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: ZVLLN

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889366.563103
FMO2-HF: Nuclear repulsion 1818111.549131
FMO2-HF: Total energy -71255.013972
FMO2-MP2: Total energy -71465.780187


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.
-23.356-13.7044.287-6.155-7.783-0.031
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 : 0.034 / q_NPA : 0.025
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].
3A3PRO00.0160.0153.515-0.4712.0160.025-1.291-1.2210.007
4A4ILE00.021-0.0054.4240.2890.465-0.001-0.015-0.1600.000
5A5VAL0-0.024-0.0107.109-0.501-0.5010.0000.0000.0000.000
6A6ILE0-0.0030.00210.871-0.018-0.0180.0000.0000.0000.000
7A7SER00.0250.01012.836-0.073-0.0730.0000.0000.0000.000
8A8GLY00.0270.01516.5730.0020.0020.0000.0000.0000.000
9A9PRO00.0500.03519.959-0.009-0.0090.0000.0000.0000.000
10A10SER0-0.039-0.00222.6880.0020.0020.0000.0000.0000.000
11A11GLY00.0380.01023.908-0.016-0.0160.0000.0000.0000.000
12A12THR00.013-0.03622.046-0.010-0.0100.0000.0000.0000.000
13A13GLY00.0000.00122.141-0.005-0.0050.0000.0000.0000.000
14A14LYS10.9230.96616.346-0.414-0.4140.0000.0000.0000.000
15A15SER00.0490.02917.2980.0300.0300.0000.0000.0000.000
16A16THR0-0.009-0.02118.4780.0070.0070.0000.0000.0000.000
17A17LEU00.0620.03315.769-0.016-0.0160.0000.0000.0000.000
18A18LEU00.0610.03512.0160.0040.0040.0000.0000.0000.000
19A19LYS10.9180.96814.503-0.199-0.1990.0000.0000.0000.000
20A20LYS10.8640.92817.099-0.193-0.1930.0000.0000.0000.000
21A21LEU00.0270.0419.312-0.039-0.0390.0000.0000.0000.000
22A22PHE00.007-0.01310.853-0.001-0.0010.0000.0000.0000.000
23A23ALA0-0.053-0.00913.748-0.034-0.0340.0000.0000.0000.000
24A24GLU-1-0.810-0.84514.6480.0740.0740.0000.0000.0000.000
25A25TYR0-0.010-0.02310.528-0.042-0.0420.0000.0000.0000.000
26A26PRO00.0220.02111.7450.1000.1000.0000.0000.0000.000
27A27ASP-1-0.911-0.95311.8890.0670.0670.0000.0000.0000.000
28A28SER0-0.014-0.0207.158-0.054-0.0540.0000.0000.0000.000
29A29PHE00.0070.0155.1850.6010.6010.0000.0000.0000.000
30A30GLY00.0290.0048.419-0.233-0.2330.0000.0000.0000.000
31A31PHE00.0380.0479.6710.1410.1410.0000.0000.0000.000
32A32SER0-0.035-0.02212.372-0.065-0.0650.0000.0000.0000.000
33A33VAL00.000-0.00213.168-0.008-0.0080.0000.0000.0000.000
34A34SER00.0290.00916.010-0.009-0.0090.0000.0000.0000.000
35A35SER0-0.0160.00018.872-0.032-0.0320.0000.0000.0000.000
36A36THR0-0.020-0.01421.7350.0100.0100.0000.0000.0000.000
37A37THR00.0130.03925.382-0.007-0.0070.0000.0000.0000.000
38A38ARG10.7530.88126.573-0.106-0.1060.0000.0000.0000.000
39A39THR00.0260.00229.303-0.001-0.0010.0000.0000.0000.000
40A40PRO00.0280.02028.7790.0050.0050.0000.0000.0000.000
41A41ARG10.9660.97629.444-0.069-0.0690.0000.0000.0000.000
42A42ALA0-0.042-0.01930.821-0.004-0.0040.0000.0000.0000.000
43A43GLY00.0170.00629.6750.0030.0030.0000.0000.0000.000
