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: 7G34K

Calculation Name: 4KRD-B-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KRD

Chain ID: B

ChEMBL ID:

UniProt ID: P53124

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2232225.464014
FMO2-HF: Nuclear repulsion 2155503.191427
FMO2-HF: Total energy -76722.272587
FMO2-MP2: Total energy -76944.354008


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(B:242:ACE )


Summations of interaction energy for fragment #1(B:242: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.
0.8561.909-0.007-0.463-0.5840
Interaction energy analysis for fragmet #1(B:242:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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].
3B244GLU -1-0.733-0.8223.8140.2761.250-0.007-0.444-0.5230.000
4B245ASN 00.003-0.0117.035-0.006-0.0060.0000.0000.0000.000
5B246PRO 00.0680.0329.214-0.035-0.0350.0000.0000.0000.000
6B247LEU 00.0140.01211.4740.0110.0110.0000.0000.0000.000
7B248LEU 0-0.067-0.03910.9240.0380.0380.0000.0000.0000.000
8B249HIS 10.8120.8909.1630.7330.7330.0000.0000.0000.000
9B250GLY 00.0350.02113.6310.0560.0560.0000.0000.0000.000
10B251ILE 0-0.040-0.00115.3500.0400.0400.0000.0000.0000.000
11B252PRO 00.0720.03814.877-0.054-0.0540.0000.0000.0000.000
12B253VAL 0-0.020-0.03711.9280.0070.0070.0000.0000.0000.000
13B254ASP -1-0.897-0.95114.467-0.154-0.1540.0000.0000.0000.000
14B255VAL 0-0.071-0.01517.4860.0200.0200.0000.0000.0000.000
15B256GLU -1-0.844-0.91319.524-0.057-0.0570.0000.0000.0000.000
16B257VAL 0-0.084-0.05621.486-0.004-0.0040.0000.0000.0000.000
17B258PRO 0-0.010-0.01422.2000.0020.0020.0000.0000.0000.000
18B259HIS 00.0210.02425.3980.0100.0100.0000.0000.0000.000
19B260ILE 0-0.044-0.02426.3380.0000.0000.0000.0000.0000.000
20B261SER 00.0600.03129.7290.0040.0040.0000.0000.0000.000
21B262VAL 00.0550.01431.785-0.002-0.0020.0000.0000.0000.000
22B263ASP -1-0.869-0.93232.930-0.020-0.0200.0000.0000.0000.000
23B264GLU -1-0.884-0.94030.449-0.052-0.0520.0000.0000.0000.000
24B265ALA 0-0.024-0.01928.564-0.003-0.0030.0000.0000.0000.000
25B266LEU 0-0.037-0.02229.447-0.001-0.0010.0000.0000.0000.000
26B267ALA 0-0.013-0.00432.0090.0000.0000.0000.0000.0000.000
27B268ASN 00.0510.00427.554-0.001-0.0010.0000.0000.0000.000
28B269PHE 00.0040.03026.676-0.001-0.0010.0000.0000.0000.000
29B270LYS 10.8370.90928.7290.0320.0320.0000.0000.0000.000
30B271GLU -1-0.864-0.95130.742-0.052-0.0520.0000.0000.0000.000
31B272THR 00.0360.00724.667-0.005-0.0050.0000.0000.0000.000
32B273ILE 0-0.030-0.01527.9510.0000.0000.0000.0000.0000.000
33B274GLU -1-0.879-0.93829.471-0.031-0.0310.0000.0000.0000.000
34B275LEU 00.013-0.00228.6630.0010.0010.0000.0000.0000.000
35B276LEU 00.0410.02524.024-0.001-0.0010.0000.0000.0000.000
36B277LEU 0-0.058-0.00828.0060.0020.0020.0000.0000.0000.000
37B278LYS 10.9460.97431.3840.0410.0410.0000.0000.0000.000
38B279LEU 00.0280.01025.6440.0010.0010.0000.0000.0000.000
39B280SER 0-0.079-0.05028.6690.0010.0010.0000.0000.0000.000
40B281GLY 0-0.018-0.00429.9580.0030.0030.0000.0000.0000.000
41B282ASN 00.0090.01231.1030.0040.0040.0000.0000.0000.000
