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: VQNY1

Calculation Name: 1KKE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KKE

Chain ID: A

ChEMBL ID:

UniProt ID: P03528

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1851735.953637
FMO2-HF: Nuclear repulsion 1773325.283998
FMO2-HF: Total energy -78410.669638
FMO2-MP2: Total energy -78639.46292


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:250:GLU)


Summations of interaction energy for fragment #1(A:250: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.
-6.141-3.681-0.004-1.188-1.2680.003
Interaction energy analysis for fragmet #1(A:250:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.942 / q_NPA : -0.978
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].
3A252SER00.0480.0243.5435.0797.385-0.003-1.183-1.1210.003
4A253TYR0-0.008-0.0134.780-2.628-2.474-0.001-0.005-0.1470.000
5A254VAL0-0.023-0.0079.201-0.370-0.3700.0000.0000.0000.000
6A255ALA00.0310.00212.7970.0910.0910.0000.0000.0000.000
7A256SER0-0.023-0.01814.153-0.537-0.5370.0000.0000.0000.000
8A257ALA0-0.0360.01014.251-1.103-1.1030.0000.0000.0000.000
9A258VAL00.0200.01313.9991.5161.5160.0000.0000.0000.000
10A259THR00.0450.01811.283-0.823-0.8230.0000.0000.0000.000
11A260PRO00.007-0.00314.042-0.984-0.9840.0000.0000.0000.000
12A261LEU0-0.0270.00914.0000.7510.7510.0000.0000.0000.000
13A262ARG10.8710.9296.806-32.125-32.1250.0000.0000.0000.000
14A263LEU00.0620.04012.192-0.735-0.7350.0000.0000.0000.000
15A264ASN00.0360.0247.8690.0430.0430.0000.0000.0000.000
16A265SER0-0.038-0.0309.891-2.134-2.1340.0000.0000.0000.000
17A266SER0-0.0060.00510.033-1.805-1.8050.0000.0000.0000.000
18A267THR0-0.007-0.02411.055-1.448-1.4480.0000.0000.0000.000
19A268LYS10.9190.95413.244-19.075-19.0750.0000.0000.0000.000
20A269VAL00.0040.01813.074-1.218-1.2180.0000.0000.0000.000
21A270LEU0-0.022-0.01713.4551.5461.5460.0000.0000.0000.000
22A271ASP-1-0.825-0.90611.80024.53524.5350.0000.0000.0000.000
23A272MET0-0.020-0.02214.668-0.029-0.0290.0000.0000.0000.000
24A273LEU0-0.059-0.0219.4410.5000.5000.0000.0000.0000.000
25A274ILE00.024-0.00113.526-1.077-1.0770.0000.0000.0000.000
26A275ASP-1-0.821-0.89715.57818.29118.2910.0000.0000.0000.000
27A276SER00.0450.00316.295-1.058-1.0580.0000.0000.0000.000
28A277SER0-0.097-0.04218.399-1.140-1.1400.0000.0000.0000.000
29A278THR0-0.016-0.01720.633-1.089-1.0890.0000.0000.0000.000
30A279LEU0-0.045-0.02120.068-0.639-0.6390.0000.0000.0000.000
31A280GLU-1-0.939-0.97120.95612.89812.8980.0000.0000.0000.000
32A281ILE0-0.026-0.01718.931-0.166-0.1660.0000.0000.0000.000
33A282ASN0-0.006-0.01023.001-0.155-0.1550.0000.0000.0000.000
