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: 72V3K

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1920909.026492
FMO2-HF: Nuclear repulsion 1848652.362115
FMO2-HF: Total energy -72256.664376
FMO2-MP2: Total energy -72472.041277


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.
-9.058-1.9740.515-3.69-3.908-0.019
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 : 0.002 / q_NPA : -0.031
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].
3A46ASN0-0.0170.0223.155-3.0651.682-0.109-2.400-2.238-0.004
4A47ASN0-0.015-0.0102.814-5.514-3.3320.626-1.263-1.546-0.015
5A48PRO00.0350.0105.3800.5730.608-0.0010.000-0.0320.000
6A49TYR0-0.002-0.0298.8580.1800.1800.0000.0000.0000.000
7A50LEU0-0.0210.0018.4630.1500.1500.0000.0000.0000.000
8A51PHE00.0940.0569.988-0.028-0.0280.0000.0000.0000.000
9A52ARG10.8960.94810.9110.1930.1930.0000.0000.0000.000
10A53SER00.0690.0309.066-0.028-0.0280.0000.0000.0000.000
11A54ASN0-0.007-0.0209.1020.0170.0170.0000.0000.0000.000
12A55LYS10.8750.9307.377-0.332-0.3320.0000.0000.0000.000
13A56PHE00.1170.0708.9140.0200.0200.0000.0000.0000.000
14A57LEU00.0660.0438.3340.1380.1380.0000.0000.0000.000
15A58THR0-0.048-0.03211.855-0.103-0.1030.0000.0000.0000.000
16A59LEU00.0690.03515.0540.0340.0340.0000.0000.0000.000
17A60PHE0-0.012-0.02217.483-0.009-0.0090.0000.0000.0000.000
18A61LYS10.8780.96016.412-0.375-0.3750.0000.0000.0000.000
19A62ASN00.031-0.00721.7250.0110.0110.0000.0000.0000.000
20A63GLN00.0370.05225.3710.0000.0000.0000.0000.0000.000
21A64HIS0-0.071-0.04726.906-0.017-0.0170.0000.0000.0000.000
22A65GLY00.0700.01925.159-0.012-0.0120.0000.0000.0000.000
23A66SER0-0.038-0.01619.8980.0210.0210.0000.0000.0000.000
24A67LEU00.0360.03519.333-0.019-0.0190.0000.0000.0000.000
25A68ARG10.7530.85414.940-0.173-0.1730.0000.0000.0000.000
26A69LEU00.0360.01014.008-0.043-0.0430.0000.0000.0000.000
27A70LEU0-0.0280.00710.6310.0800.0800.0000.0000.0000.000
28A71GLN0-0.026-0.0225.0870.4020.4020.0000.0000.0000.000
29A72ARG10.8420.9159.941-0.316-0.3160.0000.0000.0000.000
30A73PHE00.006-0.0059.371-0.043-0.0430.0000.0000.0000.000
31A74ASN0-0.063-0.06110.573-0.038-0.0380.0000.0000.0000.000
32A75GLU-1-0.840-0.8956.7350.2210.2210.0000.0000.0000.000
33A76ASP-1-0.782-0.9114.322-0.999-0.879-0.001-0.027-0.0920.000
34A77THR0-0.114-0.0376.911-0.202-0.2020.0000.0000.0000.000
35A78GLU-1-0.877-0.9409.859-0.347-0.3470.0000.0000.0000.000
36A79LYS10.8700.94113.3150.5430.5430.0000.0000.0000.000
37A80LEU0-0.039-0.00811.4580.0450.0450.0000.0000.0000.000
38A81GLU-1-0.690-0.82114.807-0.154-0.1540.0000.0000.0000.000
39A82ASN0-0.041-0.01316.6070.0100.0100.0000.0000.0000.000
40A83LEU0-0.037-0.03415.6520.0210.0210.0000.0000.0000.000
41A84ARG10.8200.89715.9600.1100.1100.0000.0000.0000.000
42A85ASP-1-0.857-0.92816.8740.0050.0050.0000.0000.0000.000
