Manual

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: P4J4N

Calculation Name: 1BGF-A-Xray25

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BGF

Chain ID: A

ChEMBL ID:

UniProt ID: P42228

Base Structure: X-ray

Registration Date: 2018-07-25

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1263686.363192
FMO2-HF: Nuclear repulsion 1208013.598284
FMO2-HF: Total energy -55672.764908
FMO2-MP2: Total energy -55833.02498


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
1.1662.494-0.027-0.648-0.6520
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.020
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].
3A2SER00.0160.0143.773-0.0231.305-0.027-0.648-0.6520.000
4A3GLN0-0.004-0.0206.9380.4120.4120.0000.0000.0000.000
5A4TRP0-0.035-0.0369.6370.1180.1180.0000.0000.0000.000
6A5ASN00.0050.0136.1770.6410.6410.0000.0000.0000.000
7A6GLN00.0880.0436.7460.1890.1890.0000.0000.0000.000
8A7VAL00.0170.0129.7810.0110.0110.0000.0000.0000.000
9A8GLN0-0.062-0.04511.315-0.072-0.0720.0000.0000.0000.000
10A9GLN0-0.081-0.0269.176-0.014-0.0140.0000.0000.0000.000
11A10LEU0-0.0360.01212.4760.0070.0070.0000.0000.0000.000
12A11GLU-1-0.966-0.98015.7380.1270.1270.0000.0000.0000.000
13A12ILE00.0660.01618.909-0.008-0.0080.0000.0000.0000.000
14A13LYS10.8850.92220.616-0.149-0.1490.0000.0000.0000.000
15A14PHE00.0040.01017.901-0.005-0.0050.0000.0000.0000.000
16A15LEU0-0.0030.00519.809-0.011-0.0110.0000.0000.0000.000
17A16GLU-1-0.942-0.96522.0660.0460.0460.0000.0000.0000.000
18A17GLN0-0.017-0.01223.334-0.004-0.0040.0000.0000.0000.000
19A18VAL00.0010.00019.956-0.002-0.0020.0000.0000.0000.000
20A19ASP-1-0.945-0.96023.400-0.014-0.0140.0000.0000.0000.000
21A20GLN00.0800.05526.213-0.010-0.0100.0000.0000.0000.000
22A21PHE0-0.084-0.03323.3530.0000.0000.0000.0000.0000.000
23A22TYR0-0.035-0.03019.185-0.024-0.0240.0000.0000.0000.000
24A23ASP-1-0.678-0.83725.604-0.024-0.0240.0000.0000.0000.000
25A24ASP-1-0.948-0.97427.941-0.047-0.0470.0000.0000.0000.000
26A25ASN0-0.165-0.09328.081-0.010-0.0100.0000.0000.0000.000
27A26PHE0-0.011-0.03218.909-0.012-0.0120.0000.0000.0000.000
28A27PRO00.0720.06224.2270.0060.0060.0000.0000.0000.000
29A28MET00.0750.02119.924-0.017-0.0170.0000.0000.0000.000
30A29GLU-1-0.836-0.93119.925-0.114-0.1140.0000.0000.0000.000
31A30ILE0-0.021-0.01219.954-0.028-0.0280.0000.0000.0000.000
32A31ARG10.7580.86912.6790.1080.1080.0000.0000.0000.000
33A32HIS00.0160.00915.059-0.035-0.0350.0000.0000.0000.000
34A33LEU0-0.040-0.02114.934-0.065-0.0650.0000.0000.0000.000
35A34LEU0-0.055-0.01615.792-0.052-0.0520.0000.0000.0000.000
36A35ALA00.0380.03711.9290.0120.0120.0000.0000.0000.000
37A36GLN00.0210.0007.682-0.296-0.2960.0000.0000.0000.000
38A37TRP00.0230.01711.5730.0620.0620.0000.0000.0000.000
39A38ILE00.016-0.00415.0770.0450.0450.0000.0000.0000.000
40A39GLU-1-0.708-0.8489.827-0.336-0.3360.0000.0000.0000.000
41A40THR0-0.053-0.01612.7450.0120.0120.0000.0000.0000.000
