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: 53R1Z

Calculation Name: 1EQ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EQ6

Chain ID: A

ChEMBL ID:

UniProt ID: P47123

Base Structure: X-ray

Registration Date: 2023-03-13

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2054047.787264
FMO2-HF: Nuclear repulsion 1980151.969817
FMO2-HF: Total energy -73895.817447
FMO2-MP2: Total energy -74113.04838


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:30:SER)


Summations of interaction energy for fragment #1(A:30:SER)
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.
-14.189-8.8630.475-2.797-3.002-0.01
Interaction energy analysis for fragmet #1(A:30:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.008
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].
3A32ASN0-0.057-0.0393.423-1.6681.3580.011-1.610-1.4260.005
4A33ASN0-0.003-0.0286.1070.2620.2620.0000.0000.0000.000
5A34LYS10.9280.9609.1021.2521.2520.0000.0000.0000.000
6A35GLU-1-0.935-0.97012.356-0.429-0.4290.0000.0000.0000.000
7A36VAL0-0.049-0.01415.173-0.023-0.0230.0000.0000.0000.000
8A37GLU-1-0.926-0.97518.297-0.278-0.2780.0000.0000.0000.000
9A38LEU0-0.034-0.02520.356-0.012-0.0120.0000.0000.0000.000
10A39TYR0-0.004-0.05523.5360.0150.0150.0000.0000.0000.000
11A40GLY0-0.022-0.01427.3070.0160.0160.0000.0000.0000.000
12A41GLY00.0350.02624.9530.0040.0040.0000.0000.0000.000
13A42ALA0-0.048-0.01025.8690.0060.0060.0000.0000.0000.000
14A43ILE0-0.015-0.00621.8230.0210.0210.0000.0000.0000.000
15A44THR00.0300.03918.931-0.015-0.0150.0000.0000.0000.000
16A45THR00.007-0.00516.3000.0200.0200.0000.0000.0000.000
17A46VAL0-0.052-0.01711.011-0.046-0.0460.0000.0000.0000.000
18A47VAL00.0270.02113.3960.0710.0710.0000.0000.0000.000
19A48PRO00.0470.0249.908-0.117-0.1170.0000.0000.0000.000
20A49PRO0-0.029-0.0099.5280.2970.2970.0000.0000.0000.000
21A50GLY00.0550.01212.630-0.081-0.0810.0000.0000.0000.000
22A51PHE0-0.0070.01812.5160.1020.1020.0000.0000.0000.000
23A52ILE0-0.032-0.01516.5720.0100.0100.0000.0000.0000.000
24A53ASP-1-0.762-0.83320.295-0.352-0.3520.0000.0000.0000.000
25A54ALA0-0.010-0.02922.5890.0180.0180.0000.0000.0000.000
26A55SER00.021-0.01525.0760.0310.0310.0000.0000.0000.000
27A56THR0-0.088-0.04625.3090.0190.0190.0000.0000.0000.000
28A57LEU0-0.094-0.05525.9380.0180.0180.0000.0000.0000.000
29A58ARG10.8150.89029.3410.2620.2620.0000.0000.0000.000
30A59GLU-1-0.899-0.93230.135-0.168-0.1680.0000.0000.0000.000
31A60VAL0-0.037-0.01027.251-0.002-0.0020.0000.0000.0000.000
32A61PRO00.005-0.00829.5700.0070.0070.0000.0000.0000.000
33A62ASP-1-0.870-0.93730.544-0.149-0.1490.0000.0000.0000.000
34A63THR0-0.056-0.02330.224-0.006-0.0060.0000.0000.0000.000
35A64GLN0-0.094-0.04326.640-0.015-0.0150.0000.0000.0000.000
36A65GLU-1-0.788-0.85723.112-0.296-0.2960.0000.0000.0000.000
37A66VAL0-0.018-0.01822.569-0.003-0.0030.0000.0000.0000.000
38A67TYR00.0350.01918.354-0.040-0.0400.0000.0000.0000.000
39A68VAL0-0.022-0.01719.2240.0110.0110.0000.0000.0000.000
