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: JQJ49

Calculation Name: 3ZLC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZLC

Chain ID: A

ChEMBL ID:

UniProt ID: Q04651

Base Structure: X-ray

Registration Date: 2023-09-24

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2837390.504378
FMO2-HF: Nuclear repulsion 2746229.977714
FMO2-HF: Total energy -91160.526663
FMO2-MP2: Total energy -91428.04863


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:51:ILE)


Summations of interaction energy for fragment #1(A:51:ILE)
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.
-12.449-8.4968.527-4.978-7.501-0.018
Interaction energy analysis for fragmet #1(A:51:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.030
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].
3A53GLN0-0.027-0.0183.811-0.6171.714-0.019-1.020-1.2910.004
4A54GLN0-0.057-0.0275.5720.5770.5770.0000.0000.0000.000
5A55TYR00.0290.0239.3090.1010.1010.0000.0000.0000.000
6A56VAL0-0.047-0.02811.9540.0450.0450.0000.0000.0000.000
7A57VAL00.009-0.01014.5810.0100.0100.0000.0000.0000.000
8A58ASP-1-0.801-0.86517.170-0.230-0.2300.0000.0000.0000.000
9A59SER0-0.083-0.04518.2660.0430.0430.0000.0000.0000.000
10A60GLN0-0.060-0.04918.7460.0120.0120.0000.0000.0000.000
11A61VAL00.0360.03320.0400.0010.0010.0000.0000.0000.000
12A62ARG10.8920.96516.4950.0210.0210.0000.0000.0000.000
13A63ASP-1-0.877-0.94222.854-0.057-0.0570.0000.0000.0000.000
14A64THR0-0.063-0.02825.273-0.003-0.0030.0000.0000.0000.000
15A65VAL0-0.020-0.00621.082-0.002-0.0020.0000.0000.0000.000
16A66GLN00.0350.02022.820-0.002-0.0020.0000.0000.0000.000
17A67ILE0-0.0020.00422.718-0.015-0.0150.0000.0000.0000.000
18A68ASN0-0.0130.00520.7270.0280.0280.0000.0000.0000.000
19A69MET0-0.005-0.00123.996-0.021-0.0210.0000.0000.0000.000
20A70ASP-1-0.792-0.86726.309-0.012-0.0120.0000.0000.0000.000
21A71ILE00.004-0.00727.486-0.012-0.0120.0000.0000.0000.000
22A72TYR00.0260.02530.1330.0080.0080.0000.0000.0000.000
23A73VAL00.027-0.00333.311-0.009-0.0090.0000.0000.0000.000
24A74ASN0-0.057-0.00935.9980.0040.0040.0000.0000.0000.000
25A75THR0-0.014-0.03639.0690.0010.0010.0000.0000.0000.000
26A76LYS10.8940.94840.4430.0210.0210.0000.0000.0000.000
27A77CYS0-0.0120.01737.8980.0030.0030.0000.0000.0000.000
28A78ASP-1-0.845-0.92141.393-0.020-0.0200.0000.0000.0000.000
29A79TRP0-0.101-0.06343.9410.0000.0000.0000.0000.0000.000
30A80LEU0-0.030-0.00937.959-0.004-0.0040.0000.0000.0000.000
31A81GLN0-0.059-0.04040.4060.0060.0060.0000.0000.0000.000
32A82ILE00.0630.02933.813-0.006-0.0060.0000.0000.0000.000
33A83ASN0-0.050-0.02536.3010.0070.0070.0000.0000.0000.000
34A84VAL00.0700.04431.705-0.006-0.0060.0000.0000.0000.000
35A85ARG10.8270.91233.7030.0960.0960.0000.0000.0000.000
