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: 7KZNK

Calculation Name: 3E7D-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3E7D

Chain ID: B

ChEMBL ID:

UniProt ID: Q2YRF5

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2121084.929321
FMO2-HF: Nuclear repulsion 2046208.808682
FMO2-HF: Total energy -74876.120639
FMO2-MP2: Total energy -75095.21225


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:4:TYR)


Summations of interaction energy for fragment #1(A:4:TYR)
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.
16.3222.4397.081-4.195-9.0030.014
Interaction energy analysis for fragmet #1(A:4:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.880 / q_NPA : 0.929
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].
3A6ARG10.9360.9552.37729.43635.2467.082-4.159-8.7330.014
4A7ASP-1-0.816-0.8884.574-23.582-23.3710.000-0.027-0.1830.000
8A11ILE0-0.082-0.0484.331-1.029-0.931-0.001-0.009-0.0870.000
5A8GLY00.0350.0057.627-1.605-1.6050.0000.0000.0000.000
6A9GLN0-0.012-0.0118.9250.8230.8230.0000.0000.0000.000
7A10ALA00.0370.0138.8970.2540.2540.0000.0000.0000.000
9A12TYR00.0290.0378.5461.6811.6810.0000.0000.0000.000
10A13ASP-1-0.792-0.88411.994-18.776-18.7760.0000.0000.0000.000
11A14ARG10.9230.9637.95729.88029.8800.0000.0000.0000.000
12A15SER0-0.036-0.02710.8830.9530.9530.0000.0000.0000.000
13A16PHE00.0350.00012.4241.1721.1720.0000.0000.0000.000
14A17ALA0-0.031-0.00914.2931.0091.0090.0000.0000.0000.000
15A18ILE0-0.026-0.01310.3600.1760.1760.0000.0000.0000.000
16A19ILE0-0.0080.00414.9790.9030.9030.0000.0000.0000.000
17A20ARG10.7540.82317.78514.82414.8240.0000.0000.0000.000
18A21ALA0-0.052-0.00617.2770.6020.6020.0000.0000.0000.000
19A22GLU-1-0.959-0.97715.634-17.912-17.9120.0000.0000.0000.000
20A23ALA0-0.0170.00020.0260.5200.5200.0000.0000.0000.000
21A24ASP-1-0.844-0.90422.721-10.357-10.3570.0000.0000.0000.000
22A25LEU00.019-0.01423.3320.0590.0590.0000.0000.0000.000
23A26ARG10.8430.91127.64110.38510.3850.0000.0000.0000.000
24A27HIS0-0.034-0.01529.0350.3810.3810.0000.0000.0000.000
25A28ILE0-0.034-0.00928.0530.1540.1540.0000.0000.0000.000
26A29PRO00.0450.03731.199-0.077-0.0770.0000.0000.0000.000
27A30ALA00.040-0.00430.831-0.257-0.2570.0000.0000.0000.000
28A31ASP-1-0.867-0.93530.546-9.310-9.3100.0000.0000.0000.000
29A32LEU00.0080.00529.996-0.149-0.1490.0000.0000.0000.000
30A33GLU-1-0.803-0.85324.705-12.967-12.9670.0000.0000.0000.000
31A34LYS10.9320.94324.31611.51511.5150.0000.0000.0000.000
32A35LEU0-0.0070.00123.962-0.508-0.5080.0000.0000.0000.000
33A36ALA00.0230.00824.570-0.369-0.3690.0000.0000.0000.000
34A37VAL00.0130.00819.777-0.474-0.4740.0000.0000.0000.000
35A38ARG10.8950.94018.47314.20114.2010.0000.0000.0000.000
36A39VAL0-0.009-0.00820.613-0.364-0.3640.0000.0000.0000.000
37A40ILE00.0340.02818.249-0.258-0.2580.0000.0000.0000.000
38A41HIS0-0.042-0.02613.4450.3600.3600.0000.0000.0000.000
39A42ALA0-0.043-0.01616.284-0.761-0.7610.0000.0000.0000.000
40A43CYS0-0.120-0.04218.5730.1560.1560.0000.0000.0000.000
41A44GLY00.0140.01816.002-0.131-0.1310.0000.0000.0000.000
42A45MET0-0.0200.00316.6270.2050.2050.0000.0000.0000.000
43A46VAL00.0850.01518.1570.5390.5390.0000.0000.0000.000
