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: PG5G1

Calculation Name: 3KNB-A-Xray22

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KNB

Chain ID: A

ChEMBL ID:

UniProt ID: O75147

Base Structure: X-ray

Registration Date: 2018-06-07

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 SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -867217.257092
FMO2-HF: Nuclear repulsion 822513.530076
FMO2-HF: Total energy -44703.727016
FMO2-MP2: Total energy -44830.142721


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:1:ACE)


Summations of interaction energy for fragment #1(A:1:ACE)
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.
-0.7710.0510.003-0.287-0.5390.001
Interaction energy analysis for fragmet #1(A:1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.008
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].
3A3GLY00.0560.0313.8490.0380.574-0.001-0.232-0.3040.001
4A4ILE0-0.051-0.0286.3860.4140.4140.0000.0000.0000.000
5A5PRO0-0.0250.0108.6460.0610.0610.0000.0000.0000.000
6A6PRO00.0230.00511.8500.0180.0180.0000.0000.0000.000
7A7LYS10.8520.94213.5390.1770.1770.0000.0000.0000.000
8A8ILE0-0.0120.00215.5940.0220.0220.0000.0000.0000.000
9A9GLU-1-0.907-0.96015.981-0.085-0.0850.0000.0000.0000.000
10A10ALA00.0000.00819.1660.0030.0030.0000.0000.0000.000
11A11LEU00.0310.03622.9860.0070.0070.0000.0000.0000.000
12A12PRO00.0030.01725.638-0.001-0.0010.0000.0000.0000.000
13A13SER00.0470.02729.394-0.005-0.0050.0000.0000.0000.000
14A14ASP-1-0.799-0.87331.492-0.042-0.0420.0000.0000.0000.000
15A15ILE0-0.038-0.00531.5270.0030.0030.0000.0000.0000.000
16A16SER00.023-0.01235.041-0.001-0.0010.0000.0000.0000.000
17A17ILE0-0.0290.00437.6790.0020.0020.0000.0000.0000.000
18A18ASP-1-0.831-0.88639.630-0.013-0.0130.0000.0000.0000.000
19A19GLU-1-0.799-0.88542.301-0.016-0.0160.0000.0000.0000.000
20A20GLY0-0.0050.00543.2880.0010.0010.0000.0000.0000.000
21A21LYS10.8420.92440.9660.0070.0070.0000.0000.0000.000
22A22VAL00.0150.00935.270-0.001-0.0010.0000.0000.0000.000
23A23LEU0-0.020-0.00433.3120.0010.0010.0000.0000.0000.000
24A24THR00.0340.00729.2920.0000.0000.0000.0000.0000.000
25A25VAL0-0.033-0.00827.5340.0010.0010.0000.0000.0000.000
26A26ALA00.0340.02024.272-0.002-0.0020.0000.0000.0000.000
27A27CYS0-0.091-0.03321.975-0.006-0.0060.0000.0000.0000.000
28A28ALA00.0740.05517.6440.0010.0010.0000.0000.0000.000
29A29PHE0-0.036-0.03314.026-0.018-0.0180.0000.0000.0000.000
30A30THR00.0620.06910.8120.0040.0040.0000.0000.0000.000
31A31GLY00.015-0.0089.8290.0000.0000.0000.0000.0000.000
32A32GLU-1-0.934-0.9353.703-0.344-0.1140.004-0.032-0.2020.000
33A33PRO00.019-0.0247.050-0.329-0.3290.0000.0000.0000.000
34A34THR0-0.007-0.0028.1070.0320.0320.0000.0000.0000.000
35A35PRO0-0.0420.01210.951-0.013-0.0130.0000.0000.0000.000
36A36GLU-1-0.894-0.94413.901-0.102-0.1020.0000.0000.0000.000
37A37VAL00.008-0.00117.319-0.013-0.0130.0000.0000.0000.000
38A38THR0-0.026-0.01619.8810.0170.0170.0000.0000.0000.000
