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

tag_button

FMODB ID: VQK21

Calculation Name: 4N0V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N0V

Chain ID: A

ChEMBL ID:

UniProt ID: A1TY67

Base Structure: X-ray

Registration Date: 2023-09-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2413129.527863
FMO2-HF: Nuclear repulsion 2330804.783173
FMO2-HF: Total energy -82324.74469
FMO2-MP2: Total energy -82562.805357


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-32.02-19.49318.614-11.48-19.66-0.075
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : 0.002
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].
3A3ILE0-0.0020.0033.797-1.0072.069-0.028-1.541-1.5060.010
4A4TYR0-0.057-0.0305.866-0.292-0.2920.0000.0000.0000.000
5A5ASP-1-0.814-0.9109.4860.2680.2680.0000.0000.0000.000
6A6THR00.0240.00511.834-0.099-0.0990.0000.0000.0000.000
7A7GLU-1-0.921-0.96014.739-0.052-0.0520.0000.0000.0000.000
8A8GLY00.0490.03016.480-0.008-0.0080.0000.0000.0000.000
9A9PHE00.001-0.00317.1320.0150.0150.0000.0000.0000.000
10A10PRO00.0330.01217.2010.0360.0360.0000.0000.0000.000
11A11ASN00.0470.00315.4580.0790.0790.0000.0000.0000.000
12A12PRO0-0.010-0.01312.5140.1270.1270.0000.0000.0000.000
13A13LEU00.0370.03512.5960.0890.0890.0000.0000.0000.000
14A14ARG10.8450.89514.286-0.548-0.5480.0000.0000.0000.000
15A15VAL00.0230.0168.3420.0770.0770.0000.0000.0000.000
16A16ARG10.8760.9089.5940.2990.2990.0000.0000.0000.000
17A17ILE00.0220.02010.761-0.012-0.0120.0000.0000.0000.000
18A18ALA00.001-0.0059.983-0.018-0.0180.0000.0000.0000.000
19A19LEU00.0040.0073.736-0.0180.1890.002-0.029-0.1800.000
20A20ALA00.0020.0097.503-0.172-0.1720.0000.0000.0000.000
21A21GLU-1-0.816-0.87710.1610.4470.4470.0000.0000.0000.000
22A22LYS10.7150.8837.092-1.410-1.4100.0000.0000.0000.000
23A23GLY0-0.0180.0028.225-0.012-0.0120.0000.0000.0000.000
24A24ALA0-0.017-0.0163.688-0.312-0.1810.002-0.028-0.1050.000
25A25THR00.016-0.0144.733-0.256-0.198-0.001-0.002-0.0550.000
26A26ASP-1-0.907-0.9516.625-0.822-0.8220.0000.0000.0000.000
27A27LYS10.8390.9242.883-0.799-0.1170.389-0.210-0.8610.000
28A28VAL00.0150.0192.280-6.210-3.1422.776-2.055-3.789-0.019
29A29VAL0-0.016-0.0013.8550.6211.2680.006-0.188-0.4650.000
30A30PHE00.014-0.0075.967-0.089-0.0890.0000.0000.0000.000
31A31VAL0-0.035-0.0218.057-0.031-0.0310.0000.0000.0000.000
32A32PRO0-0.012-0.01210.5060.1840.1840.0000.0000.0000.000
33A33VAL00.0190.02012.797-0.037-0.0370.0000.0000.0000.000
34A34ASP-1-0.864-0.94315.453-0.135-0.1350.0000.0000.0000.000
35A35VAL0-0.035-0.02217.6310.0220.0220.0000.0000.0000.000
36A36MET0-0.080-0.03220.1530.0220.0220.0000.0000.0000.000
