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: JLQ79

Calculation Name: 1V5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V5X

Chain ID: A

ChEMBL ID:

UniProt ID: P83825

Base Structure: X-ray

Registration Date: 2023-06-22

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 200
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2195174.231935
FMO2-HF: Nuclear repulsion 2120747.900601
FMO2-HF: Total energy -74426.331335
FMO2-MP2: Total energy -74648.050259


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-13.08-3.80212.219-5.274-16.225-0.041
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / 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].
3A3VAL00.0060.0002.665-4.092-0.4400.848-1.909-2.592-0.013
4A4LYS10.7400.8204.8060.2280.302-0.001-0.009-0.0640.000
5A5ILE00.0030.0008.316-0.158-0.1580.0000.0000.0000.000
6A6CYM-1-0.769-0.79811.0120.1000.1000.0000.0000.0000.000
7A7GLY0-0.006-0.04013.902-0.051-0.0510.0000.0000.0000.000
8A8ILE0-0.043-0.02014.744-0.035-0.0350.0000.0000.0000.000
9A9THR0-0.017-0.02518.3310.0260.0260.0000.0000.0000.000
10A10ARG10.7920.85721.1210.1790.1790.0000.0000.0000.000
11A11LEU00.0530.02120.903-0.012-0.0120.0000.0000.0000.000
12A12GLU-1-0.848-0.90620.960-0.173-0.1730.0000.0000.0000.000
13A13ASP-1-0.765-0.86817.546-0.218-0.2180.0000.0000.0000.000
14A14ALA00.0010.00416.523-0.043-0.0430.0000.0000.0000.000
15A15LEU00.0470.02216.306-0.022-0.0220.0000.0000.0000.000
16A16LEU0-0.063-0.01515.651-0.023-0.0230.0000.0000.0000.000
17A17ALA00.0280.00412.362-0.072-0.0720.0000.0000.0000.000
18A18GLU-1-0.826-0.91712.372-0.099-0.0990.0000.0000.0000.000
19A19ALA0-0.052-0.03013.278-0.007-0.0070.0000.0000.0000.000
20A20LEU0-0.084-0.04211.1860.0060.0060.0000.0000.0000.000
21A21GLY0-0.0030.0148.594-0.193-0.1930.0000.0000.0000.000
22A22ALA0-0.043-0.0227.956-0.235-0.2350.0000.0000.0000.000
23A23PHE00.0280.0045.0070.4630.4630.0000.0000.0000.000
24A24ALA0-0.031-0.0149.3300.1750.1750.0000.0000.0000.000
25A25LEU00.0180.00810.971-0.145-0.1450.0000.0000.0000.000
26A26GLY00.0110.01013.7600.0620.0620.0000.0000.0000.000
27A27PHE00.0100.00415.504-0.048-0.0480.0000.0000.0000.000
28A28VAL0-0.013-0.01018.8750.0210.0210.0000.0000.0000.000
29A29LEU00.0510.03821.037-0.015-0.0150.0000.0000.0000.000
30A30ALA00.0230.02123.567-0.004-0.0040.0000.0000.0000.000
31A31PRO0-0.008-0.01425.250-0.014-0.0140.0000.0000.0000.000
32A32GLY00.0090.00927.6170.0020.0020.0000.0000.0000.000
33A33SER0-0.0060.00621.836-0.014-0.0140.0000.0000.0000.000
34A34ARG10.8580.90721.0910.1100.1100.0000.0000.0000.000
35A35ARG10.7320.83718.3820.1320.1320.0000.0000.0000.000
36A36ARG10.8700.96021.998-0.006-0.0060.0000.0000.0000.000
37A37ILE0-0.0080.00522.020-0.010-0.0100.0000.0000.0000.000
38A38ALA0-0.0050.00124.9860.0100.0100.0000.0000.0000.000
39A39PRO00.0520.02026.225-0.002-0.0020.0000.0000.0000.000
40A40GLU-1-0.808-0.92526.8310.0230.0230.0000.0000.0000.000
41A41ALA0-0.021-0.00426.859-0.002-0.0020.0000.0000.0000.000
42A42ALA0-0.006-0.01022.592-0.006-0.0060.0000.0000.0000.000
43A43ARG10.8530.92623.264-0.050-0.0500.0000.0000.0000.000
44A44ALA0-0.022-0.01225.5210.0020.0020.0000.0000.0000.000
