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: 4GK9N

Calculation Name: 4KT7-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4KT7

Chain ID: B

ChEMBL ID:

UniProt ID: C7RFG6

Base Structure: X-ray

Registration Date: 2025-10-06

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 -2868825.402795
FMO2-HF: Nuclear repulsion 2778163.090721
FMO2-HF: Total energy -90662.312073
FMO2-MP2: Total energy -90931.565792


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(B:3:ASP)


Summations of interaction energy for fragment #1(B:3:ASP)
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.
-12.512-2.4670.98-4.66-6.3640.017
Interaction energy analysis for fragmet #1(B:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.131 / q_NPA : -0.082
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].
3B5LYS10.9120.9832.467-19.848-13.5980.650-3.143-3.7570.003
4B6PHE00.0670.0524.6770.3250.399-0.001-0.014-0.0590.000
5B7ILE0-0.032-0.0283.7541.7452.0970.005-0.094-0.2620.001
100B102LEU0-0.073-0.0262.995-0.5710.7930.221-0.619-0.9670.007
123B125LEU00.0670.0354.519-0.724-0.666-0.001-0.011-0.0460.000
124B126ARG10.9370.9843.1343.9545.7130.103-0.722-1.1400.006
125B127LYS10.8520.9124.080-4.808-4.6200.003-0.057-0.1330.000
6B8SER00.010-0.0157.888-1.064-1.0640.0000.0000.0000.000
7B9ALA0-0.027-0.01211.4080.5130.5130.0000.0000.0000.000
8B10ILE0-0.0050.00413.796-0.294-0.2940.0000.0000.0000.000
9B11ILE0-0.0010.00217.2290.0310.0310.0000.0000.0000.000
10B12THR0-0.023-0.01119.926-0.127-0.1270.0000.0000.0000.000
11B13ALA00.010-0.01223.063-0.052-0.0520.0000.0000.0000.000
12B14ALA00.0430.01126.513-0.063-0.0630.0000.0000.0000.000
13B15GLY0-0.0040.01128.381-0.018-0.0180.0000.0000.0000.000
14B16SER-1-0.813-0.91330.7160.5010.5010.0000.0000.0000.000
15B17GLY0-0.051-0.00229.732-0.035-0.0350.0000.0000.0000.000
16B18LEU0-0.021-0.02329.1590.0030.0030.0000.0000.0000.000
17B19ARG10.8990.95532.383-0.355-0.3550.0000.0000.0000.000
18B20MET0-0.0030.04035.3500.0110.0110.0000.0000.0000.000
19B21ARG0-0.053-0.05834.488-0.013-0.0130.0000.0000.0000.000
20B22SER00.0260.01735.820-0.007-0.0070.0000.0000.0000.000
21B23LYS10.7730.88837.404-0.341-0.3410.0000.0000.0000.000
22B24ILE00.0200.00940.909-0.001-0.0010.0000.0000.0000.000
23B25ASN00.007-0.01240.918-0.009-0.0090.0000.0000.0000.000
24B26LYS10.9220.95540.610-0.300-0.3000.0000.0000.0000.000
25B27PRO00.0040.00939.8560.0100.0100.0000.0000.0000.000
26B28TYR00.0560.02534.9900.0060.0060.0000.0000.0000.000
27B29ILE0-0.031-0.01129.984-0.028-0.0280.0000.0000.0000.000
28B30GLU-1-0.921-0.96732.8520.2360.2360.0000.0000.0000.000
29B31VAL0-0.031-0.02330.769-0.004-0.0040.0000.0000.0000.000