36A86ASP-1-0.743-0.84931.573-0.084-0.0840.0000.0000.0000.000
37A87GLN0-0.042-0.02331.381-0.003-0.0030.0000.0000.0000.000
38A88THR0-0.121-0.07133.0880.0060.0060.0000.0000.0000.000
39A89MET0-0.070-0.01734.0250.0090.0090.0000.0000.0000.000
40A90ASP-1-0.866-0.93137.552-0.060-0.0600.0000.0000.0000.000
41A91ARG10.8180.88038.2890.0660.0660.0000.0000.0000.000
42A92LYS10.8870.95533.6280.0390.0390.0000.0000.0000.000
43A93LEU0-0.038-0.02937.297-0.003-0.0030.0000.0000.0000.000
44A94VAL0-0.014-0.00333.3960.0030.0030.0000.0000.0000.000
45A95LEU0-0.073-0.04336.5850.0000.0000.0000.0000.0000.000
46A96GLU-1-0.939-0.97836.5480.0010.0010.0000.0000.0000.000
47A97GLU-1-0.856-0.92631.975-0.021-0.0210.0000.0000.0000.000
48A98LEU0-0.056-0.01630.548-0.001-0.0010.0000.0000.0000.000
49A99GLN0-0.055-0.01533.3710.0030.0030.0000.0000.0000.000
50A100LEU0-0.028-0.03134.725-0.006-0.0060.0000.0000.0000.000
51A101GLU-1-0.870-0.93436.7890.0110.0110.0000.0000.0000.000
52A102GLU-1-0.834-0.92338.237-0.025-0.0250.0000.0000.0000.000
53A103MET0-0.0390.00434.7930.0030.0030.0000.0000.0000.000
54A104PRO0-0.051-0.01139.382-0.003-0.0030.0000.0000.0000.000
55A105PHE0-0.001-0.03634.8510.0000.0000.0000.0000.0000.000
56A106PHE0-0.013-0.01332.7660.0000.0000.0000.0000.0000.000
57A107ILE00.0530.02531.474-0.003-0.0030.0000.0000.0000.000
58A108PRO00.0250.03229.0710.0040.0040.0000.0000.0000.000
59A109TYR0-0.017-0.02729.751-0.009-0.0090.0000.0000.0000.000
60A110ASP-1-0.941-0.96724.454-0.050-0.0500.0000.0000.0000.000
61A111THR0-0.0260.00424.818-0.006-0.0060.0000.0000.0000.000
62A112LYS10.7830.91420.5400.2110.2110.0000.0000.0000.000
63A113VAL00.0630.01526.5520.0050.0050.0000.0000.0000.000
64A114ASN00.008-0.02425.0850.0050.0050.0000.0000.0000.000
65A115ASP-1-0.812-0.91629.388-0.122-0.1220.0000.0000.0000.000
66A116ILE0-0.0200.00530.5110.0050.0050.0000.0000.0000.000
67A117ASN0-0.085-0.05632.2240.0090.0090.0000.0000.0000.000
68A118GLU-1-0.968-0.96635.574-0.084-0.0840.0000.0000.0000.000
69A129GLY0-0.047-0.04234.3430.0020.0020.0000.0000.0000.000
70A130GLU-1-0.829-0.89433.404-0.074-0.0740.0000.0000.0000.000
71A131ALA00.0130.01033.4580.0020.0020.0000.0000.0000.000
72A132ILE0-0.035-0.01132.8220.0000.0000.0000.0000.0000.000
73A133PRO00.0470.03836.0880.0040.0040.0000.0000.0000.000
74A134ALA00.0120.01039.3150.0020.0020.0000.0000.0000.000
75A135GLU-1-0.883-0.94740.474-0.040-0.0400.0000.0000.0000.000
76A136PHE0-0.046-0.03637.7210.0040.0040.0000.0000.0000.000
77A137ARG10.8080.89231.8310.0550.0550.0000.0000.0000.000
78A138GLU-1-0.920-0.95534.801-0.006-0.0060.0000.0000.0000.000
79A139LYS10.7900.89237.4370.0310.0310.0000.0000.0000.000
80A140LEU00.0150.01237.3670.0020.0020.0000.0000.0000.000
81A141ASP-1-0.831-0.93041.2990.0090.0090.0000.0000.0000.000
