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: L7LG9

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 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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2454120.11798
FMO2-HF: Nuclear repulsion 2367908.793287
FMO2-HF: Total energy -86211.324693
FMO2-MP2: Total energy -86461.674856


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.
1.2773.4050.002-0.426-1.7020.001
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 : -0.970 / q_NPA : -1.019
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].
3A127GLY00.0140.0063.6341.2152.333-0.025-0.149-0.9430.001
4A128ASP-1-0.940-0.9683.39737.67438.6180.029-0.217-0.7550.000
5A129THR0-0.040-0.0214.049-0.584-0.578-0.001-0.0590.0540.000
6A130PRO00.0440.0105.501-3.363-3.3630.0000.0000.0000.000
7A131LEU0-0.0030.0008.656-2.132-2.1320.0000.0000.0000.000
8A132HIS00.020-0.0069.401-0.780-0.7800.0000.0000.0000.000
9A133ILE0-0.008-0.00110.773-1.550-1.5500.0000.0000.0000.000
10A134ALA0-0.005-0.00112.595-1.262-1.2620.0000.0000.0000.000
11A135VAL0-0.040-0.02214.437-1.181-1.1810.0000.0000.0000.000
12A136VAL00.0280.01915.677-0.830-0.8300.0000.0000.0000.000
13A137GLN0-0.064-0.02615.808-0.647-0.6470.0000.0000.0000.000
14A138GLY00.0070.01018.650-0.546-0.5460.0000.0000.0000.000
15A139ASN0-0.020-0.00818.040-0.794-0.7940.0000.0000.0000.000
16A140LEU00.0540.02118.7450.5430.5430.0000.0000.0000.000
17A141PRO00.012-0.00619.9580.3420.3420.0000.0000.0000.000
18A142ALA0-0.019-0.01015.7950.3330.3330.0000.0000.0000.000
19A143VAL00.0480.02815.4130.9170.9170.0000.0000.0000.000
20A144HIS00.0160.01316.1320.8110.8110.0000.0000.0000.000
21A145ARG10.9580.98915.977-15.864-15.8640.0000.0000.0000.000
22A146LEU00.004-0.00210.4090.5500.5500.0000.0000.0000.000
23A147VAL00.0320.02213.0520.8410.8410.0000.0000.0000.000
24A148ASN0-0.030-0.02615.211-0.181-0.1810.0000.0000.0000.000
25A149LEU0-0.022-0.01112.0180.0600.0600.0000.0000.0000.000
26A150PHE0-0.056-0.0377.2651.5601.5600.0000.0000.0000.000
27A151GLN00.0320.02412.0490.0700.0700.0000.0000.0000.000
28A152GLN0-0.047-0.01715.510-0.344-0.3440.0000.0000.0000.000
29A153GLY0-0.022-0.00211.962-0.163-0.1630.0000.0000.0000.000
30A154GLY0-0.028-0.01412.3940.8640.8640.0000.0000.0000.000
31A155ARG10.8800.9444.633-33.293-33.233-0.001-0.001-0.0580.000
32A156GLU-1-0.819-0.91810.91816.07016.0700.0000.0000.0000.000
33A157LEU0-0.015-0.01310.9491.4201.4200.0000.0000.0000.000
34A158ASP-1-0.822-0.90812.76515.54115.5410.0000.0000.0000.000
35A159ILE0-0.074-0.0247.4790.3410.3410.0000.0000.0000.000
36A160TYR0-0.043-0.06210.426-0.529-0.5290.0000.0000.0000.000
