Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LZ4V9

Calculation Name: 5EOV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EOV

Chain ID: A

ChEMBL ID:

UniProt ID: P9WJ62

Base Structure: X-ray

Registration Date: 2023-09-19

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2146777.572787
FMO2-HF: Nuclear repulsion 2073152.279771
FMO2-HF: Total energy -73625.293016
FMO2-MP2: Total energy -73844.872719


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:64:SER)


Summations of interaction energy for fragment #1(A:64: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.
-43.695-34.97410.259-9.244-9.735-0.055
Interaction energy analysis for fragmet #1(A:64: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 : 0.008
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].
3A66GLY00.0550.0283.668-3.275-1.302-0.005-0.988-0.9800.003
4A67ALA00.0520.0232.181-5.853-3.8182.977-2.312-2.7000.017
5A68HIS00.0060.0004.103-1.133-0.6720.007-0.152-0.3160.000
6A69LYS10.7830.8806.079-1.473-1.4730.0000.0000.0000.000
7A70LEU00.0220.0227.571-0.189-0.1890.0000.0000.0000.000
8A71VAL00.0020.0017.194-0.152-0.1520.0000.0000.0000.000
9A72GLY00.0280.0159.5490.0240.0240.0000.0000.0000.000
10A73ALA0-0.038-0.01312.027-0.014-0.0140.0000.0000.0000.000
11A74LEU0-0.005-0.00910.971-0.027-0.0270.0000.0000.0000.000
12A75GLU-1-0.825-0.88713.232-0.456-0.4560.0000.0000.0000.000
13A76ALA0-0.041-0.01415.5750.0210.0210.0000.0000.0000.000
14A77PHE0-0.074-0.04017.4110.0310.0310.0000.0000.0000.000
15A78ALA0-0.0070.00518.601-0.009-0.0090.0000.0000.0000.000
16A79ILE0-0.039-0.00716.851-0.014-0.0140.0000.0000.0000.000
17A80ALA00.0120.00816.606-0.064-0.0640.0000.0000.0000.000
18A81VAL0-0.003-0.01413.1640.0340.0340.0000.0000.0000.000
19A82ALA00.0220.00916.483-0.011-0.0110.0000.0000.0000.000
20A83GLY0-0.024-0.01018.2540.0650.0650.0000.0000.0000.000
21A84ARG10.7680.88217.9770.3530.3530.0000.0000.0000.000
22A85ARG10.8560.90918.0860.2830.2830.0000.0000.0000.000
23A86CYS0-0.044-0.02314.5170.0320.0320.0000.0000.0000.000
24A87LEU0-0.013-0.00515.620-0.005-0.0050.0000.0000.0000.000
25A88ASP-1-0.778-0.8839.116-0.473-0.4730.0000.0000.0000.000
26A89ALA00.002-0.01612.6770.0120.0120.0000.0000.0000.000
27A90GLY00.000-0.03213.0360.0490.0490.0000.0000.0000.000
28A91ALA00.0270.0629.7420.1850.1850.0000.0000.0000.000
29A92SER0-0.059-0.0479.962-0.100-0.1000.0000.0000.0000.000
30A93THR0-0.059-0.0344.7040.6680.745-0.001-0.004-0.0730.000
31A94GLY00.0820.0425.0970.1740.1740.0000.0000.0000.000
32A95GLY0-0.041-0.0122.077-0.959-0.4002.110-1.498-1.1700.007
33A96PHE00.002-0.0112.8691.5080.1570.1071.494-0.2490.001
