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

tag_button

FMODB ID: 17J3Z

Calculation Name: 1EIA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EIA

Chain ID: A

ChEMBL ID:

UniProt ID: P69732

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2185564.940976
FMO2-HF: Nuclear repulsion 2102212.275314
FMO2-HF: Total energy -83352.665662
FMO2-MP2: Total energy -83592.981931


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:16:THR)


Summations of interaction energy for fragment #1(A:16:THR)
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.
-6.013-2.7950.288-1.656-1.849-0.009
Interaction energy analysis for fragmet #1(A:16:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.029
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].
3A18ARG10.9350.9592.712-3.836-1.2500.264-1.535-1.314-0.009
4A19GLY0-0.002-0.0015.4630.5170.5170.0000.0000.0000.000
5A20TYR0-0.013-0.0114.1340.4710.759-0.001-0.028-0.2580.000
6A21THR00.0740.0366.247-0.183-0.1830.0000.0000.0000.000
7A22THR00.0500.0299.0530.0450.0450.0000.0000.0000.000
8A23TRP0-0.0700.0008.208-0.137-0.1370.0000.0000.0000.000
9A24VAL00.0360.0048.801-0.005-0.0050.0000.0000.0000.000
10A25ASN00.0570.01611.587-0.084-0.0840.0000.0000.0000.000
11A26THR0-0.034-0.04714.302-0.058-0.0580.0000.0000.0000.000
12A27ILE0-0.062-0.01912.108-0.039-0.0390.0000.0000.0000.000
13A28GLN0-0.022-0.00915.6400.0190.0190.0000.0000.0000.000
14A29THR0-0.057-0.00217.565-0.042-0.0420.0000.0000.0000.000
15A30ASN0-0.001-0.02420.1960.0410.0410.0000.0000.0000.000
16A31GLY00.0470.01918.189-0.014-0.0140.0000.0000.0000.000
17A32LEU00.0700.09214.613-0.021-0.0210.0000.0000.0000.000
18A33LEU0-0.045-0.01817.319-0.031-0.0310.0000.0000.0000.000
19A34ASN00.009-0.00319.873-0.035-0.0350.0000.0000.0000.000
20A35GLU-1-0.854-0.93320.1340.0850.0850.0000.0000.0000.000
21A36ALA0-0.0140.01219.556-0.019-0.0190.0000.0000.0000.000
22A37SER0-0.046-0.08815.861-0.013-0.0130.0000.0000.0000.000
23A38GLN00.0440.03016.118-0.012-0.0120.0000.0000.0000.000
24A39ASN00.007-0.01117.782-0.029-0.0290.0000.0000.0000.000
25A40LEU0-0.056-0.01212.927-0.049-0.0490.0000.0000.0000.000
26A41PHE00.0340.00911.296-0.082-0.0820.0000.0000.0000.000
27A42GLY00.0000.05014.167-0.086-0.0860.0000.0000.0000.000
28A43ILE0-0.012-0.01315.118-0.054-0.0540.0000.0000.0000.000
29A44LEU0-0.011-0.0159.701-0.089-0.0890.0000.0000.0000.000
30A45SER0-0.057-0.07711.512-0.175-0.1750.0000.0000.0000.000
31A46VAL0-0.037-0.01412.5750.0370.0370.0000.0000.0000.000
32A47ASP-1-0.922-0.97813.133-0.680-0.6800.0000.0000.0000.000
33A48CYS0-0.101-0.0149.226-0.178-0.1780.0000.0000.0000.000