42A41GLN0-0.052-0.02314.3280.0500.0500.0000.0000.0000.000
43A42ASP-1-0.859-0.92217.759-0.013-0.0130.0000.0000.0000.000
44A43TRP0-0.051-0.03818.0000.0090.0090.0000.0000.0000.000
45A44GLU-1-0.775-0.90619.298-0.015-0.0150.0000.0000.0000.000
46A45VAL0-0.0180.00722.9680.0040.0040.0000.0000.0000.000
47A46ALA0-0.024-0.00624.2420.0010.0010.0000.0000.0000.000
48A47SER0-0.044-0.02125.7380.0010.0010.0000.0000.0000.000
49A48ASN0-0.020-0.01027.5830.0030.0030.0000.0000.0000.000
50A49ASN00.0380.01828.855-0.003-0.0030.0000.0000.0000.000
51A50GLU-1-0.851-0.92829.933-0.034-0.0340.0000.0000.0000.000
52A51THR0-0.0020.00330.810-0.005-0.0050.0000.0000.0000.000
53A52MET0-0.022-0.01924.271-0.004-0.0040.0000.0000.0000.000
54A53ALA00.0210.02226.852-0.009-0.0090.0000.0000.0000.000
55A54THR0-0.018-0.00627.770-0.007-0.0070.0000.0000.0000.000
56A55ILE00.0000.00025.533-0.007-0.0070.0000.0000.0000.000
57A56LEU00.0080.00821.894-0.012-0.0120.0000.0000.0000.000
58A57LEU00.0100.02024.195-0.014-0.0140.0000.0000.0000.000
59A58GLN0-0.009-0.02726.6010.0000.0000.0000.0000.0000.000
60A59ASN0-0.016-0.01622.742-0.005-0.0050.0000.0000.0000.000
61A60LEU00.0530.04021.551-0.017-0.0170.0000.0000.0000.000
62A61LEU0-0.024-0.02523.367-0.011-0.0110.0000.0000.0000.000
63A62ILE0-0.0010.02923.878-0.004-0.0040.0000.0000.0000.000
64A63GLN00.0470.01618.937-0.038-0.0380.0000.0000.0000.000
65A64LEU00.0020.00721.950-0.013-0.0130.0000.0000.0000.000
66A65ASP-1-0.803-0.90523.812-0.117-0.1170.0000.0000.0000.000
67A66GLU-1-0.958-0.95720.629-0.233-0.2330.0000.0000.0000.000
68A67GLN0-0.0060.00017.872-0.007-0.0070.0000.0000.0000.000
69A68LEU0-0.021-0.01322.1200.0050.0050.0000.0000.0000.000
70A69GLY00.0070.02125.5120.0080.0080.0000.0000.0000.000
71A70ARG10.9350.96815.6720.3820.3820.0000.0000.0000.000
72A71VAL00.0310.00922.4820.0070.0070.0000.0000.0000.000
73A72SER0-0.051-0.03624.5490.0180.0180.0000.0000.0000.000
74A73LYS10.9280.97825.1480.1680.1680.0000.0000.0000.000
75A74GLU-1-0.856-0.94020.579-0.240-0.2400.0000.0000.0000.000
76A75LYS10.9070.96225.3990.1070.1070.0000.0000.0000.000
77A76ASN00.0480.04122.9750.0230.0230.0000.0000.0000.000
78A77LEU00.012-0.01826.5940.0010.0010.0000.0000.0000.000
79A78LEU00.0430.03226.2650.0030.0030.0000.0000.0000.000
80A79LEU00.0630.02321.6190.0040.0040.0000.0000.0000.000
81A80ILE00.0020.01726.0210.0020.0020.0000.0000.0000.000
82A81HIS0-0.099-0.04328.5250.0080.0080.0000.0000.0000.000
83A82ASN00.0930.04826.9220.0110.0110.0000.0000.0000.000
84A83LEU00.0570.02223.2270.0040.0040.0000.0000.0000.000
85A84LYS10.8710.94827.3490.0950.0950.0000.0000.0000.000
86A85ARG10.9470.98030.7830.0620.0620.0000.0000.0000.000
87A86ILE00.0980.05925.4360.0050.0050.0000.0000.0000.000
88A87ARG10.8490.92129.0970.1020.1020.0000.0000.0000.000
89A88LYS10.8870.95229.8780.0610.0610.0000.0000.0000.000
90A89VAL00.0100.01630.9440.0040.0040.0000.0000.0000.000
91A90LEU00.0800.02825.8340.0040.0040.0000.0000.0000.000
