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: LJMG9

Calculation Name: 3VZI-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZI

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0J9

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2505832.809381
FMO2-HF: Nuclear repulsion 2417958.856009
FMO2-HF: Total energy -87873.953372
FMO2-MP2: Total energy -88128.982015


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:ACE )


Summations of interaction energy for fragment #1(A:-1:ACE )
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.
1.2382.187-0.004-0.343-0.6010
Interaction energy analysis for fragmet #1(A:-1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.029
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].
3A1MET 00.0590.0463.8980.5861.374-0.004-0.324-0.4600.000
4A2SER 0-0.053-0.0366.891-0.052-0.0520.0000.0000.0000.000
5A3TYR 0-0.038-0.04810.6060.0030.0030.0000.0000.0000.000
6A4GLY 00.0130.02613.3290.0110.0110.0000.0000.0000.000
7A5VAL 0-0.012-0.00515.439-0.002-0.0020.0000.0000.0000.000
8A6ARG 10.9080.93118.3100.0920.0920.0000.0000.0000.000
9A7LEU 0-0.043-0.01621.6750.0000.0000.0000.0000.0000.000
10A8HIS 0-0.0260.01623.9210.0090.0090.0000.0000.0000.000
11A9VAL 00.0550.02925.9930.0000.0000.0000.0000.0000.000
12A10TRP 0-0.015-0.01928.7170.0020.0020.0000.0000.0000.000
13A11GLY 00.0260.00932.3140.0000.0000.0000.0000.0000.000
14A12GLU -1-0.928-0.96235.312-0.009-0.0090.0000.0000.0000.000
15A13ARG 10.8630.94237.5440.0050.0050.0000.0000.0000.000
16A14ALA 00.0140.01532.897-0.001-0.0010.0000.0000.0000.000
17A15LEU 0-0.022-0.01333.6000.0010.0010.0000.0000.0000.000
18A16PHE 00.0370.02228.7740.0020.0020.0000.0000.0000.000
19A17THR 0-0.027-0.01331.7140.0000.0000.0000.0000.0000.000
20A18ARG 10.9270.94432.020-0.021-0.0210.0000.0000.0000.000
21A19PRO 0-0.026-0.00730.300-0.001-0.0010.0000.0000.0000.000
22A20GLU -1-0.813-0.89933.2800.0310.0310.0000.0000.0000.000
23A21MET 0-0.043-0.00935.807-0.001-0.0010.0000.0000.0000.000
24A22LYS 10.9500.97634.885-0.037-0.0370.0000.0000.0000.000
25A23VAL 0-0.012-0.00138.7540.0000.0000.0000.0000.0000.000
26A24GLU -1-0.939-0.97041.7040.0140.0140.0000.0000.0000.000
27A25ARG 10.8700.94137.524-0.010-0.0100.0000.0000.0000.000
28A26VAL 00.0580.01437.576-0.002-0.0020.0000.0000.0000.000
29A27SER 0-0.064-0.04634.2850.0020.0020.0000.0000.0000.000
30A28TYR 0-0.006-0.01329.7240.0020.0020.0000.0000.0000.000
31A29ASP -1-0.842-0.91333.2730.0070.0070.0000.0000.0000.000
32A30ILE 0-0.010-0.00227.561-0.004-0.0040.0000.0000.0000.000
33A31ILE 0-0.049-0.01425.4230.0030.0030.0000.0000.0000.000
34A32THR 00.0270.01625.286-0.001-0.0010.0000.0000.0000.000
35A33PRO 00.0580.02120.177-0.007-0.0070.0000.0000.0000.000
36A34SER 00.0040.02321.056-0.007-0.0070.0000.0000.0000.000
37A35ALA 00.0090.00122.102-0.004-0.0040.0000.0000.0000.000