30B32GLY00.0230.00732.576-0.001-0.0010.0000.0000.0000.000
31B33GLY0-0.030-0.00234.147-0.019-0.0190.0000.0000.0000.000
32B34ARG10.8570.92626.574-0.193-0.1930.0000.0000.0000.000
33B35LYS10.9680.98130.347-0.258-0.2580.0000.0000.0000.000
34B36VAL0-0.005-0.00627.3360.0110.0110.0000.0000.0000.000
35B37LEU00.0390.02223.7880.0240.0240.0000.0000.0000.000
36B38GLU-1-0.780-0.89424.6010.3090.3090.0000.0000.0000.000
37B39ILE0-0.048-0.00224.902-0.016-0.0160.0000.0000.0000.000
38B40THR0-0.020-0.02020.724-0.013-0.0130.0000.0000.0000.000
39B41LEU00.0040.01420.1300.0730.0730.0000.0000.0000.000
40B42ASP-1-0.763-0.84620.4020.2260.2260.0000.0000.0000.000
41B43THR0-0.072-0.02418.359-0.115-0.1150.0000.0000.0000.000
42B44VAL00.010-0.00814.831-0.028-0.0280.0000.0000.0000.000
43B45SER0-0.017-0.01315.3190.0190.0190.0000.0000.0000.000
44B46ARG10.8340.93016.922-0.191-0.1910.0000.0000.0000.000
45B47VAL00.0420.01110.602-0.201-0.2010.0000.0000.0000.000
46B48LYS10.8590.92711.9790.3850.3850.0000.0000.0000.000
47B49GLU-1-0.920-0.9656.605-1.450-1.4500.0000.0000.0000.000
48B50ILE0-0.045-0.0197.4211.6311.6310.0000.0000.0000.000
49B51ASP-1-0.824-0.8928.5561.6551.6550.0000.0000.0000.000
50B52GLU-1-0.751-0.84211.5081.5211.5210.0000.0000.0000.000
51B53ILE0-0.017-0.00613.8920.3480.3480.0000.0000.0000.000
52B54ILE0-0.0130.00116.614-0.184-0.1840.0000.0000.0000.000
53B55LEU00.005-0.00119.1710.0720.0720.0000.0000.0000.000
54B56VAL00.0120.01321.510-0.044-0.0440.0000.0000.0000.000
55B57ILE00.000-0.00224.121-0.021-0.0210.0000.0000.0000.000
56B58ARG10.8220.90527.675-0.492-0.4920.0000.0000.0000.000
57B59LYS10.9550.97831.383-0.441-0.4410.0000.0000.0000.000
58B60ASP-1-0.883-0.93233.3790.4000.4000.0000.0000.0000.000
59B61ASP-1-0.841-0.93731.8770.4380.4380.0000.0000.0000.000
60B62GLU-1-0.804-0.87231.1190.4400.4400.0000.0000.0000.000
61B63ASP-1-0.851-0.92431.7990.3260.3260.0000.0000.0000.000
62B64ILE00.0120.01132.357-0.011-0.0110.0000.0000.0000.000
63B65ILE0-0.050-0.02926.9360.0080.0080.0000.0000.0000.000
64B66LYS10.8350.92128.515-0.348-0.3480.0000.0000.0000.000
65B67ASP-1-0.862-0.92729.9650.2550.2550.0000.0000.0000.000
66B68ILE0-0.107-0.06026.499-0.014-0.0140.0000.0000.0000.000
67B69LEU0-0.029-0.03423.6720.0070.0070.0000.0000.0000.000
68B70GLU-1-0.926-0.94926.4440.1820.1820.0000.0000.0000.000
69B71LYS10.7400.89226.739-0.282-0.2820.0000.0000.0000.000
70B72TYR0-0.094-0.07622.469-0.016-0.0160.0000.0000.0000.000
71B73ASP-1-0.860-0.90623.0620.0460.0460.0000.0000.0000.000
72B74GLY0-0.032-0.03019.2840.0140.0140.0000.0000.0000.000
73B75ASN0-0.045-0.02515.436-0.005-0.0050.0000.0000.0000.000
74B76ILE00.0120.00417.5270.2020.2020.0000.0000.0000.000
