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: KVYQ3

Calculation Name: 5CM8-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5CM8

Chain ID: B

ChEMBL ID:

UniProt ID: P48555

Base Structure: X-ray

Registration Date: 2025-10-05

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1838304.416156
FMO2-HF: Nuclear repulsion 1768858.427019
FMO2-HF: Total energy -69445.989137
FMO2-MP2: Total energy -69647.511661


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:8:GLY)


Summations of interaction energy for fragment #1(A:8:GLY)
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.
-176.555-175.929-0.001-0.221-0.4050
Interaction energy analysis for fragmet #1(A:8:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.907
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].
3A10ALA00.0670.0443.848-3.014-2.388-0.001-0.221-0.4050.000
4A11LEU0-0.040-0.0186.3174.1164.1160.0000.0000.0000.000
5A12HIS00.022-0.0099.1140.8400.8400.0000.0000.0000.000
6A13LYS10.9580.98211.93024.68924.6890.0000.0000.0000.000
7A14VAL00.0440.02515.1360.2910.2910.0000.0000.0000.000
8A15ILE0-0.023-0.00718.6050.3310.3310.0000.0000.0000.000
9A16MET0-0.0210.00121.8390.0950.0950.0000.0000.0000.000
10A17VAL0-0.007-0.00625.2670.2670.2670.0000.0000.0000.000
11A18GLY00.1120.04828.544-0.004-0.0040.0000.0000.0000.000
12A19SER00.010-0.00832.143-0.136-0.1360.0000.0000.0000.000
13A20GLY00.0410.02534.962-0.141-0.1410.0000.0000.0000.000
14A21GLY0-0.029-0.01835.8220.2770.2770.0000.0000.0000.000
15A22VAL0-0.053-0.01733.1830.1140.1140.0000.0000.0000.000
16A23GLY00.0240.00433.931-0.163-0.1630.0000.0000.0000.000
17A24LYS10.8080.91128.69810.56610.5660.0000.0000.0000.000
18A25SER00.0590.02628.648-0.292-0.2920.0000.0000.0000.000
19A26ALA0-0.016-0.01029.051-0.202-0.2020.0000.0000.0000.000
20A27LEU00.0090.01627.067-0.158-0.1580.0000.0000.0000.000
21A28THR0-0.016-0.02023.472-0.526-0.5260.0000.0000.0000.000
22A29LEU0-0.037-0.01724.731-0.425-0.4250.0000.0000.0000.000
23A30GLN0-0.0100.00326.739-0.104-0.1040.0000.0000.0000.000
24A31PHE00.0290.02619.222-0.250-0.2500.0000.0000.0000.000
25A32MET0-0.088-0.01718.972-0.541-0.5410.0000.0000.0000.000
26A33TYR0-0.053-0.04723.109-0.431-0.4310.0000.0000.0000.000
27A34ASP-1-0.837-0.90425.958-11.578-11.5780.0000.0000.0000.000
28A35GLU-1-0.921-0.96228.146-9.405-9.4050.0000.0000.0000.000
29A36PHE0-0.086-0.04125.1350.2510.2510.0000.0000.0000.000
30A37VAL0-0.001-0.01228.832-0.360-0.3600.0000.0000.0000.000
31A38GLU-1-0.931-0.96330.306-9.037-9.0370.0000.0000.0000.000
32A39ASP-1-0.985-0.97629.093-10.047-10.0470.0000.0000.0000.000
33A40TYR0-0.018-0.00625.393-0.325-0.3250.0000.0000.0000.000
34A41GLU-1-0.846-0.91626.908-10.865-10.8650.0000.0000.0000.000
35A42PRO0-0.0120.00826.309-0.513-0.5130.0000.0000.0000.000