34A283SER00.0260.01025.3620.2410.2410.0000.0000.0000.000
35A284SER0-0.048-0.03427.683-0.026-0.0260.0000.0000.0000.000
36A285GLY00.0120.00824.246-0.052-0.0520.0000.0000.0000.000
37A286GLN0-0.0120.00124.4170.3150.3150.0000.0000.0000.000
38A287LEU00.0230.02821.3180.1800.1800.0000.0000.0000.000
39A288THR0-0.002-0.00124.435-0.623-0.6230.0000.0000.0000.000
40A289VAL00.0190.00425.0820.5720.5720.0000.0000.0000.000
41A290ARG10.9420.97922.922-13.654-13.6540.0000.0000.0000.000
42A291SER00.0080.01426.848-0.162-0.1620.0000.0000.0000.000
43A292THR0-0.027-0.01929.5470.1200.1200.0000.0000.0000.000
44A293SER0-0.0040.00431.223-0.364-0.3640.0000.0000.0000.000
45A294PRO00.0180.01334.1000.1480.1480.0000.0000.0000.000
46A295ASN0-0.017-0.02035.134-0.238-0.2380.0000.0000.0000.000
47A296LEU00.0180.01737.983-0.054-0.0540.0000.0000.0000.000
48A297ARG10.8910.94738.090-8.011-8.0110.0000.0000.0000.000
49A298TYR00.0500.03744.254-0.107-0.1070.0000.0000.0000.000
50A299PRO00.0550.01647.8670.0410.0410.0000.0000.0000.000
51A300ILE0-0.033-0.00544.906-0.064-0.0640.0000.0000.0000.000
52A301ALA0-0.024-0.02845.4190.0940.0940.0000.0000.0000.000
53A302ASP-1-0.852-0.93343.3907.2897.2890.0000.0000.0000.000
54A303VAL0-0.067-0.03145.348-0.172-0.1720.0000.0000.0000.000
55A304SER0-0.010-0.01447.787-0.043-0.0430.0000.0000.0000.000
56A305GLY0-0.0260.00843.361-0.004-0.0040.0000.0000.0000.000
57A306GLY00.0130.01542.7940.1920.1920.0000.0000.0000.000
58A307ILE00.0070.00240.524-0.026-0.0260.0000.0000.0000.000
59A308GLY00.012-0.00344.897-0.111-0.1110.0000.0000.0000.000
60A309MET0-0.014-0.00448.0480.0430.0430.0000.0000.0000.000
61A310SER00.008-0.00850.019-0.139-0.1390.0000.0000.0000.000
62A311PRO00.0550.00351.461-0.088-0.0880.0000.0000.0000.000
63A312ASN00.0020.00053.761-0.080-0.0800.0000.0000.0000.000
64A313TYR0-0.093-0.03853.662-0.056-0.0560.0000.0000.0000.000
65A314ARG10.9880.99754.976-5.820-5.8200.0000.0000.0000.000
66A315PHE0-0.011-0.00257.899-0.102-0.1020.0000.0000.0000.000
67A316ARG10.9260.97855.869-5.556-5.5560.0000.0000.0000.000
68A317GLN00.0200.01761.303-0.008-0.0080.0000.0000.0000.000
69A318SER0-0.035-0.01264.1440.0200.0200.0000.0000.0000.000
70A319MET00.0120.00666.121-0.063-0.0630.0000.0000.0000.000
71A320TRP0-0.047-0.01968.8520.0350.0350.0000.0000.0000.000
72A321ILE0-0.0170.00170.965-0.067-0.0670.0000.0000.0000.000
73A322GLY00.0360.01273.8410.0270.0270.0000.0000.0000.000
74A323ILE0-0.049-0.01874.936-0.067-0.0670.0000.0000.0000.000
75A324VAL00.0550.03676.4300.0540.0540.0000.0000.0000.000
76A325SER0-0.063-0.05978.386-0.057-0.0570.0000.0000.0000.000