34A97THR00.051-0.0116.582-0.159-0.1590.0000.0000.0000.000
35A98GLU-1-0.844-0.9291.943-33.759-28.7925.064-5.784-4.247-0.083
36A99VAL0-0.0010.0145.1390.5380.5380.0000.0000.0000.000
37A100LEU0-0.025-0.0167.3500.3930.3930.0000.0000.0000.000
38A101LEU0-0.017-0.0078.9730.2130.2130.0000.0000.0000.000
39A102ASP-1-0.924-0.9608.030-2.661-2.6610.0000.0000.0000.000
40A103ARG10.7330.8459.8621.1631.1630.0000.0000.0000.000
41A104GLY00.0220.00512.7480.1790.1790.0000.0000.0000.000
42A105ALA0-0.0040.00313.7720.1240.1240.0000.0000.0000.000
43A106ALA0-0.036-0.00915.566-0.053-0.0530.0000.0000.0000.000
44A107HIS0-0.025-0.00417.0730.0380.0380.0000.0000.0000.000
45A108VAL00.0080.00011.2120.0200.0200.0000.0000.0000.000
46A109VAL0-0.0060.01314.558-0.021-0.0210.0000.0000.0000.000
47A110ALA00.0240.00211.4520.0030.0030.0000.0000.0000.000
48A111ALA00.010-0.00213.3660.0270.0270.0000.0000.0000.000
49A112ASP-1-0.726-0.86913.578-0.264-0.2640.0000.0000.0000.000
50A113VAL0-0.058-0.03415.1720.0310.0310.0000.0000.0000.000
51A114GLY0-0.034-0.02816.6090.0410.0410.0000.0000.0000.000
52A115TYR0-0.053-0.01815.749-0.065-0.0650.0000.0000.0000.000
53A116GLY00.0300.00913.3260.1040.1040.0000.0000.0000.000
54A117GLN0-0.008-0.00612.579-0.068-0.0680.0000.0000.0000.000
55A118LEU0-0.0060.0168.674-0.100-0.1000.0000.0000.0000.000
56A119ALA00.0320.0218.9390.0910.0910.0000.0000.0000.000
57A120TRP00.0720.02310.715-0.101-0.1010.0000.0000.0000.000
58A121SER0-0.041-0.0169.8890.0920.0920.0000.0000.0000.000
59A122LEU0-0.022-0.0036.982-0.104-0.1040.0000.0000.0000.000
60A123ARG10.7450.84710.8940.5700.5700.0000.0000.0000.000
61A124ASN00.0160.01113.9290.1340.1340.0000.0000.0000.000
62A125ASP-1-0.786-0.85513.014-1.214-1.2140.0000.0000.0000.000
63A126PRO00.009-0.00215.0630.0530.0530.0000.0000.0000.000
64A127ARG10.8320.90312.1941.4051.4050.0000.0000.0000.000
65A128VAL0-0.037-0.02111.8350.0010.0010.0000.0000.0000.000
66A129VAL0-0.0080.00014.9880.0750.0750.0000.0000.0000.000
67A130VAL00.0060.00613.3230.0000.0000.0000.0000.0000.000
68A131LEU0-0.046-0.02215.8940.0550.0550.0000.0000.0000.000
69A132GLU-1-0.863-0.91417.686-0.250-0.2500.0000.0000.0000.000
70A133ARG10.8830.92819.3110.1310.1310.0000.0000.0000.000
71A134THR00.0250.01720.3110.0270.0270.0000.0000.0000.000
72A135ASN00.012-0.00621.5210.0070.0070.0000.0000.0000.000
73A136ALA00.1240.06818.119-0.023-0.0230.0000.0000.0000.000
74A137ARG10.8540.91420.084-0.100-0.1000.0000.0000.0000.000
75A138GLY00.0230.02523.267-0.002-0.0020.0000.0000.0000.000
76A139LEU0-0.047-0.00618.143-0.019-0.0190.0000.0000.0000.000
