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

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FMODB ID: 6Y3NZ

Calculation Name: 3ENP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ENP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3C4

Base Structure: X-ray

Registration Date: 2023-09-20

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1859679.717272
FMO2-HF: Nuclear repulsion 1790557.525103
FMO2-HF: Total energy -69122.192169
FMO2-MP2: Total energy -69322.980799


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.
-4.231-2.10311.988-4.758-9.359-0.008
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 : -0.020 / q_NPA : -0.038
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].
3A3LEU0-0.008-0.0113.8840.0462.0680.087-0.818-1.291-0.003
4A4THR0-0.029-0.0176.853-0.155-0.1550.0000.0000.0000.000
5A5HIS0-0.0040.0039.734-0.049-0.0490.0000.0000.0000.000
6A6GLN00.0820.05213.1680.0360.0360.0000.0000.0000.000
7A7LEU0-0.064-0.04016.539-0.008-0.0080.0000.0000.0000.000
8A8ASP-1-0.967-0.98419.4970.0730.0730.0000.0000.0000.000
9A9LEU0-0.013-0.01222.203-0.006-0.0060.0000.0000.0000.000
10A10PHE0-0.036-0.02222.920-0.006-0.0060.0000.0000.0000.000
11A11PRO00.0520.03119.9610.0180.0180.0000.0000.0000.000
12A12GLU-1-0.862-0.93718.9050.1310.1310.0000.0000.0000.000
13A13CYS0-0.062-0.02819.1980.0150.0150.0000.0000.0000.000
14A14ARG10.9260.96813.287-0.278-0.2780.0000.0000.0000.000
15A15VAL0-0.017-0.00813.4590.0030.0030.0000.0000.0000.000
16A16THR00.0110.0028.2400.0520.0520.0000.0000.0000.000
17A17LEU0-0.035-0.0168.436-0.081-0.0810.0000.0000.0000.000
18A18LEU00.0350.0115.143-0.102-0.1020.0000.0000.0000.000
19A19LEU0-0.035-0.0084.253-0.0380.054-0.001-0.007-0.0840.000
20A20PHE00.0290.0064.6330.1850.313-0.001-0.006-0.1210.000
21A21LYS10.9030.9607.2860.2610.2610.0000.0000.0000.000
22A22ASP-1-0.900-0.9529.6390.0300.0300.0000.0000.0000.000
23A23VAL0-0.055-0.02711.3330.0410.0410.0000.0000.0000.000
24A24LYS10.9590.96713.689-0.108-0.1080.0000.0000.0000.000
25A25ASN00.0500.02915.868-0.012-0.0120.0000.0000.0000.000
26A26ALA00.0720.04616.6820.0180.0180.0000.0000.0000.000
27A27GLY0-0.013-0.01717.6970.0040.0040.0000.0000.0000.000
28A28ASP-1-0.859-0.92920.5440.1400.1400.0000.0000.0000.000
29A29LEU0-0.023-0.01114.2010.0000.0000.0000.0000.0000.000
30A30ARG10.9290.97118.328-0.091-0.0910.0000.0000.0000.000
31A31ARG10.7820.88420.481-0.146-0.1460.0000.0000.0000.000
32A32LYS10.9720.98117.988-0.277-0.2770.0000.0000.0000.000
33A33ALA00.0190.01619.2150.0040.0040.0000.0000.0000.000
34A34MET0-0.107-0.06120.734-0.005-0.0050.0000.0000.0000.000
35A35GLU-1-0.898-0.95524.3830.1390.1390.0000.0000.0000.000
36A36GLY00.0210.03322.567-0.004-0.0040.0000.0000.0000.000
37A37THR0-0.055-0.02322.0500.0140.0140.0000.0000.0000.000
