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: ZV26N

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1861108.77761
FMO2-HF: Nuclear repulsion 1791984.846126
FMO2-HF: Total energy -69123.931484
FMO2-MP2: Total energy -69324.586438


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.
-5.302-4.77114.81-5.262-10.079-0.022
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 : -0.014 / q_NPA : -0.012
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].
3A3LEU0-0.022-0.0113.8770.0382.8610.077-1.309-1.5910.001
4A4THR0-0.001-0.0106.852-0.292-0.2920.0000.0000.0000.000
5A5HIS0-0.032-0.0179.7620.0780.0780.0000.0000.0000.000
6A6GLN00.0570.03913.188-0.028-0.0280.0000.0000.0000.000
7A7LEU0-0.027-0.01216.5690.0010.0010.0000.0000.0000.000
8A8ASP-1-0.881-0.93319.522-0.024-0.0240.0000.0000.0000.000
9A9LEU0-0.042-0.02422.2160.0040.0040.0000.0000.0000.000
10A10PHE0-0.034-0.02022.9050.0000.0000.0000.0000.0000.000
11A11PRO00.0550.02819.995-0.004-0.0040.0000.0000.0000.000
12A12GLU-1-0.839-0.92818.944-0.052-0.0520.0000.0000.0000.000
13A13CYS0-0.076-0.03319.218-0.007-0.0070.0000.0000.0000.000
14A14ARG10.8510.92613.6090.0870.0870.0000.0000.0000.000
15A15VAL0-0.013-0.00913.189-0.022-0.0220.0000.0000.0000.000
16A16THR00.003-0.0048.3190.0640.0640.0000.0000.0000.000
17A17LEU0-0.020-0.0058.426-0.028-0.0280.0000.0000.0000.000
18A18LEU00.0280.0034.643-0.508-0.452-0.001-0.007-0.0480.000
19A19LEU0-0.039-0.0104.4330.6990.803-0.001-0.011-0.0920.000
20A20PHE00.0280.0084.778-0.625-0.533-0.001-0.005-0.0870.000
21A21LYS10.8710.9497.395-0.037-0.0370.0000.0000.0000.000
22A22ASP-1-0.837-0.9159.6600.1940.1940.0000.0000.0000.000
23A23VAL0-0.035-0.01511.2670.0220.0220.0000.0000.0000.000
24A24LYS10.8570.91613.736-0.070-0.0700.0000.0000.0000.000
25A25ASN00.0530.02915.540-0.010-0.0100.0000.0000.0000.000
26A26ALA00.0640.04116.716-0.015-0.0150.0000.0000.0000.000
27A27GLY0-0.006-0.01517.620-0.008-0.0080.0000.0000.0000.000
28A28ASP-1-0.837-0.91620.261-0.039-0.0390.0000.0000.0000.000
29A29LEU0-0.033-0.01313.881-0.004-0.0040.0000.0000.0000.000
30A30ARG10.8910.93917.9320.0690.0690.0000.0000.0000.000
31A31ARG10.7470.85820.2490.0470.0470.0000.0000.0000.000
32A32LYS10.9140.95017.1780.0830.0830.0000.0000.0000.000
33A33ALA00.0140.01418.8080.0000.0000.0000.0000.0000.000
34A34MET0-0.098-0.05920.2780.0040.0040.0000.0000.0000.000
35A35GLU-1-0.865-0.93423.906-0.051-0.0510.0000.0000.0000.000
36A36GLY00.0150.03121.9270.0050.0050.0000.0000.0000.000
37A37THR0-0.055-0.02321.232-0.002-0.0020.0000.0000.0000.000
38A38ILE0-0.043-0.02113.773-0.001-0.0010.0000.0000.0000.000
39A39ASP-1-0.877-0.92115.061-0.136-0.1360.0000.0000.0000.000
40A40GLY00.008-0.01314.432-0.033-0.0330.0000.0000.0000.000