75B77ARG10.8200.89517.391-1.263-1.2630.0000.0000.0000.000
76B78TYR0-0.030-0.03421.9270.0830.0830.0000.0000.0000.000
77B79VAL00.0060.00323.091-0.021-0.0210.0000.0000.0000.000
78B80TYR0-0.065-0.06825.689-0.002-0.0020.0000.0000.0000.000
79B81GLY00.0340.00927.0640.0720.0720.0000.0000.0000.000
80B82SER0-0.027-0.02628.002-0.063-0.0630.0000.0000.0000.000
81B83THR00.002-0.00630.2660.0130.0130.0000.0000.0000.000
82B84THR00.0180.01128.368-0.019-0.0190.0000.0000.0000.000
83B85ARG10.8490.90421.278-1.301-1.3010.0000.0000.0000.000
84B86GLU-1-0.770-0.85924.0061.0991.0990.0000.0000.0000.000
85B87LEU00.0070.00424.2870.0800.0800.0000.0000.0000.000
86B88SER00.000-0.01225.6570.0020.0020.0000.0000.0000.000
87B89THR0-0.029-0.02519.5260.0680.0680.0000.0000.0000.000
88B90PHE00.0130.00220.6730.1330.1330.0000.0000.0000.000
89B91GLU-1-0.855-0.90422.4350.9540.9540.0000.0000.0000.000
90B92GLY00.020-0.00120.3850.0070.0070.0000.0000.0000.000
91B93LEU0-0.031-0.02915.9810.1370.1370.0000.0000.0000.000
92B94LYS10.7620.87018.466-0.892-0.8920.0000.0000.0000.000
93B95ALA0-0.0140.01220.455-0.056-0.0560.0000.0000.0000.000
94B96LEU0-0.057-0.01813.937-0.001-0.0010.0000.0000.0000.000
95B97ASP-1-0.815-0.89414.1041.1391.1390.0000.0000.0000.000
96B98PRO0-0.051-0.03915.0060.3120.3120.0000.0000.0000.000
97B99GLN0-0.088-0.05511.713-0.075-0.0750.0000.0000.0000.000
98B100SER0-0.059-0.02610.6800.6970.6970.0000.0000.0000.000
99B101GLU-1-0.931-0.9866.6315.0635.0630.0000.0000.0000.000
101B103VAL00.0280.0187.735-1.202-1.2020.0000.0000.0000.000
102B104LEU0-0.0030.00610.7050.1930.1930.0000.0000.0000.000
103B105THR00.0070.00112.359-0.354-0.3540.0000.0000.0000.000
104B106HIS00.0710.01016.1660.1290.1290.0000.0000.0000.000
105B107ASP-1-0.780-0.88018.5950.9260.9260.0000.0000.0000.000
106B108GLY00.0540.00822.395-0.045-0.0450.0000.0000.0000.000
107B109VAL0-0.035-0.01523.660-0.069-0.0690.0000.0000.0000.000
108B110ARG10.8200.90022.128-0.954-0.9540.0000.0000.0000.000
109B111PRO00.0250.02022.6230.0620.0620.0000.0000.0000.000
110B112PHE0-0.012-0.02323.892-0.051-0.0510.0000.0000.0000.000
111B113ALA0-0.0200.01418.684-0.037-0.0370.0000.0000.0000.000
112B114SER0-0.012-0.05318.711-0.031-0.0310.0000.0000.0000.000
113B115GLU-1-0.862-0.95414.967-0.011-0.0110.0000.0000.0000.000
114B116GLU-1-0.890-0.94414.355-0.385-0.3850.0000.0000.0000.000
115B117LEU0-0.077-0.02714.1100.1240.1240.0000.0000.0000.000
116B118PHE00.0390.02212.7220.4170.4170.0000.0000.0000.000
117B119LEU00.0560.0419.7760.7200.7200.0000.0000.0000.000
118B120LYS10.8160.9049.378-0.245-0.2450.0000.0000.0000.000
119B121THR0-0.052-0.04410.7820.3040.3040.0000.0000.0000.000
120B122ILE00.0670.0315.3241.2311.2310.0000.0000.0000.000
