FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R8MM8

Calculation Name: 1EX6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EX6

Chain ID: A

ChEMBL ID:

UniProt ID: P15454

Base Structure: X-ray

Registration Date: 2023-09-23

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889631.930554
FMO2-HF: Nuclear repulsion 1818374.992829
FMO2-HF: Total energy -71256.937726
FMO2-MP2: Total energy -71467.656495


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:SER)


Summations of interaction energy for fragment #1(A:1: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.
-35.431-34.9123.205-13.996-9.731-0.08
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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].
3A3PRO00.0040.0003.334-2.7520.7890.038-2.028-1.5510.008
4A4ILE00.0160.0003.9320.7590.9590.000-0.021-0.1790.000
5A5VAL0-0.021-0.0056.960-0.402-0.4020.0000.0000.0000.000
6A6ILE0-0.0030.00610.7190.1070.1070.0000.0000.0000.000
7A7SER00.0130.00012.713-0.095-0.0950.0000.0000.0000.000
8A8GLY00.0230.01316.4430.0310.0310.0000.0000.0000.000
9A9PRO00.0490.03119.834-0.024-0.0240.0000.0000.0000.000
10A10SER0-0.031-0.01322.5930.0020.0020.0000.0000.0000.000
11A11GLY00.0440.01223.825-0.003-0.0030.0000.0000.0000.000
12A12THR00.0280.00121.769-0.004-0.0040.0000.0000.0000.000
13A13GLY00.0070.00622.0990.0080.0080.0000.0000.0000.000
14A14LYS10.8500.93916.265-0.129-0.1290.0000.0000.0000.000
15A15SER00.0600.02717.2660.0050.0050.0000.0000.0000.000
16A16THR0-0.029-0.02518.481-0.018-0.0180.0000.0000.0000.000
17A17LEU00.0330.02515.867-0.014-0.0140.0000.0000.0000.000
18A18LEU00.0710.03911.8910.0010.0010.0000.0000.0000.000
19A19LYS10.9200.96314.543-0.050-0.0500.0000.0000.0000.000
20A20LYS10.8320.91617.168-0.105-0.1050.0000.0000.0000.000
21A21LEU00.0180.0319.1560.0010.0010.0000.0000.0000.000
22A22PHE0-0.003-0.01811.197-0.030-0.0300.0000.0000.0000.000
23A23ALA0-0.052-0.00513.839-0.022-0.0220.0000.0000.0000.000
24A24GLU-1-0.753-0.81314.7150.0740.0740.0000.0000.0000.000
25A25TYR0-0.050-0.05810.4700.0250.0250.0000.0000.0000.000
26A26PRO00.0290.02211.705-0.058-0.0580.0000.0000.0000.000
27A27ASP-1-0.911-0.94311.274-0.250-0.2500.0000.0000.0000.000
28A28SER00.0160.0036.796-0.056-0.0560.0000.0000.0000.000
29A29PHE00.0050.0105.316-0.455-0.4550.0000.0000.0000.000
30A30GLY00.0380.0118.2020.1110.1110.0000.0000.0000.000
31A31PHE00.0460.0549.401-0.108-0.1080.0000.0000.0000.000
32A32SER0-0.009-0.00912.112-0.063-0.0630.0000.0000.0000.000
33A33VAL0-0.003-0.00312.8770.0730.0730.0000.0000.0000.000
34A34SER00.0020.00815.8020.0150.0150.0000.0000.0000.000
35A35SER0-0.0070.00118.664-0.008-0.0080.0000.0000.0000.000
36A36THR0-0.016-0.02021.6840.0180.0180.0000.0000.0000.000
37A37THR00.0100.04325.268-0.004-0.0040.0000.0000.0000.000
38A38ARG10.7150.84326.2610.1040.1040.0000.0000.0000.000
39A39THR00.009-0.00829.145-0.008-0.0080.0000.0000.0000.000
40A40PRO00.0200.01928.6030.0030.0030.0000.0000.0000.000