41A41SER0-0.100-0.06315.1870.0310.0310.0000.0000.0000.000
42A42LEU0-0.015-0.00113.624-0.055-0.0550.0000.0000.0000.000
43A43ILE0-0.008-0.02613.8870.0500.0500.0000.0000.0000.000
44A44ASN00.0380.02713.705-0.054-0.0540.0000.0000.0000.000
45A45PRO00.026-0.00211.0490.0100.0100.0000.0000.0000.000
46A46THR0-0.058-0.03613.2180.0270.0270.0000.0000.0000.000
47A47VAL0-0.013-0.01815.9720.0260.0260.0000.0000.0000.000
48A48ILE0-0.036-0.01313.3880.0030.0030.0000.0000.0000.000
49A49VAL00.009-0.00114.420-0.004-0.0040.0000.0000.0000.000
50A50ASP-1-0.841-0.92013.6720.0230.0230.0000.0000.0000.000
51A51PRO00.0260.00610.198-0.033-0.0330.0000.0000.0000.000
52A52PHE00.0110.01012.940-0.016-0.0160.0000.0000.0000.000
53A53GLN00.0290.00716.174-0.002-0.0020.0000.0000.0000.000
54A54ILE0-0.008-0.01712.851-0.001-0.0010.0000.0000.0000.000
55A55LEU00.0050.00813.9420.0040.0040.0000.0000.0000.000
56A56VAL00.0370.02717.3550.0040.0040.0000.0000.0000.000
57A57ALA0-0.005-0.00118.9760.0060.0060.0000.0000.0000.000
58A58ALA00.002-0.00617.5380.0030.0030.0000.0000.0000.000
59A59ASN00.035-0.00519.6920.0050.0050.0000.0000.0000.000
60A60LYS10.9050.98022.1460.0550.0550.0000.0000.0000.000
61A61ALA0-0.019-0.01722.1180.0050.0050.0000.0000.0000.000
62A62VAL00.0400.01321.3180.0040.0040.0000.0000.0000.000
63A63HIS0-0.035-0.03024.2220.0090.0090.0000.0000.0000.000
64A64LEU0-0.0130.00727.2130.0050.0050.0000.0000.0000.000
65A65TYR00.003-0.01925.4010.0020.0020.0000.0000.0000.000
66A66LYS10.8350.92825.0930.0590.0590.0000.0000.0000.000
67A67LEU0-0.032-0.01029.3890.0040.0040.0000.0000.0000.000
68A68GLY0-0.025-0.00131.0810.0030.0030.0000.0000.0000.000
69A69LYS10.9060.95531.6940.0360.0360.0000.0000.0000.000
70A70MET0-0.0460.00526.348-0.003-0.0030.0000.0000.0000.000
71A71LYS10.8510.90729.0000.0460.0460.0000.0000.0000.000
72A72THR0-0.076-0.06526.3470.0000.0000.0000.0000.0000.000
73A73ARG10.9540.96727.7710.0530.0530.0000.0000.0000.000
74A74THR00.0260.00023.6970.0000.0000.0000.0000.0000.000
75A75LEU00.1190.06020.659-0.001-0.0010.0000.0000.0000.000
76A76SER00.0340.02818.835-0.004-0.0040.0000.0000.0000.000
77A77THR0-0.009-0.00320.046-0.010-0.0100.0000.0000.0000.000
78A78GLU-1-0.771-0.84722.685-0.067-0.0670.0000.0000.0000.000
79A79ILE00.0230.01417.2070.0070.0070.0000.0000.0000.000
80A80ILE00.0050.00218.4230.0020.0020.0000.0000.0000.000
81A81PHE0-0.039-0.02720.4410.0090.0090.0000.0000.0000.000
82A82ASN0-0.024-0.03022.4470.0150.0150.0000.0000.0000.000
83A83LEU00.0280.04117.2640.0060.0060.0000.0000.0000.000
84A84SER0-0.0250.00921.5880.0100.0100.0000.0000.0000.000
85A85PRO00.0360.01524.6670.0020.0020.0000.0000.0000.000
86A86ASN0-0.057-0.02827.6840.0070.0070.0000.0000.0000.000