121B123ASN0-0.016-0.0135.8292.0992.0990.0000.0000.0000.000
122B124ALA0-0.066-0.0246.973-0.433-0.4330.0000.0000.0000.000
126B128ASN0-0.066-0.0357.096-1.935-1.9350.0000.0000.0000.000
127B129LYS10.9911.0027.683-3.338-3.3380.0000.0000.0000.000
128B130ALA00.0670.0459.7070.0110.0110.0000.0000.0000.000
129B131VAL0-0.043-0.0089.092-0.297-0.2970.0000.0000.0000.000
130B132ILE00.0480.02112.327-0.063-0.0630.0000.0000.0000.000
131B133THR0-0.001-0.00515.312-0.227-0.2270.0000.0000.0000.000
132B134ALA00.0190.00117.431-0.070-0.0700.0000.0000.0000.000
133B135THR0-0.052-0.01220.888-0.052-0.0520.0000.0000.0000.000
134B136LYS10.8430.92723.913-0.384-0.3840.0000.0000.0000.000
135B137SER00.004-0.00426.613-0.024-0.0240.0000.0000.0000.000
136B138LYS10.8490.93829.786-0.351-0.3510.0000.0000.0000.000
137B139ASP-1-0.864-0.91932.7920.3400.3400.0000.0000.0000.000
138B140THR0-0.068-0.03233.7620.0240.0240.0000.0000.0000.000
139B141VAL00.0380.02031.714-0.009-0.0090.0000.0000.0000.000
140B142LYS10.8890.92434.929-0.320-0.3200.0000.0000.0000.000
141B143ILE0-0.0010.01233.1700.0210.0210.0000.0000.0000.000
142B144ILE0-0.018-0.01737.221-0.026-0.0260.0000.0000.0000.000
143B145ASP-1-0.776-0.88139.7570.3380.3380.0000.0000.0000.000
144B146ASP-1-0.943-0.98142.3840.3580.3580.0000.0000.0000.000
145B147ASP-1-0.938-0.95643.8170.2770.2770.0000.0000.0000.000
146B148MET0-0.126-0.06143.393-0.007-0.0070.0000.0000.0000.000
147B149TYR0-0.043-0.01245.602-0.020-0.0200.0000.0000.0000.000
148B150VAL0-0.091-0.06141.1670.0170.0170.0000.0000.0000.000
149B151ASP-1-0.880-0.92139.5960.3690.3690.0000.0000.0000.000
150B152PHE00.001-0.02034.125-0.008-0.0080.0000.0000.0000.000
151B153THR0-0.038-0.01736.9820.0030.0030.0000.0000.0000.000
152B154PRO00.0160.02132.074-0.011-0.0110.0000.0000.0000.000
153B155ASN00.0360.01331.701-0.026-0.0260.0000.0000.0000.000
154B156ARG10.9930.97430.912-0.270-0.2700.0000.0000.0000.000
155B157ASP-1-0.846-0.90629.0880.3260.3260.0000.0000.0000.000
156B158TYR0-0.020-0.02125.4590.0040.0040.0000.0000.0000.000
157B159VAL00.0050.02326.4550.0630.0630.0000.0000.0000.000
158B160TYR0-0.077-0.06222.429-0.059-0.0590.0000.0000.0000.000
159B161ASN00.0190.02125.3170.0540.0540.0000.0000.0000.000
160B162ILE00.0370.01021.4220.0060.0060.0000.0000.0000.000
161B163GLN0-0.045-0.01820.344-0.099-0.0990.0000.0000.0000.000
162B164THR0-0.0200.01218.5060.0850.0850.0000.0000.0000.000
163B165PRO00.0560.02714.282-0.200-0.2000.0000.0000.0000.000
164B166GLN0-0.040-0.02814.709-0.016-0.0160.0000.0000.0000.000
165B167ALA00.0020.0019.7160.0750.0750.0000.0000.0000.000
166B168PHE0-0.010-0.00810.474-0.117-0.1170.0000.0000.0000.000