41A41ARG10.9270.96529.1390.0780.0780.0000.0000.0000.000
42A42ALA0-0.005-0.00730.508-0.005-0.0050.0000.0000.0000.000
43A43GLY00.0210.00829.2580.0030.0030.0000.0000.0000.000
44A44GLU-1-0.799-0.86025.761-0.117-0.1170.0000.0000.0000.000
45A45VAL0-0.010-0.02323.2220.0060.0060.0000.0000.0000.000
46A46ASN00.0720.02722.619-0.027-0.0270.0000.0000.0000.000
47A47GLY0-0.0020.02119.528-0.004-0.0040.0000.0000.0000.000
48A48LYS10.8210.90217.9480.1460.1460.0000.0000.0000.000
49A49ASP-1-0.867-0.92418.782-0.172-0.1720.0000.0000.0000.000
50A50TYR00.021-0.01020.4920.0030.0030.0000.0000.0000.000
51A51ASN0-0.0280.00317.5470.0020.0020.0000.0000.0000.000
52A52PHE0-0.031-0.02821.7130.0110.0110.0000.0000.0000.000
53A53VAL00.0220.00424.273-0.002-0.0020.0000.0000.0000.000
54A54SER00.005-0.03327.0890.0110.0110.0000.0000.0000.000
55A55VAL00.021-0.01629.674-0.003-0.0030.0000.0000.0000.000
56A56ASP-1-0.885-0.94331.281-0.061-0.0610.0000.0000.0000.000
57A57GLU-1-0.839-0.88327.253-0.121-0.1210.0000.0000.0000.000
58A58PHE00.009-0.00723.998-0.006-0.0060.0000.0000.0000.000
59A59LYS10.9790.97627.0210.0520.0520.0000.0000.0000.000
60A60SER0-0.121-0.05928.3490.0030.0030.0000.0000.0000.000
61A61MET00.0370.02421.8360.0020.0020.0000.0000.0000.000
62A62ILE0-0.067-0.01224.438-0.001-0.0010.0000.0000.0000.000
63A63LYS10.9250.96926.3200.0690.0690.0000.0000.0000.000
64A64ASN0-0.074-0.03124.6910.0190.0190.0000.0000.0000.000
65A65ASN0-0.049-0.02222.8820.0000.0000.0000.0000.0000.000
66A66GLU-1-0.830-0.92020.259-0.168-0.1680.0000.0000.0000.000
67A67PHE0-0.080-0.04718.990-0.039-0.0390.0000.0000.0000.000
68A68ILE0-0.021-0.00113.7320.0140.0140.0000.0000.0000.000
69A69GLU-1-0.846-0.90718.009-0.059-0.0590.0000.0000.0000.000
70A70TRP00.0460.02120.560-0.025-0.0250.0000.0000.0000.000
71A71ALA0-0.025-0.00323.5120.0160.0160.0000.0000.0000.000
72A72GLN00.008-0.00626.669-0.012-0.0120.0000.0000.0000.000
73A73PHE00.0130.00225.1040.0080.0080.0000.0000.0000.000
74A74SER0-0.003-0.00730.830-0.004-0.0040.0000.0000.0000.000
75A75GLY00.0250.02233.5940.0000.0000.0000.0000.0000.000
76A76ASN0-0.047-0.02729.835-0.007-0.0070.0000.0000.0000.000
77A77TYR0-0.010-0.00927.2810.0060.0060.0000.0000.0000.000
78A78TYR00.0120.01423.425-0.009-0.0090.0000.0000.0000.000
79A79GLY00.1050.04721.2800.0170.0170.0000.0000.0000.000
80A80SER0-0.055-0.03815.793-0.029-0.0290.0000.0000.0000.000
81A81THR00.0660.03117.2190.0100.0100.0000.0000.0000.000
82A82VAL00.0750.01713.679-0.075-0.0750.0000.0000.0000.000
83A83ALA00.0190.00913.014-0.122-0.1220.0000.0000.0000.000
84A84SER0-0.022-0.02013.304-0.085-0.0850.0000.0000.0000.000
85A85VAL0-0.003-0.0089.083-0.116-0.1160.0000.0000.0000.000
86A86LYS10.9170.9598.6110.3110.3110.0000.0000.0000.000
87A87GLN00.0540.0348.337-0.288-0.2880.0000.0000.0000.000
88A88VAL0-0.0110.0066.621-0.013-0.0130.0000.0000.0000.000
89A89SER00.0450.0184.0160.6690.771-0.001-0.024-0.0760.000