77A326TYR00.0670.05080.1340.0260.0260.0000.0000.0000.000
78A327SER0-0.002-0.00181.778-0.052-0.0520.0000.0000.0000.000
79A328GLY00.0690.02683.4710.0380.0380.0000.0000.0000.000
80A329SER0-0.038-0.01586.045-0.042-0.0420.0000.0000.0000.000
81A330GLY00.0200.01688.083-0.050-0.0500.0000.0000.0000.000
82A331LEU0-0.038-0.00688.7760.0000.0000.0000.0000.0000.000
83A332ASN00.0350.00084.0000.0870.0870.0000.0000.0000.000
84A333TRP0-0.072-0.02984.279-0.028-0.0280.0000.0000.0000.000
85A334ARG10.9330.96480.707-3.900-3.9000.0000.0000.0000.000
86A335VAL00.0220.02181.840-0.055-0.0550.0000.0000.0000.000
87A336GLN00.0030.00778.4160.0540.0540.0000.0000.0000.000
88A337VAL0-0.020-0.01376.569-0.046-0.0460.0000.0000.0000.000
89A338ASN00.0160.00375.6890.0430.0430.0000.0000.0000.000
90A339SER0-0.002-0.00172.811-0.045-0.0450.0000.0000.0000.000
91A340ASP-1-0.888-0.92570.6484.5254.5250.0000.0000.0000.000
92A341ILE0-0.033-0.03065.554-0.009-0.0090.0000.0000.0000.000
93A342PHE0-0.006-0.01865.5880.0490.0490.0000.0000.0000.000
94A343ILE0-0.017-0.01759.732-0.011-0.0110.0000.0000.0000.000
95A344VAL0-0.023-0.01761.2410.0250.0250.0000.0000.0000.000
96A345ASP-1-0.874-0.93757.9375.4625.4620.0000.0000.0000.000
97A346ASP-1-0.919-0.95556.4715.8225.8220.0000.0000.0000.000
98A347TYR0-0.041-0.01459.235-0.080-0.0800.0000.0000.0000.000
99A348ILE0-0.023-0.00162.8260.0420.0420.0000.0000.0000.000
100A349HIS00.0280.04864.786-0.121-0.1210.0000.0000.0000.000
101A350ILE00.0150.00768.2370.0100.0100.0000.0000.0000.000
102A351CYS0-0.015-0.01370.815-0.036-0.0360.0000.0000.0000.000
103A352LEU00.0200.00073.598-0.019-0.0190.0000.0000.0000.000
104A353PRO00.0140.01676.577-0.023-0.0230.0000.0000.0000.000
105A354ALA00.000-0.00979.641-0.008-0.0080.0000.0000.0000.000
106A355PHE0-0.048-0.02180.8870.0020.0020.0000.0000.0000.000
107A356ASP-1-0.849-0.93084.6483.6173.6170.0000.0000.0000.000
108A357GLY00.0130.00386.8690.0360.0360.0000.0000.0000.000
109A358PHE0-0.033-0.02387.798-0.054-0.0540.0000.0000.0000.000
110A359SER00.0210.03390.0820.0140.0140.0000.0000.0000.000
111A360ILE0-0.0400.00087.2020.0470.0470.0000.0000.0000.000
112A361ALA00.0340.00788.225-0.051-0.0510.0000.0000.0000.000
113A362ASP-1-0.918-0.97088.6763.5833.5830.0000.0000.0000.000
114A363GLY00.022-0.00185.4110.0350.0350.0000.0000.0000.000
115A364GLY0-0.058-0.02983.852-0.037-0.0370.0000.0000.0000.000
116A365ASP-1-0.881-0.93578.5704.1454.1450.0000.0000.0000.000
117A366LEU0-0.040-0.02778.700-0.046-0.0460.0000.0000.0000.000
118A367SER00.001-0.00975.5340.0730.0730.0000.0000.0000.000
119A368LEU0-0.018-0.00672.420-0.054-0.0540.0000.0000.0000.000
120A369ASN00.0420.01272.1820.0980.0980.0000.0000.0000.000
