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: MV16Z

Calculation Name: 1CAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CAX

Chain ID: A

ChEMBL ID:

UniProt ID: P50477

Base Structure: X-ray

Registration Date: 2023-09-19

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1923135.602135
FMO2-HF: Nuclear repulsion 1850883.473662
FMO2-HF: Total energy -72252.128474
FMO2-MP2: Total energy -72468.189877


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:44:ALA)


Summations of interaction energy for fragment #1(A:44:ALA)
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.
-8.871-2.1870.305-3.505-3.482-0.017
Interaction energy analysis for fragmet #1(A:44:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.036
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].
3A46ASN00.0340.0473.161-2.8211.731-0.099-2.319-2.134-0.005
4A47ASN0-0.055-0.0342.896-5.427-3.4050.406-1.167-1.260-0.012
5A48PRO00.031-0.0085.3650.6100.646-0.0010.000-0.0340.000
6A49TYR0-0.013-0.0398.8440.1910.1910.0000.0000.0000.000
7A50LEU0-0.0190.0118.9030.1430.1430.0000.0000.0000.000
8A51PHE00.0870.0569.854-0.037-0.0370.0000.0000.0000.000
9A52ARG10.9450.96810.5360.1770.1770.0000.0000.0000.000
10A53SER00.0500.0239.024-0.061-0.0610.0000.0000.0000.000
11A54ASN0-0.013-0.0209.0200.0210.0210.0000.0000.0000.000
12A55LYS10.8430.9087.820-0.299-0.2990.0000.0000.0000.000
13A56PHE00.0910.0628.9810.0100.0100.0000.0000.0000.000
14A57LEU00.0790.0468.5560.1410.1410.0000.0000.0000.000
15A58THR0-0.108-0.05611.844-0.108-0.1080.0000.0000.0000.000
16A59LEU00.0720.04015.0690.0310.0310.0000.0000.0000.000
17A60PHE0-0.032-0.04717.486-0.006-0.0060.0000.0000.0000.000
18A61LYS10.8990.98616.746-0.375-0.3750.0000.0000.0000.000
19A62ASN00.0530.00721.7410.0090.0090.0000.0000.0000.000
20A63GLN0-0.0030.01725.3910.0000.0000.0000.0000.0000.000
21A64HIS0-0.0110.01626.908-0.015-0.0150.0000.0000.0000.000
22A65GLY00.0860.02025.143-0.012-0.0120.0000.0000.0000.000
23A66SER0-0.053-0.02419.8850.0210.0210.0000.0000.0000.000
24A67LEU00.0810.05919.451-0.021-0.0210.0000.0000.0000.000
25A68ARG10.7990.85714.747-0.207-0.2070.0000.0000.0000.000
26A69LEU00.0100.01513.990-0.041-0.0410.0000.0000.0000.000
27A70LEU00.0000.03010.5480.0790.0790.0000.0000.0000.000
28A71GLN0-0.007-0.0094.9650.4960.4960.0000.0000.0000.000
29A72ARG10.9010.9469.961-0.275-0.2750.0000.0000.0000.000
30A73PHE00.0130.0059.315-0.049-0.0490.0000.0000.0000.000
31A74ASN00.011-0.00910.467-0.036-0.0360.0000.0000.0000.000
32A75GLU-1-0.921-0.9576.6470.1400.1400.0000.0000.0000.000
33A76ASP-1-0.726-0.8664.408-1.229-1.155-0.001-0.019-0.0540.000
34A77THR0-0.127-0.0606.769-0.251-0.2510.0000.0000.0000.000
35A78GLU-1-0.908-0.9469.700-0.364-0.3640.0000.0000.0000.000
36A79LYS10.8990.96213.0910.6430.6430.0000.0000.0000.000
37A80LEU0-0.083-0.03010.9270.0480.0480.0000.0000.0000.000
38A81GLU-1-0.808-0.92614.677-0.235-0.2350.0000.0000.0000.000
