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: YR722

Calculation Name: 3C38-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C38

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KLK7

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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2516698.954718
FMO2-HF: Nuclear repulsion 2432212.385936
FMO2-HF: Total energy -84486.568782
FMO2-MP2: Total energy -84736.637714


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:52:THR)


Summations of interaction energy for fragment #1(A:52:THR)
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.
-120.737-113.1913.858-4.307-7.096-0.009
Interaction energy analysis for fragmet #1(A:52:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.919
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].
3A54VAL00.0890.0383.6050.4312.0450.054-0.676-0.9920.000
4A55GLN0-0.025-0.0141.982-13.675-9.0143.771-3.205-5.226-0.007
5A56THR0-0.004-0.0022.9775.0266.1460.034-0.416-0.738-0.002
6A57SER00.003-0.0105.3756.4276.578-0.001-0.010-0.1400.000
7A58SER00.004-0.0037.1954.2494.2490.0000.0000.0000.000
8A59LEU0-0.0100.0157.4492.5732.5730.0000.0000.0000.000
9A60ILE00.0290.0069.0693.0413.0410.0000.0000.0000.000
10A61GLN0-0.030-0.01411.2431.6921.6920.0000.0000.0000.000
11A62SER0-0.022-0.01611.8151.5761.5760.0000.0000.0000.000
12A63LEU0-0.026-0.01311.9661.5841.5840.0000.0000.0000.000
13A64PHE00.0090.00315.1491.5511.5510.0000.0000.0000.000
14A65ASP-1-0.824-0.91816.175-17.211-17.2110.0000.0000.0000.000
15A66PHE0-0.045-0.01517.6651.1041.1040.0000.0000.0000.000
16A67ARG10.9360.97819.43313.48413.4840.0000.0000.0000.000
17A68LEU00.0410.01621.2340.8100.8100.0000.0000.0000.000
18A69ALA0-0.045-0.02222.1080.7370.7370.0000.0000.0000.000
19A70ALA00.0180.01223.5970.6090.6090.0000.0000.0000.000
20A71LEU00.0270.01625.5410.5430.5430.0000.0000.0000.000
21A72ARG10.9340.98124.06312.61812.6180.0000.0000.0000.000
22A73ILE0-0.059-0.02626.0500.4550.4550.0000.0000.0000.000
23A74HIS00.011-0.00229.6030.5560.5560.0000.0000.0000.000
24A75GLN0-0.0260.00031.2930.1470.1470.0000.0000.0000.000
25A76ASP-1-0.784-0.86331.609-9.556-9.5560.0000.0000.0000.000
26A77SER0-0.069-0.01933.8650.3710.3710.0000.0000.0000.000
27A78THR00.007-0.01935.2950.3430.3430.0000.0000.0000.000
28A79ALA0-0.034-0.02437.0030.2690.2690.0000.0000.0000.000
29A80LYS10.9290.96336.7528.7378.7370.0000.0000.0000.000
30A81ASN00.0460.04540.4340.3690.3690.0000.0000.0000.000
31A82ALA00.0640.01342.1580.0720.0720.0000.0000.0000.000
32A83SER0-0.046-0.02344.4440.2150.2150.0000.0000.0000.000
33A84LEU00.0050.02440.7120.1070.1070.0000.0000.0000.000
34A85ILE00.0020.00043.6810.1180.1180.0000.0000.0000.000
35A86ASN0-0.009-0.01846.7570.2010.2010.0000.0000.0000.000
36A87ALA00.0370.02647.1460.1480.1480.0000.0000.0000.000
