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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: GNVN1

Calculation Name: 3BT3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BT3

Chain ID: A

ChEMBL ID:

UniProt ID: A9KJQ6

Base Structure: X-ray

Registration Date: 2023-03-14

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 131
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1125380.272596
FMO2-HF: Nuclear repulsion 1072549.207392
FMO2-HF: Total energy -52831.065204
FMO2-MP2: Total energy -52983.855815


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:134:GLU)


Summations of interaction energy for fragment #1(A:134:GLU)
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.
80.70479.66619.548-6.212-12.297-0.02
Interaction energy analysis for fragmet #1(A:134:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.947
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].
3A136GLY0-0.025-0.0053.771-5.145-2.753-0.019-1.125-1.2470.004
4A137TYR0-0.003-0.0022.351-3.108-9.06518.808-3.768-9.084-0.018
5A138VAL00.0170.0132.7678.40610.7170.759-1.258-1.811-0.006
6A139VAL00.0240.0074.019-6.839-6.6230.000-0.061-0.1550.000
7A140ARG10.9040.9526.185-29.312-29.3120.0000.0000.0000.000
8A141GLU-1-0.802-0.8949.53818.64718.6470.0000.0000.0000.000
9A142ASN0-0.065-0.05010.1360.8890.8890.0000.0000.0000.000
10A143GLY00.0360.04812.200-0.241-0.2410.0000.0000.0000.000
11A144PRO0-0.0020.00115.8920.3450.3450.0000.0000.0000.000
12A145VAL00.0130.00717.019-0.517-0.5170.0000.0000.0000.000
13A146TYR0-0.017-0.02819.575-0.196-0.1960.0000.0000.0000.000
14A147PHE0-0.039-0.01620.938-0.025-0.0250.0000.0000.0000.000
15A148THR00.020-0.00525.855-0.359-0.3590.0000.0000.0000.000
16A149LYS10.9150.95429.415-9.187-9.1870.0000.0000.0000.000
17A150ASP-1-0.871-0.94132.5408.4478.4470.0000.0000.0000.000
18A151MET00.0000.03728.2120.0650.0650.0000.0000.0000.000
19A152ASP-1-0.760-0.87131.4679.0689.0680.0000.0000.0000.000
20A153LYS10.9090.96834.280-8.853-8.8530.0000.0000.0000.000
21A154THR0-0.031-0.04529.060-0.092-0.0920.0000.0000.0000.000
22A155VAL00.023-0.00129.5370.1730.1730.0000.0000.0000.000
23A156LYS10.9840.99931.731-8.424-8.4240.0000.0000.0000.000
24A157TRP00.0220.03030.4300.0140.0140.0000.0000.0000.000
25A158PHE0-0.014-0.02626.9140.0340.0340.0000.0000.0000.000
26A159GLU-1-0.941-0.95831.7139.4319.4310.0000.0000.0000.000
27A160GLU-1-0.980-1.00533.9148.0188.0180.0000.0000.0000.000
28A161ILE0-0.060-0.02034.893-0.154-0.1540.0000.0000.0000.000
29A162LEU0-0.044-0.03929.2930.0100.0100.0000.0000.0000.000
30A163GLY0-0.0200.01432.1000.1500.1500.0000.0000.0000.000
31A164TRP0-0.060-0.03824.2130.4500.4500.0000.0000.0000.000
32A165SER00.0220.00628.797-0.480-0.4800.0000.0000.0000.000
33A166GLY0-0.001-0.01428.1630.4900.4900.0000.0000.0000.000
34A167ASP-1-0.958-0.96627.96410.16910.1690.0000.0000.0000.000
35A168ILE0-0.071-0.03427.7440.4270.4270.0000.0000.0000.000
