Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4JL4N

Calculation Name: 2VZN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VZN

Chain ID: A

ChEMBL ID:

UniProt ID: P35778

Base Structure: X-ray

Registration Date: 2023-09-22

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2631632.2145
FMO2-HF: Nuclear repulsion 2542618.449817
FMO2-HF: Total energy -89013.764683
FMO2-MP2: Total energy -89265.796217


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-9.156-3.2260.317-2.644-3.6040.005
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.006
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].
3A4CYS0-0.096-0.0303.047-2.5661.0890.136-1.786-2.0050.009
4A5ASN0-0.002-0.0092.608-0.5090.5450.164-0.331-0.8880.000
5A6LEU00.0220.0234.3680.0830.330-0.001-0.038-0.2070.000
6A7GLN00.021-0.0057.0230.3820.3820.0000.0000.0000.000
7A8SER0-0.052-0.02610.0940.2470.2470.0000.0000.0000.000
8A9CYS00.0010.0029.292-0.066-0.0660.0000.0000.0000.000
9A10LYS10.9300.9756.8350.5710.5710.0000.0000.0000.000
10A11ARG10.9410.97811.6650.7370.7370.0000.0000.0000.000
11A12ASN0-0.028-0.01214.2170.1060.1060.0000.0000.0000.000
12A13ASN0-0.020-0.00614.8180.0410.0410.0000.0000.0000.000
13A14ALA00.0000.01613.5820.0320.0320.0000.0000.0000.000
14A15ILE00.0070.0029.801-0.019-0.0190.0000.0000.0000.000
15A16HIS0-0.004-0.0206.1910.1500.1500.0000.0000.0000.000
16A17THR00.028-0.0089.1660.2420.2420.0000.0000.0000.000
17A18MET0-0.032-0.0175.4320.4900.4900.0000.0000.0000.000
18A20GLN00.0230.0157.2070.3160.3160.0000.0000.0000.000
19A21TYR00.0230.01510.9550.1800.1800.0000.0000.0000.000
20A22THR00.0430.0128.284-0.243-0.2430.0000.0000.0000.000
21A23SER00.0140.00110.4100.0330.0330.0000.0000.0000.000
22A24PRO0-0.037-0.02113.165-0.103-0.1030.0000.0000.0000.000
23A25THR0-0.006-0.00614.5180.0020.0020.0000.0000.0000.000
24A26PRO0-0.007-0.00617.624-0.021-0.0210.0000.0000.0000.000
25A27GLY00.0310.02719.2860.0380.0380.0000.0000.0000.000
26A28PRO00.000-0.01420.5690.0040.0040.0000.0000.0000.000
27A29MET00.0100.01023.0370.0230.0230.0000.0000.0000.000
28A30CYS0-0.185-0.05518.9370.0330.0330.0000.0000.0000.000
29A31LEU00.0400.01624.8540.0100.0100.0000.0000.0000.000
30A32GLU-1-0.860-0.93928.312-0.123-0.1230.0000.0000.0000.000
31A33TYR00.0190.01623.139-0.010-0.0100.0000.0000.0000.000
32A34SER0-0.040-0.03326.1870.0170.0170.0000.0000.0000.000
33A35ASN0-0.013-0.03625.418-0.021-0.0210.0000.0000.0000.000
34A36VAL00.0280.01719.209-0.019-0.0190.0000.0000.0000.000
35A37GLY0-0.0210.01119.5190.0130.0130.0000.0000.0000.000
36A38PHE0-0.053-0.04219.6710.0240.0240.0000.0000.0000.000
37A39THR00.027-0.01822.0630.0040.0040.0000.0000.0000.000