36A43THR0-0.036-0.02526.746-0.208-0.2080.0000.0000.0000.000
37A44LYS10.8480.92022.70411.84711.8470.0000.0000.0000.000
38A45ALA00.014-0.00318.584-0.132-0.1320.0000.0000.0000.000
39A46ASP-1-0.926-0.97218.265-16.712-16.7120.0000.0000.0000.000
40A47SER0-0.043-0.01819.336-0.200-0.2000.0000.0000.0000.000
41A48TYR00.0500.02320.2260.4180.4180.0000.0000.0000.000
42A49ARG10.8330.88811.79920.93620.9360.0000.0000.0000.000
43A50LYS10.8810.95116.21615.45915.4590.0000.0000.0000.000
44A51LYS10.7990.89811.76221.98121.9810.0000.0000.0000.000
45A52VAL00.0230.00213.6951.6021.6020.0000.0000.0000.000
46A53VAL0-0.0070.00513.488-1.704-1.7040.0000.0000.0000.000
47A54LEU00.0280.01812.4191.5911.5910.0000.0000.0000.000
48A55ASP-1-0.796-0.87013.829-19.502-19.5020.0000.0000.0000.000
49A56GLY0-0.035-0.02214.873-0.139-0.1390.0000.0000.0000.000
50A57GLU-1-0.953-0.9728.112-37.051-37.0510.0000.0000.0000.000
51A58GLU-1-0.885-0.9429.508-22.543-22.5430.0000.0000.0000.000
52A59VAL0-0.022-0.0138.469-5.461-5.4610.0000.0000.0000.000
53A60GLN0-0.022-0.0159.8193.7543.7540.0000.0000.0000.000
54A61ILE00.0050.00611.755-1.424-1.4240.0000.0000.0000.000
55A62ASP-1-0.868-0.92814.324-18.645-18.6450.0000.0000.0000.000
56A63ILE00.0200.01016.015-0.061-0.0610.0000.0000.0000.000
57A64LEU00.0040.00919.7050.5130.5130.0000.0000.0000.000
58A65ASP-1-0.749-0.90021.758-11.293-11.2930.0000.0000.0000.000
59A66THR0-0.021-0.01525.3870.2470.2470.0000.0000.0000.000
60A67ALA0-0.027-0.01728.2120.4390.4390.0000.0000.0000.000
61A68GLY0-0.025-0.00530.546-0.074-0.0740.0000.0000.0000.000
62A69GLN0-0.050-0.03327.6200.0780.0780.0000.0000.0000.000
63A70GLU-1-0.767-0.89632.369-9.827-9.8270.0000.0000.0000.000
64A71ASP-1-0.852-0.90633.744-8.368-8.3680.0000.0000.0000.000
65A72TYR0-0.093-0.03432.5250.1290.1290.0000.0000.0000.000
66A73ALA0-0.016-0.00933.230-0.245-0.2450.0000.0000.0000.000
67A74ALA00.0420.00931.612-0.126-0.1260.0000.0000.0000.000
68A75ILE0-0.022-0.00828.096-0.277-0.2770.0000.0000.0000.000
69A76ARG10.8710.93826.5679.5359.5350.0000.0000.0000.000
70A77ASP-1-0.856-0.92825.713-11.389-11.3890.0000.0000.0000.000
71A78ASN0-0.079-0.05421.940-0.371-0.3710.0000.0000.0000.000
72A79TYR0-0.019-0.00321.862-0.713-0.7130.0000.0000.0000.000
73A80PHE00.0710.02421.091-0.737-0.7370.0000.0000.0000.000
74A81ARG10.8850.96720.50212.16212.1620.0000.0000.0000.000
75A82SER0-0.038-0.03916.450-0.001-0.0010.0000.0000.0000.000
76A83GLY00.0260.02616.691-1.016-1.0160.0000.0000.0000.000
77A84GLU-1-0.865-0.93911.246-27.341-27.3410.0000.0000.0000.000
78A85GLY00.0650.03215.7810.0280.0280.0000.0000.0000.000
79A86PHE0-0.051-0.02218.4440.1310.1310.0000.0000.0000.000
80A87LEU00.0000.00122.1650.0760.0760.0000.0000.0000.000
81A88CYS-1-0.880-0.93124.873-10.488-10.4880.0000.0000.0000.000
