FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 3K89L

Calculation Name: 1K1A-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1K1A

Chain ID: A

ChEMBL ID:

UniProt ID: P20749

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
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. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2450987.276324
FMO2-HF: Nuclear repulsion 2364775.711526
FMO2-HF: Total energy -86211.564799
FMO2-MP2: Total energy -86461.790684


3D Structure Molmil
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.
-48.364-47.63515.789-9.937-6.58-0.11
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 : 0 / q_Mulliken : -0.184 / q_NPA : -0.110
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].
3A127GLY00.0110.0143.838-1.686-0.599-0.005-0.412-0.6700.000
4A128ASP-1-0.878-0.9131.723-63.884-64.31015.795-9.504-5.864-0.110
5A129THR0-0.043-0.0284.3601.1591.227-0.001-0.021-0.0460.000
6A130PRO00.016-0.0016.1952.6052.6050.0000.0000.0000.000
7A131LEU00.0200.0109.1501.4561.4560.0000.0000.0000.000
8A132HIS00.023-0.0029.9070.1010.1010.0000.0000.0000.000
9A133ILE00.0010.00810.7860.8040.8040.0000.0000.0000.000
10A134ALA0-0.014-0.00913.1280.6830.6830.0000.0000.0000.000
11A135VAL0-0.018-0.00815.0710.5430.5430.0000.0000.0000.000
12A136VAL00.0090.00516.2560.3580.3580.0000.0000.0000.000
13A137GLN0-0.063-0.03415.6640.2370.2370.0000.0000.0000.000
14A138GLY00.0320.02418.9670.2000.2000.0000.0000.0000.000
15A139ASN0-0.016-0.00818.0090.3100.3100.0000.0000.0000.000
16A140LEU00.0560.02218.951-0.228-0.2280.0000.0000.0000.000
17A141PRO00.0120.00020.368-0.080-0.0800.0000.0000.0000.000
18A142ALA0-0.023-0.00815.759-0.116-0.1160.0000.0000.0000.000
19A143VAL00.0320.00615.700-0.414-0.4140.0000.0000.0000.000
20A144HIS00.0320.03316.386-0.255-0.2550.0000.0000.0000.000
21A145ARG10.9410.97813.8733.9303.9300.0000.0000.0000.000
22A146LEU0-0.027-0.01510.399-0.157-0.1570.0000.0000.0000.000
23A147VAL00.0290.01713.209-0.259-0.2590.0000.0000.0000.000
24A148ASN0-0.009-0.00615.5370.1780.1780.0000.0000.0000.000
25A149LEU00.001-0.00911.5090.0900.0900.0000.0000.0000.000
26A150PHE0-0.069-0.0387.929-0.682-0.6820.0000.0000.0000.000
27A151GLN00.0210.01812.5710.3670.3670.0000.0000.0000.000
28A152GLN0-0.053-0.03115.5120.2090.2090.0000.0000.0000.000
29A153GLY0-0.029-0.00512.3120.2740.2740.0000.0000.0000.000
30A154GLY0-0.018-0.00412.9520.1910.1910.0000.0000.0000.000
31A155ARG10.8610.9385.6019.6769.6760.0000.0000.0000.000
32A156GLU-1-0.862-0.93012.207-1.756-1.7560.0000.0000.0000.000
33A157LEU00.011-0.01011.967-0.864-0.8640.0000.0000.0000.000
34A158ASP-1-0.838-0.90713.878-2.455-2.4550.0000.0000.0000.000
35A159ILE0-0.054-0.0228.5210.0430.0430.0000.0000.0000.000
