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: 2J37R

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 OptAll
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 -1920562.922003
FMO2-HF: Nuclear repulsion 1848303.551262
FMO2-HF: Total energy -72259.370741
FMO2-MP2: Total energy -72474.436212


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.
-5.463-0.6841.636-2.761-3.653-0.022
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 : -0.030 / q_NPA : -0.023
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].
3A46ASN0-0.017-0.0072.9630.8612.2490.055-0.538-0.9040.000
4A47ASN0-0.0100.0022.541-2.823-1.1061.317-1.316-1.717-0.013
5A48PRO00.0350.0185.2370.3200.343-0.001-0.001-0.0210.000
6A49TYR00.018-0.0348.8470.1390.1390.0000.0000.0000.000
7A50LEU0-0.0320.0017.8850.1110.1110.0000.0000.0000.000
8A51PHE00.0980.0469.031-0.008-0.0080.0000.0000.0000.000
9A52ARG10.8630.94910.514-0.018-0.0180.0000.0000.0000.000
10A53SER00.0600.0278.3510.0540.0540.0000.0000.0000.000
11A54ASN0-0.001-0.0168.448-0.037-0.0370.0000.0000.0000.000
12A55LYS10.8910.9407.152-0.531-0.5310.0000.0000.0000.000
13A56PHE00.0760.0398.924-0.041-0.0410.0000.0000.0000.000
14A57LEU00.0460.0348.1390.0890.0890.0000.0000.0000.000
15A58THR0-0.022-0.02211.332-0.094-0.0940.0000.0000.0000.000
16A59LEU00.0420.02514.6360.0160.0160.0000.0000.0000.000
17A60PHE00.0200.01317.175-0.011-0.0110.0000.0000.0000.000
18A61LYS10.8770.92616.060-0.371-0.3710.0000.0000.0000.000
19A62ASN00.0210.00621.5070.0110.0110.0000.0000.0000.000
20A63GLN00.0320.01324.9910.0040.0040.0000.0000.0000.000
21A64HIS0-0.012-0.00127.404-0.012-0.0120.0000.0000.0000.000
22A65GLY00.0660.02025.266-0.010-0.0100.0000.0000.0000.000
23A66SER0-0.094-0.03519.7440.0210.0210.0000.0000.0000.000
24A67LEU00.0600.03318.875-0.016-0.0160.0000.0000.0000.000
25A68ARG10.8000.89814.626-0.222-0.2220.0000.0000.0000.000
26A69LEU00.0370.01613.186-0.036-0.0360.0000.0000.0000.000
27A70LEU0-0.0160.01410.1590.0930.0930.0000.0000.0000.000
28A71GLN0-0.043-0.0253.4380.1350.3120.002-0.029-0.1500.000
29A72ARG10.8220.8838.884-0.039-0.0390.0000.0000.0000.000
30A73PHE00.002-0.0098.826-0.040-0.0400.0000.0000.0000.000
31A74ASN0-0.018-0.0299.939-0.010-0.0100.0000.0000.0000.000
32A75GLU-1-0.828-0.8926.211-0.060-0.0600.0000.0000.0000.000
33A76ASP-1-0.809-0.9012.901-2.981-1.5070.263-0.877-0.861-0.009
34A77THR0-0.015-0.0046.068-0.143-0.1430.0000.0000.0000.000
35A78GLU-1-0.876-0.9439.166-0.319-0.3190.0000.0000.0000.000
36A79LYS10.8540.93312.6350.4480.4480.0000.0000.0000.000
37A80LEU00.0100.01110.7040.0510.0510.0000.0000.0000.000
38A81GLU-1-0.729-0.82414.066-0.248-0.2480.0000.0000.0000.000
39A82ASN0-0.038-0.02615.7040.0090.0090.0000.0000.0000.000
40A83LEU0-0.017-0.01515.0600.0240.0240.0000.0000.0000.000
41A84ARG10.8230.90714.7340.1910.1910.0000.0000.0000.000
