FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: J3889

Calculation Name: 3D5N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D5N

Chain ID: A

ChEMBL ID:

UniProt ID: Q97W15

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1935552.247851
FMO2-HF: Nuclear repulsion 1865546.272236
FMO2-HF: Total energy -70005.975615
FMO2-MP2: Total energy -70209.21958


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.
-9.667-4.88.709-4.135-9.44-0.012
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 : 0.006 / q_NPA : 0.011
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].
3A3ILE00.007-0.0073.0290.4653.2051.996-1.428-3.3070.004
4A4GLY00.0640.0525.511-0.834-0.796-0.001-0.018-0.0190.000
5A5VAL0-0.058-0.0369.3080.2990.2990.0000.0000.0000.000
6A6ILE00.0150.00812.170-0.056-0.0560.0000.0000.0000.000
7A7ILE0-0.001-0.00215.2180.0450.0450.0000.0000.0000.000
8A8LEU0-0.012-0.00918.144-0.016-0.0160.0000.0000.0000.000
9A9ALA00.0400.00620.9130.0080.0080.0000.0000.0000.000
10A10ALA0-0.061-0.00824.260-0.005-0.0050.0000.0000.0000.000
11A11GLY00.0460.01326.4970.0060.0060.0000.0000.0000.000
12A12GLU-1-0.803-0.87724.643-0.007-0.0070.0000.0000.0000.000
13A13GLY00.0070.00529.0370.0050.0050.0000.0000.0000.000
14A14LYS10.8930.93831.160-0.012-0.0120.0000.0000.0000.000
15A15ARG10.8260.89725.822-0.024-0.0240.0000.0000.0000.000
16A16PHE00.0390.00527.797-0.005-0.0050.0000.0000.0000.000
17A17GLY00.0480.00928.2450.0000.0000.0000.0000.0000.000
18A18GLY00.0340.01429.2770.0000.0000.0000.0000.0000.000
19A19ASP-1-0.785-0.88231.160-0.013-0.0130.0000.0000.0000.000
20A20LYS10.7550.85431.505-0.007-0.0070.0000.0000.0000.000
21A21LEU0-0.050-0.01926.4280.0010.0010.0000.0000.0000.000
22A22LEU00.0160.01129.429-0.005-0.0050.0000.0000.0000.000
23A23ALA0-0.0130.01432.0930.0000.0000.0000.0000.0000.000
24A24LYS10.8720.92131.2110.0280.0280.0000.0000.0000.000
25A25ILE00.0490.02728.1050.0040.0040.0000.0000.0000.000
26A26ASP-1-0.798-0.87729.509-0.011-0.0110.0000.0000.0000.000
27A27ASN0-0.011-0.01031.211-0.004-0.0040.0000.0000.0000.000
28A28THR0-0.033-0.01127.170-0.005-0.0050.0000.0000.0000.000
29A29PRO00.0460.00828.4130.0060.0060.0000.0000.0000.000
30A30ILE00.0170.02026.640-0.006-0.0060.0000.0000.0000.000
31A31ILE00.0440.02522.8640.0000.0000.0000.0000.0000.000
32A32MET00.0070.00722.859-0.005-0.0050.0000.0000.0000.000
33A33ARG10.7740.88122.334-0.001-0.0010.0000.0000.0000.000
34A34THR0-0.010-0.02819.878-0.001-0.0010.0000.0000.0000.000
35A35ILE00.0130.00818.192-0.004-0.0040.0000.0000.0000.000
36A36ARG10.9440.97417.3890.0280.0280.0000.0000.0000.000
37A37ILE0-0.058-0.01415.952-0.021-0.0210.0000.0000.0000.000
38A38TYR00.037-0.00212.7370.0050.0050.0000.0000.0000.000
39A39GLY0-0.059-0.02212.717-0.085-0.0850.0000.0000.0000.000
