FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 5JJNZ

Calculation Name: 4GVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q7A2Q1

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptAll
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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2420967.625002
FMO2-HF: Nuclear repulsion 2338197.371483
FMO2-HF: Total energy -82770.253519
FMO2-MP2: Total energy -83009.567722


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:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-36.525-38.18423.299-11.465-10.175-0.098
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.056
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].
3A4LYS10.8490.9193.8710.8352.697-0.007-0.815-1.0400.004
4A5VAL0-0.011-0.0135.3761.0941.157-0.001-0.003-0.0580.000
5A6LEU0-0.0180.0078.161-0.092-0.0920.0000.0000.0000.000
6A7PHE0-0.017-0.02711.5190.1470.1470.0000.0000.0000.000
7A8VAL0-0.032-0.01713.8370.0330.0330.0000.0000.0000.000
8A9ASP-1-0.791-0.90517.605-0.411-0.4110.0000.0000.0000.000
9A10ASP-1-0.830-0.91320.290-0.384-0.3840.0000.0000.0000.000
10A11HIS00.0050.01423.1080.0070.0070.0000.0000.0000.000
11A12GLU-1-0.811-0.88421.184-0.566-0.5660.0000.0000.0000.000
12A13MET0-0.025-0.01820.915-0.036-0.0360.0000.0000.0000.000
13A14VAL0-0.0090.00020.287-0.004-0.0040.0000.0000.0000.000
14A15ARG10.7540.84416.3970.6580.6580.0000.0000.0000.000
15A16ILE00.0320.01316.456-0.074-0.0740.0000.0000.0000.000
16A17GLY0-0.016-0.00616.855-0.032-0.0320.0000.0000.0000.000
17A18ILE0-0.021-0.01614.0360.0080.0080.0000.0000.0000.000
18A19SER00.009-0.01812.436-0.112-0.1120.0000.0000.0000.000
19A20SER0-0.027-0.00212.125-0.120-0.1200.0000.0000.0000.000
20A21TYR0-0.030-0.00212.2680.0990.0990.0000.0000.0000.000
21A22LEU0-0.001-0.0018.9940.0690.0690.0000.0000.0000.000
22A23SER0-0.004-0.0138.181-0.080-0.0800.0000.0000.0000.000
23A24THR0-0.089-0.0508.7440.0950.0950.0000.0000.0000.000
24A25GLN0-0.041-0.0166.9240.4930.4930.0000.0000.0000.000
25A26SER00.0280.0054.891-0.828-0.711-0.001-0.018-0.0980.000
26A27ASP-1-0.807-0.8682.2871.3972.3701.833-1.186-1.620-0.006
27A28ILE0-0.036-0.0152.586-2.798-1.7191.759-0.998-1.840-0.020
28A29GLU-1-0.842-0.8941.620-32.354-38.10819.717-8.439-5.524-0.076
29A30VAL0-0.020-0.0104.4770.3840.385-0.001-0.0060.0050.000
30A31VAL0-0.0100.0026.1520.2360.2360.0000.0000.0000.000
31A32GLY00.0110.0058.5990.3870.3870.0000.0000.0000.000
32A33GLU-1-0.810-0.87612.340-1.036-1.0360.0000.0000.0000.000
33A34GLY0-0.007-0.00715.1000.0440.0440.0000.0000.0000.000
34A35ALA0-0.003-0.00118.717-0.008-0.0080.0000.0000.0000.000