40A69ASN0-0.063-0.02213.366-0.053-0.0530.0000.0000.0000.000
41A70SER0-0.059-0.04816.9040.0830.0830.0000.0000.0000.000
42A71ARG10.7790.8738.9511.9411.9410.0000.0000.0000.000
43A72ARG10.7940.85816.4380.6140.6140.0000.0000.0000.000
44A73ASP-1-0.885-0.95416.284-0.545-0.5450.0000.0000.0000.000
45A74GLU-1-0.943-0.95316.093-0.510-0.5100.0000.0000.0000.000
46A75GLU-1-0.909-0.92813.853-0.954-0.9540.0000.0000.0000.000
47A76GLU-1-0.931-0.96410.666-0.799-0.7990.0000.0000.0000.000
48A77PHE0-0.049-0.0327.530-0.062-0.0620.0000.0000.0000.000
49A78GLU-1-0.880-0.9433.298-2.770-2.2730.031-0.119-0.409-0.001
50A79ASP-1-0.911-0.9392.603-10.692-9.0590.435-1.059-1.009-0.014
51A80GLY00.0060.0024.9950.6970.786-0.001-0.002-0.0860.000
52A81LEU0-0.060-0.0356.4840.6310.6310.0000.0000.0000.000
53A82ALA0-0.016-0.0169.583-0.040-0.0400.0000.0000.0000.000
54A83THR00.000-0.00812.755-0.111-0.1110.0000.0000.0000.000
55A84ASN00.0010.00515.6870.0060.0060.0000.0000.0000.000
56A85GLU-1-0.738-0.85012.946-0.758-0.7580.0000.0000.0000.000
57A86SER0-0.023-0.01316.709-0.015-0.0150.0000.0000.0000.000
58A87ILE0-0.015-0.01314.4210.0240.0240.0000.0000.0000.000
59A88ILE00.0280.02118.732-0.008-0.0080.0000.0000.0000.000
60A89VAL0-0.040-0.01520.1950.0160.0160.0000.0000.0000.000
61A90ASP-1-0.760-0.89322.641-0.145-0.1450.0000.0000.0000.000
62A91LEU0-0.066-0.01826.2070.0160.0160.0000.0000.0000.000
63A92LEU00.000-0.00228.4540.0050.0050.0000.0000.0000.000
64A93GLU-1-0.871-0.93430.855-0.048-0.0480.0000.0000.0000.000
65A94THR0-0.067-0.03432.2030.0040.0040.0000.0000.0000.000
66A95VAL0-0.0080.00931.5890.0020.0020.0000.0000.0000.000
67A96ASP-1-0.907-0.94334.085-0.002-0.0020.0000.0000.0000.000
68A97LYS10.8690.93033.137-0.024-0.0240.0000.0000.0000.000
69A98SER0-0.002-0.01033.418-0.001-0.0010.0000.0000.0000.000
70A99ASP-1-0.860-0.92630.8250.0970.0970.0000.0000.0000.000
71A100LEU0-0.029-0.00524.175-0.007-0.0070.0000.0000.0000.000
72A101LYS10.8870.94226.486-0.157-0.1570.0000.0000.0000.000
73A102GLU-1-0.938-0.98327.6550.0500.0500.0000.0000.0000.000
74A103ALA0-0.013-0.00129.149-0.010-0.0100.0000.0000.0000.000
75A104TRP0-0.029-0.03521.463-0.003-0.0030.0000.0000.0000.000
76A105GLN0-0.023-0.02826.641-0.012-0.0120.0000.0000.0000.000
77A106PHE00.0030.01128.372-0.004-0.0040.0000.0000.0000.000
78A107HIS10.9050.91927.0310.0240.0240.0000.0000.0000.000
79A108VAL0-0.0160.00124.064-0.014-0.0140.0000.0000.0000.000
80A109GLU-1-0.883-0.94226.711-0.004-0.0040.0000.0000.0000.000
81A110ASP-1-0.857-0.92130.150-0.044-0.0440.0000.0000.0000.000
82A111LEU0-0.068-0.02823.965-0.012-0.0120.0000.0000.0000.000
83A112THR0-0.021-0.03626.467-0.004-0.0040.0000.0000.0000.000
84A113GLU-1-0.950-0.97428.743-0.022-0.0220.0000.0000.0000.000
85A114LEU0-0.058-0.01029.230-0.002-0.0020.0000.0000.0000.000
86A115ASN0-0.061-0.02527.021-0.016-0.0160.0000.0000.0000.000
87A116GLY0-0.053-0.02931.2130.0040.0040.0000.0000.0000.000
88A117THR0-0.029-0.03829.2190.0070.0070.0000.0000.0000.000
89A118THR0-0.049-0.02932.1380.0010.0010.0000.0000.0000.000
90A119LYS10.9420.97131.540-0.062-0.0620.0000.0000.0000.000