121A370PHE00.0570.01567.502-0.010-0.0100.0000.0000.0000.000
122A371VAL0-0.0070.00967.0650.0760.0760.0000.0000.0000.000
123A372THR0-0.056-0.03868.3460.0000.0000.0000.0000.0000.000
124A373GLY00.0690.03370.342-0.028-0.0280.0000.0000.0000.000
125A374LEU0-0.045-0.00464.426-0.025-0.0250.0000.0000.0000.000
126A375LEU00.0010.01266.4680.0160.0160.0000.0000.0000.000
127A376PRO00.0090.01561.8220.0700.0700.0000.0000.0000.000
128A377PRO0-0.034-0.04158.317-0.036-0.0360.0000.0000.0000.000
129A378LEU0-0.056-0.01959.9330.0590.0590.0000.0000.0000.000
130A379LEU00.0440.02557.604-0.052-0.0520.0000.0000.0000.000
131A380THR00.0340.01861.8320.0230.0230.0000.0000.0000.000
132A381GLY00.0260.01759.907-0.028-0.0280.0000.0000.0000.000
133A382ASP-1-0.836-0.90658.3045.5565.5560.0000.0000.0000.000
134A383THR0-0.030-0.03160.686-0.028-0.0280.0000.0000.0000.000
135A384GLU-1-0.869-0.91859.4785.3455.3450.0000.0000.0000.000
136A385PRO00.0200.00161.7970.0660.0660.0000.0000.0000.000
137A386ALA00.001-0.00959.3770.0580.0580.0000.0000.0000.000
138A387PHE0-0.030-0.01959.9530.0680.0680.0000.0000.0000.000
139A388HIS10.9000.93757.278-5.552-5.5520.0000.0000.0000.000
140A389ASN0-0.021-0.01062.789-0.017-0.0170.0000.0000.0000.000
141A390ASP-1-0.869-0.89863.8745.0245.0240.0000.0000.0000.000
142A391VAL0-0.092-0.05666.694-0.035-0.0350.0000.0000.0000.000
143A392VAL0-0.045-0.01767.3480.0180.0180.0000.0000.0000.000
144A393THR0-0.003-0.01270.694-0.061-0.0610.0000.0000.0000.000
145A394TYR0-0.001-0.00466.5870.0030.0030.0000.0000.0000.000
146A395GLY00.0220.00771.228-0.040-0.0400.0000.0000.0000.000
147A396ALA0-0.013-0.00872.620-0.041-0.0410.0000.0000.0000.000
148A397GLN0-0.034-0.00876.029-0.022-0.0220.0000.0000.0000.000
149A398THR0-0.013-0.00578.707-0.046-0.0460.0000.0000.0000.000
150A399VAL00.0090.00480.7940.0120.0120.0000.0000.0000.000
151A400ALA00.001-0.00183.693-0.038-0.0380.0000.0000.0000.000
152A401ILE00.0090.00785.1160.0110.0110.0000.0000.0000.000
153A402GLY0-0.010-0.00388.386-0.042-0.0420.0000.0000.0000.000
154A403LEU00.0060.01390.7680.0120.0120.0000.0000.0000.000
155A404SER00.000-0.00393.801-0.040-0.0400.0000.0000.0000.000
156A405SER00.0890.02596.6410.0280.0280.0000.0000.0000.000
157A406GLY00.0050.01298.473-0.034-0.0340.0000.0000.0000.000
158A407GLY0-0.018-0.00199.930-0.010-0.0100.0000.0000.0000.000
159A408ALA0-0.009-0.01399.1240.0350.0350.0000.0000.0000.000
160A409PRO0-0.016-0.01794.537-0.009-0.0090.0000.0000.0000.000
161A410GLN0-0.0110.00696.004-0.030-0.0300.0000.0000.0000.000
162A411TYR0-0.014-0.01490.3440.0120.0120.0000.0000.0000.000
163A412MET0-0.0070.02690.829-0.031-0.0310.0000.0000.0000.000