82A142THR0-0.113-0.05742.6600.0030.0030.0000.0000.0000.000
83A143ARG10.8530.91442.675-0.019-0.0190.0000.0000.0000.000
84A144SER00.0590.04238.574-0.001-0.0010.0000.0000.0000.000
85A145PHE00.0140.02535.3560.0020.0020.0000.0000.0000.000
86A154ALA0-0.045-0.03447.4600.0000.0000.0000.0000.0000.000
87A155HIS00.0120.00344.5850.0000.0000.0000.0000.0000.000
88A156LEU00.0460.02847.3510.0000.0000.0000.0000.0000.000
89A157PRO00.0660.02846.6980.0000.0000.0000.0000.0000.000
90A158GLU-1-0.939-0.97144.354-0.040-0.0400.0000.0000.0000.000
91A159PHE00.026-0.00141.714-0.001-0.0010.0000.0000.0000.000
92A160ASN0-0.064-0.02141.9990.0040.0040.0000.0000.0000.000
93A161GLY00.0250.00939.437-0.005-0.0050.0000.0000.0000.000
94A163HIS00.028-0.01530.317-0.005-0.0050.0000.0000.0000.000
95A164VAL0-0.026-0.02032.4600.0050.0050.0000.0000.0000.000
96A165PHE0-0.004-0.00229.401-0.005-0.0050.0000.0000.0000.000
97A166GLY00.0340.02128.6630.0070.0070.0000.0000.0000.000
98A167SER0-0.022-0.02424.861-0.005-0.0050.0000.0000.0000.000
99A168ILE0-0.025-0.01627.3490.0060.0060.0000.0000.0000.000
100A169PRO0-0.0200.01527.361-0.010-0.0100.0000.0000.0000.000
101A170VAL0-0.030-0.01526.6750.0000.0000.0000.0000.0000.000
102A171ASN0-0.007-0.03327.4380.0070.0070.0000.0000.0000.000
103A172ARG10.8500.93918.1760.1700.1700.0000.0000.0000.000
104A173VAL0-0.049-0.03525.659-0.009-0.0090.0000.0000.0000.000
105A174SER0-0.004-0.00827.696-0.003-0.0030.0000.0000.0000.000
106A175GLY00.0480.00328.6520.0150.0150.0000.0000.0000.000
107A176GLU-1-0.800-0.87129.708-0.115-0.1150.0000.0000.0000.000
108A177LEU00.0430.03028.9540.0100.0100.0000.0000.0000.000
109A178GLN0-0.060-0.03331.6320.0000.0000.0000.0000.0000.000
110A179ILE00.0770.05032.1150.0080.0080.0000.0000.0000.000
111A180THR0-0.006-0.01536.023-0.003-0.0030.0000.0000.0000.000
112A181ALA00.0670.03739.6540.0040.0040.0000.0000.0000.000
113A182LYS10.8240.93243.1390.0240.0240.0000.0000.0000.000
114A183SER0-0.006-0.02245.2150.0000.0000.0000.0000.0000.000
115A184LEU0-0.054-0.02047.7260.0000.0000.0000.0000.0000.000
116A185GLY00.0490.02650.598-0.001-0.0010.0000.0000.0000.000
117A186TYR00.0340.00753.7500.0010.0010.0000.0000.0000.000
118A187VAL00.0150.01657.0170.0010.0010.0000.0000.0000.000
119A188ALA00.028-0.00858.379-0.001-0.0010.0000.0000.0000.000
120A189SER0-0.0300.00454.420-0.001-0.0010.0000.0000.0000.000
121A190ARG10.8320.91453.2370.0280.0280.0000.0000.0000.000
122A191LYS10.9800.98348.6340.0440.0440.0000.0000.0000.000
123A192ALA00.0480.04246.8680.0010.0010.0000.0000.0000.000
124A193PRO00.0030.00148.916-0.002-0.0020.0000.0000.0000.000
125A194LEU00.008-0.01247.5440.0000.0000.0000.0000.0000.000
126A195GLU-1-0.933-0.95247.455-0.035-0.0350.0000.0000.0000.000
127A196GLU-1-0.845-0.91747.199-0.031-0.0310.0000.0000.0000.000