167B169ASP-1-0.853-0.9318.4216.8576.8570.0000.0000.0000.000
168B170LYS10.9540.9819.330-3.591-3.5910.0000.0000.0000.000
169B171LYS10.9460.96211.343-3.727-3.7270.0000.0000.0000.000
170B172LEU0-0.021-0.00912.475-0.378-0.3780.0000.0000.0000.000
171B173ILE00.0110.00313.578-0.392-0.3920.0000.0000.0000.000
172B174TYR0-0.042-0.00215.482-0.302-0.3020.0000.0000.0000.000
173B175ALA00.0600.03217.426-0.215-0.2150.0000.0000.0000.000
174B176MET0-0.044-0.01717.583-0.267-0.2670.0000.0000.0000.000
175B177TYR0-0.017-0.04319.073-0.216-0.2160.0000.0000.0000.000
176B178GLU-1-0.925-0.97221.4621.2351.2350.0000.0000.0000.000
177B179LYS10.8840.94122.392-1.339-1.3390.0000.0000.0000.000
178B180TYR00.0050.00323.830-0.084-0.0840.0000.0000.0000.000
179B181LEU0-0.022-0.00825.149-0.086-0.0860.0000.0000.0000.000
180B182ALA0-0.0410.00127.446-0.070-0.0700.0000.0000.0000.000
181B183SER0-0.057-0.04228.461-0.033-0.0330.0000.0000.0000.000
182B184GLU-1-0.913-0.95330.5090.6250.6250.0000.0000.0000.000
183B185PHE0-0.061-0.02627.486-0.032-0.0320.0000.0000.0000.000
184B186LYS10.9440.96829.159-0.630-0.6300.0000.0000.0000.000
185B187VAL0-0.006-0.00123.927-0.003-0.0030.0000.0000.0000.000
186B188THR0-0.028-0.03124.184-0.053-0.0530.0000.0000.0000.000
187B189ASP-1-0.808-0.86220.4841.4651.4650.0000.0000.0000.000
188B190ASP-1-0.770-0.84618.0781.6801.6800.0000.0000.0000.000
189B191SER0-0.061-0.05917.4700.1120.1120.0000.0000.0000.000
190B192GLN00.0930.05418.5480.0050.0050.0000.0000.0000.000
191B193LEU0-0.011-0.00419.471-0.084-0.0840.0000.0000.0000.000
192B194PHE0-0.061-0.04914.2530.0900.0900.0000.0000.0000.000
193B195GLU-1-0.937-0.96719.8021.0671.0670.0000.0000.0000.000
194B196PHE0-0.026-0.01323.267-0.076-0.0760.0000.0000.0000.000
195B197PHE0-0.051-0.02822.168-0.068-0.0680.0000.0000.0000.000
196B198ASP-1-0.923-0.95022.7451.0251.0250.0000.0000.0000.000
197B199ARG10.7980.88416.670-1.820-1.8200.0000.0000.0000.000
198B200ASP-1-0.872-0.92918.2121.2821.2820.0000.0000.0000.000
199B201GLU-1-0.950-0.96513.2092.5412.5410.0000.0000.0000.000
200B202LYS10.9490.97015.482-1.446-1.4460.0000.0000.0000.000
201B203VAL00.0510.03514.1030.4000.4000.0000.0000.0000.000
202B204LYS10.8570.93811.916-1.812-1.8120.0000.0000.0000.000
203B205VAL00.0340.01814.2370.1360.1360.0000.0000.0000.000
204B206VAL0-0.030-0.01812.522-0.117-0.1170.0000.0000.0000.000
205B207HIS00.0140.01515.796-0.067-0.0670.0000.0000.0000.000
206B208GLY00.0570.02718.519-0.015-0.0150.0000.0000.0000.000
207B209GLU-1-0.801-0.87420.0310.3580.3580.0000.0000.0000.000
208B210TYR0-0.033-0.06622.9980.0160.0160.0000.0000.0000.000
209B211SER00.0150.01926.0260.0060.0060.0000.0000.0000.000
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