39A39TRP00.0260.00223.427-0.006-0.0060.0000.0000.0000.000
40A40SER0-0.037-0.04026.2700.0040.0040.0000.0000.0000.000
41A41CYS00.0190.02629.4070.0000.0000.0000.0000.0000.000
42A42GLY00.0770.05632.8330.0010.0010.0000.0000.0000.000
43A43GLY0-0.0030.00332.0940.0010.0010.0000.0000.0000.000
44A44ARG10.8250.92432.5000.0430.0430.0000.0000.0000.000
45A45LYS10.9360.95024.5830.0800.0800.0000.0000.0000.000
46A46ILE0-0.0010.02729.0240.0060.0060.0000.0000.0000.000
47A47HIS0-0.063-0.02728.541-0.006-0.0060.0000.0000.0000.000
48A48SER00.025-0.03628.3380.0020.0020.0000.0000.0000.000
49A49GLN00.015-0.00230.2710.0020.0020.0000.0000.0000.000
50A50GLU-1-0.719-0.77833.320-0.040-0.0400.0000.0000.0000.000
51A51GLN0-0.039-0.05035.0920.0040.0040.0000.0000.0000.000
52A52GLY0-0.014-0.00237.5370.0020.0020.0000.0000.0000.000
53A53ARG10.7170.82837.0900.0230.0230.0000.0000.0000.000
54A54PHE00.0330.03632.2450.0010.0010.0000.0000.0000.000
55A55HIS0-0.011-0.02330.2430.0010.0010.0000.0000.0000.000
56A56ILE00.0130.00824.260-0.002-0.0020.0000.0000.0000.000
57A57GLU-1-0.884-0.88823.7310.0150.0150.0000.0000.0000.000
58A58ASN0-0.0190.01419.2960.0000.0000.0000.0000.0000.000
59A59THR00.007-0.01117.6360.0050.0050.0000.0000.0000.000
60A60ASP-1-0.898-0.95012.1750.0900.0900.0000.0000.0000.000
61A61ASP-1-0.832-0.89313.0100.0180.0180.0000.0000.0000.000
62A62LEU00.0010.01114.969-0.006-0.0060.0000.0000.0000.000
63A63THR0-0.035-0.02018.715-0.002-0.0020.0000.0000.0000.000
64A64THR0-0.009-0.02521.4380.0020.0020.0000.0000.0000.000
65A65LEU0-0.0130.01225.0780.0010.0010.0000.0000.0000.000
66A66ILE0-0.004-0.01928.0510.0030.0030.0000.0000.0000.000
67A67ILE0-0.0110.00731.341-0.001-0.0010.0000.0000.0000.000
68A68MET0-0.027-0.02434.3010.0020.0020.0000.0000.0000.000
69A69ASP-1-0.885-0.94737.579-0.013-0.0130.0000.0000.0000.000
70A70VAL0-0.0080.00537.707-0.001-0.0010.0000.0000.0000.000
71A71GLN00.0480.01140.3780.0000.0000.0000.0000.0000.000
72A72LYS10.9060.93041.5840.0160.0160.0000.0000.0000.000
73A73GLN0-0.016-0.00241.748-0.003-0.0030.0000.0000.0000.000
74A74ASP-1-0.692-0.79837.559-0.027-0.0270.0000.0000.0000.000
75A75GLY0-0.052-0.00337.246-0.002-0.0020.0000.0000.0000.000
76A76GLY00.0980.05037.1180.0000.0000.0000.0000.0000.000
77A77LEU0-0.046-0.01032.3180.0010.0010.0000.0000.0000.000
78A78TYR0-0.013-0.02029.827-0.003-0.0030.0000.0000.0000.000
79A79THR0-0.024-0.03825.794-0.003-0.0030.0000.0000.0000.000
80A80LEU0-0.0180.00920.9200.0030.0030.0000.0000.0000.000
81A81SER0-0.005-0.03021.933-0.003-0.0030.0000.0000.0000.000
82A82LEU0-0.0050.00315.9520.0080.0080.0000.0000.0000.000
83A83GLY00.0230.00216.768-0.007-0.0070.0000.0000.0000.000
84A84ASN00.013-0.00310.3310.0510.0510.0000.0000.0000.000
85A85GLU-1-0.922-0.9749.389-0.783-0.7830.0000.0000.0000.000
86A86PHE0-0.0180.0137.679-0.055-0.0550.0000.0000.0000.000
87A87GLY00.0260.02612.7010.0360.0360.0000.0000.0000.000
88A88SER0-0.033-0.01415.6630.0180.0180.0000.0000.0000.000
89A89ASP-1-0.748-0.85617.604-0.190-0.1900.0000.0000.0000.000