40A40ASP-1-0.842-0.91910.322-0.486-0.4860.0000.0000.0000.000
41A41LEU00.0110.0147.464-0.119-0.1190.0000.0000.0000.000
42A42GLU-1-0.798-0.8857.444-1.417-1.4170.0000.0000.0000.000
43A43LYS10.7830.89810.6170.4420.4420.0000.0000.0000.000
44A44ILE0-0.0040.01514.025-0.007-0.0070.0000.0000.0000.000
45A45ILE0-0.022-0.00916.8740.0360.0360.0000.0000.0000.000
46A46ILE0-0.0170.00419.270-0.003-0.0030.0000.0000.0000.000
47A47VAL00.0310.00422.1090.0120.0120.0000.0000.0000.000
48A48GLY00.046-0.00325.865-0.004-0.0040.0000.0000.0000.000
49A49LYS10.7860.90328.9430.0090.0090.0000.0000.0000.000
50A50TYR00.0200.02031.1060.0030.0030.0000.0000.0000.000
51A51VAL00.0360.00928.657-0.003-0.0030.0000.0000.0000.000
52A52ASN0-0.041-0.01630.902-0.005-0.0050.0000.0000.0000.000
53A53GLU-1-0.838-0.92732.852-0.040-0.0400.0000.0000.0000.000
54A54MET0-0.0240.00427.491-0.001-0.0010.0000.0000.0000.000
55A55LEU00.0270.01426.657-0.006-0.0060.0000.0000.0000.000
56A56PRO00.0240.00628.012-0.008-0.0080.0000.0000.0000.000
57A57LEU0-0.056-0.02727.359-0.001-0.0010.0000.0000.0000.000
58A58LEU0-0.025-0.02722.761-0.005-0.0050.0000.0000.0000.000
59A59MET0-0.027-0.00423.909-0.011-0.0110.0000.0000.0000.000
60A60ASP-1-0.870-0.91321.626-0.161-0.1610.0000.0000.0000.000
61A61GLN0-0.050-0.02918.376-0.054-0.0540.0000.0000.0000.000
62A62ILE00.0290.01715.8040.0180.0180.0000.0000.0000.000
63A63VAL0-0.013-0.00419.5630.0070.0070.0000.0000.0000.000
64A64ILE0-0.021-0.01019.754-0.001-0.0010.0000.0000.0000.000
65A65TYR0-0.010-0.00523.6440.0130.0130.0000.0000.0000.000
66A66ASN00.019-0.00724.898-0.006-0.0060.0000.0000.0000.000
67A67PRO0-0.002-0.00426.8220.0070.0070.0000.0000.0000.000
68A68PHE00.0160.00127.8910.0040.0040.0000.0000.0000.000
69A69TRP00.0360.02227.7740.0070.0070.0000.0000.0000.000
70A70ASN0-0.042-0.02428.7830.0050.0050.0000.0000.0000.000
71A71GLU-1-0.892-0.92428.465-0.009-0.0090.0000.0000.0000.000
72A72GLY00.014-0.01428.1460.0050.0050.0000.0000.0000.000
73A73ILE0-0.008-0.01522.100-0.003-0.0030.0000.0000.0000.000
74A74SER0-0.067-0.04021.841-0.001-0.0010.0000.0000.0000.000
75A75THR00.012-0.01321.842-0.006-0.0060.0000.0000.0000.000
76A76SER0-0.043-0.05422.348-0.014-0.0140.0000.0000.0000.000
77A77LEU0-0.043-0.01815.779-0.008-0.0080.0000.0000.0000.000
78A78LYS10.8970.96417.7460.0060.0060.0000.0000.0000.000
79A79LEU0-0.063-0.01718.887-0.018-0.0180.0000.0000.0000.000
80A80GLY00.0230.00817.512-0.022-0.0220.0000.0000.0000.000
81A81LEU00.002-0.00112.039-0.026-0.0260.0000.0000.0000.000
82A82ARG10.8980.93714.5460.0740.0740.0000.0000.0000.000
83A83PHE0-0.018-0.00313.707-0.006-0.0060.0000.0000.0000.000
84A84PHE00.0360.02410.319-0.027-0.0270.0000.0000.0000.000
85A85LYS10.9330.97710.4810.2020.2020.0000.0000.0000.000
86A86ASP-1-0.910-0.95910.371-0.467-0.4670.0000.0000.0000.000