44A47ASP-1-0.829-0.89620.810-12.051-12.0510.0000.0000.0000.000
45A48VAL00.000-0.00223.1980.6040.6040.0000.0000.0000.000
46A49ALA00.0240.00524.9770.4170.4170.0000.0000.0000.000
47A50ASN0-0.0120.00126.7500.3860.3860.0000.0000.0000.000
48A51ASP-1-0.824-0.90228.767-9.946-9.9460.0000.0000.0000.000
49A52LEU0-0.069-0.01626.8770.2460.2460.0000.0000.0000.000
50A53ALA0-0.0100.00230.8050.2060.2060.0000.0000.0000.000
51A54PHE00.007-0.01732.206-0.197-0.1970.0000.0000.0000.000
52A55SER00.0220.03835.9380.1790.1790.0000.0000.0000.000
53A56GLU-1-0.892-0.96637.733-8.308-8.3080.0000.0000.0000.000
54A57GLY0-0.039-0.01237.3610.1560.1560.0000.0000.0000.000
55A58ALA00.0100.00235.2500.0420.0420.0000.0000.0000.000
56A59GLY00.0440.01632.878-0.076-0.0760.0000.0000.0000.000
57A60LYS10.9410.95133.5147.8087.8080.0000.0000.0000.000
58A61ALA0-0.0370.00235.8810.1150.1150.0000.0000.0000.000
59A62GLY00.0480.01234.1850.0870.0870.0000.0000.0000.000
60A63ARG10.8870.93128.15810.39410.3940.0000.0000.0000.000
61A64ASN0-0.019-0.02133.752-0.137-0.1370.0000.0000.0000.000
62A65ALA00.0260.02137.1730.1260.1260.0000.0000.0000.000
63A66LEU0-0.044-0.02130.7830.0220.0220.0000.0000.0000.000
64A67LEU00.0260.00433.380-0.001-0.0010.0000.0000.0000.000
65A68ALA0-0.036-0.00435.8620.1170.1170.0000.0000.0000.000
66A69GLY00.0470.02636.7660.1850.1850.0000.0000.0000.000
67A70ALA0-0.060-0.01537.2920.0580.0580.0000.0000.0000.000
68A71PRO0-0.014-0.00336.045-0.286-0.2860.0000.0000.0000.000
69A72ILE00.017-0.00630.682-0.051-0.0510.0000.0000.0000.000
70A73LEU0-0.018-0.00534.480-0.045-0.0450.0000.0000.0000.000
71A74CYS0-0.0240.00231.866-0.211-0.2110.0000.0000.0000.000
72A75ASP-1-0.716-0.85432.724-9.081-9.0810.0000.0000.0000.000
73A76ALA0-0.017-0.01830.7690.1440.1440.0000.0000.0000.000
74A77ARG10.9110.94727.22110.11010.1100.0000.0000.0000.000
75A78MET0-0.002-0.01225.339-0.287-0.2870.0000.0000.0000.000
76A79VAL00.0050.01825.712-0.452-0.4520.0000.0000.0000.000
77A80ALA00.0460.01527.356-0.165-0.1650.0000.0000.0000.000
78A81GLU-1-0.895-0.94424.555-10.841-10.8410.0000.0000.0000.000
79A82GLY00.0000.00922.711-0.342-0.3420.0000.0000.0000.000
80A83ILE0-0.0030.01023.107-0.385-0.3850.0000.0000.0000.000
81A84THR0-0.028-0.02421.053-0.120-0.1200.0000.0000.0000.000
82A85ARG10.9110.93023.58110.70210.7020.0000.0000.0000.000
83A86SER00.0130.00922.2560.2800.2800.0000.0000.0000.000
84A87ARG10.7640.86421.32912.81312.8130.0000.0000.0000.000
85A88LEU0-0.037-0.01425.7070.1240.1240.0000.0000.0000.000
86A89PRO0-0.0250.00029.357-0.005-0.0050.0000.0000.0000.000
87A90ALA00.0050.00631.7470.1690.1690.0000.0000.0000.000
88A91ASP-1-0.919-0.94933.802-8.528-8.5280.0000.0000.0000.000
89A92ASN0-0.062-0.03232.614-0.014-0.0140.0000.0000.0000.000
90A93ARG10.9180.94833.3137.4947.4940.0000.0000.0000.000
91A94VAL00.0020.01329.8480.0460.0460.0000.0000.0000.000
92A95ILE0-0.046-0.02033.2500.1300.1300.0000.0000.0000.000
93A96TYR0-0.001-0.00733.536-0.170-0.1700.0000.0000.0000.000
94A97THR00.031-0.00735.669-0.011-0.0110.0000.0000.0000.000
95A98LEU0-0.034-0.01235.4450.1500.1500.0000.0000.0000.000
96A99SER0-0.048-0.02336.2770.0520.0520.0000.0000.0000.000
97A100ASP-1-0.783-0.85538.432-6.810-6.8100.0000.0000.0000.000
98A101PRO0-0.005-0.01341.8890.0250.0250.0000.0000.0000.000
