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: QVMMY

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 OptAll
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 -1890991.321643
FMO2-HF: Nuclear repulsion 1819733.498202
FMO2-HF: Total energy -71257.823441
FMO2-MP2: Total energy -71468.450261


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.
-38.649-42.58934.203-17.079-13.186-0.079
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 : 0.027 / q_NPA : -0.020
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].
3A3PRO00.0010.0113.105-1.0241.9240.154-1.690-1.4130.003
4A4ILE0-0.002-0.0123.5500.6250.9610.006-0.063-0.2790.000
5A5VAL00.0000.0066.676-0.412-0.4120.0000.0000.0000.000
6A6ILE0-0.019-0.00910.4920.1680.1680.0000.0000.0000.000
7A7SER00.0290.01112.386-0.106-0.1060.0000.0000.0000.000
8A8GLY00.0260.01916.0470.0320.0320.0000.0000.0000.000
9A9PRO00.0210.01119.397-0.022-0.0220.0000.0000.0000.000
10A10SER00.004-0.00221.8980.0040.0040.0000.0000.0000.000
11A11GLY00.0210.00523.4360.0000.0000.0000.0000.0000.000
12A12THR00.009-0.00221.0460.0010.0010.0000.0000.0000.000
13A13GLY00.0460.02221.4050.0040.0040.0000.0000.0000.000
14A14LYS10.8030.91915.357-0.159-0.1590.0000.0000.0000.000
15A15SER00.0520.02416.6180.0070.0070.0000.0000.0000.000
16A16THR0-0.024-0.02218.090-0.025-0.0250.0000.0000.0000.000
17A17LEU00.0050.01015.336-0.011-0.0110.0000.0000.0000.000
18A18LEU00.0540.02711.4620.0060.0060.0000.0000.0000.000
19A19LYS10.9170.96514.285-0.073-0.0730.0000.0000.0000.000
20A20LYS10.7900.89516.770-0.152-0.1520.0000.0000.0000.000
21A21LEU00.0230.0278.5940.0000.0000.0000.0000.0000.000
22A22PHE0-0.007-0.02410.636-0.026-0.0260.0000.0000.0000.000
23A23ALA0-0.033-0.00413.586-0.021-0.0210.0000.0000.0000.000
24A24GLU-1-0.780-0.83014.2070.1600.1600.0000.0000.0000.000
25A25TYR0-0.034-0.04910.1880.0420.0420.0000.0000.0000.000
26A26PRO00.0110.00710.895-0.075-0.0750.0000.0000.0000.000
27A27ASP-1-0.842-0.90710.875-0.275-0.2750.0000.0000.0000.000
28A28SER0-0.0110.0056.623-0.037-0.0370.0000.0000.0000.000
29A29PHE0-0.011-0.0024.976-0.517-0.5170.0000.0000.0000.000
30A30GLY00.0510.0197.4750.1630.1630.0000.0000.0000.000
31A31PHE00.0130.0139.015-0.143-0.1430.0000.0000.0000.000
32A32SER00.003-0.00211.766-0.037-0.0370.0000.0000.0000.000
33A33VAL00.004-0.00212.6650.0820.0820.0000.0000.0000.000
34A34SER0-0.0080.01315.7950.0180.0180.0000.0000.0000.000
35A35SER00.0110.01018.4460.0030.0030.0000.0000.0000.000
36A36THR0-0.044-0.04321.5360.0180.0180.0000.0000.0000.000
37A37THR00.0230.02625.092-0.003-0.0030.0000.0000.0000.000
38A38ARG10.7280.84625.9650.1070.1070.0000.0000.0000.000
39A39THR00.003-0.00629.240-0.008-0.0080.0000.0000.0000.000
40A40PRO00.0280.02328.4360.0040.0040.0000.0000.0000.000
41A41ARG10.8650.92729.2400.0800.0800.0000.0000.0000.000
42A42ALA00.009-0.00530.131-0.006-0.0060.0000.0000.0000.000
