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: 7GVYK

Calculation Name: 3VZI-A-Xray372

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: 2023-06-19

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2496366.807521
FMO2-HF: Nuclear repulsion 2408664.682929
FMO2-HF: Total energy -87702.124592
FMO2-MP2: Total energy -87956.663918


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-0.4093.0542.643-1.922-4.1860
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / 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].
3A2SER0-0.065-0.0453.808-0.3321.439-0.031-0.847-0.8940.001
4A3TYR0-0.044-0.0526.3910.2750.2750.0000.0000.0000.000
5A4GLY00.0120.0249.651-0.141-0.1410.0000.0000.0000.000
6A5VAL0-0.024-0.01212.339-0.060-0.0600.0000.0000.0000.000
7A6ARG00.0280.01214.671-0.009-0.0090.0000.0000.0000.000
8A7LEU0-0.058-0.02618.413-0.043-0.0430.0000.0000.0000.000
9A8HIS00.0310.03820.6490.0120.0120.0000.0000.0000.000
10A9VAL00.0570.03023.379-0.024-0.0240.0000.0000.0000.000
11A10TRP0-0.025-0.02025.9090.0080.0080.0000.0000.0000.000
12A11GLY00.0200.00629.697-0.010-0.0100.0000.0000.0000.000
13A12GLU-1-0.932-0.96432.7850.0670.0670.0000.0000.0000.000
14A13ARG10.8610.94035.386-0.065-0.0650.0000.0000.0000.000
15A14ALA00.0220.02031.5390.0000.0000.0000.0000.0000.000
16A15LEU0-0.034-0.01932.287-0.003-0.0030.0000.0000.0000.000
17A16PHE00.0430.02727.457-0.004-0.0040.0000.0000.0000.000
18A17THR0-0.032-0.01630.7180.0040.0040.0000.0000.0000.000
19A18ARG10.9290.94531.328-0.133-0.1330.0000.0000.0000.000
20A19PRO0-0.024-0.00629.990-0.010-0.0100.0000.0000.0000.000
21A20GLU-1-0.814-0.90032.8640.1190.1190.0000.0000.0000.000
22A21MET0-0.044-0.00935.611-0.004-0.0040.0000.0000.0000.000
23A22LYS10.9500.97634.525-0.064-0.0640.0000.0000.0000.000
24A23VAL0-0.014-0.00238.269-0.006-0.0060.0000.0000.0000.000
25A24GLU-1-0.944-0.97341.0010.0630.0630.0000.0000.0000.000
26A25ARG10.8700.94136.424-0.057-0.0570.0000.0000.0000.000
27A26VAL00.0560.01336.928-0.002-0.0020.0000.0000.0000.000
28A27SER0-0.060-0.04333.3760.0020.0020.0000.0000.0000.000
29A28TYR0-0.007-0.01329.2000.0030.0030.0000.0000.0000.000
30A29ASP-1-0.846-0.91632.6050.1470.1470.0000.0000.0000.000
31A30ILE0-0.0020.00326.748-0.001-0.0010.0000.0000.0000.000
32A31ILE0-0.049-0.01323.947-0.006-0.0060.0000.0000.0000.000
33A32THR00.0250.01324.6090.0150.0150.0000.0000.0000.000
34A33PRO00.0660.02619.532-0.010-0.0100.0000.0000.0000.000
35A34SER00.0020.02220.099-0.005-0.0050.0000.0000.0000.000
36A35ALA0-0.001-0.00421.175-0.021-0.0210.0000.0000.0000.000
37A36ALA00.0320.00820.242-0.015-0.0150.0000.0000.0000.000
38A37ARG10.7920.86615.535-0.180-0.1800.0000.0000.0000.000
39A38GLY0-0.012-0.00318.252-0.029-0.0290.0000.0000.0000.000
40A39ILE0-0.020-0.01020.822-0.029-0.0290.0000.0000.0000.000