90A90LYS10.8080.9235.3270.7520.7520.0000.0000.0000.000
91A91SER0-0.081-0.0618.0250.2870.2870.0000.0000.0000.000
92A92GLY00.0100.0255.7590.2510.2510.0000.0000.0000.000
93A93LYS10.8200.9135.2851.1131.1130.0000.0000.0000.000
94A94THR00.001-0.0022.872-6.163-3.8140.591-1.181-1.760-0.012
95A95CYS0-0.063-0.0344.0151.3051.4380.000-0.024-0.1090.000
96A96ILE0-0.017-0.0126.6160.3650.3650.0000.0000.0000.000
97A97LEU00.017-0.0079.098-0.069-0.0690.0000.0000.0000.000
98A98ASP-1-0.849-0.92211.9050.1780.1780.0000.0000.0000.000
99A99ILE0-0.0010.00214.763-0.035-0.0350.0000.0000.0000.000
100A100ASP-1-0.801-0.91417.2430.1020.1020.0000.0000.0000.000
101A101MET00.0390.03018.9760.0200.0200.0000.0000.0000.000
102A102GLN0-0.060-0.03820.5150.0160.0160.0000.0000.0000.000
103A103GLY00.0750.04218.462-0.008-0.0080.0000.0000.0000.000
104A104VAL0-0.071-0.02515.7030.0060.0060.0000.0000.0000.000
105A105LYS10.8630.92916.905-0.118-0.1180.0000.0000.0000.000
106A106SER0-0.0020.01618.912-0.003-0.0030.0000.0000.0000.000
107A107VAL0-0.006-0.01712.316-0.007-0.0070.0000.0000.0000.000
108A108LYS10.8220.91714.448-0.443-0.4430.0000.0000.0000.000
109A109ALA0-0.069-0.01716.6880.0010.0010.0000.0000.0000.000
110A110ILE00.0070.00715.284-0.041-0.0410.0000.0000.0000.000
111A111PRO00.0430.02314.5250.0110.0110.0000.0000.0000.000
112A112GLU-1-0.876-0.93913.6640.0420.0420.0000.0000.0000.000
113A113LEU0-0.106-0.06710.439-0.143-0.1430.0000.0000.0000.000
114A114ASN0-0.027-0.0088.5080.1680.1680.0000.0000.0000.000
115A115ALA00.0200.0167.7330.4960.4960.0000.0000.0000.000
116A116ARG10.8180.9093.242-6.850-5.7050.024-0.550-0.6190.005
117A117PHE00.0190.0048.275-0.321-0.3210.0000.0000.0000.000
118A118LEU00.0180.02010.901-0.010-0.0100.0000.0000.0000.000
119A119PHE00.0230.00912.806-0.098-0.0980.0000.0000.0000.000
120A120ILE0-0.014-0.00214.788-0.001-0.0010.0000.0000.0000.000
121A121ALA00.0390.01818.201-0.030-0.0300.0000.0000.0000.000
122A122PRO0-0.032-0.01521.801-0.002-0.0020.0000.0000.0000.000
123A123PRO00.010-0.00825.0430.0050.0050.0000.0000.0000.000
124A124SER00.0500.02527.263-0.001-0.0010.0000.0000.0000.000
125A125VAL00.0500.01929.680-0.002-0.0020.0000.0000.0000.000
126A126GLU-1-0.914-0.94231.1300.0580.0580.0000.0000.0000.000
127A127ASP-1-0.746-0.87529.3560.0770.0770.0000.0000.0000.000
128A128LEU0-0.0040.00826.354-0.003-0.0030.0000.0000.0000.000
129A129LYS10.9000.93029.525-0.050-0.0500.0000.0000.0000.000
130A130LYS10.9190.94932.357-0.068-0.0680.0000.0000.0000.000
131A131ARG10.7320.85024.957-0.102-0.1020.0000.0000.0000.000
132A132LEU0-0.106-0.05228.317-0.005-0.0050.0000.0000.0000.000
133A133GLU-1-0.858-0.92331.2730.0350.0350.0000.0000.0000.000
134A134GLY0-0.0280.00333.143-0.003-0.0030.0000.0000.0000.000
135A135ARG10.7260.84628.330-0.031-0.0310.0000.0000.0000.000
136A136GLY00.0610.04632.328-0.004-0.0040.0000.0000.0000.000
137A137THR0-0.100-0.04032.271-0.003-0.0030.0000.0000.0000.000
138A138GLU-1-0.796-0.90831.9490.0310.0310.0000.0000.0000.000