43A43GLY00.0300.01428.9190.0050.0050.0000.0000.0000.000
44A44GLU-1-0.785-0.84625.416-0.118-0.1180.0000.0000.0000.000
45A45VAL0-0.018-0.02023.2430.0060.0060.0000.0000.0000.000
46A46ASN00.0100.00122.663-0.027-0.0270.0000.0000.0000.000
47A47GLY00.0220.02119.4200.0000.0000.0000.0000.0000.000
48A48LYS10.7960.89517.9690.1370.1370.0000.0000.0000.000
49A49ASP-1-0.821-0.89918.153-0.184-0.1840.0000.0000.0000.000
50A50TYR00.011-0.01020.0770.0060.0060.0000.0000.0000.000
51A51ASN0-0.024-0.00617.4030.0070.0070.0000.0000.0000.000
52A52PHE0-0.028-0.02421.5450.0120.0120.0000.0000.0000.000
53A53VAL00.0210.01824.357-0.004-0.0040.0000.0000.0000.000
54A54SER0-0.029-0.05927.1740.0120.0120.0000.0000.0000.000
55A55VAL00.024-0.01629.502-0.005-0.0050.0000.0000.0000.000
56A56ASP-1-0.867-0.95030.866-0.070-0.0700.0000.0000.0000.000
57A57GLU-1-0.816-0.85127.253-0.126-0.1260.0000.0000.0000.000
58A58PHE00.0560.03724.113-0.006-0.0060.0000.0000.0000.000
59A59LYS10.9290.95826.9430.0610.0610.0000.0000.0000.000
60A60SER0-0.112-0.06427.9680.0030.0030.0000.0000.0000.000
61A61MET00.0390.01921.6630.0060.0060.0000.0000.0000.000
62A62ILE0-0.060-0.01824.191-0.003-0.0030.0000.0000.0000.000
63A63LYS10.9260.97326.0920.0830.0830.0000.0000.0000.000
64A64ASN0-0.080-0.04724.3840.0180.0180.0000.0000.0000.000
65A65ASN0-0.069-0.03022.8670.0010.0010.0000.0000.0000.000
66A66GLU-1-0.812-0.90119.901-0.196-0.1960.0000.0000.0000.000
67A67PHE0-0.078-0.05018.622-0.041-0.0410.0000.0000.0000.000
68A68ILE0-0.0060.01313.5060.0120.0120.0000.0000.0000.000
69A69GLU-1-0.840-0.88817.833-0.073-0.0730.0000.0000.0000.000
70A70TRP00.0340.00320.313-0.024-0.0240.0000.0000.0000.000
71A71ALA0-0.0040.01023.2920.0160.0160.0000.0000.0000.000
72A72GLN00.0250.00126.355-0.012-0.0120.0000.0000.0000.000
73A73PHE0-0.0070.00124.9150.0090.0090.0000.0000.0000.000
74A74SER0-0.003-0.01530.664-0.004-0.0040.0000.0000.0000.000
75A75GLY00.0250.02233.6510.0000.0000.0000.0000.0000.000
76A76ASN0-0.045-0.02529.737-0.007-0.0070.0000.0000.0000.000
77A77TYR00.0060.00327.3640.0050.0050.0000.0000.0000.000
78A78TYR00.0050.00923.178-0.007-0.0070.0000.0000.0000.000
79A79GLY00.0740.04420.9360.0170.0170.0000.0000.0000.000
80A80SER0-0.048-0.03315.528-0.029-0.0290.0000.0000.0000.000
81A81THR00.0710.03816.6620.0010.0010.0000.0000.0000.000
82A82VAL00.0740.02313.695-0.082-0.0820.0000.0000.0000.000
83A83ALA00.0070.00412.759-0.124-0.1240.0000.0000.0000.000
84A84SER0-0.016-0.02212.878-0.098-0.0980.0000.0000.0000.000
85A85VAL00.0140.0028.922-0.081-0.0810.0000.0000.0000.000
86A86LYS10.8530.9238.4240.3920.3920.0000.0000.0000.000
87A87GLN00.0260.0248.601-0.204-0.2040.0000.0000.0000.000
88A88VAL0-0.0150.0046.4590.0930.0930.0000.0000.0000.000
89A89SER00.0400.0223.6830.7150.848-0.001-0.037-0.0950.000
90A90LYS10.8130.9135.0460.8400.909-0.0010.000-0.0680.000
91A91SER0-0.069-0.0507.7560.3330.3330.0000.0000.0000.000