90A90SER0-0.051-0.02519.3980.0150.0150.0000.0000.0000.000
91A91ALA00.0270.02822.664-0.001-0.0010.0000.0000.0000.000
92A92THR00.0220.00124.9750.0040.0040.0000.0000.0000.000
93A93VAL00.0050.00728.4690.0030.0030.0000.0000.0000.000
94A94ASN0-0.026-0.01530.5640.0020.0020.0000.0000.0000.000
95A95ILE00.0080.00831.8670.0040.0040.0000.0000.0000.000
96A96HIS10.7950.87135.6760.0340.0340.0000.0000.0000.000
97A97ILE00.0460.02739.0380.0020.0020.0000.0000.0000.000
98A98ARG10.8490.94440.3870.0150.0150.0000.0000.0000.000
99A99SER00.071-0.00244.6430.0010.0010.0000.0000.0000.000
100A100NME0-0.0420.00046.819-0.001-0.0010.0000.0000.0000.000
101A101SO4-2-1.807-1.90237.538-0.092-0.0920.0000.0000.0000.000
102A102HOH0-0.054-0.03142.2290.0000.0000.0000.0000.0000.000
103A103HOH0-0.049-0.03328.0850.0020.0020.0000.0000.0000.000
104A104HOH0-0.003-0.00225.321-0.004-0.0040.0000.0000.0000.000
105A105HOH00.0350.01241.528-0.001-0.0010.0000.0000.0000.000
106A106HOH00.0120.02325.5400.0030.0030.0000.0000.0000.000
107A108HOH0-0.032-0.02031.225-0.001-0.0010.0000.0000.0000.000
108A109HOH0-0.020-0.02130.3870.0020.0020.0000.0000.0000.000
109A110HOH00.0190.02236.8990.0000.0000.0000.0000.0000.000
110A113HOH0-0.045-0.02338.5120.0010.0010.0000.0000.0000.000
111A114HOH0-0.005-0.01021.5240.0010.0010.0000.0000.0000.000
112A115HOH00.0170.01931.320-0.002-0.0020.0000.0000.0000.000
113A116HOH0-0.015-0.00832.3150.0000.0000.0000.0000.0000.000
114A117HOH00.0010.00141.4150.0000.0000.0000.0000.0000.000
115A118HOH0-0.024-0.02924.2310.0010.0010.0000.0000.0000.000
116A119HOH00.0200.02534.329-0.001-0.0010.0000.0000.0000.000
117A120HOH0-0.042-0.03410.976-0.031-0.0310.0000.0000.0000.000
118A121HOH00.0200.01718.367-0.001-0.0010.0000.0000.0000.000
119A123HOH00.0280.01040.6600.0000.0000.0000.0000.0000.000
120A124HOH00.0060.01021.669-0.001-0.0010.0000.0000.0000.000
121A125HOH00.0280.01023.0810.0020.0020.0000.0000.0000.000
122A126HOH0-0.051-0.02730.9670.0000.0000.0000.0000.0000.000
123A127HOH00.0530.04122.294-0.004-0.0040.0000.0000.0000.000
124A128HOH0-0.005-0.01034.350-0.002-0.0020.0000.0000.0000.000
125A129HOH0-0.008-0.00519.8360.0070.0070.0000.0000.0000.000
126A131HOH00.0140.00638.660-0.001-0.0010.0000.0000.0000.000
127A132HOH0-0.060-0.05825.7410.0000.0000.0000.0000.0000.000
128A133HOH0-0.040-0.02512.1150.0140.0140.0000.0000.0000.000
129A134HOH0-0.022-0.01924.9630.0000.0000.0000.0000.0000.000
130A135HOH00.0290.01827.299-0.003-0.0030.0000.0000.0000.000
131A136HOH0-0.013-0.01525.9850.0040.0040.0000.0000.0000.000
132A137HOH0-0.028-0.02232.2960.0000.0000.0000.0000.0000.000
133A138HOH0-0.037-0.02936.389-0.001-0.0010.0000.0000.0000.000
134A139HOH0-0.007-0.01246.182-0.001-0.0010.0000.0000.0000.000
135A140HOH0-0.017-0.0124.0940.2540.3100.000-0.023-0.0330.000
136A141HOH0-0.003-0.00538.087-0.001-0.0010.0000.0000.0000.000
137A143HOH0-0.036-0.03826.5430.0000.0000.0000.0000.0000.000
138A144HOH0-0.036-0.02013.0430.0200.0200.0000.0000.0000.000