42A85ASP-1-0.874-0.94015.810-0.054-0.0540.0000.0000.0000.000
43A86TYR0-0.0030.02117.0670.0240.0240.0000.0000.0000.000
44A87ARG10.7940.89010.834-0.157-0.1570.0000.0000.0000.000
45A88VAL00.0290.03014.861-0.001-0.0010.0000.0000.0000.000
46A89LEU00.008-0.01415.0880.0370.0370.0000.0000.0000.000
47A90GLU-1-0.842-0.89017.3430.1630.1630.0000.0000.0000.000
48A91TYR00.0100.00319.0260.0200.0200.0000.0000.0000.000
49A92CYS0-0.057-0.03322.112-0.009-0.0090.0000.0000.0000.000
50A93SER00.0630.04324.1320.0070.0070.0000.0000.0000.000
51A94LYS10.8530.91026.892-0.140-0.1400.0000.0000.0000.000
52A95PRO00.0510.04930.2100.0010.0010.0000.0000.0000.000
53A96ASN0-0.062-0.04933.7600.0050.0050.0000.0000.0000.000
54A97THR0-0.056-0.02230.8470.0040.0040.0000.0000.0000.000
55A98LEU00.0270.01032.096-0.005-0.0050.0000.0000.0000.000
56A99LEU0-0.058-0.00125.7750.0080.0080.0000.0000.0000.000
57A100LEU00.0410.00629.364-0.008-0.0080.0000.0000.0000.000
58A101PRO0-0.0100.00029.9420.0030.0030.0000.0000.0000.000
59A102HIS10.8590.94426.297-0.086-0.0860.0000.0000.0000.000
60A103HIS00.0720.06429.384-0.002-0.0020.0000.0000.0000.000
61A104SER0-0.033-0.05724.6300.0100.0100.0000.0000.0000.000
62A105ASP-1-0.831-0.88823.2690.0320.0320.0000.0000.0000.000
63A106SER0-0.020-0.03722.317-0.006-0.0060.0000.0000.0000.000
64A107ASP-1-0.778-0.87324.6840.0240.0240.0000.0000.0000.000
65A108LEU0-0.037-0.02623.2200.0060.0060.0000.0000.0000.000
66A109LEU00.0110.02024.571-0.002-0.0020.0000.0000.0000.000
67A110VAL0-0.037-0.02224.2490.0090.0090.0000.0000.0000.000
68A111LEU00.0240.00023.743-0.008-0.0080.0000.0000.0000.000
69A112VAL00.0090.00525.8430.0120.0120.0000.0000.0000.000
70A113LEU0-0.041-0.01821.818-0.004-0.0040.0000.0000.0000.000
71A114GLU-1-0.807-0.89226.0150.0990.0990.0000.0000.0000.000
72A115GLY00.0370.03128.2080.0050.0050.0000.0000.0000.000
73A116GLN00.009-0.00131.351-0.008-0.0080.0000.0000.0000.000
74A117ALA0-0.006-0.00631.4380.0060.0060.0000.0000.0000.000
75A118ILE0-0.006-0.00333.581-0.005-0.0050.0000.0000.0000.000
76A119LEU0-0.0130.00931.1420.0050.0050.0000.0000.0000.000
77A120VAL0-0.008-0.00534.211-0.004-0.0040.0000.0000.0000.000
78A121LEU00.005-0.00232.7140.0040.0040.0000.0000.0000.000
79A122VAL0-0.032-0.02935.658-0.003-0.0030.0000.0000.0000.000
80A123ASN0-0.010-0.02437.3740.0000.0000.0000.0000.0000.000
81A124PRO0-0.025-0.00839.5210.0020.0020.0000.0000.0000.000
82A125ASP-1-0.828-0.89941.3130.0240.0240.0000.0000.0000.000
83A126GLY0-0.014-0.00843.7470.0010.0010.0000.0000.0000.000
84A127ARG10.8100.88040.573-0.032-0.0320.0000.0000.0000.000
85A128ASP-1-0.863-0.90038.8760.0280.0280.0000.0000.0000.000
86A129THR0-0.009-0.01538.1490.0030.0030.0000.0000.0000.000
87A130TYR00.0020.00136.209-0.003-0.0030.0000.0000.0000.000
88A131LYS10.7980.87236.619-0.038-0.0380.0000.0000.0000.000