77A140THR0-0.022-0.03422.7080.0140.0140.0000.0000.0000.000
78A141PRO00.0230.00724.493-0.019-0.0190.0000.0000.0000.000
79A142GLU-1-0.833-0.91425.677-0.137-0.1370.0000.0000.0000.000
80A143ALA0-0.061-0.02724.020-0.014-0.0140.0000.0000.0000.000
81A144ILE0-0.0330.00120.361-0.018-0.0180.0000.0000.0000.000
82A145GLY00.0160.02021.841-0.035-0.0350.0000.0000.0000.000
83A146GLY00.0050.00624.464-0.008-0.0080.0000.0000.0000.000
84A147ARG10.8040.88623.6190.1070.1070.0000.0000.0000.000
85A148VAL00.0020.01119.207-0.021-0.0210.0000.0000.0000.000
86A149ASP-1-0.762-0.87820.734-0.278-0.2780.0000.0000.0000.000
87A150LEU0-0.006-0.00414.6600.0220.0220.0000.0000.0000.000
88A151VAL0-0.0110.00216.575-0.035-0.0350.0000.0000.0000.000
89A152VAL00.0170.01811.2470.0490.0490.0000.0000.0000.000
90A153ALA00.007-0.01013.599-0.021-0.0210.0000.0000.0000.000
91A154ASP-1-0.719-0.8489.3661.1861.1860.0000.0000.0000.000
92A155LEU00.0010.01212.2790.0810.0810.0000.0000.0000.000
93A156SER00.020-0.00114.1460.0950.0950.0000.0000.0000.000
94A157PHE0-0.027-0.02316.860-0.041-0.0410.0000.0000.0000.000
95A158ILE0-0.026-0.00619.473-0.041-0.0410.0000.0000.0000.000
96A159SER0-0.001-0.00320.8690.0090.0090.0000.0000.0000.000
97A160LEU00.0670.00918.044-0.035-0.0350.0000.0000.0000.000
98A161ALA0-0.0050.00122.187-0.031-0.0310.0000.0000.0000.000
99A162THR0-0.098-0.06524.544-0.020-0.0200.0000.0000.0000.000
100A163VAL0-0.007-0.01920.165-0.013-0.0130.0000.0000.0000.000
101A164LEU00.0180.01422.459-0.024-0.0240.0000.0000.0000.000
102A165PRO00.0160.00324.035-0.019-0.0190.0000.0000.0000.000
103A166ALA00.0280.03523.098-0.014-0.0140.0000.0000.0000.000
104A167LEU00.0020.00418.806-0.022-0.0220.0000.0000.0000.000
105A168VAL00.0130.00622.080-0.024-0.0240.0000.0000.0000.000
106A169GLY0-0.021-0.00825.337-0.011-0.0110.0000.0000.0000.000
107A170CYS0-0.045-0.02521.438-0.014-0.0140.0000.0000.0000.000
108A171ALA00.0410.03022.590-0.025-0.0250.0000.0000.0000.000
109A172SER00.0110.00623.4950.0220.0220.0000.0000.0000.000
110A173ARG10.8980.93325.7450.0840.0840.0000.0000.0000.000
111A174ASP-1-0.858-0.92326.461-0.174-0.1740.0000.0000.0000.000
112A175ALA00.0090.01721.908-0.010-0.0100.0000.0000.0000.000
113A176ASP-1-0.797-0.85419.436-0.165-0.1650.0000.0000.0000.000
114A177ILE0-0.019-0.01019.174-0.024-0.0240.0000.0000.0000.000
115A178VAL00.002-0.00915.7570.0260.0260.0000.0000.0000.000
116A179PRO0-0.019-0.00115.3950.0130.0130.0000.0000.0000.000
117A180LEU0-0.023-0.00811.8970.0130.0130.0000.0000.0000.000
118A181VAL0-0.006-0.01015.5200.0170.0170.0000.0000.0000.000
119A182LYS10.8090.89812.646-0.674-0.6740.0000.0000.0000.000
