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: KG263

Calculation Name: 2VZN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VZN

Chain ID: A

ChEMBL ID:

UniProt ID: P35778

Base Structure: X-ray

Registration Date: 2023-09-22

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2632602.044687
FMO2-HF: Nuclear repulsion 2543589.364902
FMO2-HF: Total energy -89012.679784
FMO2-MP2: Total energy -89264.794501


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-2.4382.940.243-2.302-3.3180.006
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.006
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].
3A4CYS0-0.089-0.0293.038-5.554-2.0120.108-1.766-1.8840.009
4A5ASN0-0.014-0.0133.086-1.270-0.0220.132-0.447-0.933-0.003
5A6LEU00.0640.0374.318-0.618-0.311-0.001-0.036-0.2700.000
6A7GLN0-0.004-0.0186.977-0.163-0.1630.0000.0000.0000.000
7A8SER0-0.032-0.01710.054-0.145-0.1450.0000.0000.0000.000
8A9CYS00.0420.0269.229-0.036-0.0360.0000.0000.0000.000
9A10LYS10.9050.9736.980-0.819-0.8190.0000.0000.0000.000
10A11ARG10.9350.96911.594-0.641-0.6410.0000.0000.0000.000
11A12ASN0-0.019-0.00914.142-0.080-0.0800.0000.0000.0000.000
12A13ASN0-0.011-0.00114.775-0.033-0.0330.0000.0000.0000.000
13A14ALA0-0.0040.01613.394-0.037-0.0370.0000.0000.0000.000
14A15ILE00.0110.0069.9630.1380.1380.0000.0000.0000.000
15A16HIS00.007-0.0146.961-0.155-0.1550.0000.0000.0000.000
16A17THR00.019-0.0099.917-0.045-0.0450.0000.0000.0000.000
17A18MET0-0.042-0.0135.969-0.036-0.0360.0000.0000.0000.000
18A20GLN00.0080.0117.219-0.047-0.0470.0000.0000.0000.000
19A21TYR00.0250.01210.953-0.090-0.0900.0000.0000.0000.000
20A22THR00.013-0.0058.605-0.163-0.1630.0000.0000.0000.000
21A23SER00.0060.0069.996-0.240-0.2400.0000.0000.0000.000
22A24PRO0-0.041-0.02611.9780.0190.0190.0000.0000.0000.000
23A25THR0-0.005-0.00813.4860.0540.0540.0000.0000.0000.000
24A26PRO0-0.012-0.00716.837-0.001-0.0010.0000.0000.0000.000
25A27GLY00.0300.02518.7590.0030.0030.0000.0000.0000.000
26A28PRO00.005-0.00720.1880.0040.0040.0000.0000.0000.000
27A29MET0-0.001-0.00223.1440.0110.0110.0000.0000.0000.000
28A30CYS0-0.184-0.04919.1690.0230.0230.0000.0000.0000.000
29A31LEU00.0500.01924.689-0.016-0.0160.0000.0000.0000.000
30A32GLU-1-0.856-0.93627.972-0.075-0.0750.0000.0000.0000.000
31A33TYR00.0150.01222.0560.0020.0020.0000.0000.0000.000
32A34SER0-0.043-0.03525.744-0.003-0.0030.0000.0000.0000.000
33A35ASN0-0.005-0.02524.909-0.008-0.0080.0000.0000.0000.000
34A36VAL00.0360.01718.4390.0090.0090.0000.0000.0000.000
35A37GLY0-0.0280.00718.875-0.013-0.0130.0000.0000.0000.000
36A38PHE0-0.076-0.04919.0750.0320.0320.0000.0000.0000.000
