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: G5RV1

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 OptAll
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 -1850447.554446
FMO2-HF: Nuclear repulsion 1772035.586584
FMO2-HF: Total energy -78411.967863
FMO2-MP2: Total energy -78640.615628


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.
-63.091-62.71812.57-7.378-5.5650.079
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 : -0.819 / q_NPA : -0.901
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].
3A252SER00.0330.0273.846-3.282-1.039-0.007-1.056-1.1800.005
4A253TYR0-0.027-0.0381.691-35.303-37.29012.578-6.315-4.2760.074
5A254VAL0-0.023-0.0108.081-1.641-1.6410.0000.0000.0000.000
6A255ALA00.0400.00911.900-0.292-0.2920.0000.0000.0000.000
7A256SER0-0.032-0.01613.228-0.725-0.7250.0000.0000.0000.000
8A257ALA0-0.045-0.00712.391-1.384-1.3840.0000.0000.0000.000
9A258VAL00.0160.01312.3472.0962.0960.0000.0000.0000.000
10A259THR00.0300.02410.349-0.288-0.2880.0000.0000.0000.000
11A260PRO00.015-0.00212.813-1.423-1.4230.0000.0000.0000.000
12A261LEU0-0.038-0.00912.0781.4011.4010.0000.0000.0000.000
13A262ARG10.8430.8984.586-44.022-43.905-0.001-0.007-0.1090.000
14A263LEU00.0400.02010.149-1.563-1.5630.0000.0000.0000.000
15A264ASN00.0250.0276.687-1.481-1.4810.0000.0000.0000.000
16A265SER0-0.013-0.0328.800-4.343-4.3430.0000.0000.0000.000
17A266SER0-0.041-0.01810.313-3.316-3.3160.0000.0000.0000.000
18A267THR0-0.002-0.02610.562-1.886-1.8860.0000.0000.0000.000
19A268LYS10.9000.95912.077-22.043-22.0430.0000.0000.0000.000
20A269VAL00.0280.02511.505-1.587-1.5870.0000.0000.0000.000
21A270LEU0-0.021-0.00811.5142.2772.2770.0000.0000.0000.000
22A271ASP-1-0.817-0.8889.35231.61931.6190.0000.0000.0000.000
23A272MET0-0.017-0.01612.243-0.258-0.2580.0000.0000.0000.000
24A273LEU0-0.0240.0027.1110.1310.1310.0000.0000.0000.000
25A274ILE00.015-0.00711.254-1.765-1.7650.0000.0000.0000.000
26A275ASP-1-0.770-0.85313.87518.18218.1820.0000.0000.0000.000
27A276SER00.0260.01115.473-0.744-0.7440.0000.0000.0000.000
28A277SER0-0.131-0.09017.354-1.226-1.2260.0000.0000.0000.000
29A278THR00.0090.00219.684-0.939-0.9390.0000.0000.0000.000
30A279LEU0-0.030-0.02318.755-0.607-0.6070.0000.0000.0000.000
31A280GLU-1-0.809-0.89119.59213.63013.6300.0000.0000.0000.000
32A281ILE0-0.021-0.01717.067-0.110-0.1100.0000.0000.0000.000
33A282ASN00.0140.00521.409-0.248-0.2480.0000.0000.0000.000
34A283SER00.0390.01024.0050.2830.2830.0000.0000.0000.000
35A284SER0-0.060-0.02426.043-0.020-0.0200.0000.0000.0000.000
36A285GLY00.0060.00522.515-0.077-0.0770.0000.0000.0000.000
37A286GLN0-0.015-0.00322.2020.4320.4320.0000.0000.0000.000
38A287LEU00.0170.01219.0160.0690.0690.0000.0000.0000.000
39A288THR0-0.018-0.01222.178-0.781-0.7810.0000.0000.0000.000
40A289VAL00.0060.00822.9960.6210.6210.0000.0000.0000.000
41A290ARG10.7980.89421.057-14.207-14.2070.0000.0000.0000.000
42A291SER0-0.016-0.01125.580-0.230-0.2300.0000.0000.0000.000
43A292THR0-0.0010.00428.001-0.016-0.0160.0000.0000.0000.000
44A293SER0-0.0010.00129.897-0.346-0.3460.0000.0000.0000.000
45A294PRO00.0050.01033.2550.1060.1060.0000.0000.0000.000
46A295ASN00.0330.00834.214-0.360-0.3600.0000.0000.0000.000