139A139THR00.021-0.00135.7500.0000.0000.0000.0000.0000.000
140A140GLU-1-0.852-0.91637.8220.0230.0230.0000.0000.0000.000
141A141GLU-1-0.774-0.88238.0480.0270.0270.0000.0000.0000.000
142A142SER0-0.044-0.02134.2400.0020.0020.0000.0000.0000.000
143A143ILE00.0530.02733.3780.0040.0040.0000.0000.0000.000
144A144ASN00.0400.01933.3660.0080.0080.0000.0000.0000.000
145A145LYS10.7910.87633.120-0.021-0.0210.0000.0000.0000.000
146A146ARG10.9090.96027.455-0.030-0.0300.0000.0000.0000.000
147A147LEU0-0.0100.00729.3800.0080.0080.0000.0000.0000.000
148A148SER0-0.009-0.00730.9810.0070.0070.0000.0000.0000.000
149A149ALA00.0130.00427.8570.0060.0060.0000.0000.0000.000
150A150ALA0-0.0020.00526.2870.0090.0090.0000.0000.0000.000
151A151GLN00.0090.00726.5490.0100.0100.0000.0000.0000.000
152A152ALA00.0070.00727.7380.0060.0060.0000.0000.0000.000
153A153GLU-1-0.859-0.95920.8830.1560.1560.0000.0000.0000.000
154A154LEU0-0.027-0.03623.5900.0190.0190.0000.0000.0000.000
155A155ALA00.0450.03925.0050.0110.0110.0000.0000.0000.000
156A156TYR00.021-0.01819.1810.0060.0060.0000.0000.0000.000
157A157ALA0-0.039-0.01220.7640.0250.0250.0000.0000.0000.000
158A158GLU-1-0.907-0.95021.5120.1670.1670.0000.0000.0000.000
159A159THR0-0.128-0.06722.600-0.002-0.0020.0000.0000.0000.000
160A160GLY00.0230.01119.9510.0040.0040.0000.0000.0000.000
161A161ALA0-0.0390.00018.1760.0420.0420.0000.0000.0000.000
162A162HIS0-0.021-0.02814.7320.0770.0770.0000.0000.0000.000
163A163ASP-1-0.839-0.9139.7511.3151.3150.0000.0000.0000.000
164A164LYS10.8020.89012.789-0.466-0.4660.0000.0000.0000.000
165A165VAL00.0190.00814.161-0.020-0.0200.0000.0000.0000.000
166A166ILE0-0.061-0.03814.179-0.008-0.0080.0000.0000.0000.000
167A167VAL00.0440.03518.279-0.017-0.0170.0000.0000.0000.000
168A168ASN0-0.030-0.02920.923-0.004-0.0040.0000.0000.0000.000
169A169ASP-1-0.834-0.90422.6190.1260.1260.0000.0000.0000.000
170A170ASP-1-0.812-0.92324.1610.0980.0980.0000.0000.0000.000
171A171LEU00.0050.01620.5290.0160.0160.0000.0000.0000.000
172A172ASP-1-0.837-0.91720.3880.0990.0990.0000.0000.0000.000
173A173LYS10.8800.92920.070-0.135-0.1350.0000.0000.0000.000
174A174ALA00.0140.00118.8640.0270.0270.0000.0000.0000.000
175A175TYR0-0.095-0.09014.8300.0400.0400.0000.0000.0000.000
176A176LYS10.8660.91915.462-0.222-0.2220.0000.0000.0000.000
177A177GLU-1-0.841-0.92015.0910.3460.3460.0000.0000.0000.000
178A178LEU0-0.018-0.01611.6470.0790.0790.0000.0000.0000.000
179A179LYS10.8180.89510.793-0.010-0.0100.0000.0000.0000.000
180A180ASP-1-0.848-0.91210.2350.3370.3370.0000.0000.0000.000
181A181PHE0-0.011-0.0138.5930.1130.1130.0000.0000.0000.000
182A182ILE0-0.0200.0085.4380.4160.4160.0000.0000.0000.000
183A183PHE00.0360.0155.2920.7960.7960.0000.0000.0000.000
184A184ALA0-0.0310.0136.909-0.322-0.3220.0000.0000.0000.000
185A185GLU-1-0.882-0.9131.589-24.743-31.76222.554-10.159-5.376-0.081
186A186LYS10.9060.9514.282-1.126-1.056-0.001-0.009-0.0610.000