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: YYL12

Calculation Name: 3VJP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VJP

Chain ID: A

ChEMBL ID:

UniProt ID: P40131

Base Structure: X-ray

Registration Date: 2023-06-20

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1894960.508983
FMO2-HF: Nuclear repulsion 1820139.353783
FMO2-HF: Total energy -74821.1552
FMO2-MP2: Total energy -75039.094722


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-16.592-11.8431.301-2.333-3.7160.015
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.015
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].
3A3ILE00.0420.0093.5271.2763.3070.075-0.663-1.4420.004
4A4ASN00.0650.0262.370-6.906-4.6911.211-1.543-1.8840.011
5A5ALA00.0580.0493.343-2.169-1.7810.016-0.120-0.2840.000
6A6GLN00.0390.0155.0320.2900.405-0.001-0.007-0.1060.000
7A7LEU0-0.032-0.0197.299-0.309-0.3090.0000.0000.0000.000
8A8THR0-0.014-0.0206.363-0.271-0.2710.0000.0000.0000.000
9A9THR00.0280.0678.655-0.216-0.2160.0000.0000.0000.000
10A10TRP0-0.001-0.00310.816-0.012-0.0120.0000.0000.0000.000
11A11PHE0-0.014-0.04011.710-0.081-0.0810.0000.0000.0000.000
12A12SER0-0.013-0.05811.746-0.054-0.0540.0000.0000.0000.000
13A13GLN0-0.020-0.00414.391-0.029-0.0290.0000.0000.0000.000
14A14ARG10.9130.96016.492-0.340-0.3400.0000.0000.0000.000
15A15LEU0-0.100-0.04215.974-0.007-0.0070.0000.0000.0000.000
16A16ALA00.1130.06618.9860.0050.0050.0000.0000.0000.000
17A17GLY0-0.024-0.00920.658-0.006-0.0060.0000.0000.0000.000
18A18PHE0-0.089-0.04121.3890.0020.0020.0000.0000.0000.000
19A19SER0-0.046-0.07518.1690.0330.0330.0000.0000.0000.000
20A20ASP-1-0.935-0.95818.5960.2330.2330.0000.0000.0000.000
21A21GLU-1-0.961-0.97114.6280.5010.5010.0000.0000.0000.000
22A22VAL0-0.020-0.01712.3930.0750.0750.0000.0000.0000.000
23A23VAL00.0470.0278.2140.0500.0500.0000.0000.0000.000
24A24VAL0-0.061-0.0268.709-0.062-0.0620.0000.0000.0000.000
25A25THR0-0.0150.0026.8081.1421.1420.0000.0000.0000.000
26A26LEU00.010-0.0086.629-1.166-1.1660.0000.0000.0000.000
27A27ARG10.9080.9468.356-1.549-1.5490.0000.0000.0000.000
28A28SER0-0.0010.00111.089-0.154-0.1540.0000.0000.0000.000
29A29SER00.0090.00510.8840.3140.3140.0000.0000.0000.000
30A30PRO00.0430.0017.970-0.240-0.2400.0000.0000.0000.000
31A31ASN00.0330.02610.004-0.146-0.1460.0000.0000.0000.000
32A32LEU0-0.030-0.00412.988-0.179-0.1790.0000.0000.0000.000
33A33LEU0-0.041-0.0198.3910.0510.0510.0000.0000.0000.000
34A34PRO0-0.006-0.02612.751-0.101-0.1010.0000.0000.0000.000
35A35SER00.0370.00612.009-0.038-0.0380.0000.0000.0000.000
36A36CYS0-0.0500.02112.089-0.160-0.1600.0000.0000.0000.000
37A37GLU-1-0.825-0.9077.680-3.594-3.5940.0000.0000.0000.000
38A38GLN0-0.047-0.0279.029-0.446-0.4460.0000.0000.0000.000
39A39PRO0-0.006-0.00910.9050.1190.1190.0000.0000.0000.000
40A40ALA00.0010.01714.0850.0540.0540.0000.0000.0000.000
41A41PHE00.0280.00910.3450.1100.1100.0000.0000.0000.000
42A42SER0-0.012-0.00616.231-0.074-0.0740.0000.0000.0000.000
43A43MET00.0130.00818.0970.1060.1060.0000.0000.0000.000
44A44THR0-0.040-0.01420.164-0.063-0.0630.0000.0000.0000.000