128A197LEU0-0.107-0.04243.3800.0000.0000.0000.0000.0000.000
129A198LYS10.8820.94541.5130.0410.0410.0000.0000.0000.000
130A199PHE0-0.009-0.00637.2280.0030.0030.0000.0000.0000.000
131A200ASN00.0250.01936.075-0.010-0.0100.0000.0000.0000.000
132A201HIS0-0.041-0.01830.518-0.002-0.0020.0000.0000.0000.000
133A202VAL00.0260.01128.796-0.007-0.0070.0000.0000.0000.000
134A203ILE0-0.020-0.00524.8910.0090.0090.0000.0000.0000.000
135A204ASN0-0.023-0.03625.533-0.015-0.0150.0000.0000.0000.000
136A205GLU-1-0.852-0.90621.007-0.055-0.0550.0000.0000.0000.000
137A206PHE0-0.018-0.01821.9180.0050.0050.0000.0000.0000.000
138A207SER0-0.016-0.01618.360-0.030-0.0300.0000.0000.0000.000
139A208PHE00.012-0.00118.7880.0150.0150.0000.0000.0000.000
140A209GLY0-0.008-0.00318.009-0.019-0.0190.0000.0000.0000.000
141A210ASP-1-0.875-0.92616.7540.0820.0820.0000.0000.0000.000
142A211PHE00.0330.00815.960-0.019-0.0190.0000.0000.0000.000
143A212TYR0-0.045-0.0429.7860.0320.0320.0000.0000.0000.000
144A213PRO0-0.037-0.03610.252-0.041-0.0410.0000.0000.0000.000
145A214TYR0-0.071-0.0476.7560.1940.1940.0000.0000.0000.000
146A215ILE0-0.0340.0139.331-0.142-0.1420.0000.0000.0000.000
147A216ASP-1-0.906-0.95812.314-0.369-0.3690.0000.0000.0000.000
148A217ASN0-0.070-0.03814.019-0.074-0.0740.0000.0000.0000.000
149A218PRO0-0.012-0.01116.8390.0220.0220.0000.0000.0000.000
150A219LEU0-0.001-0.01619.3370.0140.0140.0000.0000.0000.000
151A220ASP-1-0.747-0.83519.204-0.117-0.1170.0000.0000.0000.000
152A221ASN0-0.014-0.00620.801-0.001-0.0010.0000.0000.0000.000
153A222THR0-0.077-0.03523.509-0.011-0.0110.0000.0000.0000.000
154A223ALA00.0520.01826.0690.0130.0130.0000.0000.0000.000
155A224GLN0-0.023-0.00529.735-0.010-0.0100.0000.0000.0000.000
156A225PHE0-0.028-0.03032.5320.0100.0100.0000.0000.0000.000
157A226ASN00.1120.05236.1730.0000.0000.0000.0000.0000.000
158A227GLN0-0.035-0.02339.3780.0050.0050.0000.0000.0000.000
159A228ASP-1-0.880-0.92842.543-0.061-0.0610.0000.0000.0000.000
160A229GLU-1-1.022-1.00841.375-0.075-0.0750.0000.0000.0000.000
161A230PRO00.0560.04641.080-0.003-0.0030.0000.0000.0000.000
162A231LEU0-0.065-0.03941.3120.0000.0000.0000.0000.0000.000
163A232THR0-0.024-0.01637.138-0.002-0.0020.0000.0000.0000.000
164A233THR0-0.046-0.01536.7140.0040.0040.0000.0000.0000.000
165A234TYR00.0060.00532.401-0.005-0.0050.0000.0000.0000.000
166A235VAL0-0.040-0.02231.0830.0050.0050.0000.0000.0000.000
167A236TYR00.0210.01126.365-0.012-0.0120.0000.0000.0000.000
168A237TYR0-0.041-0.02626.6320.0140.0140.0000.0000.0000.000
169A238THR0-0.009-0.01622.028-0.019-0.0190.0000.0000.0000.000
170A239SER0-0.074-0.07120.1970.0330.0330.0000.0000.0000.000
171A240VAL0-0.009-0.01118.355-0.041-0.0410.0000.0000.0000.000