89A132LEU0-0.0170.00331.061-0.002-0.0020.0000.0000.0000.000
90A133ASP-1-0.816-0.90634.0450.0480.0480.0000.0000.0000.000
91A134GLN00.013-0.01029.2000.0040.0040.0000.0000.0000.000
92A135GLY0-0.035-0.01430.227-0.004-0.0040.0000.0000.0000.000
93A136ASP-1-0.844-0.89731.1550.0330.0330.0000.0000.0000.000
94A137ALA0-0.038-0.03629.1890.0050.0050.0000.0000.0000.000
95A138ILE00.0030.00729.627-0.004-0.0040.0000.0000.0000.000
96A139LYS10.7960.86928.428-0.014-0.0140.0000.0000.0000.000
97A140ILE00.0040.01128.354-0.003-0.0030.0000.0000.0000.000
98A141GLN00.0520.03228.762-0.002-0.0020.0000.0000.0000.000
99A142ALA00.0360.02528.2940.0040.0040.0000.0000.0000.000
100A143GLY0-0.038-0.00929.154-0.003-0.0030.0000.0000.0000.000
101A144THR0-0.013-0.01631.131-0.001-0.0010.0000.0000.0000.000
102A145PRO0-0.007-0.00231.1990.0060.0060.0000.0000.0000.000
103A146PHE0-0.001-0.01026.523-0.001-0.0010.0000.0000.0000.000
104A147TYR00.0170.00131.2600.0050.0050.0000.0000.0000.000
105A148LEU0-0.026-0.01027.860-0.004-0.0040.0000.0000.0000.000
106A149ILE00.0200.00831.5110.0060.0060.0000.0000.0000.000
107A150ASN00.006-0.00329.980-0.007-0.0070.0000.0000.0000.000
108A151PRO00.0550.02033.1800.0010.0010.0000.0000.0000.000
109A152ASP-1-0.930-0.95735.8780.0590.0590.0000.0000.0000.000
110A153ASN00.0340.01935.044-0.002-0.0020.0000.0000.0000.000
111A154ASN0-0.041-0.02936.4170.0000.0000.0000.0000.0000.000
112A155GLN0-0.056-0.03428.9680.0000.0000.0000.0000.0000.000
113A156ASN0-0.044-0.03028.187-0.004-0.0040.0000.0000.0000.000
114A157LEU00.0270.04027.831-0.006-0.0060.0000.0000.0000.000
115A158ARG10.8000.87220.603-0.110-0.1100.0000.0000.0000.000
116A159ILE00.0280.02024.079-0.009-0.0090.0000.0000.0000.000
117A160LEU0-0.0190.00118.6110.0170.0170.0000.0000.0000.000
118A161LYS10.9180.95120.722-0.117-0.1170.0000.0000.0000.000
119A162PHE0-0.008-0.00618.5450.0130.0130.0000.0000.0000.000
120A163ALA00.0130.00219.358-0.007-0.0070.0000.0000.0000.000
121A164ILE00.003-0.00620.090-0.008-0.0080.0000.0000.0000.000
122A165THR0-0.057-0.04418.7260.0000.0000.0000.0000.0000.000
123A166PHE00.0310.00021.938-0.010-0.0100.0000.0000.0000.000
124A167ARG10.7840.87722.368-0.054-0.0540.0000.0000.0000.000
125A168ARG10.9280.94717.599-0.028-0.0280.0000.0000.0000.000
126A169PRO00.0210.02419.5440.0110.0110.0000.0000.0000.000
127A170GLY00.0800.05115.789-0.010-0.0100.0000.0000.0000.000
128A171THR0-0.138-0.07015.3640.0260.0260.0000.0000.0000.000
129A172VAL00.0520.04417.558-0.006-0.0060.0000.0000.0000.000
130A173GLU-1-0.793-0.88319.0730.0990.0990.0000.0000.0000.000
131A174ASP-1-0.857-0.91721.7420.0980.0980.0000.0000.0000.000
132A175PHE0-0.033-0.00523.9920.0080.0080.0000.0000.0000.000
133A176PHE0-0.002-0.02123.942-0.005-0.0050.0000.0000.0000.000
134A177LEU00.0580.03528.786-0.001-0.0010.0000.0000.0000.000
135A178SER00.0300.03931.711-0.004-0.0040.0000.0000.0000.000
