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: 1NY9Z

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 OptHSide
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 -1851123.605573
FMO2-HF: Nuclear repulsion 1772712.079554
FMO2-HF: Total energy -78411.52602
FMO2-MP2: Total energy -78640.210162


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.
-15.808-12.7760.01-1.475-1.5680.004
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 : -0.915 / q_NPA : -0.958
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].
3A252SER00.0130.0083.4592.0994.7710.010-1.384-1.2990.004
4A253TYR00.007-0.0124.098-9.096-8.7360.000-0.091-0.2690.000
5A254VAL0-0.024-0.0108.813-0.664-0.6640.0000.0000.0000.000
6A255ALA00.0260.00112.4770.0970.0970.0000.0000.0000.000
7A256SER0-0.022-0.01413.993-0.564-0.5640.0000.0000.0000.000
8A257ALA0-0.0400.00613.854-1.164-1.1640.0000.0000.0000.000
9A258VAL00.0200.01213.7291.5851.5850.0000.0000.0000.000
10A259THR00.0550.02811.280-0.125-0.1250.0000.0000.0000.000
11A260PRO0-0.007-0.01313.807-1.139-1.1390.0000.0000.0000.000
12A261LEU0-0.0280.00913.6390.8500.8500.0000.0000.0000.000
13A262ARG10.8400.8876.812-33.058-33.0580.0000.0000.0000.000
14A263LEU00.0490.03211.736-0.761-0.7610.0000.0000.0000.000
15A264ASN00.0360.0207.8710.0190.0190.0000.0000.0000.000
16A265SER00.0110.00110.044-1.984-1.9840.0000.0000.0000.000
17A266SER0-0.0120.00010.175-2.192-2.1920.0000.0000.0000.000
18A267THR0-0.007-0.02311.087-1.548-1.5480.0000.0000.0000.000
19A268LYS10.9150.95513.328-19.816-19.8160.0000.0000.0000.000
20A269VAL00.0120.02113.130-1.325-1.3250.0000.0000.0000.000
21A270LEU0-0.023-0.01513.2651.6881.6880.0000.0000.0000.000
22A271ASP-1-0.803-0.87011.52425.94925.9490.0000.0000.0000.000
23A272MET0-0.019-0.02014.143-0.082-0.0820.0000.0000.0000.000
24A273LEU0-0.045-0.0119.0320.4290.4290.0000.0000.0000.000
25A274ILE00.019-0.00613.159-1.198-1.1980.0000.0000.0000.000
26A275ASP-1-0.792-0.86715.35118.03818.0380.0000.0000.0000.000
27A276SER00.0460.00516.328-0.723-0.7230.0000.0000.0000.000
28A277SER0-0.128-0.07518.201-1.124-1.1240.0000.0000.0000.000
29A278THR00.001-0.00820.448-0.976-0.9760.0000.0000.0000.000
30A279LEU0-0.043-0.02120.223-0.664-0.6640.0000.0000.0000.000
31A280GLU-1-0.823-0.91020.73913.23513.2350.0000.0000.0000.000
32A281ILE0-0.025-0.01618.682-0.196-0.1960.0000.0000.0000.000
33A282ASN0-0.009-0.01022.954-0.238-0.2380.0000.0000.0000.000
34A283SER00.0470.02225.3660.2670.2670.0000.0000.0000.000
35A284SER0-0.055-0.03327.656-0.052-0.0520.0000.0000.0000.000
36A285GLY00.0090.00624.279-0.037-0.0370.0000.0000.0000.000
37A286GLN0-0.024-0.00524.3020.2650.2650.0000.0000.0000.000
38A287LEU00.0230.02720.8980.1640.1640.0000.0000.0000.000
39A288THR00.004-0.00424.013-0.678-0.6780.0000.0000.0000.000
40A289VAL00.001-0.00324.7460.5710.5710.0000.0000.0000.000
41A290ARG10.8140.91822.291-13.670-13.6700.0000.0000.0000.000
42A291SER0-0.0030.00026.644-0.199-0.1990.0000.0000.0000.000
43A292THR0-0.006-0.00329.2420.1590.1590.0000.0000.0000.000
44A293SER0-0.0040.00331.049-0.361-0.3610.0000.0000.0000.000
45A294PRO00.0140.01033.9520.1460.1460.0000.0000.0000.000
46A295ASN00.0110.00335.194-0.323-0.3230.0000.0000.0000.000
47A296LEU00.0160.01937.852-0.058-0.0580.0000.0000.0000.000
