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: GY511

Calculation Name: 3B77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B77

Chain ID: A

ChEMBL ID:

UniProt ID: B1YJX4

Base Structure: X-ray

Registration Date: 2023-09-27

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1996148.260219
FMO2-HF: Nuclear repulsion 1919450.351099
FMO2-HF: Total energy -76697.90912
FMO2-MP2: Total energy -76924.308925


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:14:ASP)


Summations of interaction energy for fragment #1(A:14:ASP)
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.
-23.903-16.47226.324-17.989-15.7650.184
Interaction energy analysis for fragmet #1(A:14:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.787 / q_NPA : -0.882
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].
3A16GLY0-0.003-0.0103.8148.36410.6670.001-1.132-1.1720.005
4A17GLN0-0.103-0.0756.127-2.117-2.1170.0000.0000.0000.000
5A18VAL0-0.001-0.0029.214-0.480-0.4800.0000.0000.0000.000
6A19ILE0-0.040-0.01311.051-0.036-0.0360.0000.0000.0000.000
7A20HIS00.0290.02014.232-0.560-0.5600.0000.0000.0000.000
8A21PRO00.037-0.01317.9200.2090.2090.0000.0000.0000.000
9A22ASP-1-0.899-0.94720.56212.91012.9100.0000.0000.0000.000
10A23ASP-1-0.949-0.97116.87716.47816.4780.0000.0000.0000.000
11A24PHE0-0.063-0.03516.9030.8580.8580.0000.0000.0000.000
12A25ASP-1-0.815-0.91318.44814.63114.6310.0000.0000.0000.000
13A26LYS10.7790.90117.531-15.081-15.0810.0000.0000.0000.000
14A27ALA0-0.102-0.03914.4681.2441.2440.0000.0000.0000.000
15A28ALA00.0430.01613.473-0.846-0.8460.0000.0000.0000.000
16A29ALA0-0.007-0.03113.845-0.955-0.9550.0000.0000.0000.000
17A30ASP-1-0.867-0.94215.72413.53913.5390.0000.0000.0000.000
18A31ASP-1-0.896-0.93618.94314.46514.4650.0000.0000.0000.000
19A32TYR0-0.108-0.06016.973-0.634-0.6340.0000.0000.0000.000
20A33VAL0-0.043-0.01519.299-0.175-0.1750.0000.0000.0000.000
21A34LEU0-0.010-0.00221.673-0.252-0.2520.0000.0000.0000.000
22A35HIS0-0.006-0.01222.687-0.864-0.8640.0000.0000.0000.000
23A36GLU-1-0.961-0.98126.92210.64510.6450.0000.0000.0000.000
24A37ASP-1-0.981-0.99028.4529.6789.6780.0000.0000.0000.000
25A38GLY0-0.045-0.02329.344-0.095-0.0950.0000.0000.0000.000
26A39GLU-1-0.783-0.82122.46613.30213.3020.0000.0000.0000.000
27A40LYS10.9650.98223.852-12.137-12.1370.0000.0000.0000.000
28A41ILE00.009-0.00317.6590.1280.1280.0000.0000.0000.000
29A42TYR0-0.114-0.10419.882-0.345-0.3450.0000.0000.0000.000
30A43PHE00.010-0.00613.5280.0260.0260.0000.0000.0000.000
31A44LEU00.0060.02612.6130.1250.1250.0000.0000.0000.000
32A45ILE00.0120.0167.9260.0300.0300.0000.0000.0000.000
33A46LYS10.8470.9157.908-26.443-26.4430.0000.0000.0000.000
34A47SER00.0710.0392.548-0.7891.1430.271-0.995-1.2080.003
35A48LYS10.7830.8771.787-171.711-172.08525.568-14.349-10.8450.183
36A49THR0-0.010-0.0332.875-7.515-5.3090.473-0.959-1.719-0.003
37A50ASP-1-0.799-0.8464.39330.09130.307-0.001-0.014-0.2000.000
38A51GLU-1-0.783-0.8856.09427.11427.1140.0000.0000.0000.000
39A52TYR0-0.027-0.0365.433-2.472-2.4720.0000.0000.0000.000
