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: Y15L2

Calculation Name: 6K0C-D-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6K0C

Chain ID: D

ChEMBL ID:

UniProt ID: Q27511

Base Structure: X-ray

Registration Date: 2025-10-04

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1954602.885432
FMO2-HF: Nuclear repulsion 1884290.582187
FMO2-HF: Total energy -70312.303245
FMO2-MP2: Total energy -70520.866994


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:29:MET)


Summations of interaction energy for fragment #1(A:29:MET)
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.
-6.0615.628000000000132.657-17.133-27.214-0.187
Interaction energy analysis for fragmet #1(A:29:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.750 / q_NPA : 0.891
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].
3A31LYS10.8680.9232.27726.79128.6113.742-2.285-3.277-0.028
4A32GLU-1-0.815-0.8933.481-24.522-24.0150.004-0.080-0.4310.000
5A33SER0-0.0140.0035.2820.7510.773-0.0010.000-0.0210.000
6A34TYR00.0600.0073.9583.1263.263-0.001-0.009-0.1260.000
36A64ASN0-0.076-0.0712.471-6.203-5.4762.440-0.900-2.268-0.010
37A65ASP-1-0.840-0.9202.784-60.188-58.9380.868-0.763-1.355-0.013
38A66VAL00.0400.0234.7921.4061.513-0.001-0.003-0.1030.000
39A67PHE0-0.021-0.0252.1661.4592.3371.209-0.397-1.6900.001
40A68GLU-1-0.803-0.9171.996-131.033-123.44213.340-10.615-10.317-0.137
41A69ARG10.9700.9944.40829.41729.4590.0240.138-0.2040.000
43A71ALA0-0.029-0.0225.5162.2602.330-0.001-0.007-0.0620.000
116A144PHE00.0340.0065.116-0.457-0.298-0.001-0.018-0.1400.000
117A145LEU00.0550.0266.226-1.019-0.908-0.001-0.003-0.1070.000
120A148ARG10.8770.9402.14248.45546.72311.036-2.191-7.1130.000
7A35SER00.031-0.00310.0651.2741.2740.0000.0000.0000.000
8A36VAL0-0.010-0.00313.0880.8400.8400.0000.0000.0000.000
9A37TYR0-0.019-0.01911.7070.4410.4410.0000.0000.0000.000
10A38ILE00.0660.03210.3240.6610.6610.0000.0000.0000.000
11A39TYR0-0.007-0.00314.5980.7450.7450.0000.0000.0000.000
12A40ARG10.9260.96817.67114.20614.2060.0000.0000.0000.000
13A41VAL00.0650.04215.7980.4980.4980.0000.0000.0000.000
14A42LEU0-0.0110.00518.6640.3550.3550.0000.0000.0000.000
15A43LYS10.9210.94620.47211.28011.2800.0000.0000.0000.000
16A44GLN0-0.039-0.00820.9880.1340.1340.0000.0000.0000.000
17A45VAL00.0040.00321.0470.3790.3790.0000.0000.0000.000
18A46HIS0-0.019-0.00323.5270.5050.5050.0000.0000.0000.000
19A47PRO0-0.021-0.00925.549-0.141-0.1410.0000.0000.0000.000
20A48ASP-1-0.877-0.93027.126-9.841-9.8410.0000.0000.0000.000
21A49THR0-0.043-0.00624.2090.0900.0900.0000.0000.0000.000
22A50GLY00.0020.00824.074-0.316-0.3160.0000.0000.0000.000
23A51VAL00.0390.00818.010-0.140-0.1400.0000.0000.0000.000
24A52SER0-0.060-0.03920.9340.0240.0240.0000.0000.0000.000
25A53SER00.0490.00017.619-0.410-0.4100.0000.0000.0000.000
26A54LYS10.9811.00716.17813.45113.4510.0000.0000.0000.000
27A55ALA00.0540.03415.931-1.111-1.1110.0000.0000.0000.000