36A169VAL00.0370.01725.087-0.194-0.1940.0000.0000.0000.000
37A170ALA0-0.033-0.02027.673-0.176-0.1760.0000.0000.0000.000
38A171ARG10.7690.86329.408-8.902-8.9020.0000.0000.0000.000
39A172ASP-1-0.753-0.86032.3238.9558.9550.0000.0000.0000.000
40A173ASP-1-0.967-1.00133.7538.3158.3150.0000.0000.0000.000
41A174GLU-1-1.012-1.00136.8997.7287.7280.0000.0000.0000.000
42A175GLY0-0.041-0.00736.951-0.165-0.1650.0000.0000.0000.000
43A176PHE0-0.040-0.01333.9590.0930.0930.0000.0000.0000.000
44A177GLY0-0.0130.00030.8540.1080.1080.0000.0000.0000.000
45A178ASP-1-0.888-0.96627.54410.25110.2510.0000.0000.0000.000
46A179TYR0-0.038-0.05819.9150.3840.3840.0000.0000.0000.000
47A180GLY00.0540.00724.653-0.525-0.5250.0000.0000.0000.000
48A181CYS0-0.089-0.01322.6170.6310.6310.0000.0000.0000.000
49A182VAL00.0530.03124.167-0.528-0.5280.0000.0000.0000.000
50A183PHE00.011-0.02423.1100.8530.8530.0000.0000.0000.000
51A184ASP-1-0.888-0.94023.54312.87812.8780.0000.0000.0000.000
52A185TYR0-0.035-0.00320.8830.0170.0170.0000.0000.0000.000
53A186PRO00.0450.00826.927-0.068-0.0680.0000.0000.0000.000
54A187SER00.0790.01927.5840.3280.3280.0000.0000.0000.000
55A188GLU-1-1.001-0.99027.85810.39110.3910.0000.0000.0000.000
56A189VAL0-0.044-0.02423.0560.2240.2240.0000.0000.0000.000
57A190ALA00.0630.02222.2640.0320.0320.0000.0000.0000.000
58A191VAL0-0.0400.00122.9080.2530.2530.0000.0000.0000.000
59A192ALA0-0.071-0.04524.387-0.091-0.0910.0000.0000.0000.000
60A193HIS-1-0.912-1.02518.76615.93615.9360.0000.0000.0000.000
61A194LEU0-0.049-0.05019.4520.1100.1100.0000.0000.0000.000
62A195THR0-0.0630.05514.355-0.112-0.1120.0000.0000.0000.000
63A196PRO0-0.130-0.09314.3011.5161.5160.0000.0000.0000.000
64A197PHE00.1440.11416.170-1.009-1.0090.0000.0000.0000.000
65A198ARG10.8690.93316.222-14.817-14.8170.0000.0000.0000.000
66A199GLY00.0540.04218.316-0.482-0.4820.0000.0000.0000.000
67A200PHE0-0.070-0.03919.7810.8010.8010.0000.0000.0000.000
68A201HIS00.0240.02315.907-1.220-1.2200.0000.0000.0000.000
69A202LEU0-0.046-0.03021.008-0.074-0.0740.0000.0000.0000.000
70A203PHE00.0280.00718.9060.0700.0700.0000.0000.0000.000
71A204LYS10.8980.95824.740-10.008-10.0080.0000.0000.0000.000
72A205GLY0-0.047-0.03427.0740.2500.2500.0000.0000.0000.000
73A206GLU-1-0.981-1.00528.5469.3019.3010.0000.0000.0000.000
74A207PRO00.0310.03227.9700.4200.4200.0000.0000.0000.000
75A208ILE0-0.005-0.00322.837-0.030-0.0300.0000.0000.0000.000
76A209LYS10.9430.97227.183-10.061-10.0610.0000.0000.0000.000
77A210GLY00.0220.00627.8270.2000.2000.0000.0000.0000.000
78A211VAL0-0.039-0.02723.278-0.124-0.1240.0000.0000.0000.000
79A212ALA00.0010.00423.3010.3800.3800.0000.0000.0000.000
80A213GLY00.0350.01521.8090.5700.5700.0000.0000.0000.000
81A214PHE0-0.061-0.02719.258-0.647-0.6470.0000.0000.0000.000
82A215MET00.0070.01420.4420.8170.8170.0000.0000.0000.000
83A216MET0-0.0080.00220.289-0.514-0.5140.0000.0000.0000.000