36A160TYR0-0.046-0.05711.128-0.215-0.2150.0000.0000.0000.000
37A161ASN00.0320.0229.655-0.555-0.5550.0000.0000.0000.000
38A162ASN00.0460.00010.006-0.121-0.1210.0000.0000.0000.000
39A163LEU0-0.059-0.01912.6900.6120.6120.0000.0000.0000.000
40A164ARG10.8810.95114.5721.2791.2790.0000.0000.0000.000
41A165GLN00.0730.03714.729-0.035-0.0350.0000.0000.0000.000
42A166THR00.0550.02513.686-0.577-0.5770.0000.0000.0000.000
43A167PRO00.017-0.00312.4320.1920.1920.0000.0000.0000.000
44A168LEU00.0540.03115.1500.2110.2110.0000.0000.0000.000
45A169HIS0-0.012-0.01118.035-0.064-0.0640.0000.0000.0000.000
46A170LEU00.0100.01314.6890.1050.1050.0000.0000.0000.000
47A171ALA00.0030.01718.6850.1270.1270.0000.0000.0000.000
48A172VAL0-0.033-0.01220.6980.1690.1690.0000.0000.0000.000
49A173ILE0-0.0100.00520.2100.0820.0820.0000.0000.0000.000
50A174THR0-0.043-0.03620.4830.0530.0530.0000.0000.0000.000
51A175THR0-0.057-0.03723.1320.1140.1140.0000.0000.0000.000
52A176LEU00.0180.01221.1450.0700.0700.0000.0000.0000.000
53A177PRO00.0300.00724.339-0.073-0.0730.0000.0000.0000.000
54A178SER00.012-0.01425.7610.0230.0230.0000.0000.0000.000
55A179VAL00.0020.00619.579-0.028-0.0280.0000.0000.0000.000
56A180VAL00.0070.00821.569-0.093-0.0930.0000.0000.0000.000
57A181ARG10.8590.93223.3611.0701.0700.0000.0000.0000.000
58A182LEU0-0.0420.00419.4610.0250.0250.0000.0000.0000.000
59A183LEU00.015-0.00316.624-0.031-0.0310.0000.0000.0000.000
60A184VAL00.0100.01720.1180.0060.0060.0000.0000.0000.000
61A185THR0-0.067-0.04722.8420.0630.0630.0000.0000.0000.000
62A186ALA0-0.054-0.01919.2650.0630.0630.0000.0000.0000.000
63A187GLY00.0250.00519.853-0.068-0.0680.0000.0000.0000.000
64A188ALA0-0.054-0.01217.9270.0110.0110.0000.0000.0000.000
65A189SER00.038-0.00219.3030.2030.2030.0000.0000.0000.000
66A190PRO0-0.006-0.02321.400-0.073-0.0730.0000.0000.0000.000
67A191MET00.0070.02723.9550.0120.0120.0000.0000.0000.000
68A192ALA00.0200.02718.7160.0760.0760.0000.0000.0000.000
69A193LEU0-0.0080.01220.728-0.016-0.0160.0000.0000.0000.000
70A194ASP-1-0.758-0.88019.295-1.422-1.4220.0000.0000.0000.000
71A195ARG10.8750.94118.9051.1821.1820.0000.0000.0000.000
72A196HIS00.000-0.01320.8430.2100.2100.0000.0000.0000.000
73A197GLY00.0410.02223.4590.1050.1050.0000.0000.0000.000
74A198GLN0-0.027-0.02424.0770.1290.1290.0000.0000.0000.000
75A199THR00.035-0.00823.444-0.116-0.1160.0000.0000.0000.000
76A200ALA00.027-0.00122.836-0.036-0.0360.0000.0000.0000.000
77A201ALA00.0540.01824.356-0.002-0.0020.0000.0000.0000.000
78A202HIS00.0000.02627.182-0.041-0.0410.0000.0000.0000.000
79A203LEU00.0100.01921.8880.0040.0040.0000.0000.0000.000
80A204ALA00.008-0.00526.3850.0000.0000.0000.0000.0000.000
81A205CYS0-0.069-0.01728.4170.0570.0570.0000.0000.0000.000
