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: ZY2KN

Calculation Name: 5E1L-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E1L

Chain ID: A

ChEMBL ID:

UniProt ID: P75862

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1945289.173011
FMO2-HF: Nuclear repulsion 1871913.391359
FMO2-HF: Total energy -73375.781652
FMO2-MP2: Total energy -73581.278128


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:-9:ACE )


Summations of interaction energy for fragment #1(A:-9:ACE )
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.
12.705-7.53624.585-0.68-3.6630
Interaction energy analysis for fragmet #1(A:-9:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : -0.051
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].
3A-7GLY 00.0690.0493.7280.5191.525-0.005-0.411-0.5910.000
4A-6LEU 0-0.066-0.0285.5860.2260.2260.0000.0000.0000.000
5A-5VAL 00.0370.0329.162-0.042-0.0420.0000.0000.0000.000
6A-4PRO 00.006-0.00411.3290.0690.0690.0000.0000.0000.000
7A-3ARG 10.8530.87511.6870.3370.3370.0000.0000.0000.000
8A-2GLY 00.1890.15013.0480.0180.0180.0000.0000.0000.000
9A-1SER 0-0.036-0.05615.0720.0210.0210.0000.0000.0000.000
10A0HIS 00.0230.00314.1380.0270.0270.0000.0000.0000.000
11A1MET 0-0.0390.00715.4240.0140.0140.0000.0000.0000.000
12A2ARG 10.8900.94317.1080.1280.1280.0000.0000.0000.000
13A3ILE 0-0.018-0.01913.1610.0100.0100.0000.0000.0000.000
14A4LYS 11.0011.00917.3800.0510.0510.0000.0000.0000.000
15A5PRO 00.0050.00718.586-0.011-0.0110.0000.0000.0000.000
16A6ASP -1-0.915-0.95220.468-0.062-0.0620.0000.0000.0000.000
17A7ASP -1-0.901-0.96922.662-0.033-0.0330.0000.0000.0000.000
18A8ASN 0-0.077-0.03123.7280.0010.0010.0000.0000.0000.000
19A9TRP 0-0.0410.00716.222-0.012-0.0120.0000.0000.0000.000
20A10ARG 10.9490.97018.7890.1360.1360.0000.0000.0000.000
21A11TRP 00.005-0.00213.017-0.030-0.0300.0000.0000.0000.000
22A12TYR 0-0.053-0.04415.3750.0170.0170.0000.0000.0000.000
23A13TYR 00.015-0.06814.503-0.019-0.0190.0000.0000.0000.000
24A14ASP -1-0.840-0.91713.800-0.316-0.3160.0000.0000.0000.000
25A15GLU -1-0.944-1.00215.164-0.165-0.1650.0000.0000.0000.000
26A16GLU -1-1.003-0.97915.473-0.291-0.2910.0000.0000.0000.000
27A17HIS 0-0.032-0.02811.088-0.088-0.0880.0000.0000.0000.000
28A18ASP -1-0.823-0.84911.813-0.197-0.1970.0000.0000.0000.000
29A19ARG 10.8310.9195.3961.0281.0450.000-0.007-0.0090.000
30A20MET 0-0.0100.02411.1870.0160.0160.0000.0000.0000.000
31A21MET 0-0.026-0.01110.493-0.099-0.0990.0000.0000.0000.000
32A22LEU 0-0.025-0.01012.3160.0660.0660.0000.0000.0000.000
33A23ASP -1-0.885-0.93613.942-0.213-0.2130.0000.0000.0000.000
34A24LEU 0-0.023-0.03113.1510.0260.0260.0000.0000.0000.000
35A25ALA 00.0020.01817.2450.0160.0160.0000.0000.0000.000
36A26ASN 0-0.013-0.01218.053-0.005-0.0050.0000.0000.0000.000
37A27GLY 0-0.013-0.01019.3830.0040.0040.0000.0000.0000.000
38A28MET 0-0.097-0.03313.245-0.007-0.0070.0000.0000.0000.000