37A39THR00.028-0.00521.248-0.018-0.0180.0000.0000.0000.000
38A40ASP-1-0.850-0.95521.310-0.170-0.1700.0000.0000.0000.000
39A41ALA00.0280.01923.5650.0150.0150.0000.0000.0000.000
40A42GLU-1-0.854-0.92124.430-0.102-0.1020.0000.0000.0000.000
41A43LYS10.9010.96117.3680.2390.2390.0000.0000.0000.000
42A44ASP-1-0.859-0.92522.666-0.042-0.0420.0000.0000.0000.000
43A45ALA0-0.053-0.01625.3480.0150.0150.0000.0000.0000.000
44A46ILE00.0190.00421.9280.0150.0150.0000.0000.0000.000
45A47VAL0-0.0150.00521.6580.0180.0180.0000.0000.0000.000
46A48ASN00.013-0.00124.4090.0200.0200.0000.0000.0000.000
47A49LYS10.8540.94527.849-0.002-0.0020.0000.0000.0000.000
48A50HIS00.0510.02123.8810.0180.0180.0000.0000.0000.000
49A51ASN00.0810.05225.7500.0210.0210.0000.0000.0000.000
50A52GLU-1-0.917-0.92728.6240.0140.0140.0000.0000.0000.000
51A53LEU0-0.042-0.01929.4820.0020.0020.0000.0000.0000.000
52A54ARG10.8240.90825.126-0.119-0.1190.0000.0000.0000.000
53A55GLN0-0.004-0.02130.5810.0020.0020.0000.0000.0000.000
54A56ARG10.8890.94633.265-0.034-0.0340.0000.0000.0000.000
55A57VAL00.0350.02133.217-0.001-0.0010.0000.0000.0000.000
56A58ALA00.0270.01932.8230.0010.0010.0000.0000.0000.000
57A59SER0-0.077-0.04634.805-0.001-0.0010.0000.0000.0000.000
58A60GLY0-0.0080.00138.052-0.003-0.0030.0000.0000.0000.000
59A61LYS10.9290.98138.132-0.040-0.0400.0000.0000.0000.000
60A62GLU-1-0.789-0.88436.8880.0380.0380.0000.0000.0000.000
61A63MET00.0620.01339.4170.0030.0030.0000.0000.0000.000
62A64ARG10.8340.92437.712-0.038-0.0380.0000.0000.0000.000
63A65GLY00.1330.06740.0060.0040.0040.0000.0000.0000.000
64A66THR0-0.0080.01040.250-0.004-0.0040.0000.0000.0000.000
65A67ASN0-0.072-0.04242.0050.0010.0010.0000.0000.0000.000
66A68GLY00.0180.01543.6710.0000.0000.0000.0000.0000.000
67A69PRO0-0.050-0.01642.0530.0020.0020.0000.0000.0000.000
68A70GLN00.014-0.01136.9200.0070.0070.0000.0000.0000.000
69A71PRO0-0.0260.00637.684-0.003-0.0030.0000.0000.0000.000
70A72PRO00.0410.02537.2240.0030.0030.0000.0000.0000.000
71A73ALA0-0.020-0.01232.7230.0040.0040.0000.0000.0000.000
72A74VAL0-0.110-0.04833.795-0.005-0.0050.0000.0000.0000.000
73A75LYS10.8810.93429.685-0.125-0.1250.0000.0000.0000.000
74A76MET0-0.0040.00028.9090.0090.0090.0000.0000.0000.000
75A77PRO0-0.0550.01325.036-0.012-0.0120.0000.0000.0000.000
76A78ASN00.0460.00526.2910.0030.0030.0000.0000.0000.000
77A79LEU0-0.022-0.00521.6950.0140.0140.0000.0000.0000.000
78A80THR0-0.019-0.01319.689-0.016-0.0160.0000.0000.0000.000
79A81TRP00.0860.01915.9680.0350.0350.0000.0000.0000.000
80A82ASP-1-0.834-0.92912.1200.2030.2030.0000.0000.0000.000
81A83PRO00.0250.00711.805-0.005-0.0050.0000.0000.0000.000
82A84GLU-1-0.767-0.8615.9831.1511.1510.0000.0000.0000.000
