FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 9MY72

Calculation Name: 1K1B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K1B

Chain ID: A

ChEMBL ID:

UniProt ID: P20749

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2462808.643123
FMO2-HF: Nuclear repulsion 2376596.884201
FMO2-HF: Total energy -86211.758922
FMO2-MP2: Total energy -86462.150755


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:125:GLU)


Summations of interaction energy for fragment #1(A:125: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.
-0.894999999999992.3570.037-1.452-1.8370.002
Interaction energy analysis for fragmet #1(A:125:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.959 / q_NPA : -0.988
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].
3A127GLY0-0.0150.0003.5182.5464.5610.011-1.017-1.0090.002
4A128ASP-1-0.915-0.9593.42635.18736.0860.023-0.213-0.7090.001
5A129THR0-0.031-0.0203.638-1.522-1.3050.004-0.187-0.034-0.001
6A130PRO00.0270.0105.259-3.341-3.3410.0000.0000.0000.000
7A131LEU0-0.0040.0058.380-2.080-2.0800.0000.0000.0000.000
8A132HIS00.0340.0078.904-0.940-0.9400.0000.0000.0000.000
9A133ILE00.0030.00910.077-1.469-1.4690.0000.0000.0000.000
10A134ALA0-0.009-0.00712.300-1.264-1.2640.0000.0000.0000.000
11A135VAL0-0.041-0.02514.058-1.140-1.1400.0000.0000.0000.000
12A136VAL00.0280.01315.114-0.833-0.8330.0000.0000.0000.000
13A137GLN0-0.063-0.03115.544-0.729-0.7290.0000.0000.0000.000
14A138GLY00.0300.02218.311-0.570-0.5700.0000.0000.0000.000
15A139ASN0-0.022-0.00217.391-0.860-0.8600.0000.0000.0000.000
16A140LEU00.0420.01518.2260.5970.5970.0000.0000.0000.000
17A141PRO00.004-0.01019.4900.3030.3030.0000.0000.0000.000
18A142ALA0-0.040-0.01715.2870.3670.3670.0000.0000.0000.000
19A143VAL00.0390.02314.8830.8300.8300.0000.0000.0000.000
20A144HIS00.0170.01315.6520.7980.7980.0000.0000.0000.000
21A145ARG10.9680.99715.890-15.582-15.5820.0000.0000.0000.000
22A146LEU0-0.002-0.00210.1740.5870.5870.0000.0000.0000.000
23A147VAL00.0350.02012.5370.9370.9370.0000.0000.0000.000
24A148ASN0-0.030-0.01914.649-0.120-0.1200.0000.0000.0000.000
25A149LEU0-0.020-0.01412.0800.0850.0850.0000.0000.0000.000
26A150PHE0-0.045-0.0296.6711.7491.7490.0000.0000.0000.000
27A151GLN00.0150.00811.8250.1880.1880.0000.0000.0000.000
28A152GLN0-0.048-0.02815.312-0.384-0.3840.0000.0000.0000.000
29A153GLY0-0.023-0.00212.127-0.204-0.2040.0000.0000.0000.000
30A154GLY0-0.028-0.00912.2691.1351.1350.0000.0000.0000.000
31A155ARG10.8740.9444.137-35.175-35.054-0.001-0.035-0.0850.000
32A156GLU-1-0.806-0.90511.19515.88215.8820.0000.0000.0000.000
33A157LEU0-0.028-0.02210.7151.4951.4950.0000.0000.0000.000
34A158ASP-1-0.820-0.91412.27415.41515.4150.0000.0000.0000.000