92A92GLY00.0010.0155.7990.1800.1800.0000.0000.0000.000
93A93LYS10.7940.8905.0670.9970.9970.0000.0000.0000.000
94A94THR00.0230.0102.149-6.761-6.8965.967-2.223-3.608-0.016
95A95CYS0-0.047-0.0113.2052.0552.1650.0350.103-0.2480.000
96A96ILE0-0.0080.0035.9090.3750.3750.0000.0000.0000.000
97A97LEU00.032-0.0048.531-0.070-0.0700.0000.0000.0000.000
98A98ASP-1-0.849-0.91511.5410.2070.2070.0000.0000.0000.000
99A99ILE0-0.0150.00114.208-0.044-0.0440.0000.0000.0000.000
100A100ASP-1-0.790-0.89216.6730.1050.1050.0000.0000.0000.000
101A101MET00.0190.02318.5380.0150.0150.0000.0000.0000.000
102A102GLN0-0.043-0.02920.3170.0110.0110.0000.0000.0000.000
103A103GLY00.0640.02817.942-0.009-0.0090.0000.0000.0000.000
104A104VAL0-0.054-0.03315.3320.0020.0020.0000.0000.0000.000
105A105LYS10.8270.91716.677-0.110-0.1100.0000.0000.0000.000
106A106SER0-0.017-0.01518.402-0.004-0.0040.0000.0000.0000.000
107A107VAL00.006-0.01211.942-0.014-0.0140.0000.0000.0000.000
108A108LYS10.7820.90614.005-0.406-0.4060.0000.0000.0000.000
109A109ALA0-0.038-0.00116.491-0.003-0.0030.0000.0000.0000.000
110A110ILE00.0040.01515.636-0.033-0.0330.0000.0000.0000.000
111A111PRO00.0650.03114.576-0.011-0.0110.0000.0000.0000.000
112A112GLU-1-0.866-0.92313.251-0.079-0.0790.0000.0000.0000.000
113A113LEU0-0.037-0.04210.939-0.193-0.1930.0000.0000.0000.000
114A114ASN0-0.043-0.0268.5910.0410.0410.0000.0000.0000.000
115A115ALA00.0310.0267.5770.3140.3140.0000.0000.0000.000
116A116ARG10.7740.9022.376-13.251-10.6791.011-1.560-2.0230.023
117A117PHE00.005-0.0087.709-0.375-0.3750.0000.0000.0000.000
118A118LEU00.0040.01010.4750.0270.0270.0000.0000.0000.000
119A119PHE00.0200.01612.364-0.113-0.1130.0000.0000.0000.000
120A120ILE0-0.015-0.01614.3670.0050.0050.0000.0000.0000.000
121A121ALA00.0620.01817.839-0.035-0.0350.0000.0000.0000.000
122A122PRO0-0.027-0.01721.4610.0000.0000.0000.0000.0000.000
123A123PRO0-0.013-0.01024.7670.0060.0060.0000.0000.0000.000
124A124SER00.0550.03327.120-0.002-0.0020.0000.0000.0000.000
125A125VAL00.0570.01929.1600.0000.0000.0000.0000.0000.000
126A126GLU-1-0.911-0.94730.6040.0670.0670.0000.0000.0000.000
127A127ASP-1-0.790-0.89528.7610.0940.0940.0000.0000.0000.000
128A128LEU0-0.032-0.01425.678-0.002-0.0020.0000.0000.0000.000
129A129LYS10.8460.90928.939-0.055-0.0550.0000.0000.0000.000
130A130LYS10.9450.95831.879-0.081-0.0810.0000.0000.0000.000
131A131ARG10.7230.85324.546-0.122-0.1220.0000.0000.0000.000
132A132LEU0-0.052-0.01927.475-0.005-0.0050.0000.0000.0000.000
133A133GLU-1-0.800-0.89530.6420.0410.0410.0000.0000.0000.000
134A134GLY0-0.0130.00833.058-0.004-0.0040.0000.0000.0000.000
135A135ARG10.7670.86127.824-0.036-0.0360.0000.0000.0000.000
136A136GLY00.0210.02232.170-0.004-0.0040.0000.0000.0000.000
137A137THR0-0.093-0.05231.620-0.004-0.0040.0000.0000.0000.000
138A138GLU-1-0.765-0.86431.0140.0360.0360.0000.0000.0000.000
139A139THR00.0490.03834.9460.0000.0000.0000.0000.0000.000
