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: LN3M9

Calculation Name: 1V8E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V8E

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W25

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2510641.829483
FMO2-HF: Nuclear repulsion 2429987.879845
FMO2-HF: Total energy -80653.949638
FMO2-MP2: Total energy -80895.739772


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:8:PRO)


Summations of interaction energy for fragment #1(A:8:PRO)
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.
-3.165-4.20514.88-3.594-10.246-0.029
Interaction energy analysis for fragmet #1(A:8:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.011
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].
3A10ARG10.7990.8923.5831.5713.7600.007-0.982-1.2140.002
4A11LEU0-0.032-0.0295.5830.7340.7340.0000.0000.0000.000
5A12GLY00.0680.0228.5730.0930.0930.0000.0000.0000.000
6A13HIS0-0.078-0.05412.0330.0950.0950.0000.0000.0000.000
7A14ARG10.8770.94113.7710.3930.3930.0000.0000.0000.000
8A15GLY0-0.012-0.00315.4130.0600.0600.0000.0000.0000.000
9A16ALA0-0.011-0.01914.988-0.094-0.0940.0000.0000.0000.000
10A17PRO00.0450.02216.0950.0550.0550.0000.0000.0000.000
11A18LEU0-0.034-0.00917.9230.0390.0390.0000.0000.0000.000
12A19LYS10.8460.92817.4160.4300.4300.0000.0000.0000.000
13A20ALA00.0490.03121.2230.0270.0270.0000.0000.0000.000
14A21LYS10.8890.95822.1710.1730.1730.0000.0000.0000.000
15A22GLU-1-0.857-0.91220.469-0.309-0.3090.0000.0000.0000.000
16A23ASN0-0.035-0.04119.9870.0060.0060.0000.0000.0000.000
17A24THR00.0290.00521.5530.0250.0250.0000.0000.0000.000
18A25LEU00.021-0.01222.146-0.029-0.0290.0000.0000.0000.000
19A26GLU-1-0.938-0.96322.459-0.256-0.2560.0000.0000.0000.000
20A27SER00.0370.02819.492-0.035-0.0350.0000.0000.0000.000
21A28PHE0-0.001-0.01117.001-0.045-0.0450.0000.0000.0000.000
22A29ARG10.9500.98617.6200.2090.2090.0000.0000.0000.000
23A30LEU00.0050.00318.734-0.027-0.0270.0000.0000.0000.000
24A31ALA0-0.030-0.01114.036-0.035-0.0350.0000.0000.0000.000
25A32LEU0-0.014-0.01013.624-0.095-0.0950.0000.0000.0000.000
26A33GLU-1-0.939-0.97714.907-0.316-0.3160.0000.0000.0000.000
27A34ALA0-0.098-0.03913.9540.0250.0250.0000.0000.0000.000
28A35GLY0-0.011-0.00512.235-0.015-0.0150.0000.0000.0000.000
29A36LEU0-0.083-0.0308.652-0.185-0.1850.0000.0000.0000.000
30A37ASP-1-0.768-0.8615.330-3.346-3.3460.0000.0000.0000.000
31A38GLY00.036-0.0018.7520.3000.3000.0000.0000.0000.000
32A39VAL0-0.052-0.00811.317-0.097-0.0970.0000.0000.0000.000
33A40GLH0-0.031-0.03012.1150.0120.0120.0000.0000.0000.000
34A41LEU0-0.002-0.00413.7850.0220.0220.0000.0000.0000.000
35A42ASP-1-0.756-0.85417.564-0.331-0.3310.0000.0000.0000.000