38A38ILE0-0.057-0.02714.4240.0260.0260.0000.0000.0000.000
39A39ASP-1-0.844-0.90715.9130.3180.3180.0000.0000.0000.000
40A40GLY0-0.003-0.01914.9180.0360.0360.0000.0000.0000.000
41A41SER0-0.089-0.05215.463-0.027-0.0270.0000.0000.0000.000
42A42LEU0-0.0180.00213.9740.0150.0150.0000.0000.0000.000
43A43ILE0-0.004-0.02313.754-0.024-0.0240.0000.0000.0000.000
44A44ASN00.0370.01113.584-0.024-0.0240.0000.0000.0000.000
45A45PRO00.0230.00711.030-0.007-0.0070.0000.0000.0000.000
46A46THR0-0.053-0.02213.177-0.023-0.0230.0000.0000.0000.000
47A47VAL00.004-0.01215.976-0.003-0.0030.0000.0000.0000.000
48A48ILE0-0.036-0.01613.1940.0180.0180.0000.0000.0000.000
49A49VAL00.0100.00114.456-0.028-0.0280.0000.0000.0000.000
50A50ASP-1-0.845-0.92813.7000.0000.0000.0000.0000.0000.000
51A51PRO00.0310.01310.2950.0100.0100.0000.0000.0000.000
52A52PHE00.0110.00912.9510.0290.0290.0000.0000.0000.000
53A53GLN00.0470.01716.176-0.001-0.0010.0000.0000.0000.000
54A54ILE0-0.010-0.01712.7150.0080.0080.0000.0000.0000.000
55A55LEU00.0060.00614.0260.0150.0150.0000.0000.0000.000
56A56VAL00.0210.02817.3030.0040.0040.0000.0000.0000.000
57A57ALA00.0050.00318.9090.0000.0000.0000.0000.0000.000
58A58ALA00.0160.01217.4710.0020.0020.0000.0000.0000.000
59A59ASN00.0640.01919.5960.0060.0060.0000.0000.0000.000
60A60LYS10.9390.98822.168-0.065-0.0650.0000.0000.0000.000
61A61ALA0-0.020-0.01722.152-0.005-0.0050.0000.0000.0000.000
62A62VAL00.0350.01121.355-0.002-0.0020.0000.0000.0000.000
63A63HIS0-0.005-0.01224.376-0.010-0.0100.0000.0000.0000.000
64A64LEU0-0.0090.00527.271-0.008-0.0080.0000.0000.0000.000
65A65TYR00.000-0.01625.428-0.002-0.0020.0000.0000.0000.000
66A66LYS10.8250.91025.394-0.123-0.1230.0000.0000.0000.000
67A67LEU0-0.025-0.00929.520-0.006-0.0060.0000.0000.0000.000
68A68GLY0-0.0260.00131.368-0.004-0.0040.0000.0000.0000.000
69A69LYS10.9140.95931.879-0.061-0.0610.0000.0000.0000.000
70A70MET0-0.0430.00226.5370.0020.0020.0000.0000.0000.000
71A71LYS10.9070.93928.949-0.062-0.0620.0000.0000.0000.000
72A72THR0-0.063-0.06726.4160.0000.0000.0000.0000.0000.000
73A73ARG10.9590.96128.032-0.091-0.0910.0000.0000.0000.000
74A74THR00.0240.00223.7680.0030.0030.0000.0000.0000.000
75A75LEU00.1260.06620.964-0.006-0.0060.0000.0000.0000.000
76A76SER00.0270.01918.8630.0000.0000.0000.0000.0000.000
77A77THR0-0.011-0.01120.138-0.009-0.0090.0000.0000.0000.000
78A78GLU-1-0.760-0.82422.7780.0790.0790.0000.0000.0000.000
79A79ILE00.0190.01517.090-0.014-0.0140.0000.0000.0000.000
80A80ILE00.003-0.00118.255-0.012-0.0120.0000.0000.0000.000
81A81PHE0-0.049-0.03120.293-0.015-0.0150.0000.0000.0000.000
82A82ASN0-0.079-0.06422.135-0.017-0.0170.0000.0000.0000.000
83A83LEU00.0320.03817.054-0.007-0.0070.0000.0000.0000.000
84A84SER0-0.0310.02221.498-0.012-0.0120.0000.0000.0000.000