172A241VAL0-0.007-0.00513.3820.0010.0010.0000.0000.0000.000
173A242PRO00.0210.03114.720-0.010-0.0100.0000.0000.0000.000
174A243THR0-0.007-0.0229.386-0.045-0.0450.0000.0000.0000.000
175A244LEU00.0180.0319.6010.1300.1300.0000.0000.0000.000
176A245PHE00.0700.0315.287-0.175-0.1750.0000.0000.0000.000
177A246LYS10.9280.9425.8980.1550.1550.0000.0000.0000.000
178A247LYS10.8850.9352.102-8.110-7.3520.970-0.540-1.1880.006
179A248LEU0-0.047-0.0156.451-0.032-0.0320.0000.0000.0000.000
180A249GLY00.0280.0349.646-0.034-0.0340.0000.0000.0000.000
181A250ALA0-0.025-0.03411.693-0.081-0.0810.0000.0000.0000.000
182A251GLU-1-0.923-0.96913.8670.3050.3050.0000.0000.0000.000
183A252VAL0-0.027-0.00212.572-0.022-0.0220.0000.0000.0000.000
184A253ASP-1-0.867-0.95114.845-0.118-0.1180.0000.0000.0000.000
185A254THR0-0.0290.00111.6570.0140.0140.0000.0000.0000.000
186A255ASN00.0260.00814.040-0.071-0.0710.0000.0000.0000.000
187A256GLN00.0280.0369.5880.0160.0160.0000.0000.0000.000
188A257TYR0-0.025-0.03114.373-0.003-0.0030.0000.0000.0000.000
189A258SER0-0.0080.01416.887-0.013-0.0130.0000.0000.0000.000
190A259VAL00.047-0.00218.6150.0290.0290.0000.0000.0000.000
191A260ASN0-0.081-0.02222.2820.0000.0000.0000.0000.0000.000
192A261ASP-1-0.810-0.91825.398-0.190-0.1900.0000.0000.0000.000
193A262TYR0-0.067-0.04128.4630.0050.0050.0000.0000.0000.000
194A263ARG10.9120.96131.2040.1450.1450.0000.0000.0000.000
195A264TYR0-0.046-0.02335.168-0.002-0.0020.0000.0000.0000.000
196A265LEU00.0770.05038.8800.0040.0040.0000.0000.0000.000
197A266TYR00.1000.04142.0290.0020.0020.0000.0000.0000.000
198A267LYS10.8330.89844.4030.0860.0860.0000.0000.0000.000
199A268ASP-1-0.833-0.90643.027-0.086-0.0860.0000.0000.0000.000
200A269VAL00.0270.01140.9280.0010.0010.0000.0000.0000.000
201A270ALA0-0.023-0.00743.8990.0030.0030.0000.0000.0000.000
202A271ALA0-0.039-0.02647.1040.0030.0030.0000.0000.0000.000
203A272LYS10.7930.88444.2870.0780.0780.0000.0000.0000.000
204A273GLY00.0720.04941.965-0.002-0.0020.0000.0000.0000.000
205A274ASP-1-0.884-0.95038.866-0.093-0.0930.0000.0000.0000.000
206A275LYS10.8520.93641.6810.0650.0650.0000.0000.0000.000
207A276MET0-0.061-0.01141.7280.0030.0030.0000.0000.0000.000
208A277PRO00.0260.00940.731-0.003-0.0030.0000.0000.0000.000
209A278GLY00.0270.00638.1200.0050.0050.0000.0000.0000.000
210A279ILE0-0.0070.01431.744-0.006-0.0060.0000.0000.0000.000
211A280PHE0-0.071-0.03832.6600.0060.0060.0000.0000.0000.000
212A281PHE00.0730.04226.649-0.009-0.0090.0000.0000.0000.000
213A282LYS10.8290.90128.6580.1300.1300.0000.0000.0000.000
214A283TYR00.0420.03824.578-0.013-0.0130.0000.0000.0000.000
215A284ASN00.013-0.00524.1360.0200.0200.0000.0000.0000.000
216A285PHE00.0400.01820.751-0.016-0.0160.0000.0000.0000.000
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