164A413SER0-0.025-0.01587.5950.0460.0460.0000.0000.0000.000
165A414LYS10.8330.91985.507-3.743-3.7430.0000.0000.0000.000
166A415ASN00.0100.00280.5460.0490.0490.0000.0000.0000.000
167A416LEU00.0170.00577.080-0.013-0.0130.0000.0000.0000.000
168A417TRP0-0.020-0.00574.6990.0190.0190.0000.0000.0000.000
169A418VAL0-0.0010.00469.756-0.024-0.0240.0000.0000.0000.000
170A419GLU-1-0.884-0.93872.5194.2814.2810.0000.0000.0000.000
171A420GLN00.0440.02269.243-0.008-0.0080.0000.0000.0000.000
172A421TRP0-0.0060.01063.331-0.039-0.0390.0000.0000.0000.000
173A422GLN00.0190.00167.3930.1220.1220.0000.0000.0000.000
174A423ASP-1-0.895-0.94665.8004.8164.8160.0000.0000.0000.000
175A424GLY00.014-0.01166.437-0.025-0.0250.0000.0000.0000.000
176A425VAL0-0.049-0.01867.248-0.052-0.0520.0000.0000.0000.000
177A426LEU0-0.020-0.00269.0400.0290.0290.0000.0000.0000.000
178A427ARG10.8430.92571.257-4.443-4.4430.0000.0000.0000.000
179A428LEU0-0.005-0.00973.5930.0450.0450.0000.0000.0000.000
180A429ARG10.9160.97876.197-4.074-4.0740.0000.0000.0000.000
181A430VAL00.002-0.01478.8400.0010.0010.0000.0000.0000.000
182A431GLU-1-0.865-0.95382.1623.9143.9140.0000.0000.0000.000
183A432GLY00.0440.03584.7750.0160.0160.0000.0000.0000.000
184A433GLY00.026-0.00387.2150.0000.0000.0000.0000.0000.000
185A434GLY0-0.0330.00689.779-0.038-0.0380.0000.0000.0000.000
186A435SER00.008-0.00892.1430.0370.0370.0000.0000.0000.000
187A436ILE00.0030.00394.165-0.037-0.0370.0000.0000.0000.000
188A437THR0-0.004-0.00596.3230.0380.0380.0000.0000.0000.000
189A438HIS0-0.061-0.02092.6480.0200.0200.0000.0000.0000.000
190A439SER00.007-0.00495.479-0.005-0.0050.0000.0000.0000.000
191A440ASN0-0.026-0.01692.639-0.009-0.0090.0000.0000.0000.000
192A441SER00.026-0.02789.037-0.004-0.0040.0000.0000.0000.000
193A442LYS10.8670.94989.008-3.525-3.5250.0000.0000.0000.000
194A443TRP00.0370.00582.4620.0150.0150.0000.0000.0000.000
195A444PRO00.0100.01182.983-0.004-0.0040.0000.0000.0000.000
196A445ALA00.0240.00679.5960.0300.0300.0000.0000.0000.000
197A446MET0-0.065-0.02578.077-0.016-0.0160.0000.0000.0000.000
198A447THR00.0240.01372.2200.0400.0400.0000.0000.0000.000
199A448VAL0-0.0170.00071.065-0.015-0.0150.0000.0000.0000.000
200A449SER00.015-0.04268.2550.0240.0240.0000.0000.0000.000
201A450TYR0-0.077-0.06165.053-0.077-0.0770.0000.0000.0000.000
202A451PRO0-0.0120.01261.6470.0400.0400.0000.0000.0000.000
203A452ARG10.8770.93356.976-5.558-5.5580.0000.0000.0000.000
204A453SER0-0.032-0.01457.8700.1160.1160.0000.0000.0000.000
205A454PHE0-0.019-0.00452.0750.0370.0370.0000.0000.0000.000
206A455THR0-0.015-0.00748.6550.0610.0610.0000.0000.0000.000