45A45GLY0-0.005-0.00722.0450.0010.0010.0000.0000.0000.000
46A46SER0-0.037-0.01523.887-0.009-0.0090.0000.0000.0000.000
47A47ALA00.0210.02223.131-0.009-0.0090.0000.0000.0000.000
48A48LYS10.8800.93320.585-0.722-0.7220.0000.0000.0000.000
49A49LEU00.0020.01920.0320.0030.0030.0000.0000.0000.000
50A50TRP00.0760.03517.0740.0670.0670.0000.0000.0000.000
51A51GLY00.0080.00416.958-0.062-0.0620.0000.0000.0000.000
52A52ASN0-0.032-0.00615.8820.2040.2040.0000.0000.0000.000
53A53VAL00.0060.02115.625-0.124-0.1240.0000.0000.0000.000
54A54ASN00.0410.01016.0700.2120.2120.0000.0000.0000.000
55A55VAL00.006-0.00213.041-0.103-0.1030.0000.0000.0000.000
56A56VAL0-0.038-0.03216.2490.0300.0300.0000.0000.0000.000
57A57ALA00.0380.04213.910-0.047-0.0470.0000.0000.0000.000
58A58ARG10.9320.94815.857-0.143-0.1430.0000.0000.0000.000
59A60ALA00.0150.03118.2350.0020.0020.0000.0000.0000.000
60A61ASN00.000-0.02121.5920.0460.0460.0000.0000.0000.000
61A62GLU-1-0.910-0.94416.9510.0420.0420.0000.0000.0000.000
62A63LYS10.9250.96019.517-0.217-0.2170.0000.0000.0000.000
63A64ARG10.9290.97116.132-0.258-0.2580.0000.0000.0000.000
64A65TYR0-0.006-0.01517.129-0.010-0.0100.0000.0000.0000.000
65A66LEU00.0340.02711.2410.0260.0260.0000.0000.0000.000
66A67GLN00.0050.00613.888-0.064-0.0640.0000.0000.0000.000
67A68VAL00.0170.00210.7120.3150.3150.0000.0000.0000.000
68A69ASN0-0.082-0.07311.359-0.237-0.2370.0000.0000.0000.000
69A70VAL0-0.0070.00811.4240.2400.2400.0000.0000.0000.000
70A71GLN00.000-0.01212.537-0.271-0.2710.0000.0000.0000.000
71A72ALA00.0390.03214.257-0.027-0.0270.0000.0000.0000.000
72A73THR00.0390.01216.715-0.013-0.0130.0000.0000.0000.000
73A74GLY00.0570.04919.271-0.035-0.0350.0000.0000.0000.000
74A75ASN0-0.032-0.01922.4200.0130.0130.0000.0000.0000.000
75A76TYR00.0010.00426.2000.0140.0140.0000.0000.0000.000
76A77VAL00.0180.01028.328-0.016-0.0160.0000.0000.0000.000
77A78ALA0-0.026-0.01031.7790.0130.0130.0000.0000.0000.000
78A79VAL0-0.006-0.00633.483-0.016-0.0160.0000.0000.0000.000
79A80ALA0-0.009-0.00636.9280.0070.0070.0000.0000.0000.000
80A81ALA00.004-0.00438.578-0.005-0.0050.0000.0000.0000.000
81A82PRO00.0050.00841.8500.0060.0060.0000.0000.0000.000
82A83ILE0-0.046-0.01740.677-0.008-0.0080.0000.0000.0000.000
83A84ALA00.0280.02544.4410.0060.0060.0000.0000.0000.000
84A85ARG10.9370.96046.428-0.141-0.1410.0000.0000.0000.000
85A86GLY0-0.028-0.00746.635-0.006-0.0060.0000.0000.0000.000
86A87GLY00.0040.02546.435-0.007-0.0070.0000.0000.0000.000
87A88LYS10.9600.98144.750-0.094-0.0940.0000.0000.0000.000
88A89LEU00.0160.02038.1400.0000.0000.0000.0000.0000.000
89A90THR0-0.076-0.04842.050-0.005-0.0050.0000.0000.0000.000
90A91PRO00.0690.00140.5000.0060.0060.0000.0000.0000.000
91A92ALA00.0110.02941.2660.0020.0020.0000.0000.0000.000
92A93ASN00.008-0.00242.0450.0060.0060.0000.0000.0000.000
93A94VAL0-0.0040.00936.9330.0120.0120.0000.0000.0000.000
94A95THR00.0280.01134.318-0.010-0.0100.0000.0000.0000.000
95A96LEU0-0.0010.01130.0730.0150.0150.0000.0000.0000.000
96A97LYS10.9420.97428.584-0.257-0.2570.0000.0000.0000.000