40A53CYS00.0000.00010.953-0.496-0.4960.0000.0000.0000.000
41A54PHE00.0170.01212.175-0.592-0.5920.0000.0000.0000.000
42A55THR00.0620.01117.056-0.349-0.3490.0000.0000.0000.000
43A56ASN00.0020.00620.7030.4180.4180.0000.0000.0000.000
44A57LEU00.0040.00123.355-0.381-0.3810.0000.0000.0000.000
45A58ALA0-0.008-0.01220.241-0.285-0.2850.0000.0000.0000.000
46A59LEU0-0.0060.03412.7980.2140.2140.0000.0000.0000.000
47A60VAL0-0.014-0.01315.631-0.256-0.2560.0000.0000.0000.000
48A61HIS0-0.0030.0068.063-1.561-1.5610.0000.0000.0000.000
49A62LEU0-0.0110.00711.039-1.032-1.0320.0000.0000.0000.000
50A63ASP-1-0.875-0.9538.80128.37128.3710.0000.0000.0000.000
51A64GLY00.0590.0137.585-2.200-2.2000.0000.0000.0000.000
52A65GLU-1-0.853-0.8976.99124.31424.3140.0000.0000.0000.000
53A66SER0-0.077-0.0568.450-2.149-2.1490.0000.0000.0000.000
54A67ALA00.0440.0246.8473.1073.1070.0000.0000.0000.000
55A68VAL0-0.017-0.0177.8891.7401.7400.0000.0000.0000.000
56A69SER0-0.020-0.02010.491-2.810-2.8100.0000.0000.0000.000
57A70SER00.0130.01111.158-1.422-1.4220.0000.0000.0000.000
58A71LYS10.8400.91912.194-20.377-20.3770.0000.0000.0000.000
59A72ARG10.8600.9377.464-32.237-32.2370.0000.0000.0000.000
60A73VAL00.0050.01412.456-1.751-1.7510.0000.0000.0000.000
61A74LEU0-0.0310.00913.2901.0051.0050.0000.0000.0000.000
62A75TYR0-0.038-0.02312.605-1.688-1.6880.0000.0000.0000.000
63A76ARG10.8360.86016.419-13.159-13.1590.0000.0000.0000.000
64A77TYR0-0.030-0.00914.494-0.374-0.3740.0000.0000.0000.000
65A78PRO00.019-0.00519.4800.0540.0540.0000.0000.0000.000
66A79TYR00.0510.01118.743-0.022-0.0220.0000.0000.0000.000
67A80ALA0-0.064-0.03522.975-0.192-0.1920.0000.0000.0000.000
68A81HIS0-0.030-0.00924.846-0.355-0.3550.0000.0000.0000.000
69A82TYR0-0.056-0.02420.2470.0810.0810.0000.0000.0000.000
70A83PRO0-0.012-0.01521.4940.2900.2900.0000.0000.0000.000
71A84ILE00.0280.02617.9910.3770.3770.0000.0000.0000.000
72A85ARG10.9210.96019.296-12.118-12.1180.0000.0000.0000.000
73A86HIS0-0.010-0.01118.5710.4540.4540.0000.0000.0000.000
74A87VAL00.0020.01417.0370.5900.5900.0000.0000.0000.000
75A88MET0-0.041-0.02115.170-0.707-0.7070.0000.0000.0000.000
76A89PHE0-0.016-0.02613.1100.5690.5690.0000.0000.0000.000
77A90GLU-1-0.836-0.89812.27916.47516.4750.0000.0000.0000.000
78A91THR0-0.037-0.01812.9010.6540.6540.0000.0000.0000.000
79A92ALA00.0310.01813.0090.2620.2620.0000.0000.0000.000
80A93GLY00.0230.01614.227-1.175-1.1750.0000.0000.0000.000
81A94THR0-0.079-0.06816.3620.6490.6490.0000.0000.0000.000
82A95VAL0-0.041-0.03114.7060.2280.2280.0000.0000.0000.000
83A96ASP-1-0.824-0.87611.51820.55420.5540.0000.0000.0000.000
84A97LEU0-0.002-0.0229.030-1.338-1.3380.0000.0000.0000.000
85A98ASP-1-0.880-0.9416.43231.64931.6490.0000.0000.0000.000
86A99VAL0-0.061-0.0219.384-2.201-2.2010.0000.0000.0000.000
87A100GLU-1-0.714-0.8047.39122.53722.5370.0000.0000.0000.000
88A101ILE0-0.072-0.0329.431-1.936-1.9360.0000.0000.0000.000
89A102LYS10.8450.88810.123-17.197-17.1970.0000.0000.0000.000
90A103PHE0-0.040-0.02312.137-0.971-0.9710.0000.0000.0000.000