38A36ALA 00.0240.00321.738-0.007-0.0070.0000.0000.0000.000
39A37ARG 10.7880.86416.533-0.068-0.0680.0000.0000.0000.000
40A38GLY 0-0.0030.00119.632-0.007-0.0070.0000.0000.0000.000
41A39ILE 0-0.019-0.00922.128-0.005-0.0050.0000.0000.0000.000
42A40LEU 0-0.011-0.01117.579-0.008-0.0080.0000.0000.0000.000
43A41GLU -1-0.903-0.96617.2250.0220.0220.0000.0000.0000.000
44A42ALA 0-0.0180.01119.612-0.003-0.0030.0000.0000.0000.000
45A43ILE 0-0.045-0.02021.544-0.004-0.0040.0000.0000.0000.000
46A44HIS 0-0.063-0.08515.7470.0110.0110.0000.0000.0000.000
47A45TRP 00.1040.06414.242-0.011-0.0110.0000.0000.0000.000
48A46LYS 10.9140.95214.7830.0430.0430.0000.0000.0000.000
49A47PRO 00.0750.04013.839-0.001-0.0010.0000.0000.0000.000
50A48ALA 00.0070.03410.4360.0400.0400.0000.0000.0000.000
51A49ILE 0-0.043-0.0148.999-0.048-0.0480.0000.0000.0000.000
52A50ARG 10.9880.9999.478-0.262-0.2620.0000.0000.0000.000
53A51TRP 0-0.011-0.00310.926-0.050-0.0500.0000.0000.0000.000
54A52VAL 0-0.014-0.02010.8100.0440.0440.0000.0000.0000.000
55A53VAL 0-0.006-0.00713.560-0.035-0.0350.0000.0000.0000.000
56A54ASP -1-0.792-0.89214.218-0.064-0.0640.0000.0000.0000.000
57A55SER 0-0.049-0.02417.0900.0100.0100.0000.0000.0000.000
58A56ILE 00.0280.02120.867-0.007-0.0070.0000.0000.0000.000
59A57GLN 00.0220.02424.116-0.001-0.0010.0000.0000.0000.000
60A58VAL 0-0.014-0.02527.143-0.001-0.0010.0000.0000.0000.000
61A59LEU 0-0.019-0.01430.367-0.001-0.0010.0000.0000.0000.000
62A60LYS 10.9130.96432.8280.0180.0180.0000.0000.0000.000
63A61PRO 00.0270.01235.5530.0020.0020.0000.0000.0000.000
64A62ILE 00.0220.02034.0280.0000.0000.0000.0000.0000.000
65A63CYS 0-0.024-0.00437.6340.0010.0010.0000.0000.0000.000
66A64PHE 00.007-0.00536.7420.0000.0000.0000.0000.0000.000
67A65GLU -1-0.832-0.93841.485-0.003-0.0030.0000.0000.0000.000
68A66SER 0-0.027-0.00843.1330.0010.0010.0000.0000.0000.000
69A67ILE 0-0.036-0.01042.839-0.001-0.0010.0000.0000.0000.000
70A68ARG 10.8810.92045.240-0.006-0.0060.0000.0000.0000.000
71A69ARG 10.8580.94839.888-0.004-0.0040.0000.0000.0000.000
72A70ASN 0-0.004-0.02746.6170.0000.0000.0000.0000.0000.000
73A71GLU -1-0.793-0.87844.6020.0050.0050.0000.0000.0000.000
74A72VAL 0-0.047-0.01948.6340.0010.0010.0000.0000.0000.000
75A73GLY 00.0660.03152.070-0.001-0.0010.0000.0000.0000.000
76A74SER 0-0.008-0.02055.1080.0000.0000.0000.0000.0000.000
77A75LYS 10.9380.96758.665-0.002-0.0020.0000.0000.0000.000
78A76LEU 0-0.076-0.02354.3230.0000.0000.0000.0000.0000.000
79A77SER 00.0160.01857.4190.0000.0000.0000.0000.0000.000
80A78ALA 00.0670.02959.3900.0000.0000.0000.0000.0000.000
81A79ALA 00.0270.00061.5550.0000.0000.0000.0000.0000.000
82A80SER 00.0110.00861.7580.0000.0000.0000.0000.0000.000
83A81ILE 00.0700.04358.6820.0000.0000.0000.0000.0000.000
84A82SER 0-0.0070.00162.8410.0000.0000.0000.0000.0000.000
85A83LYS 10.9530.95666.148-0.004-0.0040.0000.0000.0000.000
