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: 9MYV2

Calculation Name: 1VI5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VI5

Chain ID: A

ChEMBL ID:

UniProt ID: O29132

Base Structure: X-ray

Registration Date: 2023-09-26

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2282290.766921
FMO2-HF: Nuclear repulsion 2205431.851693
FMO2-HF: Total energy -76858.915228
FMO2-MP2: Total energy -77086.42044


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
-51.904-47.9450.065-2.083-1.9410.014
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.992 / q_NPA : -1.007
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].
3A7GLU-1-0.891-0.9423.76923.67025.8170.034-1.055-1.1260.005
4A8TYR0-0.025-0.0025.401-0.825-0.8250.0000.0000.0000.000
5A9LEU0-0.053-0.0299.588-1.445-1.4450.0000.0000.0000.000
6A10VAL00.0090.00812.622-2.013-2.0130.0000.0000.0000.000
7A11PRO00.0440.03110.9122.2332.2330.0000.0000.0000.000
8A12PRO00.019-0.0068.148-1.219-1.2190.0000.0000.0000.000
9A13ASP-1-0.871-0.94211.20319.14519.1450.0000.0000.0000.000
10A14ASP-1-0.844-0.91914.39515.85315.8530.0000.0000.0000.000
11A15TYR0-0.048-0.06612.188-1.679-1.6790.0000.0000.0000.000
12A16LEU0-0.049-0.02912.620-0.972-0.9720.0000.0000.0000.000
13A17ALA00.003-0.00416.381-0.917-0.9170.0000.0000.0000.000
14A18ALA0-0.021-0.01118.929-0.827-0.8270.0000.0000.0000.000
15A19GLY0-0.006-0.00119.368-0.576-0.5760.0000.0000.0000.000
16A20VAL0-0.012-0.00616.162-0.360-0.3600.0000.0000.0000.000
17A21HIS00.0500.03215.6470.1360.1360.0000.0000.0000.000
18A22ILE0-0.087-0.03117.646-0.189-0.1890.0000.0000.0000.000
19A23GLY00.0580.03821.144-0.320-0.3200.0000.0000.0000.000
20A24THR00.013-0.00823.004-0.615-0.6150.0000.0000.0000.000
21A25GLN00.000-0.02425.7540.3080.3080.0000.0000.0000.000
22A26ILE0-0.0040.00627.797-0.118-0.1180.0000.0000.0000.000
23A27LYS10.9230.98721.276-13.877-13.8770.0000.0000.0000.000
24A28THR00.003-0.00225.861-0.235-0.2350.0000.0000.0000.000
25A29GLY00.005-0.00825.0840.4500.4500.0000.0000.0000.000
26A30ASP-1-0.814-0.88824.17712.56712.5670.0000.0000.0000.000
27A31MET00.0250.01220.7150.9790.9790.0000.0000.0000.000
28A32LYS10.9300.97420.226-13.955-13.9550.0000.0000.0000.000
29A33LYS10.8670.94117.216-15.235-15.2350.0000.0000.0000.000
30A34PHE00.0250.00015.4921.3451.3450.0000.0000.0000.000
31A35ILE0-0.041-0.00516.892-0.020-0.0200.0000.0000.0000.000
32A36PHE00.0140.02511.719-0.454-0.4540.0000.0000.0000.000
33A37LYS10.9290.97115.570-15.133-15.1330.0000.0000.0000.000
34A38VAL00.020-0.00418.248-0.216-0.2160.0000.0000.0000.000
35A39ARG10.8410.90020.468-12.602-12.6020.0000.0000.0000.000
36A40GLN00.0280.00622.550-0.558-0.5580.0000.0000.0000.000
37A41ASP-1-0.799-0.87024.99411.67011.6700.0000.0000.0000.000
38A42GLY00.0360.02726.306-0.279-0.2790.0000.0000.0000.000
39A43LEU0-0.057-0.01424.3110.0810.0810.0000.0000.0000.000
40A44TYR00.000-0.01721.7940.7150.7150.0000.0000.0000.000
41A45VAL0-0.028-0.00915.890-0.013-0.0130.0000.0000.0000.000
42A46LEU0-0.025-0.02117.3210.6460.6460.0000.0000.0000.000
43A47ASP-1-0.842-0.92811.08728.44228.4420.0000.0000.0000.000
44A48ILE00.0640.02411.0590.1380.1380.0000.0000.0000.000