37A37GLY00.0410.04222.6830.0130.0130.0000.0000.0000.000
38A38GLY0-0.065-0.03822.937-0.005-0.0050.0000.0000.0000.000
39A39GLU-1-0.832-0.91316.445-0.422-0.4220.0000.0000.0000.000
40A40HIS0-0.011-0.00317.281-0.041-0.0410.0000.0000.0000.000
41A41ARG10.8410.90218.2970.0420.0420.0000.0000.0000.000
42A42THR0-0.0040.01718.9540.0060.0060.0000.0000.0000.000
43A43THR00.010-0.01419.7770.0210.0210.0000.0000.0000.000
44A44ASP-1-0.877-0.93216.537-0.353-0.3530.0000.0000.0000.000
45A45PHE0-0.047-0.01212.443-0.024-0.0240.0000.0000.0000.000
46A46ARG10.8940.91715.1250.0660.0660.0000.0000.0000.000
47A47ALA0-0.039-0.00516.0070.0460.0460.0000.0000.0000.000
48A48LYS10.8640.9419.6540.9330.9330.0000.0000.0000.000
49A49ASN00.001-0.01412.7440.1370.1370.0000.0000.0000.000
50A50PRO00.0230.01914.664-0.031-0.0310.0000.0000.0000.000
51A51ASP-1-0.930-0.96416.8800.3260.3260.0000.0000.0000.000
52A52ALA0-0.077-0.03917.740-0.013-0.0130.0000.0000.0000.000
53A53THR0-0.041-0.01816.2430.0020.0020.0000.0000.0000.000
54A54VAL00.0410.03213.276-0.018-0.0180.0000.0000.0000.000
55A55PRO0-0.051-0.0439.5070.0050.0050.0000.0000.0000.000
56A56VAL0-0.010-0.0108.4940.0940.0940.0000.0000.0000.000
57A57LEU0-0.0020.0112.472-1.231-0.3991.313-0.375-1.770-0.002
58A58GLU-1-0.777-0.8794.454-1.940-1.706-0.001-0.045-0.1880.000
59A59LEU00.005-0.0162.509-4.514-1.9972.330-2.057-2.790-0.022
60A60ASP-1-0.848-0.9281.976-14.816-14.2176.376-3.655-3.320-0.048
61A61ASP-1-0.936-0.9454.1510.2970.4120.000-0.048-0.0670.000
62A62GLY0-0.013-0.0016.6870.1380.1380.0000.0000.0000.000
63A63THR0-0.049-0.0417.4780.0980.0980.0000.0000.0000.000
64A64CYS0-0.056-0.0206.859-0.097-0.0970.0000.0000.0000.000
65A65ILE0-0.022-0.0047.1670.0520.0520.0000.0000.0000.000
66A66ALA00.0560.0259.1040.0480.0480.0000.0000.0000.000
67A67GLN00.0190.00611.8550.1320.1320.0000.0000.0000.000
68A68CYS00.0060.02112.4230.1370.1370.0000.0000.0000.000
69A69ASN00.0320.01312.0910.2480.2480.0000.0000.0000.000
70A70ALA00.0400.03311.9420.1170.1170.0000.0000.0000.000
71A71ILE00.0120.0026.8280.3060.3060.0000.0000.0000.000
72A72THR0-0.019-0.0317.7790.6920.6920.0000.0000.0000.000
73A73GLU-1-0.895-0.9409.7901.3041.3040.0000.0000.0000.000
74A74TYR0-0.0070.0073.086-2.694-2.0741.283-0.523-1.3800.005
75A75LEU0-0.005-0.0173.658-0.1430.5020.348-0.169-0.8240.000
76A76ASP-1-0.740-0.8556.3150.7240.7240.0000.0000.0000.000
77A77GLY0-0.0250.0039.344-0.293-0.2930.0000.0000.0000.000
78A78VAL0-0.037-0.0194.677-0.407-0.297-0.001-0.008-0.1000.000
79A79PHE0-0.038-0.0132.067-0.561-1.5753.820-0.547-2.2600.001
80A80ASP-1-0.875-0.9297.5900.8200.8200.0000.0000.0000.000
81A81GLY0-0.004-0.01110.7560.0210.0210.0000.0000.0000.000
82A82PRO0-0.055-0.04513.3390.0280.0280.0000.0000.0000.000