43A86TYR00.0110.02117.8570.0140.0140.0000.0000.0000.000
44A87ARG10.8150.90311.875-0.255-0.2550.0000.0000.0000.000
45A88VAL00.0370.03515.541-0.007-0.0070.0000.0000.0000.000
46A89LEU0-0.010-0.01915.9770.0410.0410.0000.0000.0000.000
47A90GLU-1-0.836-0.90117.2050.1170.1170.0000.0000.0000.000
48A91TYR0-0.006-0.00319.3380.0240.0240.0000.0000.0000.000
49A92CYS0-0.039-0.02222.490-0.014-0.0140.0000.0000.0000.000
50A93SER00.0570.02324.5030.0080.0080.0000.0000.0000.000
51A94LYS10.8990.92927.013-0.129-0.1290.0000.0000.0000.000
52A95PRO00.0410.04830.4160.0020.0020.0000.0000.0000.000
53A96ASN00.0040.00134.0490.0050.0050.0000.0000.0000.000
54A97THR0-0.057-0.06530.8290.0050.0050.0000.0000.0000.000
55A98LEU00.0390.02732.360-0.006-0.0060.0000.0000.0000.000
56A99LEU0-0.0420.01826.0960.0090.0090.0000.0000.0000.000
57A100LEU00.004-0.01129.795-0.006-0.0060.0000.0000.0000.000
58A101PRO00.0170.01230.1830.0060.0060.0000.0000.0000.000
59A102HIS10.8210.93126.491-0.109-0.1090.0000.0000.0000.000
60A103HIS00.0650.03929.753-0.006-0.0060.0000.0000.0000.000
61A104SER0-0.046-0.05525.1640.0120.0120.0000.0000.0000.000
62A105ASP-1-0.812-0.87523.9170.0830.0830.0000.0000.0000.000
63A106SER0-0.037-0.03623.279-0.008-0.0080.0000.0000.0000.000
64A107ASP-1-0.790-0.87225.6020.0370.0370.0000.0000.0000.000
65A108LEU0-0.038-0.01523.8500.0070.0070.0000.0000.0000.000
66A109LEU00.0230.02425.157-0.006-0.0060.0000.0000.0000.000
67A110VAL0-0.064-0.04125.2380.0070.0070.0000.0000.0000.000
68A111LEU00.0680.03524.678-0.008-0.0080.0000.0000.0000.000
69A112VAL0-0.0180.00726.6990.0110.0110.0000.0000.0000.000
70A113LEU0-0.043-0.00422.690-0.006-0.0060.0000.0000.0000.000
71A114GLU-1-0.753-0.88526.6860.0650.0650.0000.0000.0000.000
72A115GLY0-0.0030.02128.9620.0080.0080.0000.0000.0000.000
73A116GLN00.0670.03231.802-0.006-0.0060.0000.0000.0000.000
74A117ALA0-0.022-0.00732.1010.0060.0060.0000.0000.0000.000
75A118ILE0-0.003-0.00534.266-0.005-0.0050.0000.0000.0000.000
76A119LEU00.0130.00632.0120.0060.0060.0000.0000.0000.000
77A120VAL00.0000.00735.158-0.005-0.0050.0000.0000.0000.000
78A121LEU0-0.039-0.03733.3910.0050.0050.0000.0000.0000.000
79A122VAL0-0.031-0.02136.321-0.003-0.0030.0000.0000.0000.000
80A123ASN0-0.001-0.00837.4460.0030.0030.0000.0000.0000.000
81A124PRO0-0.022-0.00939.9810.0020.0020.0000.0000.0000.000
82A125ASP-1-0.908-0.96341.8620.0340.0340.0000.0000.0000.000
83A126GLY0-0.014-0.00743.432-0.003-0.0030.0000.0000.0000.000
84A127ARG10.8610.93341.075-0.040-0.0400.0000.0000.0000.000
85A128ASP-1-0.816-0.88439.8660.0320.0320.0000.0000.0000.000
86A129THR0-0.005-0.01639.2610.0040.0040.0000.0000.0000.000
87A130TYR00.0010.00737.149-0.004-0.0040.0000.0000.0000.000
88A131LYS10.7980.88337.601-0.031-0.0310.0000.0000.0000.000
89A132LEU0-0.035-0.00731.622-0.002-0.0020.0000.0000.0000.000