47A296LEU0-0.0030.01437.032-0.102-0.1020.0000.0000.0000.000
48A297ARG10.8550.90937.366-7.979-7.9790.0000.0000.0000.000
49A298TYR00.0510.04143.538-0.075-0.0750.0000.0000.0000.000
50A299PRO00.0630.03247.2930.0290.0290.0000.0000.0000.000
51A300ILE0-0.048-0.02343.859-0.044-0.0440.0000.0000.0000.000
52A301ALA0-0.026-0.02744.6130.0720.0720.0000.0000.0000.000
53A302ASP-1-0.804-0.89442.6267.3667.3660.0000.0000.0000.000
54A303VAL0-0.067-0.03344.484-0.168-0.1680.0000.0000.0000.000
55A304SER0-0.049-0.02846.069-0.148-0.1480.0000.0000.0000.000
56A305GLY0-0.017-0.01042.0300.0230.0230.0000.0000.0000.000
57A306GLY00.005-0.00141.7490.1610.1610.0000.0000.0000.000
58A307ILE0-0.039-0.01739.306-0.101-0.1010.0000.0000.0000.000
59A308GLY00.0330.01643.605-0.102-0.1020.0000.0000.0000.000
60A309MET0-0.026-0.00546.9590.0350.0350.0000.0000.0000.000
61A310SER00.0220.01049.481-0.116-0.1160.0000.0000.0000.000
62A311PRO00.0530.01450.779-0.086-0.0860.0000.0000.0000.000
63A312ASN00.0280.00152.847-0.025-0.0250.0000.0000.0000.000
64A313TYR0-0.113-0.06752.840-0.027-0.0270.0000.0000.0000.000
65A314ARG10.9910.99054.054-5.830-5.8300.0000.0000.0000.000
66A315PHE0-0.038-0.01857.058-0.109-0.1090.0000.0000.0000.000
67A316ARG10.8370.92356.296-5.512-5.5120.0000.0000.0000.000
68A317GLN0-0.022-0.01660.473-0.007-0.0070.0000.0000.0000.000
69A318SER0-0.041-0.02663.3470.0350.0350.0000.0000.0000.000
70A319MET00.0190.01265.573-0.060-0.0600.0000.0000.0000.000
71A320TRP0-0.047-0.01568.3030.0400.0400.0000.0000.0000.000
72A321ILE0-0.019-0.01870.717-0.068-0.0680.0000.0000.0000.000
73A322GLY00.0390.02173.7130.0170.0170.0000.0000.0000.000
74A323ILE0-0.047-0.01974.705-0.059-0.0590.0000.0000.0000.000
75A324VAL00.0620.04476.1590.0510.0510.0000.0000.0000.000
76A325SER0-0.034-0.03878.154-0.050-0.0500.0000.0000.0000.000
77A326TYR00.0600.03879.7050.0250.0250.0000.0000.0000.000
78A327SER0-0.009-0.00281.802-0.056-0.0560.0000.0000.0000.000
79A328GLY00.0750.02783.4500.0330.0330.0000.0000.0000.000
80A329SER0-0.021-0.01486.083-0.046-0.0460.0000.0000.0000.000
81A330GLY00.0130.01187.623-0.049-0.0490.0000.0000.0000.000
82A331LEU0-0.0340.00088.805-0.010-0.0100.0000.0000.0000.000
83A332ASN00.0480.02483.8770.0790.0790.0000.0000.0000.000
84A333TRP0-0.045-0.01884.135-0.019-0.0190.0000.0000.0000.000
85A334ARG10.8810.91781.114-3.838-3.8380.0000.0000.0000.000
86A335VAL00.0150.01781.546-0.055-0.0550.0000.0000.0000.000
87A336GLN0-0.031-0.00577.8440.0350.0350.0000.0000.0000.000
88A337VAL0-0.012-0.00476.860-0.046-0.0460.0000.0000.0000.000
89A338ASN00.004-0.00375.2070.0290.0290.0000.0000.0000.000
90A339SER00.017-0.00372.337-0.052-0.0520.0000.0000.0000.000
91A340ASP-1-0.854-0.91069.8154.5914.5910.0000.0000.0000.000
92A341ILE0-0.032-0.01865.127-0.024-0.0240.0000.0000.0000.000
93A342PHE00.000-0.00564.7140.0490.0490.0000.0000.0000.000
94A343ILE0-0.028-0.02458.995-0.016-0.0160.0000.0000.0000.000
95A344VAL0-0.026-0.01460.4510.0270.0270.0000.0000.0000.000
96A345ASP-1-0.823-0.92356.9715.5555.5550.0000.0000.0000.000
97A346ASP-1-0.880-0.90855.0485.8235.8230.0000.0000.0000.000
98A347TYR0-0.051-0.02058.154-0.052-0.0520.0000.0000.0000.000
99A348ILE0-0.0190.00261.9830.0290.0290.0000.0000.0000.000
100A349HIS00.0250.01863.968-0.133-0.1330.0000.0000.0000.000