82A206GLU-1-0.844-0.92227.098-1.014-1.0140.0000.0000.0000.000
83A207HIS0-0.072-0.04025.393-0.039-0.0390.0000.0000.0000.000
84A208ARG10.8620.94529.7280.7280.7280.0000.0000.0000.000
85A209SER00.0580.02728.9710.0280.0280.0000.0000.0000.000
86A210PRO00.0640.01331.338-0.027-0.0270.0000.0000.0000.000
87A211THR0-0.028-0.00231.201-0.004-0.0040.0000.0000.0000.000
88A212CYS0-0.0270.00926.137-0.028-0.0280.0000.0000.0000.000
89A213LEU00.0450.02828.414-0.028-0.0280.0000.0000.0000.000
90A214ARG10.9590.98130.6140.7430.7430.0000.0000.0000.000
91A215ALA0-0.043-0.01627.5210.0140.0140.0000.0000.0000.000
92A216LEU00.0140.01824.504-0.026-0.0260.0000.0000.0000.000
93A217LEU00.008-0.00428.0790.0230.0230.0000.0000.0000.000
94A218ASP-1-0.821-0.89131.530-0.764-0.7640.0000.0000.0000.000
95A219SER0-0.072-0.05827.3070.0170.0170.0000.0000.0000.000
96A220ALA00.0190.02027.378-0.046-0.0460.0000.0000.0000.000
97A221ALA00.0080.02427.8730.0650.0650.0000.0000.0000.000
98A222PRO00.025-0.00129.7490.0080.0080.0000.0000.0000.000
99A223GLY00.0160.01331.9860.0130.0130.0000.0000.0000.000
100A224THR0-0.072-0.04626.612-0.018-0.0180.0000.0000.0000.000
101A225LEU0-0.039-0.03027.323-0.071-0.0710.0000.0000.0000.000
102A226ASP-1-0.851-0.93729.402-0.481-0.4810.0000.0000.0000.000
103A227LEU0-0.021-0.02230.878-0.057-0.0570.0000.0000.0000.000
104A228GLU-1-0.827-0.91733.323-0.473-0.4730.0000.0000.0000.000
105A229ALA0-0.0020.00328.9960.0310.0310.0000.0000.0000.000
106A230ARG10.7850.88930.8270.4150.4150.0000.0000.0000.000
107A231ASN00.0220.02428.1180.0510.0510.0000.0000.0000.000
108A232TYR0-0.025-0.03023.2630.0510.0510.0000.0000.0000.000
109A233ASP-1-0.885-0.91229.268-0.452-0.4520.0000.0000.0000.000
110A234GLY0-0.007-0.02032.0890.0430.0430.0000.0000.0000.000
111A235LEU0-0.046-0.02032.9150.0220.0220.0000.0000.0000.000
112A236THR00.1050.04132.498-0.050-0.0500.0000.0000.0000.000
113A237ALA00.0350.00531.415-0.018-0.0180.0000.0000.0000.000
114A238LEU00.0640.02832.929-0.018-0.0180.0000.0000.0000.000
115A239HIS0-0.0070.00435.908-0.019-0.0190.0000.0000.0000.000
116A240VAL0-0.019-0.00231.1580.0080.0080.0000.0000.0000.000
117A241ALA00.0190.01234.4780.0010.0010.0000.0000.0000.000
118A242VAL00.0120.00335.9850.0050.0050.0000.0000.0000.000
119A243ASN00.0010.00236.8850.0380.0380.0000.0000.0000.000
120A244THR0-0.079-0.03933.858-0.011-0.0110.0000.0000.0000.000
121A245GLU-1-0.849-0.91637.162-0.483-0.4830.0000.0000.0000.000
122A246CYS0-0.088-0.01336.857-0.001-0.0010.0000.0000.0000.000
123A247GLN00.0740.02038.9110.0110.0110.0000.0000.0000.000
124A248GLU-1-0.840-0.92538.357-0.604-0.6040.0000.0000.0000.000
125A249THR0-0.065-0.05433.998-0.018-0.0180.0000.0000.0000.000
126A250VAL0-0.004-0.00336.6800.0030.0030.0000.0000.0000.000