82A89VAL00.0120.00928.3340.1510.1510.0000.0000.0000.000
83A90PHE0-0.015-0.01930.7830.2750.2750.0000.0000.0000.000
84A91SER0-0.009-0.00834.606-0.058-0.0580.0000.0000.0000.000
85A92ILE00.0210.01837.0700.0840.0840.0000.0000.0000.000
86A93THR0-0.021-0.02339.6530.2330.2330.0000.0000.0000.000
87A94ASP-1-0.895-0.95141.118-7.405-7.4050.0000.0000.0000.000
88A95ASP-1-0.873-0.91941.847-7.356-7.3560.0000.0000.0000.000
89A96GLU-1-0.902-0.95840.944-7.826-7.8260.0000.0000.0000.000
90A97SER0-0.001-0.00836.749-0.228-0.2280.0000.0000.0000.000
91A98PHE00.0190.01836.351-0.271-0.2710.0000.0000.0000.000
92A99GLN0-0.058-0.03737.369-0.080-0.0800.0000.0000.0000.000
93A100ALA00.0300.01636.123-0.079-0.0790.0000.0000.0000.000
94A101THR00.0490.02132.310-0.098-0.0980.0000.0000.0000.000
95A102GLN0-0.070-0.03432.922-0.222-0.2220.0000.0000.0000.000
96A103GLU-1-0.985-0.97734.572-8.893-8.8930.0000.0000.0000.000
97A104PHE00.018-0.00930.030-0.238-0.2380.0000.0000.0000.000
98A105ARG10.9470.99126.60311.10911.1090.0000.0000.0000.000
99A106GLU-1-0.813-0.89229.259-10.080-10.0800.0000.0000.0000.000
100A107GLN0-0.021-0.02430.181-0.388-0.3880.0000.0000.0000.000
101A108ILE00.0060.00024.216-0.233-0.2330.0000.0000.0000.000
102A109LEU00.0160.02225.819-0.412-0.4120.0000.0000.0000.000
103A110ARG10.7900.88927.5689.3939.3930.0000.0000.0000.000
104A111VAL0-0.078-0.04224.6810.0440.0440.0000.0000.0000.000
105A112LYS10.7960.90918.50615.62415.6240.0000.0000.0000.000
106A113ASN0-0.0030.00424.0340.5070.5070.0000.0000.0000.000
107A114ASP-1-0.815-0.90020.232-15.248-15.2480.0000.0000.0000.000
108A115GLU-1-0.901-0.95423.755-11.092-11.0920.0000.0000.0000.000
109A116SER0-0.115-0.05522.3240.1760.1760.0000.0000.0000.000
110A117ILE00.0080.00818.875-0.796-0.7960.0000.0000.0000.000
111A118PRO00.0300.01216.6200.5890.5890.0000.0000.0000.000
112A119PHE00.027-0.00519.8870.0500.0500.0000.0000.0000.000
113A120LEU00.0110.00822.5340.1260.1260.0000.0000.0000.000
114A121LEU0-0.0290.00425.4130.0980.0980.0000.0000.0000.000
115A122VAL0-0.010-0.01627.8750.0950.0950.0000.0000.0000.000
116A123GLY00.0370.02430.8040.1080.1080.0000.0000.0000.000
117A124ASN0-0.056-0.06031.772-0.245-0.2450.0000.0000.0000.000
118A125LYS0-0.0170.00433.9910.1520.1520.0000.0000.0000.000
119A126CYS-1-0.899-0.96335.702-7.817-7.8170.0000.0000.0000.000
120A127ASP-1-0.850-0.91038.186-8.042-8.0420.0000.0000.0000.000
121A128LEU00.0160.00939.8850.0410.0410.0000.0000.0000.000
122A129ASN0-0.007-0.01143.2010.0270.0270.0000.0000.0000.000
123A130ASP-1-0.883-0.93745.402-6.815-6.8150.0000.0000.0000.000
124A131LYS10.8270.90244.2927.2947.2940.0000.0000.0000.000
125A132ARG10.7250.84738.5438.1848.1840.0000.0000.0000.000
126A133LYS10.8270.90744.1057.1107.1100.0000.0000.0000.000
127A134VAL00.0210.02039.8200.1110.1110.0000.0000.0000.000