35A159ILE0-0.067-0.0227.0140.1900.1900.0000.0000.0000.000
36A160TYR0-0.035-0.0549.855-0.345-0.3450.0000.0000.0000.000
37A161ASN00.0340.0238.2441.3501.3500.0000.0000.0000.000
38A162ASN0-0.006-0.0368.094-1.088-1.0880.0000.0000.0000.000
39A163LEU0-0.072-0.02110.954-1.027-1.0270.0000.0000.0000.000
40A164ARG10.8280.90012.872-15.423-15.4230.0000.0000.0000.000
41A165GLN00.0690.03713.147-0.326-0.3260.0000.0000.0000.000
42A166THR0-0.004-0.00812.1701.1331.1330.0000.0000.0000.000
43A167PRO00.0290.00211.306-0.680-0.6800.0000.0000.0000.000
44A168LEU00.0250.01813.919-0.702-0.7020.0000.0000.0000.000
45A169HIS00.000-0.01016.562-0.080-0.0800.0000.0000.0000.000
46A170LEU00.0300.01913.233-0.490-0.4900.0000.0000.0000.000
47A171ALA0-0.0100.01017.272-0.427-0.4270.0000.0000.0000.000
48A172VAL0-0.040-0.01619.433-0.567-0.5670.0000.0000.0000.000
49A173ILE0-0.0110.00418.680-0.334-0.3340.0000.0000.0000.000
50A174THR0-0.038-0.02919.238-0.234-0.2340.0000.0000.0000.000
51A175THR0-0.079-0.04821.927-0.471-0.4710.0000.0000.0000.000
52A176LEU00.0090.01119.953-0.294-0.2940.0000.0000.0000.000
53A177PRO00.0430.01023.2650.2640.2640.0000.0000.0000.000
54A178SER0-0.003-0.01824.927-0.030-0.0300.0000.0000.0000.000
55A179VAL00.0210.00818.5730.1360.1360.0000.0000.0000.000
56A180VAL00.0160.01420.5510.3800.3800.0000.0000.0000.000
57A181ARG10.8270.90822.245-9.359-9.3590.0000.0000.0000.000
58A182LEU0-0.0330.00718.5900.0400.0400.0000.0000.0000.000
59A183LEU00.015-0.00315.6150.2550.2550.0000.0000.0000.000
60A184VAL00.0120.01719.0740.2220.2220.0000.0000.0000.000
61A185THR0-0.080-0.05321.710-0.010-0.0100.0000.0000.0000.000
62A186ALA0-0.053-0.01818.260-0.070-0.0700.0000.0000.0000.000
63A187GLY00.013-0.00218.9740.5000.5000.0000.0000.0000.000
64A188ALA0-0.0360.00116.9630.0440.0440.0000.0000.0000.000
65A189SER00.0600.01518.317-0.917-0.9170.0000.0000.0000.000
66A190PRO0-0.001-0.01920.2450.2020.2020.0000.0000.0000.000
67A191MET00.0040.02322.807-0.199-0.1990.0000.0000.0000.000
68A192ALA00.0190.02717.3930.0620.0620.0000.0000.0000.000
69A193LEU0-0.0180.00719.187-0.283-0.2830.0000.0000.0000.000
70A194ASP-1-0.742-0.87817.71013.42213.4220.0000.0000.0000.000
71A195ARG10.8710.96117.905-13.388-13.3880.0000.0000.0000.000
72A196HIS0-0.004-0.02019.099-0.256-0.2560.0000.0000.0000.000
73A197GLY00.0190.00721.768-0.519-0.5190.0000.0000.0000.000
74A198GLN0-0.032-0.03022.450-0.541-0.5410.0000.0000.0000.000
75A199THR00.0500.00221.8120.4800.4800.0000.0000.0000.000
76A200ALA00.0170.00121.399-0.044-0.0440.0000.0000.0000.000
77A201ALA00.0530.01622.893-0.199-0.1990.0000.0000.0000.000
78A202HIS00.0010.02925.5920.0530.0530.0000.0000.0000.000
79A203LEU00.0260.02220.395-0.173-0.1730.0000.0000.0000.000