45A49ARG10.8240.9293.157-63.773-61.9610.031-1.028-0.8150.009
46A50LYS10.8650.9209.647-29.174-29.1740.0000.0000.0000.000
47A51LEU0-0.0040.01012.293-0.896-0.8960.0000.0000.0000.000
48A52ASP-1-0.696-0.79510.44127.44327.4430.0000.0000.0000.000
49A53GLU-1-0.798-0.8958.12235.94235.9420.0000.0000.0000.000
50A54ARG10.8580.91411.796-19.836-19.8360.0000.0000.0000.000
51A55ILE00.0200.01615.284-1.334-1.3340.0000.0000.0000.000
52A56ARG10.8370.9029.425-31.655-31.6550.0000.0000.0000.000
53A57VAL0-0.040-0.01914.705-1.040-1.0400.0000.0000.0000.000
54A58ALA00.0150.00117.037-1.027-1.0270.0000.0000.0000.000
55A59ALA00.0310.01918.860-0.882-0.8820.0000.0000.0000.000
56A60LYS10.9630.98218.772-16.579-16.5790.0000.0000.0000.000
57A61PHE0-0.038-0.01320.614-0.568-0.5680.0000.0000.0000.000
58A62LEU00.0400.00922.757-0.605-0.6050.0000.0000.0000.000
59A63SER0-0.066-0.04523.497-0.486-0.4860.0000.0000.0000.000
60A64ARG10.8920.94624.212-12.802-12.8020.0000.0000.0000.000
61A65TYR0-0.0060.01727.236-0.129-0.1290.0000.0000.0000.000
62A66GLU-1-0.846-0.90830.4418.8448.8440.0000.0000.0000.000
63A67PRO0-0.005-0.01732.252-0.003-0.0030.0000.0000.0000.000
64A68SER00.0260.00733.3100.1780.1780.0000.0000.0000.000
65A69LYS10.8060.90234.099-8.840-8.8400.0000.0000.0000.000
66A70ILE0-0.016-0.00428.6360.2260.2260.0000.0000.0000.000
67A71LEU00.0050.01332.193-0.224-0.2240.0000.0000.0000.000
68A72LEU0-0.042-0.01828.5750.2850.2850.0000.0000.0000.000
69A73VAL0-0.034-0.02131.698-0.409-0.4090.0000.0000.0000.000
70A74ALA00.010-0.00731.8880.3910.3910.0000.0000.0000.000
71A75ALA00.0270.02233.681-0.253-0.2530.0000.0000.0000.000
72A76ARG10.7910.88929.459-10.929-10.9290.0000.0000.0000.000
73A77GLN00.0580.02233.7290.0360.0360.0000.0000.0000.000
74A78TYR0-0.029-0.02730.608-0.014-0.0140.0000.0000.0000.000
75A79ALA00.0200.01630.1240.2520.2520.0000.0000.0000.000
76A80HIS0-0.014-0.01031.0630.0300.0300.0000.0000.0000.000
77A81LYS10.8020.89932.048-9.639-9.6390.0000.0000.0000.000
78A82PRO00.0040.00827.6190.0420.0420.0000.0000.0000.000
79A83VAL00.0360.02329.5490.2180.2180.0000.0000.0000.000
80A84GLN00.0100.01931.0300.1860.1860.0000.0000.0000.000
81A85MET0-0.018-0.01230.383-0.115-0.1150.0000.0000.0000.000
82A86PHE00.016-0.00524.8420.2090.2090.0000.0000.0000.000
83A87SER00.000-0.00929.1610.0640.0640.0000.0000.0000.000
84A88LYS10.8670.94732.301-9.486-9.4860.0000.0000.0000.000
85A89VAL0-0.032-0.00227.468-0.116-0.1160.0000.0000.0000.000
86A90VAL0-0.015-0.00527.1300.0350.0350.0000.0000.0000.000
87A91GLY00.0340.01630.045-0.051-0.0510.0000.0000.0000.000
88A92SER0-0.034-0.00731.266-0.052-0.0520.0000.0000.0000.000
89A93ASP-1-0.757-0.86933.3038.3108.3100.0000.0000.0000.000
90A94TYR0-0.071-0.04634.1630.3270.3270.0000.0000.0000.000
91A95ILE00.0190.02035.810-0.295-0.2950.0000.0000.0000.000
92A96VAL0-0.013-0.01035.1240.2920.2920.0000.0000.0000.000
93A97GLY0-0.0050.00937.643-0.270-0.2700.0000.0000.0000.000
94A98ARG10.9070.93639.174-7.037-7.0370.0000.0000.0000.000
95A99PHE00.0870.04337.607-0.110-0.1100.0000.0000.0000.000
96A100ILE0-0.041-0.00640.732-0.100-0.1000.0000.0000.0000.000