83A83SER00.0430.05013.3490.0770.0770.0000.0000.0000.000
84A84LEU00.038-0.00411.052-0.126-0.1260.0000.0000.0000.000
85A85THR0-0.014-0.03013.519-0.099-0.0990.0000.0000.0000.000
86A86GLY0-0.0030.00716.063-0.074-0.0740.0000.0000.0000.000
87A87ALA00.014-0.00417.6510.0690.0690.0000.0000.0000.000
88A88SER0-0.008-0.00719.518-0.050-0.0500.0000.0000.0000.000
89A89PRO00.0550.00922.5620.0200.0200.0000.0000.0000.000
90A90LYS10.9961.00524.295-0.286-0.2860.0000.0000.0000.000
91A91GLU-1-0.808-0.89521.1140.5190.5190.0000.0000.0000.000
92A92ARG10.8830.93215.457-0.924-0.9240.0000.0000.0000.000
93A93ALA0-0.027-0.00521.2190.0110.0110.0000.0000.0000.000
94A94VAL0-0.029-0.01924.056-0.013-0.0130.0000.0000.0000.000
95A95ILE00.0480.02718.638-0.017-0.0170.0000.0000.0000.000
96A96ALA00.0030.01020.5840.0010.0010.0000.0000.0000.000
97A97MET0-0.024-0.00421.508-0.027-0.0270.0000.0000.0000.000
98A98MET0-0.035-0.02023.995-0.027-0.0270.0000.0000.0000.000
99A99ASN00.0520.04517.766-0.036-0.0360.0000.0000.0000.000
100A100ILE00.0220.01320.846-0.015-0.0150.0000.0000.0000.000
101A101ARG10.8840.94723.292-0.310-0.3100.0000.0000.0000.000
102A102ALA00.0480.02922.792-0.027-0.0270.0000.0000.0000.000
103A103GLU-1-0.856-0.93518.7730.5290.5290.0000.0000.0000.000
104A104SER0-0.054-0.04022.729-0.031-0.0310.0000.0000.0000.000
105A105GLY00.0000.00825.770-0.025-0.0250.0000.0000.0000.000
106A106LEU00.0040.00225.797-0.023-0.0230.0000.0000.0000.000
107A107MET0-0.0120.01119.864-0.027-0.0270.0000.0000.0000.000
108A108ASN0-0.001-0.02422.155-0.022-0.0220.0000.0000.0000.000
109A109ALA0-0.0080.03125.096-0.023-0.0230.0000.0000.0000.000
110A110VAL00.0310.00326.599-0.024-0.0240.0000.0000.0000.000
111A111GLY00.0110.00325.306-0.020-0.0200.0000.0000.0000.000
112A112ALA0-0.045-0.02326.174-0.023-0.0230.0000.0000.0000.000
113A113TYR00.009-0.00329.074-0.018-0.0180.0000.0000.0000.000
114A114PHE00.0070.00625.831-0.014-0.0140.0000.0000.0000.000
115A115HIS10.8220.88123.630-0.118-0.1180.0000.0000.0000.000
116A116HIS00.0390.03629.094-0.018-0.0180.0000.0000.0000.000
117A117ALA0-0.025-0.01132.447-0.008-0.0080.0000.0000.0000.000
118A118THR0-0.058-0.01631.612-0.009-0.0090.0000.0000.0000.000
119A119ARG10.9760.97632.7670.0070.0070.0000.0000.0000.000
120A120GLY00.0310.02529.372-0.005-0.0050.0000.0000.0000.000
121A121LEU0-0.056-0.04523.451-0.006-0.0060.0000.0000.0000.000
122A122GLY0-0.011-0.00127.817-0.016-0.0160.0000.0000.0000.000
123A123PRO00.007-0.01030.3780.0030.0030.0000.0000.0000.000
124A124ASP-1-0.890-0.92829.761-0.046-0.0460.0000.0000.0000.000
125A125LEU0-0.028-0.02124.3380.0020.0020.0000.0000.0000.000
126A126GLU-1-0.772-0.84027.8000.0730.0730.0000.0000.0000.000
