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: 3Z9VL

Calculation Name: 3EXR-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3EXR

Chain ID: A

ChEMBL ID:

UniProt ID: Q93DA8

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2524456.642602
FMO2-HF: Nuclear repulsion 2441610.561885
FMO2-HF: Total energy -82846.080717
FMO2-MP2: Total energy -83087.637113


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-453.741-450.04619.865-11.968-11.593-0.158
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.700 / q_NPA : 1.835
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].
3A5LEU00.0310.0192.839-9.559-6.5910.463-1.296-2.135-0.011
4A6PRO00.0380.0364.8184.1594.231-0.001-0.006-0.0650.000
218A220TRP0-0.001-0.0103.739-1.419-0.5280.003-0.408-0.486-0.002
219A221GLY-1-0.907-0.9361.862-213.132-213.36819.400-10.258-8.907-0.145
5A7ASN0-0.034-0.0127.7202.8362.8360.0000.0000.0000.000
6A8LEU0-0.034-0.00510.8701.7341.7340.0000.0000.0000.000
7A9GLN00.005-0.02913.905-1.106-1.1060.0000.0000.0000.000
8A10VAL0-0.039-0.02016.9370.7200.7200.0000.0000.0000.000
9A11ALA00.0570.03420.6180.3940.3940.0000.0000.0000.000
10A12LEU0-0.084-0.04223.3100.7870.7870.0000.0000.0000.000
11A13ASP-1-0.885-0.95426.714-22.717-22.7170.0000.0000.0000.000
12A14HIS00.0100.00227.8510.8280.8280.0000.0000.0000.000
13A15SER00.0380.01532.1540.1030.1030.0000.0000.0000.000
14A16ASN0-0.029-0.02634.8240.3960.3960.0000.0000.0000.000
15A17LEU00.1130.06233.223-0.445-0.4450.0000.0000.0000.000
16A18LYS10.9940.99433.36015.52815.5280.0000.0000.0000.000
17A19GLY0-0.0120.01233.154-0.274-0.2740.0000.0000.0000.000
18A20ALA00.0810.04229.345-0.484-0.4840.0000.0000.0000.000
19A21ILE00.0310.01328.639-0.724-0.7240.0000.0000.0000.000
20A22THR0-0.045-0.03929.456-0.371-0.3710.0000.0000.0000.000
21A23ALA0-0.0080.00227.088-0.432-0.4320.0000.0000.0000.000
22A24ALA00.0540.03624.895-0.868-0.8680.0000.0000.0000.000
23A25VAL0-0.007-0.01324.855-0.879-0.8790.0000.0000.0000.000
24A26SER0-0.111-0.05826.385-0.422-0.4220.0000.0000.0000.000
25A27VAL00.017-0.01021.131-0.319-0.3190.0000.0000.0000.000
26A28GLY00.0350.02720.756-1.438-1.4380.0000.0000.0000.000
27A29ASN0-0.019-0.03020.109-1.143-1.1430.0000.0000.0000.000
28A30GLU-1-0.863-0.89917.563-32.366-32.3660.0000.0000.0000.000
29A31VAL0-0.0190.01215.864-2.019-2.0190.0000.0000.0000.000
30A32ASP-1-0.781-0.85911.784-48.544-48.5440.0000.0000.0000.000
31A33VAL0-0.028-0.01814.1260.6920.6920.0000.0000.0000.000
32A34ILE0-0.019-0.00816.7910.8820.8820.0000.0000.0000.000
33A35GLU-1-0.833-0.90620.606-28.538-28.5380.0000.0000.0000.000
34A36ALA00.005-0.00422.4630.8530.8530.0000.0000.0000.000
35A37GLY00.0800.03926.098-0.077-0.0770.0000.0000.0000.000
36A38THR0-0.018-0.03626.9670.8570.8570.0000.0000.0000.000
37A39VAL0-0.040-0.02229.4730.7200.7200.0000.0000.0000.000
38A40CYS0-0.049-0.00130.2170.6980.6980.0000.0000.0000.000
39A41LEU00.0150.00327.4140.6780.6780.0000.0000.0000.000
40A42LEU0-0.037-0.02231.8050.5290.5290.0000.0000.0000.000
41A43GLN0-0.088-0.03734.8290.7660.7660.0000.0000.0000.000
42A44VAL0-0.076-0.04433.0780.4670.4670.0000.0000.0000.000
43A45GLY00.0200.02934.5380.2080.2080.0000.0000.0000.000
44A46SER00.000-0.01830.631-0.239-0.2390.0000.0000.0000.000
45A47GLU-1-0.852-0.91130.810-17.664-17.6640.0000.0000.0000.000
46A48LEU00.001-0.00428.768-0.220-0.2200.0000.0000.0000.000
47A49VAL00.001-0.00325.335-0.511-0.5110.0000.0000.0000.000
48A50GLU-1-0.801-0.88126.872-19.654-19.6540.0000.0000.0000.000
49A51VAL0-0.047-0.02829.150-0.129-0.1290.0000.0000.0000.000