86A84ALA 00.0570.04964.2720.0000.0000.0000.0000.0000.000
87A85ILE 00.0170.01163.4580.0000.0000.0000.0000.0000.000
88A86LYS 10.8690.93567.015-0.005-0.0050.0000.0000.0000.000
89A87ALA 0-0.037-0.01369.4000.0000.0000.0000.0000.0000.000
90A88GLY 00.0020.01868.8930.0000.0000.0000.0000.0000.000
91A89ARG 10.8230.90166.143-0.006-0.0060.0000.0000.0000.000
92A90THR 00.0720.00961.7060.0000.0000.0000.0000.0000.000
93A91ASP -1-0.835-0.90161.6360.0070.0070.0000.0000.0000.000
94A92GLU -1-0.918-0.96460.7010.0060.0060.0000.0000.0000.000
95A93LEU 0-0.009-0.00860.1190.0000.0000.0000.0000.0000.000
96A94VAL 0-0.037-0.00856.3710.0000.0000.0000.0000.0000.000
97A95LYS 10.9930.99756.001-0.006-0.0060.0000.0000.0000.000
98A96TYR 0-0.023-0.02355.6580.0000.0000.0000.0000.0000.000
99A97VAL 00.0220.02752.8960.0000.0000.0000.0000.0000.000
100A98GLU -1-0.962-1.00351.5220.0110.0110.0000.0000.0000.000
101A99GLU -1-0.820-0.94550.6950.0050.0050.0000.0000.0000.000
102A100ASP -1-0.882-0.92450.5700.0090.0090.0000.0000.0000.000
103A101ARG 10.9570.97047.327-0.014-0.0140.0000.0000.0000.000
104A102GLN 0-0.024-0.01446.2180.0010.0010.0000.0000.0000.000
105A103GLN 0-0.0160.01246.7400.0000.0000.0000.0000.0000.000
106A104ARG 10.7790.90140.051-0.009-0.0090.0000.0000.0000.000
107A105ALA 00.0140.01043.1080.0000.0000.0000.0000.0000.000
108A106ALA 0-0.0040.00540.2610.0010.0010.0000.0000.0000.000
109A107THR 00.0080.01740.867-0.002-0.0020.0000.0000.0000.000
110A108VAL 0-0.029-0.01138.0880.0010.0010.0000.0000.0000.000
111A109LEU 00.0270.01633.452-0.001-0.0010.0000.0000.0000.000
112A110ARG 10.9220.95337.5970.0050.0050.0000.0000.0000.000
113A111GLU -1-0.988-1.00438.340-0.011-0.0110.0000.0000.0000.000
114A112VAL 00.0160.02932.800-0.001-0.0010.0000.0000.0000.000
115A113GLY 00.020-0.03231.934-0.002-0.0020.0000.0000.0000.000
116A114TYR 00.0250.01127.3790.0030.0030.0000.0000.0000.000
117A115ILE 00.0110.00824.145-0.004-0.0040.0000.0000.0000.000
118A116ILE 0-0.007-0.00420.2940.0040.0040.0000.0000.0000.000
119A117ALA 00.0090.01419.236-0.012-0.0120.0000.0000.0000.000
120A118ALA 00.0190.01716.0580.0170.0170.0000.0000.0000.000
121A119HIS 10.8290.9219.5310.0890.0890.0000.0000.0000.000
122A120PHE 00.0150.0169.3640.0350.0350.0000.0000.0000.000
123A121GLU -1-0.911-0.9715.7770.1520.1520.0000.0000.0000.000
124A122MET 0-0.069-0.0394.2430.0540.1270.000-0.014-0.0580.000
125A123THR 0-0.031-0.0304.8020.3100.3980.000-0.005-0.0830.000
126A124ASP -1-0.885-0.9546.7160.3940.3940.0000.0000.0000.000
127A125LYS 10.9110.9557.924-0.294-0.2940.0000.0000.0000.000
128A126ALA 0-0.080-0.0227.642-0.071-0.0710.0000.0000.0000.000
129A127GLY 00.0450.0239.6630.0340.0340.0000.0000.0000.000
130A128PRO 00.008-0.00811.447-0.058-0.0580.0000.0000.0000.000
131A129ASP -1-0.890-0.94013.176-0.162-0.1620.0000.0000.0000.000
132A130ASP -1-0.908-0.93510.781-0.136-0.1360.0000.0000.0000.000