37A161ASN00.0490.0318.8731.4081.4080.0000.0000.0000.000
38A162ASN00.018-0.0118.571-0.829-0.8290.0000.0000.0000.000
39A163LEU0-0.079-0.02411.737-1.056-1.0560.0000.0000.0000.000
40A164ARG10.8660.93813.468-15.778-15.7780.0000.0000.0000.000
41A165GLN00.0750.04013.790-0.287-0.2870.0000.0000.0000.000
42A166THR00.0210.01912.8141.1671.1670.0000.0000.0000.000
43A167PRO00.0370.00311.687-0.699-0.6990.0000.0000.0000.000
44A168LEU00.0340.01814.367-0.714-0.7140.0000.0000.0000.000
45A169HIS0-0.001-0.00617.157-0.084-0.0840.0000.0000.0000.000
46A170LEU00.0250.01113.887-0.518-0.5180.0000.0000.0000.000
47A171ALA0-0.0170.00917.915-0.438-0.4380.0000.0000.0000.000
48A172VAL0-0.047-0.01919.970-0.583-0.5830.0000.0000.0000.000
49A173ILE0-0.0170.00119.304-0.321-0.3210.0000.0000.0000.000
50A174THR0-0.036-0.02419.860-0.165-0.1650.0000.0000.0000.000
51A175THR0-0.084-0.04722.493-0.536-0.5360.0000.0000.0000.000
52A176LEU00.0120.01420.613-0.241-0.2410.0000.0000.0000.000
53A177PRO00.0640.01623.7790.2800.2800.0000.0000.0000.000
54A178SER0-0.005-0.01525.310-0.052-0.0520.0000.0000.0000.000
55A179VAL00.0250.00718.9710.1310.1310.0000.0000.0000.000
56A180VAL00.0040.00921.1210.3350.3350.0000.0000.0000.000
57A181ARG10.8380.91422.808-9.390-9.3900.0000.0000.0000.000
58A182LEU0-0.0310.00919.145-0.010-0.0100.0000.0000.0000.000
59A183LEU00.0230.00316.2090.2440.2440.0000.0000.0000.000
60A184VAL00.0100.01519.6850.1830.1830.0000.0000.0000.000
61A185THR0-0.066-0.04222.351-0.037-0.0370.0000.0000.0000.000
62A186ALA0-0.065-0.02418.918-0.088-0.0880.0000.0000.0000.000
63A187GLY00.0130.00019.6110.4480.4480.0000.0000.0000.000
64A188ALA0-0.060-0.01517.5820.2190.2190.0000.0000.0000.000
65A189SER00.0480.01018.767-0.936-0.9360.0000.0000.0000.000
66A190PRO0-0.013-0.02520.5120.2490.2490.0000.0000.0000.000
67A191MET00.0040.02322.857-0.296-0.2960.0000.0000.0000.000
68A192ALA00.0080.02817.8590.0160.0160.0000.0000.0000.000
69A193LEU0-0.0180.00919.923-0.226-0.2260.0000.0000.0000.000
70A194ASP-1-0.734-0.87418.33213.48913.4890.0000.0000.0000.000
71A195ARG10.8800.94718.420-13.783-13.7830.0000.0000.0000.000
72A196HIS0-0.017-0.01719.939-0.362-0.3620.0000.0000.0000.000
73A197GLY00.025-0.00222.419-0.527-0.5270.0000.0000.0000.000
74A198GLN0-0.022-0.00923.141-0.647-0.6470.0000.0000.0000.000
75A199THR00.0450.00522.4810.4760.4760.0000.0000.0000.000
76A200ALA00.0350.00022.178-0.061-0.0610.0000.0000.0000.000
77A201ALA00.0480.01523.690-0.188-0.1880.0000.0000.0000.000
78A202HIS00.0140.02726.2250.0180.0180.0000.0000.0000.000
79A203LEU00.0170.01721.165-0.169-0.1690.0000.0000.0000.000
80A204ALA00.0150.00025.619-0.123-0.1230.0000.0000.0000.000
