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: 4Y2YN

Calculation Name: 5C5S-C-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5C5S

Chain ID: C

ChEMBL ID:

UniProt ID: Q13459

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2436478.947156
FMO2-HF: Nuclear repulsion 2353314.595089
FMO2-HF: Total energy -83164.352067
FMO2-MP2: Total energy -83403.475134


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:112:VAL)


Summations of interaction energy for fragment #1(A:112:VAL)
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.
-27.388-25.683-0.018-0.667-1.0210
Interaction energy analysis for fragmet #1(A:112:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.735 / q_NPA : 0.843
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].
3A114PRO0-0.002-0.0073.8143.4255.130-0.018-0.667-1.0210.000
4A115GLY00.0400.0356.5492.0092.0090.0000.0000.0000.000
5A116HIS00.0310.0048.5082.4572.4570.0000.0000.0000.000
6A117PHE0-0.053-0.0289.9902.5972.5970.0000.0000.0000.000
7A118GLY00.0280.0168.088-3.317-3.3170.0000.0000.0000.000
8A119VAL0-0.045-0.0137.852-1.546-1.5460.0000.0000.0000.000
9A120CYS0-0.012-0.01710.2011.4231.4230.0000.0000.0000.000
10A121VAL00.0470.01513.258-0.363-0.3630.0000.0000.0000.000
11A122ASP-1-0.861-0.94016.355-15.777-15.7770.0000.0000.0000.000
12A123SER0-0.026-0.01312.412-0.067-0.0670.0000.0000.0000.000
13A124LEU0-0.051-0.01911.902-1.146-1.1460.0000.0000.0000.000
14A125THR0-0.073-0.01915.5350.7430.7430.0000.0000.0000.000
15A126SER0-0.040-0.03919.102-0.339-0.3390.0000.0000.0000.000
16A127ASP-1-0.926-0.95621.671-12.305-12.3050.0000.0000.0000.000
17A128LYS10.9740.98123.32510.89910.8990.0000.0000.0000.000
18A129ALA0-0.073-0.01124.5000.3750.3750.0000.0000.0000.000
19A130SER00.0140.01823.3950.1360.1360.0000.0000.0000.000
20A131VAL00.039-0.00522.552-0.446-0.4460.0000.0000.0000.000
21A132PRO00.0000.00417.494-0.159-0.1590.0000.0000.0000.000
22A133ILE00.0320.01218.1230.4190.4190.0000.0000.0000.000
23A134VAL0-0.013-0.00815.0090.5650.5650.0000.0000.0000.000
24A135LEU0-0.0240.00518.3250.5270.5270.0000.0000.0000.000
25A136GLU-1-0.759-0.86720.860-11.192-11.1920.0000.0000.0000.000
26A137LYS10.8560.93820.19215.00915.0090.0000.0000.0000.000
27A138LEU0-0.045-0.02618.6960.3450.3450.0000.0000.0000.000
28A139LEU0-0.027-0.01322.9840.5040.5040.0000.0000.0000.000
29A140GLU-1-0.895-0.94026.078-10.592-10.5920.0000.0000.0000.000
30A141HIS00.0690.02825.6090.3030.3030.0000.0000.0000.000
31A142VAL0-0.024-0.02626.0680.4230.4230.0000.0000.0000.000
32A143GLU-1-0.806-0.88528.684-10.021-10.0210.0000.0000.0000.000
33A144MET0-0.0230.00330.8540.5140.5140.0000.0000.0000.000