85A85PRO00.0580.02124.5830.0030.0030.0000.0000.0000.000
86A86ASN0-0.033-0.00727.620-0.002-0.0020.0000.0000.0000.000
87A87ASN00.0990.04429.0580.0050.0050.0000.0000.0000.000
88A88ASN0-0.0190.00731.2770.0070.0070.0000.0000.0000.000
89A89ILE00.1060.04427.7820.0010.0010.0000.0000.0000.000
90A90SER0-0.056-0.03027.4430.0020.0020.0000.0000.0000.000
91A91GLU-1-0.951-1.00727.7070.0370.0370.0000.0000.0000.000
92A92ALA00.0380.02324.872-0.003-0.0030.0000.0000.0000.000
93A93LEU00.0380.00822.7890.0000.0000.0000.0000.0000.000
94A94LYS10.8970.97022.444-0.040-0.0400.0000.0000.0000.000
95A95LYS10.9260.96723.108-0.028-0.0280.0000.0000.0000.000
96A96PHE00.0450.02119.086-0.006-0.0060.0000.0000.0000.000
97A97GLY00.0180.02418.0650.0060.0060.0000.0000.0000.000
98A98ILE0-0.0120.01515.171-0.012-0.0120.0000.0000.0000.000
99A99SER0-0.076-0.06318.357-0.002-0.0020.0000.0000.0000.000
100A100ALA0-0.009-0.03119.8650.0030.0030.0000.0000.0000.000
101A101ASN0-0.011-0.00521.0830.0130.0130.0000.0000.0000.000
102A102ASP-1-0.797-0.87016.2410.0400.0400.0000.0000.0000.000
103A103THR0-0.003-0.01215.3660.0110.0110.0000.0000.0000.000
104A104SER0-0.018-0.01111.553-0.035-0.0350.0000.0000.0000.000
105A105ILE0-0.007-0.00410.5010.0100.0100.0000.0000.0000.000
106A106LEU00.0270.0198.129-0.027-0.0270.0000.0000.0000.000
107A107ILE00.0020.0009.133-0.002-0.0020.0000.0000.0000.000
108A108VAL00.000-0.0019.9570.0270.0270.0000.0000.0000.000
109A109TYR00.0350.01310.2870.0510.0510.0000.0000.0000.000
110A110ILE0-0.001-0.00714.1570.0190.0190.0000.0000.0000.000
111A111GLU-1-0.909-0.94014.1280.4810.4810.0000.0000.0000.000
112A112GLU-1-0.782-0.85517.7190.1280.1280.0000.0000.0000.000
113A113GLY0-0.057-0.06320.502-0.003-0.0030.0000.0000.0000.000
114A114GLU-1-0.869-0.90422.2790.1140.1140.0000.0000.0000.000
115A115LYS10.7940.87021.212-0.165-0.1650.0000.0000.0000.000
116A116GLN0-0.052-0.04817.344-0.002-0.0020.0000.0000.0000.000
117A117ILE00.0270.04513.507-0.006-0.0060.0000.0000.0000.000
118A118ASN00.015-0.02012.6850.0900.0900.0000.0000.0000.000
119A119GLN0-0.048-0.0436.928-0.020-0.0200.0000.0000.0000.000
120A120GLU-1-0.832-0.90210.2930.7670.7670.0000.0000.0000.000
121A121TYR00.0540.04511.180-0.059-0.0590.0000.0000.0000.000
122A122LEU0-0.0010.01511.211-0.041-0.0410.0000.0000.0000.000
123A123ILE0-0.027-0.0266.6870.0030.0030.0000.0000.0000.000
124A124SER0-0.080-0.06010.376-0.099-0.0990.0000.0000.0000.000
125A125GLN0-0.0210.00813.518-0.120-0.1200.0000.0000.0000.000
126A126VAL0-0.073-0.03610.489-0.111-0.1110.0000.0000.0000.000
127A127GLU-1-0.884-0.91812.5800.2880.2880.0000.0000.0000.000
128A128GLY0-0.087-0.07911.531-0.079-0.0790.0000.0000.0000.000
129A129HIS00.0480.0385.9770.3120.3120.0000.0000.0000.000