81A205CYS0-0.078-0.02927.675-0.350-0.3500.0000.0000.0000.000
82A206GLU-1-0.884-0.93326.13810.63310.6330.0000.0000.0000.000
83A207HIS0-0.067-0.03624.7010.0660.0660.0000.0000.0000.000
84A208ARG10.8590.94028.832-8.503-8.5030.0000.0000.0000.000
85A209SER00.0590.03228.732-0.093-0.0930.0000.0000.0000.000
86A210PRO00.0500.00930.5300.1600.1600.0000.0000.0000.000
87A211THR0-0.028-0.01130.8050.0320.0320.0000.0000.0000.000
88A212CYS0-0.0090.00626.3070.2010.2010.0000.0000.0000.000
89A213LEU00.0490.02627.8280.1920.1920.0000.0000.0000.000
90A214ARG10.9550.97929.963-7.983-7.9830.0000.0000.0000.000
91A215ALA0-0.016-0.00227.179-0.019-0.0190.0000.0000.0000.000
92A216LEU00.0060.01923.7950.1260.1260.0000.0000.0000.000
93A217LEU00.004-0.00827.4010.0030.0030.0000.0000.0000.000
94A218ASP-1-0.823-0.88630.7368.4578.4570.0000.0000.0000.000
95A219SER0-0.063-0.05526.616-0.073-0.0730.0000.0000.0000.000
96A220ALA0-0.0080.01326.8180.2390.2390.0000.0000.0000.000
97A221ALA00.0230.02727.308-0.329-0.3290.0000.0000.0000.000
98A222PRO00.0360.00329.2170.0610.0610.0000.0000.0000.000
99A223GLY00.0000.00331.1970.0900.0900.0000.0000.0000.000
100A224THR0-0.069-0.03926.0840.2380.2380.0000.0000.0000.000
101A225LEU0-0.016-0.01827.0390.3040.3040.0000.0000.0000.000
102A226ASP-1-0.845-0.93928.7748.5418.5410.0000.0000.0000.000
103A227LEU0-0.030-0.02830.3400.2290.2290.0000.0000.0000.000
104A228GLU-1-0.791-0.89232.5327.9127.9120.0000.0000.0000.000
105A229ALA0-0.0180.00428.2760.0150.0150.0000.0000.0000.000
106A230ARG10.7700.87230.260-8.329-8.3290.0000.0000.0000.000
107A231ASN00.0160.01327.1540.0110.0110.0000.0000.0000.000
108A232TYR0-0.015-0.01921.925-0.022-0.0220.0000.0000.0000.000
109A233ASP-1-0.881-0.91127.9949.2289.2280.0000.0000.0000.000
110A234GLY0-0.008-0.01130.956-0.345-0.3450.0000.0000.0000.000
111A235LEU0-0.040-0.01432.183-0.244-0.2440.0000.0000.0000.000
112A236THR00.0840.04031.6510.2990.2990.0000.0000.0000.000
113A237ALA00.030-0.01030.5750.0010.0010.0000.0000.0000.000
114A238LEU00.0550.02832.122-0.048-0.0480.0000.0000.0000.000
115A239HIS00.0160.02835.1110.0590.0590.0000.0000.0000.000
116A240VAL0-0.019-0.00330.433-0.086-0.0860.0000.0000.0000.000
117A241ALA00.0140.00333.765-0.060-0.0600.0000.0000.0000.000
118A242VAL00.004-0.00635.252-0.140-0.1400.0000.0000.0000.000
119A243ASN00.0050.00435.895-0.294-0.2940.0000.0000.0000.000
120A244THR0-0.088-0.03233.016-0.015-0.0150.0000.0000.0000.000
121A245GLU-1-0.812-0.88536.3687.0597.0590.0000.0000.0000.000
122A246CYS0-0.107-0.01836.227-0.041-0.0410.0000.0000.0000.000
123A247GLN00.038-0.00438.211-0.092-0.0920.0000.0000.0000.000