136A179SER0-0.001-0.00430.7280.0070.0070.0000.0000.0000.000
137A180THR0-0.022-0.01527.2350.0070.0070.0000.0000.0000.000
138A181LYS10.8280.89627.665-0.115-0.1150.0000.0000.0000.000
139A182ARG10.8060.89418.714-0.228-0.2280.0000.0000.0000.000
140A183LEU00.0280.01023.2850.0050.0050.0000.0000.0000.000
141A184PRO00.0510.03826.456-0.001-0.0010.0000.0000.0000.000
142A185SER00.0270.01429.3930.0010.0010.0000.0000.0000.000
143A186TYR0-0.006-0.00629.783-0.003-0.0030.0000.0000.0000.000
144A187LEU00.0160.00531.473-0.004-0.0040.0000.0000.0000.000
145A188SER0-0.029-0.03432.912-0.002-0.0020.0000.0000.0000.000
146A189ALA0-0.024-0.00231.8070.0000.0000.0000.0000.0000.000
147A190PHE0-0.049-0.00933.900-0.004-0.0040.0000.0000.0000.000
148A191SER00.0090.00337.3840.0010.0010.0000.0000.0000.000
149A192LYS10.8990.93640.382-0.036-0.0360.0000.0000.0000.000
150A193ASN00.0360.00143.1670.0000.0000.0000.0000.0000.000
151A194PHE0-0.039-0.01340.179-0.002-0.0020.0000.0000.0000.000
152A195LEU00.0190.02638.972-0.001-0.0010.0000.0000.0000.000
153A196GLU-1-0.780-0.88842.9180.0350.0350.0000.0000.0000.000
154A197ALA00.0070.00246.655-0.001-0.0010.0000.0000.0000.000
155A198SER0-0.095-0.06543.194-0.001-0.0010.0000.0000.0000.000
156A199TYR0-0.056-0.03639.8380.0010.0010.0000.0000.0000.000
157A200ASP-1-0.964-0.95346.6760.0260.0260.0000.0000.0000.000
158A201SER0-0.0150.00647.7500.0000.0000.0000.0000.0000.000
159A202PRO0-0.011-0.01348.5290.0000.0000.0000.0000.0000.000
160A203TYR0-0.014-0.05340.0760.0010.0010.0000.0000.0000.000
161A204ASP-1-0.963-0.96344.5340.0500.0500.0000.0000.0000.000
162A205GLU-1-0.930-0.98145.7320.0380.0380.0000.0000.0000.000
163A206ILE00.0600.04541.8790.0020.0020.0000.0000.0000.000
164A207GLU-1-0.875-0.92439.9960.0640.0640.0000.0000.0000.000
165A208GLN0-0.039-0.02040.3570.0060.0060.0000.0000.0000.000
166A209THR0-0.053-0.03141.9790.0000.0000.0000.0000.0000.000
167A210LEU0-0.070-0.02936.9430.0010.0010.0000.0000.0000.000
168A211LEU0-0.081-0.02134.4100.0070.0070.0000.0000.0000.000
169A212GLN00.0220.00334.411-0.004-0.0040.0000.0000.0000.000
170A213GLU-1-0.888-0.92433.2850.1040.1040.0000.0000.0000.000
171A214GLU-1-0.801-0.91631.1610.0960.0960.0000.0000.0000.000
172A215GLN0-0.080-0.05129.9640.0070.0070.0000.0000.0000.000
173A216GLU-1-0.838-0.89628.6230.1340.1340.0000.0000.0000.000
174A217GLY0-0.043-0.02727.3720.0070.0070.0000.0000.0000.000
175A218VAL0-0.0020.00423.802-0.007-0.0070.0000.0000.0000.000
176A219ILE0-0.055-0.02323.925-0.007-0.0070.0000.0000.0000.000
177A220VAL00.0730.03628.0680.0050.0050.0000.0000.0000.000
178A221LYS10.8380.92131.632-0.089-0.0890.0000.0000.0000.000
179A222MET00.0380.02734.722-0.002-0.0020.0000.0000.0000.000
180A223PRO00.0430.01337.6850.0010.0010.0000.0000.0000.000
181A224LYS10.9520.98237.509-0.053-0.0530.0000.0000.0000.000