87A87TYR0-0.042-0.0496.860-0.184-0.1840.0000.0000.0000.000
88A88ASP-1-0.836-0.9192.322-5.733-4.0103.313-1.881-3.155-0.018
89A89ALA0-0.029-0.0154.243-0.2590.0540.001-0.029-0.2840.000
90A90VAL0-0.0050.0046.082-0.233-0.2330.0000.0000.0000.000
91A91LEU0-0.002-0.0019.0350.0740.0740.0000.0000.0000.000
92A92VAL0-0.016-0.00610.931-0.139-0.1390.0000.0000.0000.000
93A93ALA00.0250.00014.4110.0240.0240.0000.0000.0000.000
94A94LEU0-0.009-0.00216.760-0.017-0.0170.0000.0000.0000.000
95A95GLY00.0430.00520.605-0.004-0.0040.0000.0000.0000.000
96A96ASP-1-0.870-0.93222.8920.0150.0150.0000.0000.0000.000
97A97MET00.0080.00921.4750.0130.0130.0000.0000.0000.000
98A98PRO0-0.0260.00221.8270.0020.0020.0000.0000.0000.000
99A99PHE0-0.022-0.02723.037-0.006-0.0060.0000.0000.0000.000
100A100VAL0-0.0170.01717.4550.0050.0050.0000.0000.0000.000
101A101THR00.008-0.02818.923-0.022-0.0220.0000.0000.0000.000
102A102LYS10.9060.93513.1390.2580.2580.0000.0000.0000.000
103A103GLU-1-0.782-0.88814.1400.1280.1280.0000.0000.0000.000
104A104ASP-1-0.768-0.82715.0660.1560.1560.0000.0000.0000.000
105A105VAL00.0180.00610.7990.0670.0670.0000.0000.0000.000
106A106ASN0-0.025-0.01710.4050.0560.0560.0000.0000.0000.000
107A107LYS10.8550.92210.211-0.074-0.0740.0000.0000.0000.000
108A108ILE0-0.0010.0099.8620.1080.1080.0000.0000.0000.000
109A109ILE00.0250.0084.8010.2980.2980.0000.0000.0000.000
110A110ASN0-0.038-0.0206.2930.6020.6020.0000.0000.0000.000
111A111THR0-0.041-0.0268.149-0.011-0.0110.0000.0000.0000.000
112A112PHE0-0.042-0.0052.311-1.851-1.7983.400-0.779-2.6750.002
113A113LYS10.8890.9245.807-1.032-1.0320.0000.0000.0000.000
114A114PRO00.0390.0075.5780.0230.0230.0000.0000.0000.000
115A115ASN00.0040.0086.949-0.001-0.0010.0000.0000.0000.000
116A116CYS0-0.099-0.0217.844-0.044-0.0440.0000.0000.0000.000
117A117LYS10.9090.9418.163-0.028-0.0280.0000.0000.0000.000
118A118ALA0-0.018-0.0069.8560.0190.0190.0000.0000.0000.000
119A119VAL0-0.0070.0028.634-0.055-0.0550.0000.0000.0000.000
120A120ILE0-0.034-0.02011.476-0.022-0.0220.0000.0000.0000.000
121A121PRO00.0370.03314.249-0.008-0.0080.0000.0000.0000.000
122A122THR0-0.045-0.03316.524-0.027-0.0270.0000.0000.0000.000
123A123HIS00.0450.01120.148-0.014-0.0140.0000.0000.0000.000
124A124LYS10.8660.91023.348-0.091-0.0910.0000.0000.0000.000
125A125GLY00.0180.02324.736-0.009-0.0090.0000.0000.0000.000
126A126GLU-1-0.880-0.92624.9320.0900.0900.0000.0000.0000.000
127A127ARG10.9400.95819.112-0.168-0.1680.0000.0000.0000.000
128A128GLY0-0.005-0.00419.577-0.020-0.0200.0000.0000.0000.000
129A129ASN0-0.065-0.01917.1540.0430.0430.0000.0000.0000.000
130A130PRO00.0350.01013.784-0.018-0.0180.0000.0000.0000.000
131A131VAL0-0.001-0.01813.2840.0430.0430.0000.0000.0000.000
132A132LEU0-0.0040.0165.956-0.113-0.1130.0000.0000.0000.000
