A81THR0-0.035-0.02725.8860.0040.0040.0000.0000.0000.000
83A82PHE0-0.016-0.01028.656-0.001-0.0010.0000.0000.0000.000
84A83HIS00.0470.01931.4100.0010.0010.0000.0000.0000.000
85A84ASP-1-0.955-0.93934.173-0.045-0.0450.0000.0000.0000.000
86A92GLY0-0.029-0.02634.202-0.003-0.0030.0000.0000.0000.000
87A93LYS10.8880.95428.9300.0560.0560.0000.0000.0000.000
88A94ASN0-0.026-0.01225.367-0.019-0.0190.0000.0000.0000.000
89A95ILE0-0.072-0.02523.3160.0120.0120.0000.0000.0000.000
90A96VAL00.0240.03320.453-0.016-0.0160.0000.0000.0000.000
91A97PHE0-0.001-0.01018.0740.0300.0300.0000.0000.0000.000
92A98VAL00.005-0.00714.891-0.033-0.0330.0000.0000.0000.000
93A99PHE00.018-0.01011.8910.0520.0520.0000.0000.0000.000
94A100GLU-1-0.902-0.96410.7620.0740.0740.0000.0000.0000.000
95A101GLY00.006-0.0248.2240.1580.1580.0000.0000.0000.000
96A102GLU-1-0.795-0.9022.604-1.317-0.3670.243-0.373-0.821-0.001
97A103GLY0-0.105-0.0454.633-0.0290.062-0.001-0.004-0.0850.000
98A104ILE0-0.027-0.0093.6990.0110.1910.001-0.031-0.1500.000
99A105LYS10.8740.9407.312-0.068-0.0680.0000.0000.0000.000
100A106VAL00.0200.0069.194-0.039-0.0390.0000.0000.0000.000
101A107CYS0-0.036-0.00411.8490.0760.0760.0000.0000.0000.000
102A108HIS00.0360.01615.637-0.023-0.0230.0000.0000.0000.000
103A109LEU00.025-0.01918.0070.0410.0410.0000.0000.0000.000
104A110GLY00.0140.01421.3750.0230.0230.0000.0000.0000.000
105A111ASP-1-0.866-0.94623.602-0.210-0.2100.0000.0000.0000.000
106A112LEU0-0.040-0.01124.6460.0150.0150.0000.0000.0000.000
107A113GLY00.0730.02227.142-0.010-0.0100.0000.0000.0000.000
108A114HIS10.7380.84929.5590.0850.0850.0000.0000.0000.000
109A115VAL00.0690.02828.172-0.007-0.0070.0000.0000.0000.000
110A116LEU0-0.0120.01622.9310.0090.0090.0000.0000.0000.000
111A117THR00.0260.01627.5570.0040.0040.0000.0000.0000.000
112A118PRO00.0720.01028.011-0.001-0.0010.0000.0000.0000.000
113A119ALA00.0420.04027.7560.0040.0040.0000.0000.0000.000
114A120GLN00.0690.02325.793-0.003-0.0030.0000.0000.0000.000
115A121VAL00.0050.00623.216-0.003-0.0030.0000.0000.0000.000
116A122GLU-1-0.986-0.98122.7560.0300.0300.0000.0000.0000.000
117A123GLU-1-0.985-0.99323.1280.0180.0180.0000.0000.0000.000
118A124ILE0-0.033-0.02918.6620.0040.0040.0000.0000.0000.000
119A125GLY0-0.0010.00818.4010.0060.0060.0000.0000.0000.000
120A126GLU-1-0.936-0.98916.4540.0190.0190.0000.0000.0000.000
121A127ILE0-0.029-0.01613.973-0.003-0.0030.0000.0000.0000.000
122A128ASP-1-0.851-0.9129.707-0.032-0.0320.0000.0000.0000.000
123A129VAL00.002-0.0119.119-0.051-0.0510.0000.0000.0000.000
124A130LEU0-0.014-0.00812.1270.0440.0440.0000.0000.0000.000
125A131LEU00.0160.01813.902-0.047-0.0470.0000.0000.0000.000
126A132VAL0-0.006-0.01417.4310.0530.0530.0000.0000.0000.000
127A133PRO00.0080.02021.032-0.029-0.0290.0000.0000.0000.000
128A134VAL00.003-0.02023.7150.0140.0140.0000.0000.0000.000
129A135GLY00.0160.00526.4870.0060.0060.0000.0000.0000.000
130A136GLY0-0.032-0.02629.2060.0080.0080.0000.0000.0000.000
131A137THR0-0.044-0.00132.0400.0130.0130.0000.0000.0000.000
132A138TYR0-0.025-0.03331.1370.0120.0120.0000.0000.0000.000
133A139THR00.0030.00727.371-0.003-0.0030.0000.0000.0000.000
134A140ILE00.0010.02825.3680.0050.0050.0000.0000.0000.000
135A141GLY00.0430.02429.079-0.017-0.0170.0000.0000.0000.000
136A142PRO00.0050.00027.4850.0000.0000.0000.0000.0000.000
137A143LYS10.9600.95427.5230.1260.1260.0000.0000.0000.000
138A144GLU-1-0.821-0.90528.886-0.122-0.1220.0000.0000.0000.000
139A145ALA00.0070.01124.1390.0040.0040.0000.0000.0000.000
140A146LYS10.8700.94223.9900.1500.1500.0000.0000.0000.000
141A147GLU-1-0.915-0.94824.598-0.088-0.0880.0000.0000.0000.000
142A148VAL00.0130.00522.2950.0130.0130.0000.0000.0000.000