84A217ILE0-0.020-0.01923.1330.1700.1700.0000.0000.0000.000
85A218GLU-1-0.927-0.96226.08111.62611.6260.0000.0000.0000.000
86A219GLY0-0.0250.00228.751-0.182-0.1820.0000.0000.0000.000
87A220ILE0-0.006-0.02030.223-0.158-0.1580.0000.0000.0000.000
88A221ASP-1-0.848-0.92032.4928.7098.7090.0000.0000.0000.000
89A222ALA0-0.029-0.01434.579-0.226-0.2260.0000.0000.0000.000
90A223LEU00.0350.02630.253-0.160-0.1600.0000.0000.0000.000
91A224HIS00.0130.00034.088-0.333-0.3330.0000.0000.0000.000
92A225LYS10.9170.96336.459-7.844-7.8440.0000.0000.0000.000
93A226TYR0-0.0090.01035.164-0.199-0.1990.0000.0000.0000.000
94A227VAL00.0250.01134.403-0.110-0.1100.0000.0000.0000.000
95A228LYS10.8770.94537.396-8.038-8.0380.0000.0000.0000.000
96A229GLU-1-0.919-0.97140.8187.3217.3210.0000.0000.0000.000
97A230ASN0-0.106-0.03938.098-0.341-0.3410.0000.0000.0000.000
98A231GLY0-0.0150.00041.191-0.007-0.0070.0000.0000.0000.000
99A232TRP0-0.052-0.01035.863-0.149-0.1490.0000.0000.0000.000
100A233ASP-1-0.825-0.94840.1077.4817.4810.0000.0000.0000.000
101A234GLN0-0.125-0.04637.4550.0580.0580.0000.0000.0000.000
102A235ILE00.006-0.00734.0770.3330.3330.0000.0000.0000.000
103A236SER0-0.027-0.00334.478-0.133-0.1330.0000.0000.0000.000
104A237ASP-1-0.895-0.95836.4258.0308.0300.0000.0000.0000.000
105A238ILE0-0.026-0.01333.9090.2580.2580.0000.0000.0000.000
106A239TYR0-0.039-0.02131.525-0.178-0.1780.0000.0000.0000.000
107A240THR0-0.019-0.02532.6790.3030.3030.0000.0000.0000.000
108A241GLN0-0.003-0.00328.317-0.325-0.3250.0000.0000.0000.000
109A242PRO0-0.026-0.02329.7240.0010.0010.0000.0000.0000.000
110A243TRP0-0.071-0.03224.3140.0360.0360.0000.0000.0000.000
111A244GLY00.0270.02626.3460.3890.3890.0000.0000.0000.000
112A245ALA00.006-0.00126.6870.1900.1900.0000.0000.0000.000
113A246ARG10.8370.92128.812-9.516-9.5160.0000.0000.0000.000
114A247GLU-1-0.741-0.86727.80612.02512.0250.0000.0000.0000.000
115A248CYS0-0.0300.01230.206-0.476-0.4760.0000.0000.0000.000
116A249SER0-0.024-0.01529.9780.3790.3790.0000.0000.0000.000
117A250ILE00.0310.01530.544-0.390-0.3900.0000.0000.0000.000
118A251THR0-0.0020.00731.0850.4270.4270.0000.0000.0000.000
119A252THR00.0360.00729.379-0.316-0.3160.0000.0000.0000.000
120A253THR0-0.016-0.00332.677-0.262-0.2620.0000.0000.0000.000
121A254ASP-1-0.835-0.88630.9129.8349.8340.0000.0000.0000.000
122A255GLY0-0.020-0.00432.846-0.010-0.0100.0000.0000.0000.000
123A256CYS0-0.056-0.00827.328-0.012-0.0120.0000.0000.0000.000
124A257ILE0-0.0030.00928.346-0.224-0.2240.0000.0000.0000.000
125A258LEU00.0030.00325.5230.6270.6270.0000.0000.0000.000
126A259ARG10.8010.86924.776-12.827-12.8270.0000.0000.0000.000
127A260PHE00.0460.02425.3590.5290.5290.0000.0000.0000.000
128A261PHE0-0.005-0.02021.071-0.390-0.3900.0000.0000.0000.000
129A262GLU-1-0.760-0.87826.23210.87410.8740.0000.0000.0000.000
130A263SER0-0.026-0.01225.483-0.132-0.1320.0000.0000.0000.000
131A264ILE0-0.040-0.01627.511-0.324-0.3240.0000.0000.0000.000