99A102SER0-0.034-0.03544.5500.1440.1440.0000.0000.0000.000
100A103VAL00.0220.00941.6810.0920.0920.0000.0000.0000.000
101A104PRO0-0.086-0.05843.3230.0260.0260.0000.0000.0000.000
102A105GLU-1-0.799-0.86945.627-5.844-5.8440.0000.0000.0000.000
103A106LEU00.0150.00346.8700.0980.0980.0000.0000.0000.000
104A107ALA0-0.012-0.00845.2590.0560.0560.0000.0000.0000.000
105A108LYS10.8330.89747.3205.8815.8810.0000.0000.0000.000
106A109LYS10.9290.97050.3695.9325.9320.0000.0000.0000.000
107A110ILE0-0.056-0.03146.7190.1040.1040.0000.0000.0000.000
108A111GLY00.0120.03150.7390.0070.0070.0000.0000.0000.000
109A112ASN00.0400.02044.998-0.192-0.1920.0000.0000.0000.000
110A113THR0-0.008-0.02641.2450.0050.0050.0000.0000.0000.000
111A114ARG10.9870.98440.9317.1937.1930.0000.0000.0000.000
112A115SER0-0.004-0.01637.2080.0050.0050.0000.0000.0000.000
113A116ALA00.0220.02839.687-0.072-0.0720.0000.0000.0000.000
114A117ALA00.0510.01442.6800.0460.0460.0000.0000.0000.000
115A118ALA0-0.025-0.01140.0030.0780.0780.0000.0000.0000.000
116A119LEU00.0110.02439.646-0.054-0.0540.0000.0000.0000.000
117A120ASP-1-0.816-0.88642.916-6.400-6.4000.0000.0000.0000.000
118A121LEU0-0.027-0.02343.2550.0700.0700.0000.0000.0000.000
119A122TRP0-0.032-0.03437.102-0.094-0.0940.0000.0000.0000.000
120A123LEU00.0230.02242.930-0.027-0.0270.0000.0000.0000.000
121A124PRO0-0.039-0.02145.4280.0410.0410.0000.0000.0000.000
122A125HIS0-0.010-0.00941.168-0.038-0.0380.0000.0000.0000.000
123A126ILE00.0280.01441.703-0.184-0.1840.0000.0000.0000.000
124A127GLU-1-0.895-0.92242.543-6.584-6.5840.0000.0000.0000.000
125A128GLY0-0.015-0.00842.286-0.071-0.0710.0000.0000.0000.000
126A129SER0-0.067-0.04938.562-0.243-0.2430.0000.0000.0000.000
127A130ILE0-0.0040.00532.602-0.043-0.0430.0000.0000.0000.000
128A131VAL00.0130.00935.347-0.087-0.0870.0000.0000.0000.000
129A132ALA00.007-0.00230.958-0.188-0.1880.0000.0000.0000.000
130A133ILE0-0.014-0.00832.815-0.040-0.0400.0000.0000.0000.000
131A134GLY00.0580.01729.796-0.107-0.1070.0000.0000.0000.000
132A135ASN0-0.095-0.07129.018-0.579-0.5790.0000.0000.0000.000
133A136ALA00.0010.00531.8570.0880.0880.0000.0000.0000.000
134A137PRO00.0320.01635.2970.1250.1250.0000.0000.0000.000
135A138THR00.0190.01237.8260.1040.1040.0000.0000.0000.000
136A139ALA0-0.0030.00937.6960.1810.1810.0000.0000.0000.000
137A140LEU0-0.015-0.00236.4650.0720.0720.0000.0000.0000.000
138A141PHE00.0360.01240.1300.1100.1100.0000.0000.0000.000
139A142ARG10.8060.89543.1856.6376.6370.0000.0000.0000.000
140A143LEU00.014-0.00140.1610.1190.1190.0000.0000.0000.000
141A144PHE00.0040.00140.7590.0760.0760.0000.0000.0000.000
142A145GLU-1-0.857-0.91545.840-6.369-6.3690.0000.0000.0000.000
143A146LEU0-0.044-0.02445.0560.1330.1330.0000.0000.0000.000
144A147LEU0-0.033-0.01643.5880.0740.0740.0000.0000.0000.000
145A148ASP-1-0.816-0.88448.119-6.258-6.2580.0000.0000.0000.000
146A149ALA0-0.086-0.03551.0550.1430.1430.0000.0000.0000.000
147A150GLY0-0.014-0.00151.6310.0920.0920.0000.0000.0000.000
148A151ALA0-0.047-0.02247.7880.0210.0210.0000.0000.0000.000
149A152PRO00.005-0.00446.951-0.051-0.0510.0000.0000.0000.000
150A153LYS10.9110.94144.9286.5626.5620.0000.0000.0000.000
151A154PRO0-0.0100.00639.6810.0010.0010.0000.0000.0000.000