34A145HIS0-0.058-0.03329.6000.3980.3980.0000.0000.0000.000
35A146GLY0-0.016-0.00631.0100.1370.1370.0000.0000.0000.000
36A147LEU00.0220.01931.9820.1350.1350.0000.0000.0000.000
37A148TYR00.0480.02834.5110.1570.1570.0000.0000.0000.000
38A149THR0-0.070-0.04132.4890.1320.1320.0000.0000.0000.000
39A150GLU-1-0.829-0.89934.984-7.960-7.9600.0000.0000.0000.000
40A151GLY0-0.047-0.03434.321-0.162-0.1620.0000.0000.0000.000
41A152LEU00.0190.01429.661-0.365-0.3650.0000.0000.0000.000
42A153TYR00.052-0.00325.162-0.107-0.1070.0000.0000.0000.000
43A154ARG10.8620.94628.2038.5428.5420.0000.0000.0000.000
44A155LYS10.8540.92930.1288.9748.9740.0000.0000.0000.000
45A156SER0-0.004-0.00525.109-0.455-0.4550.0000.0000.0000.000
46A157GLY00.0100.01524.8800.3740.3740.0000.0000.0000.000
47A158ALA00.0280.01224.926-0.104-0.1040.0000.0000.0000.000
48A159ALA00.0730.03620.976-0.526-0.5260.0000.0000.0000.000
49A160ASN0-0.021-0.01719.549-0.696-0.6960.0000.0000.0000.000
50A161ARG10.8740.91719.13213.07413.0740.0000.0000.0000.000
51A162THR00.000-0.00918.826-0.120-0.1200.0000.0000.0000.000
52A163ARG10.9690.98414.40917.42517.4250.0000.0000.0000.000
53A164GLU-1-0.873-0.92314.707-16.888-16.8880.0000.0000.0000.000
54A165LEU00.0210.01815.642-0.926-0.9260.0000.0000.0000.000
55A166ARG10.8040.8718.69926.87126.8710.0000.0000.0000.000
56A167GLN0-0.019-0.0138.769-1.816-1.8160.0000.0000.0000.000
57A168ALA0-0.033-0.01511.807-1.313-1.3130.0000.0000.0000.000
58A169LEU0-0.002-0.00814.223-0.056-0.0560.0000.0000.0000.000
59A170GLN00.0060.0216.8752.1972.1970.0000.0000.0000.000
60A171THR0-0.013-0.0138.101-1.158-1.1580.0000.0000.0000.000
61A172ASP-1-0.816-0.92010.677-18.126-18.1260.0000.0000.0000.000
62A173PRO0-0.008-0.00914.0451.2261.2260.0000.0000.0000.000
63A174ALA0-0.0120.00416.8561.1161.1160.0000.0000.0000.000
64A175ALA00.0240.00918.4100.8740.8740.0000.0000.0000.000
65A176VAL0-0.042-0.01817.0660.6530.6530.0000.0000.0000.000
66A177LYS10.9370.98619.97713.73113.7310.0000.0000.0000.000
67A178LEU00.0540.01921.046-0.057-0.0570.0000.0000.0000.000
68A179GLU-1-0.830-0.92024.127-11.867-11.8670.0000.0000.0000.000
69A180ASN0-0.071-0.02624.2710.6210.6210.0000.0000.0000.000
70A181PHE0-0.036-0.02119.721-0.211-0.2110.0000.0000.0000.000
71A182PRO00.0030.00924.6290.3550.3550.0000.0000.0000.000
72A183ILE00.1160.04825.821-0.452-0.4520.0000.0000.0000.000
73A184HIS00.0540.02026.417-0.503-0.5030.0000.0000.0000.000
74A185ALA0-0.022-0.00922.197-0.258-0.2580.0000.0000.0000.000
75A186ILE00.0210.02821.839-0.720-0.7200.0000.0000.0000.000
76A187THR0-0.036-0.01922.398-0.205-0.2050.0000.0000.0000.000
77A188GLY0-0.037-0.02622.073-0.058-0.0580.0000.0000.0000.000