87A87ASN00.049-0.00929.160-0.006-0.0060.0000.0000.0000.000
88A88ASN0-0.0160.01131.406-0.004-0.0040.0000.0000.0000.000
89A89ILE00.1200.04827.845-0.003-0.0030.0000.0000.0000.000
90A90SER0-0.048-0.02727.586-0.004-0.0040.0000.0000.0000.000
91A91GLU-1-0.869-0.92427.845-0.046-0.0460.0000.0000.0000.000
92A92ALA00.0300.01625.071-0.002-0.0020.0000.0000.0000.000
93A93LEU00.0410.01122.933-0.008-0.0080.0000.0000.0000.000
94A94LYS10.8980.96622.5810.0370.0370.0000.0000.0000.000
95A95LYS10.8570.91923.2160.0470.0470.0000.0000.0000.000
96A96PHE00.0400.01819.092-0.001-0.0010.0000.0000.0000.000
97A97GLY00.0130.02218.184-0.027-0.0270.0000.0000.0000.000
98A98ILE00.0040.01915.2880.0070.0070.0000.0000.0000.000
99A99SER0-0.103-0.08218.4980.0210.0210.0000.0000.0000.000
100A100ALA00.028-0.01419.991-0.004-0.0040.0000.0000.0000.000
101A101ASN0-0.028-0.01221.1900.0020.0020.0000.0000.0000.000
102A102ASP-1-0.775-0.84316.412-0.099-0.0990.0000.0000.0000.000
103A103THR00.0230.00315.412-0.005-0.0050.0000.0000.0000.000
104A104SER0-0.040-0.02111.3780.0210.0210.0000.0000.0000.000
105A105ILE0-0.004-0.00210.6010.0300.0300.0000.0000.0000.000
106A106LEU00.0230.0168.128-0.170-0.1700.0000.0000.0000.000
107A107ILE00.0050.0049.1090.1600.1600.0000.0000.0000.000
108A108VAL0-0.007-0.0089.803-0.131-0.1310.0000.0000.0000.000
109A109TYR00.0210.0089.6960.0400.0400.0000.0000.0000.000
110A110ILE0-0.004-0.01013.9080.0010.0010.0000.0000.0000.000
111A111GLU-1-0.865-0.90714.324-0.111-0.1110.0000.0000.0000.000
112A112GLU-1-0.802-0.89017.746-0.058-0.0580.0000.0000.0000.000
113A113GLY0-0.049-0.05720.5240.0010.0010.0000.0000.0000.000
114A114GLU-1-0.857-0.89222.031-0.055-0.0550.0000.0000.0000.000
115A115LYS10.7630.85021.3740.0700.0700.0000.0000.0000.000
116A116GLN00.011-0.00816.765-0.007-0.0070.0000.0000.0000.000
117A117ILE00.0360.03813.4360.0050.0050.0000.0000.0000.000
118A118ASN0-0.034-0.01412.519-0.019-0.0190.0000.0000.0000.000
119A119GLN00.002-0.0086.4210.0420.0420.0000.0000.0000.000
120A120GLU-1-0.808-0.9179.778-0.082-0.0820.0000.0000.0000.000
121A121TYR00.0430.03710.7670.0240.0240.0000.0000.0000.000
122A122LEU00.0080.00410.5000.0060.0060.0000.0000.0000.000
123A123ILE0-0.032-0.0235.988-0.021-0.0210.0000.0000.0000.000
124A124SER0-0.078-0.0429.3880.0350.0350.0000.0000.0000.000
125A125GLN00.0190.03212.5440.0220.0220.0000.0000.0000.000
126A126VAL0-0.065-0.03310.1010.0100.0100.0000.0000.0000.000
127A127GLU-1-0.887-0.92011.9200.0790.0790.0000.0000.0000.000
128A128GLY0-0.094-0.08111.368-0.012-0.0120.0000.0000.0000.000
129A129HIS00.0470.0366.929-0.092-0.0920.0000.0000.0000.000
130A130GLN00.0080.0032.047-2.500-2.0512.276-1.193-1.533-0.003
131A131VAL0-0.0110.0043.6381.7953.0180.028-0.485-0.765-0.001