35A36SER00.0250.00921.7050.0460.0460.0000.0000.0000.000
36A37GLY00.0850.01021.732-0.049-0.0490.0000.0000.0000.000
37A38LYS10.9200.94822.5230.3320.3320.0000.0000.0000.000
38A39GLU-1-0.802-0.87819.770-0.598-0.5980.0000.0000.0000.000
39A40ALA00.0100.01718.025-0.064-0.0640.0000.0000.0000.000
40A41ILE0-0.007-0.01218.206-0.045-0.0450.0000.0000.0000.000
41A42ALA0-0.046-0.01119.981-0.008-0.0080.0000.0000.0000.000
42A43LYS10.8810.91115.3250.7370.7370.0000.0000.0000.000
43A44ALA00.0090.01314.811-0.128-0.1280.0000.0000.0000.000
44A45HIS0-0.026-0.03115.361-0.048-0.0480.0000.0000.0000.000
45A46GLU-1-0.996-0.99016.184-0.673-0.6730.0000.0000.0000.000
46A47LEU0-0.028-0.02611.0730.0180.0180.0000.0000.0000.000
47A48LYS10.8010.91310.6360.4750.4750.0000.0000.0000.000
48A49PRO00.0090.0219.096-0.162-0.1620.0000.0000.0000.000
49A50ASP-1-0.805-0.9006.097-2.445-2.4450.0000.0000.0000.000
50A51LEU0-0.054-0.0259.1270.3730.3730.0000.0000.0000.000
51A52ILE00.0150.01010.603-0.222-0.2220.0000.0000.0000.000
52A53LEU0-0.0330.00212.5410.1400.1400.0000.0000.0000.000
53A54MET00.001-0.00714.275-0.036-0.0360.0000.0000.0000.000
54A55ASP-1-0.759-0.86517.871-0.312-0.3120.0000.0000.0000.000
55A56LEU0-0.012-0.01921.2030.0010.0010.0000.0000.0000.000
56A57LEU0-0.086-0.04924.3070.0220.0220.0000.0000.0000.000
57A58MET00.0190.02622.001-0.014-0.0140.0000.0000.0000.000
58A59GLU-1-0.957-0.96625.977-0.262-0.2620.0000.0000.0000.000
59A60ASP-1-0.816-0.90426.187-0.352-0.3520.0000.0000.0000.000
60A61MET0-0.086-0.03325.7800.0130.0130.0000.0000.0000.000
61A62ASP-1-0.717-0.82326.477-0.266-0.2660.0000.0000.0000.000
62A63GLY00.043-0.00423.086-0.016-0.0160.0000.0000.0000.000
63A64VAL0-0.017-0.00222.989-0.021-0.0210.0000.0000.0000.000
64A65GLU-1-0.855-0.91125.535-0.243-0.2430.0000.0000.0000.000
65A66ALA00.0320.00821.980-0.008-0.0080.0000.0000.0000.000
66A67THR0-0.041-0.03720.459-0.042-0.0420.0000.0000.0000.000
67A68THR0-0.022-0.01621.9680.0050.0050.0000.0000.0000.000
68A69GLN0-0.065-0.05624.4290.0080.0080.0000.0000.0000.000
69A70ILE00.0090.02117.730-0.012-0.0120.0000.0000.0000.000
70A71LYS10.7890.87016.7910.3980.3980.0000.0000.0000.000
71A72LYS10.8260.91221.1090.3110.3110.0000.0000.0000.000
72A73ASP-1-0.871-0.92121.898-0.285-0.2850.0000.0000.0000.000
73A74LEU0-0.071-0.04216.8520.0030.0030.0000.0000.0000.000
74A75PRO00.0170.01217.172-0.052-0.0520.0000.0000.0000.000
75A76GLN0-0.046-0.03413.9520.0000.0000.0000.0000.0000.000
76A77ILE0-0.0300.01612.779-0.028-0.0280.0000.0000.0000.000
77A78LYS10.8610.92812.1180.3880.3880.0000.0000.0000.000
78A79VAL00.001-0.00614.040-0.113-0.1130.0000.0000.0000.000