36A43VAL0-0.016-0.01920.1070.0160.0160.0000.0000.0000.000
37A44TRP0-0.002-0.00523.1950.0130.0130.0000.0000.0000.000
38A45PRO0-0.073-0.03226.5760.0000.0000.0000.0000.0000.000
39A46THR00.020-0.01629.4040.0010.0010.0000.0000.0000.000
40A47ARG10.7990.88332.5600.0780.0780.0000.0000.0000.000
41A48ASP-1-0.882-0.92635.481-0.091-0.0910.0000.0000.0000.000
42A49GLY0-0.086-0.04132.6040.0020.0020.0000.0000.0000.000
43A50VAL0-0.0210.00629.823-0.003-0.0030.0000.0000.0000.000
44A51PHE00.002-0.00625.3030.0000.0000.0000.0000.0000.000
45A52ALA00.0210.01526.591-0.009-0.0090.0000.0000.0000.000
46A53VAL0-0.033-0.01921.622-0.007-0.0070.0000.0000.0000.000
47A54ARG10.8250.88223.8940.1620.1620.0000.0000.0000.000
48A55HIS00.0540.02121.230-0.011-0.0110.0000.0000.0000.000
49A56ASP-1-0.857-0.92223.478-0.152-0.1520.0000.0000.0000.000
50A57PRO0-0.0060.01426.9830.0020.0020.0000.0000.0000.000
51A58ASP-1-0.882-0.94129.252-0.108-0.1080.0000.0000.0000.000
52A59THR0-0.024-0.03931.832-0.007-0.0070.0000.0000.0000.000
53A60PRO0-0.029-0.02733.9780.0060.0060.0000.0000.0000.000
54A61LEU0-0.012-0.00136.8500.0060.0060.0000.0000.0000.000
55A62GLY00.0110.02437.1180.0060.0060.0000.0000.0000.000
56A63PRO00.0010.02033.763-0.007-0.0070.0000.0000.0000.000
57A64VAL00.0460.00829.3680.0050.0050.0000.0000.0000.000
58A65PHE0-0.046-0.02032.4880.0050.0050.0000.0000.0000.000
59A66GLN0-0.060-0.03633.7840.0060.0060.0000.0000.0000.000
60A67VAL00.0120.01535.5240.0050.0050.0000.0000.0000.000
61A68ASP-1-0.754-0.84435.478-0.083-0.0830.0000.0000.0000.000
62A69TYR00.002-0.04130.0230.0000.0000.0000.0000.0000.000
63A70ALA0-0.017-0.01634.408-0.004-0.0040.0000.0000.0000.000
64A71ASP-1-0.873-0.93237.068-0.084-0.0840.0000.0000.0000.000
65A72LEU0-0.018-0.02031.926-0.003-0.0030.0000.0000.0000.000
66A73LYS10.8120.91030.4260.1480.1480.0000.0000.0000.000
67A74ALA0-0.029-0.01134.517-0.001-0.0010.0000.0000.0000.000
68A75GLN0-0.032-0.01035.9330.0060.0060.0000.0000.0000.000
69A76GLU-1-0.885-0.94630.279-0.161-0.1610.0000.0000.0000.000
70A77PRO00.0310.01832.392-0.008-0.0080.0000.0000.0000.000
71A78ASP-1-0.894-0.94228.674-0.184-0.1840.0000.0000.0000.000
72A79LEU00.0220.01927.343-0.016-0.0160.0000.0000.0000.000
73A80PRO0-0.0110.01824.3570.0130.0130.0000.0000.0000.000
74A81ARG10.8520.92627.0790.1270.1270.0000.0000.0000.000
75A82LEU00.019-0.00921.054-0.008-0.0080.0000.0000.0000.000
76A83GLU-1-0.839-0.91623.405-0.154-0.1540.0000.0000.0000.000
77A84GLU-1-0.876-0.94724.948-0.166-0.1660.0000.0000.0000.000
78A85VAL0-0.0080.00119.263-0.010-0.0100.0000.0000.0000.000
79A86LEU0-0.023-0.02019.072-0.019-0.0190.0000.0000.0000.000
80A87ALA00.0210.01921.0130.0020.0020.0000.0000.0000.000
81A88LEU00.0030.00419.7740.0090.0090.0000.0000.0000.000