39A29LEU 00.0550.03213.2350.0290.0290.0000.0000.0000.000
40A30PHE 00.008-0.0116.442-0.094-0.0940.0000.0000.0000.000
41A31ARG 00.0090.0166.772-0.525-0.5250.0000.0000.0000.000
42A32SER 0-0.021-0.0156.015-0.237-0.2370.0000.0000.0000.000
43A33ARG 0-0.0420.0241.81813.343-9.96823.2571.522-1.4680.010
44A34PHE 0-0.045-0.0355.5960.0440.0440.0000.0000.0000.000
45A35ALA 00.0700.0309.416-0.064-0.0640.0000.0000.0000.000
46A36ARG 11.0511.03311.9250.1520.1520.0000.0000.0000.000
47A37LYS 10.8640.93212.945-0.044-0.0440.0000.0000.0000.000
48A38MET 0-0.121-0.0649.8240.0380.0380.0000.0000.0000.000
49A39LEU 00.0220.03312.8900.0240.0240.0000.0000.0000.000
50A40THR 0-0.008-0.01916.414-0.008-0.0080.0000.0000.0000.000
51A41PRO 00.005-0.02919.702-0.010-0.0100.0000.0000.0000.000
52A42ASP -1-0.875-0.92321.033-0.008-0.0080.0000.0000.0000.000
53A43ALA 0-0.050-0.02116.800-0.007-0.0070.0000.0000.0000.000
54A44PHE 0-0.076-0.03817.505-0.018-0.0180.0000.0000.0000.000
55A45SER 0-0.037-0.01720.773-0.002-0.0020.0000.0000.0000.000
56A46PRO 0-0.031-0.01320.7530.0030.0030.0000.0000.0000.000
57A47ALA 00.0360.03220.8170.0110.0110.0000.0000.0000.000
58A48GLY 00.0130.01020.990-0.011-0.0110.0000.0000.0000.000
59A49PHE 0-0.0090.01416.3500.0090.0090.0000.0000.0000.000
60A50CYS 0-0.0040.01720.9920.0030.0030.0000.0000.0000.000
61A51VAL 00.0610.00122.7760.0030.0030.0000.0000.0000.000
62A52ASP -1-0.889-0.94023.6330.0260.0260.0000.0000.0000.000
63A53ASP -1-0.745-0.88318.8730.0140.0140.0000.0000.0000.000
64A54ALA 0-0.006-0.00619.1940.0070.0070.0000.0000.0000.000
65A55ALA 0-0.019-0.01020.9790.0070.0070.0000.0000.0000.000
66A56LEU 0-0.003-0.00118.0860.0120.0120.0000.0000.0000.000
67A57TYR 0-0.007-0.00214.2870.0150.0150.0000.0000.0000.000
68A58PHE 00.013-0.01817.5640.0110.0110.0000.0000.0000.000
69A59SER 0-0.0380.00320.2510.0110.0110.0000.0000.0000.000
70A60PHE 00.025-0.00215.0700.0150.0150.0000.0000.0000.000
71A61GLU -1-0.928-0.96615.9240.0680.0680.0000.0000.0000.000
72A62GLU -1-1.007-1.01616.9190.0790.0790.0000.0000.0000.000
73A63LYS 10.9060.97717.749-0.116-0.1160.0000.0000.0000.000
74A64CYS 00.0020.01013.9150.0310.0310.0000.0000.0000.000
75A65ARG 10.9100.96315.817-0.064-0.0640.0000.0000.0000.000
76A66ASP -1-0.897-0.94518.0170.1090.1090.0000.0000.0000.000
77A67PHE 0-0.036-0.01612.9710.0140.0140.0000.0000.0000.000
78A68ASN 0-0.016-0.00914.996-0.037-0.0370.0000.0000.0000.000
79A69LEU 0-0.028-0.0149.0950.0530.0530.0000.0000.0000.000
80A70SER 00.000-0.0059.430-0.089-0.0890.0000.0000.0000.000
81A71LYS 10.9740.95611.609-0.002-0.0020.0000.0000.0000.000
82A72GLU -1-0.888-0.9337.279-0.514-0.5140.0000.0000.0000.000
83A73GLN 00.0580.0216.321-0.076-0.0760.0000.0000.0000.000
84A74LYS 10.8610.9508.062-0.058-0.0580.0000.0000.0000.000
85A75ALA 00.0140.01810.9020.0150.0150.0000.0000.0000.000
86A76GLU -1-0.833-0.9363.032-1.570-0.4380.432-0.943-0.621-0.008