34A49THR00.0750.0358.5850.1910.1910.0000.0000.0000.000
35A50SER00.027-0.02710.3170.0260.0260.0000.0000.0000.000
36A51GLU-1-0.884-0.9296.2490.7720.7720.0000.0000.0000.000
37A52GLU-1-0.855-0.9295.461-2.767-2.7670.0000.0000.0000.000
38A53MET0-0.009-0.0066.662-0.017-0.0170.0000.0000.0000.000
39A54ASN00.0550.0428.993-0.010-0.0100.0000.0000.0000.000
40A55ALA00.0390.0253.3280.0000.2640.026-0.084-0.2070.000
41A56PHE0-0.022-0.0205.428-0.045-0.0450.0000.0000.0000.000
42A57LEU0-0.003-0.0047.180-0.004-0.0040.0000.0000.0000.000
43A58ASP-1-0.965-0.9956.6471.6601.6600.0000.0000.0000.000
44A59VAL0-0.053-0.0184.460-0.104-0.024-0.001-0.009-0.0700.000
45A60VAL0-0.067-0.0167.418-0.230-0.2300.0000.0000.0000.000
46A61PRO00.0360.00710.951-0.013-0.0130.0000.0000.0000.000
47A62GLY00.0340.02713.2310.0020.0020.0000.0000.0000.000
48A63GLN0-0.0360.00216.245-0.088-0.0880.0000.0000.0000.000
49A64ALA00.0280.01118.076-0.011-0.0110.0000.0000.0000.000
50A65GLY00.0240.00918.977-0.008-0.0080.0000.0000.0000.000
51A66GLN00.0680.03419.497-0.001-0.0010.0000.0000.0000.000
52A67LYS10.9410.96011.866-0.938-0.9380.0000.0000.0000.000
53A68GLN00.0140.01017.4340.0500.0500.0000.0000.0000.000
54A69ILE0-0.0090.02420.010-0.024-0.0240.0000.0000.0000.000
55A70LEU0-0.031-0.01715.163-0.019-0.0190.0000.0000.0000.000
56A71LEU00.009-0.02014.262-0.006-0.0060.0000.0000.0000.000
57A72ASP-1-0.825-0.90418.2120.2570.2570.0000.0000.0000.000
58A73ALA0-0.087-0.03921.308-0.031-0.0310.0000.0000.0000.000
59A74ILE0-0.001-0.02316.086-0.028-0.0280.0000.0000.0000.000
60A75ASP-1-0.794-0.88420.2280.2870.2870.0000.0000.0000.000
61A76LYS10.9140.97922.119-0.177-0.1770.0000.0000.0000.000
62A77ILE0-0.070-0.02822.127-0.016-0.0160.0000.0000.0000.000
63A78ALA0-0.003-0.00921.301-0.017-0.0170.0000.0000.0000.000
64A79ASP-1-0.877-0.94523.4060.1530.1530.0000.0000.0000.000
65A80ASP-1-0.931-0.93726.5140.0570.0570.0000.0000.0000.000
66A81TRP0-0.047-0.04125.259-0.019-0.0190.0000.0000.0000.000
67A82ASP-1-0.749-0.89825.7790.0990.0990.0000.0000.0000.000
68A83ASN0-0.059-0.02328.275-0.009-0.0090.0000.0000.0000.000
69A84ARG10.7880.88530.495-0.064-0.0640.0000.0000.0000.000
70A85HIS10.7980.90028.737-0.043-0.0430.0000.0000.0000.000
71A86PRO00.0440.04629.6240.0040.0040.0000.0000.0000.000
72A87LEU0-0.015-0.02627.330-0.010-0.0100.0000.0000.0000.000
73A88PRO00.0220.01729.7870.0050.0050.0000.0000.0000.000
74A89ASN0-0.016-0.02031.587-0.005-0.0050.0000.0000.0000.000
75A90ALA00.0000.02026.384-0.007-0.0070.0000.0000.0000.000
76A91PRO0-0.012-0.00224.3910.0110.0110.0000.0000.0000.000
77A92LEU00.0430.00622.2450.0080.0080.0000.0000.0000.000