38A40ASP-1-0.809-0.91821.668-0.287-0.2870.0000.0000.0000.000
39A41ALA00.0450.03124.101-0.006-0.0060.0000.0000.0000.000
40A42GLU-1-0.819-0.88725.069-0.247-0.2470.0000.0000.0000.000
41A43LYS10.8110.90219.2700.3200.3200.0000.0000.0000.000
42A44ASP-1-0.859-0.92722.965-0.259-0.2590.0000.0000.0000.000
43A45ALA0-0.063-0.02125.4670.0030.0030.0000.0000.0000.000
44A46ILE00.0260.00822.1210.0020.0020.0000.0000.0000.000
45A47VAL0-0.0110.00621.576-0.007-0.0070.0000.0000.0000.000
46A48ASN0-0.014-0.02024.2380.0110.0110.0000.0000.0000.000
47A49LYS10.8230.91127.8990.2180.2180.0000.0000.0000.000
48A50HIS00.0530.02123.933-0.009-0.0090.0000.0000.0000.000
49A51ASN00.0620.04824.938-0.007-0.0070.0000.0000.0000.000
50A52GLU-1-0.858-0.88628.125-0.181-0.1810.0000.0000.0000.000
51A53LEU0-0.035-0.01729.3100.0140.0140.0000.0000.0000.000
52A54ARG10.8030.89024.1820.3470.3470.0000.0000.0000.000
53A55GLN0-0.008-0.02829.9050.0190.0190.0000.0000.0000.000
54A56ARG10.8650.93132.5690.1750.1750.0000.0000.0000.000
55A57VAL00.0560.02932.4620.0120.0120.0000.0000.0000.000
56A58ALA00.0300.01831.9540.0090.0090.0000.0000.0000.000
57A59SER0-0.082-0.04533.9680.0120.0120.0000.0000.0000.000
58A60GLY0-0.012-0.00437.2210.0090.0090.0000.0000.0000.000
59A61LYS10.9150.96038.0980.1470.1470.0000.0000.0000.000
60A62GLU-1-0.779-0.83536.253-0.159-0.1590.0000.0000.0000.000
61A63MET00.0500.01038.7570.0010.0010.0000.0000.0000.000
62A64ARG10.8260.89637.0090.1680.1680.0000.0000.0000.000
63A65GLY00.1250.05439.219-0.007-0.0070.0000.0000.0000.000
64A66THR0-0.028-0.00239.3860.0090.0090.0000.0000.0000.000
65A67ASN0-0.080-0.04241.2970.0060.0060.0000.0000.0000.000
66A68GLY00.0260.02342.9810.0050.0050.0000.0000.0000.000
67A69PRO0-0.055-0.01841.403-0.007-0.0070.0000.0000.0000.000
68A70GLN00.0150.00436.087-0.008-0.0080.0000.0000.0000.000
69A71PRO0-0.0170.00537.0510.0040.0040.0000.0000.0000.000
70A72PRO00.0370.02936.501-0.010-0.0100.0000.0000.0000.000
71A73ALA0-0.023-0.00831.9770.0000.0000.0000.0000.0000.000
72A74VAL0-0.111-0.05233.4290.0070.0070.0000.0000.0000.000
73A75LYS10.8180.90029.1580.1750.1750.0000.0000.0000.000
74A76MET00.0130.00828.112-0.016-0.0160.0000.0000.0000.000
75A77PRO0-0.0470.01124.1600.0120.0120.0000.0000.0000.000
76A78ASN00.0470.01325.426-0.024-0.0240.0000.0000.0000.000
77A79LEU0-0.021-0.00620.974-0.014-0.0140.0000.0000.0000.000
78A80THR00.0130.00319.3860.0190.0190.0000.0000.0000.000
79A81TRP00.0750.02116.366-0.061-0.0610.0000.0000.0000.000
80A82ASP-1-0.802-0.88911.724-1.053-1.0530.0000.0000.0000.000
81A83PRO00.0460.01311.968-0.091-0.0910.0000.0000.0000.000
82A84GLU-1-0.744-0.8335.435-3.902-3.9020.0000.0000.0000.000