37A88LEU00.0080.01644.8940.0830.0830.0000.0000.0000.000
38A89VAL0-0.030-0.02648.4390.0920.0920.0000.0000.0000.000
39A90SER0-0.058-0.03151.4110.1660.1660.0000.0000.0000.000
40A91ARG10.8420.91749.5376.4806.4800.0000.0000.0000.000
41A92ASP-1-0.822-0.88552.319-6.062-6.0620.0000.0000.0000.000
42A93SER00.010-0.00348.982-0.078-0.0780.0000.0000.0000.000
43A94SER00.0410.01248.143-0.095-0.0950.0000.0000.0000.000
44A95ARG10.8090.91149.3336.1486.1480.0000.0000.0000.000
45A96LEU0-0.060-0.03644.650-0.111-0.1110.0000.0000.0000.000
46A97ASP-1-0.829-0.89644.081-7.158-7.1580.0000.0000.0000.000
47A98GLU-1-0.929-0.96243.791-6.837-6.8370.0000.0000.0000.000
48A99PHE0-0.013-0.00540.673-0.154-0.1540.0000.0000.0000.000
49A100PHE00.006-0.02938.294-0.204-0.2040.0000.0000.0000.000
50A101SER00.0480.03439.237-0.208-0.2080.0000.0000.0000.000
51A102SER0-0.004-0.01640.172-0.075-0.0750.0000.0000.0000.000
52A103VAL0-0.105-0.04735.834-0.132-0.1320.0000.0000.0000.000
53A104ASP-1-0.774-0.84435.181-9.251-9.2510.0000.0000.0000.000
54A105GLU-1-0.962-0.97335.715-7.860-7.8600.0000.0000.0000.000
55A106LEU0-0.029-0.02135.231-0.085-0.0850.0000.0000.0000.000
56A107GLU-1-0.837-0.90030.200-10.899-10.8990.0000.0000.0000.000
57A108LEU0-0.0040.01331.558-0.336-0.3360.0000.0000.0000.000
58A109SER0-0.023-0.00327.267-0.030-0.0300.0000.0000.0000.000
59A110ASN0-0.141-0.10126.385-0.899-0.8990.0000.0000.0000.000
60A111ALA00.0730.04828.6190.0720.0720.0000.0000.0000.000
61A112PRO0-0.081-0.05629.515-0.417-0.4170.0000.0000.0000.000
62A113ASP-1-0.806-0.88828.339-11.094-11.0940.0000.0000.0000.000
63A114LEU0-0.031-0.01631.5500.3020.3020.0000.0000.0000.000
64A115ARG10.7780.84334.0618.7358.7350.0000.0000.0000.000
65A116PHE00.0480.02936.7970.1770.1770.0000.0000.0000.000
66A117ILE0-0.017-0.01139.333-0.152-0.1520.0000.0000.0000.000
67A118SER0-0.0130.00041.7420.1230.1230.0000.0000.0000.000
68A119SER00.007-0.01443.5500.0550.0550.0000.0000.0000.000
69A120HIS00.0180.00745.7210.0580.0580.0000.0000.0000.000
70A121ASP-1-0.778-0.84545.015-7.181-7.1810.0000.0000.0000.000
71A122ASN0-0.024-0.00146.093-0.039-0.0390.0000.0000.0000.000
72A123ILE00.0150.00642.655-0.126-0.1260.0000.0000.0000.000
73A124LEU0-0.091-0.04445.7070.1730.1730.0000.0000.0000.000
74A125TRP00.001-0.02939.9080.0230.0230.0000.0000.0000.000
75A126ASP-1-0.814-0.91140.861-7.944-7.9440.0000.0000.0000.000
76A127ASP-1-0.787-0.88737.175-8.490-8.4900.0000.0000.0000.000
77A128GLY0-0.0020.01440.8580.0500.0500.0000.0000.0000.000
78A129ASN0-0.039-0.03735.9950.0800.0800.0000.0000.0000.000
79A130ALA0-0.002-0.01137.038-0.170-0.1700.0000.0000.0000.000
80A131SER0-0.014-0.00538.059-0.056-0.0560.0000.0000.0000.000
81A132PHE0-0.0040.01133.4540.0380.0380.0000.0000.0000.000
82A133TYR00.0050.00330.781-0.122-0.1220.0000.0000.0000.000
83A134GLY00.0880.05335.795-0.128-0.1280.0000.0000.0000.000