120A183PRO00.0680.02318.697-0.028-0.0280.0000.0000.0000.000
121A184GLN0-0.005-0.00916.746-0.080-0.0800.0000.0000.0000.000
122A185PHE0-0.055-0.02216.8300.0030.0030.0000.0000.0000.000
123A186GLU-1-0.778-0.85721.9100.1780.1780.0000.0000.0000.000
124A187VAL0-0.065-0.01024.756-0.026-0.0260.0000.0000.0000.000
125A188GLY00.0430.02027.4590.0000.0000.0000.0000.0000.000
126A189LYS10.9380.94130.040-0.147-0.1470.0000.0000.0000.000
127A190GLY0-0.005-0.01130.765-0.015-0.0150.0000.0000.0000.000
128A191GLN0-0.0020.01029.7660.0020.0020.0000.0000.0000.000
129A192VAL00.0160.02724.3310.0130.0130.0000.0000.0000.000
130A193GLY00.0210.01326.322-0.021-0.0210.0000.0000.0000.000
131A194PRO00.027-0.00825.9770.0240.0240.0000.0000.0000.000
132A195GLY00.0440.02923.1580.0160.0160.0000.0000.0000.000
133A196GLY0-0.0110.01121.6990.0410.0410.0000.0000.0000.000
134A197VAL0-0.002-0.00420.2730.0280.0280.0000.0000.0000.000
135A198VAL00.0030.01422.676-0.041-0.0410.0000.0000.0000.000
136A199HIS00.014-0.00224.380-0.001-0.0010.0000.0000.0000.000
137A200ASP-1-0.807-0.89926.1230.2060.2060.0000.0000.0000.000
138A201PRO00.0420.01326.3600.0090.0090.0000.0000.0000.000
139A202GLN00.0420.02127.434-0.012-0.0120.0000.0000.0000.000
140A203LEU0-0.026-0.00727.844-0.011-0.0110.0000.0000.0000.000
141A204ARG10.8430.93421.916-0.349-0.3490.0000.0000.0000.000
142A205ALA00.0550.02224.716-0.004-0.0040.0000.0000.0000.000
143A206ARG10.8990.92926.868-0.178-0.1780.0000.0000.0000.000
144A207SER0-0.003-0.00923.874-0.008-0.0080.0000.0000.0000.000
145A208VAL00.0070.00721.883-0.010-0.0100.0000.0000.0000.000
146A209LEU00.0130.00324.348-0.021-0.0210.0000.0000.0000.000
147A210ALA0-0.0180.00127.383-0.018-0.0180.0000.0000.0000.000
148A211VAL0-0.0050.00221.897-0.017-0.0170.0000.0000.0000.000
149A212ALA00.0260.01425.336-0.019-0.0190.0000.0000.0000.000
150A213ARG10.8790.93426.497-0.078-0.0780.0000.0000.0000.000
151A214ARG10.8090.90527.286-0.070-0.0700.0000.0000.0000.000
152A215ALA00.0300.00925.212-0.013-0.0130.0000.0000.0000.000
153A216GLN0-0.018-0.01727.242-0.007-0.0070.0000.0000.0000.000
154A217GLU-1-0.825-0.89230.5140.0450.0450.0000.0000.0000.000
155A218LEU0-0.043-0.01127.580-0.004-0.0040.0000.0000.0000.000
156A219GLY0-0.0060.00330.562-0.012-0.0120.0000.0000.0000.000
157A220TRP0-0.040-0.03124.081-0.011-0.0110.0000.0000.0000.000
158A221HIS00.0650.04527.7620.0220.0220.0000.0000.0000.000
159A222SER00.0370.00925.533-0.001-0.0010.0000.0000.0000.000
160A223VAL0-0.041-0.01724.213-0.003-0.0030.0000.0000.0000.000
161A224GLY00.0350.01922.922-0.007-0.0070.0000.0000.0000.000
162A225VAL0-0.031-0.01621.1300.0060.0060.0000.0000.0000.000