124A248GLU-1-0.846-0.93437.3197.4427.4420.0000.0000.0000.000
125A249THR00.016-0.01532.935-0.026-0.0260.0000.0000.0000.000
126A250VAL00.0300.01835.8220.0330.0330.0000.0000.0000.000
127A251GLN0-0.043-0.02738.377-0.058-0.0580.0000.0000.0000.000
128A252LEU0-0.038-0.01033.964-0.019-0.0190.0000.0000.0000.000
129A253LEU0-0.006-0.01732.7400.0560.0560.0000.0000.0000.000
130A254LEU0-0.0010.00236.548-0.023-0.0230.0000.0000.0000.000
131A255GLU-1-0.912-0.94039.6047.1307.1300.0000.0000.0000.000
132A256ARG10.7420.84634.230-8.185-8.1850.0000.0000.0000.000
133A257GLY00.0030.00836.9640.1520.1520.0000.0000.0000.000
134A258ALA0-0.053-0.01236.3730.0190.0190.0000.0000.0000.000
135A259ASP-1-0.856-0.92437.8416.8946.8940.0000.0000.0000.000
136A260ILE0-0.028-0.02340.0590.0980.0980.0000.0000.0000.000
137A261ASP-1-0.893-0.95942.3436.4056.4050.0000.0000.0000.000
138A262ALA0-0.0020.01838.171-0.020-0.0200.0000.0000.0000.000
139A263VAL0-0.023-0.02440.3290.0030.0030.0000.0000.0000.000
140A264ASP-1-0.805-0.86136.2667.8207.8200.0000.0000.0000.000
141A265ILE00.0290.00335.161-0.153-0.1530.0000.0000.0000.000
142A266LYS10.8470.92933.087-8.902-8.9020.0000.0000.0000.000
143A267SER0-0.059-0.06537.716-0.226-0.2260.0000.0000.0000.000
144A268GLY00.0350.00740.510-0.201-0.2010.0000.0000.0000.000
145A269ARG10.7850.87641.712-7.010-7.0100.0000.0000.0000.000
146A270SER00.0870.04441.4430.1520.1520.0000.0000.0000.000
147A271PRO00.0500.01339.683-0.032-0.0320.0000.0000.0000.000
148A272LEU00.0240.02441.823-0.035-0.0350.0000.0000.0000.000
149A273ILE0-0.009-0.02145.192-0.078-0.0780.0000.0000.0000.000
150A274HIS0-0.010-0.00539.234-0.081-0.0810.0000.0000.0000.000
151A275ALA00.0340.03042.888-0.007-0.0070.0000.0000.0000.000
152A276VAL0-0.049-0.03244.309-0.107-0.1070.0000.0000.0000.000
153A277GLU-1-0.847-0.89444.8306.4256.4250.0000.0000.0000.000
154A278ASN0-0.0070.00840.137-0.047-0.0470.0000.0000.0000.000
155A279ASN0-0.108-0.06644.341-0.111-0.1110.0000.0000.0000.000
156A280SER00.014-0.01443.886-0.111-0.1110.0000.0000.0000.000
157A281LEU0-0.035-0.03646.429-0.040-0.0400.0000.0000.0000.000
158A282SER00.0240.01045.597-0.103-0.1030.0000.0000.0000.000
159A283MET00.0320.03841.6330.0130.0130.0000.0000.0000.000
160A284VAL0-0.010-0.00744.906-0.034-0.0340.0000.0000.0000.000
161A285GLN0-0.044-0.03747.902-0.029-0.0290.0000.0000.0000.000
162A286LEU00.0100.02142.534-0.059-0.0590.0000.0000.0000.000
163A287LEU00.0340.01242.082-0.007-0.0070.0000.0000.0000.000
164A288LEU0-0.022-0.02046.047-0.050-0.0500.0000.0000.0000.000
165A289GLN0-0.066-0.01948.734-0.018-0.0180.0000.0000.0000.000
166A290HIS0-0.063-0.04144.7940.0120.0120.0000.0000.0000.000