78A189VAL0-0.002-0.00916.611-0.416-0.4160.0000.0000.0000.000
79A190LEU00.0330.03418.198-0.732-0.7320.0000.0000.0000.000
80A191LYS10.8580.91119.82711.87611.8760.0000.0000.0000.000
81A192GLN0-0.115-0.05514.0410.8250.8250.0000.0000.0000.000
82A193TRP00.028-0.00514.4650.2010.2010.0000.0000.0000.000
83A194LEU00.0140.00015.598-0.390-0.3900.0000.0000.0000.000
84A195ARG10.8810.93017.11214.42114.4210.0000.0000.0000.000
85A196GLU-1-0.796-0.85711.044-24.494-24.4940.0000.0000.0000.000
86A197LEU00.0150.02811.977-1.449-1.4490.0000.0000.0000.000
87A198PRO0-0.030-0.00811.4150.7990.7990.0000.0000.0000.000
88A199GLU-1-0.836-0.91813.361-13.224-13.2240.0000.0000.0000.000
89A200PRO0-0.048-0.01117.011-0.337-0.3370.0000.0000.0000.000
90A201LEU00.0400.01019.4570.2830.2830.0000.0000.0000.000
91A202MET0-0.040-0.00621.2020.2190.2190.0000.0000.0000.000
92A203THR0-0.006-0.00521.7120.5910.5910.0000.0000.0000.000
93A204PHE0-0.025-0.03417.6760.3260.3260.0000.0000.0000.000
94A205ALA0-0.037-0.01623.2250.4340.4340.0000.0000.0000.000
95A206GLN00.0880.04325.6920.6160.6160.0000.0000.0000.000
96A207TYR0-0.0080.00625.6450.3360.3360.0000.0000.0000.000
97A208GLY00.012-0.00427.6930.2860.2860.0000.0000.0000.000
98A209ASP-1-0.802-0.88630.695-8.603-8.6030.0000.0000.0000.000
99A210PHE00.036-0.00727.8160.2820.2820.0000.0000.0000.000
100A211LEU0-0.056-0.02030.1980.2060.2060.0000.0000.0000.000
101A212ARG10.8780.91533.4338.8968.8960.0000.0000.0000.000
102A213ALA00.0040.00835.3910.2570.2570.0000.0000.0000.000
103A214VAL0-0.037-0.02735.0710.2200.2200.0000.0000.0000.000
104A215GLU-1-0.923-0.94836.591-7.988-7.9880.0000.0000.0000.000
105A216LEU0-0.0280.00339.6950.2360.2360.0000.0000.0000.000
106A217PRO0-0.014-0.00442.346-0.003-0.0030.0000.0000.0000.000
107A218GLU-1-0.850-0.89945.772-6.296-6.2960.0000.0000.0000.000
108A219LYS10.9730.96741.5507.2177.2170.0000.0000.0000.000
109A220GLN00.0110.00743.125-0.281-0.2810.0000.0000.0000.000
110A221GLU0-0.012-0.04343.626-0.077-0.0770.0000.0000.0000.000
111A222GLN0-0.016-0.00239.925-0.181-0.1810.0000.0000.0000.000
112A223LEU0-0.032-0.01338.658-0.240-0.2400.0000.0000.0000.000
113A224ALA00.002-0.00538.922-0.193-0.1930.0000.0000.0000.000
114A225ALA00.0160.01638.329-0.126-0.1260.0000.0000.0000.000
115A226ILE0-0.004-0.01633.712-0.230-0.2300.0000.0000.0000.000
116A227TYR0-0.040-0.06134.234-0.248-0.2480.0000.0000.0000.000
117A228ALA00.0030.01735.413-0.121-0.1210.0000.0000.0000.000
118A229VAL00.005-0.00330.766-0.136-0.1360.0000.0000.0000.000
119A230LEU0-0.073-0.04030.246-0.351-0.3510.0000.0000.0000.000
120A231GLU-1-0.934-0.95330.568-8.719-8.7190.0000.0000.0000.000
121A232HIS0-0.056-0.02530.031-0.304-0.3040.0000.0000.0000.000