48A297ARG10.8620.92137.988-8.017-8.0170.0000.0000.0000.000
49A298TYR00.0600.03844.137-0.101-0.1010.0000.0000.0000.000
50A299PRO00.0540.02047.7490.0350.0350.0000.0000.0000.000
51A300ILE0-0.042-0.01244.738-0.061-0.0610.0000.0000.0000.000
52A301ALA0-0.021-0.02545.2710.0940.0940.0000.0000.0000.000
53A302ASP-1-0.843-0.92143.0907.3167.3160.0000.0000.0000.000
54A303VAL0-0.061-0.03445.192-0.169-0.1690.0000.0000.0000.000
55A304SER0-0.012-0.01247.568-0.048-0.0480.0000.0000.0000.000
56A305GLY0-0.0250.00243.184-0.001-0.0010.0000.0000.0000.000
57A306GLY00.0050.01142.6120.1960.1960.0000.0000.0000.000
58A307ILE0-0.007-0.00840.245-0.029-0.0290.0000.0000.0000.000
59A308GLY00.0190.00344.724-0.109-0.1090.0000.0000.0000.000
60A309MET0-0.020-0.00547.8920.0380.0380.0000.0000.0000.000
61A310SER00.005-0.00649.888-0.134-0.1340.0000.0000.0000.000
62A311PRO00.0550.00851.318-0.085-0.0850.0000.0000.0000.000
63A312ASN0-0.002-0.00753.706-0.056-0.0560.0000.0000.0000.000
64A313TYR0-0.097-0.06153.522-0.058-0.0580.0000.0000.0000.000
65A314ARG10.9951.00054.836-5.804-5.8040.0000.0000.0000.000
66A315PHE0-0.016-0.00457.758-0.103-0.1030.0000.0000.0000.000
67A316ARG10.9130.96456.405-5.554-5.5540.0000.0000.0000.000
68A317GLN0-0.027-0.01261.179-0.007-0.0070.0000.0000.0000.000
69A318SER0-0.036-0.01364.0070.0200.0200.0000.0000.0000.000
70A319MET00.0100.00966.014-0.065-0.0650.0000.0000.0000.000
71A320TRP0-0.044-0.01468.7610.0330.0330.0000.0000.0000.000
72A321ILE0-0.025-0.00870.877-0.070-0.0700.0000.0000.0000.000
73A322GLY00.0420.01573.7670.0260.0260.0000.0000.0000.000
74A323ILE0-0.051-0.02574.864-0.066-0.0660.0000.0000.0000.000
75A324VAL00.0580.03976.3640.0540.0540.0000.0000.0000.000
76A325SER0-0.044-0.04378.443-0.053-0.0530.0000.0000.0000.000
77A326TYR00.0620.04680.0710.0270.0270.0000.0000.0000.000
78A327SER0-0.008-0.00981.799-0.053-0.0530.0000.0000.0000.000
79A328GLY00.0670.02883.4140.0380.0380.0000.0000.0000.000
80A329SER0-0.037-0.01585.990-0.044-0.0440.0000.0000.0000.000
81A330GLY00.0210.01788.046-0.049-0.0490.0000.0000.0000.000
82A331LEU0-0.038-0.00688.7810.0000.0000.0000.0000.0000.000
83A332ASN00.0560.02084.1640.0830.0830.0000.0000.0000.000
84A333TRP0-0.052-0.01684.006-0.030-0.0300.0000.0000.0000.000
85A334ARG10.9010.93180.845-3.879-3.8790.0000.0000.0000.000
86A335VAL00.0160.02281.768-0.054-0.0540.0000.0000.0000.000
87A336GLN0-0.0140.00578.2560.0440.0440.0000.0000.0000.000
88A337VAL0-0.016-0.01076.818-0.044-0.0440.0000.0000.0000.000
89A338ASN00.003-0.00675.5930.0250.0250.0000.0000.0000.000
90A339SER00.0220.01072.405-0.042-0.0420.0000.0000.0000.000
91A340ASP-1-0.850-0.90870.5774.5804.5800.0000.0000.0000.000
92A341ILE0-0.038-0.02965.446-0.010-0.0100.0000.0000.0000.000
93A342PHE00.000-0.01165.4640.0440.0440.0000.0000.0000.000
94A343ILE0-0.021-0.01759.664-0.013-0.0130.0000.0000.0000.000
95A344VAL0-0.030-0.01861.1150.0270.0270.0000.0000.0000.000
96A345ASP-1-0.859-0.93757.8055.4875.4870.0000.0000.0000.000
97A346ASP-1-0.887-0.91456.0935.8315.8310.0000.0000.0000.000
98A347TYR0-0.048-0.01959.119-0.052-0.0520.0000.0000.0000.000
99A348ILE0-0.0130.00362.7110.0400.0400.0000.0000.0000.000
100A349HIS00.0120.01864.679-0.130-0.1300.0000.0000.0000.000