97A101PRO0-0.061-0.03343.4630.0680.0680.0000.0000.0000.000
98A102GLY00.0260.01543.678-0.215-0.2150.0000.0000.0000.000
99A103THR0-0.042-0.04440.408-0.047-0.0470.0000.0000.0000.000
100A104LEU00.000-0.00637.0160.0770.0770.0000.0000.0000.000
101A105THR0-0.038-0.03941.499-0.057-0.0570.0000.0000.0000.000
102A106ASN0-0.011-0.00644.210-0.220-0.2200.0000.0000.0000.000
103A107PRO00.0460.01947.155-0.026-0.0260.0000.0000.0000.000
104A108MET0-0.057-0.01848.582-0.147-0.1470.0000.0000.0000.000
105A109LEU0-0.075-0.01445.792-0.119-0.1190.0000.0000.0000.000
106A110SER0-0.050-0.05148.6010.0520.0520.0000.0000.0000.000
107A111GLU-1-0.827-0.91344.5156.8986.8980.0000.0000.0000.000
108A112TYR0-0.084-0.05243.7760.2440.2440.0000.0000.0000.000
109A113ARG10.7670.86439.294-7.984-7.9840.0000.0000.0000.000
110A114GLU-1-0.855-0.90240.0397.5477.5470.0000.0000.0000.000
111A115PRO0-0.046-0.01034.5630.0700.0700.0000.0000.0000.000
112A116GLU-1-0.834-0.92033.4709.1739.1730.0000.0000.0000.000
113A117VAL0-0.064-0.03027.6410.3910.3910.0000.0000.0000.000
114A118VAL00.0380.02630.716-0.216-0.2160.0000.0000.0000.000
115A119PHE0-0.043-0.03124.2220.5730.5730.0000.0000.0000.000
116A120VAL00.0000.01128.780-0.259-0.2590.0000.0000.0000.000
117A121ASN00.003-0.00827.7760.3360.3360.0000.0000.0000.000
118A122ASP-1-0.779-0.89228.23211.11111.1110.0000.0000.0000.000
119A123PRO00.0490.03127.620-0.394-0.3940.0000.0000.0000.000
120A124ALA0-0.025-0.00830.685-0.297-0.2970.0000.0000.0000.000
121A125ILE0-0.080-0.04333.112-0.361-0.3610.0000.0000.0000.000
122A126ASP-1-0.729-0.87232.2079.5949.5940.0000.0000.0000.000
123A127LYS10.9680.97934.759-8.537-8.5370.0000.0000.0000.000
124A128GLN0-0.053-0.01635.656-0.073-0.0730.0000.0000.0000.000
125A129ALA00.0420.02034.992-0.076-0.0760.0000.0000.0000.000
126A130VAL0-0.015-0.00131.8380.0720.0720.0000.0000.0000.000
127A131SER0-0.006-0.01434.263-0.018-0.0180.0000.0000.0000.000
128A132GLU-1-0.724-0.84237.4227.6797.6790.0000.0000.0000.000
129A133ALA00.0110.01533.834-0.091-0.0910.0000.0000.0000.000
130A134THR0-0.029-0.04234.4410.0420.0420.0000.0000.0000.000
131A135ALA0-0.080-0.03835.880-0.089-0.0890.0000.0000.0000.000
132A136VAL0-0.019-0.00138.279-0.213-0.2130.0000.0000.0000.000
133A137GLY0-0.0240.00135.3170.0080.0080.0000.0000.0000.000
134A138ILE0-0.037-0.01132.9390.2400.2400.0000.0000.0000.000
135A139PRO0-0.014-0.00828.2650.1440.1440.0000.0000.0000.000
136A140VAL00.0200.00728.589-0.073-0.0730.0000.0000.0000.000
137A141VAL0-0.008-0.01223.3220.5670.5670.0000.0000.0000.000
138A142ALA00.0230.00224.481-0.559-0.5590.0000.0000.0000.000
139A143LEU0-0.0310.01022.4480.7490.7490.0000.0000.0000.000
140A144CYS0-0.088-0.04122.628-0.727-0.7270.0000.0000.0000.000
141A145ASP-1-0.655-0.82422.35013.53813.5380.0000.0000.0000.000
142A146SER0-0.046-0.05722.791-0.072-0.0720.0000.0000.0000.000
143A147ASN00.0140.00524.1260.0080.0080.0000.0000.0000.000
144A148ASN0-0.018-0.01125.982-0.217-0.2170.0000.0000.0000.000
145A149SER0-0.0020.00726.3850.3940.3940.0000.0000.0000.000
146A150SER0-0.075-0.08324.6340.1620.1620.0000.0000.0000.000
147A151ALA0-0.043-0.01726.7070.0700.0700.0000.0000.0000.000
