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: 2234R

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 OptHSide
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 -2496182.549527
FMO2-HF: Nuclear repulsion 2408478.825624
FMO2-HF: Total energy -87703.723903
FMO2-MP2: Total energy -87958.19852


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.
-1.6022.1152.416-1.964-4.1710
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 : -0.007 / q_NPA : -0.010
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].
3A2SER0-0.057-0.0383.808-0.1231.734-0.031-0.898-0.9280.001
4A3TYR0-0.031-0.0376.3850.2120.2120.0000.0000.0000.000
5A4GLY00.0130.0239.652-0.150-0.1500.0000.0000.0000.000
6A5VAL0-0.028-0.01812.416-0.043-0.0430.0000.0000.0000.000
7A6ARG00.0570.01714.660-0.019-0.0190.0000.0000.0000.000
8A7LEU0-0.043-0.02218.403-0.039-0.0390.0000.0000.0000.000
9A8HIS00.0350.03720.6340.0050.0050.0000.0000.0000.000
10A9VAL00.0430.02123.135-0.023-0.0230.0000.0000.0000.000
11A10TRP0-0.011-0.00925.8910.0060.0060.0000.0000.0000.000
12A11GLY00.0190.00029.679-0.009-0.0090.0000.0000.0000.000
13A12GLU-1-0.909-0.94332.7650.0810.0810.0000.0000.0000.000
14A13ARG10.7730.86635.387-0.076-0.0760.0000.0000.0000.000
15A14ALA00.0260.02031.5170.0010.0010.0000.0000.0000.000
16A15LEU0-0.034-0.01832.291-0.004-0.0040.0000.0000.0000.000
17A16PHE00.0560.02927.648-0.006-0.0060.0000.0000.0000.000
18A17THR0-0.035-0.01730.7300.0020.0020.0000.0000.0000.000
19A18ARG10.9450.96931.342-0.126-0.1260.0000.0000.0000.000
20A19PRO0-0.037-0.01229.987-0.009-0.0090.0000.0000.0000.000
21A20GLU-1-0.830-0.92032.8780.1030.1030.0000.0000.0000.000
22A21MET0-0.036-0.00935.626-0.004-0.0040.0000.0000.0000.000
23A22LYS10.9450.97334.809-0.044-0.0440.0000.0000.0000.000
24A23VAL0-0.022-0.00738.282-0.006-0.0060.0000.0000.0000.000
25A24GLU-1-0.914-0.96041.0130.0560.0560.0000.0000.0000.000
26A25ARG10.8550.94336.079-0.054-0.0540.0000.0000.0000.000
27A26VAL00.0480.00937.2310.0000.0000.0000.0000.0000.000
28A27SER0-0.041-0.02433.3530.0010.0010.0000.0000.0000.000
29A28TYR0-0.023-0.02129.7550.0030.0030.0000.0000.0000.000
30A29ASP-1-0.852-0.92732.6200.1460.1460.0000.0000.0000.000
31A30ILE0-0.021-0.00926.9160.0020.0020.0000.0000.0000.000
32A31ILE0-0.039-0.00924.551-0.008-0.0080.0000.0000.0000.000
33A32THR00.0160.00624.6440.0140.0140.0000.0000.0000.000
34A33PRO00.0590.02019.564-0.004-0.0040.0000.0000.0000.000
35A34SER00.0230.03620.1130.0020.0020.0000.0000.0000.000
36A35ALA0-0.012-0.00821.188-0.018-0.0180.0000.0000.0000.000
37A36ALA00.0190.01020.438-0.009-0.0090.0000.0000.0000.000
38A37ARG10.7590.82415.303-0.137-0.1370.0000.0000.0000.000
39A38GLY0-0.0020.00418.251-0.024-0.0240.0000.0000.0000.000
40A39ILE0-0.031-0.01920.819-0.025-0.0250.0000.0000.0000.000