97A98ARG11.0191.00622.928-0.233-0.2330.0000.0000.0000.000
98A99GLY0-0.040-0.02824.074-0.009-0.0090.0000.0000.0000.000
99A100ARG10.8680.88316.727-0.847-0.8470.0000.0000.0000.000
100A101LEU00.0390.02020.330-0.005-0.0050.0000.0000.0000.000
101A102ASP-1-0.809-0.86417.5300.8650.8650.0000.0000.0000.000
102A103GLN0-0.077-0.03819.017-0.017-0.0170.0000.0000.0000.000
103A104LEU0-0.0270.01522.431-0.050-0.0500.0000.0000.0000.000
104A105PRO00.0150.02525.3340.0250.0250.0000.0000.0000.000
105A106PRO00.0260.03826.920-0.008-0.0080.0000.0000.0000.000
106A107ARG10.9330.95927.896-0.308-0.3080.0000.0000.0000.000
107A108THR00.019-0.03327.695-0.031-0.0310.0000.0000.0000.000
108A109VAL0-0.038-0.02828.8430.0060.0060.0000.0000.0000.000
109A110LEU00.0050.00024.9040.0060.0060.0000.0000.0000.000
110A111ASP-1-0.790-0.89328.5920.1470.1470.0000.0000.0000.000
111A112ILE00.0380.00730.891-0.001-0.0010.0000.0000.0000.000
112A113ARG10.8810.94531.058-0.133-0.1330.0000.0000.0000.000
113A114GLN00.008-0.00730.9260.0030.0030.0000.0000.0000.000
114A115ILE0-0.044-0.01735.3140.0000.0000.0000.0000.0000.000
115A116GLN00.0350.03437.822-0.006-0.0060.0000.0000.0000.000
116A117ASP-1-0.953-1.01040.6570.1010.1010.0000.0000.0000.000
117A118ALA00.0270.02840.0830.0020.0020.0000.0000.0000.000
118A119VAL0-0.001-0.00942.129-0.004-0.0040.0000.0000.0000.000
119A120SER00.0370.00442.0920.0110.0110.0000.0000.0000.000
120A121LEU0-0.027-0.01340.876-0.009-0.0090.0000.0000.0000.000
121A122ARG10.8870.93639.676-0.209-0.2090.0000.0000.0000.000
122A123ASP-1-0.844-0.91843.5100.1420.1420.0000.0000.0000.000
123A124LEU0-0.052-0.03438.2960.0110.0110.0000.0000.0000.000
124A125ALA00.0480.03239.769-0.011-0.0110.0000.0000.0000.000
125A126PRO00.013-0.01338.5290.0090.0090.0000.0000.0000.000
126A127GLY0-0.0110.00034.4850.0050.0050.0000.0000.0000.000
127A128GLN0-0.010-0.00433.1240.0100.0100.0000.0000.0000.000
128A129PRO00.0260.01229.993-0.011-0.0110.0000.0000.0000.000
129A130VAL00.0430.02632.157-0.002-0.0020.0000.0000.0000.000
130A131GLN00.0160.01631.5310.0100.0100.0000.0000.0000.000
131A132LEU00.000-0.01831.875-0.014-0.0140.0000.0000.0000.000
132A133THR0-0.041-0.01734.433-0.009-0.0090.0000.0000.0000.000
133A134MET0-0.051-0.01535.342-0.011-0.0110.0000.0000.0000.000
134A135ILE0-0.0050.01237.023-0.010-0.0100.0000.0000.0000.000
135A136ARG10.9710.98440.145-0.122-0.1220.0000.0000.0000.000
136A137GLN0-0.061-0.03536.8080.0000.0000.0000.0000.0000.000
137A138ALA00.0370.03941.644-0.002-0.0020.0000.0000.0000.000
138A139TRP0-0.051-0.04443.094-0.001-0.0010.0000.0000.0000.000
139A140ARG10.8870.96541.039-0.087-0.0870.0000.0000.0000.000
140A141VAL00.0420.02643.257-0.007-0.0070.0000.0000.0000.000
141A142LYS10.9580.96745.354-0.068-0.0680.0000.0000.0000.000
142A143ALA0-0.0050.00348.610-0.003-0.0030.0000.0000.0000.000
143A144GLY0-0.016-0.00750.101-0.002-0.0020.0000.0000.0000.000
144A145GLN00.0110.00248.743-0.002-0.0020.0000.0000.0000.000
145A146ARG10.9150.96349.590-0.039-0.0390.0000.0000.0000.000
146A147VAL00.0010.00044.5690.0020.0020.0000.0000.0000.000
147A148GLN00.0190.00442.326-0.009-0.0090.0000.0000.0000.000