133A131ASN 00.003-0.0119.366-0.086-0.0860.0000.0000.0000.000
134A132VAL 00.0860.0287.8380.0770.0770.0000.0000.0000.000
135A133GLY 00.0390.02410.5220.0970.0970.0000.0000.0000.000
136A134LYS 10.9300.97313.9010.2160.2160.0000.0000.0000.000
137A135HIS 0-0.040-0.03611.8180.0570.0570.0000.0000.0000.000
138A136LEU 00.0360.01913.8820.0370.0370.0000.0000.0000.000
139A137ASP -1-0.934-0.96415.416-0.130-0.1300.0000.0000.0000.000
140A138ILE 0-0.076-0.03717.3100.0320.0320.0000.0000.0000.000
141A139PHE 00.0490.02317.5930.0180.0180.0000.0000.0000.000
142A140ASN 00.0760.03018.6700.0290.0290.0000.0000.0000.000
143A141ARG 10.8870.95521.4200.1310.1310.0000.0000.0000.000
144A142ARG 10.9300.98720.9950.0840.0840.0000.0000.0000.000
145A143ALA 00.0630.03823.0320.0100.0100.0000.0000.0000.000
146A144ARG 10.9070.95822.8600.1290.1290.0000.0000.0000.000
147A145ARG 10.8370.89826.2270.0870.0870.0000.0000.0000.000
148A146GLY 00.0300.04528.2330.0050.0050.0000.0000.0000.000
149A147GLN 0-0.057-0.03626.672-0.001-0.0010.0000.0000.0000.000
150A148CYS 0-0.057-0.03825.110-0.004-0.0040.0000.0000.0000.000
151A149PHE 0-0.031-0.00123.6670.0020.0020.0000.0000.0000.000
152A150GLN 0-0.017-0.00825.0330.0060.0060.0000.0000.0000.000
153A151ALA 00.0410.00827.271-0.003-0.0030.0000.0000.0000.000
154A152PRO 00.0230.03326.1500.0050.0050.0000.0000.0000.000
155A153CYS 0-0.0270.01027.8960.0010.0010.0000.0000.0000.000
156A154LEU 00.0040.00528.5850.0000.0000.0000.0000.0000.000
157A155GLY 00.0060.00829.3730.0020.0020.0000.0000.0000.000
158A156THR 0-0.035-0.04330.4650.0030.0030.0000.0000.0000.000
159A157ARG 11.0000.96332.341-0.012-0.0120.0000.0000.0000.000
160A158GLU -1-0.974-0.97533.4550.0060.0060.0000.0000.0000.000
161A159PHE 0-0.027-0.00734.290-0.001-0.0010.0000.0000.0000.000
162A160PRO 00.0490.03432.8880.0000.0000.0000.0000.0000.000
163A161ALA 0-0.004-0.00429.2470.0000.0000.0000.0000.0000.000
164A162SER 0-0.0070.00230.742-0.003-0.0030.0000.0000.0000.000
165A163PHE 0-0.016-0.03627.0390.0000.0000.0000.0000.0000.000
166A164ALA 00.0060.01128.452-0.001-0.0010.0000.0000.0000.000
167A165LEU 0-0.054-0.02821.7220.0000.0000.0000.0000.0000.000
168A166LEU 0-0.008-0.00124.6210.0040.0040.0000.0000.0000.000
169A167GLY 0-0.029-0.02324.067-0.010-0.0100.0000.0000.0000.000
170A168ASP -1-0.898-0.91921.151-0.158-0.1580.0000.0000.0000.000
171A169ASP -1-0.949-0.98022.826-0.106-0.1060.0000.0000.0000.000
172A170ASP -1-0.925-1.01525.348-0.050-0.0500.0000.0000.0000.000
173A171THR 00.0650.09826.450-0.005-0.0050.0000.0000.0000.000
174A172PRO 00.0120.00527.2010.0020.0020.0000.0000.0000.000
175A173PRO 00.0420.04429.8960.0030.0030.0000.0000.0000.000
176A174ALA 0-0.055-0.03632.4350.0030.0030.0000.0000.0000.000
177A175SER 0-0.021-0.01434.2560.0010.0010.0000.0000.0000.000
178A176ASP -1-0.840-0.92637.213-0.011-0.0110.0000.0000.0000.000
179A177PRO 00.0020.00438.2360.0010.0010.0000.0000.0000.000