128A135PRO00.008-0.00642.250-0.092-0.0920.0000.0000.0000.000
129A136LEU00.0630.03136.461-0.088-0.0880.0000.0000.0000.000
130A137SER0-0.041-0.02238.716-0.209-0.2090.0000.0000.0000.000
131A138GLU-1-0.894-0.95639.988-7.601-7.6010.0000.0000.0000.000
132A139CYS0-0.0060.00736.175-0.133-0.1330.0000.0000.0000.000
133A140GLN0-0.009-0.01135.000-0.135-0.1350.0000.0000.0000.000
134A141LEU0-0.071-0.03735.587-0.169-0.1690.0000.0000.0000.000
135A142ARG10.9170.97634.3798.5658.5650.0000.0000.0000.000
136A143ALA00.0170.01131.131-0.179-0.1790.0000.0000.0000.000
137A144GLN00.0440.02831.243-0.336-0.3360.0000.0000.0000.000
138A145GLN0-0.077-0.04932.5690.2460.2460.0000.0000.0000.000
139A146TRP0-0.031-0.01729.8560.0310.0310.0000.0000.0000.000
140A147ALA0-0.020-0.00728.220-0.380-0.3800.0000.0000.0000.000
141A148VAL00.0020.01725.752-0.422-0.4220.0000.0000.0000.000
142A149PRO0-0.006-0.00624.7540.5380.5380.0000.0000.0000.000
143A150TYR0-0.039-0.05627.985-0.082-0.0820.0000.0000.0000.000
144A151VAL0-0.044-0.02427.156-0.102-0.1020.0000.0000.0000.000
145A152GLU-1-0.758-0.82230.370-8.657-8.6570.0000.0000.0000.000
146A153THR00.004-0.00928.875-0.135-0.1350.0000.0000.0000.000
147A154SER-1-0.651-0.77832.308-8.908-8.9080.0000.0000.0000.000
148A155ALA0-0.021-0.00532.783-0.348-0.3480.0000.0000.0000.000
149A156LYS10.7900.87233.7439.3149.3140.0000.0000.0000.000
150A157THR0-0.060-0.05135.789-0.023-0.0230.0000.0000.0000.000
151A158ARG10.8050.87925.73811.77711.7770.0000.0000.0000.000
152A159GLU-1-0.917-0.94930.881-9.733-9.7330.0000.0000.0000.000
153A160ASN0-0.012-0.03328.806-0.443-0.4430.0000.0000.0000.000
154A161VAL00.0150.01826.411-0.402-0.4020.0000.0000.0000.000
155A162ASP-1-0.789-0.90123.364-13.996-13.9960.0000.0000.0000.000
156A163LYS10.7730.90122.71712.34912.3490.0000.0000.0000.000
157A164VAL00.0480.01823.147-0.514-0.5140.0000.0000.0000.000
158A165PHE00.0310.01820.049-0.483-0.4830.0000.0000.0000.000
159A166PHE0-0.036-0.02818.211-1.160-1.1600.0000.0000.0000.000
160A167ASP-1-0.808-0.90118.278-14.845-14.8450.0000.0000.0000.000
161A168LEU00.0250.02318.459-0.529-0.5290.0000.0000.0000.000
162A169MET0-0.033-0.00413.504-0.538-0.5380.0000.0000.0000.000
163A170ARG10.7590.83914.24515.22015.2200.0000.0000.0000.000
164A171GLU-1-0.903-0.94615.704-16.114-16.1140.0000.0000.0000.000
165A172ILE0-0.018-0.01411.485-0.708-0.7080.0000.0000.0000.000
166A173ARG10.8790.96210.49725.29525.2950.0000.0000.0000.000
167A174SER0-0.017-0.00712.011-1.143-1.1430.0000.0000.0000.000
168A175ARG10.8180.87714.03916.05716.0570.0000.0000.0000.000
169A176LYS10.7810.8797.96332.01232.0120.0000.0000.0000.000
170A177THR0-0.113-0.0559.587-3.053-3.0530.0000.0000.0000.000
171A178GLU-1-0.942-0.95711.624-16.775-16.7750.0000.0000.0000.000
172A179ASP-2-1.924-1.94311.278-45.381-45.3810.0000.0000.0000.000