80A204ALA00.0130.00024.902-0.136-0.1360.0000.0000.0000.000
81A205CYS0-0.071-0.02326.972-0.358-0.3580.0000.0000.0000.000
82A206GLU-1-0.869-0.93025.57510.55010.5500.0000.0000.0000.000
83A207HIS0-0.063-0.03524.0260.0540.0540.0000.0000.0000.000
84A208ARG10.8520.93028.099-8.491-8.4910.0000.0000.0000.000
85A209SER00.0640.03728.031-0.093-0.0930.0000.0000.0000.000
86A210PRO00.0460.00529.8150.1570.1570.0000.0000.0000.000
87A211THR0-0.031-0.00329.8720.0320.0320.0000.0000.0000.000
88A212CYS0-0.0120.00725.4950.1920.1920.0000.0000.0000.000
89A213LEU00.0500.02527.2080.1630.1630.0000.0000.0000.000
90A214ARG10.8430.91329.284-7.891-7.8910.0000.0000.0000.000
91A215ALA0-0.014-0.00726.639-0.012-0.0120.0000.0000.0000.000
92A216LEU0-0.0010.01223.2370.1370.1370.0000.0000.0000.000
93A217LEU00.016-0.00226.917-0.007-0.0070.0000.0000.0000.000
94A218ASP-1-0.824-0.87730.3618.3038.3030.0000.0000.0000.000
95A219SER0-0.063-0.05626.315-0.109-0.1090.0000.0000.0000.000
96A220ALA00.0020.01626.3590.2900.2900.0000.0000.0000.000
97A221ALA00.0220.02826.936-0.340-0.3400.0000.0000.0000.000
98A222PRO00.016-0.00528.8820.0660.0660.0000.0000.0000.000
99A223GLY00.0160.01530.9510.0530.0530.0000.0000.0000.000
100A224THR0-0.068-0.04425.2960.2380.2380.0000.0000.0000.000
101A225LEU0-0.029-0.03125.8660.3860.3860.0000.0000.0000.000
102A226ASP-1-0.844-0.93228.0848.5258.5250.0000.0000.0000.000
103A227LEU0-0.018-0.01929.5160.2660.2660.0000.0000.0000.000
104A228GLU-1-0.809-0.90331.8877.9367.9360.0000.0000.0000.000
105A229ALA00.0220.01927.5350.0320.0320.0000.0000.0000.000
106A230ARG10.7210.84229.382-8.318-8.3180.0000.0000.0000.000
107A231ASN00.0290.02326.5700.0110.0110.0000.0000.0000.000
108A232TYR0-0.008-0.00521.927-0.023-0.0230.0000.0000.0000.000
109A233ASP-1-0.883-0.90527.8419.2399.2390.0000.0000.0000.000
110A234GLY00.007-0.00730.657-0.330-0.3300.0000.0000.0000.000
111A235LEU0-0.026-0.01131.440-0.258-0.2580.0000.0000.0000.000
112A236THR00.0850.03730.9890.3140.3140.0000.0000.0000.000
113A237ALA00.029-0.00129.9340.0480.0480.0000.0000.0000.000
114A238LEU00.0470.01931.367-0.038-0.0380.0000.0000.0000.000
115A239HIS00.0270.02234.2740.0820.0820.0000.0000.0000.000
116A240VAL0-0.021-0.00229.515-0.070-0.0700.0000.0000.0000.000
117A241ALA00.0150.00932.835-0.069-0.0690.0000.0000.0000.000
118A242VAL00.0140.00234.403-0.120-0.1200.0000.0000.0000.000
119A243ASN00.0130.01335.352-0.283-0.2830.0000.0000.0000.000
120A244THR0-0.067-0.02832.0820.0390.0390.0000.0000.0000.000
121A245GLU-1-0.812-0.89035.4097.0597.0590.0000.0000.0000.000
122A246CYS0-0.090-0.00735.260-0.060-0.0600.0000.0000.0000.000
123A247GLN00.013-0.01837.269-0.071-0.0710.0000.0000.0000.000
124A248GLU-1-0.809-0.90436.7517.4087.4080.0000.0000.0000.000
