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: 9GJR2

Calculation Name: 3WRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WRV

Chain ID: A

ChEMBL ID:

UniProt ID: A7M6E7

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972308.352873
FMO2-HF: Nuclear repulsion 1900141.402075
FMO2-HF: Total energy -72166.950798
FMO2-MP2: Total energy -72375.813911


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:7:ASN)


Summations of interaction energy for fragment #1(A:7: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.
-28.263-27.6110.814-5.609-5.857-0.048
Interaction energy analysis for fragmet #1(A:7:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.043
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].
3A9PRO0-0.0090.0073.336-4.942-2.9220.063-1.113-0.9710.002
4A10ARG10.9100.9664.3783.9894.189-0.001-0.007-0.1910.000
5A11VAL00.0010.0146.4450.2540.2540.0000.0000.0000.000
6A12PHE00.0260.0126.2370.2690.2690.0000.0000.0000.000
7A13CYS0-0.040-0.01611.6200.1850.1850.0000.0000.0000.000
8A14ILE00.0280.01213.4880.0650.0650.0000.0000.0000.000
9A15GLY00.018-0.00916.6530.0980.0980.0000.0000.0000.000
10A16THR0-0.0320.00519.698-0.031-0.0310.0000.0000.0000.000
11A17ALA00.0590.01120.3730.0550.0550.0000.0000.0000.000
12A18ASP-1-0.802-0.86922.367-0.409-0.4090.0000.0000.0000.000
13A19THR0-0.049-0.04125.4520.0440.0440.0000.0000.0000.000
14A20LYS10.8710.93824.0330.4650.4650.0000.0000.0000.000
15A21PHE00.0080.01721.003-0.032-0.0320.0000.0000.0000.000
16A22ASP-1-0.904-0.95522.949-0.332-0.3320.0000.0000.0000.000
17A23GLU-1-0.787-0.93324.763-0.404-0.4040.0000.0000.0000.000
18A24LEU0-0.006-0.00418.200-0.020-0.0200.0000.0000.0000.000
19A25ARG10.9090.95519.7430.2310.2310.0000.0000.0000.000
20A26PHE0-0.0110.00120.3950.0050.0050.0000.0000.0000.000
21A27LEU00.0210.01319.4960.0170.0170.0000.0000.0000.000
22A28SER00.022-0.00915.935-0.082-0.0820.0000.0000.0000.000
23A29GLU-1-0.813-0.89517.006-0.347-0.3470.0000.0000.0000.000
24A30HIS0-0.022-0.01819.1200.0440.0440.0000.0000.0000.000
25A31VAL0-0.0080.01614.6510.0180.0180.0000.0000.0000.000
26A32ARG10.7960.87814.0310.3350.3350.0000.0000.0000.000
27A33SER00.0070.00615.5750.0320.0320.0000.0000.0000.000
28A34SER00.016-0.00318.5600.0700.0700.0000.0000.0000.000
29A35LEU00.0030.00312.1540.0290.0290.0000.0000.0000.000
30A36ASN0-0.113-0.06214.1940.1470.1470.0000.0000.0000.000
31A37SER0-0.041-0.02116.5190.0570.0570.0000.0000.0000.000
32A38PHE0-0.012-0.01918.7230.0350.0350.0000.0000.0000.000
33A39SER0-0.072-0.00715.2660.0240.0240.0000.0000.0000.000
34A40ASN0-0.037-0.01217.2620.1060.1060.0000.0000.0000.000
35A41LYS10.9990.98213.484-0.215-0.2150.0000.0000.0000.000
36A42SER0-0.053-0.04514.7560.0900.0900.0000.0000.0000.000
37A43SER0-0.041-0.01211.6730.0420.0420.0000.0000.0000.000
38A44PHE00.025-0.0057.2950.1950.1950.0000.0000.0000.000
39A45LYS10.8810.9608.121-0.195-0.1950.0000.0000.0000.000
40A46VAL00.0680.0497.783-0.081-0.0810.0000.0000.0000.000
41A47GLY0-0.0110.0076.7820.4450.4450.0000.0000.0000.000
42A48VAL0-0.022-0.0327.907-0.395-0.3950.0000.0000.0000.000