41A40LEU0-0.001-0.00515.280-0.019-0.0190.0000.0000.0000.000
42A41GLU-1-0.902-0.96615.7710.0080.0080.0000.0000.0000.000
43A42ALA0-0.0260.00817.637-0.036-0.0360.0000.0000.0000.000
44A43ILE0-0.038-0.01818.328-0.027-0.0270.0000.0000.0000.000
45A44HIS0-0.066-0.08712.386-0.008-0.0080.0000.0000.0000.000
46A45TRP00.1030.06513.2470.0030.0030.0000.0000.0000.000
47A46LYS10.9070.95012.3660.3320.3320.0000.0000.0000.000
48A47PRO00.0700.03612.242-0.007-0.0070.0000.0000.0000.000
49A48ALA00.0050.0318.3490.0180.0180.0000.0000.0000.000
50A49ILE0-0.035-0.0087.096-0.232-0.2320.0000.0000.0000.000
51A50ARG10.9770.9948.473-0.382-0.3820.0000.0000.0000.000
52A51TRP0-0.011-0.0029.5020.1020.1020.0000.0000.0000.000
53A52VAL0-0.019-0.02210.296-0.035-0.0350.0000.0000.0000.000
54A53VAL0-0.009-0.00912.5230.0290.0290.0000.0000.0000.000
55A54ASP-1-0.790-0.89213.2010.9350.9350.0000.0000.0000.000
56A55SER0-0.046-0.02316.148-0.026-0.0260.0000.0000.0000.000
57A56ILE00.0240.01919.736-0.016-0.0160.0000.0000.0000.000
58A57GLN00.0510.04022.7580.0210.0210.0000.0000.0000.000
59A58VAL0-0.030-0.03225.516-0.018-0.0180.0000.0000.0000.000
60A59LEU0-0.010-0.00827.863-0.001-0.0010.0000.0000.0000.000
61A60LYS10.9040.95830.901-0.127-0.1270.0000.0000.0000.000
62A61PRO00.0240.01134.0130.0060.0060.0000.0000.0000.000
63A62ILE00.0190.01933.097-0.006-0.0060.0000.0000.0000.000
64A63CYS0-0.023-0.00436.464-0.006-0.0060.0000.0000.0000.000
65A64PHE00.007-0.00536.014-0.001-0.0010.0000.0000.0000.000
66A65GLU-1-0.833-0.93840.4370.0680.0680.0000.0000.0000.000
67A66SER0-0.028-0.00942.0240.0000.0000.0000.0000.0000.000
68A67ILE0-0.028-0.00641.428-0.004-0.0040.0000.0000.0000.000
69A68ARG10.8720.91544.037-0.046-0.0460.0000.0000.0000.000
70A69ARG10.8850.95438.612-0.046-0.0460.0000.0000.0000.000
71A70ASN0-0.020-0.06045.3760.0030.0030.0000.0000.0000.000
72A71GLU-1-0.899-0.93147.2030.0180.0180.0000.0000.0000.000
73A72VAL0-0.0160.02449.585-0.001-0.0010.0000.0000.0000.000
74A73GLY0-0.023-0.01552.110-0.002-0.0020.0000.0000.0000.000
75A74SER0-0.005-0.01855.7730.0010.0010.0000.0000.0000.000
76A75LYS10.8460.94158.549-0.019-0.0190.0000.0000.0000.000
77A76LEU00.0450.04953.151-0.001-0.0010.0000.0000.0000.000
78A77SER00.0330.00856.3360.0020.0020.0000.0000.0000.000
79A78ALA00.0620.02858.324-0.001-0.0010.0000.0000.0000.000
80A79ALA00.0370.00660.567-0.001-0.0010.0000.0000.0000.000
81A80SER00.0080.01260.987-0.001-0.0010.0000.0000.0000.000
82A81ILE00.0640.03757.787-0.002-0.0020.0000.0000.0000.000
83A82SER0-0.0110.00061.954-0.001-0.0010.0000.0000.0000.000
84A83LYS10.9590.95965.258-0.021-0.0210.0000.0000.0000.000
85A84ALA00.0320.03763.447-0.001-0.0010.0000.0000.0000.000
86A85ILE00.0230.01462.718-0.001-0.0010.0000.0000.0000.000
87A86LYS10.8780.94066.272-0.025-0.0250.0000.0000.0000.000