42B283ARG 10.9261.00223.5610.0780.0780.0000.0000.0000.000
43B284LYS 10.9460.97129.5820.0280.0280.0000.0000.0000.000
44B285CYS 0-0.075-0.02224.598-0.004-0.0040.0000.0000.0000.000
45B286THR 00.0540.02721.4600.0020.0020.0000.0000.0000.000
46B287GLY 0-0.046-0.00723.7620.0080.0080.0000.0000.0000.000
47B288PHE 00.012-0.00520.627-0.002-0.0020.0000.0000.0000.000
48B289ASN 00.013-0.01217.043-0.014-0.0140.0000.0000.0000.000
49B290THR 0-0.001-0.01519.6330.0050.0050.0000.0000.0000.000
50B291ARG 10.8460.90322.355-0.038-0.0380.0000.0000.0000.000
51B292VAL 00.0910.04822.687-0.006-0.0060.0000.0000.0000.000
52B293GLU -1-0.731-0.83118.5520.0610.0610.0000.0000.0000.000
53B294LYS 10.9690.99523.184-0.030-0.0300.0000.0000.0000.000
54B295LYS 10.9120.95826.291-0.040-0.0400.0000.0000.0000.000
55B296GLU -1-0.872-0.93924.1490.0560.0560.0000.0000.0000.000
56B297TYR 00.030-0.00524.881-0.004-0.0040.0000.0000.0000.000
57B298SER 0-0.085-0.04726.959-0.004-0.0040.0000.0000.0000.000
58B299ASN 0-0.043-0.03829.140-0.005-0.0050.0000.0000.0000.000
59B300PHE 00.014-0.00825.549-0.002-0.0020.0000.0000.0000.000
60B301TYR 0-0.0150.00431.137-0.003-0.0030.0000.0000.0000.000
61B302MET 0-0.056-0.02134.1100.0030.0030.0000.0000.0000.000
62B303LYS 10.9770.97937.199-0.008-0.0080.0000.0000.0000.000
63B304SER 00.0390.03440.484-0.002-0.0020.0000.0000.0000.000
64B305LYS 10.9990.99539.6760.0080.0080.0000.0000.0000.000
65B306PRO 0-0.016-0.01438.7320.0010.0010.0000.0000.0000.000
66B307THR 00.0260.01341.409-0.001-0.0010.0000.0000.0000.000
67B308LEU 00.0140.02240.993-0.001-0.0010.0000.0000.0000.000
68B309SER 00.0170.00840.4070.0000.0000.0000.0000.0000.000
69B310SER 00.0540.00034.9410.0020.0020.0000.0000.0000.000
70B311ALA 00.0500.02736.4540.0010.0010.0000.0000.0000.000
71B312ASP -1-0.789-0.90037.899-0.010-0.0100.0000.0000.0000.000
72B313PHE 0-0.079-0.03334.5500.0020.0020.0000.0000.0000.000
73B314LEU 00.028-0.00131.8300.0020.0020.0000.0000.0000.000
74B315LYS 10.9380.98435.8090.0140.0140.0000.0000.0000.000
75B316ARG 10.9120.96238.761-0.003-0.0030.0000.0000.0000.000
76B317ILE 0-0.053-0.04333.2480.0020.0020.0000.0000.0000.000
77B318GLN 00.1020.07134.0620.0030.0030.0000.0000.0000.000
78B319ASP -1-0.898-0.93636.361-0.004-0.0040.0000.0000.0000.000
79B320LYS 10.8440.92638.810-0.004-0.0040.0000.0000.0000.000
80B321CYS 0-0.104-0.04334.4180.0030.0030.0000.0000.0000.000
81B322GLU -1-0.908-0.94335.6330.0040.0040.0000.0000.0000.000
82B323TYR 0-0.046-0.03930.4330.0020.0020.0000.0000.0000.000
83B324GLN 00.1060.04528.949-0.004-0.0040.0000.0000.0000.000
84B325PRO 00.0460.00528.5480.0010.0010.0000.0000.0000.000
85B326THR 00.0390.01023.237-0.005-0.0050.0000.0000.0000.000
86B327VAL 00.0260.03424.3010.0000.0000.0000.0000.0000.000
87B328TYR 00.011-0.02325.4730.0020.0020.0000.0000.0000.000
88B329LEU 00.0110.02823.062-0.003-0.0030.0000.0000.0000.000
89B330VAL 00.0350.01819.940-0.008-0.0080.0000.0000.0000.000
90B331ALA 0-0.020-0.00721.3420.0020.0020.0000.0000.0000.000
91B332THR 0-0.015-0.03323.3650.0010.0010.0000.0000.0000.000
92B333PHE 00.0490.02114.176-0.004-0.0040.0000.0000.0000.000