90A133ASP-1-0.832-0.89634.6430.0380.0380.0000.0000.0000.000
91A134GLN00.025-0.02430.8270.0030.0030.0000.0000.0000.000
92A135GLY0-0.060-0.03031.020-0.004-0.0040.0000.0000.0000.000
93A136ASP-1-0.862-0.91531.7870.0250.0250.0000.0000.0000.000
94A137ALA0-0.021-0.05229.5660.0040.0040.0000.0000.0000.000
95A138ILE0-0.0040.00130.340-0.003-0.0030.0000.0000.0000.000
96A139LYS10.8100.88829.594-0.025-0.0250.0000.0000.0000.000
97A140ILE0-0.021-0.00229.178-0.001-0.0010.0000.0000.0000.000
98A141GLN00.0480.01729.715-0.001-0.0010.0000.0000.0000.000
99A142ALA00.0190.01728.8250.0050.0050.0000.0000.0000.000
100A143GLY0-0.058-0.03129.844-0.004-0.0040.0000.0000.0000.000
101A144THR00.0040.01031.594-0.006-0.0060.0000.0000.0000.000
102A145PRO0-0.002-0.00431.8050.0060.0060.0000.0000.0000.000
103A146PHE00.0110.00326.701-0.002-0.0020.0000.0000.0000.000
104A147TYR00.010-0.01531.8740.0060.0060.0000.0000.0000.000
105A148LEU00.0000.00628.259-0.005-0.0050.0000.0000.0000.000
106A149ILE00.0020.00032.0020.0050.0050.0000.0000.0000.000
107A150ASN0-0.005-0.00530.639-0.008-0.0080.0000.0000.0000.000
108A151PRO00.006-0.00433.8440.0020.0020.0000.0000.0000.000
109A152ASP-1-0.935-0.98236.9290.0500.0500.0000.0000.0000.000
110A153ASN00.0290.03035.692-0.003-0.0030.0000.0000.0000.000
111A154ASN0-0.055-0.02236.7720.0010.0010.0000.0000.0000.000
112A155GLN0-0.040-0.05029.0900.0000.0000.0000.0000.0000.000
113A156ASN0-0.072-0.03928.837-0.002-0.0020.0000.0000.0000.000
114A157LEU00.0140.03528.284-0.005-0.0050.0000.0000.0000.000
115A158ARG10.8260.89621.294-0.066-0.0660.0000.0000.0000.000
116A159ILE00.0300.01924.615-0.008-0.0080.0000.0000.0000.000
117A160LEU0-0.029-0.00219.3630.0160.0160.0000.0000.0000.000
118A161LYS10.9280.94520.990-0.136-0.1360.0000.0000.0000.000
119A162PHE0-0.0050.00719.1290.0150.0150.0000.0000.0000.000
120A163ALA00.007-0.00420.171-0.002-0.0020.0000.0000.0000.000
121A164ILE00.0230.00421.203-0.009-0.0090.0000.0000.0000.000
122A165THR0-0.048-0.02220.1950.0070.0070.0000.0000.0000.000
123A166PHE00.0940.03123.059-0.009-0.0090.0000.0000.0000.000
124A167ARG10.7970.87522.676-0.118-0.1180.0000.0000.0000.000
125A168ARG10.9260.96417.725-0.140-0.1400.0000.0000.0000.000
126A169PRO00.0050.00520.5440.0170.0170.0000.0000.0000.000
127A170GLY00.1020.04917.123-0.002-0.0020.0000.0000.0000.000
128A171THR0-0.125-0.06716.3080.0540.0540.0000.0000.0000.000
129A172VAL0-0.0030.01718.048-0.014-0.0140.0000.0000.0000.000
130A173GLU-1-0.812-0.90719.9520.1940.1940.0000.0000.0000.000
131A174ASP-1-0.882-0.93522.2810.1250.1250.0000.0000.0000.000
132A175PHE0-0.0090.00924.5190.0080.0080.0000.0000.0000.000
133A176PHE0-0.003-0.01424.454-0.008-0.0080.0000.0000.0000.000
134A177LEU00.0650.03829.1480.0010.0010.0000.0000.0000.000
135A178SER00.0220.02631.911-0.003-0.0030.0000.0000.0000.000