92A91GLN0-0.022-0.01030.3030.0020.0020.0000.0000.0000.000
93A92GLY00.0240.02333.0150.0030.0030.0000.0000.0000.000
94A93LYS10.9200.96630.4260.0440.0440.0000.0000.0000.000
95A94PHE0-0.050-0.03331.3450.0020.0020.0000.0000.0000.000
96A95HIS0-0.057-0.02832.7710.0030.0030.0000.0000.0000.000
97A96GLY0-0.0200.00435.3260.0040.0040.0000.0000.0000.000
98A97ASN00.0310.01033.7360.0000.0000.0000.0000.0000.000
99A98PRO00.0840.03029.9190.0000.0000.0000.0000.0000.000
100A99MET00.0380.01528.854-0.003-0.0030.0000.0000.0000.000
101A100HIS0-0.043-0.00828.8110.0030.0030.0000.0000.0000.000
102A101VAL0-0.011-0.00225.3680.0020.0020.0000.0000.0000.000
103A102ALA00.0020.01524.441-0.002-0.0020.0000.0000.0000.000
104A103VAL00.0160.03324.2290.0040.0040.0000.0000.0000.000
105A104VAL0-0.031-0.00424.7710.0060.0060.0000.0000.0000.000
106A105ILE00.0060.01419.6880.0050.0050.0000.0000.0000.000
107A106SER00.012-0.01120.4310.0050.0050.0000.0000.0000.000
108A107ASN0-0.038-0.03020.8840.0180.0180.0000.0000.0000.000
109A108CYS00.0050.02020.1530.0150.0150.0000.0000.0000.000
110A109LEU0-0.0010.00614.9390.0160.0160.0000.0000.0000.000
111A110ARG10.9460.96516.917-0.048-0.0480.0000.0000.0000.000
112A111GLU-1-0.784-0.87119.2410.1090.1090.0000.0000.0000.000
113A112GLU-1-0.741-0.83114.8020.0090.0090.0000.0000.0000.000
114A113ARG10.8480.91014.400-0.048-0.0480.0000.0000.0000.000
115A114ARG10.8210.90616.151-0.072-0.0720.0000.0000.0000.000
116A115ILE00.0260.00818.0320.0210.0210.0000.0000.0000.000
117A116LEU0-0.008-0.00811.8580.0120.0120.0000.0000.0000.000
118A117ALA0-0.0350.00015.5920.0410.0410.0000.0000.0000.000
119A118ALA0-0.040-0.01617.332-0.002-0.0020.0000.0000.0000.000
120A119ALA0-0.0390.02016.781-0.020-0.0200.0000.0000.0000.000
121A120ASN00.002-0.01118.5770.0310.0310.0000.0000.0000.000
122A121MET0-0.042-0.02611.9600.0090.0090.0000.0000.0000.000
123A122PRO0-0.053-0.00516.926-0.022-0.0220.0000.0000.0000.000
124A123ILE-1-0.922-0.95717.0760.3930.3930.0000.0000.0000.000
125A125HOH00.0370.02020.241-0.001-0.0010.0000.0000.0000.000
126A126HOH0-0.058-0.05324.2040.0050.0050.0000.0000.0000.000
127A127HOH0-0.0010.00322.808-0.008-0.0080.0000.0000.0000.000
128A128HOH0-0.015-0.01433.2340.0000.0000.0000.0000.0000.000
129A129HOH0-0.033-0.02426.450-0.002-0.0020.0000.0000.0000.000
130A130HOH00.0320.02114.158-0.010-0.0100.0000.0000.0000.000
131A131HOH0-0.016-0.02028.696-0.003-0.0030.0000.0000.0000.000
132A133HOH0-0.033-0.02416.053-0.020-0.0200.0000.0000.0000.000
133A134HOH0-0.046-0.02819.1650.0090.0090.0000.0000.0000.000
134A136HOH0-0.020-0.01430.9170.0020.0020.0000.0000.0000.000
135A137HOH0-0.031-0.02114.424-0.005-0.0050.0000.0000.0000.000
136A138HOH0-0.045-0.03623.3140.0050.0050.0000.0000.0000.000
137A141HOH00.0380.02219.479-0.005-0.0050.0000.0000.0000.000
138A142HOH0-0.021-0.01931.4020.0010.0010.0000.0000.0000.000
139A144HOH00.000-0.02717.341-0.012-0.0120.0000.0000.0000.000