91A120TRP00.012-0.00125.2460.0030.0030.0000.0000.0000.000
92A121GLU-1-0.973-0.98324.4600.1530.1530.0000.0000.0000.000
93A122ALA00.007-0.00422.417-0.014-0.0140.0000.0000.0000.000
94A123LEU0-0.033-0.01918.9650.0220.0220.0000.0000.0000.000
95A124GLN0-0.017-0.01214.2800.0440.0440.0000.0000.0000.000
96A125GLU-1-0.850-0.92418.8540.1210.1210.0000.0000.0000.000
97A126ASP-1-0.836-0.87816.8600.5030.5030.0000.0000.0000.000
98A127THR0-0.0200.00219.733-0.052-0.0520.0000.0000.0000.000
99A128VAL0-0.043-0.02017.0830.0340.0340.0000.0000.0000.000
100A129GLN0-0.031-0.03419.517-0.004-0.0040.0000.0000.0000.000
101A130GLN00.016-0.00922.672-0.030-0.0300.0000.0000.0000.000
102A131GLY00.0060.00426.182-0.012-0.0120.0000.0000.0000.000
103A132THR00.0020.00325.078-0.007-0.0070.0000.0000.0000.000
104A133LYS10.9551.00419.205-0.022-0.0220.0000.0000.0000.000
105A134PHE00.0180.00721.1960.0410.0410.0000.0000.0000.000
106A135THR00.012-0.00416.404-0.033-0.0330.0000.0000.0000.000
107A136GLY00.0390.01018.2650.0450.0450.0000.0000.0000.000
108A137LEU0-0.056-0.00914.116-0.058-0.0580.0000.0000.0000.000
109A138VAL00.0140.00518.3900.0340.0340.0000.0000.0000.000
110A139MET00.0150.01421.591-0.028-0.0280.0000.0000.0000.000
111A140GLU-1-0.786-0.85823.820-0.009-0.0090.0000.0000.0000.000
112A141VAL0-0.030-0.01627.2940.0060.0060.0000.0000.0000.000
113A142ALA0-0.058-0.03629.5910.0020.0020.0000.0000.0000.000
114A143ASN00.0550.02232.148-0.003-0.0030.0000.0000.0000.000
115A144LYS10.9530.96634.5160.0320.0320.0000.0000.0000.000
116A145TRP0-0.052-0.01833.9610.0030.0030.0000.0000.0000.000
117A146GLY0-0.035-0.00837.6750.0010.0010.0000.0000.0000.000
118A147LYS10.8390.91535.4760.0050.0050.0000.0000.0000.000
119A148PRO00.0400.03731.258-0.009-0.0090.0000.0000.0000.000
120A149ASP-1-0.856-0.91629.3890.0210.0210.0000.0000.0000.000
121A150LEU0-0.095-0.05831.000-0.002-0.0020.0000.0000.0000.000
122A151ALA0-0.041-0.02629.595-0.008-0.0080.0000.0000.0000.000
123A152GLN0-0.046-0.03421.9060.0090.0090.0000.0000.0000.000
124A153THR00.0480.03522.6330.0000.0000.0000.0000.0000.000
125A154VAL0-0.002-0.00221.511-0.026-0.0260.0000.0000.0000.000
126A155VAL0-0.0130.00317.6410.0300.0300.0000.0000.0000.000
127A156ILE00.016-0.00319.271-0.047-0.0470.0000.0000.0000.000
128A157GLY0-0.0090.00616.4830.0550.0550.0000.0000.0000.000
129A158VAL00.0330.00917.511-0.046-0.0460.0000.0000.0000.000
130A159ALA0-0.027-0.01717.9060.0510.0510.0000.0000.0000.000
131A160LEU0-0.0140.02519.978-0.024-0.0240.0000.0000.0000.000
132A161ILE0-0.035-0.02919.5420.0310.0310.0000.0000.0000.000
133A162ARG10.7880.86723.577-0.021-0.0210.0000.0000.0000.000
134A163LEU0-0.032-0.00725.0490.0080.0080.0000.0000.0000.000
135A164THR00.025-0.01428.644-0.004-0.0040.0000.0000.0000.000
136A165GLN0-0.068-0.02731.736-0.005-0.0050.0000.0000.0000.000
137A166PHE0-0.021-0.02530.723-0.001-0.0010.0000.0000.0000.000
138A167ASP-1-0.893-0.92333.374-0.041-0.0410.0000.0000.0000.000
139A168THR0-0.0160.00128.755-0.008-0.0080.0000.0000.0000.000