101A350ILE00.0110.00967.5040.0250.0250.0000.0000.0000.000
102A351CYS0-0.034-0.02070.196-0.032-0.0320.0000.0000.0000.000
103A352LEU00.0150.00973.140-0.025-0.0250.0000.0000.0000.000
104A353PRO00.0330.01676.122-0.022-0.0220.0000.0000.0000.000
105A354ALA0-0.007-0.00779.100-0.008-0.0080.0000.0000.0000.000
106A355PHE0-0.052-0.02480.1380.0030.0030.0000.0000.0000.000
107A356ASP-1-0.789-0.87684.2973.5643.5640.0000.0000.0000.000
108A357GLY00.0390.01886.2480.0430.0430.0000.0000.0000.000
109A358PHE0-0.017-0.00887.683-0.055-0.0550.0000.0000.0000.000
110A359SER00.003-0.00489.6860.0200.0200.0000.0000.0000.000
111A360ILE0-0.045-0.01286.6920.0410.0410.0000.0000.0000.000
112A361ALA00.0280.01187.850-0.051-0.0510.0000.0000.0000.000
113A362ASP-1-0.828-0.90688.2273.5973.5970.0000.0000.0000.000
114A363GLY00.043-0.00985.3280.0280.0280.0000.0000.0000.000
115A364GLY0-0.055-0.02083.380-0.037-0.0370.0000.0000.0000.000
116A365ASP-1-0.863-0.91378.5644.1024.1020.0000.0000.0000.000
117A366LEU0-0.016-0.00578.446-0.033-0.0330.0000.0000.0000.000
118A367SER0-0.019-0.01675.2400.0660.0660.0000.0000.0000.000
119A368LEU0-0.007-0.00172.103-0.053-0.0530.0000.0000.0000.000
120A369ASN00.0350.01371.5080.1150.1150.0000.0000.0000.000
121A370PHE00.0570.02367.055-0.008-0.0080.0000.0000.0000.000
122A371VAL00.0220.03567.0830.0890.0890.0000.0000.0000.000
123A372THR0-0.062-0.04368.280-0.019-0.0190.0000.0000.0000.000
124A373GLY00.0670.03170.172-0.022-0.0220.0000.0000.0000.000
125A374LEU0-0.0450.00063.903-0.029-0.0290.0000.0000.0000.000
126A375LEU00.0060.00766.2880.0230.0230.0000.0000.0000.000
127A376PRO00.0130.02161.3270.0630.0630.0000.0000.0000.000
128A377PRO0-0.021-0.02357.798-0.041-0.0410.0000.0000.0000.000
129A378LEU0-0.028-0.00359.1080.0760.0760.0000.0000.0000.000
130A379LEU00.0380.02057.204-0.058-0.0580.0000.0000.0000.000
131A380THR00.027-0.00361.1160.0180.0180.0000.0000.0000.000
132A381GLY00.0230.02159.375-0.033-0.0330.0000.0000.0000.000
133A382ASP-1-0.823-0.89358.2445.5425.5420.0000.0000.0000.000
134A383THR0-0.020-0.02560.223-0.035-0.0350.0000.0000.0000.000
135A384GLU-1-0.834-0.86959.1165.2975.2970.0000.0000.0000.000
136A385PRO00.008-0.00361.4320.0700.0700.0000.0000.0000.000
137A386ALA0-0.016-0.01559.2230.0530.0530.0000.0000.0000.000
138A387PHE0-0.039-0.02059.9480.0550.0550.0000.0000.0000.000
139A388HIS10.8860.94657.952-5.442-5.4420.0000.0000.0000.000
140A389ASN0-0.036-0.01162.537-0.013-0.0130.0000.0000.0000.000
141A390ASP-1-0.821-0.89962.9915.0285.0280.0000.0000.0000.000
142A391VAL0-0.043-0.02366.316-0.031-0.0310.0000.0000.0000.000
143A392VAL0-0.064-0.02967.1770.0190.0190.0000.0000.0000.000
144A393THR0-0.005-0.01370.591-0.067-0.0670.0000.0000.0000.000
145A394TYR00.0200.01266.3510.0160.0160.0000.0000.0000.000
146A395GLY00.016-0.00270.778-0.037-0.0370.0000.0000.0000.000
147A396ALA0-0.034-0.01272.078-0.041-0.0410.0000.0000.0000.000
148A397GLN0-0.034-0.00974.974-0.034-0.0340.0000.0000.0000.000
149A398THR0-0.024-0.01378.243-0.044-0.0440.0000.0000.0000.000
150A399VAL00.000-0.00280.4120.0070.0070.0000.0000.0000.000
151A400ALA00.0020.00583.301-0.039-0.0390.0000.0000.0000.000
152A401ILE00.0150.00084.3350.0160.0160.0000.0000.0000.000
153A402GLY00.014-0.00287.905-0.042-0.0420.0000.0000.0000.000