93B334LEU 0-0.063-0.02518.427-0.001-0.0010.0000.0000.0000.000
94B335ILE 0-0.033-0.01820.1790.0030.0030.0000.0000.0000.000
95B336ASP -1-0.800-0.90919.191-0.085-0.0850.0000.0000.0000.000
96B337THR 0-0.024-0.02614.801-0.025-0.0250.0000.0000.0000.000
97B338LEU 0-0.032-0.00717.0350.0080.0080.0000.0000.0000.000
98B339PHE 0-0.037-0.03619.5480.0020.0020.0000.0000.0000.000
99B340LEU 00.0270.03119.206-0.002-0.0020.0000.0000.0000.000
100B341THR 0-0.012-0.01214.343-0.016-0.0160.0000.0000.0000.000
101B342ARG 10.7460.84714.6100.2540.2540.0000.0000.0000.000
102B343ASP -1-0.859-0.92214.811-0.219-0.2190.0000.0000.0000.000
103B344GLY 0-0.005-0.01714.856-0.040-0.0400.0000.0000.0000.000
104B345ASN 0-0.027-0.00815.936-0.048-0.0480.0000.0000.0000.000
105B346ASN 00.013-0.00514.679-0.026-0.0260.0000.0000.0000.000
106B347ILE 00.0450.04217.1270.0180.0180.0000.0000.0000.000
107B348LEU 00.0150.01118.768-0.005-0.0050.0000.0000.0000.000
108B349GLN 0-0.034-0.02319.3050.0320.0320.0000.0000.0000.000
109B350LEU 0-0.019-0.02520.3550.0000.0000.0000.0000.0000.000
110B351LYS 10.8620.93115.6950.0460.0460.0000.0000.0000.000
111B352LEU 0-0.016-0.02121.1380.0110.0110.0000.0000.0000.000
112B353ASN 0-0.035-0.02724.144-0.003-0.0030.0000.0000.0000.000
113B354LEU 00.0260.03027.4750.0060.0060.0000.0000.0000.000
114B355GLN 0-0.046-0.05128.972-0.003-0.0030.0000.0000.0000.000
115B356GLU -1-0.834-0.93932.592-0.015-0.0150.0000.0000.0000.000
116B357LYS 10.7920.88235.1130.0030.0030.0000.0000.0000.000
117B358GLU -1-0.796-0.87730.171-0.001-0.0010.0000.0000.0000.000
118B359VAL 00.0590.04431.2320.0030.0030.0000.0000.0000.000
119B360HIS 10.8960.95431.893-0.001-0.0010.0000.0000.0000.000
120B361ARG 10.8980.93132.001-0.013-0.0130.0000.0000.0000.000
121B362MET 00.0450.04425.6770.0050.0050.0000.0000.0000.000
122B363ILE 00.0110.01328.0580.0020.0020.0000.0000.0000.000
123B364ILE 0-0.047-0.02529.6910.0020.0020.0000.0000.0000.000
124B365ALA 0-0.008-0.00426.6930.0030.0030.0000.0000.0000.000
125B366ALA 00.0370.01624.7950.0050.0050.0000.0000.0000.000
126B367VAL 00.0250.01325.2580.0010.0010.0000.0000.0000.000
127B368ARG 10.8270.93427.355-0.031-0.0310.0000.0000.0000.000
128B369LEU 00.007-0.00921.6090.0040.0040.0000.0000.0000.000
129B370SER 0-0.017-0.03122.7070.0070.0070.0000.0000.0000.000
130B371THR 0-0.013-0.01623.7070.0030.0030.0000.0000.0000.000
131B372LYS 10.8510.91424.610-0.051-0.0510.0000.0000.0000.000
132B373LEU 0-0.062-0.02218.0900.0090.0090.0000.0000.0000.000
133B374LEU 0-0.078-0.03320.8100.0010.0010.0000.0000.0000.000
134B375GLU -1-0.927-0.96023.1670.0170.0170.0000.0000.0000.000
135B376ASP -1-0.894-0.93025.8720.0570.0570.0000.0000.0000.000
136B377PHE 0-0.065-0.03127.7330.0020.0020.0000.0000.0000.000
137B378VAL 0-0.0030.00728.049-0.004-0.0040.0000.0000.0000.000
138B379HIS 00.0610.04431.2110.0020.0020.0000.0000.0000.000
139B380SER 00.0890.04133.3850.0030.0030.0000.0000.0000.000
140B381HIS 00.026-0.01732.166-0.002-0.0020.0000.0000.0000.000
141B382GLU -1-0.967-0.98235.1470.0210.0210.0000.0000.0000.000
142B383TYR 0-0.028-0.02537.159-0.001-0.0010.0000.0000.0000.000