44A44GLU-1-0.840-0.90126.1360.0970.0970.0000.0000.0000.000
45A45VAL0-0.024-0.03223.271-0.010-0.0100.0000.0000.0000.000
46A46ASN00.0550.01522.7890.0130.0130.0000.0000.0000.000
47A47GLY0-0.0150.01619.470-0.011-0.0110.0000.0000.0000.000
48A48LYS10.8960.94317.998-0.077-0.0770.0000.0000.0000.000
49A49ASP-1-0.888-0.93519.1230.1080.1080.0000.0000.0000.000
50A50TYR00.022-0.01220.8520.0220.0220.0000.0000.0000.000
51A51ASN0-0.0150.01017.517-0.037-0.0370.0000.0000.0000.000
52A52PHE0-0.064-0.03821.6890.0120.0120.0000.0000.0000.000
53A53VAL00.0320.01724.199-0.007-0.0070.0000.0000.0000.000
54A54SER0-0.018-0.08626.9440.0020.0020.0000.0000.0000.000
55A55VAL00.007-0.01829.4970.0050.0050.0000.0000.0000.000
56A56ASP-1-0.882-0.94131.1070.0580.0580.0000.0000.0000.000
57A57GLU-1-0.812-0.84026.9040.0470.0470.0000.0000.0000.000
58A58PHE00.011-0.00623.9410.0030.0030.0000.0000.0000.000
59A59LYS10.9770.98226.783-0.075-0.0750.0000.0000.0000.000
60A60SER0-0.129-0.06328.0150.0010.0010.0000.0000.0000.000
61A61MET00.0620.04121.443-0.001-0.0010.0000.0000.0000.000
62A62ILE0-0.099-0.03424.0970.0110.0110.0000.0000.0000.000
63A63LYS10.9160.96626.045-0.056-0.0560.0000.0000.0000.000
64A64ASN0-0.034-0.01224.6220.0010.0010.0000.0000.0000.000
65A65ASN0-0.028-0.01222.5180.0090.0090.0000.0000.0000.000
66A66GLU-1-0.867-0.94219.9440.0880.0880.0000.0000.0000.000
67A67PHE0-0.075-0.04818.6540.0110.0110.0000.0000.0000.000
68A68ILE0-0.026-0.00713.6530.0100.0100.0000.0000.0000.000
69A69GLU-1-0.847-0.88218.1380.3360.3360.0000.0000.0000.000
70A70TRP00.0310.01320.680-0.019-0.0190.0000.0000.0000.000
71A71ALA0-0.022-0.00523.6120.0000.0000.0000.0000.0000.000
72A72GLN00.001-0.01126.765-0.015-0.0150.0000.0000.0000.000
73A73PHE0-0.003-0.00425.3910.0000.0000.0000.0000.0000.000
74A74SER0-0.015-0.01230.894-0.004-0.0040.0000.0000.0000.000
75A75GLY00.0210.02333.684-0.006-0.0060.0000.0000.0000.000
76A76ASN0-0.028-0.01830.153-0.009-0.0090.0000.0000.0000.000
77A77TYR0-0.005-0.00527.3090.0080.0080.0000.0000.0000.000
78A78TYR0-0.0010.00223.580-0.008-0.0080.0000.0000.0000.000
79A79GLY00.1090.04521.360-0.003-0.0030.0000.0000.0000.000
80A80SER0-0.042-0.05315.934-0.012-0.0120.0000.0000.0000.000
81A81THR00.0490.02216.8750.0040.0040.0000.0000.0000.000
82A82VAL00.0830.02513.3800.0110.0110.0000.0000.0000.000
83A83ALA00.0290.01512.677-0.020-0.0200.0000.0000.0000.000
84A84SER0-0.010-0.00513.000-0.062-0.0620.0000.0000.0000.000
85A85VAL0-0.012-0.0179.0030.0120.0120.0000.0000.0000.000
86A86LYS10.9360.9678.336-0.086-0.0860.0000.0000.0000.000
87A87GLN00.0320.0148.088-0.256-0.2560.0000.0000.0000.000
88A88VAL0-0.025-0.0067.053-0.119-0.1190.0000.0000.0000.000
89A89SER00.0560.0153.8220.2460.360-0.001-0.027-0.0860.000
90A90LYS10.8470.9525.152-0.268-0.210-0.0010.000-0.0560.000
91A91SER0-0.066-0.0477.937-0.047-0.0470.0000.0000.0000.000
92A92GLY00.0040.0235.8010.0660.0660.0000.0000.0000.000
