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: 8594Y

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 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 200
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2190119.014977
FMO2-HF: Nuclear repulsion 2115694.981568
FMO2-HF: Total energy -74424.033409
FMO2-MP2: Total energy -74646.030775


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.
-10.522-3.91715.33-5.512-16.418-0.044
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 : -0.026 / q_NPA : -0.004
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].
3A3VAL00.0340.0232.765-3.517-0.2040.458-1.631-2.139-0.008
4A4LYS10.8050.8914.8030.4870.578-0.001-0.010-0.0790.000
5A5ILE00.0000.0068.243-0.140-0.1400.0000.0000.0000.000
6A6CYM-1-0.780-0.83010.9680.0090.0090.0000.0000.0000.000
7A7GLY0-0.037-0.06213.689-0.045-0.0450.0000.0000.0000.000
8A8ILE0-0.038-0.01715.065-0.022-0.0220.0000.0000.0000.000
9A9THR0-0.021-0.01518.3150.0260.0260.0000.0000.0000.000
10A10ARG10.8710.93121.1110.1990.1990.0000.0000.0000.000
11A11LEU00.0550.02420.986-0.016-0.0160.0000.0000.0000.000
12A12GLU-1-0.899-0.95821.042-0.186-0.1860.0000.0000.0000.000
13A13ASP-1-0.792-0.90017.657-0.259-0.2590.0000.0000.0000.000
14A14ALA0-0.020-0.00816.728-0.042-0.0420.0000.0000.0000.000
15A15LEU00.0520.02116.532-0.015-0.0150.0000.0000.0000.000
16A16LEU0-0.0420.00715.472-0.012-0.0120.0000.0000.0000.000
17A17ALA00.016-0.00212.508-0.062-0.0620.0000.0000.0000.000
18A18GLU-1-0.856-0.92511.976-0.075-0.0750.0000.0000.0000.000
19A19ALA0-0.022-0.01412.6050.0120.0120.0000.0000.0000.000
20A20LEU0-0.106-0.05810.6700.0220.0220.0000.0000.0000.000
21A21GLY00.0040.0178.231-0.173-0.1730.0000.0000.0000.000
22A22ALA0-0.057-0.0177.404-0.160-0.1600.0000.0000.0000.000
23A23PHE00.004-0.0085.0310.4990.4990.0000.0000.0000.000
24A24ALA0-0.030-0.0169.3780.1620.1620.0000.0000.0000.000
25A25LEU00.0190.01410.928-0.166-0.1660.0000.0000.0000.000
26A26GLY0-0.008-0.00513.5750.0720.0720.0000.0000.0000.000
27A27PHE00.0220.00915.309-0.044-0.0440.0000.0000.0000.000
28A28VAL0-0.029-0.01818.8050.0210.0210.0000.0000.0000.000
29A29LEU00.0160.00420.792-0.008-0.0080.0000.0000.0000.000
30A30ALA00.0320.02623.4210.0050.0050.0000.0000.0000.000
31A31PRO0-0.048-0.07225.045-0.017-0.0170.0000.0000.0000.000
32A32GLY00.0500.03028.1590.0020.0020.0000.0000.0000.000
33A33SER0-0.0130.00321.699-0.016-0.0160.0000.0000.0000.000
34A34ARG10.8960.93621.1360.1770.1770.0000.0000.0000.000
35A35ARG10.7840.86918.2440.2180.2180.0000.0000.0000.000
36A36ARG10.9091.00621.9280.0300.0300.0000.0000.0000.000
37A37ILE00.0240.01522.283-0.010-0.0100.0000.0000.0000.000
38A38ALA0-0.0310.00025.2010.0090.0090.0000.0000.0000.000
39A39PRO00.0660.03626.199-0.003-0.0030.0000.0000.0000.000
40A40GLU-1-0.799-0.92926.8550.0100.0100.0000.0000.0000.000
41A41ALA0-0.033-0.01226.6630.0000.0000.0000.0000.0000.000
42A42ALA0-0.012-0.01822.534-0.003-0.0030.0000.0000.0000.000
43A43ARG10.9250.98923.310-0.046-0.0460.0000.0000.0000.000
44A44ALA0-0.0060.00425.6900.0050.0050.0000.0000.0000.000
45A45ILE0-0.046-0.03420.901-0.002-0.0020.0000.0000.0000.000