82A89LYS10.8280.92015.3160.2290.2290.0000.0000.0000.000
83A90GLU-1-0.983-0.98919.434-0.122-0.1220.0000.0000.0000.000
84A91ALA0-0.049-0.01721.1320.0160.0160.0000.0000.0000.000
85A92PHE0-0.019-0.01215.743-0.004-0.0040.0000.0000.0000.000
86A93PRO00.0520.02416.666-0.030-0.0300.0000.0000.0000.000
87A94GLN0-0.041-0.03712.2220.0140.0140.0000.0000.0000.000
88A95ALA0-0.0020.03112.115-0.062-0.0620.0000.0000.0000.000
89A96VAL0-0.048-0.0169.0830.1430.1430.0000.0000.0000.000
90A97PHE0-0.015-0.02312.400-0.101-0.1010.0000.0000.0000.000
91A98ASN00.0320.02311.6740.1460.1460.0000.0000.0000.000
92A99VAL00.004-0.00913.767-0.013-0.0130.0000.0000.0000.000
93A100GLU-1-0.785-0.88716.633-0.271-0.2710.0000.0000.0000.000
94A101LEU0-0.048-0.03018.0720.0150.0150.0000.0000.0000.000
95A102LYS10.8230.91120.0870.2590.2590.0000.0000.0000.000
96A103SER0-0.054-0.04723.5930.0080.0080.0000.0000.0000.000
97A104PHE00.0780.06226.596-0.003-0.0030.0000.0000.0000.000
98A105PRO0-0.017-0.03127.8850.0070.0070.0000.0000.0000.000
99A106GLY00.0490.03430.1810.0040.0040.0000.0000.0000.000
100A107LEU0-0.014-0.01931.5400.0050.0050.0000.0000.0000.000
101A108GLY0-0.0060.00728.174-0.004-0.0040.0000.0000.0000.000
102A109GLU-1-0.866-0.94628.088-0.067-0.0670.0000.0000.0000.000
103A110GLU-1-0.971-0.98829.978-0.066-0.0660.0000.0000.0000.000
104A111ALA00.0290.01327.9360.0000.0000.0000.0000.0000.000
105A112ALA00.0500.01825.843-0.005-0.0050.0000.0000.0000.000
106A113ARG10.9000.95026.8390.0560.0560.0000.0000.0000.000
107A114ARG10.9190.96529.3640.0790.0790.0000.0000.0000.000
108A115LEU00.0340.02421.8010.0010.0010.0000.0000.0000.000
109A116ALA00.001-0.00424.690-0.003-0.0030.0000.0000.0000.000
110A117ALA0-0.049-0.02525.7600.0050.0050.0000.0000.0000.000
111A118LEU0-0.0070.00725.7860.0040.0040.0000.0000.0000.000
112A119LEU0-0.003-0.01620.367-0.004-0.0040.0000.0000.0000.000
113A120ARG10.9570.98722.9640.0420.0420.0000.0000.0000.000
114A121GLY0-0.031-0.02423.483-0.001-0.0010.0000.0000.0000.000
115A122ARG10.8890.97220.7950.1330.1330.0000.0000.0000.000
116A123GLU-1-0.903-0.95017.585-0.004-0.0040.0000.0000.0000.000
117A124GLY0-0.035-0.02214.062-0.025-0.0250.0000.0000.0000.000
118A125VAL0-0.0020.00214.556-0.075-0.0750.0000.0000.0000.000
119A126TRP0-0.035-0.0219.0610.0410.0410.0000.0000.0000.000
120A127VAL00.0030.00915.241-0.044-0.0440.0000.0000.0000.000
121A128SER00.0050.00714.3680.0190.0190.0000.0000.0000.000
122A129SER00.040-0.00116.5140.0070.0070.0000.0000.0000.000
123A130PHE00.0350.02617.7330.0100.0100.0000.0000.0000.000
124A131ASP-1-0.817-0.91020.540-0.078-0.0780.0000.0000.0000.000
125A132PRO00.023-0.00123.1910.0030.0030.0000.0000.0000.000
126A133LEU00.0110.00524.1540.0100.0100.0000.0000.0000.000