78A93VAL00.001-0.00519.1950.0340.0340.0000.0000.0000.000
79A94ALA0-0.031-0.00118.967-0.017-0.0170.0000.0000.0000.000
80A95PRO00.0040.00220.843-0.005-0.0050.0000.0000.0000.000
81A96PRO00.0300.01420.964-0.012-0.0120.0000.0000.0000.000
82A97GLN00.0220.00822.007-0.018-0.0180.0000.0000.0000.000
83A98GLY00.0270.02025.1980.0130.0130.0000.0000.0000.000
84A99PRO0-0.002-0.00324.690-0.005-0.0050.0000.0000.0000.000
85A100ILE00.0260.02519.3260.0140.0140.0000.0000.0000.000
86A101PRO0-0.0070.00423.484-0.003-0.0030.0000.0000.0000.000
87A102MET00.0440.01322.1270.0080.0080.0000.0000.0000.000
88A103THR00.0370.02223.1760.0070.0070.0000.0000.0000.000
89A104ALA00.0880.03521.9470.0030.0030.0000.0000.0000.000
90A105ARG10.8570.92319.338-0.201-0.2010.0000.0000.0000.000
91A106PHE0-0.014-0.02018.1260.0330.0330.0000.0000.0000.000
92A107ILE00.0240.04317.395-0.005-0.0050.0000.0000.0000.000
93A108ARG10.8400.92415.473-0.322-0.3220.0000.0000.0000.000
94A109GLY0-0.029-0.04213.7080.0870.0870.0000.0000.0000.000
95A110LEU00.0120.01913.4720.0550.0550.0000.0000.0000.000
96A111GLY0-0.0340.00715.1430.0050.0050.0000.0000.0000.000
97A112VAL0-0.082-0.04514.809-0.049-0.0490.0000.0000.0000.000
98A113PRO00.0440.03713.4530.0480.0480.0000.0000.0000.000
99A114ARG10.9400.9514.8510.2740.2740.0000.0000.0000.000
100A115GLU-1-0.888-0.95511.218-0.316-0.3160.0000.0000.0000.000
101A116ARG10.8740.91313.9090.0610.0610.0000.0000.0000.000
102A117GLN0-0.023-0.00611.340-0.016-0.0160.0000.0000.0000.000
103A118MET0-0.046-0.0309.385-0.044-0.0440.0000.0000.0000.000
104A119GLU-1-0.920-0.94414.070-0.185-0.1850.0000.0000.0000.000
105A120PRO00.0750.01717.8410.0130.0130.0000.0000.0000.000
106A121ALA0-0.044-0.01820.2010.0190.0190.0000.0000.0000.000
107A122PHE00.0230.01214.3180.0350.0350.0000.0000.0000.000
108A123ASP-1-0.842-0.91617.969-0.271-0.2710.0000.0000.0000.000
109A124GLN0-0.010-0.01318.8760.0100.0100.0000.0000.0000.000
110A125PHE0-0.014-0.00717.8720.0200.0200.0000.0000.0000.000
111A126ARG10.9400.97013.9340.4020.4020.0000.0000.0000.000
112A127GLN0-0.001-0.00316.0290.0390.0390.0000.0000.0000.000
113A128THR0-0.022-0.00318.5560.0170.0170.0000.0000.0000.000
114A129TYR0-0.046-0.03312.870-0.014-0.0140.0000.0000.0000.000
115A130ARG10.9090.94714.9840.2040.2040.0000.0000.0000.000
116A131GLN0-0.026-0.01816.630-0.005-0.0050.0000.0000.0000.000
117A132TRP00.0590.03218.7330.0280.0280.0000.0000.0000.000
118A133ILE00.0220.01813.0530.0210.0210.0000.0000.0000.000
119A134ILE0-0.0230.00517.2910.0170.0170.0000.0000.0000.000
120A135GLU-1-0.922-0.97919.3290.0740.0740.0000.0000.0000.000
121A136ALA0-0.030-0.00818.8610.0040.0040.0000.0000.0000.000