39A82ASN0-0.025-0.00116.4820.0130.0130.0000.0000.0000.000
40A83LEU0-0.076-0.04515.4340.0250.0250.0000.0000.0000.000
41A84ARG10.9040.96315.5970.1210.1210.0000.0000.0000.000
42A85ASP-1-0.844-0.92716.823-0.011-0.0110.0000.0000.0000.000
43A86TYR0-0.0060.01117.8100.0160.0160.0000.0000.0000.000
44A87ARG10.8290.89812.247-0.214-0.2140.0000.0000.0000.000
45A88VAL00.0380.03515.543-0.006-0.0060.0000.0000.0000.000
46A89LEU00.001-0.00116.0100.0400.0400.0000.0000.0000.000
47A90GLU-1-0.882-0.93617.3730.1240.1240.0000.0000.0000.000
48A91TYR0-0.004-0.01019.4020.0300.0300.0000.0000.0000.000
49A92CYS0-0.005-0.01022.435-0.014-0.0140.0000.0000.0000.000
50A93SER00.0000.00424.4590.0070.0070.0000.0000.0000.000
51A94LYS10.9740.96227.453-0.131-0.1310.0000.0000.0000.000
52A95PRO0-0.0140.03630.3910.0010.0010.0000.0000.0000.000
53A96ASN0-0.019-0.01834.0170.0030.0030.0000.0000.0000.000
54A97THR0-0.048-0.05931.2610.0050.0050.0000.0000.0000.000
55A98LEU00.0470.02632.333-0.006-0.0060.0000.0000.0000.000
56A99LEU0-0.0580.00926.2300.0090.0090.0000.0000.0000.000
57A100LEU00.011-0.01329.770-0.007-0.0070.0000.0000.0000.000
58A101PRO00.0170.02230.1610.0050.0050.0000.0000.0000.000
59A102HIS10.7980.90226.622-0.106-0.1060.0000.0000.0000.000
60A103HIS00.0600.03929.018-0.007-0.0070.0000.0000.0000.000
61A104SER0-0.037-0.02624.3780.0060.0060.0000.0000.0000.000
62A105ASP-1-0.799-0.88623.3220.0860.0860.0000.0000.0000.000
63A106SER0-0.010-0.01823.181-0.006-0.0060.0000.0000.0000.000
64A107ASP-1-0.800-0.88825.5280.0340.0340.0000.0000.0000.000
65A108LEU0-0.018-0.01723.4560.0050.0050.0000.0000.0000.000
66A109LEU0-0.0080.00725.157-0.006-0.0060.0000.0000.0000.000
67A110VAL0-0.078-0.04325.2470.0070.0070.0000.0000.0000.000
68A111LEU00.0780.03224.112-0.007-0.0070.0000.0000.0000.000
69A112VAL0-0.0190.05426.7310.0110.0110.0000.0000.0000.000
70A113LEU0-0.046-0.00322.796-0.005-0.0050.0000.0000.0000.000
71A114GLU-1-0.758-0.89726.3770.0710.0710.0000.0000.0000.000
72A115GLY00.0250.01929.0100.0080.0080.0000.0000.0000.000
73A116GLN00.0250.00831.860-0.005-0.0050.0000.0000.0000.000
74A117ALA00.005-0.00432.2480.0060.0060.0000.0000.0000.000
75A118ILE00.0000.01234.320-0.005-0.0050.0000.0000.0000.000
76A119LEU00.0050.00732.1170.0060.0060.0000.0000.0000.000
77A120VAL00.0290.02335.121-0.005-0.0050.0000.0000.0000.000
78A121LEU0-0.055-0.04833.1190.0050.0050.0000.0000.0000.000
79A122VAL0-0.038-0.02736.117-0.003-0.0030.0000.0000.0000.000
80A123ASN00.0340.01037.3930.0010.0010.0000.0000.0000.000
81A124PRO0-0.0350.00939.9240.0030.0030.0000.0000.0000.000
82A125ASP-1-0.903-0.97641.8120.0320.0320.0000.0000.0000.000
83A126GLY0-0.014-0.00643.391-0.002-0.0020.0000.0000.0000.000
84A127ARG10.8730.94041.009-0.039-0.0390.0000.0000.0000.000
85A128ASP-1-0.837-0.91240.0500.0300.0300.0000.0000.0000.000
86A129THR0-0.034-0.02039.2030.0040.0040.0000.0000.0000.000