91A104GLU-1-0.857-0.91813.93214.12414.1240.0000.0000.0000.000
92A105ILE00.0120.00115.276-0.587-0.5870.0000.0000.0000.000
93A106GLY00.002-0.00317.7040.1820.1820.0000.0000.0000.000
94A107GLY0-0.060-0.03819.550-0.262-0.2620.0000.0000.0000.000
95A108LYS10.8540.95111.943-19.126-19.1260.0000.0000.0000.000
96A109HIS0-0.018-0.01212.7220.3250.3250.0000.0000.0000.000
97A110TYR0-0.036-0.0409.3390.3860.3860.0000.0000.0000.000
98A111SER0-0.064-0.0587.213-0.599-0.5990.0000.0000.0000.000
99A112ILE0-0.001-0.0045.7441.3131.3130.0000.0000.0000.000
100A113ASP-1-0.833-0.9003.44526.51927.6670.012-0.540-0.621-0.004
101A114VAL0-0.051-0.0405.7163.3473.3470.0000.0000.0000.000
102A115ASP-1-0.718-0.8328.47023.49623.4960.0000.0000.0000.000
103A116LYS10.8630.92510.289-21.515-21.5150.0000.0000.0000.000
104A117LYS10.7670.87012.700-25.265-25.2650.0000.0000.0000.000
105A118GLN0-0.028-0.01712.0780.4920.4920.0000.0000.0000.000
106A119LEU00.0410.03615.217-0.368-0.3680.0000.0000.0000.000
107A120GLU-1-0.854-0.92916.10912.77912.7790.0000.0000.0000.000
108A121HIS00.0560.03216.4520.0460.0460.0000.0000.0000.000
109A122VAL00.0360.01912.225-0.383-0.3830.0000.0000.0000.000
110A123LYS10.7390.85115.223-13.894-13.8940.0000.0000.0000.000
111A124ASP-1-0.789-0.89218.09212.48112.4810.0000.0000.0000.000
112A125LEU0-0.0020.01713.564-0.604-0.6040.0000.0000.0000.000
113A126TYR0-0.004-0.00516.507-0.607-0.6070.0000.0000.0000.000
114A127LYS10.8280.90817.847-12.705-12.7050.0000.0000.0000.000
115A128ALA00.0120.00520.045-0.489-0.4890.0000.0000.0000.000
116A129LEU00.0300.01515.217-0.515-0.5150.0000.0000.0000.000
117A130LEU0-0.0270.00019.805-0.407-0.4070.0000.0000.0000.000
118A131ALA0-0.0020.00022.008-0.476-0.4760.0000.0000.0000.000
119A132ILE0-0.020-0.00921.172-0.460-0.4600.0000.0000.0000.000
120A133ALA00.0150.00521.684-0.357-0.3570.0000.0000.0000.000
121A134GLU-1-0.969-0.97323.6829.3149.3140.0000.0000.0000.000
122A135LYS10.8810.93327.050-9.162-9.1620.0000.0000.0000.000
123A136GLN00.0050.00223.741-0.050-0.0500.0000.0000.0000.000
124A137TYR0-0.005-0.00427.376-0.386-0.3860.0000.0000.0000.000
125A138GLU-1-0.882-0.93528.9318.2178.2170.0000.0000.0000.000
126A139GLY00.0140.00831.332-0.296-0.2960.0000.0000.0000.000
127A140GLN0-0.018-0.02329.573-0.301-0.3010.0000.0000.0000.000
128A141LYS10.8150.89432.615-8.403-8.4030.0000.0000.0000.000
129A142MET0-0.004-0.00135.313-0.335-0.3350.0000.0000.0000.000
130A143LEU0-0.0040.00233.325-0.251-0.2510.0000.0000.0000.000
131A144GLU-1-0.832-0.88535.0537.8157.8150.0000.0000.0000.000
132A145PHE00.0100.00538.638-0.214-0.2140.0000.0000.0000.000
133A146ALA00.0280.04140.250-0.224-0.2240.0000.0000.0000.000
134A147ASN00.0170.00538.641-0.253-0.2530.0000.0000.0000.000
135A148SER0-0.049-0.03542.325-0.174-0.1740.0000.0000.0000.000
136A149SER0-0.022-0.02744.693-0.190-0.1900.0000.0000.0000.000
137A150LEU0-0.0190.01345.551-0.156-0.1560.0000.0000.0000.000
138A151ASN00.028-0.00545.241-0.191-0.1910.0000.0000.0000.000
139A152HIS00.0060.01347.685-0.197-0.1970.0000.0000.0000.000
140A153SER00.0180.00650.613-0.154-0.1540.0000.0000.0000.000