127A134ALA00.0050.01324.0240.0070.0070.0000.0000.0000.000
128A135LEU00.0150.00719.2750.0050.0050.0000.0000.0000.000
129A136LEU0-0.0180.00223.0430.0120.0120.0000.0000.0000.000
130A137ALA0-0.062-0.03126.0140.0090.0090.0000.0000.0000.000
131A138LEU00.010-0.00221.4130.0060.0060.0000.0000.0000.000
132A139ARG10.8140.92218.5060.0100.0100.0000.0000.0000.000
133A140LYS10.9300.96224.1700.0280.0280.0000.0000.0000.000
134A141ALA0-0.061-0.03627.4270.0060.0060.0000.0000.0000.000
135A142ALA0-0.006-0.00423.8430.0020.0020.0000.0000.0000.000
136A143PRO0-0.026-0.02223.173-0.002-0.0020.0000.0000.0000.000
137A144GLY0-0.014-0.00321.3660.0110.0110.0000.0000.0000.000
138A145LEU0-0.0090.02018.5120.0030.0030.0000.0000.0000.000
139A146PRO00.0180.00714.3540.0030.0030.0000.0000.0000.000
140A147LEU0-0.022-0.01616.282-0.040-0.0400.0000.0000.0000.000
141A148GLY00.0210.01113.9760.0240.0240.0000.0000.0000.000
142A149PHE0-0.023-0.02414.890-0.009-0.0090.0000.0000.0000.000
143A150LEU0-0.0150.01014.057-0.010-0.0100.0000.0000.0000.000
144A151MET0-0.059-0.01515.6980.0430.0430.0000.0000.0000.000
145A152ALA00.0240.00316.616-0.027-0.0270.0000.0000.0000.000
146A153GLU-1-0.952-0.96919.155-0.099-0.0990.0000.0000.0000.000
147A154ASP-1-0.832-0.90418.984-0.059-0.0590.0000.0000.0000.000
148A155HIS00.0410.02219.9810.0240.0240.0000.0000.0000.000
149A156SER00.030-0.03418.2600.0080.0080.0000.0000.0000.000
150A157ALA0-0.046-0.02120.0810.0150.0150.0000.0000.0000.000
151A158LEU00.015-0.00222.4770.0090.0090.0000.0000.0000.000
152A159LEU00.0130.01616.8650.0060.0060.0000.0000.0000.000
153A160PRO0-0.106-0.06220.6520.0110.0110.0000.0000.0000.000
154A161CYS0-0.043-0.02023.0460.0070.0070.0000.0000.0000.000
155A162LEU0-0.0100.01720.591-0.007-0.0070.0000.0000.0000.000
156A163GLY0-0.021-0.00521.3670.0150.0150.0000.0000.0000.000
157A164VAL0-0.036-0.02916.574-0.016-0.0160.0000.0000.0000.000
158A165GLU-1-0.769-0.87713.3760.0460.0460.0000.0000.0000.000
159A166ALA00.0120.00110.7880.0520.0520.0000.0000.0000.000
160A167VAL0-0.0100.00711.588-0.008-0.0080.0000.0000.0000.000
161A168HIS0-0.002-0.01510.872-0.041-0.0410.0000.0000.0000.000
162A169PRO00.0080.01810.4170.0140.0140.0000.0000.0000.000
163A170HIS00.1340.07211.909-0.074-0.0740.0000.0000.0000.000
164A171HIS0-0.004-0.04411.3390.0290.0290.0000.0000.0000.000
165A172ALA0-0.030-0.01512.5730.0360.0360.0000.0000.0000.000
166A173LEU0-0.063-0.02715.1220.0350.0350.0000.0000.0000.000
167A174VAL0-0.046-0.0029.9010.0360.0360.0000.0000.0000.000
168A175THR00.0630.02313.2930.0000.0000.0000.0000.0000.000
169A176GLU-1-0.902-0.96013.6840.1620.1620.0000.0000.0000.000
170A177GLU-1-0.956-0.98714.7300.0520.0520.0000.0000.0000.000