41A40LEU00.0060.00315.245-0.011-0.0110.0000.0000.0000.000
42A41GLU-1-0.858-0.93215.8260.0260.0260.0000.0000.0000.000
43A42ALA0-0.0350.00217.605-0.033-0.0330.0000.0000.0000.000
44A43ILE0-0.0080.00018.150-0.021-0.0210.0000.0000.0000.000
45A44HIS0-0.043-0.05112.302-0.020-0.0200.0000.0000.0000.000
46A45TRP00.0930.06512.8350.0170.0170.0000.0000.0000.000
47A46LYS10.9230.95412.4330.2910.2910.0000.0000.0000.000
48A47PRO00.0840.04112.209-0.011-0.0110.0000.0000.0000.000
49A48ALA0-0.0100.0238.389-0.025-0.0250.0000.0000.0000.000
50A49ILE0-0.030-0.0037.141-0.276-0.2760.0000.0000.0000.000
51A50ARG10.9280.9748.409-0.373-0.3730.0000.0000.0000.000
52A51TRP0-0.021-0.0139.5110.1180.1180.0000.0000.0000.000
53A52VAL0-0.025-0.02710.231-0.050-0.0500.0000.0000.0000.000
54A53VAL00.006-0.00412.5380.0520.0520.0000.0000.0000.000
55A54ASP-1-0.800-0.87913.2070.9710.9710.0000.0000.0000.000
56A55SER0-0.026-0.01516.148-0.032-0.0320.0000.0000.0000.000
57A56ILE0-0.0110.00619.736-0.009-0.0090.0000.0000.0000.000
58A57GLN00.0360.03522.7580.0170.0170.0000.0000.0000.000
59A58VAL0-0.022-0.02925.516-0.016-0.0160.0000.0000.0000.000
60A59LEU0-0.016-0.00827.8640.0000.0000.0000.0000.0000.000
61A60LYS10.8600.93630.901-0.142-0.1420.0000.0000.0000.000
62A61PRO00.0130.00534.0130.0040.0040.0000.0000.0000.000
63A62ILE00.0170.01933.133-0.005-0.0050.0000.0000.0000.000
64A63CYS0-0.043-0.00836.464-0.007-0.0070.0000.0000.0000.000
65A64PHE00.0230.00036.288-0.001-0.0010.0000.0000.0000.000
66A65GLU-1-0.726-0.84440.4370.0770.0770.0000.0000.0000.000
67A66SER0-0.013-0.00442.0370.0010.0010.0000.0000.0000.000
68A67ILE0-0.024-0.00941.630-0.003-0.0030.0000.0000.0000.000
69A68ARG10.7840.85444.048-0.044-0.0440.0000.0000.0000.000
70A69ARG10.8970.95838.462-0.052-0.0520.0000.0000.0000.000
71A70ASN0-0.034-0.05445.2640.0030.0030.0000.0000.0000.000
72A71GLU-1-0.892-0.92547.0460.0230.0230.0000.0000.0000.000
73A72VAL0-0.0160.01449.674-0.001-0.0010.0000.0000.0000.000
74A73GLY00.0100.00652.260-0.001-0.0010.0000.0000.0000.000
75A74SER0-0.008-0.01855.8230.0020.0020.0000.0000.0000.000
76A75LYS10.8640.93958.516-0.018-0.0180.0000.0000.0000.000
77A76LEU00.0180.02753.341-0.001-0.0010.0000.0000.0000.000
78A77SER00.0470.02356.3460.0020.0020.0000.0000.0000.000
79A78ALA00.0650.02258.335-0.002-0.0020.0000.0000.0000.000
80A79ALA00.0410.01060.578-0.001-0.0010.0000.0000.0000.000
81A80SER0-0.044-0.02660.735-0.001-0.0010.0000.0000.0000.000
82A81ILE00.0610.03657.914-0.002-0.0020.0000.0000.0000.000
83A82SER0-0.0020.00561.965-0.002-0.0020.0000.0000.0000.000
84A83LYS10.9560.95965.269-0.021-0.0210.0000.0000.0000.000
85A84ALA00.0360.03763.466-0.001-0.0010.0000.0000.0000.000
86A85ILE00.0270.01062.547-0.001-0.0010.0000.0000.0000.000
87A86LYS10.8800.94566.283-0.024-0.0240.0000.0000.0000.000