83A85LEU00.004-0.0049.324-0.073-0.0730.0000.0000.0000.000
84A86ALA00.0110.01111.539-0.038-0.0380.0000.0000.0000.000
85A87THR0-0.083-0.0318.796-0.124-0.1240.0000.0000.0000.000
86A88ILE00.0220.0046.802-0.061-0.0610.0000.0000.0000.000
87A89ALA0-0.047-0.01610.2270.0650.0650.0000.0000.0000.000
88A90GLN0-0.014-0.02913.6350.0310.0310.0000.0000.0000.000
89A91ARG10.8710.9538.7301.0041.0040.0000.0000.0000.000
90A92TRP00.0460.00813.1280.0140.0140.0000.0000.0000.000
91A93ALA00.0170.01415.2030.0190.0190.0000.0000.0000.000
92A94ASN0-0.038-0.00915.7410.0490.0490.0000.0000.0000.000
93A95GLN00.0130.00315.5360.0090.0090.0000.0000.0000.000
94A97THR00.0390.00821.2400.0110.0110.0000.0000.0000.000
95A98PHE0-0.083-0.03122.1770.0060.0060.0000.0000.0000.000
96A99GLU-1-0.884-0.93821.9390.1040.1040.0000.0000.0000.000
97A100HIS0-0.042-0.03619.661-0.015-0.0150.0000.0000.0000.000
98A101ASP-1-0.723-0.81914.2010.1920.1920.0000.0000.0000.000
99A102ALA00.0220.00315.2110.0290.0290.0000.0000.0000.000
100A103CYS0-0.095-0.04011.7970.1270.1270.0000.0000.0000.000
101A104ARG10.8710.93910.908-0.292-0.2920.0000.0000.0000.000
102A105ASN0-0.025-0.04210.214-0.084-0.0840.0000.0000.0000.000
103A106VAL00.0280.0266.9250.1160.1160.0000.0000.0000.000
104A107GLU-1-0.888-0.9544.0286.4976.7780.004-0.053-0.2310.000
105A108ARG10.7960.9077.543-1.115-1.1150.0000.0000.0000.000
106A109PHE00.011-0.00310.994-0.179-0.1790.0000.0000.0000.000
107A110ALA00.0140.01411.8520.0920.0920.0000.0000.0000.000
108A111VAL00.007-0.00211.602-0.038-0.0380.0000.0000.0000.000
109A112GLY00.0100.00714.550-0.008-0.0080.0000.0000.0000.000
110A113GLN0-0.037-0.06116.1050.0010.0010.0000.0000.0000.000
111A114ASN0-0.0040.03019.1630.0130.0130.0000.0000.0000.000
112A115ILE00.0310.03020.857-0.018-0.0180.0000.0000.0000.000
113A116ALA00.0020.00823.2330.0050.0050.0000.0000.0000.000
114A117ALA00.0100.00325.179-0.012-0.0120.0000.0000.0000.000
115A118THR0-0.035-0.00627.6500.0060.0060.0000.0000.0000.000
116A119SER00.0780.02230.808-0.009-0.0090.0000.0000.0000.000
117A120SER0-0.054-0.01633.4190.0010.0010.0000.0000.0000.000
118A121SER00.0560.03535.772-0.003-0.0030.0000.0000.0000.000
119A122GLY00.0530.03936.5140.0000.0000.0000.0000.0000.000
120A123LYS10.9590.97333.4420.0680.0680.0000.0000.0000.000
121A124ASN0-0.012-0.00231.586-0.004-0.0040.0000.0000.0000.000
122A125LYS10.8420.91333.0980.0560.0560.0000.0000.0000.000
123A126SER00.0640.03731.0670.0050.0050.0000.0000.0000.000
124A127THR00.0000.00129.933-0.005-0.0050.0000.0000.0000.000
125A128PRO00.043-0.00325.3560.0060.0060.0000.0000.0000.000
126A129ASN00.0190.00327.4840.0080.0080.0000.0000.0000.000
127A130GLU-1-0.862-0.92829.800-0.012-0.0120.0000.0000.0000.000