83A85LEU00.000-0.0029.326-0.192-0.1920.0000.0000.0000.000
84A86ALA00.0250.01811.3680.0230.0230.0000.0000.0000.000
85A87THR0-0.069-0.0269.556-0.021-0.0210.0000.0000.0000.000
86A88ILE00.004-0.0046.4940.0570.0570.0000.0000.0000.000
87A89ALA0-0.036-0.00710.1440.1520.1520.0000.0000.0000.000
88A90GLN0-0.019-0.03213.8210.1190.1190.0000.0000.0000.000
89A91ARG10.8380.93010.0010.9790.9790.0000.0000.0000.000
90A92TRP00.0330.01313.1920.0740.0740.0000.0000.0000.000
91A93ALA00.0150.00914.8220.0980.0980.0000.0000.0000.000
92A94ASN0-0.020-0.01316.1130.0770.0770.0000.0000.0000.000
93A95GLN00.002-0.00515.1940.1160.1160.0000.0000.0000.000
94A97THR00.0430.03220.3390.0360.0360.0000.0000.0000.000
95A98PHE0-0.064-0.04021.499-0.039-0.0390.0000.0000.0000.000
96A99GLU-1-0.895-0.94220.604-0.323-0.3230.0000.0000.0000.000
97A100HIS0-0.035-0.03418.566-0.001-0.0010.0000.0000.0000.000
98A101ASP-1-0.727-0.81513.197-1.048-1.0480.0000.0000.0000.000
99A102ALA00.0220.00114.452-0.015-0.0150.0000.0000.0000.000
100A103CYS0-0.041-0.02611.178-0.108-0.1080.0000.0000.0000.000
101A104ARG10.8490.9269.7540.8110.8110.0000.0000.0000.000
102A105ASN0-0.006-0.0149.603-0.096-0.0960.0000.0000.0000.000
103A106VAL00.0310.0316.462-0.712-0.7120.0000.0000.0000.000
104A107GLU-1-0.888-0.9603.325-7.224-6.2500.018-0.489-0.504-0.004
105A108ARG10.7280.8357.3501.8461.8460.0000.0000.0000.000
106A109PHE00.0220.00310.5730.2550.2550.0000.0000.0000.000
107A110ALA00.0060.00611.458-0.246-0.2460.0000.0000.0000.000
108A111VAL0-0.005-0.00610.8690.0760.0760.0000.0000.0000.000
109A112GLY00.0270.01413.8990.0340.0340.0000.0000.0000.000
110A113GLN0-0.029-0.04815.337-0.019-0.0190.0000.0000.0000.000
111A114ASN00.0070.02118.3390.0340.0340.0000.0000.0000.000
112A115ILE00.0270.02819.235-0.038-0.0380.0000.0000.0000.000
113A116ALA00.0140.02522.6480.0360.0360.0000.0000.0000.000
114A117ALA00.0250.01024.868-0.018-0.0180.0000.0000.0000.000
115A118THR0-0.0210.00327.3430.0180.0180.0000.0000.0000.000
116A119SER00.001-0.02930.707-0.009-0.0090.0000.0000.0000.000
117A120SER0-0.0250.00233.2930.0070.0070.0000.0000.0000.000
118A121SER00.0620.03835.8270.0000.0000.0000.0000.0000.000
119A122GLY00.0380.02836.7890.0050.0050.0000.0000.0000.000
120A123LYS10.9590.96933.6280.1030.1030.0000.0000.0000.000
121A124ASN0-0.016-0.01931.5900.0010.0010.0000.0000.0000.000
122A125LYS10.8470.91733.4720.1480.1480.0000.0000.0000.000
123A126SER00.0720.04331.3350.0030.0030.0000.0000.0000.000
124A127THR0-0.037-0.05730.210-0.017-0.0170.0000.0000.0000.000
125A128PRO00.0430.00125.464-0.001-0.0010.0000.0000.0000.000
126A129ASN00.0170.00227.605-0.019-0.0190.0000.0000.0000.000
127A130GLU-1-0.789-0.85329.898-0.186-0.1860.0000.0000.0000.000