93A93LYS10.8560.9485.7960.0240.0240.0000.0000.0000.000
94A94THR00.0060.0032.397-3.760-2.2112.045-1.397-2.197-0.006
95A95CYS0-0.074-0.0344.550-0.832-0.708-0.001-0.035-0.0880.000
96A96ILE0-0.011-0.0116.6810.4430.4430.0000.0000.0000.000
97A97LEU00.001-0.0189.146-0.222-0.2220.0000.0000.0000.000
98A98ASP-1-0.884-0.93911.9980.5240.5240.0000.0000.0000.000
99A99ILE0-0.0050.00414.301-0.063-0.0630.0000.0000.0000.000
100A100ASP-1-0.825-0.91917.3610.3440.3440.0000.0000.0000.000
101A101MET00.0150.00319.1290.0350.0350.0000.0000.0000.000
102A102GLN0-0.026-0.02920.4480.0100.0100.0000.0000.0000.000
103A103GLY00.0850.05518.608-0.007-0.0070.0000.0000.0000.000
104A104VAL0-0.071-0.02815.5640.0340.0340.0000.0000.0000.000
105A105LYS10.9230.95516.630-0.251-0.2510.0000.0000.0000.000
106A106SER00.0260.03018.921-0.022-0.0220.0000.0000.0000.000
107A107VAL00.003-0.00512.4590.0050.0050.0000.0000.0000.000
108A108LYS10.8560.93714.837-0.634-0.6340.0000.0000.0000.000
109A109ALA0-0.057-0.01316.298-0.025-0.0250.0000.0000.0000.000
110A110ILE00.0060.00615.214-0.052-0.0520.0000.0000.0000.000
111A111PRO00.0370.01314.2010.0870.0870.0000.0000.0000.000
112A112GLU-1-0.892-0.94313.3900.2930.2930.0000.0000.0000.000
113A113LEU0-0.115-0.06410.214-0.066-0.0660.0000.0000.0000.000
114A114ASN0-0.020-0.0057.7430.2670.2670.0000.0000.0000.000
115A115ALA0-0.0150.0037.3960.6800.6800.0000.0000.0000.000
116A116ARG10.8090.8943.559-4.389-3.6890.016-0.283-0.4320.002
117A117PHE0-0.008-0.0137.929-0.175-0.1750.0000.0000.0000.000
118A118LEU00.0080.01610.869-0.111-0.1110.0000.0000.0000.000
119A119PHE00.0360.01812.526-0.053-0.0530.0000.0000.0000.000
120A120ILE0-0.011-0.00514.990-0.036-0.0360.0000.0000.0000.000
121A121ALA00.0280.01018.280-0.020-0.0200.0000.0000.0000.000
122A122PRO0-0.044-0.01821.745-0.007-0.0070.0000.0000.0000.000
123A123PRO00.030-0.00425.1000.0010.0010.0000.0000.0000.000
124A124SER00.0490.02027.165-0.006-0.0060.0000.0000.0000.000
125A125VAL00.0490.02329.7230.0040.0040.0000.0000.0000.000
126A126GLU-1-0.914-0.94231.1370.1030.1030.0000.0000.0000.000
127A127ASP-1-0.787-0.92329.8030.1350.1350.0000.0000.0000.000
128A128LEU00.0050.00626.6670.0030.0030.0000.0000.0000.000
129A129LYS10.9760.96729.615-0.107-0.1070.0000.0000.0000.000
130A130LYS10.9340.99032.448-0.121-0.1210.0000.0000.0000.000
131A131ARG10.7840.88825.817-0.171-0.1710.0000.0000.0000.000
132A132LEU0-0.130-0.06128.2730.0020.0020.0000.0000.0000.000
133A133GLU-1-0.871-0.93431.3410.1030.1030.0000.0000.0000.000
134A134GLY0-0.050-0.00833.182-0.007-0.0070.0000.0000.0000.000
135A135ARG10.7590.87027.732-0.159-0.1590.0000.0000.0000.000
136A136GLY00.0700.05432.362-0.005-0.0050.0000.0000.0000.000
137A137THR0-0.093-0.08732.423-0.001-0.0010.0000.0000.0000.000
138A138GLU-1-0.845-0.89532.5700.1410.1410.0000.0000.0000.000
139A139THR00.0300.01235.815-0.004-0.0040.0000.0000.0000.000