132A132SER0-0.001-0.0111.937-7.235-8.13312.303-6.036-5.368-0.019
133A133LEU00.1030.0322.7393.6150.2970.1293.784-0.5950.000
134A134LYS10.8940.9595.021-0.597-0.5970.0000.0000.0000.000
135A135ASN0-0.014-0.0186.505-0.038-0.0380.0000.0000.0000.000
136A136LEU00.0310.0178.143-0.019-0.0190.0000.0000.0000.000
137A137PRO00.009-0.0119.9890.0190.0190.0000.0000.0000.000
138A138GLU-1-0.895-0.94111.1940.2290.2290.0000.0000.0000.000
139A139ILE0-0.026-0.0079.8790.0070.0070.0000.0000.0000.000
140A140MET0-0.063-0.00213.757-0.007-0.0070.0000.0000.0000.000
141A141ASN00.0660.02515.8600.0270.0270.0000.0000.0000.000
142A142ILE00.1010.03919.462-0.007-0.0070.0000.0000.0000.000
143A143THR0-0.005-0.00721.4950.0010.0010.0000.0000.0000.000
144A144GLU-1-0.829-0.90121.754-0.036-0.0360.0000.0000.0000.000
145A145VAL00.0230.02119.426-0.002-0.0020.0000.0000.0000.000
146A146LYS10.8170.88722.5220.0000.0000.0000.0000.0000.000
147A147LYS10.7960.89426.0050.0330.0330.0000.0000.0000.000
148A148ILE0-0.062-0.04022.7950.0020.0020.0000.0000.0000.000
149A149TYR00.019-0.00921.079-0.002-0.0020.0000.0000.0000.000
150A150LYS10.8520.94226.6520.0300.0300.0000.0000.0000.000
151A151LEU00.0550.04524.7390.0010.0010.0000.0000.0000.000
152A152SER00.0390.02429.3050.0000.0000.0000.0000.0000.000
153A153SER00.0420.00929.7060.0000.0000.0000.0000.0000.000
154A154GLN0-0.065-0.02529.8200.0010.0010.0000.0000.0000.000
155A155GLU-1-0.840-0.91825.7050.0050.0050.0000.0000.0000.000
156A156GLU-1-0.789-0.87026.6290.0130.0130.0000.0000.0000.000
157A157SER0-0.042-0.01423.0430.0030.0030.0000.0000.0000.000
158A158ILE00.0420.02317.109-0.005-0.0050.0000.0000.0000.000
159A159GLY00.0010.01320.539-0.007-0.0070.0000.0000.0000.000
160A160THR00.058-0.00321.526-0.004-0.0040.0000.0000.0000.000
161A161LEU0-0.041-0.03722.638-0.006-0.0060.0000.0000.0000.000
162A162LEU0-0.011-0.00917.949-0.009-0.0090.0000.0000.0000.000
163A163ASP-1-0.840-0.90321.596-0.008-0.0080.0000.0000.0000.000
164A164ALA0-0.018-0.01124.623-0.004-0.0040.0000.0000.0000.000
165A165ILE0-0.042-0.02220.934-0.004-0.0040.0000.0000.0000.000
166A166ILE00.0210.00420.394-0.007-0.0070.0000.0000.0000.000
167A167CYS0-0.041-0.00824.362-0.001-0.0010.0000.0000.0000.000
168A168ARG10.8270.90526.3780.0230.0230.0000.0000.0000.000
169A169MET0-0.055-0.02520.471-0.001-0.0010.0000.0000.0000.000
170A170SER0-0.057-0.03626.026-0.002-0.0020.0000.0000.0000.000
171A171THR0-0.068-0.04528.4910.0020.0020.0000.0000.0000.000
172A172LYS10.8180.93926.5820.0610.0610.0000.0000.0000.000
173A173ASP-1-0.922-0.95930.976-0.040-0.0400.0000.0000.0000.000
174A174VAL00.0450.01632.932-0.001-0.0010.0000.0000.0000.000
175A175LEU0-0.0150.02334.7080.0000.0000.0000.0000.0000.000