79A80LEU0-0.035-0.02013.6240.0890.0890.0000.0000.0000.000
80A81MET0-0.033-0.00116.408-0.030-0.0300.0000.0000.0000.000
81A82LEU00.0110.00316.8870.0390.0390.0000.0000.0000.000
82A83THR00.0620.00920.5400.0040.0040.0000.0000.0000.000
83A84SER0-0.0020.00524.3060.0010.0010.0000.0000.0000.000
84A85PHE0-0.007-0.00427.0480.0180.0180.0000.0000.0000.000
85A86ILE00.0090.00925.265-0.014-0.0140.0000.0000.0000.000
86A87GLU-1-0.810-0.90128.983-0.130-0.1300.0000.0000.0000.000
87A88ASP-1-0.830-0.89830.495-0.100-0.1000.0000.0000.0000.000
88A89LYS10.8060.87431.0950.1380.1380.0000.0000.0000.000
89A90GLU-1-0.742-0.83929.130-0.173-0.1730.0000.0000.0000.000
90A91VAL00.0060.00125.237-0.014-0.0140.0000.0000.0000.000
91A92TYR0-0.014-0.02727.0380.0000.0000.0000.0000.0000.000
92A93ARG10.7890.86828.9830.1990.1990.0000.0000.0000.000
93A94ALA00.0280.01724.176-0.010-0.0100.0000.0000.0000.000
94A95LEU0-0.036-0.02123.634-0.009-0.0090.0000.0000.0000.000
95A96ASP-1-0.804-0.89125.630-0.118-0.1180.0000.0000.0000.000
96A97ALA0-0.0130.01825.3640.0050.0050.0000.0000.0000.000
97A98GLY0-0.010-0.01122.707-0.020-0.0200.0000.0000.0000.000
98A99VAL0-0.022-0.00919.983-0.026-0.0260.0000.0000.0000.000
99A100ASP-1-0.766-0.84516.694-0.314-0.3140.0000.0000.0000.000
100A101SER00.024-0.00416.0660.0790.0790.0000.0000.0000.000
101A102TYR0-0.007-0.00118.842-0.045-0.0450.0000.0000.0000.000
102A103ILE0-0.018-0.01217.4390.0420.0420.0000.0000.0000.000
103A104LEU00.0260.01521.662-0.028-0.0280.0000.0000.0000.000
104A105LYS10.7700.85420.6970.3840.3840.0000.0000.0000.000
105A106THR0-0.003-0.00421.888-0.013-0.0130.0000.0000.0000.000
106A107THR0-0.068-0.03218.6740.0370.0370.0000.0000.0000.000
107A108SER0-0.027-0.04419.119-0.039-0.0390.0000.0000.0000.000
108A109ALA00.0900.03115.530-0.006-0.0060.0000.0000.0000.000
109A110LYS10.8870.93214.329-0.051-0.0510.0000.0000.0000.000
110A111ASP-1-0.840-0.88014.205-0.010-0.0100.0000.0000.0000.000
111A112ILE00.0240.01313.6470.0080.0080.0000.0000.0000.000
112A113ALA00.0250.02010.327-0.066-0.0660.0000.0000.0000.000
113A114ASP-1-0.859-0.93710.2460.2510.2510.0000.0000.0000.000
114A115ALA00.0060.01012.3250.0280.0280.0000.0000.0000.000
115A116VAL00.0240.0248.0340.0070.0070.0000.0000.0000.000
116A117ARG10.7740.8567.146-0.458-0.4580.0000.0000.0000.000
117A118LYS10.7940.8949.129-0.055-0.0550.0000.0000.0000.000
118A119THR00.0290.00112.6220.0540.0540.0000.0000.0000.000
119A120SER0-0.072-0.0457.9240.0220.0220.0000.0000.0000.000
120A121ARG10.7840.8849.859-0.382-0.3820.0000.0000.0000.000
121A122GLY00.0010.00610.9690.0480.0480.0000.0000.0000.000
122A123GLU-1-0.856-0.90414.2130.2030.2030.0000.0000.0000.000