122A233LEU0-0.081-0.02525.351-0.388-0.3880.0000.0000.0000.000
123A234PRO00.0250.01222.1850.1740.1740.0000.0000.0000.000
124A235GLU-1-0.865-0.93124.606-11.522-11.5220.0000.0000.0000.000
125A236ALA00.0470.03119.9280.0180.0180.0000.0000.0000.000
126A237ASN0-0.056-0.04120.308-0.464-0.4640.0000.0000.0000.000
127A238HIS00.0070.02022.764-0.106-0.1060.0000.0000.0000.000
128A239ASN00.1060.04425.379-0.074-0.0740.0000.0000.0000.000
129A240SER0-0.028-0.03121.867-0.037-0.0370.0000.0000.0000.000
130A241LEU0-0.019-0.01024.0160.0400.0400.0000.0000.0000.000
131A242GLU-1-0.925-0.95926.155-9.619-9.6190.0000.0000.0000.000
132A243ARG10.7520.82226.23911.42311.4230.0000.0000.0000.000
133A244LEU00.0100.01023.9440.1290.1290.0000.0000.0000.000
134A245ILE0-0.010-0.01627.3760.2870.2870.0000.0000.0000.000
135A246PHE00.0120.00030.6670.3710.3710.0000.0000.0000.000
136A247HIS00.0170.01728.7760.1450.1450.0000.0000.0000.000
137A248LEU0-0.014-0.02227.9780.2720.2720.0000.0000.0000.000
138A249VAL0-0.014-0.00431.7610.2940.2940.0000.0000.0000.000
139A250LYS10.9090.97132.9959.3679.3670.0000.0000.0000.000
140A251VAL0-0.0170.00531.4330.1420.1420.0000.0000.0000.000
141A252ALA00.0010.00734.7850.2350.2350.0000.0000.0000.000
142A253LEU0-0.042-0.03137.2520.2820.2820.0000.0000.0000.000
143A254LEU00.0090.00937.6990.2110.2110.0000.0000.0000.000
144A255GLU-1-0.888-0.93639.193-7.729-7.7290.0000.0000.0000.000
145A256ASP-1-0.902-0.95240.159-7.064-7.0640.0000.0000.0000.000
146A257VAL0-0.059-0.02840.1310.0850.0850.0000.0000.0000.000
147A258ASN00.002-0.02235.7580.0030.0030.0000.0000.0000.000
148A259ARG10.8240.90036.8187.2267.2260.0000.0000.0000.000
149A260MET0-0.067-0.01932.036-0.061-0.0610.0000.0000.0000.000
150A261SER00.1020.06536.294-0.087-0.0870.0000.0000.0000.000
151A262PRO00.010-0.01235.510-0.223-0.2230.0000.0000.0000.000
152A263GLY00.0600.03934.583-0.211-0.2110.0000.0000.0000.000
153A264ALA0-0.062-0.03234.316-0.201-0.2010.0000.0000.0000.000
154A265LEU00.0030.00030.867-0.320-0.3200.0000.0000.0000.000
155A266ALA00.0340.01830.028-0.392-0.3920.0000.0000.0000.000
156A267ILE0-0.002-0.00330.071-0.262-0.2620.0000.0000.0000.000
157A268ILE0-0.073-0.02126.545-0.297-0.2970.0000.0000.0000.000
158A269PHE00.032-0.00724.397-0.536-0.5360.0000.0000.0000.000
159A270ALA00.0400.03425.440-0.369-0.3690.0000.0000.0000.000
160A271PRO00.000-0.00624.592-0.260-0.2600.0000.0000.0000.000
161A272CYS0-0.117-0.04621.395-0.662-0.6620.0000.0000.0000.000
162A273LEU0-0.0150.00921.161-0.514-0.5140.0000.0000.0000.000
163A274LEU00.0120.00323.582-0.105-0.1050.0000.0000.0000.000
164A275ARG10.8760.93216.48515.71615.7160.0000.0000.0000.000