122A137MET0-0.010-0.02615.1670.0130.0130.0000.0000.0000.000
123A138SER0-0.0430.00120.022-0.003-0.0030.0000.0000.0000.000
124A139GLU-1-0.873-0.95323.4910.1040.1040.0000.0000.0000.000
125A140GLY00.0280.00222.3950.0020.0020.0000.0000.0000.000
126A141ILE0-0.002-0.01021.263-0.002-0.0020.0000.0000.0000.000
127A142LYS10.8610.93024.433-0.097-0.0970.0000.0000.0000.000
128A143VAL0-0.034-0.00126.105-0.006-0.0060.0000.0000.0000.000
129A144MET0-0.035-0.02824.0090.0010.0010.0000.0000.0000.000
130A145ILE00.0150.02927.362-0.006-0.0060.0000.0000.0000.000
131A146GLY00.0180.01129.822-0.008-0.0080.0000.0000.0000.000
132A147LYS10.7990.90228.735-0.148-0.1480.0000.0000.0000.000
133A148PRO0-0.017-0.01830.2530.0090.0090.0000.0000.0000.000
134A149LYS10.9780.99526.950-0.186-0.1860.0000.0000.0000.000
135A150ALA00.0380.01832.006-0.008-0.0080.0000.0000.0000.000
136A151GLN00.0530.01927.792-0.008-0.0080.0000.0000.0000.000
137A152ASN0-0.055-0.01529.762-0.001-0.0010.0000.0000.0000.000
138A153ILE00.0060.02432.862-0.007-0.0070.0000.0000.0000.000
139A154ARG10.9781.00235.233-0.054-0.0540.0000.0000.0000.000
140A155GLN0-0.0130.02437.7880.0000.0000.0000.0000.0000.000
141A156GLY0-0.010-0.01941.342-0.002-0.0020.0000.0000.0000.000
142A157ALA00.025-0.01743.544-0.001-0.0010.0000.0000.0000.000
143A158LYS10.9240.96145.099-0.025-0.0250.0000.0000.0000.000
144A159GLU-1-0.837-0.89943.9120.0530.0530.0000.0000.0000.000
145A160PRO00.0410.03346.9390.0000.0000.0000.0000.0000.000
146A161TYR00.036-0.01841.3050.0030.0030.0000.0000.0000.000
147A162PRO00.030-0.00645.3200.0030.0030.0000.0000.0000.000
148A163GLU-1-0.840-0.91346.6600.0460.0460.0000.0000.0000.000
149A164PHE0-0.064-0.02938.2340.0040.0040.0000.0000.0000.000
150A165VAL00.004-0.00142.1270.0050.0050.0000.0000.0000.000
151A166ASP-1-0.883-0.92942.3540.0640.0640.0000.0000.0000.000
152A167ARG10.8720.93940.893-0.056-0.0560.0000.0000.0000.000
153A168LEU0-0.0070.00435.6460.0060.0060.0000.0000.0000.000
154A169LEU00.0290.00438.1220.0080.0080.0000.0000.0000.000
155A170SER0-0.085-0.03339.8730.0060.0060.0000.0000.0000.000
156A171GLN00.008-0.00534.3340.0010.0010.0000.0000.0000.000
157A172ILE0-0.015-0.00734.4970.0080.0080.0000.0000.0000.000
158A173LYS10.9500.98535.611-0.078-0.0780.0000.0000.0000.000
159A174SER00.033-0.00537.1660.0040.0040.0000.0000.0000.000
160A175GLU-1-0.865-0.90331.4680.1450.1450.0000.0000.0000.000
161A176GLY0-0.083-0.04432.6390.0100.0100.0000.0000.0000.000
162A177HIS10.7860.88829.030-0.152-0.1520.0000.0000.0000.000
163A178PRO00.0240.02930.365-0.010-0.0100.0000.0000.0000.000
164A179GLN00.1220.01333.327-0.003-0.0030.0000.0000.0000.000