152A155ALA0-0.014-0.00138.9940.1260.1260.0000.0000.0000.000
153A156LEU0-0.070-0.03633.182-0.100-0.1000.0000.0000.0000.000
154A157ILE00.0050.00836.624-0.009-0.0090.0000.0000.0000.000
155A158ILE0-0.005-0.00429.843-0.100-0.1000.0000.0000.0000.000
156A159GLY00.0330.01333.2050.0280.0280.0000.0000.0000.000
157A160MET0-0.025-0.02028.507-0.212-0.2120.0000.0000.0000.000
158A161PRO0-0.0010.02030.044-0.341-0.3410.0000.0000.0000.000
159A162VAL00.0140.00427.410-0.066-0.0660.0000.0000.0000.000
160A163GLY0-0.019-0.00730.7330.2110.2110.0000.0000.0000.000
161A164PHE0-0.027-0.04830.4480.0720.0720.0000.0000.0000.000
162A165VAL00.0220.01435.1250.1790.1790.0000.0000.0000.000
163A166GLY00.0560.03538.121-0.048-0.0480.0000.0000.0000.000
164A167ALA0-0.0040.00333.8510.0280.0280.0000.0000.0000.000
165A168ALA00.0010.01035.566-0.095-0.0950.0000.0000.0000.000
166A169GLU-1-0.824-0.92236.410-7.904-7.9040.0000.0000.0000.000
167A170SER0-0.031-0.02338.1170.0700.0700.0000.0000.0000.000
168A171LYS10.7760.88831.7079.5989.5980.0000.0000.0000.000
169A172ASP-1-0.897-0.95537.409-8.171-8.1710.0000.0000.0000.000
170A173GLU-1-0.850-0.91139.674-6.702-6.7020.0000.0000.0000.000
171A174LEU0-0.058-0.02637.0120.0900.0900.0000.0000.0000.000
172A175ALA0-0.028-0.02638.3630.0380.0380.0000.0000.0000.000
173A176ALA0-0.046-0.00940.3630.0920.0920.0000.0000.0000.000
174A177ASN00.0150.00044.0160.1320.1320.0000.0000.0000.000
175A178SER0-0.0040.00541.9090.0510.0510.0000.0000.0000.000
176A179ARG10.7520.82743.5746.6386.6380.0000.0000.0000.000
177A180GLY0-0.0130.00446.0760.0910.0910.0000.0000.0000.000
178A181VAL0-0.0280.00640.7150.0350.0350.0000.0000.0000.000
179A182PRO00.0050.00938.977-0.056-0.0560.0000.0000.0000.000
180A183TYR00.0390.01636.487-0.144-0.1440.0000.0000.0000.000
181A184VAL00.007-0.00930.694-0.073-0.0730.0000.0000.0000.000
182A185ILE0-0.0160.00532.592-0.052-0.0520.0000.0000.0000.000
183A186VAL00.0080.00527.234-0.218-0.2180.0000.0000.0000.000
184A187ARG10.9370.96830.5159.1489.1480.0000.0000.0000.000
185A188GLY00.0600.03231.425-0.270-0.2700.0000.0000.0000.000
186A189ARG10.9620.96530.9278.9568.9560.0000.0000.0000.000
187A190ARG10.7800.85324.26311.55311.5530.0000.0000.0000.000
188A191GLY00.0640.01226.7180.3550.3550.0000.0000.0000.000
189A192GLY00.0250.01025.820-0.472-0.4720.0000.0000.0000.000
190A193SER0-0.004-0.01725.509-0.019-0.0190.0000.0000.0000.000
191A194ALA00.0070.01420.7500.0260.0260.0000.0000.0000.000
192A195MET00.0220.02522.789-0.008-0.0080.0000.0000.0000.000
193A196THR00.0300.00224.3550.1970.1970.0000.0000.0000.000
194A197ALA00.0150.00623.9240.1900.1900.0000.0000.0000.000
195A198ALA0-0.048-0.01721.575-0.044-0.0440.0000.0000.0000.000
196A199ALA00.0380.01323.237-0.046-0.0460.0000.0000.0000.000
197A200VAL00.0330.01326.6170.1470.1470.0000.0000.0000.000
198A201ASN0-0.012-0.00822.3260.3430.3430.0000.0000.0000.000
199A202ALA0-0.0130.00724.334-0.270-0.2700.0000.0000.0000.000
200A203LEU0-0.042-0.00725.4080.1090.1090.0000.0000.0000.000
201A204ALA0-0.0150.00927.2560.2620.2620.0000.0000.0000.000
202A205SER00.0730.03024.9560.1330.1330.0000.0000.0000.000
203A206GLU-1-0.946-0.96627.014-10.283-10.2830.0000.0000.0000.000
204A207ARG-1-0.842-0.88520.512-13.835-13.8350.0000.0000.0000.000