28A56MET00.0250.03413.751-1.306-1.3060.0000.0000.0000.000
29A57SER0-0.013-0.00912.055-1.716-1.7160.0000.0000.0000.000
30A58ILE00.0430.03011.053-2.646-2.6460.0000.0000.0000.000
31A59MET00.0380.03310.838-1.933-1.9330.0000.0000.0000.000
32A60ASN0-0.022-0.0418.148-1.772-1.7720.0000.0000.0000.000
33A61SER00.0190.0266.615-2.386-2.3860.0000.0000.0000.000
34A62PHE00.0750.0516.277-3.830-3.8300.0000.0000.0000.000
35A63VAL00.0170.0055.861-0.992-0.9920.0000.0000.0000.000
42A70ILE0-0.0020.0047.4893.1123.1120.0000.0000.0000.000
44A72ALA00.0330.0307.2012.1682.1680.0000.0000.0000.000
45A73GLU-1-0.751-0.8478.864-18.268-18.2680.0000.0000.0000.000
46A74ALA0-0.017-0.01510.8111.7831.7830.0000.0000.0000.000
47A75SER0-0.029-0.03610.0511.2511.2510.0000.0000.0000.000
48A76ARG10.8100.88312.67919.42719.4270.0000.0000.0000.000
49A77LEU0-0.012-0.00814.9811.2751.2750.0000.0000.0000.000
50A78ALA0-0.015-0.01015.4650.9710.9710.0000.0000.0000.000
51A79HIS0-0.025-0.00814.7131.5901.5900.0000.0000.0000.000
52A80TYR0-0.0040.01819.0870.4330.4330.0000.0000.0000.000
53A81ASN0-0.080-0.03720.3531.1551.1550.0000.0000.0000.000
54A82LYS10.9670.97422.4339.7189.7180.0000.0000.0000.000
55A83ARG10.9530.97422.18511.73811.7380.0000.0000.0000.000
56A84SER00.0450.02217.706-0.137-0.1370.0000.0000.0000.000
57A85THR0-0.036-0.01417.170-0.513-0.5130.0000.0000.0000.000
58A86ILE00.0330.01911.860-0.054-0.0540.0000.0000.0000.000
59A87SER0-0.098-0.09115.8710.4390.4390.0000.0000.0000.000
60A88SER00.0350.00216.484-0.543-0.5430.0000.0000.0000.000
61A89ARG10.9740.99917.58712.14412.1440.0000.0000.0000.000
62A90GLU-1-0.749-0.83915.613-14.145-14.1450.0000.0000.0000.000
63A91ILE0-0.020-0.00711.268-0.568-0.5680.0000.0000.0000.000
64A92GLN00.0420.03214.361-0.402-0.4020.0000.0000.0000.000
65A93THR0-0.039-0.03017.3200.3480.3480.0000.0000.0000.000
66A94ALA00.0350.01612.621-0.078-0.0780.0000.0000.0000.000
67A95VAL0-0.007-0.01613.233-0.549-0.5490.0000.0000.0000.000
68A96ARG10.9200.95614.82912.69812.6980.0000.0000.0000.000
69A97LEU0-0.0030.01416.1140.6220.6220.0000.0000.0000.000
70A98ILE0-0.073-0.02110.614-0.664-0.6640.0000.0000.0000.000
71A99LEU0-0.040-0.01512.683-0.519-0.5190.0000.0000.0000.000
72A100PRO00.0480.02416.0660.6750.6750.0000.0000.0000.000
73A101GLY00.0390.01819.6710.0710.0710.0000.0000.0000.000
74A102GLU-1-0.831-0.91322.408-11.029-11.0290.0000.0000.0000.000
75A103LEU00.0240.00916.691-0.186-0.1860.0000.0000.0000.000
76A104ALA0-0.016-0.00818.008-0.286-0.2860.0000.0000.0000.000
77A105LYS10.8290.90319.04611.31111.3110.0000.0000.0000.000
78A106HIS10.8630.92420.85012.14312.1430.0000.0000.0000.000
79A107ALA00.0520.03215.7640.0920.0920.0000.0000.0000.000
80A108VAL0-0.028-0.01817.7870.0530.0530.0000.0000.0000.000
81A109SER0-0.0160.01319.6860.3430.3430.0000.0000.0000.000
82A110GLU-1-0.765-0.87518.393-11.935-11.9350.0000.0000.0000.000
83A111GLY00.002-0.00617.363-0.011-0.0110.0000.0000.0000.000
84A112THR0-0.058-0.04218.0240.3080.3080.0000.0000.0000.000