87A77LEU 0-0.035-0.0127.2030.0700.0700.0000.0000.0000.000
88A78VAL 0-0.0050.0008.227-0.040-0.0400.0000.0000.0000.000
89A79LEU 00.0170.0049.388-0.018-0.0180.0000.0000.0000.000
90A80ASN 00.0180.0044.636-0.077-0.0780.000-0.0020.0030.000
91A81ALA 00.0170.0138.665-0.009-0.0090.0000.0000.0000.000
92A82LEU 0-0.022-0.01011.864-0.027-0.0270.0000.0000.0000.000
93A83VAL 0-0.0010.01110.568-0.021-0.0210.0000.0000.0000.000
94A84ALA 0-0.056-0.04011.574-0.008-0.0080.0000.0000.0000.000
95A85ILE 0-0.003-0.00613.192-0.018-0.0180.0000.0000.0000.000
96A86ARG 10.8550.93415.947-0.041-0.0410.0000.0000.0000.000
97A87TYR 00.0220.00314.986-0.013-0.0130.0000.0000.0000.000
98A88LEU 0-0.0310.01812.131-0.006-0.0060.0000.0000.0000.000
99A89LYS 10.8670.94315.618-0.027-0.0270.0000.0000.0000.000
100A90PRO 00.0400.03017.5110.0230.0230.0000.0000.0000.000
101A91GLN 0-0.028-0.02315.1340.0110.0110.0000.0000.0000.000
102A92MET 0-0.006-0.01218.532-0.012-0.0120.0000.0000.0000.000
103A93PRO 0-0.003-0.01519.3210.0220.0220.0000.0000.0000.000
104A94LYS 10.9150.96415.192-0.267-0.2670.0000.0000.0000.000
105A95SER 00.041-0.01120.4560.0010.0010.0000.0000.0000.000
106A96TRP 00.0060.00822.5920.0020.0020.0000.0000.0000.000
107A97HIS 00.0190.01418.880-0.008-0.0080.0000.0000.0000.000
108A98PHE 0-0.0080.00916.2240.0140.0140.0000.0000.0000.000
109A99VAL 00.0780.03921.939-0.017-0.0170.0000.0000.0000.000
110A100SER 0-0.104-0.05424.6850.0050.0050.0000.0000.0000.000
111A101HIS 00.001-0.02024.169-0.013-0.0130.0000.0000.0000.000
112A102GLY 0-0.0180.01829.161-0.006-0.0060.0000.0000.0000.000
113A103GLU -1-0.925-0.96230.8130.0900.0900.0000.0000.0000.000
114A104MET 0-0.054-0.03128.0380.0080.0080.0000.0000.0000.000
115A105TRP 0-0.0050.00621.479-0.004-0.0040.0000.0000.0000.000
116A106VAL 0-0.013-0.02426.0860.0060.0060.0000.0000.0000.000
117A107PRO 0-0.0240.01521.428-0.003-0.0030.0000.0000.0000.000
118A108MET 00.012-0.01423.076-0.014-0.0140.0000.0000.0000.000
119A109PRO 00.002-0.00119.5500.0160.0160.0000.0000.0000.000
120A110GLY 0-0.047-0.03317.913-0.016-0.0160.0000.0000.0000.000
121A111ASP -1-0.854-0.92418.6770.1490.1490.0000.0000.0000.000
122A112ALA 0-0.0070.00017.2400.0310.0310.0000.0000.0000.000
123A113ALA 0-0.020-0.01717.173-0.030-0.0300.0000.0000.0000.000
124A114CYS 0-0.045-0.00517.3030.0380.0380.0000.0000.0000.000
125A115VAL 00.0090.01416.841-0.022-0.0220.0000.0000.0000.000
126A116TRP 00.0360.01419.0820.0150.0150.0000.0000.0000.000
127A117LEU 0-0.024-0.01016.463-0.008-0.0080.0000.0000.0000.000
128A118SER 0-0.017-0.01720.524-0.013-0.0130.0000.0000.0000.000
129A119ASP -1-0.937-0.97121.7320.1500.1500.0000.0000.0000.000
130A120THR 00.0020.00019.807-0.008-0.0080.0000.0000.0000.000
131A121HIS 0-0.015-0.00123.019-0.001-0.0010.0000.0000.0000.000
132A122GLU -1-0.929-0.96615.6690.2960.2960.0000.0000.0000.000