88A87ALA0-0.040-0.01568.579-0.001-0.0010.0000.0000.0000.000
89A88GLY00.0060.01968.230-0.001-0.0010.0000.0000.0000.000
90A89ARG10.8270.90465.389-0.016-0.0160.0000.0000.0000.000
91A90THR00.0800.01461.1390.0010.0010.0000.0000.0000.000
92A91ASP-1-0.827-0.89760.9870.0150.0150.0000.0000.0000.000
93A92GLU-1-0.916-0.97559.9910.0170.0170.0000.0000.0000.000
94A93LEU0-0.002-0.00359.3170.0010.0010.0000.0000.0000.000
95A94VAL0-0.031-0.00455.7860.0020.0020.0000.0000.0000.000
96A95LYS10.9930.99655.300-0.013-0.0130.0000.0000.0000.000
97A96TYR0-0.066-0.06854.8250.0000.0000.0000.0000.0000.000
98A97VAL00.0190.02652.2300.0020.0020.0000.0000.0000.000
99A98GLU-1-0.964-1.00550.8040.0190.0190.0000.0000.0000.000
100A99GLU-1-0.816-0.92849.8790.0260.0260.0000.0000.0000.000
101A100ASP-1-0.888-0.93149.7060.0430.0430.0000.0000.0000.000
102A101ARG10.9560.96746.581-0.025-0.0250.0000.0000.0000.000
103A102GLN0-0.001-0.00245.3560.0020.0020.0000.0000.0000.000
104A103GLN0-0.0170.01045.714-0.002-0.0020.0000.0000.0000.000
105A104ARG10.8650.95738.950-0.034-0.0340.0000.0000.0000.000
106A105ALA00.0100.00542.0620.0030.0030.0000.0000.0000.000
107A106ALA0-0.0020.00639.1670.0020.0020.0000.0000.0000.000
108A107THR00.0130.02039.907-0.003-0.0030.0000.0000.0000.000
109A108VAL0-0.028-0.01036.9870.0050.0050.0000.0000.0000.000
110A109LEU00.0270.01832.420-0.002-0.0020.0000.0000.0000.000
111A110ARG10.9170.94936.374-0.086-0.0860.0000.0000.0000.000
112A111GLU-1-0.988-1.00436.3100.0950.0950.0000.0000.0000.000
113A112VAL00.0130.02730.8400.0070.0070.0000.0000.0000.000
114A113GLY00.010-0.03629.638-0.010-0.0100.0000.0000.0000.000
115A114TYR00.0100.00025.5180.0050.0050.0000.0000.0000.000
116A115ILE00.0320.02521.811-0.015-0.0150.0000.0000.0000.000
117A116ILE0-0.025-0.01318.3900.0180.0180.0000.0000.0000.000
118A117ALA00.0290.02517.115-0.005-0.0050.0000.0000.0000.000
119A118ALA00.0070.00914.1740.0130.0130.0000.0000.0000.000
120A119HIS10.8370.9257.709-1.177-1.1770.0000.0000.0000.000
121A120PHE00.0040.0095.905-0.045-0.0450.0000.0000.0000.000
122A121GLU-1-0.902-0.9644.6401.6051.835-0.001-0.028-0.2020.000
123A122MET0-0.059-0.0332.345-0.4440.3912.110-0.777-2.1670.000
124A123THR0-0.032-0.0294.386-0.0380.095-0.001-0.026-0.1070.000
125A124ASP-1-0.882-0.9537.012-0.760-0.7600.0000.0000.0000.000
126A125LYS10.8990.9478.8610.3450.3450.0000.0000.0000.000
127A126ALA0-0.070-0.0176.5170.0620.0620.0000.0000.0000.000
128A127GLY00.0370.0198.423-0.061-0.0610.0000.0000.0000.000
129A128PRO00.007-0.0098.038-0.263-0.2630.0000.0000.0000.000
130A129ASP-1-0.899-0.9458.838-1.103-1.1030.0000.0000.0000.000
131A130ASP-1-0.909-0.9387.662-0.745-0.7450.0000.0000.0000.000
132A131ASN00.011-0.0044.896-0.221-0.2210.0000.0000.0000.000