46A46GLY00.0170.01421.5620.0010.0010.0000.0000.0000.000
47A47GLU-1-0.955-0.97922.6140.0480.0480.0000.0000.0000.000
48A48ALA0-0.044-0.01823.6120.0030.0030.0000.0000.0000.000
49A49LEU0-0.073-0.02117.792-0.010-0.0100.0000.0000.0000.000
50A50GLY00.0270.01518.6890.0170.0170.0000.0000.0000.000
51A51PRO0-0.047-0.04818.7810.0050.0050.0000.0000.0000.000
52A52PHE0-0.096-0.04714.4000.0410.0410.0000.0000.0000.000
53A53VAL00.0690.04812.7890.0280.0280.0000.0000.0000.000
54A54VAL0-0.040-0.01912.920-0.002-0.0020.0000.0000.0000.000
55A55ARG10.8900.94814.301-0.184-0.1840.0000.0000.0000.000
56A56VAL0-0.003-0.01513.1930.0350.0350.0000.0000.0000.000
57A57GLY00.0520.02316.425-0.045-0.0450.0000.0000.0000.000
58A58VAL0-0.038-0.02016.8510.0200.0200.0000.0000.0000.000
59A59PHE00.0410.00919.541-0.016-0.0160.0000.0000.0000.000
60A60ARG10.8800.91621.3930.0310.0310.0000.0000.0000.000
61A61ASP-1-0.887-0.94424.5730.0040.0040.0000.0000.0000.000
62A62GLN0-0.005-0.00326.253-0.006-0.0060.0000.0000.0000.000
63A63PRO00.0530.02728.1750.0090.0090.0000.0000.0000.000
64A64PRO00.0550.01528.3840.0010.0010.0000.0000.0000.000
65A65GLU-1-0.945-0.97029.4660.0530.0530.0000.0000.0000.000
66A66GLU-1-0.917-0.95929.3400.0290.0290.0000.0000.0000.000
67A67VAL0-0.008-0.00424.3110.0030.0030.0000.0000.0000.000
68A68LEU0-0.0170.00226.3820.0050.0050.0000.0000.0000.000
69A69ARG10.9851.00228.039-0.048-0.0480.0000.0000.0000.000
70A70LEU00.0230.01026.626-0.003-0.0030.0000.0000.0000.000
71A71MET0-0.085-0.02820.843-0.008-0.0080.0000.0000.0000.000
72A72GLU-1-0.950-0.95625.1730.0890.0890.0000.0000.0000.000
73A73GLU-1-0.970-0.98927.9140.0310.0310.0000.0000.0000.000
74A74ALA0-0.017-0.02424.235-0.005-0.0050.0000.0000.0000.000
75A75ARG10.8300.91424.420-0.086-0.0860.0000.0000.0000.000
76A76LEU0-0.017-0.00319.8230.0070.0070.0000.0000.0000.000
77A77GLN00.027-0.00217.9950.0200.0200.0000.0000.0000.000
78A78VAL0-0.001-0.00115.1340.0320.0320.0000.0000.0000.000
79A79ALA00.0520.03618.074-0.040-0.0400.0000.0000.0000.000
80A80GLN0-0.029-0.03914.1590.0540.0540.0000.0000.0000.000
81A81LEU00.0130.01217.905-0.033-0.0330.0000.0000.0000.000
82A82HIS00.036-0.01915.5530.0220.0220.0000.0000.0000.000
83A83GLY0-0.078-0.02120.247-0.020-0.0200.0000.0000.0000.000
84A84GLU-1-0.982-0.97423.2570.0230.0230.0000.0000.0000.000
85A85GLU-1-0.766-0.89723.7780.0540.0540.0000.0000.0000.000
86A86PRO00.0200.02325.4940.0060.0060.0000.0000.0000.000
87A87PRO00.0600.02725.1240.0100.0100.0000.0000.0000.000
88A88GLU-1-0.819-0.92926.1580.0930.0930.0000.0000.0000.000
89A89TRP0-0.006-0.00927.4660.0050.0050.0000.0000.0000.000
90A90ALA00.0040.00522.6260.0070.0070.0000.0000.0000.000
91A91GLU-1-0.890-0.95924.0600.1920.1920.0000.0000.0000.000
92A92ALA0-0.047-0.02326.1280.0080.0080.0000.0000.0000.000
93A93VAL00.014-0.00723.2840.0030.0030.0000.0000.0000.000
94A94GLY00.004-0.00122.5870.0120.0120.0000.0000.0000.000
95A95ARG10.8430.94023.485-0.129-0.1290.0000.0000.0000.000
96A96PHE0-0.083-0.04525.348-0.003-0.0030.0000.0000.0000.000
97A97TYR00.000-0.00321.0020.0080.0080.0000.0000.0000.000
98A98PRO0-0.0220.00517.056-0.001-0.0010.0000.0000.0000.000