127A251GLN0-0.026-0.02139.3730.0200.0200.0000.0000.0000.000
128A252LEU0-0.033-0.01134.5310.0050.0050.0000.0000.0000.000
129A253LEU00.002-0.01233.529-0.006-0.0060.0000.0000.0000.000
130A254LEU0-0.0010.01537.2750.0170.0170.0000.0000.0000.000
131A255GLU-1-0.917-0.95540.201-0.538-0.5380.0000.0000.0000.000
132A256ARG10.7310.84734.9570.6970.6970.0000.0000.0000.000
133A257GLY00.0070.01437.530-0.011-0.0110.0000.0000.0000.000
134A258ALA0-0.032-0.01336.9340.0100.0100.0000.0000.0000.000
135A259ASP-1-0.879-0.94538.548-0.333-0.3330.0000.0000.0000.000
136A260ILE0-0.024-0.01740.688-0.018-0.0180.0000.0000.0000.000
137A261ASP-1-0.864-0.94143.248-0.304-0.3040.0000.0000.0000.000
138A262ALA0-0.0220.00439.4420.0180.0180.0000.0000.0000.000
139A263VAL0-0.007-0.01041.069-0.015-0.0150.0000.0000.0000.000
140A264ASP-1-0.784-0.85537.388-0.360-0.3600.0000.0000.0000.000
141A265ILE00.0090.00135.8060.0210.0210.0000.0000.0000.000
142A266LYS10.8280.91633.7150.4070.4070.0000.0000.0000.000
143A267SER0-0.093-0.07238.8860.0190.0190.0000.0000.0000.000
144A268GLY00.0320.02541.7860.0130.0130.0000.0000.0000.000
145A269ARG10.8110.88641.5120.3390.3390.0000.0000.0000.000
146A270SER00.1220.06742.287-0.021-0.0210.0000.0000.0000.000
147A271PRO00.020-0.00140.3330.0040.0040.0000.0000.0000.000
148A272LEU00.0380.02842.649-0.006-0.0060.0000.0000.0000.000
149A273ILE0-0.015-0.01546.0350.0070.0070.0000.0000.0000.000
150A274HIS0-0.020-0.01240.003-0.002-0.0020.0000.0000.0000.000
151A275ALA00.0280.02243.913-0.003-0.0030.0000.0000.0000.000
152A276VAL0-0.039-0.02845.3290.0040.0040.0000.0000.0000.000
153A277GLU-1-0.862-0.92045.951-0.283-0.2830.0000.0000.0000.000
154A278ASN00.003-0.00841.3600.0210.0210.0000.0000.0000.000
155A279ASN0-0.081-0.04645.5100.0060.0060.0000.0000.0000.000
156A280SER00.010-0.00744.8620.0030.0030.0000.0000.0000.000
157A281LEU0-0.027-0.02347.3810.0030.0030.0000.0000.0000.000
158A282SER00.0400.02046.4940.0140.0140.0000.0000.0000.000
159A283MET00.0100.03642.572-0.009-0.0090.0000.0000.0000.000
160A284VAL0-0.012-0.01145.8090.0070.0070.0000.0000.0000.000
161A285GLN0-0.026-0.02348.894-0.001-0.0010.0000.0000.0000.000
162A286LEU00.0200.02243.2760.0080.0080.0000.0000.0000.000
163A287LEU00.0230.01142.883-0.002-0.0020.0000.0000.0000.000
164A288LEU0-0.015-0.01246.8670.0090.0090.0000.0000.0000.000
165A289GLN0-0.066-0.02349.1930.0170.0170.0000.0000.0000.000
166A290HIS0-0.069-0.04345.728-0.010-0.0100.0000.0000.0000.000
167A291GLY00.0000.00347.850-0.002-0.0020.0000.0000.0000.000
168A292ALA0-0.0100.00347.1580.0090.0090.0000.0000.0000.000
169A293ASN00.010-0.01048.6930.0190.0190.0000.0000.0000.000
170A294VAL0-0.016-0.02050.741-0.001-0.0010.0000.0000.0000.000
171A295ASN0-0.055-0.02252.9970.0060.0060.0000.0000.0000.000