127A127THR0-0.024-0.01428.9590.0000.0000.0000.0000.0000.000
128A128TRP0-0.022-0.01831.4290.0010.0010.0000.0000.0000.000
129A129GLN0-0.051-0.01532.0760.0030.0030.0000.0000.0000.000
130A130CYS0-0.029-0.01534.116-0.005-0.0050.0000.0000.0000.000
131A131PRO00.0670.01635.5890.0100.0100.0000.0000.0000.000
132A132ASP-1-0.884-0.92737.1720.0730.0730.0000.0000.0000.000
133A133TRP0-0.033-0.01830.7250.0040.0040.0000.0000.0000.000
134A134GLY00.0490.01333.0420.0100.0100.0000.0000.0000.000
135A135ASN0-0.029-0.03934.0370.0060.0060.0000.0000.0000.000
136A136LYS10.9660.99836.464-0.123-0.1230.0000.0000.0000.000
137A137GLN0-0.016-0.01930.7570.0190.0190.0000.0000.0000.000
138A138LYS10.9981.01432.683-0.080-0.0800.0000.0000.0000.000
139A139GLU-1-0.922-0.95934.1140.1100.1100.0000.0000.0000.000
140A140VAL0-0.071-0.02931.2630.0040.0040.0000.0000.0000.000
141A141ALA00.0270.01830.6410.0100.0100.0000.0000.0000.000
142A142GLN0-0.035-0.03631.6490.0040.0040.0000.0000.0000.000
143A143SER0-0.029-0.01534.486-0.002-0.0020.0000.0000.0000.000
144A144THR0-0.033-0.01628.6280.0070.0070.0000.0000.0000.000
145A145MET0-0.071-0.01430.4450.0060.0060.0000.0000.0000.000
146A146ALA00.0450.02232.0030.0020.0020.0000.0000.0000.000
147A147TYR00.0190.01329.4310.0110.0110.0000.0000.0000.000
148A148LEU00.007-0.01326.9740.0070.0070.0000.0000.0000.000
149A149ASN00.0300.02030.6260.0050.0050.0000.0000.0000.000
150A150GLU-1-0.934-0.97133.0780.1470.1470.0000.0000.0000.000
151A151VAL0-0.065-0.02428.8530.0020.0020.0000.0000.0000.000
152A152LEU0-0.027-0.02126.9700.0030.0030.0000.0000.0000.000
153A153ALA0-0.0080.01531.030-0.005-0.0050.0000.0000.0000.000
154A154GLU-1-1.010-1.00033.6140.1680.1680.0000.0000.0000.000
155A155ASN0-0.104-0.04628.6880.0130.0130.0000.0000.0000.000
156A156GLU-1-0.969-0.97226.2670.2370.2370.0000.0000.0000.000
157A157PHE0-0.009-0.02322.9730.0020.0020.0000.0000.0000.000
158A158LEU0-0.010-0.02123.564-0.009-0.0090.0000.0000.0000.000
159A159ALA0-0.040-0.02622.848-0.009-0.0090.0000.0000.0000.000
160A160GLY0-0.0040.00824.8840.0010.0010.0000.0000.0000.000
161A161ASP-1-0.907-0.95325.6020.3090.3090.0000.0000.0000.000
162A162ARG10.8080.89117.636-0.548-0.5480.0000.0000.0000.000
163A163PHE0-0.025-0.00215.8590.0010.0010.0000.0000.0000.000
164A164THR0-0.059-0.03517.2180.0530.0530.0000.0000.0000.000
165A165VAL00.0550.00814.996-0.027-0.0270.0000.0000.0000.000
166A166ALA0-0.0030.00816.562-0.037-0.0370.0000.0000.0000.000
167A167ASP-1-0.734-0.87219.7270.3690.3690.0000.0000.0000.000
168A168ILE00.0260.02113.758-0.043-0.0430.0000.0000.0000.000
169A169THR0-0.075-0.05717.928-0.025-0.0250.0000.0000.0000.000
170A170ALA00.0200.00519.545-0.046-0.0460.0000.0000.0000.000