101A350ILE00.0140.00868.0690.0090.0090.0000.0000.0000.000
102A351CYS0-0.024-0.01870.711-0.038-0.0380.0000.0000.0000.000
103A352LEU00.0150.00273.486-0.019-0.0190.0000.0000.0000.000
104A353PRO00.0160.01576.474-0.022-0.0220.0000.0000.0000.000
105A354ALA0-0.006-0.01079.533-0.009-0.0090.0000.0000.0000.000
106A355PHE0-0.044-0.02080.8020.0000.0000.0000.0000.0000.000
107A356ASP-1-0.815-0.88784.5523.5873.5870.0000.0000.0000.000
108A357GLY00.0170.00686.7860.0360.0360.0000.0000.0000.000
109A358PHE0-0.030-0.02487.718-0.053-0.0530.0000.0000.0000.000
110A359SER00.0190.02390.0060.0130.0130.0000.0000.0000.000
111A360ILE0-0.041-0.00587.0320.0460.0460.0000.0000.0000.000
112A361ALA00.0290.00788.158-0.052-0.0520.0000.0000.0000.000
113A362ASP-1-0.876-0.93888.6043.5883.5880.0000.0000.0000.000
114A363GLY00.011-0.00385.4380.0330.0330.0000.0000.0000.000
115A364GLY0-0.068-0.03583.788-0.037-0.0370.0000.0000.0000.000
116A365ASP-1-0.857-0.91178.5454.1284.1280.0000.0000.0000.000
117A366LEU0-0.042-0.02978.820-0.045-0.0450.0000.0000.0000.000
118A367SER0-0.017-0.01675.5190.0700.0700.0000.0000.0000.000
119A368LEU0-0.0060.00472.364-0.052-0.0520.0000.0000.0000.000
120A369ASN00.0360.01071.8870.1120.1120.0000.0000.0000.000
121A370PHE00.0590.01667.510-0.010-0.0100.0000.0000.0000.000
122A371VAL0-0.0040.01367.2250.0800.0800.0000.0000.0000.000
123A372THR0-0.062-0.04268.2970.0010.0010.0000.0000.0000.000
124A373GLY00.0780.03670.267-0.028-0.0280.0000.0000.0000.000
125A374LEU0-0.049-0.00664.178-0.024-0.0240.0000.0000.0000.000
126A375LEU00.0070.01666.4450.0150.0150.0000.0000.0000.000
127A376PRO00.0110.01561.6840.0680.0680.0000.0000.0000.000
128A377PRO0-0.035-0.04058.221-0.037-0.0370.0000.0000.0000.000
129A378LEU0-0.046-0.01259.8540.0560.0560.0000.0000.0000.000
130A379LEU00.0510.02857.737-0.051-0.0510.0000.0000.0000.000
131A380THR00.0360.01361.7640.0260.0260.0000.0000.0000.000
132A381GLY00.0240.01559.848-0.028-0.0280.0000.0000.0000.000
133A382ASP-1-0.838-0.89958.4325.5505.5500.0000.0000.0000.000
134A383THR0-0.034-0.03160.609-0.030-0.0300.0000.0000.0000.000
135A384GLU-1-0.830-0.87659.2335.3605.3600.0000.0000.0000.000
136A385PRO00.0200.00461.7180.0660.0660.0000.0000.0000.000
137A386ALA0-0.004-0.00859.3940.0560.0560.0000.0000.0000.000
138A387PHE0-0.036-0.02360.0130.0690.0690.0000.0000.0000.000
139A388HIS10.8970.93857.500-5.521-5.5210.0000.0000.0000.000
140A389ASN0-0.028-0.01462.793-0.024-0.0240.0000.0000.0000.000
141A390ASP-1-0.862-0.88863.6965.0165.0160.0000.0000.0000.000
142A391VAL0-0.065-0.04066.807-0.032-0.0320.0000.0000.0000.000
143A392VAL0-0.052-0.02467.3650.0190.0190.0000.0000.0000.000
144A393THR0-0.007-0.01270.760-0.063-0.0630.0000.0000.0000.000
145A394TYR00.008-0.00366.7060.0250.0250.0000.0000.0000.000
146A395GLY00.0140.00671.223-0.038-0.0380.0000.0000.0000.000
147A396ALA0-0.016-0.00672.594-0.039-0.0390.0000.0000.0000.000
148A397GLN0-0.037-0.00975.478-0.026-0.0260.0000.0000.0000.000
149A398THR0-0.022-0.01078.666-0.045-0.0450.0000.0000.0000.000
150A399VAL00.0080.00380.6750.0120.0120.0000.0000.0000.000
151A400ALA00.0020.00183.586-0.038-0.0380.0000.0000.0000.000
152A401ILE00.0100.00784.7090.0110.0110.0000.0000.0000.000
153A402GLY00.0010.00288.285-0.042-0.0420.0000.0000.0000.000