171A178ALA00.0250.02514.9260.0170.0170.0000.0000.0000.000
172A179VAL00.0120.0039.9110.0100.0100.0000.0000.0000.000
173A180ALA00.0070.01012.6890.0550.0550.0000.0000.0000.000
174A181GLY0-0.020-0.01115.0880.0210.0210.0000.0000.0000.000
175A182TRP00.012-0.02611.5810.0070.0070.0000.0000.0000.000
176A183ARG10.8090.8846.367-0.588-0.5880.0000.0000.0000.000
177A184LYS10.9190.98113.397-0.109-0.1090.0000.0000.0000.000
178A185ARG10.8720.93916.264-0.093-0.0930.0000.0000.0000.000
179A186GLY0-0.011-0.00214.013-0.014-0.0140.0000.0000.0000.000
180A187LEU0-0.063-0.01612.8000.0100.0100.0000.0000.0000.000
181A188PHE00.0010.0054.8570.1170.1170.0000.0000.0000.000
182A189VAL00.004-0.0067.528-0.133-0.1330.0000.0000.0000.000
183A190VAL0-0.022-0.0106.090-0.167-0.1670.0000.0000.0000.000
184A191ALA00.0220.0216.6630.1600.1600.0000.0000.0000.000
185A192TRP0-0.059-0.0178.442-0.190-0.1900.0000.0000.0000.000
186A193THR00.0140.01011.1380.0890.0890.0000.0000.0000.000
187A194VAL00.0090.0018.7260.0800.0800.0000.0000.0000.000
188A195ASN00.0040.00310.968-0.163-0.1630.0000.0000.0000.000
189A196GLU-1-0.916-0.96112.658-0.268-0.2680.0000.0000.0000.000
190A197GLU-1-0.864-0.94310.940-0.372-0.3720.0000.0000.0000.000
191A198GLY0-0.003-0.00710.6830.0010.0010.0000.0000.0000.000
192A199GLU-1-0.705-0.84111.112-0.268-0.2680.0000.0000.0000.000
193A200ALA00.011-0.0027.230-0.008-0.0080.0000.0000.0000.000
194A201ARG10.8900.9416.5730.2510.2510.0000.0000.0000.000
195A202ARG10.7690.8788.2660.2920.2920.0000.0000.0000.000
196A203LEU00.000-0.0077.1240.0670.0670.0000.0000.0000.000
197A204LEU00.0260.0041.9942.075-2.2238.105-1.165-2.641-0.005
198A205ALA0-0.049-0.0054.8260.2200.283-0.001-0.005-0.0570.000
199A206LEU0-0.043-0.0217.9390.0950.0950.0000.0000.0000.000
200A207GLY0-0.014-0.0035.8640.0570.0570.0000.0000.0000.000
201A208LEU0-0.046-0.0214.7170.0710.254-0.001-0.044-0.1390.000
202A209ASP-1-0.763-0.8572.516-2.0040.1181.293-1.405-2.010-0.018
203A210GLY0-0.009-0.0032.431-3.149-0.9551.744-1.858-2.080-0.015
204A211LEU0-0.041-0.0153.2001.1321.059-0.0050.510-0.4320.000
205A212ILE00.0210.0215.362-0.178-0.205-0.001-0.0010.0290.000
206A213GLY00.026-0.0048.8570.1470.1470.0000.0000.0000.000
207A214ASP-1-0.782-0.90011.144-0.523-0.5230.0000.0000.0000.000
208A215ARG10.8640.94112.7840.4640.4640.0000.0000.0000.000
209A216PRO00.0560.01711.048-0.088-0.0880.0000.0000.0000.000
210A217GLU-1-0.862-0.94710.478-0.666-0.6660.0000.0000.0000.000
211A218VAL0-0.041-0.0119.3060.0100.0100.0000.0000.0000.000
212A219LEU0-0.003-0.0096.374-0.069-0.0690.0000.0000.0000.000
213A220LEU0-0.027-0.0055.886-0.461-0.4610.0000.0000.0000.000
214A221PRO0-0.038-0.0157.473-0.134-0.1340.0000.0000.0000.000
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