99A99VAL00.0560.03318.341-0.020-0.0200.0000.0000.0000.000
100A100ILE0-0.038-0.01812.1340.0550.0550.0000.0000.0000.000
101A101LYS10.9010.96915.826-0.118-0.1180.0000.0000.0000.000
102A102ALA0-0.028-0.00715.9990.0210.0210.0000.0000.0000.000
103A103PHE00.023-0.00116.6400.0020.0020.0000.0000.0000.000
104A104PRO00.0100.02116.925-0.017-0.0170.0000.0000.0000.000
105A105LEU0-0.005-0.00714.0080.0090.0090.0000.0000.0000.000
106A106GLU-1-0.958-0.98718.307-0.113-0.1130.0000.0000.0000.000
107A107GLY00.032-0.02619.5570.0020.0020.0000.0000.0000.000
108A108PRO0-0.070-0.02218.126-0.013-0.0130.0000.0000.0000.000
109A109ALA00.0420.00616.0960.0150.0150.0000.0000.0000.000
110A110ARG10.9610.97618.0550.0280.0280.0000.0000.0000.000
111A111PRO00.014-0.00317.8810.0160.0160.0000.0000.0000.000
112A112GLU-1-0.876-0.92918.9610.0670.0670.0000.0000.0000.000
113A113TRP00.0570.03217.3640.0010.0010.0000.0000.0000.000
114A114ALA0-0.106-0.04816.1720.0300.0300.0000.0000.0000.000
115A115ASP-1-0.859-0.94117.4640.1470.1470.0000.0000.0000.000
116A116TYR0-0.090-0.05719.4590.0050.0050.0000.0000.0000.000
117A117PRO00.0030.00619.5400.0350.0350.0000.0000.0000.000
118A118ALA0-0.014-0.00417.180-0.007-0.0070.0000.0000.0000.000
119A119GLN0-0.032-0.02514.8470.0820.0820.0000.0000.0000.000
120A120ALA0-0.054-0.03311.0240.1230.1230.0000.0000.0000.000
121A121LEU00.0180.03512.273-0.081-0.0810.0000.0000.0000.000
122A122LEU0-0.003-0.01111.1150.0660.0660.0000.0000.0000.000
123A123LEU0-0.0020.00210.687-0.060-0.0600.0000.0000.0000.000
124A124ASP-1-0.826-0.93812.400-0.254-0.2540.0000.0000.0000.000
125A125GLY00.0560.02714.8740.0070.0070.0000.0000.0000.000
126A126LYS10.9210.97117.0220.1260.1260.0000.0000.0000.000
127A127ARG10.8910.93720.8240.1950.1950.0000.0000.0000.000
128A128PRO00.0590.05418.701-0.019-0.0190.0000.0000.0000.000
129A129GLY00.0400.02017.6460.0030.0030.0000.0000.0000.000
130A130SER0-0.071-0.05818.6300.0000.0000.0000.0000.0000.000
131A131GLY0-0.003-0.01216.966-0.001-0.0010.0000.0000.0000.000
132A132GLU-1-0.917-0.94117.802-0.277-0.2770.0000.0000.0000.000
133A133ALA00.0060.01314.5930.0000.0000.0000.0000.0000.000
134A134TYR0-0.038-0.02511.2480.0440.0440.0000.0000.0000.000
135A135PRO0-0.0110.01114.414-0.064-0.0640.0000.0000.0000.000
136A136ARG10.9670.9629.1380.7570.7570.0000.0000.0000.000
137A137ALA0-0.015-0.01911.4650.0000.0000.0000.0000.0000.000
138A138TRP00.0150.03313.9130.0300.0300.0000.0000.0000.000
139A139ALA00.0960.05010.4890.0420.0420.0000.0000.0000.000
140A140LYS10.8840.95111.9530.4020.4020.0000.0000.0000.000
141A141PRO0-0.0080.01213.2590.0310.0310.0000.0000.0000.000
142A142LEU00.0710.03813.0150.0250.0250.0000.0000.0000.000
143A143LEU00.0000.0157.4370.0500.0500.0000.0000.0000.000
144A144ALA0-0.032-0.01410.9120.0430.0430.0000.0000.0000.000
145A145THR0-0.049-0.05613.7280.0440.0440.0000.0000.0000.000
146A146GLY0-0.0010.01111.9310.0270.0270.0000.0000.0000.000
147A147ARG10.8680.96212.043-0.202-0.2020.0000.0000.0000.000
148A148ARG10.9250.9649.275-0.983-0.9830.0000.0000.0000.000
149A149VAL00.0370.0218.210-0.071-0.0710.0000.0000.0000.000