125A249THR0-0.021-0.03232.2100.0950.0950.0000.0000.0000.000
126A250VAL00.0110.00535.1370.0290.0290.0000.0000.0000.000
127A251GLN0-0.035-0.02137.778-0.110-0.1100.0000.0000.0000.000
128A252LEU0-0.032-0.00832.994-0.021-0.0210.0000.0000.0000.000
129A253LEU00.005-0.00932.0910.0700.0700.0000.0000.0000.000
130A254LEU0-0.0060.01135.859-0.030-0.0300.0000.0000.0000.000
131A255GLU-1-0.844-0.91038.3317.3267.3260.0000.0000.0000.000
132A256ARG10.7540.85633.709-8.159-8.1590.0000.0000.0000.000
133A257GLY00.0030.01636.2470.1420.1420.0000.0000.0000.000
134A258ALA0-0.024-0.01035.5730.0280.0280.0000.0000.0000.000
135A259ASP-1-0.870-0.93537.1596.8636.8630.0000.0000.0000.000
136A260ILE0-0.017-0.01639.5130.0960.0960.0000.0000.0000.000
137A261ASP-1-0.831-0.90241.8026.3796.3790.0000.0000.0000.000
138A262ALA00.0110.01437.555-0.030-0.0300.0000.0000.0000.000
139A263VAL0-0.007-0.00439.4430.0440.0440.0000.0000.0000.000
140A264ASP-1-0.772-0.83335.8607.7937.7930.0000.0000.0000.000
141A265ILE00.019-0.00434.687-0.159-0.1590.0000.0000.0000.000
142A266LYS10.8330.92232.344-8.944-8.9440.0000.0000.0000.000
143A267SER0-0.087-0.07337.318-0.171-0.1710.0000.0000.0000.000
144A268GLY00.0380.01740.053-0.201-0.2010.0000.0000.0000.000
145A269ARG10.7720.85740.867-7.031-7.0310.0000.0000.0000.000
146A270SER00.0620.01940.7420.1780.1780.0000.0000.0000.000
147A271PRO00.0200.00738.904-0.045-0.0450.0000.0000.0000.000
148A272LEU00.0420.03041.099-0.026-0.0260.0000.0000.0000.000
149A273ILE0-0.011-0.02244.433-0.104-0.1040.0000.0000.0000.000
150A274HIS0-0.018-0.01638.075-0.052-0.0520.0000.0000.0000.000
151A275ALA00.0330.02842.114-0.029-0.0290.0000.0000.0000.000
152A276VAL0-0.045-0.03543.572-0.101-0.1010.0000.0000.0000.000
153A277GLU-1-0.852-0.88544.2186.3976.3970.0000.0000.0000.000
154A278ASN00.0010.00139.595-0.023-0.0230.0000.0000.0000.000
155A279ASN0-0.098-0.06143.606-0.121-0.1210.0000.0000.0000.000
156A280SER00.002-0.01643.130-0.136-0.1360.0000.0000.0000.000
157A281LEU0-0.027-0.02545.660-0.038-0.0380.0000.0000.0000.000
158A282SER00.0230.01044.807-0.101-0.1010.0000.0000.0000.000
159A283MET00.0270.03140.8960.0140.0140.0000.0000.0000.000
160A284VAL0-0.005-0.00644.084-0.035-0.0350.0000.0000.0000.000
161A285GLN0-0.047-0.03947.147-0.035-0.0350.0000.0000.0000.000
162A286LEU00.0060.02241.697-0.056-0.0560.0000.0000.0000.000
163A287LEU00.0270.01041.272-0.002-0.0020.0000.0000.0000.000
164A288LEU0-0.022-0.02045.267-0.052-0.0520.0000.0000.0000.000
165A289GLN0-0.069-0.02548.0280.0000.0000.0000.0000.0000.000
166A290HIS0-0.055-0.03443.8060.0300.0300.0000.0000.0000.000
167A291GLY0-0.0020.00446.4430.0550.0550.0000.0000.0000.000
168A292ALA0-0.026-0.00345.744-0.017-0.0170.0000.0000.0000.000