43A49THR0-0.043-0.0507.8980.0210.0210.0000.0000.0000.000
44A50VAL0-0.036-0.00310.451-0.042-0.0420.0000.0000.0000.000
45A51VAL00.021-0.00211.626-0.057-0.0570.0000.0000.0000.000
46A52ASP-1-0.776-0.86213.999-0.583-0.5830.0000.0000.0000.000
47A53VAL00.019-0.00616.910-0.040-0.0400.0000.0000.0000.000
48A54SER0-0.105-0.06019.1940.0770.0770.0000.0000.0000.000
49A55THR00.0330.01022.2580.0090.0090.0000.0000.0000.000
50A56SER0-0.118-0.10124.8310.0500.0500.0000.0000.0000.000
51A57TRP00.0400.00726.172-0.019-0.0190.0000.0000.0000.000
52A58LYS10.8380.93226.4940.3310.3310.0000.0000.0000.000
53A59GLU-1-0.860-0.91723.346-0.313-0.3130.0000.0000.0000.000
54A60THR0-0.049-0.04020.4570.0380.0380.0000.0000.0000.000
55A61ASN00.008-0.00818.934-0.068-0.0680.0000.0000.0000.000
56A62SER0-0.016-0.00117.3000.0020.0020.0000.0000.0000.000
57A63CYS00.0000.00117.0450.0310.0310.0000.0000.0000.000
58A64ALA0-0.010-0.00417.523-0.028-0.0280.0000.0000.0000.000
59A65ASP-1-0.828-0.88316.837-0.161-0.1610.0000.0000.0000.000
60A66PHE0-0.054-0.01013.4050.0260.0260.0000.0000.0000.000
61A67ASP-1-0.839-0.9057.862-1.825-1.8250.0000.0000.0000.000
62A68PHE0-0.012-0.01611.191-0.140-0.1400.0000.0000.0000.000
63A69VAL00.0210.0189.364-0.013-0.0130.0000.0000.0000.000
64A70PRO00.0190.00912.3580.0280.0280.0000.0000.0000.000
65A71SER00.0740.01915.266-0.086-0.0860.0000.0000.0000.000
66A72LYS10.8160.89114.6130.6190.6190.0000.0000.0000.000
67A73ASP-1-0.809-0.90611.878-0.815-0.8150.0000.0000.0000.000
68A74VAL00.0050.01513.320-0.121-0.1210.0000.0000.0000.000
69A75LEU00.005-0.01714.390-0.006-0.0060.0000.0000.0000.000
70A76SER0-0.082-0.02914.0730.0320.0320.0000.0000.0000.000
71A77CYS0-0.069-0.02112.097-0.013-0.0130.0000.0000.0000.000
72A78HIS00.0260.02714.100-0.125-0.1250.0000.0000.0000.000
73A79THR0-0.037-0.00917.3710.0880.0880.0000.0000.0000.000
74A80LEU0-0.037-0.02920.510-0.012-0.0120.0000.0000.0000.000
75A81GLY00.0460.01523.7140.0140.0140.0000.0000.0000.000
76A82GLU-1-0.949-0.98225.682-0.401-0.4010.0000.0000.0000.000
77A83GLU-1-0.816-0.90623.470-0.559-0.5590.0000.0000.0000.000
78A84THR0-0.022-0.02327.0860.0260.0260.0000.0000.0000.000
79A85MET0-0.069-0.02929.2320.0330.0330.0000.0000.0000.000
80A86GLY0-0.0100.00531.1940.0140.0140.0000.0000.0000.000
81A87THR0-0.026-0.02732.5390.0090.0090.0000.0000.0000.000
82A88PHE0-0.027-0.00329.4290.0020.0020.0000.0000.0000.000
83A89ALA00.0070.00934.5850.0150.0150.0000.0000.0000.000
84A90ASP-1-0.847-0.91833.612-0.303-0.3030.0000.0000.0000.000
85A91THR00.0550.00831.203-0.011-0.0110.0000.0000.0000.000
86A92ARG10.8970.96228.7900.3320.3320.0000.0000.0000.000
87A93GLY00.015-0.00528.916-0.034-0.0340.0000.0000.0000.000
88A94LEU00.0290.02728.996-0.024-0.0240.0000.0000.0000.000
89A95ALA00.003-0.00426.080-0.030-0.0300.0000.0000.0000.000
90A96ILE0-0.039-0.02724.474-0.052-0.0520.0000.0000.0000.000
91A97ALA00.0140.01424.086-0.055-0.0550.0000.0000.0000.000
92A98ILE00.0270.01222.341-0.044-0.0440.0000.0000.0000.000
93A99MET0-0.0340.01219.158-0.099-0.0990.0000.0000.0000.000
94A100SER0-0.069-0.03419.206-0.098-0.0980.0000.0000.0000.000