128A131MET00.0050.00526.5510.0020.0020.0000.0000.0000.000
129A132ILE0-0.0080.00625.304-0.006-0.0060.0000.0000.0000.000
130A133LEU0-0.027-0.02328.2890.0030.0030.0000.0000.0000.000
131A134LEU0-0.032-0.01730.9850.0100.0100.0000.0000.0000.000
132A135TRP00.007-0.01522.596-0.002-0.0020.0000.0000.0000.000
133A136TYR00.004-0.03229.2040.0070.0070.0000.0000.0000.000
134A137ASN0-0.018-0.02231.1320.0190.0190.0000.0000.0000.000
135A138GLU-1-0.715-0.85329.564-0.270-0.2700.0000.0000.0000.000
136A139VAL0-0.054-0.01833.5080.0080.0080.0000.0000.0000.000
137A140LYS10.8610.92535.0990.1610.1610.0000.0000.0000.000
138A141ASP-1-0.874-0.91635.776-0.162-0.1620.0000.0000.0000.000
139A142PHE0-0.026-0.02032.068-0.005-0.0050.0000.0000.0000.000
140A143ASP-1-0.758-0.83836.178-0.133-0.1330.0000.0000.0000.000
141A144ASN00.0510.00836.553-0.015-0.0150.0000.0000.0000.000
142A145ARG10.8090.85637.0930.1270.1270.0000.0000.0000.000
143A146TRP00.0110.00933.155-0.003-0.0030.0000.0000.0000.000
144A147ILE0-0.023-0.00132.553-0.014-0.0140.0000.0000.0000.000
145A148SER0-0.0040.00231.820-0.011-0.0110.0000.0000.0000.000
146A149SER0-0.031-0.02231.2130.0020.0020.0000.0000.0000.000
147A150PHE0-0.001-0.00526.9940.0060.0060.0000.0000.0000.000
148A151PRO00.009-0.00429.9810.0030.0030.0000.0000.0000.000
149A152SER0-0.009-0.01529.407-0.012-0.0120.0000.0000.0000.000
150A153ASP-1-0.855-0.92129.934-0.193-0.1930.0000.0000.0000.000
151A154ASP-1-0.843-0.92727.869-0.284-0.2840.0000.0000.0000.000
152A155ASN0-0.026-0.03230.302-0.006-0.0060.0000.0000.0000.000
153A156ILE0-0.041-0.01231.850-0.001-0.0010.0000.0000.0000.000
154A157LEU0-0.025-0.00724.545-0.010-0.0100.0000.0000.0000.000
155A158MET0-0.015-0.00728.087-0.014-0.0140.0000.0000.0000.000
156A159LYS10.8450.93029.6400.1780.1780.0000.0000.0000.000
157A160VAL0-0.037-0.02030.8950.0040.0040.0000.0000.0000.000
158A161GLY00.0720.05126.749-0.006-0.0060.0000.0000.0000.000
159A162HIS0-0.022-0.00924.048-0.060-0.0600.0000.0000.0000.000
160A163TYR0-0.009-0.01226.239-0.013-0.0130.0000.0000.0000.000
161A164THR0-0.029-0.03926.5540.0010.0010.0000.0000.0000.000
162A165GLN00.0240.01220.262-0.050-0.0500.0000.0000.0000.000
163A166ILE0-0.0180.00423.772-0.016-0.0160.0000.0000.0000.000
164A167VAL0-0.030-0.01225.5720.0010.0010.0000.0000.0000.000
165A168TRP00.0500.05122.3880.0200.0200.0000.0000.0000.000
166A169ALA00.0260.01024.113-0.023-0.0230.0000.0000.0000.000
167A170LYS10.9200.94621.9360.2780.2780.0000.0000.0000.000
168A171THR0-0.0040.00918.982-0.013-0.0130.0000.0000.0000.000
169A172THR0-0.019-0.02118.9080.0390.0390.0000.0000.0000.000
170A173LYS10.8570.93615.0760.5130.5130.0000.0000.0000.000