133A132VAL00.1080.0402.633-0.485-0.0150.567-0.243-0.794-0.001
134A133GLY00.0350.0225.332-0.046-0.022-0.001-0.001-0.0220.000
135A134LYS10.9170.9668.5470.7630.7630.0000.0000.0000.000
136A135HIS0-0.039-0.0378.3050.2100.2100.0000.0000.0000.000
137A136LEU00.0410.0248.8660.0390.0390.0000.0000.0000.000
138A137ASP-1-0.935-0.96510.521-0.030-0.0300.0000.0000.0000.000
139A138ILE0-0.082-0.04113.184-0.003-0.0030.0000.0000.0000.000
140A139PHE00.0510.02413.4090.0080.0080.0000.0000.0000.000
141A140ASN00.0800.03413.5930.0130.0130.0000.0000.0000.000
142A141ARG10.8830.95216.6240.1420.1420.0000.0000.0000.000
143A142ARG10.9250.98417.5990.1010.1010.0000.0000.0000.000
144A143ALA00.0650.04018.959-0.002-0.0020.0000.0000.0000.000
145A144ARG10.9140.96117.515-0.138-0.1380.0000.0000.0000.000
146A145ARG10.8280.89321.1700.0020.0020.0000.0000.0000.000
147A146GLY00.0290.04423.929-0.008-0.0080.0000.0000.0000.000
148A147GLN0-0.061-0.03822.690-0.020-0.0200.0000.0000.0000.000
149A148CYS0-0.052-0.03421.7920.0080.0080.0000.0000.0000.000
150A149PHE0-0.031-0.00121.055-0.015-0.0150.0000.0000.0000.000
151A150GLN0-0.024-0.01122.998-0.008-0.0080.0000.0000.0000.000
152A151ALA00.0400.00724.7810.0080.0080.0000.0000.0000.000
153A152PRO00.0370.03923.7130.0010.0010.0000.0000.0000.000
154A153CYS0-0.0400.00425.620-0.005-0.0050.0000.0000.0000.000
155A154LEU00.0120.01026.8980.0150.0150.0000.0000.0000.000
156A155GLY00.0080.00928.005-0.001-0.0010.0000.0000.0000.000
157A156THR0-0.043-0.04729.204-0.005-0.0050.0000.0000.0000.000
158A157ARG11.0070.96630.955-0.020-0.0200.0000.0000.0000.000
159A158GLU-1-0.986-0.98332.0160.0430.0430.0000.0000.0000.000
160A159PHE0-0.026-0.00732.675-0.003-0.0030.0000.0000.0000.000
161A160PRO00.0500.03530.6520.0050.0050.0000.0000.0000.000
162A161ALA0-0.005-0.00326.7330.0070.0070.0000.0000.0000.000
163A162SER0-0.0100.00027.840-0.012-0.0120.0000.0000.0000.000
164A163PHE0-0.011-0.03323.2510.0110.0110.0000.0000.0000.000
165A164ALA0-0.0090.00324.575-0.016-0.0160.0000.0000.0000.000
166A165LEU0-0.057-0.03017.2850.0110.0110.0000.0000.0000.000
167A166LEU0-0.0010.00420.655-0.020-0.0200.0000.0000.0000.000
168A167GLY0-0.040-0.02819.8440.0110.0110.0000.0000.0000.000
169A168ASP-1-0.890-0.91717.1270.5690.5690.0000.0000.0000.000
170A169ASP-1-0.921-0.95519.3150.4290.4290.0000.0000.0000.000
171A170ASP-1-0.831-0.90122.0540.2470.2470.0000.0000.0000.000
172A171THR0-0.101-0.07521.7890.0240.0240.0000.0000.0000.000
173A172PRO00.0290.01124.534-0.007-0.0070.0000.0000.0000.000
174A173PRO00.0050.01728.3310.0040.0040.0000.0000.0000.000
175A174ALA0-0.033-0.03930.571-0.019-0.0190.0000.0000.0000.000
176A175SER0-0.030-0.00632.254-0.006-0.0060.0000.0000.0000.000
177A176ASP-1-0.853-0.92935.3260.1330.1330.0000.0000.0000.000
178A177PRO0-0.0010.00236.6800.0080.0080.0000.0000.0000.000