45A45ILE0-0.039-0.02320.637-0.007-0.0070.0000.0000.0000.000
46A46GLY00.0150.00421.436-0.002-0.0020.0000.0000.0000.000
47A47GLU-1-0.863-0.91522.4930.0580.0580.0000.0000.0000.000
48A48ALA0-0.040-0.01624.1510.0000.0000.0000.0000.0000.000
49A49LEU0-0.0410.00117.487-0.015-0.0150.0000.0000.0000.000
50A50GLY00.0470.02018.9980.0200.0200.0000.0000.0000.000
51A51PRO0-0.033-0.02619.3780.0080.0080.0000.0000.0000.000
52A52PHE0-0.062-0.03814.9160.0390.0390.0000.0000.0000.000
53A53VAL00.0390.04112.6710.0360.0360.0000.0000.0000.000
54A54VAL0-0.041-0.02512.8930.0040.0040.0000.0000.0000.000
55A55ARG10.8320.90714.408-0.147-0.1470.0000.0000.0000.000
56A56VAL00.000-0.00413.3340.0340.0340.0000.0000.0000.000
57A57GLY00.0550.02416.661-0.045-0.0450.0000.0000.0000.000
58A58VAL0-0.053-0.03316.7630.0260.0260.0000.0000.0000.000
59A59PHE00.019-0.00719.620-0.025-0.0250.0000.0000.0000.000
60A60ARG10.8450.91021.946-0.037-0.0370.0000.0000.0000.000
61A61ASP-1-0.843-0.92324.5170.0460.0460.0000.0000.0000.000
62A62GLN0-0.025-0.01826.052-0.003-0.0030.0000.0000.0000.000
63A63PRO00.0330.02828.0730.0100.0100.0000.0000.0000.000
64A64PRO00.0340.00328.4690.0020.0020.0000.0000.0000.000
65A65GLU-1-0.874-0.94329.5460.0810.0810.0000.0000.0000.000
66A66GLU-1-0.896-0.93830.0030.0510.0510.0000.0000.0000.000
67A67VAL0-0.014-0.00624.4010.0010.0010.0000.0000.0000.000
68A68LEU0-0.005-0.00226.5630.0070.0070.0000.0000.0000.000
69A69ARG10.8600.92728.239-0.057-0.0570.0000.0000.0000.000
70A70LEU0-0.005-0.00726.785-0.003-0.0030.0000.0000.0000.000
71A71MET0-0.044-0.00220.780-0.007-0.0070.0000.0000.0000.000
72A72GLU-1-0.839-0.88825.3200.0900.0900.0000.0000.0000.000
73A73GLU-1-0.868-0.92328.1040.0500.0500.0000.0000.0000.000
74A74ALA0-0.022-0.01824.458-0.007-0.0070.0000.0000.0000.000
75A75ARG10.7330.84124.592-0.095-0.0950.0000.0000.0000.000
76A76LEU0-0.0230.00920.2350.0040.0040.0000.0000.0000.000
77A77GLN00.019-0.00418.3100.0050.0050.0000.0000.0000.000
78A78VAL0-0.021-0.01515.0170.0350.0350.0000.0000.0000.000
79A79ALA00.0490.03418.306-0.036-0.0360.0000.0000.0000.000
80A80GLN0-0.029-0.03714.3320.0700.0700.0000.0000.0000.000
81A81LEU00.0210.01917.865-0.038-0.0380.0000.0000.0000.000
82A82HIS00.025-0.00815.4160.0400.0400.0000.0000.0000.000
83A83GLY0-0.032-0.01820.078-0.026-0.0260.0000.0000.0000.000
84A84GLU-1-0.939-0.95622.4750.1030.1030.0000.0000.0000.000
85A85GLU-1-0.724-0.86623.0290.1070.1070.0000.0000.0000.000
86A86PRO00.0270.04024.9910.0110.0110.0000.0000.0000.000
87A87PRO00.0400.01424.8940.0110.0110.0000.0000.0000.000
88A88GLU-1-0.851-0.94425.9330.1250.1250.0000.0000.0000.000
89A89TRP0-0.025-0.02427.0010.0010.0010.0000.0000.0000.000
90A90ALA00.0090.01222.1660.0050.0050.0000.0000.0000.000
91A91GLU-1-0.819-0.90723.8840.2130.2130.0000.0000.0000.000
92A92ALA0-0.061-0.02225.9690.0040.0040.0000.0000.0000.000
93A93VAL0-0.002-0.01522.877-0.001-0.0010.0000.0000.0000.000
94A94GLY00.0370.00022.5030.0100.0100.0000.0000.0000.000
95A95ARG10.7570.87423.438-0.146-0.1460.0000.0000.0000.000
96A96PHE0-0.053-0.01825.249-0.009-0.0090.0000.0000.0000.000
97A97TYR00.0070.00821.1780.0040.0040.0000.0000.0000.000