172A296ALA00.0030.02148.6640.0110.0110.0000.0000.0000.000
173A297GLN0-0.084-0.07150.3640.0020.0020.0000.0000.0000.000
174A298MET00.0150.02247.519-0.009-0.0090.0000.0000.0000.000
175A299TYR00.003-0.01641.7260.0180.0180.0000.0000.0000.000
176A300SER0-0.0060.00248.5350.0120.0120.0000.0000.0000.000
177A301GLY00.0710.03151.6600.0100.0100.0000.0000.0000.000
178A302SER0-0.039-0.01352.1960.0040.0040.0000.0000.0000.000
179A303SER00.0620.01551.685-0.011-0.0110.0000.0000.0000.000
180A304ALA00.0670.03150.736-0.001-0.0010.0000.0000.0000.000
181A305LEU00.0270.00752.020-0.003-0.0030.0000.0000.0000.000
182A306HIS0-0.0110.00954.565-0.006-0.0060.0000.0000.0000.000
183A307SER00.0020.00350.2000.0090.0090.0000.0000.0000.000
184A308ALA00.0050.00553.192-0.002-0.0020.0000.0000.0000.000
185A309SER0-0.048-0.04454.8140.0020.0020.0000.0000.0000.000
186A310GLY00.0550.02457.0110.0040.0040.0000.0000.0000.000
187A311ARG10.8460.92348.4250.2920.2920.0000.0000.0000.000
188A312GLY00.0000.00755.9990.0000.0000.0000.0000.0000.000
189A313LEU0-0.0110.00751.9730.0000.0000.0000.0000.0000.000
190A314LEU00.010-0.01056.363-0.004-0.0040.0000.0000.0000.000
191A315PRO0-0.016-0.01455.4910.0040.0040.0000.0000.0000.000
192A316LEU00.0690.06150.5910.0000.0000.0000.0000.0000.000
193A317VAL00.0150.00455.0330.0030.0030.0000.0000.0000.000
194A318ARG10.9320.96358.0350.2320.2320.0000.0000.0000.000
195A319THR0-0.006-0.00553.7570.0030.0030.0000.0000.0000.000
196A320LEU00.0190.01952.4460.0000.0000.0000.0000.0000.000
197A321VAL00.0330.01156.3740.0030.0030.0000.0000.0000.000
198A322ARG10.8980.94159.6430.2330.2330.0000.0000.0000.000
199A323SER00.0000.00055.602-0.004-0.0040.0000.0000.0000.000
200A324GLY00.0100.01757.311-0.002-0.0020.0000.0000.0000.000
201A325ALA0-0.045-0.02156.8440.0040.0040.0000.0000.0000.000
202A326ASP-1-0.794-0.87658.320-0.159-0.1590.0000.0000.0000.000
203A327SER0-0.024-0.02960.0180.0010.0010.0000.0000.0000.000
204A328SER0-0.093-0.07762.3750.0080.0080.0000.0000.0000.000
205A329LEU00.0430.02855.8850.0080.0080.0000.0000.0000.000
206A330LYS10.8790.92359.9520.1180.1180.0000.0000.0000.000
207A331ASN00.0070.01755.5950.0060.0060.0000.0000.0000.000
208A332CYS00.006-0.01254.9410.0060.0060.0000.0000.0000.000
209A333HIS0-0.099-0.04857.0330.0140.0140.0000.0000.0000.000
210A334ASN0-0.033-0.01759.3890.0040.0040.0000.0000.0000.000
211A335ASP-1-0.809-0.89459.579-0.136-0.1360.0000.0000.0000.000
212A336THR00.0190.00560.102-0.005-0.0050.0000.0000.0000.000
213A337PRO0-0.008-0.00458.2780.0010.0010.0000.0000.0000.000
214A338LEU00.0420.02260.531-0.003-0.0030.0000.0000.0000.000
215A339MET0-0.117-0.01763.2740.0020.0020.0000.0000.0000.000
216A340VAL00.0240.01558.2890.0020.0020.0000.0000.0000.000
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