84A135ILE0-0.107-0.04834.2990.0620.0620.0000.0000.0000.000
85A136ALA00.0030.00638.7190.1680.1680.0000.0000.0000.000
86A137GLN00.008-0.02141.687-0.152-0.1520.0000.0000.0000.000
87A138GLN00.0470.00943.582-0.066-0.0660.0000.0000.0000.000
88A139GLU-1-0.840-0.91239.276-7.802-7.8020.0000.0000.0000.000
89A140LEU00.0350.02638.119-0.191-0.1910.0000.0000.0000.000
90A141ASN0-0.023-0.02340.399-0.061-0.0610.0000.0000.0000.000
91A142LYS10.7970.88339.9447.6427.6420.0000.0000.0000.000
92A143LEU0-0.032-0.02034.965-0.172-0.1720.0000.0000.0000.000
93A144ILE0-0.0090.01337.118-0.164-0.1640.0000.0000.0000.000
94A145ARG10.8010.85239.0017.1417.1410.0000.0000.0000.000
95A146ARG10.8590.92334.3928.9198.9190.0000.0000.0000.000
96A147VAL0-0.0010.01332.624-0.228-0.2280.0000.0000.0000.000
97A148ALA00.0220.02034.7290.1690.1690.0000.0000.0000.000
98A149ILE0-0.034-0.01931.1830.2670.2670.0000.0000.0000.000
99A150SER00.0140.00334.386-0.053-0.0530.0000.0000.0000.000
100A151GLY0-0.0080.00631.853-0.033-0.0330.0000.0000.0000.000
101A152ASN0-0.004-0.00127.212-0.068-0.0680.0000.0000.0000.000
102A153TRP0-0.024-0.03025.3720.4350.4350.0000.0000.0000.000
103A154HIS0-0.044-0.02227.0760.0770.0770.0000.0000.0000.000
104A155LEU0-0.0120.00723.845-0.059-0.0590.0000.0000.0000.000
105A156VAL0-0.024-0.01127.3780.3580.3580.0000.0000.0000.000
106A157GLN00.0470.02229.342-0.213-0.2130.0000.0000.0000.000
107A158THR0-0.014-0.00832.0130.4010.4010.0000.0000.0000.000
108A159PRO0-0.028-0.01434.802-0.199-0.1990.0000.0000.0000.000
109A160SER00.0090.00035.9940.0330.0330.0000.0000.0000.000
110A161GLU-1-0.932-0.96237.958-7.938-7.9380.0000.0000.0000.000
111A162GLY00.008-0.00836.8110.0700.0700.0000.0000.0000.000
112A163LYS10.7920.90028.23410.91410.9140.0000.0000.0000.000
113A164SER0-0.010-0.00230.9790.0180.0180.0000.0000.0000.000
114A165VAL00.0250.01730.911-0.424-0.4240.0000.0000.0000.000
115A166HIS00.0310.02026.785-0.042-0.0420.0000.0000.0000.000
116A167ILE00.008-0.00328.123-0.161-0.1610.0000.0000.0000.000
117A168LEU00.0220.02722.715-0.021-0.0210.0000.0000.0000.000
118A169MET0-0.014-0.01327.2560.3270.3270.0000.0000.0000.000
119A170ARG10.7810.86728.40810.31810.3180.0000.0000.0000.000
120A171ARG10.8850.97131.3098.6638.6630.0000.0000.0000.000
121A172SER0-0.020-0.04234.231-0.050-0.0500.0000.0000.0000.000
122A173SER0-0.014-0.02736.2270.1330.1330.0000.0000.0000.000
123A174LEU00.0020.02839.801-0.045-0.0450.0000.0000.0000.000
124A175ILE0-0.043-0.02342.1240.1390.1390.0000.0000.0000.000
125A176GLU-1-0.896-0.94644.908-6.336-6.3360.0000.0000.0000.000
126A177ALA0-0.008-0.01347.731-0.047-0.0470.0000.0000.0000.000
127A178GLY00.011-0.00348.6930.1130.1130.0000.0000.0000.000
128A179THR0-0.076-0.03347.0370.0800.0800.0000.0000.0000.000
129A180GLY00.0690.05749.3160.1050.1050.0000.0000.0000.000