133A133ILE0-0.022-0.0139.6860.0470.0470.0000.0000.0000.000
134A134SER00.0290.0056.1350.0600.0600.0000.0000.0000.000
135A135LYS10.8830.9035.8810.6200.6200.0000.0000.0000.000
136A136SER0-0.093-0.0498.004-0.049-0.0490.0000.0000.0000.000
137A137LEU00.018-0.00210.198-0.022-0.0220.0000.0000.0000.000
138A138PHE0-0.0050.0138.432-0.025-0.0250.0000.0000.0000.000
139A139ASN0-0.006-0.00613.087-0.012-0.0120.0000.0000.0000.000
140A140GLU-1-0.830-0.90515.7880.0250.0250.0000.0000.0000.000
141A141ILE0-0.036-0.01314.561-0.005-0.0050.0000.0000.0000.000
142A142GLU-1-0.850-0.95616.823-0.043-0.0430.0000.0000.0000.000
143A143LYS10.7840.88619.174-0.019-0.0190.0000.0000.0000.000
144A144LEU0-0.061-0.00619.944-0.001-0.0010.0000.0000.0000.000
145A145ARG10.9640.97622.697-0.011-0.0110.0000.0000.0000.000
146A146GLY00.0890.05426.1590.0060.0060.0000.0000.0000.000
147A147ASP-1-0.800-0.85226.3630.0220.0220.0000.0000.0000.000
148A148VAL0-0.040-0.00724.0040.0070.0070.0000.0000.0000.000
149A149GLY00.0820.03422.202-0.002-0.0020.0000.0000.0000.000
150A150ALA00.0590.00916.8980.0010.0010.0000.0000.0000.000
151A151ARG10.9650.98618.705-0.081-0.0810.0000.0000.0000.000
152A152VAL0-0.019-0.01420.4160.0020.0020.0000.0000.0000.000
153A153ILE0-0.004-0.00116.691-0.009-0.0090.0000.0000.0000.000
154A154LEU00.0460.01614.414-0.001-0.0010.0000.0000.0000.000
155A155ASN0-0.063-0.03217.8810.0040.0040.0000.0000.0000.000
156A156LYS10.8980.95619.998-0.075-0.0750.0000.0000.0000.000
157A157ILE00.0220.03414.355-0.010-0.0100.0000.0000.0000.000
158A158LYS10.8640.91517.833-0.089-0.0890.0000.0000.0000.000
159A159ILE00.0380.01117.3400.0190.0190.0000.0000.0000.000
160A160GLU-1-0.817-0.89217.7130.1320.1320.0000.0000.0000.000
161A161GLU-1-0.863-0.91913.6390.1170.1170.0000.0000.0000.000
162A162LEU0-0.058-0.01812.7560.0460.0460.0000.0000.0000.000
163A164PHE00.0230.00313.4610.0210.0210.0000.0000.0000.000
164A165ILE00.0030.00413.3240.0040.0040.0000.0000.0000.000
165A166GLU-1-0.804-0.88816.9860.1370.1370.0000.0000.0000.000
166A167CYS0-0.054-0.01616.8740.0250.0250.0000.0000.0000.000
167A168SER0-0.022-0.03919.491-0.018-0.0180.0000.0000.0000.000
168A169GLU-1-0.815-0.90522.1590.0600.0600.0000.0000.0000.000
169A170GLY00.0470.02023.0070.0000.0000.0000.0000.0000.000
170A171VAL0-0.013-0.00618.260-0.003-0.0030.0000.0000.0000.000
171A172LEU0-0.072-0.02420.8800.0080.0080.0000.0000.0000.000
172A173ILE0-0.031-0.00923.923-0.007-0.0070.0000.0000.0000.000
173A174ASP-1-0.827-0.90224.9950.0400.0400.0000.0000.0000.000
174A175ILE0-0.025-0.03426.646-0.001-0.0010.0000.0000.0000.000
175A176ASP-1-0.779-0.87429.7450.0120.0120.0000.0000.0000.000
176A177LYS10.7430.88126.546-0.074-0.0740.0000.0000.0000.000
177A178LYS10.7600.87029.211-0.044-0.0440.0000.0000.0000.000