150A150ILE0-0.028-0.0166.9120.4380.4380.0000.0000.0000.000
151A151LEU00.0040.0035.491-0.332-0.3320.0000.0000.0000.000
152A152ALA00.059-0.0277.753-0.072-0.0720.0000.0000.0000.000
153A153GLY00.0480.01210.422-0.079-0.0790.0000.0000.0000.000
154A154GLY0-0.040-0.02112.627-0.049-0.0490.0000.0000.0000.000
155A155ILE0-0.0520.0636.802-0.048-0.0480.0000.0000.0000.000
156A156ALA00.0480.00010.0840.0570.0570.0000.0000.0000.000
157A157PRO00.0120.0039.493-0.184-0.1840.0000.0000.0000.000
158A158GLU-1-0.897-0.94810.530-0.719-0.7190.0000.0000.0000.000
159A159ASN00.0100.00010.766-0.112-0.1120.0000.0000.0000.000
160A160LEU0-0.0090.0115.645-0.074-0.0740.0000.0000.0000.000
161A161GLU-1-0.889-0.9616.969-1.120-1.1200.0000.0000.0000.000
162A162GLU-1-0.885-0.9248.170-0.723-0.7230.0000.0000.0000.000
163A163VAL00.016-0.0145.1850.0080.0080.0000.0000.0000.000
164A164LEU0-0.026-0.0102.394-1.659-0.9912.243-0.466-2.444-0.002
165A165ALA00.0080.0173.959-0.191-0.0130.000-0.003-0.1740.000
166A166LEU0-0.099-0.0585.8870.2040.2040.0000.0000.0000.000
167A167ARG10.9010.9712.6460.4720.9590.366-0.229-0.6240.000
168A168PRO00.0160.0212.228-0.835-0.3672.479-0.513-2.4330.000
169A169TYR0-0.014-0.0122.444-3.788-1.7181.784-1.655-2.199-0.024
170A170ALA0-0.011-0.0292.9821.4892.3002.240-1.270-1.780-0.003
171A171LEU0-0.0010.0032.109-0.491-2.7625.6390.445-3.813-0.006
172A172ASP-1-0.829-0.9264.422-0.541-0.494-0.001-0.012-0.0350.000
173A173LEU00.006-0.0086.138-0.118-0.1180.0000.0000.0000.000
174A174ALA00.0740.0149.7040.0970.0970.0000.0000.0000.000
175A175SER00.008-0.00313.442-0.011-0.0110.0000.0000.0000.000
176A176GLY0-0.0140.00512.6070.0190.0190.0000.0000.0000.000
177A177VAL0-0.024-0.01711.111-0.060-0.0600.0000.0000.0000.000
178A178GLU-1-0.735-0.84314.162-0.243-0.2430.0000.0000.0000.000
179A179GLU-1-0.945-0.95917.597-0.261-0.2610.0000.0000.0000.000
180A180ALA0-0.002-0.01320.8870.0210.0210.0000.0000.0000.000
181A181PRO0-0.079-0.03320.338-0.017-0.0170.0000.0000.0000.000
182A182GLY00.004-0.00619.6550.0260.0260.0000.0000.0000.000
183A183VAL0-0.0110.01620.7310.0140.0140.0000.0000.0000.000
184A184LYS10.8470.92015.1970.2610.2610.0000.0000.0000.000
185A185SER00.0350.04217.1680.0140.0140.0000.0000.0000.000
186A186ALA00.0680.00416.595-0.059-0.0590.0000.0000.0000.000
187A187GLU-1-0.961-0.97416.283-0.526-0.5260.0000.0000.0000.000
188A188LYS10.9520.96914.6630.3930.3930.0000.0000.0000.000
189A189LEU0-0.014-0.00512.015-0.136-0.1360.0000.0000.0000.000
190A190ARG10.9780.98011.3360.2100.2100.0000.0000.0000.000
191A191ALA00.0720.03611.973-0.090-0.0900.0000.0000.0000.000
192A192LEU00.0070.0037.088-0.118-0.1180.0000.0000.0000.000
193A193PHE00.029-0.0146.423-0.394-0.3940.0000.0000.0000.000
194A194ALA0-0.0230.0058.1240.0130.0130.0000.0000.0000.000
195A195ARG10.8230.9128.3541.1001.1000.0000.0000.0000.000
196A196LEU00.0140.0042.883-0.785-0.0420.123-0.168-0.698-0.001
197A197ALA00.0190.0275.7000.1560.1560.0000.0000.0000.000
198A198SER0-0.040-0.0206.9680.3540.3540.0000.0000.0000.000
199A199LEU0-0.114-0.0466.5630.2100.2100.0000.0000.0000.000
200A200ARG10.9410.9785.7650.2310.2310.0000.0000.0000.000