128A131MET00.0110.01026.3260.0080.0080.0000.0000.0000.000
129A132ILE0-0.0010.01025.3490.0090.0090.0000.0000.0000.000
130A133LEU0-0.038-0.03128.5040.0100.0100.0000.0000.0000.000
131A134LEU0-0.027-0.01631.4040.0050.0050.0000.0000.0000.000
132A135TRP00.012-0.00422.9470.0060.0060.0000.0000.0000.000
133A136TYR0-0.044-0.05229.7380.0070.0070.0000.0000.0000.000
134A137ASN0-0.011-0.01931.6330.0030.0030.0000.0000.0000.000
135A138GLU-1-0.741-0.86530.3600.0780.0780.0000.0000.0000.000
136A139VAL0-0.065-0.02134.2510.0020.0020.0000.0000.0000.000
137A140LYS10.8590.92535.822-0.033-0.0330.0000.0000.0000.000
138A141ASP-1-0.922-0.94836.7290.0520.0520.0000.0000.0000.000
139A142PHE0-0.026-0.02032.9810.0060.0060.0000.0000.0000.000
140A143ASP-1-0.815-0.90836.8850.0660.0660.0000.0000.0000.000
141A144ASN00.0500.01737.1480.0070.0070.0000.0000.0000.000
142A145ARG10.8360.90637.597-0.063-0.0630.0000.0000.0000.000
143A146TRP00.0140.01233.7060.0040.0040.0000.0000.0000.000
144A147ILE0-0.027-0.00433.0050.0090.0090.0000.0000.0000.000
145A148SER0-0.042-0.01732.2820.0100.0100.0000.0000.0000.000
146A149SER00.004-0.01431.5130.0070.0070.0000.0000.0000.000
147A150PHE0-0.0060.00627.207-0.008-0.0080.0000.0000.0000.000
148A151PRO00.011-0.00330.4170.0050.0050.0000.0000.0000.000
149A152SER00.004-0.01329.9770.0050.0050.0000.0000.0000.000
150A153ASP-1-0.908-0.95530.6220.1050.1050.0000.0000.0000.000
151A154ASP-1-0.843-0.92829.1800.1330.1330.0000.0000.0000.000
152A155ASN00.0400.01631.197-0.002-0.0020.0000.0000.0000.000
153A156ILE0-0.055-0.02032.482-0.005-0.0050.0000.0000.0000.000
154A157LEU0-0.015-0.00325.492-0.001-0.0010.0000.0000.0000.000
155A158MET00.002-0.00729.0650.0000.0000.0000.0000.0000.000
156A159LYS10.8630.95430.709-0.073-0.0730.0000.0000.0000.000
157A160VAL0-0.014-0.01031.344-0.006-0.0060.0000.0000.0000.000
158A161GLY00.0540.04027.6910.0030.0030.0000.0000.0000.000
159A162HIS00.0420.02025.3400.0090.0090.0000.0000.0000.000
160A163TYR00.001-0.01326.9370.0010.0010.0000.0000.0000.000
161A164THR0-0.042-0.04927.0620.0000.0000.0000.0000.0000.000
162A165GLN00.0380.01621.0710.0300.0300.0000.0000.0000.000
163A166ILE0-0.0140.00624.5200.0060.0060.0000.0000.0000.000
164A167VAL0-0.051-0.02126.193-0.001-0.0010.0000.0000.0000.000
165A168TRP00.0510.04723.093-0.002-0.0020.0000.0000.0000.000
166A169ALA00.0300.00824.8470.0080.0080.0000.0000.0000.000
167A170LYS10.9200.94322.491-0.215-0.2150.0000.0000.0000.000
168A171THR0-0.0020.01619.7220.0170.0170.0000.0000.0000.000
169A172THR0-0.022-0.03119.835-0.021-0.0210.0000.0000.0000.000
170A173LYS10.8890.95816.168-0.247-0.2470.0000.0000.0000.000