139A145HOH0-0.017-0.00517.816-0.004-0.0040.0000.0000.0000.000
140A146HOH0-0.033-0.03527.872-0.002-0.0020.0000.0000.0000.000
141A150HOH0-0.0030.00622.5770.0070.0070.0000.0000.0000.000
142A151HOH0-0.051-0.04315.2870.0220.0220.0000.0000.0000.000
143A154HOH00.0300.02111.082-0.018-0.0180.0000.0000.0000.000
144A155HOH00.0110.02236.9850.0000.0000.0000.0000.0000.000
145A159HOH00.0290.02032.037-0.001-0.0010.0000.0000.0000.000
146A160HOH0-0.047-0.06432.9940.0000.0000.0000.0000.0000.000
147A161HOH0-0.020-0.01328.504-0.001-0.0010.0000.0000.0000.000
148A162HOH00.0070.01245.1690.0000.0000.0000.0000.0000.000
149A163HOH0-0.059-0.04845.9530.0000.0000.0000.0000.0000.000
150A164HOH00.0090.01631.1130.0000.0000.0000.0000.0000.000
151A165HOH0-0.033-0.03415.800-0.016-0.0160.0000.0000.0000.000
152A167HOH0-0.044-0.02231.6610.0010.0010.0000.0000.0000.000
153A169HOH00.0350.0237.855-0.013-0.0130.0000.0000.0000.000
154A170HOH0-0.028-0.02430.6890.0010.0010.0000.0000.0000.000
155A172HOH0-0.051-0.03323.890-0.003-0.0030.0000.0000.0000.000
156A174HOH0-0.040-0.02414.5300.0140.0140.0000.0000.0000.000
157A176HOH0-0.008-0.01440.4940.0000.0000.0000.0000.0000.000
158A177HOH0-0.016-0.02012.794-0.019-0.0190.0000.0000.0000.000
159A180HOH0-0.047-0.03122.4970.0050.0050.0000.0000.0000.000
160A182HOH00.0140.01542.159-0.001-0.0010.0000.0000.0000.000
161A186HOH0-0.007-0.01320.1890.0030.0030.0000.0000.0000.000
162A187HOH0-0.004-0.01045.563-0.001-0.0010.0000.0000.0000.000
163A191HOH0-0.025-0.01637.3260.0010.0010.0000.0000.0000.000
164A193HOH00.0300.03329.778-0.002-0.0020.0000.0000.0000.000
165A194HOH0-0.029-0.02236.5220.0000.0000.0000.0000.0000.000
166A196HOH00.0120.0187.540-0.042-0.0420.0000.0000.0000.000
167A198HOH0-0.027-0.02334.0540.0020.0020.0000.0000.0000.000
168A199HOH00.0170.00630.040-0.002-0.0020.0000.0000.0000.000
169A203HOH0-0.021-0.00743.132-0.001-0.0010.0000.0000.0000.000
170A207HOH0-0.016-0.00943.797-0.001-0.0010.0000.0000.0000.000
171A208HOH00.0430.03126.976-0.001-0.0010.0000.0000.0000.000
172A211HOH0-0.042-0.04912.001-0.010-0.0100.0000.0000.0000.000
173A214HOH00.0280.02531.578-0.001-0.0010.0000.0000.0000.000
174A215HOH0-0.045-0.03135.0780.0010.0010.0000.0000.0000.000
175A216HOH0-0.024-0.02742.9350.0010.0010.0000.0000.0000.000
176A218HOH0-0.047-0.04922.006-0.002-0.0020.0000.0000.0000.000
177A230HOH0-0.0090.01116.679-0.011-0.0110.0000.0000.0000.000
178A235HOH0-0.035-0.04915.8780.0020.0020.0000.0000.0000.000
179A236HOH0-0.044-0.02521.1470.0050.0050.0000.0000.0000.000
180A241HOH0-0.020-0.02446.545-0.001-0.0010.0000.0000.0000.000
181A245HOH0-0.008-0.02510.0650.0000.0000.0000.0000.0000.000
182A247HOH00.0350.0378.520-0.033-0.0330.0000.0000.0000.000
183A250HOH0-0.039-0.01839.9850.0010.0010.0000.0000.0000.000
184A251HOH0-0.036-0.02240.9620.0010.0010.0000.0000.0000.000
185A252HOH0-0.021-0.01044.6790.0010.0010.0000.0000.0000.000
186A257HOH0-0.005-0.03035.8880.0020.0020.0000.0000.0000.000
187A258HOH0-0.052-0.02936.082-0.001-0.0010.0000.0000.0000.000