140A146HOH0-0.028-0.02020.714-0.010-0.0100.0000.0000.0000.000
141A150HOH00.0140.01117.893-0.003-0.0030.0000.0000.0000.000
142A157HOH0-0.039-0.02311.3890.0130.0130.0000.0000.0000.000
143A159HOH0-0.012-0.00721.9100.0050.0050.0000.0000.0000.000
144A161HOH0-0.023-0.01934.0860.0020.0020.0000.0000.0000.000
145A162HOH0-0.031-0.02325.210-0.001-0.0010.0000.0000.0000.000
146A163HOH00.0050.00521.1470.0020.0020.0000.0000.0000.000
147A164HOH0-0.030-0.02333.6110.0000.0000.0000.0000.0000.000
148A166HOH0-0.029-0.02225.7850.0040.0040.0000.0000.0000.000
149A167HOH0-0.035-0.02035.8690.0020.0020.0000.0000.0000.000
150A168HOH0-0.009-0.00432.889-0.001-0.0010.0000.0000.0000.000
151A169HOH0-0.048-0.03215.696-0.019-0.0190.0000.0000.0000.000
152A170HOH0-0.046-0.02527.5850.0020.0020.0000.0000.0000.000
153A173HOH0-0.021-0.0238.751-0.113-0.1130.0000.0000.0000.000
154A174HOH00.0350.01736.3350.0000.0000.0000.0000.0000.000
155A175HOH00.0390.02433.886-0.001-0.0010.0000.0000.0000.000
156A176HOH0-0.079-0.07627.5870.0010.0010.0000.0000.0000.000
157A177HOH00.0160.00616.545-0.012-0.0120.0000.0000.0000.000
158A180HOH00.0270.01436.075-0.002-0.0020.0000.0000.0000.000
159A183HOH0-0.042-0.03632.7800.0020.0020.0000.0000.0000.000
160A184HOH0-0.044-0.03716.2300.0170.0170.0000.0000.0000.000
161A186HOH0-0.066-0.04327.6960.0040.0040.0000.0000.0000.000
162A192HOH00.0200.01516.250-0.011-0.0110.0000.0000.0000.000
163A193HOH0-0.027-0.0276.4320.1010.1010.0000.0000.0000.000
164A198HOH0-0.025-0.02332.0430.0000.0000.0000.0000.0000.000
165A199HOH0-0.028-0.01728.4850.0000.0000.0000.0000.0000.000
166A201HOH0-0.034-0.01837.4330.0010.0010.0000.0000.0000.000
167A205HOH0-0.031-0.02528.1970.0020.0020.0000.0000.0000.000
168A207HOH0-0.019-0.02716.114-0.007-0.0070.0000.0000.0000.000
169A210HOH00.0030.00727.1760.0040.0040.0000.0000.0000.000
170A211HOH00.0060.01613.7700.0080.0080.0000.0000.0000.000
171A222HOH0-0.023-0.01719.528-0.010-0.0100.0000.0000.0000.000
172A229HOH00.0300.03815.822-0.019-0.0190.0000.0000.0000.000
173A230HOH0-0.043-0.02329.2460.0030.0030.0000.0000.0000.000
174A231HOH00.0380.02221.070-0.002-0.0020.0000.0000.0000.000
175A233HOH00.0090.00435.175-0.002-0.0020.0000.0000.0000.000
176A236HOH0-0.019-0.01516.239-0.014-0.0140.0000.0000.0000.000
177A244HOH00.0380.02130.7190.0020.0020.0000.0000.0000.000
178A246HOH00.0230.01620.6270.0090.0090.0000.0000.0000.000
179A253HOH0-0.006-0.01110.232-0.014-0.0140.0000.0000.0000.000
180A254HOH0-0.067-0.05322.025-0.006-0.0060.0000.0000.0000.000
181A257HOH0-0.028-0.01712.932-0.043-0.0430.0000.0000.0000.000
182A258HOH00.0390.02433.424-0.002-0.0020.0000.0000.0000.000
183A259HOH0-0.027-0.01630.728-0.001-0.0010.0000.0000.0000.000
184A262HOH00.0460.03419.903-0.002-0.0020.0000.0000.0000.000
185A266HOH0-0.023-0.01530.9820.0000.0000.0000.0000.0000.000
186A278HOH00.0250.01515.9360.0080.0080.0000.0000.0000.000
187A280HOH00.0310.01924.8240.0050.0050.0000.0000.0000.000