165A276CYS0-0.026-0.00622.995-0.129-0.1290.0000.0000.0000.000
166A277PRO00.0590.02322.063-0.532-0.5320.0000.0000.0000.000
167A278ASP-1-0.816-0.90022.590-11.065-11.0650.0000.0000.0000.000
168A279ASN0-0.003-0.01918.426-0.603-0.6030.0000.0000.0000.000
169A280SER0-0.043-0.03218.278-0.239-0.2390.0000.0000.0000.000
170A281ASP-1-0.798-0.85520.039-10.698-10.6980.0000.0000.0000.000
171A282PRO00.004-0.01322.3680.3190.3190.0000.0000.0000.000
172A283LEU0-0.045-0.01525.1350.3480.3480.0000.0000.0000.000
173A284THR00.007-0.02927.6590.5130.5130.0000.0000.0000.000
174A285SER0-0.028-0.01626.5340.2010.2010.0000.0000.0000.000
175A286MET0-0.014-0.00428.4410.1750.1750.0000.0000.0000.000
176A287LYS10.7760.89229.5529.9639.9630.0000.0000.0000.000
177A288ASP-1-0.770-0.88930.429-9.020-9.0200.0000.0000.0000.000
178A289VAL00.0120.01529.423-0.021-0.0210.0000.0000.0000.000
179A290LEU00.0270.00831.488-0.063-0.0630.0000.0000.0000.000
180A291LYS10.8540.93733.3038.5648.5640.0000.0000.0000.000
181A292ILE00.0550.02627.3080.0580.0580.0000.0000.0000.000
182A293THR0-0.050-0.03830.927-0.137-0.1370.0000.0000.0000.000
183A294THR0-0.013-0.01832.4750.1100.1100.0000.0000.0000.000
184A295CYS0-0.0090.01431.4720.1220.1220.0000.0000.0000.000
185A296VAL00.0400.02028.5650.0460.0460.0000.0000.0000.000
186A297GLU-1-0.844-0.91131.879-7.989-7.9890.0000.0000.0000.000
187A298MET0-0.057-0.01535.1040.2280.2280.0000.0000.0000.000
188A299LEU00.0490.04130.9950.1440.1440.0000.0000.0000.000
189A300ILE0-0.004-0.00731.3370.1240.1240.0000.0000.0000.000
190A301LYS10.8220.87735.1117.9637.9630.0000.0000.0000.000
191A302GLU-1-0.755-0.83338.313-7.211-7.2110.0000.0000.0000.000
192A303GLN00.0370.03034.4080.2970.2970.0000.0000.0000.000
193A304MET00.0130.00637.7210.1190.1190.0000.0000.0000.000
194A305ARG10.7970.86639.5877.2407.2400.0000.0000.0000.000
195A306LYS10.9000.94838.1888.1348.1340.0000.0000.0000.000
196A307TYR00.0030.00937.7320.0080.0080.0000.0000.0000.000
197A308LYS10.9310.95541.4187.3257.3250.0000.0000.0000.000
198A309VAL00.0030.00644.6570.1130.1130.0000.0000.0000.000
199A310LYS10.8540.91742.8047.0597.0590.0000.0000.0000.000
200A311MET0-0.028-0.00542.5220.0160.0160.0000.0000.0000.000
201A312GLU-1-0.914-0.94945.927-6.188-6.1880.0000.0000.0000.000
202A313GLU-1-0.853-0.92347.889-6.608-6.6080.0000.0000.0000.000
203A314ILE0-0.024-0.02043.3110.0250.0250.0000.0000.0000.000
204A315SER0-0.092-0.04247.7240.0580.0580.0000.0000.0000.000
205A316GLN0-0.037-0.00750.1190.2180.2180.0000.0000.0000.000
206A317LEU0-0.048-0.02452.641-0.063-0.0630.0000.0000.0000.000
207A318GLU-1-1.008-1.00954.009-5.737-5.7370.0000.0000.0000.000
208A319ALA-1-0.958-0.96452.854-6.166-6.1660.0000.0000.0000.000