88A87ALA0-0.038-0.01068.503-0.001-0.0010.0000.0000.0000.000
89A88GLY00.0110.02168.240-0.001-0.0010.0000.0000.0000.000
90A89ARG10.7720.86165.234-0.014-0.0140.0000.0000.0000.000
91A90THR00.0810.01461.1280.0010.0010.0000.0000.0000.000
92A91ASP-1-0.721-0.82360.9960.0120.0120.0000.0000.0000.000
93A92GLU-1-0.876-0.94859.9990.0160.0160.0000.0000.0000.000
94A93LEU00.0060.00059.3260.0010.0010.0000.0000.0000.000
95A94VAL0-0.0220.00155.8560.0020.0020.0000.0000.0000.000
96A95LYS10.9080.93955.309-0.011-0.0110.0000.0000.0000.000
97A96TYR0-0.034-0.02854.8340.0000.0000.0000.0000.0000.000
98A97VAL00.0250.02552.2630.0020.0020.0000.0000.0000.000
99A98GLU-1-0.979-1.00550.8210.0140.0140.0000.0000.0000.000
100A99GLU-1-0.826-0.93149.8870.0250.0250.0000.0000.0000.000
101A100ASP-1-0.874-0.89849.7800.0400.0400.0000.0000.0000.000
102A101ARG10.9590.96746.537-0.018-0.0180.0000.0000.0000.000
103A102GLN00.0000.00045.3650.0020.0020.0000.0000.0000.000
104A103GLN0-0.0270.01245.7220.0030.0030.0000.0000.0000.000
105A104ARG10.8830.95339.370-0.031-0.0310.0000.0000.0000.000
106A105ALA00.0190.00142.0720.0030.0030.0000.0000.0000.000
107A106ALA0-0.0120.00139.1800.0010.0010.0000.0000.0000.000
108A107THR00.0120.01839.839-0.003-0.0030.0000.0000.0000.000
109A108VAL0-0.023-0.00937.0000.0040.0040.0000.0000.0000.000
110A109LEU00.0160.01432.458-0.001-0.0010.0000.0000.0000.000
111A110ARG10.8200.88536.374-0.096-0.0960.0000.0000.0000.000
112A111GLU-1-0.914-0.96536.3090.1140.1140.0000.0000.0000.000
113A112VAL00.0220.02531.2460.0070.0070.0000.0000.0000.000
114A113GLY00.028-0.02429.624-0.008-0.0080.0000.0000.0000.000
115A114TYR00.0090.00325.626-0.001-0.0010.0000.0000.0000.000
116A115ILE00.0130.01421.788-0.009-0.0090.0000.0000.0000.000
117A116ILE0-0.029-0.01618.3080.0130.0130.0000.0000.0000.000
118A117ALA00.0350.02717.2400.0070.0070.0000.0000.0000.000
119A118ALA00.0050.00614.257-0.003-0.0030.0000.0000.0000.000
120A119HIS10.8040.8887.696-1.130-1.1300.0000.0000.0000.000
121A120PHE00.0020.0005.862-0.065-0.0650.0000.0000.0000.000
122A121GLU-1-0.809-0.8964.8001.1111.299-0.001-0.029-0.1570.000
123A122MET0-0.060-0.0382.452-0.3920.6591.808-0.757-2.1020.000
124A123THR0-0.020-0.0224.380-0.217-0.074-0.001-0.026-0.1170.000
125A124ASP-1-0.812-0.9046.988-1.221-1.2210.0000.0000.0000.000
126A125LYS10.7990.8838.8550.6280.6280.0000.0000.0000.000
127A126ALA0-0.054-0.0126.2500.1670.1670.0000.0000.0000.000
128A127GLY00.0480.0318.246-0.137-0.1370.0000.0000.0000.000
129A128PRO00.011-0.0128.292-0.185-0.1850.0000.0000.0000.000
130A129ASP-1-0.880-0.9279.408-0.845-0.8450.0000.0000.0000.000
131A130ASP-1-0.892-0.9218.061-0.561-0.5610.0000.0000.0000.000
132A131ASN00.0190.0085.527-0.078-0.0780.0000.0000.0000.000
133A132VAL00.1110.0402.607-0.799-0.3450.642-0.253-0.844-0.001