148A152ASP-1-0.809-0.87630.2339.6319.6310.0000.0000.0000.000
149A153VAL0-0.043-0.03324.9600.0040.0040.0000.0000.0000.000
150A154ASP-1-0.811-0.88325.54712.02812.0280.0000.0000.0000.000
151A155LEU0-0.082-0.04319.3480.8850.8850.0000.0000.0000.000
152A156VAL00.012-0.00520.189-0.084-0.0840.0000.0000.0000.000
153A157ILE00.0240.02218.6011.1531.1530.0000.0000.0000.000
154A158PRO0-0.048-0.01716.367-0.741-0.7410.0000.0000.0000.000
155A159THR00.028-0.01618.0831.1261.1260.0000.0000.0000.000
156A160ASN0-0.0210.00620.357-1.184-1.1840.0000.0000.0000.000
157A161ASN0-0.0010.00522.747-0.041-0.0410.0000.0000.0000.000
158A162LYS10.7910.86425.723-12.003-12.0030.0000.0000.0000.000
159A163GLY0-0.0010.00025.631-0.406-0.4060.0000.0000.0000.000
160A164ARG10.8280.90226.079-10.042-10.0420.0000.0000.0000.000
161A165ARG10.8500.90922.853-12.330-12.3300.0000.0000.0000.000
162A166ALA0-0.0030.01021.6080.4020.4020.0000.0000.0000.000
163A167LEU00.011-0.00622.3350.4020.4020.0000.0000.0000.000
164A168ALA00.0070.01524.6810.1740.1740.0000.0000.0000.000
165A169ILE00.0120.00517.9300.0850.0850.0000.0000.0000.000
166A170VAL00.0220.01419.2890.5400.5400.0000.0000.0000.000
167A171TYR00.0260.00521.2400.1740.1740.0000.0000.0000.000
168A172TRP0-0.025-0.02118.9690.3460.3460.0000.0000.0000.000
169A173LEU0-0.010-0.00516.6320.0480.0480.0000.0000.0000.000
170A174LEU0-0.031-0.01219.9060.2300.2300.0000.0000.0000.000
171A175ALA00.0130.00621.613-0.126-0.1260.0000.0000.0000.000
172A176ARG10.7870.89516.094-17.924-17.9240.0000.0000.0000.000
173A177GLU-1-0.765-0.88117.27118.65318.6530.0000.0000.0000.000
174A178ILE00.0020.00620.600-0.069-0.0690.0000.0000.0000.000
175A179ALA0-0.0110.00023.689-0.318-0.3180.0000.0000.0000.000
176A180LYS10.8540.91116.423-18.906-18.9060.0000.0000.0000.000
177A181ILE0-0.076-0.03819.4570.0000.0000.0000.0000.0000.000
178A182ARG10.8080.89423.045-11.404-11.4040.0000.0000.0000.000
179A183GLY0-0.0190.00825.616-0.416-0.4160.0000.0000.0000.000
180A184GLN0-0.070-0.02727.148-0.418-0.4180.0000.0000.0000.000
181A185ASP-1-0.852-0.93327.57311.09011.0900.0000.0000.0000.000
182A186PHE0-0.035-0.03324.2670.0080.0080.0000.0000.0000.000
183A187THR0-0.010-0.01026.2850.3190.3190.0000.0000.0000.000
184A188TYR0-0.0340.01527.614-0.355-0.3550.0000.0000.0000.000
185A189SER00.016-0.00725.3750.5640.5640.0000.0000.0000.000
186A190ILE00.022-0.00520.550-0.084-0.0840.0000.0000.0000.000
187A191GLU-1-0.791-0.89425.12311.72411.7240.0000.0000.0000.000
188A192ASP-1-0.819-0.87328.46010.05910.0590.0000.0000.0000.000
189A193PHE00.0230.00726.753-0.257-0.2570.0000.0000.0000.000
190A194GLU-1-0.793-0.89627.08511.17611.1760.0000.0000.0000.000
191A195ALA0-0.0150.00029.398-0.369-0.3690.0000.0000.0000.000
192A196GLU-1-0.813-0.88032.4768.8268.8260.0000.0000.0000.000
193A197LEU0-0.013-0.01333.269-0.020-0.0200.0000.0000.0000.000
194A198GLU-1-0.906-0.95437.1057.0987.0980.0000.0000.0000.000
195A199GLY0-0.011-0.00639.6940.0930.0930.0000.0000.0000.000
196A200GLY0-0.023-0.00136.8940.0360.0360.0000.0000.0000.000
197A201SER0-0.016-0.01333.879-0.185-0.1850.0000.0000.0000.000
198A202HIS10.8760.93236.567-8.123-8.1230.0000.0000.0000.000