154A403LEU0-0.0040.01090.4450.0120.0120.0000.0000.0000.000
155A404SER00.0080.00393.709-0.040-0.0400.0000.0000.0000.000
156A405SER00.0850.01996.5560.0330.0330.0000.0000.0000.000
157A406GLY00.0120.01798.390-0.034-0.0340.0000.0000.0000.000
158A407GLY0-0.017-0.00199.841-0.010-0.0100.0000.0000.0000.000
159A408ALA0-0.008-0.01299.0250.0350.0350.0000.0000.0000.000
160A409PRO0-0.020-0.01894.460-0.010-0.0100.0000.0000.0000.000
161A410GLN0-0.0180.00495.901-0.031-0.0310.0000.0000.0000.000
162A411TYR0-0.015-0.01490.2210.0320.0320.0000.0000.0000.000
163A412MET00.0060.02790.775-0.031-0.0310.0000.0000.0000.000
164A413SER0-0.021-0.01487.5610.0460.0460.0000.0000.0000.000
165A414LYS10.8450.93085.618-3.711-3.7110.0000.0000.0000.000
166A415ASN0-0.001-0.00480.5530.0580.0580.0000.0000.0000.000
167A416LEU00.0260.01077.094-0.013-0.0130.0000.0000.0000.000
168A417TRP0-0.0100.00274.7790.0180.0180.0000.0000.0000.000
169A418VAL00.0000.00169.616-0.023-0.0230.0000.0000.0000.000
170A419GLU-1-0.839-0.90272.5604.2804.2800.0000.0000.0000.000
171A420GLN00.0030.00468.944-0.026-0.0260.0000.0000.0000.000
172A421TRP0-0.011-0.00163.113-0.038-0.0380.0000.0000.0000.000
173A422GLN00.0260.00167.3420.0670.0670.0000.0000.0000.000
174A423ASP-1-0.891-0.94365.7564.8064.8060.0000.0000.0000.000
175A424GLY00.017-0.00766.384-0.025-0.0250.0000.0000.0000.000
176A425VAL0-0.052-0.02067.196-0.051-0.0510.0000.0000.0000.000
177A426LEU0-0.0120.00368.7490.0280.0280.0000.0000.0000.000
178A427ARG10.8160.89571.190-4.430-4.4300.0000.0000.0000.000
179A428LEU0-0.007-0.01273.2670.0450.0450.0000.0000.0000.000
180A429ARG10.8510.92276.122-4.066-4.0660.0000.0000.0000.000
181A430VAL0-0.001-0.01878.8130.0030.0030.0000.0000.0000.000
182A431GLU-1-0.835-0.91882.1083.8983.8980.0000.0000.0000.000
183A432GLY00.0370.03184.8100.0170.0170.0000.0000.0000.000
184A433GLY00.030-0.00487.2430.0000.0000.0000.0000.0000.000
185A434GLY0-0.048-0.00189.784-0.038-0.0380.0000.0000.0000.000
186A435SER0-0.005-0.03691.9890.0350.0350.0000.0000.0000.000
187A436ILE0-0.0010.00394.128-0.038-0.0380.0000.0000.0000.000
188A437THR0-0.004-0.00296.2440.0380.0380.0000.0000.0000.000
189A438HIS0-0.061-0.01592.5200.0200.0200.0000.0000.0000.000
190A439SER00.005-0.01595.422-0.006-0.0060.0000.0000.0000.000
191A440ASN0-0.034-0.01392.550-0.007-0.0070.0000.0000.0000.000
192A441SER00.035-0.01088.837-0.003-0.0030.0000.0000.0000.000
193A442LYS10.8260.90088.892-3.545-3.5450.0000.0000.0000.000
194A443TRP00.0410.00682.2770.0170.0170.0000.0000.0000.000
195A444PRO00.0110.01282.989-0.004-0.0040.0000.0000.0000.000
196A445ALA00.014-0.00179.5230.0290.0290.0000.0000.0000.000
197A446MET0-0.057-0.01777.832-0.019-0.0190.0000.0000.0000.000
198A447THR00.0410.01872.0740.0200.0200.0000.0000.0000.000
199A448VAL0-0.0170.00371.083-0.013-0.0130.0000.0000.0000.000
200A449SER00.020-0.01968.1370.0240.0240.0000.0000.0000.000
201A450TYR0-0.084-0.06664.922-0.078-0.0780.0000.0000.0000.000
202A451PRO00.0030.01261.5580.0390.0390.0000.0000.0000.000
203A452ARG10.8650.91756.509-5.582-5.5820.0000.0000.0000.000
204A453SER0-0.050-0.04258.0130.1190.1190.0000.0000.0000.000
205A454PHE0-0.038-0.01652.3320.0380.0380.0000.0000.0000.000
206A455THR0-0.007-0.00148.6310.0640.0640.0000.0000.0000.000