171A174ILE00.0260.01917.326-0.037-0.0370.0000.0000.0000.000
172A175GLY00.0300.01714.7910.0160.0160.0000.0000.0000.000
173A176CYS0-0.115-0.04215.867-0.064-0.0640.0000.0000.0000.000
174A177GLY00.0550.01616.973-0.025-0.0250.0000.0000.0000.000
175A178ARG10.8190.90317.8240.3180.3180.0000.0000.0000.000
176A179ILE0-0.0080.02020.8430.0010.0010.0000.0000.0000.000
177A180MET00.0080.02522.8320.0050.0050.0000.0000.0000.000
178A181PHE00.006-0.00425.128-0.004-0.0040.0000.0000.0000.000
179A182LYS10.8010.91727.9470.1200.1200.0000.0000.0000.000
180A183GLU-1-0.735-0.83530.087-0.194-0.1940.0000.0000.0000.000
181A184PRO00.023-0.01330.6940.0100.0100.0000.0000.0000.000
182A185ASP-1-0.842-0.90533.718-0.130-0.1300.0000.0000.0000.000
183A186ASN0-0.060-0.04235.1930.0030.0030.0000.0000.0000.000
184A187TRP0-0.0060.01435.023-0.002-0.0020.0000.0000.0000.000
185A188THR0-0.076-0.04831.138-0.003-0.0030.0000.0000.0000.000
186A189LYS10.8920.94027.2600.2130.2130.0000.0000.0000.000
187A190HIS0-0.051-0.02926.708-0.013-0.0130.0000.0000.0000.000
188A191TYR00.0040.00019.7180.0090.0090.0000.0000.0000.000
189A192LEU00.011-0.00621.576-0.014-0.0140.0000.0000.0000.000
190A193VAL00.0140.01516.6500.0040.0040.0000.0000.0000.000
191A195ASN00.0790.03912.2340.1300.1300.0000.0000.0000.000
192A196TYR0-0.021-0.03216.0150.0340.0340.0000.0000.0000.000
193A197GLY00.0380.03914.623-0.104-0.1040.0000.0000.0000.000
194A198PRO0-0.022-0.02615.4470.0750.0750.0000.0000.0000.000
195A199ALA0-0.001-0.00516.1700.0600.0600.0000.0000.0000.000
196A200GLY0-0.009-0.01317.7750.0450.0450.0000.0000.0000.000
197A201ASN0-0.034-0.02521.283-0.007-0.0070.0000.0000.0000.000
198A202VAL0-0.0180.00221.031-0.002-0.0020.0000.0000.0000.000
199A203LEU00.0220.00423.6010.0310.0310.0000.0000.0000.000
200A204GLY00.0560.04226.4260.0070.0070.0000.0000.0000.000
201A205ALA0-0.056-0.02925.5310.0180.0180.0000.0000.0000.000
202A206PRO00.0000.01527.5920.0030.0030.0000.0000.0000.000
203A207ILE0-0.041-0.01227.506-0.021-0.0210.0000.0000.0000.000
204A208TYR0-0.041-0.06227.726-0.017-0.0170.0000.0000.0000.000
205A209GLU-1-0.844-0.91330.092-0.158-0.1580.0000.0000.0000.000
206A210ILE00.0640.03232.8030.0050.0050.0000.0000.0000.000
207A211LYS10.9740.99236.1810.1340.1340.0000.0000.0000.000
208A212LYS10.8750.92538.1640.1280.1280.0000.0000.0000.000
209A213HIS00.0340.01741.9810.0020.0020.0000.0000.0000.000
210A214HIS00.0240.00644.5630.0030.0030.0000.0000.0000.000
211A215HIS00.0370.01446.8870.0010.0010.0000.0000.0000.000
212A216HIS0-0.009-0.01750.0350.0030.0030.0000.0000.0000.000
213A217HIS0-0.051-0.00947.3950.0000.0000.0000.0000.0000.000
214A218HIS00.0200.02650.683-0.002-0.0020.0000.0000.0000.000