141A154VAL0-0.0110.01350.556-0.126-0.1260.0000.0000.0000.000
142A155THR0-0.067-0.05252.221-0.115-0.1150.0000.0000.0000.000
143A156ILE0-0.082-0.03754.284-0.105-0.1050.0000.0000.0000.000
144A157LEU0-0.012-0.01655.241-0.102-0.1020.0000.0000.0000.000
145A158GLY00.0030.02457.438-0.051-0.0510.0000.0000.0000.000
146A159GLY0-0.065-0.02858.857-0.063-0.0630.0000.0000.0000.000
147A160LEU00.0460.03160.443-0.062-0.0620.0000.0000.0000.000
148A161ARG10.9510.96764.277-4.435-4.4350.0000.0000.0000.000
149A162GLN0-0.002-0.00966.7360.0020.0020.0000.0000.0000.000
150A163GLY0-0.050-0.03368.3870.0200.0200.0000.0000.0000.000
151A164ASP-1-0.906-0.94069.2884.4574.4570.0000.0000.0000.000
152A165MET00.0110.02263.6830.0650.0650.0000.0000.0000.000
153A166ASN0-0.007-0.00865.056-0.013-0.0130.0000.0000.0000.000
154A167VAL00.0570.02163.2460.0770.0770.0000.0000.0000.000
155A168PRO00.0210.01061.7920.0790.0790.0000.0000.0000.000
156A169GLN0-0.0010.00058.9280.0600.0600.0000.0000.0000.000
157A170THR00.026-0.00359.3180.0730.0730.0000.0000.0000.000
158A171PHE0-0.040-0.02055.9090.0770.0770.0000.0000.0000.000
159A172LYS10.8830.93255.882-5.212-5.2120.0000.0000.0000.000
160A173ASP-1-0.784-0.89254.4175.4465.4460.0000.0000.0000.000
161A174LEU0-0.0150.00653.9400.0830.0830.0000.0000.0000.000
162A175SER0-0.037-0.03151.7810.1150.1150.0000.0000.0000.000
163A176GLN0-0.099-0.04948.1870.0910.0910.0000.0000.0000.000
164A177GLU-1-0.888-0.94048.9966.0126.0120.0000.0000.0000.000
165A178SER0-0.058-0.02148.2610.1790.1790.0000.0000.0000.000
166A179PHE00.005-0.00343.1480.1930.1930.0000.0000.0000.000
167A180ASP-1-0.795-0.91044.3576.6126.6120.0000.0000.0000.000
168A181TRP0-0.033-0.00644.0400.1480.1480.0000.0000.0000.000
169A182LEU0-0.027-0.03141.8950.1790.1790.0000.0000.0000.000
170A183GLN0-0.036-0.00740.0900.3300.3300.0000.0000.0000.000
171A184GLY00.011-0.00239.2290.2040.2040.0000.0000.0000.000
172A185HIS00.0120.00139.1000.3410.3410.0000.0000.0000.000
173A186TYR0-0.0290.00031.8220.2330.2330.0000.0000.0000.000
174A187TYR00.003-0.01534.5630.3860.3860.0000.0000.0000.000
175A188LYS10.8840.96834.659-7.260-7.2600.0000.0000.0000.000
176A189TRP0-0.035-0.03833.8340.1460.1460.0000.0000.0000.000
177A190ASN0-0.041-0.00930.4110.3610.3610.0000.0000.0000.000
178A191GLN0-0.046-0.02129.002-0.162-0.1620.0000.0000.0000.000
179A192LYS10.9620.95928.007-9.072-9.0720.0000.0000.0000.000
180A193ASP-1-0.793-0.86326.63510.86210.8620.0000.0000.0000.000
181A194PHE00.005-0.00624.346-0.361-0.3610.0000.0000.0000.000
182A195GLY00.0760.02325.1410.3700.3700.0000.0000.0000.000
183A196SER0-0.0210.00026.2360.2750.2750.0000.0000.0000.000
184A197PHE0-0.022-0.02024.838-0.149-0.1490.0000.0000.0000.000
185A198TYR00.030-0.00318.7490.2870.2870.0000.0000.0000.000
186A199GLU-1-0.881-0.92423.60010.71610.7160.0000.0000.0000.000
187A200LYS10.8770.95426.697-9.761-9.7610.0000.0000.0000.000
188A201TYR0-0.038-0.04423.418-0.415-0.4150.0000.0000.0000.000
189A202ILE00.0070.02020.0700.2390.2390.0000.0000.0000.000
190A203ASN0-0.067-0.00823.196-0.028-0.0280.0000.0000.0000.000