171A171TYR0-0.056-0.03119.712-0.041-0.0410.0000.0000.0000.000
172A172ALA00.0440.01618.866-0.038-0.0380.0000.0000.0000.000
173A173GLY00.004-0.00820.991-0.037-0.0370.0000.0000.0000.000
174A174LEU0-0.003-0.00724.036-0.033-0.0330.0000.0000.0000.000
175A175VAL00.0650.04122.340-0.025-0.0250.0000.0000.0000.000
176A176PHE0-0.027-0.01923.290-0.030-0.0300.0000.0000.0000.000
177A177ALA0-0.020-0.02325.064-0.022-0.0220.0000.0000.0000.000
178A178GLU-1-0.779-0.85828.2680.1030.1030.0000.0000.0000.000
179A179PHE0-0.054-0.01526.250-0.018-0.0180.0000.0000.0000.000
180A180ALA0-0.054-0.03228.261-0.016-0.0160.0000.0000.0000.000
181A181LYS10.8810.94129.995-0.058-0.0580.0000.0000.0000.000
182A182VAL0-0.067-0.02831.444-0.004-0.0040.0000.0000.0000.000
183A183ASP-1-0.891-0.94632.7660.0890.0890.0000.0000.0000.000
184A184ILE00.018-0.00129.7340.0090.0090.0000.0000.0000.000
185A185PRO0-0.036-0.01934.042-0.007-0.0070.0000.0000.0000.000
186A186GLY00.0400.01436.3790.0060.0060.0000.0000.0000.000
187A187HIS0-0.009-0.01238.154-0.004-0.0040.0000.0000.0000.000
188A188LEU0-0.063-0.01134.2340.0030.0030.0000.0000.0000.000
189A189ASP-1-0.827-0.92634.4370.1340.1340.0000.0000.0000.000
190A190HIS00.0370.01932.8850.0070.0070.0000.0000.0000.000
191A191LEU0-0.013-0.01228.4800.0130.0130.0000.0000.0000.000
192A192LEU0-0.021-0.01429.5520.0080.0080.0000.0000.0000.000
193A193ALA0-0.023-0.00630.387-0.001-0.0010.0000.0000.0000.000
194A194TRP0-0.063-0.03622.945-0.007-0.0070.0000.0000.0000.000
195A195ARG10.8350.89725.744-0.142-0.1420.0000.0000.0000.000
196A196ALA0-0.030-0.00925.5040.0040.0040.0000.0000.0000.000
197A197ARG10.9430.96525.880-0.196-0.1960.0000.0000.0000.000
198A198VAL0-0.010-0.00520.3660.0140.0140.0000.0000.0000.000
199A199ALA0-0.001-0.00621.1680.0130.0130.0000.0000.0000.000
200A200ALA0-0.0190.00122.193-0.013-0.0130.0000.0000.0000.000
201A201ARG10.8040.89116.995-0.417-0.4170.0000.0000.0000.000
202A202PRO00.008-0.00816.957-0.002-0.0020.0000.0000.0000.000
203A203SER0-0.076-0.04313.837-0.043-0.0430.0000.0000.0000.000
204A204ILE0-0.047-0.02014.9880.0240.0240.0000.0000.0000.000
205A205THR0-0.0430.00717.544-0.046-0.0460.0000.0000.0000.000
206A206GLY00.0220.00319.569-0.017-0.0170.0000.0000.0000.000
207A207ALA0-0.025-0.03722.650-0.010-0.0100.0000.0000.0000.000
208A208GLU-1-0.815-0.88919.4310.1510.1510.0000.0000.0000.000
209A209ASN0-0.050-0.01921.4940.0130.0130.0000.0000.0000.000
210A210LEU0-0.021-0.00820.503-0.003-0.0030.0000.0000.0000.000
211A211TYR0-0.026-0.02719.266-0.021-0.0210.0000.0000.0000.000
212A212PHE00.0150.00022.2670.0010.0010.0000.0000.0000.000
213A213GLN00.0120.01224.1570.0000.0000.0000.0000.0000.000