140A169ASP-1-0.750-0.85328.194-0.010-0.0100.0000.0000.0000.000
141A170VAL0-0.012-0.00622.999-0.011-0.0110.0000.0000.0000.000
142A171VAL00.011-0.00423.5670.0210.0210.0000.0000.0000.000
143A172ILE0-0.009-0.00217.537-0.025-0.0250.0000.0000.0000.000
144A173SER0-0.014-0.00619.8510.0360.0360.0000.0000.0000.000
145A174ILE00.004-0.00513.911-0.051-0.0510.0000.0000.0000.000
146A175ASN0-0.014-0.00617.7490.0780.0780.0000.0000.0000.000
147A176VAL00.0260.00115.123-0.076-0.0760.0000.0000.0000.000
148A177PRO0-0.0060.00417.7540.0610.0610.0000.0000.0000.000
149A178LEU0-0.012-0.00117.426-0.034-0.0340.0000.0000.0000.000
150A179THR00.0370.03217.6210.0090.0090.0000.0000.0000.000
151A180LYS10.9680.96720.2240.0460.0460.0000.0000.0000.000
152A181GLU-1-0.889-0.96018.943-0.057-0.0570.0000.0000.0000.000
153A182GLU-1-0.717-0.80714.741-0.153-0.1530.0000.0000.0000.000
154A183ALA00.0390.01918.7290.0340.0340.0000.0000.0000.000
155A184SER0-0.133-0.08621.7920.0260.0260.0000.0000.0000.000
156A185GLN00.006-0.01015.885-0.037-0.0370.0000.0000.0000.000
157A186ALA00.0640.03620.7320.0260.0260.0000.0000.0000.000
158A187SER0-0.019-0.00521.5950.0160.0160.0000.0000.0000.000
159A188ASN0-0.105-0.04623.422-0.008-0.0080.0000.0000.0000.000
160A189LYS10.9010.93823.346-0.165-0.1650.0000.0000.0000.000
161A190GLU-1-0.916-0.94318.7580.3440.3440.0000.0000.0000.000
162A191LEU00.0170.00213.837-0.055-0.0550.0000.0000.0000.000
163A192PRO0-0.0070.00114.9440.0820.0820.0000.0000.0000.000
164A193ALA00.0560.0149.6090.0220.0220.0000.0000.0000.000
165A194ARG10.7920.8729.7950.4690.4690.0000.0000.0000.000
166A195CYS0-0.015-0.00310.892-0.118-0.1180.0000.0000.0000.000
167A196HIS0-0.0090.0037.725-0.272-0.2720.0000.0000.0000.000
168A197ALA0-0.008-0.0087.0870.1800.1800.0000.0000.0000.000
169A198VAL00.0480.0167.990-0.195-0.1950.0000.0000.0000.000
170A199TYR0-0.024-0.02510.952-0.076-0.0760.0000.0000.0000.000
171A200GLN0-0.017-0.0114.0110.5590.640-0.001-0.007-0.0720.000
172A201LEU00.0260.0148.620-0.071-0.0710.0000.0000.0000.000
173A202LEU0-0.0130.0039.5520.0330.0330.0000.0000.0000.000
174A203GLN0-0.023-0.02411.2960.1330.1330.0000.0000.0000.000
175A204GLU-1-0.866-0.8977.756-1.076-1.0760.0000.0000.0000.000
176A205MET0-0.0020.00711.310-0.019-0.0190.0000.0000.0000.000
177A206VAL00.0250.01414.2530.0290.0290.0000.0000.0000.000
178A207ARG10.8400.9219.746-0.289-0.2890.0000.0000.0000.000
179A208LYS10.8230.8789.4690.7170.7170.0000.0000.0000.000
180A209PHE00.0410.04315.337-0.036-0.0360.0000.0000.0000.000
181A210HIS0-0.078-0.04118.3280.0400.0400.0000.0000.0000.000
182A211VAL00.0370.02021.405-0.018-0.0180.0000.0000.0000.000
183A212VAL0-0.059-0.02723.5040.0160.0160.0000.0000.0000.000
184A213ASP-1-0.858-0.91625.979-0.121-0.1210.0000.0000.0000.000
185A214THR0-0.023-0.02229.501-0.002-0.0020.0000.0000.0000.000
186A215SER0-0.122-0.06231.3470.0070.0070.0000.0000.0000.000
187A216LEU00.0080.01028.4200.0010.0010.0000.0000.0000.000
188A217PHE0-0.034-0.02327.9960.0020.0020.0000.0000.0000.000
189A218ALA0-0.0050.00333.8770.0050.0050.0000.0000.0000.000