130A181GLN0-0.010-0.02646.361-0.178-0.1780.0000.0000.0000.000
131A182VAL0-0.038-0.02444.0520.0010.0010.0000.0000.0000.000
132A183VAL00.0380.03046.4170.1270.1270.0000.0000.0000.000
133A184GLY0-0.012-0.02144.8410.1080.1080.0000.0000.0000.000
134A185TYR0-0.045-0.01939.337-0.043-0.0430.0000.0000.0000.000
135A186LEU00.0430.03336.5480.0740.0740.0000.0000.0000.000
136A187TYR0-0.018-0.02635.646-0.173-0.1730.0000.0000.0000.000
137A188VAL00.007-0.00230.7910.1480.1480.0000.0000.0000.000
138A189GLY00.000-0.00730.704-0.137-0.1370.0000.0000.0000.000
139A190ILE0-0.0030.01024.692-0.001-0.0010.0000.0000.0000.000
140A191VAL0-0.044-0.02127.888-0.073-0.0730.0000.0000.0000.000
141A192LEU00.014-0.01122.614-0.377-0.3770.0000.0000.0000.000
142A193ASN0-0.049-0.03224.733-0.596-0.5960.0000.0000.0000.000
143A194ASP-1-0.796-0.90526.322-10.818-10.8180.0000.0000.0000.000
144A195ASN0-0.0100.01124.504-0.171-0.1710.0000.0000.0000.000
145A196PHE00.023-0.00522.030-0.669-0.6690.0000.0000.0000.000
146A197ALA00.0000.00621.918-0.614-0.6140.0000.0000.0000.000
147A198LEU00.0070.00920.314-0.456-0.4560.0000.0000.0000.000
148A199LEU0-0.017-0.01016.720-0.896-0.8960.0000.0000.0000.000
149A200GLU-1-0.773-0.85617.061-18.051-18.0510.0000.0000.0000.000
150A201ASN0-0.038-0.00317.347-0.845-0.8450.0000.0000.0000.000
151A202ILE00.0410.02413.255-0.953-0.9530.0000.0000.0000.000
152A203ARG10.7750.86313.01517.13917.1390.0000.0000.0000.000
153A204SER0-0.001-0.01312.806-1.231-1.2310.0000.0000.0000.000
154A205GLY0-0.022-0.00313.740-0.661-0.6610.0000.0000.0000.000
155A206SER0-0.057-0.0578.722-1.728-1.7280.0000.0000.0000.000
156A207ASN0-0.097-0.0488.559-2.113-2.1130.0000.0000.0000.000
157A208SER00.0190.0179.323-1.578-1.5780.0000.0000.0000.000
158A209GLU-1-0.800-0.86510.236-19.709-19.7090.0000.0000.0000.000
159A210ASN0-0.043-0.04112.6102.5322.5320.0000.0000.0000.000
160A211LEU0-0.0100.01011.171-1.955-1.9550.0000.0000.0000.000
161A212VAL0-0.020-0.01414.7451.4901.4900.0000.0000.0000.000
162A213LEU0-0.0010.02616.896-0.855-0.8550.0000.0000.0000.000
163A214ALA00.020-0.00118.9740.9360.9360.0000.0000.0000.000
164A215VAL0-0.004-0.00120.963-0.356-0.3560.0000.0000.0000.000
165A216ASP-1-0.882-0.94522.463-12.108-12.1080.0000.0000.0000.000
166A217THR00.0010.00021.925-0.593-0.5930.0000.0000.0000.000
167A218THR0-0.026-0.01124.1000.2350.2350.0000.0000.0000.000
168A219PRO0-0.022-0.01522.678-0.340-0.3400.0000.0000.0000.000
169A220LEU0-0.062-0.02022.8810.6690.6690.0000.0000.0000.000
170A221VAL00.0320.01721.1970.5010.5010.0000.0000.0000.000
171A222SER00.0290.00119.804-1.001-1.0010.0000.0000.0000.000
172A223THR00.0610.02617.1600.1500.1500.0000.0000.0000.000
173A224LEU0-0.080-0.01917.7970.0380.0380.0000.0000.0000.000
174A225LYS10.8370.89818.58416.27916.2790.0000.0000.0000.000