163A226LYS10.9000.94617.006-0.256-0.2560.0000.0000.0000.000
164A227ALA0-0.0080.00417.5490.0220.0220.0000.0000.0000.000
165A228SER00.005-0.02512.160-0.021-0.0210.0000.0000.0000.000
166A229PRO0-0.0030.00210.4770.0350.0350.0000.0000.0000.000
167A230LEU0-0.041-0.0197.2720.2100.2100.0000.0000.0000.000
168A231PRO00.0040.02411.449-0.068-0.0680.0000.0000.0000.000
169A232GLY00.0530.02711.9440.2200.2200.0000.0000.0000.000
170A233PRO0-0.022-0.02411.732-0.053-0.0530.0000.0000.0000.000
171A234SER0-0.014-0.00613.477-0.027-0.0270.0000.0000.0000.000
172A235GLY00.0190.01116.126-0.076-0.0760.0000.0000.0000.000
173A236ASN0-0.039-0.03217.340-0.095-0.0950.0000.0000.0000.000
174A237VAL00.0210.01816.3510.0900.0900.0000.0000.0000.000
175A238GLU-1-0.818-0.90913.0890.8460.8460.0000.0000.0000.000
176A239TYR00.008-0.00716.6040.0110.0110.0000.0000.0000.000
177A240PHE00.0350.02510.648-0.023-0.0230.0000.0000.0000.000
178A241LEU00.004-0.00316.847-0.013-0.0130.0000.0000.0000.000
179A242TRP0-0.015-0.01719.626-0.010-0.0100.0000.0000.0000.000
180A243LEU0-0.012-0.01420.9030.0110.0110.0000.0000.0000.000
181A244ARG10.8020.86123.0450.1130.1130.0000.0000.0000.000
182A245THR0-0.056-0.01325.8210.0120.0120.0000.0000.0000.000
183A246GLN00.0030.00128.419-0.002-0.0020.0000.0000.0000.000
184A247THR0-0.016-0.01928.090-0.013-0.0130.0000.0000.0000.000
185A248ASP-1-0.781-0.84429.988-0.072-0.0720.0000.0000.0000.000
186A249ARG10.8280.87526.9070.0880.0880.0000.0000.0000.000
187A250ALA0-0.0020.00529.5760.0060.0060.0000.0000.0000.000
188A251LEU0-0.025-0.00526.6580.0050.0050.0000.0000.0000.000
189A252SER00.0110.01030.6260.0050.0050.0000.0000.0000.000
190A253ALA00.0350.01132.6840.0060.0060.0000.0000.0000.000
191A254LYS11.0130.99832.936-0.046-0.0460.0000.0000.0000.000
192A255GLY00.0190.02331.9610.0050.0050.0000.0000.0000.000
193A256LEU00.001-0.00326.4960.0060.0060.0000.0000.0000.000
194A257GLU-1-0.922-0.97228.5620.0910.0910.0000.0000.0000.000
195A258ASP-1-0.841-0.91130.0190.0930.0930.0000.0000.0000.000
196A259ALA00.0090.01025.4870.0140.0140.0000.0000.0000.000
197A260VAL0-0.023-0.01325.0750.0220.0220.0000.0000.0000.000
198A261HIS00.0180.01125.7250.0280.0280.0000.0000.0000.000
199A262ARG10.8560.93125.737-0.075-0.0750.0000.0000.0000.000
200A263ALA00.0210.02121.4740.0230.0230.0000.0000.0000.000
201A264ILE0-0.082-0.06322.0590.0440.0440.0000.0000.0000.000
202A265SER0-0.067-0.04224.0320.0240.0240.0000.0000.0000.000
203A266GLU-1-0.919-0.94621.2420.1920.1920.0000.0000.0000.000
204A267GLY0-0.0240.00320.1260.0230.0230.0000.0000.0000.000
205A268PRO0-0.034-0.01914.897-0.026-0.0260.0000.0000.0000.000