87A130TYR00.0100.01037.126-0.003-0.0030.0000.0000.0000.000
88A131LYS10.8990.95037.649-0.031-0.0310.0000.0000.0000.000
89A132LEU0-0.027-0.00931.607-0.002-0.0020.0000.0000.0000.000
90A133ASP-1-0.875-0.93834.6890.0380.0380.0000.0000.0000.000
91A134GLN00.020-0.07330.8490.0020.0020.0000.0000.0000.000
92A135GLY0-0.053-0.01931.030-0.004-0.0040.0000.0000.0000.000
93A136ASP-1-0.850-0.90431.7900.0250.0250.0000.0000.0000.000
94A137ALA0-0.042-0.06829.2670.0040.0040.0000.0000.0000.000
95A138ILE0-0.0150.00030.352-0.003-0.0030.0000.0000.0000.000
96A139LYS10.9580.97629.996-0.017-0.0170.0000.0000.0000.000
97A140ILE0-0.033-0.00128.984-0.001-0.0010.0000.0000.0000.000
98A141GLN00.010-0.01129.729-0.002-0.0020.0000.0000.0000.000
99A142ALA00.0190.01428.4020.0050.0050.0000.0000.0000.000
100A143GLY0-0.060-0.02429.782-0.004-0.0040.0000.0000.0000.000
101A144THR0-0.0060.00631.534-0.005-0.0050.0000.0000.0000.000
102A145PRO00.007-0.00231.7500.0070.0070.0000.0000.0000.000
103A146PHE00.0060.00726.527-0.002-0.0020.0000.0000.0000.000
104A147TYR0-0.004-0.02531.8330.0070.0070.0000.0000.0000.000
105A148LEU0-0.0070.00728.039-0.005-0.0050.0000.0000.0000.000
106A149ILE00.0130.00931.9540.0050.0050.0000.0000.0000.000
107A150ASN0-0.0110.00031.152-0.009-0.0090.0000.0000.0000.000
108A151PRO0-0.030-0.02333.8010.0020.0020.0000.0000.0000.000
109A152ASP-1-0.934-0.96136.8850.0510.0510.0000.0000.0000.000
110A153ASN00.0290.01635.578-0.003-0.0030.0000.0000.0000.000
111A154ASN0-0.050-0.01436.7530.0020.0020.0000.0000.0000.000
112A155GLN0-0.053-0.04028.630-0.002-0.0020.0000.0000.0000.000
113A156ASN0-0.093-0.05928.4750.0010.0010.0000.0000.0000.000
114A157LEU00.0240.03728.320-0.004-0.0040.0000.0000.0000.000
115A158ARG10.7790.87922.450-0.064-0.0640.0000.0000.0000.000
116A159ILE00.0340.02623.903-0.008-0.0080.0000.0000.0000.000
117A160LEU0-0.018-0.00519.3680.0160.0160.0000.0000.0000.000
118A161LYS10.9190.94321.020-0.121-0.1210.0000.0000.0000.000
119A162PHE0-0.0090.01118.5770.0130.0130.0000.0000.0000.000
120A163ALA00.014-0.00520.238-0.002-0.0020.0000.0000.0000.000
121A164ILE00.0190.00921.184-0.011-0.0110.0000.0000.0000.000
122A165THR0-0.067-0.04620.0020.0060.0060.0000.0000.0000.000
123A166PHE00.0860.05223.042-0.009-0.0090.0000.0000.0000.000
124A167ARG10.8620.92322.799-0.100-0.1000.0000.0000.0000.000
125A168ARG10.9430.98817.582-0.115-0.1150.0000.0000.0000.000
126A169PRO00.0570.02120.4590.0150.0150.0000.0000.0000.000
127A170GLY00.0640.02517.085-0.005-0.0050.0000.0000.0000.000
128A171THR0-0.147-0.08716.2400.0440.0440.0000.0000.0000.000
129A172VAL0-0.0180.01218.147-0.013-0.0130.0000.0000.0000.000
130A173GLU-1-0.932-0.96419.9170.1990.1990.0000.0000.0000.000
131A174ASP-1-0.875-0.94722.2490.1210.1210.0000.0000.0000.000
132A175PHE0-0.0090.00724.4930.0060.0060.0000.0000.0000.000
133A176PHE0-0.028-0.03224.654-0.008-0.0080.0000.0000.0000.000
134A177LEU00.0500.03029.1420.0000.0000.0000.0000.0000.000