134A133GLY00.0400.0235.316-0.248-0.224-0.001-0.001-0.0230.000
135A134LYS10.8230.8918.5390.4880.4880.0000.0000.0000.000
136A135HIS0-0.024-0.0338.1100.1220.1220.0000.0000.0000.000
137A136LEU00.0480.0258.708-0.029-0.0290.0000.0000.0000.000
138A137ASP-1-0.850-0.90510.5040.1480.1480.0000.0000.0000.000
139A138ILE0-0.075-0.04013.162-0.046-0.0460.0000.0000.0000.000
140A139PHE00.0570.02813.333-0.014-0.0140.0000.0000.0000.000
141A140ASN00.0380.01213.464-0.030-0.0300.0000.0000.0000.000
142A141ARG10.7980.89616.293-0.055-0.0550.0000.0000.0000.000
143A142ARG10.8960.94017.315-0.001-0.0010.0000.0000.0000.000
144A143ALA00.0530.03318.924-0.014-0.0140.0000.0000.0000.000
145A144ARG10.9100.96317.212-0.314-0.3140.0000.0000.0000.000
146A145ARG10.8590.91821.131-0.111-0.1110.0000.0000.0000.000
147A146GLY00.0290.04423.897-0.014-0.0140.0000.0000.0000.000
148A147GLN0-0.058-0.03522.633-0.021-0.0210.0000.0000.0000.000
149A148CYS0-0.083-0.05421.7680.0140.0140.0000.0000.0000.000
150A149PHE0-0.041-0.00121.013-0.018-0.0180.0000.0000.0000.000
151A150GLN00.0060.00222.970-0.018-0.0180.0000.0000.0000.000
152A151ALA00.0480.01724.7540.0130.0130.0000.0000.0000.000
153A152PRO00.0500.04023.605-0.005-0.0050.0000.0000.0000.000
154A153CYS0-0.070-0.02825.594-0.007-0.0070.0000.0000.0000.000
155A154LEU00.0290.01826.8730.0140.0140.0000.0000.0000.000
156A155GLY00.0130.01228.015-0.003-0.0030.0000.0000.0000.000
157A156THR0-0.039-0.04029.215-0.008-0.0080.0000.0000.0000.000
158A157ARG10.9890.97130.993-0.020-0.0200.0000.0000.0000.000
159A158GLU-1-0.948-0.96131.9830.0460.0460.0000.0000.0000.000
160A159PHE0-0.023-0.00832.751-0.002-0.0020.0000.0000.0000.000
161A160PRO00.0450.03230.6190.0050.0050.0000.0000.0000.000
162A161ALA0-0.0050.00026.7100.0060.0060.0000.0000.0000.000
163A162SER0-0.017-0.00227.817-0.009-0.0090.0000.0000.0000.000
164A163PHE0-0.004-0.03222.9500.0110.0110.0000.0000.0000.000
165A164ALA0-0.0130.00124.579-0.015-0.0150.0000.0000.0000.000
166A165LEU0-0.062-0.03217.3590.0090.0090.0000.0000.0000.000
167A166LEU0-0.024-0.00220.649-0.025-0.0250.0000.0000.0000.000
168A167GLY0-0.031-0.02219.8360.0230.0230.0000.0000.0000.000
169A168ASP-1-0.868-0.91516.9180.7360.7360.0000.0000.0000.000
170A169ASP-1-0.937-0.96119.3150.5160.5160.0000.0000.0000.000
171A170ASP-1-0.843-0.91822.0790.2920.2920.0000.0000.0000.000
172A171THR0-0.112-0.06921.9340.0080.0080.0000.0000.0000.000
173A172PRO00.0330.02324.551-0.009-0.0090.0000.0000.0000.000
174A173PRO00.000-0.01228.4350.0010.0010.0000.0000.0000.000
175A174ALA00.0080.01030.510-0.020-0.0200.0000.0000.0000.000
176A175SER0-0.033-0.02232.279-0.007-0.0070.0000.0000.0000.000
177A176ASP-1-0.862-0.92735.3490.1470.1470.0000.0000.0000.000
178A177PRO0-0.0030.00036.7050.0070.0070.0000.0000.0000.000