85A113LYS10.8570.94421.45511.89411.8940.0000.0000.0000.000
86A114ALA00.0360.02018.3610.2910.2910.0000.0000.0000.000
87A115VAL0-0.046-0.03918.2090.1110.1110.0000.0000.0000.000
88A116THR00.0130.01320.7040.3510.3510.0000.0000.0000.000
89A117LYS10.8570.92823.02810.83510.8350.0000.0000.0000.000
90A118TYR-1-0.886-1.00218.708-12.770-12.7700.0000.0000.0000.000
91A119THR0-0.052-0.06522.6270.1570.1570.0000.0000.0000.000
92A120SER00.0020.01125.3860.3990.3990.0000.0000.0000.000
93A121SER0-0.062-0.02327.0360.3270.3270.0000.0000.0000.000
94A122LYS0-0.0040.05921.202-0.173-0.1730.0000.0000.0000.000
95A123SER00.0410.02827.4520.0280.0280.0000.0000.0000.000
96A124LYS10.9690.97828.5878.6578.6570.0000.0000.0000.000
97A125VAL0-0.0140.00227.623-0.295-0.2950.0000.0000.0000.000
98A126VAL00.0410.00524.571-0.033-0.0330.0000.0000.0000.000
99A127SER0-0.0080.00920.319-0.148-0.1480.0000.0000.0000.000
100A128ARG10.9110.94715.76114.22814.2280.0000.0000.0000.000
101A129SER0-0.033-0.04215.3980.0050.0050.0000.0000.0000.000
102A130ALA00.0410.03118.0980.1260.1260.0000.0000.0000.000
103A131ARG0-0.058-0.04121.7140.6210.6210.0000.0000.0000.000
104A132ALA00.014-0.00218.6260.2620.2620.0000.0000.0000.000
105A133GLY0-0.0170.00520.5880.0920.0920.0000.0000.0000.000
106A134LEU0-0.055-0.01115.263-0.108-0.1080.0000.0000.0000.000
107A135GLN00.005-0.02016.7430.2220.2220.0000.0000.0000.000
108A136PHE0-0.005-0.0109.448-0.528-0.5280.0000.0000.0000.000
109A137PRO0-0.0300.01710.0550.7530.7530.0000.0000.0000.000
110A138VAL00.0680.03311.382-1.088-1.0880.0000.0000.0000.000
111A139GLY0-0.009-0.00912.647-0.367-0.3670.0000.0000.0000.000
112A140ARG10.8420.9228.80522.05422.0540.0000.0000.0000.000
113A141ILE00.0580.0367.385-0.907-0.9070.0000.0000.0000.000
114A142HIS00.011-0.0068.794-0.237-0.2370.0000.0000.0000.000
115A143ARG10.8720.9529.11721.77321.7730.0000.0000.0000.000
118A146LYS10.8400.9388.23216.35416.3540.0000.0000.0000.000
119A147GLN00.0000.0007.142-0.587-0.5870.0000.0000.0000.000
121A149THR0-0.048-0.0195.835-0.903-0.9030.0000.0000.0000.000
122A150THR00.0260.0049.1030.6570.6570.0000.0000.0000.000
123A151SER00.0090.01511.5230.9100.9100.0000.0000.0000.000
124A152SER00.0260.02014.625-0.144-0.1440.0000.0000.0000.000
125A153GLY00.0380.03216.6660.7810.7810.0000.0000.0000.000
126A154ARG10.8930.93716.41812.02512.0250.0000.0000.0000.000
127A155VAL00.0840.05611.7900.1170.1170.0000.0000.0000.000
128A156GLY0-0.001-0.00515.0860.4030.4030.0000.0000.0000.000
129A157ALA00.003-0.00915.752-0.697-0.6970.0000.0000.0000.000
130A158THR00.0630.02115.980-0.705-0.7050.0000.0000.0000.000
131A159ALA00.0500.03813.402-0.131-0.1310.0000.0000.0000.000
132A160ALA0-0.0010.00511.497-0.932-0.9320.0000.0000.0000.000
133A161VAL0-0.0140.00012.315-0.619-0.6190.0000.0000.0000.000
134A162TYR00.0450.00514.417-0.299-0.2990.0000.0000.0000.000
135A163SER00.004-0.0159.017-0.644-0.6440.0000.0000.0000.000
136A164ALA0-0.047-0.02610.558-0.829-0.8290.0000.0000.0000.000