140A140GLU-1-0.855-0.94036.8150.0250.0250.0000.0000.0000.000
141A141GLU-1-0.769-0.87837.4940.0280.0280.0000.0000.0000.000
142A142SER0-0.073-0.03133.5540.0010.0010.0000.0000.0000.000
143A143ILE00.0100.00132.8100.0040.0040.0000.0000.0000.000
144A144ASN00.0320.01333.0220.0080.0080.0000.0000.0000.000
145A145LYS10.8310.91432.372-0.022-0.0220.0000.0000.0000.000
146A146ARG10.8610.93427.806-0.033-0.0330.0000.0000.0000.000
147A147LEU00.0090.00328.6140.0090.0090.0000.0000.0000.000
148A148SER0-0.016-0.01830.1970.0070.0070.0000.0000.0000.000
149A149ALA00.0090.00727.0290.0060.0060.0000.0000.0000.000
150A150ALA0-0.002-0.00525.4500.0110.0110.0000.0000.0000.000
151A151GLN00.002-0.00225.8960.0110.0110.0000.0000.0000.000
152A152ALA00.0180.01127.5210.0070.0070.0000.0000.0000.000
153A153GLU-1-0.851-0.95620.0540.1660.1660.0000.0000.0000.000
154A154LEU0-0.037-0.02222.7130.0230.0230.0000.0000.0000.000
155A155ALA00.0480.03724.1100.0130.0130.0000.0000.0000.000
156A156TYR00.0490.00519.4380.0040.0040.0000.0000.0000.000
157A157ALA0-0.034-0.01020.0000.0190.0190.0000.0000.0000.000
158A158GLU-1-0.913-0.96420.8430.1690.1690.0000.0000.0000.000
159A159THR0-0.127-0.07122.124-0.002-0.0020.0000.0000.0000.000
160A160GLY00.0280.01819.593-0.002-0.0020.0000.0000.0000.000
161A161ALA0-0.058-0.01317.8690.0370.0370.0000.0000.0000.000
162A162HIS0-0.013-0.03014.0720.0690.0690.0000.0000.0000.000
163A163ASP-1-0.803-0.9028.8931.4201.4200.0000.0000.0000.000
164A164LYS10.8060.89012.213-0.526-0.5260.0000.0000.0000.000
165A165VAL00.0340.02413.827-0.005-0.0050.0000.0000.0000.000
166A166ILE0-0.029-0.01313.6270.0110.0110.0000.0000.0000.000
167A167VAL00.0340.03117.814-0.020-0.0200.0000.0000.0000.000
168A168ASN0-0.028-0.03020.5890.0100.0100.0000.0000.0000.000
169A169ASP-1-0.798-0.89422.1790.1520.1520.0000.0000.0000.000
170A170ASP-1-0.801-0.90723.7480.1280.1280.0000.0000.0000.000
171A171LEU0-0.0010.01820.2970.0190.0190.0000.0000.0000.000
172A172ASP-1-0.810-0.91120.0400.1500.1500.0000.0000.0000.000
173A173LYS10.8560.91819.724-0.166-0.1660.0000.0000.0000.000
174A174ALA00.004-0.00518.4310.0350.0350.0000.0000.0000.000
175A175TYR0-0.048-0.06714.1410.0510.0510.0000.0000.0000.000
176A176LYS10.7990.88414.836-0.286-0.2860.0000.0000.0000.000
177A177GLU-1-0.835-0.89714.6210.4160.4160.0000.0000.0000.000
178A178LEU0-0.017-0.00710.9890.0980.0980.0000.0000.0000.000
179A179LYS10.8350.90010.391-0.055-0.0550.0000.0000.0000.000
180A180ASP-1-0.817-0.8949.7940.4820.4820.0000.0000.0000.000
181A181PHE0-0.026-0.0198.0420.1880.1880.0000.0000.0000.000
182A182ILE0-0.018-0.0014.9900.4760.4760.0000.0000.0000.000
183A183PHE00.0390.0154.9750.9861.092-0.001-0.003-0.1030.000
184A184ALA00.0000.0266.614-0.334-0.3340.0000.0000.0000.000
185A185GLU-1-0.877-0.8991.537-24.130-34.24827.034-11.601-5.315-0.089
186A186LYS10.8850.9434.455-0.716-0.677-0.001-0.005-0.0340.000