171A174ILE00.0340.02717.8030.0230.0230.0000.0000.0000.000
172A175GLY00.0300.01614.877-0.025-0.0250.0000.0000.0000.000
173A176CYS0-0.118-0.04315.942-0.001-0.0010.0000.0000.0000.000
174A177GLY00.0480.01216.697-0.050-0.0500.0000.0000.0000.000
175A178ARG10.8570.92617.5950.1600.1600.0000.0000.0000.000
176A179ILE0-0.0120.01620.534-0.034-0.0340.0000.0000.0000.000
177A180MET0-0.0190.00722.5520.0220.0220.0000.0000.0000.000
178A181PHE0-0.008-0.01624.970-0.014-0.0140.0000.0000.0000.000
179A182LYS10.7970.92627.7670.0770.0770.0000.0000.0000.000
180A183GLU-1-0.847-0.92630.066-0.031-0.0310.0000.0000.0000.000
181A184PRO0-0.001-0.02430.933-0.002-0.0020.0000.0000.0000.000
182A185ASP-1-0.829-0.90533.818-0.024-0.0240.0000.0000.0000.000
183A186ASN0-0.053-0.04335.243-0.003-0.0030.0000.0000.0000.000
184A187TRP0-0.0150.01635.164-0.003-0.0030.0000.0000.0000.000
185A188THR0-0.077-0.05230.925-0.006-0.0060.0000.0000.0000.000
186A189LYS11.0321.03226.9670.0260.0260.0000.0000.0000.000
187A190HIS0-0.025-0.02526.873-0.020-0.0200.0000.0000.0000.000
188A191TYR0-0.005-0.01020.6340.0170.0170.0000.0000.0000.000
189A192LEU00.000-0.01021.556-0.021-0.0210.0000.0000.0000.000
190A193VAL00.0370.02516.7710.0200.0200.0000.0000.0000.000
191A195ASN00.0860.04512.8470.0400.0400.0000.0000.0000.000
192A196TYR0-0.016-0.04316.478-0.025-0.0250.0000.0000.0000.000
193A197GLY00.0330.03915.4170.0600.0600.0000.0000.0000.000
194A198PRO0-0.025-0.02616.041-0.039-0.0390.0000.0000.0000.000
195A199ALA0-0.004-0.01416.654-0.052-0.0520.0000.0000.0000.000
196A200GLY0-0.011-0.01118.2870.0000.0000.0000.0000.0000.000
197A201ASN0-0.025-0.00621.8400.0100.0100.0000.0000.0000.000
198A202VAL0-0.0160.00221.4410.0090.0090.0000.0000.0000.000
199A203LEU00.0110.00023.972-0.015-0.0150.0000.0000.0000.000
200A204GLY00.0580.04626.8260.0060.0060.0000.0000.0000.000
201A205ALA0-0.055-0.02825.785-0.008-0.0080.0000.0000.0000.000
202A206PRO00.0000.01227.866-0.008-0.0080.0000.0000.0000.000
203A207ILE0-0.044-0.01027.9580.0110.0110.0000.0000.0000.000
204A208TYR0-0.045-0.06228.3220.0060.0060.0000.0000.0000.000
205A209GLU-1-0.885-0.94430.6850.1150.1150.0000.0000.0000.000
206A210ILE00.0600.03433.368-0.006-0.0060.0000.0000.0000.000
207A211LYS10.9760.99536.773-0.065-0.0650.0000.0000.0000.000
208A212LYS10.8710.92338.818-0.082-0.0820.0000.0000.0000.000
209A213HIS00.0270.00942.6220.0000.0000.0000.0000.0000.000
210A214HIS00.006-0.00445.271-0.001-0.0010.0000.0000.0000.000
211A215HIS00.0410.01247.585-0.003-0.0030.0000.0000.0000.000
212A216HIS0-0.027-0.01250.729-0.003-0.0030.0000.0000.0000.000
213A217HIS0-0.0250.00748.907-0.001-0.0010.0000.0000.0000.000
214A218HIS00.0260.02251.4570.0000.0000.0000.0000.0000.000