154A403LEU0-0.0110.00689.900-0.003-0.0030.0000.0000.0000.000
155A404SER0-0.005-0.00793.047-0.037-0.0370.0000.0000.0000.000
156A405SER00.0710.02296.0390.0260.0260.0000.0000.0000.000
157A406GLY00.0060.01997.752-0.040-0.0400.0000.0000.0000.000
158A407GLY0-0.013-0.00999.270-0.006-0.0060.0000.0000.0000.000
159A408ALA0-0.009-0.01598.4570.0350.0350.0000.0000.0000.000
160A409PRO0-0.033-0.01493.539-0.008-0.0080.0000.0000.0000.000
161A410GLN0-0.014-0.00295.269-0.025-0.0250.0000.0000.0000.000
162A411TYR0-0.012-0.01589.5870.0300.0300.0000.0000.0000.000
163A412MET00.0030.02790.718-0.017-0.0170.0000.0000.0000.000
164A413SER0-0.013-0.00787.2170.0490.0490.0000.0000.0000.000
165A414LYS10.7820.89585.290-3.693-3.6930.0000.0000.0000.000
166A415ASN0-0.001-0.00379.9180.0580.0580.0000.0000.0000.000
167A416LEU00.0200.01476.485-0.019-0.0190.0000.0000.0000.000
168A417TRP0-0.027-0.01474.5570.0200.0200.0000.0000.0000.000
169A418VAL00.0050.00269.215-0.019-0.0190.0000.0000.0000.000
170A419GLU-1-0.834-0.89572.0834.2654.2650.0000.0000.0000.000
171A420GLN00.0210.00768.730-0.032-0.0320.0000.0000.0000.000
172A421TRP0-0.013-0.00662.725-0.032-0.0320.0000.0000.0000.000
173A422GLN0-0.016-0.03166.8200.0430.0430.0000.0000.0000.000
174A423ASP-1-0.869-0.92365.7734.7194.7190.0000.0000.0000.000
175A424GLY00.012-0.00266.022-0.010-0.0100.0000.0000.0000.000
176A425VAL0-0.060-0.03166.811-0.044-0.0440.0000.0000.0000.000
177A426LEU0-0.0030.00968.3580.0310.0310.0000.0000.0000.000
178A427ARG10.8100.88570.740-4.406-4.4060.0000.0000.0000.000
179A428LEU0-0.001-0.01472.7140.0510.0510.0000.0000.0000.000
180A429ARG10.8390.91775.714-4.060-4.0600.0000.0000.0000.000
181A430VAL0-0.005-0.02678.3860.0090.0090.0000.0000.0000.000
182A431GLU-1-0.856-0.90581.6493.8743.8740.0000.0000.0000.000
183A432GLY00.0440.03284.3560.0210.0210.0000.0000.0000.000
184A433GLY00.006-0.00486.9550.0020.0020.0000.0000.0000.000
185A434GLY0-0.0100.01489.537-0.039-0.0390.0000.0000.0000.000
186A435SER0-0.030-0.05291.4520.0470.0470.0000.0000.0000.000
187A436ILE0-0.0020.00493.753-0.036-0.0360.0000.0000.0000.000
188A437THR00.000-0.00296.1690.0340.0340.0000.0000.0000.000
189A438HIS0-0.039-0.00692.1350.0180.0180.0000.0000.0000.000
190A439SER00.0190.00695.4980.0010.0010.0000.0000.0000.000
191A440ASN0-0.036-0.01491.821-0.009-0.0090.0000.0000.0000.000
192A441SER00.017-0.00788.413-0.006-0.0060.0000.0000.0000.000
193A442LYS10.7950.88488.462-3.524-3.5240.0000.0000.0000.000
194A443TRP00.0440.00982.0050.0150.0150.0000.0000.0000.000
195A444PRO00.0210.01382.488-0.004-0.0040.0000.0000.0000.000
196A445ALA00.007-0.00778.8890.0260.0260.0000.0000.0000.000
197A446MET0-0.055-0.02277.384-0.018-0.0180.0000.0000.0000.000
198A447THR00.0230.01671.5250.0260.0260.0000.0000.0000.000
199A448VAL0-0.0080.00870.946-0.021-0.0210.0000.0000.0000.000
200A449SER00.029-0.01667.5570.0220.0220.0000.0000.0000.000
201A450TYR0-0.087-0.06364.434-0.079-0.0790.0000.0000.0000.000
202A451PRO00.0040.01961.0660.0450.0450.0000.0000.0000.000
203A452ARG10.8710.92455.835-5.596-5.5960.0000.0000.0000.000
204A453SER0-0.043-0.04557.7540.1120.1120.0000.0000.0000.000
205A454PHE0-0.032-0.02652.2030.0490.0490.0000.0000.0000.000
206A455THR0-0.0140.00348.0600.0650.0650.0000.0000.0000.000