95A101LYS10.8740.91419.4810.6700.6700.0000.0000.0000.000
96A102ALA00.0020.01017.266-0.073-0.0730.0000.0000.0000.000
97A103LEU0-0.037-0.02714.107-0.167-0.1670.0000.0000.0000.000
98A104GLU-1-0.839-0.91414.440-1.072-1.0720.0000.0000.0000.000
99A105THR00.001-0.00113.970-0.130-0.1300.0000.0000.0000.000
100A106PHE00.0490.0218.719-0.288-0.2880.0000.0000.0000.000
101A107LEU0-0.044-0.0269.870-0.538-0.5380.0000.0000.0000.000
102A108SER00.0120.01510.577-0.312-0.3120.0000.0000.0000.000
103A109ILE00.0050.0067.810-0.030-0.0300.0000.0000.0000.000
104A110ALA00.0040.0056.297-0.569-0.5690.0000.0000.0000.000
105A111ASN0-0.074-0.0717.112-0.688-0.6880.0000.0000.0000.000
106A112ASP-1-0.901-0.9389.795-1.526-1.5260.0000.0000.0000.000
107A113GLU-1-1.020-1.0035.323-4.925-4.9250.0000.0000.0000.000
108A114GLN0-0.070-0.0415.266-1.617-1.6170.0000.0000.0000.000
109A115ASN00.0260.0271.888-15.807-17.42510.753-4.482-4.653-0.050
110A116LEU0-0.056-0.0134.5941.0451.096-0.001-0.007-0.0420.000
111A117ALA00.010-0.0228.1290.6870.6870.0000.0000.0000.000
112A118GLY00.012-0.00510.2080.4760.4760.0000.0000.0000.000
113A119VAL0-0.037-0.01212.122-0.282-0.2820.0000.0000.0000.000
114A120ILE00.0280.02314.5250.1960.1960.0000.0000.0000.000
115A121GLY00.0780.02416.869-0.093-0.0930.0000.0000.0000.000
116A122LEU0-0.0500.00319.5130.0850.0850.0000.0000.0000.000
117A123GLY00.025-0.00122.829-0.028-0.0280.0000.0000.0000.000
118A124GLY00.0160.02225.4930.0250.0250.0000.0000.0000.000
119A125SER00.0380.02028.295-0.036-0.0360.0000.0000.0000.000
120A126GLY00.0270.01228.460-0.015-0.0150.0000.0000.0000.000
121A127GLY00.0570.02024.355-0.026-0.0260.0000.0000.0000.000
122A128THR00.0260.01723.861-0.058-0.0580.0000.0000.0000.000
123A129SER0-0.0100.00125.050-0.021-0.0210.0000.0000.0000.000
124A130LEU0-0.0250.01320.148-0.020-0.0200.0000.0000.0000.000
125A131LEU00.0220.00418.598-0.054-0.0540.0000.0000.0000.000
126A132SER0-0.020-0.01920.342-0.054-0.0540.0000.0000.0000.000
127A133SER0-0.023-0.01121.923-0.015-0.0150.0000.0000.0000.000
128A134ALA00.0350.03417.370-0.005-0.0050.0000.0000.0000.000
129A135PHE00.010-0.00716.715-0.113-0.1130.0000.0000.0000.000
130A136ARG10.8440.90518.6140.6000.6000.0000.0000.0000.000
131A137SER0-0.066-0.01817.8170.0080.0080.0000.0000.0000.000
132A138LEU00.0080.00313.748-0.067-0.0670.0000.0000.0000.000
133A139PRO00.0290.01215.6410.1300.1300.0000.0000.0000.000
134A140ILE0-0.0100.00018.237-0.058-0.0580.0000.0000.0000.000
135A141GLY0-0.025-0.01418.8890.0080.0080.0000.0000.0000.000
136A142ILE0-0.008-0.00113.425-0.011-0.0110.0000.0000.0000.000
137A143PRO00.0030.00214.6480.1030.1030.0000.0000.0000.000
138A144LYS10.7860.87916.1300.9260.9260.0000.0000.0000.000
139A145VAL00.0150.00718.5910.1200.1200.0000.0000.0000.000
140A146ILE00.0350.00420.248-0.052-0.0520.0000.0000.0000.000
141A147ILE0-0.043-0.01422.7680.0710.0710.0000.0000.0000.000
142A148SER00.038-0.00825.1210.0100.0100.0000.0000.0000.000
143A149THR0-0.030-0.03227.7920.0170.0170.0000.0000.0000.000
144A150VAL0-0.012-0.01930.4340.0280.0280.0000.0000.0000.000
145A151ALA0-0.0170.00929.5940.0080.0080.0000.0000.0000.000