98A98PRO0-0.031-0.00917.0180.0070.0070.0000.0000.0000.000
99A99VAL00.0250.03217.931-0.018-0.0180.0000.0000.0000.000
100A100ILE0-0.046-0.02812.2320.0670.0670.0000.0000.0000.000
101A101LYS10.8280.91215.716-0.184-0.1840.0000.0000.0000.000
102A102ALA0-0.027-0.00515.6920.0390.0390.0000.0000.0000.000
103A103PHE00.0230.00516.270-0.015-0.0150.0000.0000.0000.000
104A104PRO0-0.0180.01116.8360.0000.0000.0000.0000.0000.000
105A105LEU0-0.006-0.01613.8830.0000.0000.0000.0000.0000.000
106A106GLU-1-0.877-0.93718.109-0.042-0.0420.0000.0000.0000.000
107A107GLY00.006-0.00219.778-0.008-0.0080.0000.0000.0000.000
108A108PRO0-0.047-0.02017.8670.0010.0010.0000.0000.0000.000
109A109ALA00.0270.00915.2510.0130.0130.0000.0000.0000.000
110A110ARG10.9350.97517.339-0.045-0.0450.0000.0000.0000.000
111A111PRO00.005-0.00717.7090.0190.0190.0000.0000.0000.000
112A112GLU-1-0.895-0.94018.6830.1100.1100.0000.0000.0000.000
113A113TRP00.0310.00717.1390.0040.0040.0000.0000.0000.000
114A114ALA0-0.036-0.02116.5340.0340.0340.0000.0000.0000.000
115A115ASP-1-0.879-0.93317.4840.2000.2000.0000.0000.0000.000
116A116TYR0-0.030-0.03019.443-0.001-0.0010.0000.0000.0000.000
117A117PRO00.0160.01419.5290.0370.0370.0000.0000.0000.000
118A118ALA0-0.011-0.00317.154-0.005-0.0050.0000.0000.0000.000
119A119GLN00.001-0.00515.3700.0750.0750.0000.0000.0000.000
120A120ALA0-0.055-0.03310.9890.1070.1070.0000.0000.0000.000
121A121LEU00.0140.01911.860-0.091-0.0910.0000.0000.0000.000
122A122LEU0-0.009-0.00111.3690.0980.0980.0000.0000.0000.000
123A123LEU00.0320.01310.993-0.094-0.0940.0000.0000.0000.000
124A124ASP-1-0.727-0.87112.447-0.062-0.0620.0000.0000.0000.000
125A125GLY00.0330.00714.886-0.010-0.0100.0000.0000.0000.000
126A126LYS10.7860.88417.3690.0450.0450.0000.0000.0000.000
127A127ARG10.8650.91820.6490.1090.1090.0000.0000.0000.000
128A128PRO00.0720.06518.871-0.019-0.0190.0000.0000.0000.000
129A129GLY00.0270.02117.188-0.009-0.0090.0000.0000.0000.000
130A130SER0-0.045-0.04318.225-0.025-0.0250.0000.0000.0000.000
131A131GLY00.0350.00017.444-0.009-0.0090.0000.0000.0000.000
132A132GLU-1-0.883-0.90917.136-0.176-0.1760.0000.0000.0000.000
133A133ALA00.0140.01314.9070.0060.0060.0000.0000.0000.000
134A134TYR0-0.046-0.03711.3720.0140.0140.0000.0000.0000.000
135A135PRO0-0.0020.00914.386-0.047-0.0470.0000.0000.0000.000
136A136ARG10.9070.9229.7500.5450.5450.0000.0000.0000.000
137A137ALA0-0.013-0.00311.7080.0020.0020.0000.0000.0000.000
138A138TRP00.015-0.00114.2710.0230.0230.0000.0000.0000.000
139A139ALA00.1040.05610.2490.0370.0370.0000.0000.0000.000
140A140LYS10.9200.96511.4230.2910.2910.0000.0000.0000.000
141A141PRO0-0.010-0.00213.1190.0240.0240.0000.0000.0000.000
142A142LEU00.0490.03812.8880.0180.0180.0000.0000.0000.000
143A143LEU00.0050.0047.1150.0470.0470.0000.0000.0000.000
144A144ALA0-0.032-0.01610.7870.0290.0290.0000.0000.0000.000
145A145THR0-0.036-0.03213.7380.0270.0270.0000.0000.0000.000
146A146GLY0-0.0040.00511.4910.0220.0220.0000.0000.0000.000
147A147ARG10.7870.89511.733-0.274-0.2740.0000.0000.0000.000
148A148ARG10.9350.9678.976-0.886-0.8860.0000.0000.0000.000
149A149VAL00.0160.0147.990-0.005-0.0050.0000.0000.0000.000