175A226GLY0-0.036-0.00523.1750.6190.6190.0000.0000.0000.000
176A227ASN0-0.047-0.03022.8520.3390.3390.0000.0000.0000.000
177A228GLU-1-0.739-0.85318.717-14.963-14.9630.0000.0000.0000.000
178A229PRO0-0.030-0.01619.1160.4960.4960.0000.0000.0000.000
179A230TYR0-0.035-0.02015.3150.4840.4840.0000.0000.0000.000
180A231SER00.0270.00820.454-0.053-0.0530.0000.0000.0000.000
181A232LEU00.0530.00820.875-0.533-0.5330.0000.0000.0000.000
182A233ASP-1-0.885-0.92621.577-12.690-12.6900.0000.0000.0000.000
183A234TYR0-0.006-0.02115.2880.1860.1860.0000.0000.0000.000
184A235VAL00.0110.00416.011-0.561-0.5610.0000.0000.0000.000
185A236VAL0-0.0110.00817.650-0.705-0.7050.0000.0000.0000.000
186A237HIS10.7740.88620.02713.15913.1590.0000.0000.0000.000
187A238SER0-0.022-0.00315.741-0.132-0.1320.0000.0000.0000.000
188A239ALA0-0.007-0.00715.6950.2770.2770.0000.0000.0000.000
189A240LYS10.8710.9198.70328.70128.7010.0000.0000.0000.000
190A241ASP-1-0.806-0.8677.062-36.648-36.6480.0000.0000.0000.000
191A242ALA00.0530.0489.5490.2320.2320.0000.0000.0000.000
192A243MET0-0.040-0.0395.167-0.319-0.3190.0000.0000.0000.000
193A244ARG10.7770.87310.11617.77017.7700.0000.0000.0000.000
194A245ASP-1-0.833-0.89113.423-16.010-16.0100.0000.0000.0000.000
195A246SER0-0.017-0.01013.209-1.295-1.2950.0000.0000.0000.000
196A247PHE00.015-0.00413.8900.1830.1830.0000.0000.0000.000
197A248ILE00.0090.0347.8060.4670.4670.0000.0000.0000.000
198A249VAL00.0260.01510.945-0.698-0.6980.0000.0000.0000.000
199A250GLY0-0.0050.0068.696-0.776-0.7760.0000.0000.0000.000
200A251GLN0-0.018-0.0389.5372.1932.1930.0000.0000.0000.000
201A252THR00.0260.01910.478-2.727-2.7270.0000.0000.0000.000
202A253PHE0-0.038-0.00512.3411.1651.1650.0000.0000.0000.000
203A254LEU00.0080.01614.771-0.629-0.6290.0000.0000.0000.000
204A255GLU-1-0.913-0.95315.676-16.527-16.5270.0000.0000.0000.000
205A256VAL00.004-0.01218.099-0.097-0.0970.0000.0000.0000.000
206A257GLU-1-0.850-0.91721.446-12.081-12.0810.0000.0000.0000.000
207A258SER0-0.037-0.01319.0360.2180.2180.0000.0000.0000.000
208A259VAL0-0.0110.00420.1010.1520.1520.0000.0000.0000.000
209A260PRO00.0020.00118.219-0.159-0.1590.0000.0000.0000.000
210A261THR0-0.039-0.02719.2150.9910.9910.0000.0000.0000.000
211A262TYR0-0.022-0.03719.524-0.582-0.5820.0000.0000.0000.000
212A263LEU0-0.021-0.00919.8580.0590.0590.0000.0000.0000.000
213A264CYS0-0.0080.02416.320-1.330-1.3300.0000.0000.0000.000
214A265VAL00.0430.01212.9110.7040.7040.0000.0000.0000.000
215A266TYR00.0260.00613.292-1.888-1.8880.0000.0000.0000.000
216A267SER0-0.004-0.0148.2251.3631.3630.0000.0000.0000.000
217A268ILE0-0.010-0.00810.916-0.495-0.4950.0000.0000.0000.000
218A269GLN0-0.017-0.0137.471-1.687-1.6870.0000.0000.0000.000
219A270THR0-0.047-0.04210.2000.3390.3390.0000.0000.0000.000
220A271ASN-1-0.944-0.96110.453-26.607-26.6070.0000.0000.0000.000