143A149ALA00.006-0.01520.3510.0050.0050.0000.0000.0000.000
144A150ASP-1-0.883-0.94620.579-0.126-0.1260.0000.0000.0000.000
145A151LEU0-0.050-0.01722.7730.0180.0180.0000.0000.0000.000
146A152LEU0-0.0120.00118.6870.0150.0150.0000.0000.0000.000
147A153ASN0-0.033-0.01217.988-0.014-0.0140.0000.0000.0000.000
148A154ALA00.0060.02115.8870.0030.0030.0000.0000.0000.000
149A155LYS10.8980.95512.6480.0540.0540.0000.0000.0000.000
150A156VAL00.0360.02410.230-0.024-0.0240.0000.0000.0000.000
151A157ILE0-0.019-0.00713.4390.0360.0360.0000.0000.0000.000
152A158ILE00.007-0.00312.405-0.043-0.0430.0000.0000.0000.000
153A159PRO0-0.0260.00616.9140.0500.0500.0000.0000.0000.000
154A160MET0-0.027-0.01519.721-0.062-0.0620.0000.0000.0000.000
155A161HIS0-0.016-0.02121.6000.0120.0120.0000.0000.0000.000
156A162TYR00.0160.01320.3120.0320.0320.0000.0000.0000.000
157A163LYS10.8000.91726.6490.2060.2060.0000.0000.0000.000
158A164THR00.0320.01924.822-0.021-0.0210.0000.0000.0000.000
159A165LYS10.9300.95627.6340.2810.2810.0000.0000.0000.000
160A166TYR00.028-0.01629.0500.0160.0160.0000.0000.0000.000
161A167LEU00.0380.04627.6970.0160.0160.0000.0000.0000.000
162A168LYS11.0040.98529.9030.1800.1800.0000.0000.0000.000
163A169PHE00.001-0.00532.5920.0020.0020.0000.0000.0000.000
164A170ASN00.0100.00834.520-0.002-0.0020.0000.0000.0000.000
165A171LEU0-0.0010.01628.8860.0010.0010.0000.0000.0000.000
166A172LEU0-0.020-0.01430.838-0.002-0.0020.0000.0000.0000.000
167A173PRO0-0.016-0.01428.868-0.017-0.0170.0000.0000.0000.000
168A174VAL00.0980.04622.4390.0120.0120.0000.0000.0000.000
169A175ASP-1-0.875-0.94725.907-0.318-0.3180.0000.0000.0000.000
170A176ASP-1-0.917-0.96827.636-0.193-0.1930.0000.0000.0000.000
171A177PHE0-0.020-0.02221.3050.0160.0160.0000.0000.0000.000
172A178LEU0-0.010-0.00922.0540.0070.0070.0000.0000.0000.000
173A179LYS10.9170.97025.4290.1850.1850.0000.0000.0000.000
174A180LEU0-0.104-0.04026.7040.0210.0210.0000.0000.0000.000
175A181PHE0-0.016-0.01722.2850.0160.0160.0000.0000.0000.000
176A182ASP-1-0.888-0.93624.213-0.176-0.1760.0000.0000.0000.000
177A183SER0-0.077-0.03521.086-0.015-0.0150.0000.0000.0000.000
178A184TYR0-0.022-0.01819.4990.0040.0040.0000.0000.0000.000
179A185GLU-1-0.875-0.93013.112-1.045-1.0450.0000.0000.0000.000
180A186ARG10.9070.95917.1800.4930.4930.0000.0000.0000.000
181A187VAL00.0320.02111.685-0.051-0.0510.0000.0000.0000.000
182A188GLY00.0300.02313.1370.1320.1320.0000.0000.0000.000
183A189ASN00.018-0.00212.978-0.079-0.0790.0000.0000.0000.000
184A190ILE00.006-0.0077.0210.0610.0610.0000.0000.0000.000
185A191LEU0-0.0120.0048.1390.0700.0700.0000.0000.0000.000
186A192GLU-1-0.920-0.9642.327-23.677-19.4911.628-2.709-3.104-0.034
187A193LEU0-0.045-0.0214.3030.3920.9110.000-0.151-0.3680.000
188A194PHE00.027-0.0042.218-3.492-2.87610.571-4.559-6.629-0.027
189A195GLU-1-0.939-0.9663.3214.4164.5080.0110.357-0.4590.000
190A196LYS10.9440.9825.032-1.404-1.401-0.001-0.0030.0010.000
191A197PRO0-0.005-0.0056.7630.0650.0650.0000.0000.0000.000
192A198LYS10.9610.9879.815-0.303-0.3030.0000.0000.0000.000
193A199GLU-1-0.943-0.97912.795-0.115-0.1150.0000.0000.0000.000
194A200ARG10.7770.89114.2770.1360.1360.0000.0000.0000.000
195A201LYS10.8940.94711.5470.9060.9060.0000.0000.0000.000
196A202VAL00.0140.02115.628-0.035-0.0350.0000.0000.0000.000
197A203VAL00.005-0.00612.655-0.020-0.0200.0000.0000.0000.000
198A204VAL0-0.020-0.01815.9540.0360.0360.0000.0000.0000.000
199A205MET0-0.0080.00511.270-0.013-0.0130.0000.0000.0000.000
200A206GLU-1-0.956-0.99215.992-0.522-0.5220.0000.0000.0000.000
201A207VAL0-0.028-0.00616.598-0.083-0.0830.0000.0000.0000.000
202A208GLN0-0.0090.00115.4790.0710.0710.0000.0000.0000.000