167A291GLY00.0050.01046.9030.0710.0710.0000.0000.0000.000
168A292ALA0-0.0220.00246.4350.0040.0040.0000.0000.0000.000
169A293ASN00.0290.01247.848-0.262-0.2620.0000.0000.0000.000
170A294VAL0-0.031-0.02749.6290.0620.0620.0000.0000.0000.000
171A295ASN0-0.019-0.01051.962-0.026-0.0260.0000.0000.0000.000
172A296ALA00.0080.02347.558-0.015-0.0150.0000.0000.0000.000
173A297GLN0-0.061-0.05449.520-0.045-0.0450.0000.0000.0000.000
174A298MET0-0.0030.01046.5070.1450.1450.0000.0000.0000.000
175A299TYR00.010-0.01440.738-0.185-0.1850.0000.0000.0000.000
176A300SER0-0.032-0.01047.572-0.091-0.0910.0000.0000.0000.000
177A301GLY00.0920.03750.558-0.149-0.1490.0000.0000.0000.000
178A302SER0-0.043-0.01251.312-0.141-0.1410.0000.0000.0000.000
179A303SER00.0910.03950.7910.1080.1080.0000.0000.0000.000
180A304ALA00.0780.02749.6210.0040.0040.0000.0000.0000.000
181A305LEU00.0250.00551.025-0.023-0.0230.0000.0000.0000.000
182A306HIS00.0130.01453.6320.0130.0130.0000.0000.0000.000
183A307SER0-0.005-0.01049.303-0.087-0.0870.0000.0000.0000.000
184A308ALA0-0.012-0.00752.208-0.017-0.0170.0000.0000.0000.000
185A309SER0-0.048-0.04553.604-0.080-0.0800.0000.0000.0000.000
186A310GLY00.0560.02855.733-0.070-0.0700.0000.0000.0000.000
187A311ARG10.8520.91946.934-6.295-6.2950.0000.0000.0000.000
188A312GLY0-0.034-0.01654.553-0.001-0.0010.0000.0000.0000.000
189A313LEU0-0.0010.01550.355-0.041-0.0410.0000.0000.0000.000
190A314LEU0-0.001-0.01454.855-0.025-0.0250.0000.0000.0000.000
191A315PRO00.006-0.00354.137-0.061-0.0610.0000.0000.0000.000
192A316LEU00.0730.04549.347-0.042-0.0420.0000.0000.0000.000
193A317VAL00.0220.01653.874-0.022-0.0220.0000.0000.0000.000
194A318ARG10.9060.95056.920-5.106-5.1060.0000.0000.0000.000
195A319THR00.0200.00952.801-0.056-0.0560.0000.0000.0000.000
196A320LEU00.0270.02951.447-0.018-0.0180.0000.0000.0000.000
197A321VAL00.0220.00855.405-0.030-0.0300.0000.0000.0000.000
198A322ARG10.8990.94858.994-4.931-4.9310.0000.0000.0000.000
199A323SER0-0.034-0.02854.835-0.023-0.0230.0000.0000.0000.000
200A324GLY00.0080.01456.5740.0420.0420.0000.0000.0000.000
201A325ALA0-0.049-0.01855.7530.0050.0050.0000.0000.0000.000
202A326ASP-1-0.801-0.87957.1634.9864.9860.0000.0000.0000.000
203A327SER0-0.058-0.03958.7500.0480.0480.0000.0000.0000.000
204A328SER0-0.091-0.07361.025-0.053-0.0530.0000.0000.0000.000
205A329LEU00.0420.02854.780-0.024-0.0240.0000.0000.0000.000
206A330LYS10.8580.90759.028-4.875-4.8750.0000.0000.0000.000
207A331ASN00.0020.01054.653-0.011-0.0110.0000.0000.0000.000
208A332CYS0-0.025-0.02253.536-0.075-0.0750.0000.0000.0000.000
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