179A178ALA0-0.038-0.02537.9370.0010.0010.0000.0000.0000.000
180A179LEU0-0.048-0.04132.3710.0020.0020.0000.0000.0000.000
181A180SER00.0220.02033.2390.0110.0110.0000.0000.0000.000
182A181GLY0-0.0020.00434.147-0.013-0.0130.0000.0000.0000.000
183A182GLU-1-0.831-0.89431.1840.2880.2880.0000.0000.0000.000
184A183ARG10.8150.89132.310-0.199-0.1990.0000.0000.0000.000
185A184ASP-1-0.801-0.87832.0630.2130.2130.0000.0000.0000.000
186A185LEU0-0.008-0.00729.430-0.012-0.0120.0000.0000.0000.000
187A186GLY00.0130.01732.128-0.011-0.0110.0000.0000.0000.000
188A187TRP0-0.062-0.03227.1610.0120.0120.0000.0000.0000.000
189A188MET0-0.013-0.00426.315-0.012-0.0120.0000.0000.0000.000
190A189LEU0-0.017-0.00424.7350.0110.0110.0000.0000.0000.000
191A190HIS0-0.068-0.03917.881-0.033-0.0330.0000.0000.0000.000
192A191ASP-1-0.721-0.86617.8620.1990.1990.0000.0000.0000.000
193A192ILE0-0.055-0.02120.641-0.002-0.0020.0000.0000.0000.000
194A193ASP-1-0.828-0.89319.1830.1200.1200.0000.0000.0000.000
195A194PHE0-0.004-0.01215.055-0.018-0.0180.0000.0000.0000.000
196A195ALA0-0.039-0.00617.078-0.044-0.0440.0000.0000.0000.000
197A196ASP-1-0.806-0.89618.6610.0060.0060.0000.0000.0000.000
198A197GLY00.0120.00620.719-0.009-0.0090.0000.0000.0000.000
199A198MET0-0.094-0.06421.693-0.002-0.0020.0000.0000.0000.000
200A199THR0-0.056-0.03324.4190.0170.0170.0000.0000.0000.000
201A200PRO0-0.028-0.00823.8040.0120.0120.0000.0000.0000.000
202A201ARG10.8980.92820.407-0.168-0.1680.0000.0000.0000.000
203A202PHE00.006-0.00124.269-0.001-0.0010.0000.0000.0000.000
204A203PHE00.0980.04523.3480.0140.0140.0000.0000.0000.000
205A204ARG10.8110.88425.506-0.211-0.2110.0000.0000.0000.000
206A205ALA00.0120.02226.5610.0220.0220.0000.0000.0000.000
207A206ARG10.8780.90426.315-0.336-0.3360.0000.0000.0000.000
208A207MET0-0.053-0.01127.2390.0200.0200.0000.0000.0000.000
209A208VAL00.007-0.00927.895-0.015-0.0150.0000.0000.0000.000
210A209ASP-1-0.851-0.90928.6030.2620.2620.0000.0000.0000.000
211A210GLY00.0420.01029.5860.0060.0060.0000.0000.0000.000
212A211LEU0-0.0030.01222.1330.0030.0030.0000.0000.0000.000
213A212VAL0-0.019-0.00424.340-0.014-0.0140.0000.0000.0000.000
214A213ALA0-0.017-0.01420.9530.0200.0200.0000.0000.0000.000
215A214VAL0-0.017-0.02718.280-0.049-0.0490.0000.0000.0000.000
216A215PRO0-0.0080.01117.9800.0580.0580.0000.0000.0000.000
217A216PRO00.0440.02913.904-0.011-0.0110.0000.0000.0000.000
218A217PRO0-0.036-0.03813.134-0.055-0.0550.0000.0000.0000.000
219A218GLN0-0.071-0.02712.942-0.134-0.1340.0000.0000.0000.000
220A219ASP-1-0.801-0.89816.5800.5610.5610.0000.0000.0000.000
221A220GLY0-0.029-0.00219.711-0.047-0.0470.0000.0000.0000.000
222A221GLY0-0.039-0.01721.905-0.008-0.0080.0000.0000.0000.000
223A222VAL0-0.105-0.05422.851-0.016-0.0160.0000.0000.0000.000