143B384PHE 00.1080.04131.650-0.001-0.0010.0000.0000.0000.000
144B385SER 0-0.029-0.03735.985-0.002-0.0020.0000.0000.0000.000
145B386LYS 10.9350.97037.445-0.020-0.0200.0000.0000.0000.000
146B387VAL 00.0120.02837.308-0.002-0.0020.0000.0000.0000.000
147B388CYS 0-0.033-0.00735.024-0.003-0.0030.0000.0000.0000.000
148B389GLY 0-0.0140.00837.718-0.001-0.0010.0000.0000.0000.000
149B390ILE 0-0.056-0.01534.6690.0000.0000.0000.0000.0000.000
150B391SER 00.0190.00238.9810.0020.0020.0000.0000.0000.000
151B392LYS 11.0361.00236.737-0.026-0.0260.0000.0000.0000.000
152B393ARG 10.9731.00135.300-0.031-0.0310.0000.0000.0000.000
153B394LEU 0-0.032-0.02134.0840.0030.0030.0000.0000.0000.000
154B395LEU 00.0680.03331.4630.0010.0010.0000.0000.0000.000
155B396THR 00.0360.01730.4390.0000.0000.0000.0000.0000.000
156B397LYS 10.8970.95729.430-0.029-0.0290.0000.0000.0000.000
157B398LEU 0-0.025-0.00928.9270.0020.0020.0000.0000.0000.000
158B399GLU -1-0.807-0.89926.5110.0490.0490.0000.0000.0000.000
159B400VAL 00.0240.01124.6880.0040.0040.0000.0000.0000.000
160B401SER 00.0180.01823.9410.0040.0040.0000.0000.0000.000
161B402LEU 0-0.0090.00822.1050.0000.0000.0000.0000.0000.000
162B403LEU 00.0330.01419.1550.0010.0010.0000.0000.0000.000
163B404ILE 0-0.018-0.01819.1320.0120.0120.0000.0000.0000.000
164B405CYS 0-0.083-0.04619.1120.0030.0030.0000.0000.0000.000
165B406VAL 00.0270.03117.015-0.008-0.0080.0000.0000.0000.000
166B407CYS 0-0.047-0.00615.1590.0110.0110.0000.0000.0000.000
167B408ASN 00.0300.02112.8500.0410.0410.0000.0000.0000.000
168B409THR 0-0.077-0.02511.261-0.019-0.0190.0000.0000.0000.000
169B410LYS 10.8930.9354.080-0.382-0.3030.000-0.019-0.0610.000
170B411LEU 00.0630.01810.381-0.074-0.0740.0000.0000.0000.000
171B412MET 0-0.0380.00210.0590.0090.0090.0000.0000.0000.000
172B413VAL 00.1070.05012.853-0.050-0.0500.0000.0000.0000.000
173B414SER 00.003-0.00313.421-0.010-0.0100.0000.0000.0000.000
174B415ASN 00.1540.05515.5560.0040.0040.0000.0000.0000.000
175B416ARG 10.8320.90310.2120.4610.4610.0000.0000.0000.000
176B417LYS 10.7810.91010.5440.0670.0670.0000.0000.0000.000
177B418LEU 00.0200.01616.3550.0050.0050.0000.0000.0000.000
178B419ALA 00.0280.01918.7520.0030.0030.0000.0000.0000.000
179B420ALA 00.006-0.01316.8250.0020.0020.0000.0000.0000.000
180B421SER 0-0.046-0.00418.9540.0060.0060.0000.0000.0000.000
181B422LYS 10.9310.97621.6350.0740.0740.0000.0000.0000.000
182B423LEU 0-0.032-0.02819.6950.0000.0000.0000.0000.0000.000
183B424LEU 00.0160.00217.954-0.005-0.0050.0000.0000.0000.000
184B425LEU 0-0.0060.02422.1420.0050.0050.0000.0000.0000.000
185B426ASN 00.0110.00025.5860.0120.0120.0000.0000.0000.000
186B427GLU -1-0.770-0.85521.202-0.176-0.1760.0000.0000.0000.000
187B428LEU 0-0.017-0.00124.2670.0060.0060.0000.0000.0000.000
188B429ARG 10.8330.90226.6320.0710.0710.0000.0000.0000.000
189B430SER 0-0.093-0.04727.6380.0040.0040.0000.0000.0000.000
190B431PHE 0-0.004-0.00624.5130.0010.0010.0000.0000.0000.000
191B432CYS 0-0.117-0.03929.9520.0060.0060.0000.0000.0000.000
192B433NME 00.0260.02532.5970.0030.0030.0000.0000.0000.000