169A293ASN00.022-0.00647.283-0.255-0.2550.0000.0000.0000.000
170A294VAL0-0.020-0.01649.3330.0550.0550.0000.0000.0000.000
171A295ASN0-0.041-0.00951.571-0.042-0.0420.0000.0000.0000.000
172A296ALA00.0180.02147.037-0.009-0.0090.0000.0000.0000.000
173A297GLN0-0.084-0.07148.683-0.053-0.0530.0000.0000.0000.000
174A298MET00.0110.02045.4950.1510.1510.0000.0000.0000.000
175A299TYR0-0.017-0.02640.410-0.181-0.1810.0000.0000.0000.000
176A300SER00.0070.01347.345-0.079-0.0790.0000.0000.0000.000
177A301GLY00.0620.03150.389-0.144-0.1440.0000.0000.0000.000
178A302SER0-0.024-0.01550.840-0.129-0.1290.0000.0000.0000.000
179A303SER00.0640.01950.2160.1100.1100.0000.0000.0000.000
180A304ALA00.0740.03549.0700.0040.0040.0000.0000.0000.000
181A305LEU00.0230.00750.324-0.022-0.0220.0000.0000.0000.000
182A306HIS00.0010.01352.9230.0180.0180.0000.0000.0000.000
183A307SER0-0.002-0.02248.538-0.080-0.0800.0000.0000.0000.000
184A308ALA0-0.007-0.00451.270-0.004-0.0040.0000.0000.0000.000
185A309SER0-0.039-0.04352.788-0.068-0.0680.0000.0000.0000.000
186A310GLY00.0650.02855.108-0.068-0.0680.0000.0000.0000.000
187A311ARG10.8480.92846.029-6.308-6.3080.0000.0000.0000.000
188A312GLY0-0.0020.00353.652-0.022-0.0220.0000.0000.0000.000
189A313LEU0-0.0150.00849.795-0.061-0.0610.0000.0000.0000.000
190A314LEU00.001-0.01754.193-0.007-0.0070.0000.0000.0000.000
191A315PRO00.001-0.00553.319-0.060-0.0600.0000.0000.0000.000
192A316LEU00.0620.05848.628-0.037-0.0370.0000.0000.0000.000
193A317VAL00.0190.01053.078-0.025-0.0250.0000.0000.0000.000
194A318ARG10.9200.95456.154-5.092-5.0920.0000.0000.0000.000
195A319THR00.0170.01251.827-0.054-0.0540.0000.0000.0000.000
196A320LEU00.0240.02350.804-0.023-0.0230.0000.0000.0000.000
197A321VAL00.0230.00554.762-0.032-0.0320.0000.0000.0000.000
198A322ARG10.8670.92357.914-4.950-4.9500.0000.0000.0000.000
199A323SER0-0.0020.00254.071-0.012-0.0120.0000.0000.0000.000
200A324GLY00.0070.01655.9210.0370.0370.0000.0000.0000.000
201A325ALA0-0.045-0.02555.3020.0120.0120.0000.0000.0000.000
202A326ASP-1-0.782-0.86956.7234.9634.9630.0000.0000.0000.000
203A327SER0-0.041-0.03058.4660.0470.0470.0000.0000.0000.000
204A328SER0-0.102-0.08760.683-0.059-0.0590.0000.0000.0000.000
205A329LEU00.0470.02454.173-0.023-0.0230.0000.0000.0000.000
206A330LYS10.8090.87558.064-4.869-4.8690.0000.0000.0000.000
207A331ASN0-0.041-0.01654.4060.0030.0030.0000.0000.0000.000
208A332CYS0-0.048-0.04453.345-0.067-0.0670.0000.0000.0000.000
209A333HIS0-0.063-0.03055.807-0.061-0.0610.0000.0000.0000.000
210A334ASN00.0250.00657.898-0.155-0.1550.0000.0000.0000.000
211A335ASP-1-0.770-0.84358.0705.1165.1160.0000.0000.0000.000
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