150A150ILE0-0.024-0.0176.7760.4380.4380.0000.0000.0000.000
151A151LEU0-0.021-0.0035.776-0.427-0.4270.0000.0000.0000.000
152A152ALA00.0740.0238.1130.0470.0470.0000.0000.0000.000
153A153GLY00.0270.01410.782-0.058-0.0580.0000.0000.0000.000
154A154GLY00.003-0.00312.713-0.042-0.0420.0000.0000.0000.000
155A155ILE0-0.058-0.0136.641-0.069-0.0690.0000.0000.0000.000
156A156ALA00.0170.00610.0350.0430.0430.0000.0000.0000.000
157A157PRO00.0240.0189.490-0.155-0.1550.0000.0000.0000.000
158A158GLU-1-0.856-0.92610.541-0.734-0.7340.0000.0000.0000.000
159A159ASN00.0260.01410.576-0.096-0.0960.0000.0000.0000.000
160A160LEU00.0250.0184.765-0.122-0.049-0.001-0.001-0.0710.000
161A161GLU-1-0.805-0.8946.352-1.198-1.1980.0000.0000.0000.000
162A162GLU-1-0.891-0.9277.713-0.609-0.6090.0000.0000.0000.000
163A163VAL00.006-0.0174.9400.0730.0730.0000.0000.0000.000
164A164LEU0-0.0120.0042.539-2.088-0.8121.751-0.612-2.415-0.001
165A165ALA00.0070.0043.717-0.0270.1310.0000.035-0.1940.000
166A166LEU0-0.087-0.0475.6950.2490.2490.0000.0000.0000.000
167A167ARG10.8800.9562.4920.3590.7930.756-0.389-0.8010.000
168A168PRO00.0330.0332.364-0.940-0.3282.251-0.337-2.525-0.001
169A169TYR0-0.006-0.0052.559-3.340-1.1880.940-1.397-1.695-0.020
170A170ALA0-0.009-0.0152.9940.9811.3591.858-0.884-1.3510.000
171A171LEU00.0180.0102.462-1.439-1.7083.2200.509-3.460-0.005
172A172ASP-1-0.780-0.8974.787-0.484-0.4570.000-0.016-0.0120.000
173A173LEU0-0.0080.0016.490-0.104-0.1040.0000.0000.0000.000
174A174ALA00.0440.01510.0340.0480.0480.0000.0000.0000.000
175A175SER0-0.001-0.02413.710-0.042-0.0420.0000.0000.0000.000
176A176GLY0-0.0130.00212.4570.0060.0060.0000.0000.0000.000
177A177VAL0-0.006-0.02111.143-0.057-0.0570.0000.0000.0000.000
178A178GLU-1-0.718-0.79514.009-0.169-0.1690.0000.0000.0000.000
179A179GLU-1-0.863-0.91017.416-0.274-0.2740.0000.0000.0000.000
180A180ALA00.0090.00720.9320.0210.0210.0000.0000.0000.000
181A181PRO0-0.076-0.03020.442-0.012-0.0120.0000.0000.0000.000
182A182GLY00.0430.01619.7500.0200.0200.0000.0000.0000.000
183A183VAL0-0.0230.00820.5790.0060.0060.0000.0000.0000.000
184A184LYS10.7900.86415.1090.1960.1960.0000.0000.0000.000
185A185SER0-0.012-0.01517.2430.0100.0100.0000.0000.0000.000
186A186ALA00.021-0.00916.586-0.061-0.0610.0000.0000.0000.000
187A187GLU-1-0.933-0.96316.826-0.523-0.5230.0000.0000.0000.000
188A188LYS10.9690.98514.4900.3340.3340.0000.0000.0000.000
189A189LEU00.0100.00311.505-0.144-0.1440.0000.0000.0000.000
190A190ARG10.9610.98211.6370.2560.2560.0000.0000.0000.000
191A191ALA00.0150.01412.213-0.106-0.1060.0000.0000.0000.000
192A192LEU0-0.017-0.0067.156-0.118-0.1180.0000.0000.0000.000
193A193PHE00.0480.0096.880-0.429-0.4290.0000.0000.0000.000
194A194ALA0-0.0060.0088.165-0.105-0.1050.0000.0000.0000.000
195A195ARG10.7470.8458.8541.0401.0400.0000.0000.0000.000
196A196LEU0-0.006-0.0092.392-0.948-0.2370.597-0.264-1.045-0.001
197A197ALA0-0.0030.0075.5690.0060.0060.0000.0000.0000.000
198A198SER0-0.004-0.0037.4430.3390.3390.0000.0000.0000.000
199A199LEU0-0.080-0.0286.6410.2350.2350.0000.0000.0000.000
200A200ARG10.8690.9425.6320.7130.7130.0000.0000.0000.000