135A178SER0-0.003-0.00331.854-0.003-0.0030.0000.0000.0000.000
136A179SER00.0380.02430.9650.0090.0090.0000.0000.0000.000
137A180THR0-0.061-0.01327.9440.0070.0070.0000.0000.0000.000
138A181LYS10.8260.91527.726-0.131-0.1310.0000.0000.0000.000
139A182ARG10.8700.95120.661-0.247-0.2470.0000.0000.0000.000
140A183LEU00.0440.01223.0290.0050.0050.0000.0000.0000.000
141A184PRO00.0290.01626.778-0.006-0.0060.0000.0000.0000.000
142A185SER00.0580.04329.9410.0030.0030.0000.0000.0000.000
143A186TYR00.0810.02530.268-0.002-0.0020.0000.0000.0000.000
144A187LEU0-0.038-0.01531.840-0.002-0.0020.0000.0000.0000.000
145A188SER0-0.046-0.01733.555-0.005-0.0050.0000.0000.0000.000
146A189ALA0-0.034-0.01232.0180.0000.0000.0000.0000.0000.000
147A190PHE0-0.064-0.01334.129-0.003-0.0030.0000.0000.0000.000
148A191SER00.0560.01337.6290.0010.0010.0000.0000.0000.000
149A192LYS11.0331.02540.686-0.056-0.0560.0000.0000.0000.000
150A193ASN0-0.006-0.00343.843-0.002-0.0020.0000.0000.0000.000
151A194PHE0-0.046-0.01440.857-0.002-0.0020.0000.0000.0000.000
152A195LEU00.020-0.01039.101-0.002-0.0020.0000.0000.0000.000
153A196GLU-1-0.846-0.93743.1700.0510.0510.0000.0000.0000.000
154A197ALA00.0290.01846.970-0.001-0.0010.0000.0000.0000.000
155A198SER0-0.119-0.05143.611-0.001-0.0010.0000.0000.0000.000
156A199TYR0-0.046-0.05740.1000.0000.0000.0000.0000.0000.000
157A200ASP-1-0.990-0.97746.7630.0370.0370.0000.0000.0000.000
158A201SER0-0.027-0.00747.847-0.001-0.0010.0000.0000.0000.000
159A202PRO0-0.053-0.02349.4690.0000.0000.0000.0000.0000.000
160A203TYR00.0210.02040.1740.0020.0020.0000.0000.0000.000
161A204ASP-1-0.912-0.93544.9610.0680.0680.0000.0000.0000.000
162A205GLU-1-0.910-1.06945.6550.0510.0510.0000.0000.0000.000
163A206ILE00.0230.04242.2350.0020.0020.0000.0000.0000.000
164A207GLU-1-0.818-0.91540.9970.0830.0830.0000.0000.0000.000
165A208GLN0-0.0290.04540.8590.0070.0070.0000.0000.0000.000
166A209THR0-0.183-0.08242.312-0.002-0.0020.0000.0000.0000.000
167A210LEU0-0.041-0.00736.9900.0010.0010.0000.0000.0000.000
168A211LEU0-0.110-0.04533.6120.0080.0080.0000.0000.0000.000
169A212GLN00.0550.00434.532-0.003-0.0030.0000.0000.0000.000
170A213GLU-1-0.885-0.97533.4790.1210.1210.0000.0000.0000.000
171A214GLU-1-0.816-0.88231.6160.1080.1080.0000.0000.0000.000
172A215GLN00.0640.03730.5530.0120.0120.0000.0000.0000.000
173A216GLU-1-1.026-0.99329.2040.1400.1400.0000.0000.0000.000
174A217GLY0-0.038-0.10928.329-0.003-0.0030.0000.0000.0000.000
175A218VAL0-0.022-0.00824.703-0.007-0.0070.0000.0000.0000.000
176A219ILE0-0.030-0.00724.339-0.009-0.0090.0000.0000.0000.000
177A220VAL00.1280.07528.3210.0040.0040.0000.0000.0000.000
178A221LYS10.9871.00431.821-0.081-0.0810.0000.0000.0000.000
179A222MET00.0080.00534.760-0.003-0.0030.0000.0000.0000.000
180A223PRO00.0540.07137.9200.0000.0000.0000.0000.0000.000
181A224LYS10.8450.87537.313-0.055-0.0550.0000.0000.0000.000