146A152SER0-0.034-0.00531.2860.0130.0130.0000.0000.0000.000
147A153GLY00.030-0.00235.0630.0120.0120.0000.0000.0000.000
148A154GLN0-0.033-0.00335.569-0.009-0.0090.0000.0000.0000.000
149A155THR00.0340.00530.779-0.012-0.0120.0000.0000.0000.000
150A156GLU-1-0.888-0.93130.853-0.364-0.3640.0000.0000.0000.000
151A157SER0-0.016-0.00931.183-0.027-0.0270.0000.0000.0000.000
152A158TYR00.0090.00327.040-0.017-0.0170.0000.0000.0000.000
153A159ILE00.0600.03226.100-0.051-0.0510.0000.0000.0000.000
154A160GLY00.0040.02627.048-0.029-0.0290.0000.0000.0000.000
155A161THR0-0.013-0.01627.3430.0350.0350.0000.0000.0000.000
156A162SER0-0.091-0.04723.197-0.021-0.0210.0000.0000.0000.000
157A163ASP-1-0.738-0.85820.885-0.846-0.8460.0000.0000.0000.000
158A164LEU0-0.034-0.01121.398-0.014-0.0140.0000.0000.0000.000
159A165VAL0-0.0090.00423.0820.0700.0700.0000.0000.0000.000
160A166LEU0-0.004-0.00624.224-0.033-0.0330.0000.0000.0000.000
161A167PHE00.009-0.00624.9340.0360.0360.0000.0000.0000.000
162A168PRO00.0420.02127.655-0.004-0.0040.0000.0000.0000.000
163A169SER0-0.018-0.02828.659-0.001-0.0010.0000.0000.0000.000
164A170VAL0-0.033-0.02130.7960.0140.0140.0000.0000.0000.000
165A171VAL0-0.0240.00032.5110.0110.0110.0000.0000.0000.000
166A172ASP-1-0.847-0.92934.645-0.201-0.2010.0000.0000.0000.000
167A173ILE0-0.060-0.01134.7190.0120.0120.0000.0000.0000.000
168A174CYS0-0.009-0.00930.540-0.029-0.0290.0000.0000.0000.000
169A175GLY00.0190.02929.5800.0180.0180.0000.0000.0000.000
170A176ILE0-0.0120.00326.634-0.012-0.0120.0000.0000.0000.000
171A177ASN0-0.017-0.03430.5040.0090.0090.0000.0000.0000.000
172A178ASN00.007-0.00332.878-0.013-0.0130.0000.0000.0000.000
173A179VAL00.0670.02533.426-0.009-0.0090.0000.0000.0000.000
174A180SER00.0500.03230.439-0.014-0.0140.0000.0000.0000.000
175A181LYS10.9510.98028.7160.2240.2240.0000.0000.0000.000
176A182VAL00.0120.02228.238-0.023-0.0230.0000.0000.0000.000
177A183VAL0-0.0010.01028.810-0.012-0.0120.0000.0000.0000.000
178A184LEU0-0.0130.00224.402-0.039-0.0390.0000.0000.0000.000
179A185SER0-0.005-0.01424.009-0.035-0.0350.0000.0000.0000.000
180A186ASN0-0.0150.00224.089-0.023-0.0230.0000.0000.0000.000
181A187ALA00.0000.00623.376-0.025-0.0250.0000.0000.0000.000
182A188GLY00.0300.00420.202-0.063-0.0630.0000.0000.0000.000
183A189ALA00.0100.00619.722-0.062-0.0620.0000.0000.0000.000
184A190ALA0-0.009-0.01521.298-0.010-0.0100.0000.0000.0000.000
185A191PHE0-0.020-0.01414.204-0.016-0.0160.0000.0000.0000.000
186A192ALA00.001-0.00316.527-0.079-0.0790.0000.0000.0000.000
187A193GLY00.0230.00317.229-0.030-0.0300.0000.0000.0000.000
188A194MET0-0.054-0.02018.8140.0110.0110.0000.0000.0000.000
189A195VAL0-0.010-0.00212.353-0.036-0.0360.0000.0000.0000.000
190A196ILE0-0.020-0.01313.869-0.058-0.0580.0000.0000.0000.000
191A197GLY00.0150.02115.9760.0420.0420.0000.0000.0000.000
192A198ARG10.9180.96911.7071.7121.7120.0000.0000.0000.000
193A199LEU0-0.053-0.02210.566-0.053-0.0530.0000.0000.0000.000
194A200GLU-1-0.883-0.93514.437-0.255-0.2550.0000.0000.0000.000
195A201SER0-0.051-0.01917.2620.0990.0990.0000.0000.0000.000