148A149VAL0-0.038-0.03040.4560.0080.0080.0000.0000.0000.000
149A150ILE00.0240.01436.446-0.007-0.0070.0000.0000.0000.000
150A151ALA0-0.003-0.00536.1860.0110.0110.0000.0000.0000.000
151A152ASN0-0.0200.00132.106-0.022-0.0220.0000.0000.0000.000
152A153GLY00.0220.00332.3080.0150.0150.0000.0000.0000.000
153A154GLU-1-0.966-0.98728.564-0.057-0.0570.0000.0000.0000.000
154A155GLY00.0150.01431.059-0.007-0.0070.0000.0000.0000.000
155A156PHE0-0.048-0.02732.974-0.002-0.0020.0000.0000.0000.000
156A157SER00.0180.01534.6230.0100.0100.0000.0000.0000.000
157A158VAL0-0.016-0.00936.816-0.005-0.0050.0000.0000.0000.000
158A159ASN00.0490.02239.5260.0110.0110.0000.0000.0000.000
159A160ALA0-0.026-0.01442.166-0.004-0.0040.0000.0000.0000.000
160A161GLU-1-0.851-0.92244.7490.0410.0410.0000.0000.0000.000
161A162GLY00.0470.01747.102-0.001-0.0010.0000.0000.0000.000
162A163GLN0-0.081-0.02647.978-0.001-0.0010.0000.0000.0000.000
163A164ALA00.0420.03746.5990.0030.0030.0000.0000.0000.000
164A165MET0-0.045-0.03946.869-0.003-0.0030.0000.0000.0000.000
165A166ASN0-0.019-0.01242.950-0.002-0.0020.0000.0000.0000.000
166A167ASN00.0150.01246.251-0.006-0.0060.0000.0000.0000.000
167A168ALA00.0160.01640.9960.0060.0060.0000.0000.0000.000
168A169ALA0-0.0180.00139.795-0.007-0.0070.0000.0000.0000.000
169A170VAL00.0650.02235.6990.0020.0020.0000.0000.0000.000
170A171ALA0-0.059-0.04532.9470.0110.0110.0000.0000.0000.000
171A172GLN0-0.0260.00334.5130.0050.0050.0000.0000.0000.000
172A173ASN0-0.031-0.02536.909-0.010-0.0100.0000.0000.0000.000
173A174ALA00.0120.00738.242-0.003-0.0030.0000.0000.0000.000
174A175ARG10.9420.96241.117-0.107-0.1070.0000.0000.0000.000
175A176VAL00.0300.01343.011-0.003-0.0030.0000.0000.0000.000
176A177ARG10.9510.97445.372-0.058-0.0580.0000.0000.0000.000
177A178MET00.0230.01044.6280.0000.0000.0000.0000.0000.000
178A179THR00.0680.03148.0260.0000.0000.0000.0000.0000.000
179A180SER0-0.031-0.01348.5540.0000.0000.0000.0000.0000.000
180A181GLY00.0100.00751.016-0.001-0.0010.0000.0000.0000.000
181A182GLN0-0.0270.00043.1010.0000.0000.0000.0000.0000.000
182A183ILE0-0.031-0.02644.7730.0020.0020.0000.0000.0000.000
183A184VAL00.0110.01340.0480.0030.0030.0000.0000.0000.000
184A185SER0-0.051-0.02538.5560.0050.0050.0000.0000.0000.000
185A186GLY00.0890.04136.570-0.001-0.0010.0000.0000.0000.000
186A187THR0-0.044-0.01433.2530.0090.0090.0000.0000.0000.000
187A188VAL0-0.0020.01636.136-0.009-0.0090.0000.0000.0000.000
188A189ASP-1-0.740-0.87535.3030.0990.0990.0000.0000.0000.000
189A190SER0-0.002-0.02336.188-0.002-0.0020.0000.0000.0000.000
190A191ASP-1-0.901-0.94138.0320.0640.0640.0000.0000.0000.000
191A192GLY0-0.101-0.05440.162-0.006-0.0060.0000.0000.0000.000
192A193ASN0-0.0020.01239.447-0.006-0.0060.0000.0000.0000.000
193A194ILE0-0.025-0.01939.1170.0100.0100.0000.0000.0000.000
194A195LEU0-0.0030.00533.372-0.007-0.0070.0000.0000.0000.000
195A196ILE0-0.011-0.02335.1940.0130.0130.0000.0000.0000.000
196A197ASN0-0.021-0.01227.630-0.025-0.0250.0000.0000.0000.000
197A198LEU0-0.0070.00928.8560.0060.0060.0000.0000.0000.000