123A124SER00.011-0.00516.003-0.040-0.0400.0000.0000.0000.000
124A125VAL0-0.089-0.04615.8870.0530.0530.0000.0000.0000.000
125A126PHE00.032-0.00619.014-0.029-0.0290.0000.0000.0000.000
126A127GLU-1-0.753-0.87822.258-0.137-0.1370.0000.0000.0000.000
127A128PRO00.012-0.00423.6600.0140.0140.0000.0000.0000.000
128A129GLU-1-0.951-0.96926.196-0.066-0.0660.0000.0000.0000.000
129A130VAL0-0.041-0.02826.5380.0030.0030.0000.0000.0000.000
130A131LEU0-0.0270.01222.8560.0060.0060.0000.0000.0000.000
131A132VAL0-0.001-0.01226.3270.0050.0050.0000.0000.0000.000
132A133LYS10.8530.91429.1890.0800.0800.0000.0000.0000.000
133A134MET00.0260.02925.871-0.001-0.0010.0000.0000.0000.000
134A135ARG10.9780.99021.923-0.018-0.0180.0000.0000.0000.000
135A136ASN0-0.020-0.01126.9670.0100.0100.0000.0000.0000.000
136A137ARG10.7580.86529.0800.0900.0900.0000.0000.0000.000
137A138MET00.0090.00021.625-0.001-0.0010.0000.0000.0000.000
138A139LYS10.8700.92427.273-0.008-0.0080.0000.0000.0000.000
139A140LYS10.8640.90929.2710.0210.0210.0000.0000.0000.000
140A141ARG10.8930.93825.9570.1230.1230.0000.0000.0000.000
141A142ALA00.0230.02127.1350.0000.0000.0000.0000.0000.000
142A143GLU-1-0.789-0.87228.906-0.002-0.0020.0000.0000.0000.000
143A144LEU0-0.062-0.00332.1410.0030.0030.0000.0000.0000.000
144A145TYR00.012-0.00828.6950.0020.0020.0000.0000.0000.000
145A146GLU-1-0.927-0.96333.2150.0120.0120.0000.0000.0000.000
146A147MET0-0.031-0.00635.5680.0050.0050.0000.0000.0000.000
147A148LEU0-0.081-0.02933.781-0.003-0.0030.0000.0000.0000.000
148A149THR0-0.027-0.05137.8670.0060.0060.0000.0000.0000.000
149A150GLU-1-0.888-0.95337.8450.0040.0040.0000.0000.0000.000
150A151ARG10.8230.89437.7680.0220.0220.0000.0000.0000.000
151A152GLU-1-0.803-0.86737.893-0.038-0.0380.0000.0000.0000.000
152A153MET00.0650.04631.715-0.010-0.0100.0000.0000.0000.000
153A154GLU-1-0.837-0.90533.711-0.023-0.0230.0000.0000.0000.000
154A155ILE0-0.054-0.03534.587-0.007-0.0070.0000.0000.0000.000
155A156LEU00.0210.01530.486-0.008-0.0080.0000.0000.0000.000
156A157LEU00.0370.02128.680-0.011-0.0110.0000.0000.0000.000
157A158LEU0-0.052-0.02930.202-0.008-0.0080.0000.0000.0000.000
158A159ILE0-0.044-0.03431.101-0.009-0.0090.0000.0000.0000.000
159A160ALA00.0170.01426.945-0.013-0.0130.0000.0000.0000.000
160A161LYS10.8770.94126.7510.0440.0440.0000.0000.0000.000
161A162GLY00.0360.02528.441-0.005-0.0050.0000.0000.0000.000
162A163TYR0-0.0260.00929.6920.0030.0030.0000.0000.0000.000
163A164SER00.016-0.02733.3310.0000.0000.0000.0000.0000.000
164A165ASN00.032-0.01736.3020.0020.0020.0000.0000.0000.000
165A166GLN00.0530.02139.3040.0080.0080.0000.0000.0000.000