179A178ALA0-0.035-0.02237.9470.0020.0020.0000.0000.0000.000
180A179LEU0-0.067-0.05532.2610.0040.0040.0000.0000.0000.000
181A180SER0-0.0140.00133.2150.0120.0120.0000.0000.0000.000
182A181GLY0-0.0110.00034.105-0.010-0.0100.0000.0000.0000.000
183A182GLU-1-0.889-0.96131.5470.2770.2770.0000.0000.0000.000
184A183ARG10.8770.94732.294-0.192-0.1920.0000.0000.0000.000
185A184ASP-1-0.804-0.89032.0630.2270.2270.0000.0000.0000.000
186A185LEU0-0.006-0.00529.137-0.012-0.0120.0000.0000.0000.000
187A186GLY00.0110.01532.102-0.011-0.0110.0000.0000.0000.000
188A187TRP0-0.061-0.03027.0770.0120.0120.0000.0000.0000.000
189A188MET0-0.023-0.00626.530-0.016-0.0160.0000.0000.0000.000
190A189LEU0-0.004-0.00524.5890.0130.0130.0000.0000.0000.000
191A190HIS0-0.069-0.04317.659-0.036-0.0360.0000.0000.0000.000
192A191ASP-1-0.711-0.87217.9470.2360.2360.0000.0000.0000.000
193A192ILE0-0.063-0.02220.4400.0000.0000.0000.0000.0000.000
194A193ASP-1-0.891-0.95419.3400.2030.2030.0000.0000.0000.000
195A194PHE0-0.025-0.02615.131-0.015-0.0150.0000.0000.0000.000
196A195ALA0-0.054-0.00917.067-0.041-0.0410.0000.0000.0000.000
197A196ASP-1-0.826-0.92718.6520.0670.0670.0000.0000.0000.000
198A197GLY0-0.010-0.00420.716-0.015-0.0150.0000.0000.0000.000
199A198MET0-0.094-0.05021.684-0.009-0.0090.0000.0000.0000.000
200A199THR0-0.045-0.01524.2160.0130.0130.0000.0000.0000.000
201A200PRO0-0.0030.00423.7910.0160.0160.0000.0000.0000.000
202A201ARG11.0060.99520.223-0.257-0.2570.0000.0000.0000.000
203A202PHE0-0.010-0.00324.253-0.006-0.0060.0000.0000.0000.000
204A203PHE00.0900.04223.3340.0200.0200.0000.0000.0000.000
205A204ARG10.8220.90025.487-0.230-0.2300.0000.0000.0000.000
206A205ALA00.0150.02026.5470.0230.0230.0000.0000.0000.000
207A206ARG10.9280.95226.569-0.339-0.3390.0000.0000.0000.000
208A207MET0-0.057-0.01327.2390.0180.0180.0000.0000.0000.000
209A208VAL00.020-0.00427.791-0.014-0.0140.0000.0000.0000.000
210A209ASP-1-0.851-0.91128.5800.2490.2490.0000.0000.0000.000
211A210GLY00.0150.00129.5620.0020.0020.0000.0000.0000.000
212A211LEU0-0.0090.00622.3270.0030.0030.0000.0000.0000.000
213A212VAL0-0.0050.00424.148-0.010-0.0100.0000.0000.0000.000
214A213ALA0-0.014-0.01320.9160.0180.0180.0000.0000.0000.000
215A214VAL0-0.027-0.03118.254-0.045-0.0450.0000.0000.0000.000
216A215PRO0-0.0290.00217.9610.0590.0590.0000.0000.0000.000
217A216PRO00.0740.03913.791-0.021-0.0210.0000.0000.0000.000
218A217PRO0-0.040-0.03713.006-0.054-0.0540.0000.0000.0000.000
219A218GLN0-0.081-0.03012.435-0.143-0.1430.0000.0000.0000.000
220A219ASP-1-0.801-0.90616.5610.6300.6300.0000.0000.0000.000
221A220GLY0-0.0270.01119.691-0.048-0.0480.0000.0000.0000.000
222A221GLY0-0.028-0.01321.923-0.014-0.0140.0000.0000.0000.000
223A222VAL0-0.101-0.05122.832-0.014-0.0140.0000.0000.0000.000