130A130GLN00.0050.0052.629-0.706-0.2441.626-0.906-1.1820.006
131A131VAL0-0.034-0.0093.504-1.711-0.4640.044-0.566-0.725-0.003
132A132SER0-0.014-0.0142.136-6.034-5.69010.081-5.103-5.323-0.010
133A133LEU00.1100.0372.9712.5700.4030.1522.648-0.6330.002
134A134LYS10.8860.9555.0790.2670.2670.0000.0000.0000.000
135A135ASN00.0310.0176.5250.1760.1760.0000.0000.0000.000
136A136LEU00.0160.0118.3210.0510.0510.0000.0000.0000.000
137A137PRO00.002-0.01610.0880.0510.0510.0000.0000.0000.000
138A138GLU-1-0.947-0.97211.142-0.324-0.3240.0000.0000.0000.000
139A139ILE0-0.037-0.0119.7440.0160.0160.0000.0000.0000.000
140A140MET0-0.078-0.00913.8380.0440.0440.0000.0000.0000.000
141A141ASN00.0670.02615.9320.0030.0030.0000.0000.0000.000
142A142ILE00.0970.03519.5200.0120.0120.0000.0000.0000.000
143A143THR0-0.009-0.01021.5730.0070.0070.0000.0000.0000.000
144A144GLU-1-0.868-0.92321.9050.0070.0070.0000.0000.0000.000
145A145VAL00.0310.02719.3950.0080.0080.0000.0000.0000.000
146A146LYS10.8200.89522.5460.0340.0340.0000.0000.0000.000
147A147LYS10.8220.90826.0450.0010.0010.0000.0000.0000.000
148A148ILE0-0.078-0.04422.6300.0050.0050.0000.0000.0000.000
149A149TYR00.012-0.02521.1410.0030.0030.0000.0000.0000.000
150A150LYS10.8930.96726.646-0.009-0.0090.0000.0000.0000.000
151A151LEU00.0550.05224.8730.0010.0010.0000.0000.0000.000
152A152SER00.0410.02729.3470.0000.0000.0000.0000.0000.000
153A153SER00.0610.01429.784-0.002-0.0020.0000.0000.0000.000
154A154GLN0-0.079-0.03129.921-0.002-0.0020.0000.0000.0000.000
155A155GLU-1-0.850-0.91426.191-0.034-0.0340.0000.0000.0000.000
156A156GLU-1-0.883-0.93726.686-0.017-0.0170.0000.0000.0000.000
157A157SER0-0.0010.04223.146-0.003-0.0030.0000.0000.0000.000
158A158ILE00.0700.03417.1750.0050.0050.0000.0000.0000.000
159A159GLY0-0.0090.00420.5850.0060.0060.0000.0000.0000.000
160A160THR00.086-0.00421.5590.0050.0050.0000.0000.0000.000
161A161LEU0-0.052-0.04322.6460.0050.0050.0000.0000.0000.000
162A162LEU00.005-0.00317.9420.0040.0040.0000.0000.0000.000
163A163ASP-1-0.846-0.90921.6260.0120.0120.0000.0000.0000.000
164A164ALA0-0.016-0.01224.6450.0050.0050.0000.0000.0000.000
165A165ILE0-0.046-0.02420.7540.0040.0040.0000.0000.0000.000
166A166ILE00.009-0.00120.4960.0070.0070.0000.0000.0000.000
167A167CYS0-0.018-0.00624.3690.0050.0050.0000.0000.0000.000
168A168ARG10.8040.87926.303-0.008-0.0080.0000.0000.0000.000
169A169MET0-0.074-0.03820.5060.0000.0000.0000.0000.0000.000
170A170SER0-0.048-0.01625.9830.0060.0060.0000.0000.0000.000
171A171THR0-0.073-0.04428.441-0.001-0.0010.0000.0000.0000.000
172A172LYS10.7890.91726.539-0.053-0.0530.0000.0000.0000.000
173A173ASP-1-0.998-1.01130.8990.0470.0470.0000.0000.0000.000
174A174VAL00.0340.01632.6940.0030.0030.0000.0000.0000.000
175A175LEU0-0.0320.00634.6190.0000.0000.0000.0000.0000.000