166A167GLU-1-0.795-0.83835.138-0.089-0.0890.0000.0000.0000.000
167A168ILE00.0030.00835.3150.0060.0060.0000.0000.0000.000
168A169ALA0-0.021-0.00838.3310.0060.0060.0000.0000.0000.000
169A170SER0-0.027-0.03240.7850.0050.0050.0000.0000.0000.000
170A171ALA0-0.028-0.00237.7830.0040.0040.0000.0000.0000.000
171A172SER0-0.020-0.01539.3820.0060.0060.0000.0000.0000.000
172A173HIS0-0.0090.01141.3990.0030.0030.0000.0000.0000.000
173A174ILE0-0.0170.00142.0880.0020.0020.0000.0000.0000.000
174A175THR00.0420.02045.321-0.004-0.0040.0000.0000.0000.000
175A176ILE00.0730.02843.323-0.001-0.0010.0000.0000.0000.000
176A177LYS10.9500.98044.6290.0420.0420.0000.0000.0000.000
177A178THR00.0130.01345.0170.0000.0000.0000.0000.0000.000
178A179VAL00.0260.02339.7360.0000.0000.0000.0000.0000.000
179A180LYS10.9290.95741.1780.0710.0710.0000.0000.0000.000
180A181THR0-0.045-0.02942.428-0.002-0.0020.0000.0000.0000.000
181A182HIS00.0560.02240.010-0.001-0.0010.0000.0000.0000.000
182A183VAL00.0030.00537.054-0.001-0.0010.0000.0000.0000.000
183A184SER00.0040.00138.347-0.004-0.0040.0000.0000.0000.000
184A185ASN0-0.047-0.02240.508-0.002-0.0020.0000.0000.0000.000
185A186ILE00.0170.00734.4790.0010.0010.0000.0000.0000.000
186A187LEU0-0.026-0.01034.509-0.001-0.0010.0000.0000.0000.000
187A188SER0-0.026-0.00836.496-0.001-0.0010.0000.0000.0000.000
188A189LYS10.7850.86237.6230.0330.0330.0000.0000.0000.000
189A190LEU0-0.026-0.00131.4130.0040.0040.0000.0000.0000.000
190A191GLU-1-0.845-0.89833.068-0.076-0.0760.0000.0000.0000.000
191A192VAL0-0.035-0.00230.623-0.009-0.0090.0000.0000.0000.000
192A193GLN00.014-0.00633.9060.0120.0120.0000.0000.0000.000
193A194ASP-1-0.805-0.89131.809-0.158-0.1580.0000.0000.0000.000
194A195ARG10.8400.90032.1320.1100.1100.0000.0000.0000.000
195A196THR0-0.022-0.02927.4890.0010.0010.0000.0000.0000.000
196A197GLN00.0510.00227.8600.0030.0030.0000.0000.0000.000
197A198ALA0-0.0100.00528.2940.0040.0040.0000.0000.0000.000
198A199VAL0-0.043-0.02125.2820.0110.0110.0000.0000.0000.000
199A200ILE00.0160.01423.0060.0070.0070.0000.0000.0000.000
200A201TYR0-0.041-0.03823.9830.0030.0030.0000.0000.0000.000
201A202ALA00.003-0.00225.6020.0130.0130.0000.0000.0000.000
202A203PHE00.0100.00120.5800.0140.0140.0000.0000.0000.000
203A204GLN0-0.020-0.00218.953-0.010-0.0100.0000.0000.0000.000
204A205HIS0-0.076-0.03321.6390.0150.0150.0000.0000.0000.000
205A206ASN0-0.063-0.03220.7110.0110.0110.0000.0000.0000.000
206A207LEU00.0050.01422.4830.0180.0180.0000.0000.0000.000
207A208ILE0-0.029-0.01423.5680.0100.0100.0000.0000.0000.000
208A209GLN0-0.022-0.00319.081-0.022-0.0220.0000.0000.0000.000