140A140GLU-1-0.843-0.91637.9070.0880.0880.0000.0000.0000.000
141A141GLU-1-0.846-0.93738.1500.1060.1060.0000.0000.0000.000
142A142SER0-0.032-0.02234.6960.0090.0090.0000.0000.0000.000
143A143ILE00.0410.02933.4890.0110.0110.0000.0000.0000.000
144A144ASN00.0430.02133.4750.0110.0110.0000.0000.0000.000
145A145LYS10.8530.92033.104-0.112-0.1120.0000.0000.0000.000
146A146ARG10.9170.96327.612-0.163-0.1630.0000.0000.0000.000
147A147LEU0-0.0180.00629.5000.0130.0130.0000.0000.0000.000
148A148SER00.0150.00231.0660.0050.0050.0000.0000.0000.000
149A149ALA0-0.028-0.01327.9610.0060.0060.0000.0000.0000.000
150A150ALA00.0170.01726.3890.0180.0180.0000.0000.0000.000
151A151GLN00.0160.01226.4730.0090.0090.0000.0000.0000.000
152A152ALA00.0030.00427.6180.0010.0010.0000.0000.0000.000
153A153GLU-1-0.892-0.97021.4580.3440.3440.0000.0000.0000.000
154A154LEU0-0.035-0.04123.2680.0190.0190.0000.0000.0000.000
155A155ALA00.0470.04324.7150.0040.0040.0000.0000.0000.000
156A156TYR0-0.020-0.02618.857-0.012-0.0120.0000.0000.0000.000
157A157ALA0-0.046-0.01820.4660.0270.0270.0000.0000.0000.000
158A158GLU-1-0.897-0.94521.2600.2170.2170.0000.0000.0000.000
159A159THR0-0.137-0.06822.289-0.008-0.0080.0000.0000.0000.000
160A160GLY00.0220.01119.7360.0030.0030.0000.0000.0000.000
161A161ALA0-0.054-0.00817.9410.0410.0410.0000.0000.0000.000
162A162HIS0-0.019-0.03714.3900.1310.1310.0000.0000.0000.000
163A163ASP-1-0.842-0.90110.5281.1561.1560.0000.0000.0000.000
164A164LYS10.9070.95012.128-0.464-0.4640.0000.0000.0000.000
165A165VAL0-0.002-0.00213.9230.0330.0330.0000.0000.0000.000
166A166ILE0-0.050-0.02914.023-0.033-0.0330.0000.0000.0000.000
167A167VAL00.0340.03318.0890.0070.0070.0000.0000.0000.000
168A168ASN0-0.032-0.02021.157-0.025-0.0250.0000.0000.0000.000
169A169ASP-1-0.905-0.96422.6860.1490.1490.0000.0000.0000.000
170A170ASP-1-0.868-0.94724.2030.1050.1050.0000.0000.0000.000
171A171LEU00.0170.00520.5870.0170.0170.0000.0000.0000.000
172A172ASP-1-0.878-0.92720.3880.1340.1340.0000.0000.0000.000
173A173LYS10.9170.96820.059-0.157-0.1570.0000.0000.0000.000
174A174ALA00.0320.00918.7580.0100.0100.0000.0000.0000.000
175A175TYR0-0.149-0.15014.6760.0540.0540.0000.0000.0000.000
176A176LYS10.8910.95315.451-0.097-0.0970.0000.0000.0000.000
177A177GLU-1-0.920-0.97614.7770.2210.2210.0000.0000.0000.000
178A178LEU0-0.023-0.02111.5420.0350.0350.0000.0000.0000.000
179A179LYS10.8960.95310.7670.0500.0500.0000.0000.0000.000
180A180ASP-1-0.892-0.9479.984-0.039-0.0390.0000.0000.0000.000
181A181PHE0-0.024-0.0178.374-0.073-0.0730.0000.0000.0000.000
182A182ILE0-0.0160.0125.6600.0760.0760.0000.0000.0000.000
183A183PHE00.0400.0134.956-0.331-0.253-0.001-0.002-0.0750.000
184A184ALA0-0.0330.0136.877-0.435-0.4350.0000.0000.0000.000
185A185GLU-1-0.965-0.9962.161-15.726-11.4332.207-3.094-3.406-0.034
186A186LYS10.9510.9814.1220.5980.671-0.001-0.011-0.0620.000