133A123GLN 0-0.031-0.02218.670-0.011-0.0110.0000.0000.0000.000
134A124VAL 0-0.033-0.01613.3080.0340.0340.0000.0000.0000.000
135A125ASN 00.012-0.00813.817-0.056-0.0560.0000.0000.0000.000
136A126LEU 0-0.038-0.03212.6710.1030.1030.0000.0000.0000.000
137A127LEU 00.0270.02411.879-0.047-0.0470.0000.0000.0000.000
138A128VAL 00.0130.00514.0180.0230.0230.0000.0000.0000.000
139A129VAL 0-0.026-0.02512.897-0.013-0.0130.0000.0000.0000.000
140A130GLU -1-0.913-0.96116.2760.1000.1000.0000.0000.0000.000
141A131SER 0-0.009-0.01719.4490.0160.0160.0000.0000.0000.000
142A132GLY 00.0310.02022.285-0.011-0.0110.0000.0000.0000.000
143A133GLU -1-0.918-0.96425.0050.0850.0850.0000.0000.0000.000
144A134ASN 0-0.009-0.02326.942-0.001-0.0010.0000.0000.0000.000
145A135ALA 0-0.022-0.01121.8760.0060.0060.0000.0000.0000.000
146A136ALA 00.0530.05219.650-0.010-0.0100.0000.0000.0000.000
147A137LEU 0-0.042-0.01814.6340.0190.0190.0000.0000.0000.000
148A138CYS 0-0.011-0.00114.348-0.018-0.0180.0000.0000.0000.000
149A139LEU 00.0030.0058.5890.0150.0150.0000.0000.0000.000
150A140LEU 0-0.0280.0027.171-0.112-0.1120.0000.0000.0000.000
151A141ALA 00.0280.0128.3200.1830.1830.0000.0000.0000.000
152A142GLN 00.0420.0259.327-0.217-0.2170.0000.0000.0000.000
153A143PRO 00.016-0.0026.3920.2880.2880.0000.0000.0000.000
154A144CYS 0-0.036-0.0275.9020.5110.5110.0000.0000.0000.000
155A145VAL 00.0630.0418.040-0.158-0.1580.0000.0000.0000.000
156A146VAL 00.0050.01210.2230.0450.0450.0000.0000.0000.000
157A147ILE 00.0440.01512.839-0.040-0.0400.0000.0000.0000.000
158A148ALA 0-0.022-0.01815.010-0.009-0.0090.0000.0000.0000.000
159A149GLY 0-0.0070.00316.530-0.019-0.0190.0000.0000.0000.000
160A150ARG 10.9180.96711.218-0.268-0.2680.0000.0000.0000.000
161A151ALA 00.0120.0058.8300.0200.0200.0000.0000.0000.000
162A152MET 0-0.055-0.0247.230-0.109-0.1090.0000.0000.0000.000
163A153GLN 00.003-0.0182.500-0.606-0.4580.853-0.557-0.4440.000
164A154LEU 0-0.029-0.0143.840-0.312-0.2450.003-0.051-0.0190.000
165A155GLY 0-0.021-0.0123.3310.6151.3160.045-0.231-0.514-0.002
166A156ASP -1-0.788-0.8745.5761.1391.1390.0000.0000.0000.000
167A157ALA 00.010-0.0016.996-0.139-0.1390.0000.0000.0000.000
168A158ILE 0-0.069-0.04110.621-0.038-0.0380.0000.0000.0000.000
169A159LYS 10.9330.99213.817-0.147-0.1470.0000.0000.0000.000
170A160ILE 0-0.037-0.01915.783-0.003-0.0030.0000.0000.0000.000
171A161MET 00.0000.00119.593-0.012-0.0120.0000.0000.0000.000
172A162ASN 00.0900.01323.0860.0230.0230.0000.0000.0000.000
173A163ASP -1-0.837-0.90024.6660.1230.1230.0000.0000.0000.000
174A164ARG 10.7850.88822.023-0.137-0.1370.0000.0000.0000.000
175A165LEU 0-0.040-0.00618.6660.0150.0150.0000.0000.0000.000
176A166LYS 10.9300.97522.035-0.134-0.1340.0000.0000.0000.000
177A167PRO 00.0230.02721.7390.0200.0200.0000.0000.0000.000
178A168GLN 00.005-0.03016.8860.0300.0300.0000.0000.0000.000
179A169NME 0-0.0110.00721.840-0.013-0.0130.0000.0000.0000.000