180A178ALA 0-0.028-0.01839.3130.0020.0020.0000.0000.0000.000
181A179LEU 0-0.072-0.05733.8070.0020.0020.0000.0000.0000.000
182A180SER 0-0.018-0.00234.3660.0010.0010.0000.0000.0000.000
183A181GLY 0-0.0030.00335.2570.0020.0020.0000.0000.0000.000
184A182GLU -1-0.891-0.96331.878-0.001-0.0010.0000.0000.0000.000
185A183ARG 10.8850.95032.6820.0040.0040.0000.0000.0000.000
186A184ASP -1-0.804-0.89032.2180.0220.0220.0000.0000.0000.000
187A185LEU 0-0.010-0.00729.466-0.001-0.0010.0000.0000.0000.000
188A186GLY 00.0160.01832.0300.0010.0010.0000.0000.0000.000
189A187TRP 0-0.055-0.02626.5420.0000.0000.0000.0000.0000.000
190A188MET 0-0.021-0.00626.834-0.004-0.0040.0000.0000.0000.000
191A189LEU 0-0.002-0.00324.9960.0050.0050.0000.0000.0000.000
192A190HIS 0-0.072-0.04617.665-0.001-0.0010.0000.0000.0000.000
193A191ASP -1-0.718-0.87518.6140.0650.0650.0000.0000.0000.000
194A192ILE 0-0.059-0.02120.7800.0030.0030.0000.0000.0000.000
195A193ASP -1-0.889-0.95319.0340.1800.1800.0000.0000.0000.000
196A194PHE 0-0.032-0.02915.0130.0020.0020.0000.0000.0000.000
197A195ALA 0-0.053-0.00917.0670.0010.0010.0000.0000.0000.000
198A196ASP -1-0.819-0.92418.2140.1070.1070.0000.0000.0000.000
199A197GLY 0-0.013-0.00520.599-0.014-0.0140.0000.0000.0000.000
200A198MET 0-0.090-0.04821.753-0.015-0.0150.0000.0000.0000.000
201A199THR 0-0.040-0.01323.936-0.008-0.0080.0000.0000.0000.000
202A200PRO 0-0.0020.00423.7540.0080.0080.0000.0000.0000.000
203A201ARG 10.9970.99219.402-0.141-0.1410.0000.0000.0000.000
204A202PHE 0-0.009-0.00424.059-0.008-0.0080.0000.0000.0000.000
205A203PHE 00.0950.04023.0620.0080.0080.0000.0000.0000.000
206A204ARG 10.8280.90525.189-0.033-0.0330.0000.0000.0000.000
207A205ALA 00.0090.01726.5320.0000.0000.0000.0000.0000.000
208A206ARG 10.9330.95526.472-0.009-0.0090.0000.0000.0000.000
209A207MET 0-0.062-0.01627.524-0.002-0.0020.0000.0000.0000.000
210A208VAL 00.025-0.00128.6360.0020.0020.0000.0000.0000.000
211A209ASP -1-0.849-0.90929.773-0.019-0.0190.0000.0000.0000.000
212A210GLY 00.015-0.00130.902-0.004-0.0040.0000.0000.0000.000
213A211LEU 0-0.042-0.01123.8830.0010.0010.0000.0000.0000.000
214A212VAL 00.0130.01424.5890.0050.0050.0000.0000.0000.000
215A213ALA 0-0.021-0.01721.159-0.003-0.0030.0000.0000.0000.000
216A214VAL 0-0.025-0.03018.5060.0070.0070.0000.0000.0000.000
217A215PRO 0-0.0240.00517.996-0.001-0.0010.0000.0000.0000.000
218A216PRO 00.0690.03613.3350.0010.0010.0000.0000.0000.000
219A217PRO 0-0.042-0.03812.8250.0070.0070.0000.0000.0000.000
220A218GLN 0-0.079-0.02810.839-0.038-0.0380.0000.0000.0000.000
221A219ASP -1-0.802-0.90715.4160.1000.1000.0000.0000.0000.000
222A220GLY 0-0.0200.01418.5680.0010.0010.0000.0000.0000.000
223A221GLY 0-0.030-0.01821.036-0.012-0.0120.0000.0000.0000.000
224A222VAL 0-0.109-0.06922.1680.0060.0060.0000.0000.0000.000
225A223NME 00.0050.02424.826-0.007-0.0070.0000.0000.0000.000