165A180GLU-1-0.913-0.94432.1980.1490.1490.0000.0000.0000.000
166A181ILE0-0.0010.00127.521-0.001-0.0010.0000.0000.0000.000
167A182SER0-0.025-0.01631.268-0.004-0.0040.0000.0000.0000.000
168A183LYS10.9190.98334.391-0.092-0.0920.0000.0000.0000.000
169A184PHE00.0600.02928.206-0.004-0.0040.0000.0000.0000.000
170A185LEU0-0.0220.03529.379-0.004-0.0040.0000.0000.0000.000
171A186THR00.0500.01832.859-0.005-0.0050.0000.0000.0000.000
172A187ASP-1-0.865-0.92235.1490.0800.0800.0000.0000.0000.000
173A188THR0-0.026-0.07731.206-0.006-0.0060.0000.0000.0000.000
174A189LEU0-0.022-0.01131.282-0.005-0.0050.0000.0000.0000.000
175A190THR0-0.030-0.03034.833-0.006-0.0060.0000.0000.0000.000
176A191ILE00.0620.05736.024-0.006-0.0060.0000.0000.0000.000
177A192GLN0-0.005-0.02830.226-0.004-0.0040.0000.0000.0000.000
178A193ASN0-0.119-0.08233.445-0.002-0.0020.0000.0000.0000.000
179A194ALA00.0150.01736.175-0.002-0.0020.0000.0000.0000.000
180A195ASN0-0.008-0.00938.818-0.001-0.0010.0000.0000.0000.000
181A196GLU-1-0.939-0.99639.7000.0340.0340.0000.0000.0000.000
182A197GLU-1-0.946-0.97841.2480.0230.0230.0000.0000.0000.000
183A198CYS0-0.045-0.00843.059-0.002-0.0020.0000.0000.0000.000
184A199ARG10.9110.95236.698-0.039-0.0390.0000.0000.0000.000
185A200ASN0-0.063-0.03540.8160.0010.0010.0000.0000.0000.000
186A201ALA00.0360.03542.409-0.002-0.0020.0000.0000.0000.000
187A202MET00.0250.01040.6270.0010.0010.0000.0000.0000.000
188A203ARG10.8990.97138.087-0.021-0.0210.0000.0000.0000.000
189A204HIS0-0.076-0.04841.270-0.001-0.0010.0000.0000.0000.000
190A205LEU0-0.028-0.00241.6870.0010.0010.0000.0000.0000.000
191A206ARG10.9110.96036.133-0.053-0.0530.0000.0000.0000.000
192A207PRO0-0.035-0.02233.723-0.001-0.0010.0000.0000.0000.000
193A208GLU-1-0.891-0.96234.5770.0790.0790.0000.0000.0000.000
194A209ASP-1-0.841-0.88538.2150.0500.0500.0000.0000.0000.000
195A210THR0-0.043-0.04541.6010.0030.0030.0000.0000.0000.000
196A211LEU00.010-0.01442.531-0.001-0.0010.0000.0000.0000.000
197A212GLU-1-0.926-0.96044.3690.0400.0400.0000.0000.0000.000
198A213GLU-1-0.827-0.90845.5720.0430.0430.0000.0000.0000.000
199A214LYS10.7900.89338.890-0.069-0.0690.0000.0000.0000.000
200A215MET0-0.040-0.03545.035-0.003-0.0030.0000.0000.0000.000
201A216TYR0-0.0170.00147.663-0.003-0.0030.0000.0000.0000.000
202A217ALA0-0.010-0.01046.418-0.002-0.0020.0000.0000.0000.000
203A219ARG10.8810.96248.199-0.027-0.0270.0000.0000.0000.000
204A220ASP-1-0.949-0.98351.5250.0260.0260.0000.0000.0000.000
205A221ILE00.0010.02647.058-0.001-0.0010.0000.0000.0000.000
206A222GLY0-0.038-0.01850.272-0.002-0.0020.0000.0000.0000.000