136A179SER00.0370.02030.9490.0100.0100.0000.0000.0000.000
137A180THR0-0.032-0.01127.5450.0070.0070.0000.0000.0000.000
138A181LYS10.8670.90827.607-0.133-0.1330.0000.0000.0000.000
139A182ARG10.8220.92719.488-0.259-0.2590.0000.0000.0000.000
140A183LEU00.0440.01523.3510.0060.0060.0000.0000.0000.000
141A184PRO00.0400.02626.741-0.006-0.0060.0000.0000.0000.000
142A185SER00.0430.00829.9150.0030.0030.0000.0000.0000.000
143A186TYR00.0660.03630.243-0.002-0.0020.0000.0000.0000.000
144A187LEU0-0.040-0.01331.828-0.002-0.0020.0000.0000.0000.000
145A188SER0-0.044-0.03933.472-0.004-0.0040.0000.0000.0000.000
146A189ALA0-0.040-0.01731.9720.0000.0000.0000.0000.0000.000
147A190PHE0-0.064-0.01934.100-0.003-0.0030.0000.0000.0000.000
148A191SER00.0660.02637.6050.0010.0010.0000.0000.0000.000
149A192LYS10.9160.95840.654-0.057-0.0570.0000.0000.0000.000
150A193ASN00.0250.00343.807-0.001-0.0010.0000.0000.0000.000
151A194PHE0-0.028-0.00340.692-0.002-0.0020.0000.0000.0000.000
152A195LEU00.018-0.00339.063-0.002-0.0020.0000.0000.0000.000
153A196GLU-1-0.793-0.88843.1510.0530.0530.0000.0000.0000.000
154A197ALA00.0330.02346.948-0.001-0.0010.0000.0000.0000.000
155A198SER0-0.118-0.06243.590-0.001-0.0010.0000.0000.0000.000
156A199TYR0-0.054-0.05940.1250.0000.0000.0000.0000.0000.000
157A200ASP-1-0.965-0.96246.7570.0390.0390.0000.0000.0000.000
158A201SER0-0.055-0.01547.812-0.001-0.0010.0000.0000.0000.000
159A202PRO0-0.045-0.01049.4400.0000.0000.0000.0000.0000.000
160A203TYR00.003-0.04640.4420.0010.0010.0000.0000.0000.000
161A204ASP-1-0.952-0.94744.9220.0690.0690.0000.0000.0000.000
162A205GLU-1-0.898-1.00445.6110.0520.0520.0000.0000.0000.000
163A206ILE00.0560.06542.2580.0020.0020.0000.0000.0000.000
164A207GLU-1-0.801-0.88640.4650.0880.0880.0000.0000.0000.000
165A208GLN0-0.0070.00440.8230.0070.0070.0000.0000.0000.000
166A209THR0-0.174-0.08942.299-0.003-0.0030.0000.0000.0000.000
167A210LEU0-0.064-0.03437.4420.0010.0010.0000.0000.0000.000
168A211LEU0-0.108-0.03834.3220.0090.0090.0000.0000.0000.000
169A212GLN00.013-0.01234.773-0.004-0.0040.0000.0000.0000.000
170A213GLU-1-0.908-0.95233.7080.1240.1240.0000.0000.0000.000
171A214GLU-1-0.799-0.90331.7610.1050.1050.0000.0000.0000.000
172A215GLN00.0430.04530.5150.0120.0120.0000.0000.0000.000
173A216GLU-1-0.936-0.92329.1680.1420.1420.0000.0000.0000.000
174A217GLY0-0.058-0.09728.334-0.002-0.0020.0000.0000.0000.000
175A218VAL0-0.027-0.01224.447-0.007-0.0070.0000.0000.0000.000
176A219ILE0-0.068-0.01924.309-0.009-0.0090.0000.0000.0000.000
177A220VAL00.1250.08028.3260.0040.0040.0000.0000.0000.000
178A221LYS10.8200.89531.819-0.086-0.0860.0000.0000.0000.000
179A222MET0-0.013-0.02334.762-0.003-0.0030.0000.0000.0000.000
180A223PRO00.0170.05937.9300.0000.0000.0000.0000.0000.000
181A224LYS10.9900.98936.631-0.054-0.0540.0000.0000.0000.000