137A165ALA00.0360.01811.802-0.173-0.1730.0000.0000.0000.000
138A166ILE0-0.0080.01210.9720.1930.1930.0000.0000.0000.000
139A167LEU0-0.004-0.0026.752-0.302-0.3020.0000.0000.0000.000
140A168GLU-1-0.794-0.87510.719-14.866-14.8660.0000.0000.0000.000
141A169TYR0-0.035-0.04413.8880.1810.1810.0000.0000.0000.000
142A170LEU00.0300.01111.4940.1870.1870.0000.0000.0000.000
143A171THR0-0.062-0.05311.905-0.421-0.4210.0000.0000.0000.000
144A172ALA0-0.010-0.01414.3210.4380.4380.0000.0000.0000.000
145A173GLU-1-0.778-0.86317.793-12.837-12.8370.0000.0000.0000.000
146A174VAL0-0.003-0.00414.9780.3550.3550.0000.0000.0000.000
147A175LEU0-0.048-0.04416.3680.3040.3040.0000.0000.0000.000
148A176GLU-1-0.901-0.93919.249-11.074-11.0740.0000.0000.0000.000
149A177LEU00.0740.04120.6660.4470.4470.0000.0000.0000.000
150A178ALA0-0.036-0.02220.3320.2950.2950.0000.0000.0000.000
151A179GLY00.002-0.01422.3290.2680.2680.0000.0000.0000.000
152A180ASN0-0.0190.00324.6260.6840.6840.0000.0000.0000.000
153A181ALA00.0670.03624.9930.3240.3240.0000.0000.0000.000
154A182SER0-0.050-0.04625.3360.1610.1610.0000.0000.0000.000
155A183LYS10.9750.99827.3269.5899.5890.0000.0000.0000.000
156A184ASP-1-0.873-0.92529.988-9.514-9.5140.0000.0000.0000.000
157A185LEU0-0.072-0.04628.9490.2950.2950.0000.0000.0000.000
158A186LYS10.8350.91831.5979.0989.0980.0000.0000.0000.000
159A187VAL0-0.0120.00628.7420.0970.0970.0000.0000.0000.000
160A188LYS10.9100.94928.9949.2659.2650.0000.0000.0000.000
161A189ARG10.8980.93422.76312.25812.2580.0000.0000.0000.000
162A190ILE00.0950.06719.927-0.037-0.0370.0000.0000.0000.000
163A191THR0-0.025-0.04121.608-0.525-0.5250.0000.0000.0000.000
164A192PRO00.024-0.01318.471-0.127-0.1270.0000.0000.0000.000
165A193ARG10.9851.01119.72512.01812.0180.0000.0000.0000.000
166A194HIS00.0660.05922.495-0.292-0.2920.0000.0000.0000.000
167A195LEU00.0410.02215.7090.0330.0330.0000.0000.0000.000
168A196HIS0-0.020-0.00719.190-0.474-0.4740.0000.0000.0000.000
169A197LEU0-0.037-0.03420.2850.1100.1100.0000.0000.0000.000
170A198ALA00.0100.01520.1410.2600.2600.0000.0000.0000.000
171A199ILE0-0.007-0.00915.1960.0130.0130.0000.0000.0000.000
172A200ARG10.8910.94319.37014.86414.8640.0000.0000.0000.000
173A201GLY0-0.0050.01622.2780.4620.4620.0000.0000.0000.000
174A202ASP-1-0.831-0.90821.129-13.466-13.4660.0000.0000.0000.000
175A203GLU-1-0.893-0.94321.437-12.548-12.5480.0000.0000.0000.000
176A204GLU-1-0.777-0.86519.954-13.820-13.8200.0000.0000.0000.000
177A205LEU0-0.016-0.02716.077-1.325-1.3250.0000.0000.0000.000
178A206ASP-1-0.829-0.90416.520-17.317-17.3170.0000.0000.0000.000
179A207THR0-0.003-0.00717.539-0.903-0.9030.0000.0000.0000.000
180A208LEU0-0.048-0.02012.229-1.040-1.0400.0000.0000.0000.000
181A209ILE0-0.077-0.04312.030-2.113-2.1130.0000.0000.0000.000
182A210LYS10.8480.90212.98515.76615.7660.0000.0000.0000.000
183A211ALA0-0.043-0.00514.083-0.135-0.1350.0000.0000.0000.000
184A212THR-1-0.988-0.9838.365-34.573-34.5730.0000.0000.0000.000