50A52LEU0-0.026-0.02224.940-0.239-0.2390.0000.0000.0000.000
51A53ARG10.7800.85720.08627.05327.0530.0000.0000.0000.000
52A54SER0-0.049-0.02225.577-0.260-0.2600.0000.0000.0000.000
53A55LEU0-0.058-0.02626.9440.1040.1040.0000.0000.0000.000
54A56PHE0-0.038-0.02221.893-0.390-0.3900.0000.0000.0000.000
55A57PRO00.0350.02922.222-0.996-0.9960.0000.0000.0000.000
56A58ASP-1-0.897-0.95118.262-29.299-29.2990.0000.0000.0000.000
57A59LYS10.7840.91616.83332.11432.1140.0000.0000.0000.000
58A60ILE00.0170.01812.4870.9950.9950.0000.0000.0000.000
59A61ILE0-0.002-0.00117.1770.6640.6640.0000.0000.0000.000
60A62VAL00.0160.01018.6210.1470.1470.0000.0000.0000.000
61A63ALA00.0190.00621.2551.0551.0550.0000.0000.0000.000
62A64ASP-1-0.724-0.83223.835-24.147-24.1470.0000.0000.0000.000
63A65THR0-0.004-0.04025.1320.8790.8790.0000.0000.0000.000
64A66LYS10.7710.88724.96024.65424.6540.0000.0000.0000.000
65A67CYS0-0.0290.01727.5720.7590.7590.0000.0000.0000.000
66A68ALA00.0590.01328.522-0.518-0.5180.0000.0000.0000.000
67A69ASP-1-0.848-0.92931.253-16.872-16.8720.0000.0000.0000.000
68A70ALA0-0.021-0.02632.876-0.283-0.2830.0000.0000.0000.000
69A71GLY00.0570.00129.577-0.116-0.1160.0000.0000.0000.000
70A72GLY0-0.0020.00729.011-0.508-0.5080.0000.0000.0000.000
71A73THR0-0.008-0.01130.027-0.256-0.2560.0000.0000.0000.000
72A74VAL00.0020.00129.332-0.055-0.0550.0000.0000.0000.000
73A75ALA00.0560.02625.701-0.266-0.2660.0000.0000.0000.000
74A76LYS10.9981.00227.11417.87817.8780.0000.0000.0000.000
75A77ASN0-0.028-0.02829.097-0.046-0.0460.0000.0000.0000.000
76A78ASN0-0.039-0.03526.6540.2450.2450.0000.0000.0000.000
77A79ALA00.0490.03324.939-0.391-0.3910.0000.0000.0000.000
78A80VAL0-0.027-0.01925.919-0.164-0.1640.0000.0000.0000.000
79A81ARG10.7480.87328.66718.66518.6650.0000.0000.0000.000
80A82GLY00.0510.03225.070-0.171-0.1710.0000.0000.0000.000
81A83ALA0-0.013-0.00822.990-0.995-0.9950.0000.0000.0000.000
82A84ASP-1-0.758-0.83617.390-31.023-31.0230.0000.0000.0000.000
83A85TRP00.0110.00212.572-0.429-0.4290.0000.0000.0000.000
84A86MET0-0.0150.03419.5131.5541.5540.0000.0000.0000.000
85A87THR00.006-0.01221.324-0.243-0.2430.0000.0000.0000.000
86A88CYS0-0.061-0.01323.1931.3571.3570.0000.0000.0000.000
87A89ILE0-0.0020.00624.421-0.835-0.8350.0000.0000.0000.000
88A90CYS00.0100.00725.0160.1810.1810.0000.0000.0000.000
89A91SER0-0.023-0.01326.3910.0600.0600.0000.0000.0000.000
90A92ALA0-0.0080.01727.6390.7210.7210.0000.0000.0000.000
91A93THR00.0160.01728.856-0.488-0.4880.0000.0000.0000.000
92A94ILE00.0710.02826.133-0.249-0.2490.0000.0000.0000.000
93A95PRO0-0.038-0.03028.115-0.456-0.4560.0000.0000.0000.000
94A96THR00.0030.02129.508-0.014-0.0140.0000.0000.0000.000
95A97MET00.0210.01124.769-0.545-0.5450.0000.0000.0000.000
96A98LYS10.9430.98125.01521.01021.0100.0000.0000.0000.000
97A99ALA0-0.062-0.02726.141-0.201-0.2010.0000.0000.0000.000
98A100ALA00.0200.00625.6990.0060.0060.0000.0000.0000.000
99A101ARG10.7960.86819.37326.53426.5340.0000.0000.0000.000
100A102LYS10.9490.97022.92820.42620.4260.0000.0000.0000.000
101A103ALA0-0.0120.00225.0610.0740.0740.0000.0000.0000.000
102A104ILE0-0.033-0.00921.1430.4030.4030.0000.0000.0000.000
103A105GLU-1-0.836-0.90319.614-27.532-27.5320.0000.0000.0000.000
104A106ASP-1-1.001-0.99721.949-20.499-20.4990.0000.0000.0000.000
105A107ILE0-0.060-0.03025.0580.4170.4170.0000.0000.0000.000
106A108ASN0-0.047-0.03219.391-0.668-0.6680.0000.0000.0000.000
107A109PRO00.0220.01319.774-1.081-1.0810.0000.0000.0000.000
108A110ASP-1-0.934-0.95616.344-30.599-30.5990.0000.0000.0000.000
109A111LYS10.8120.88414.32630.26030.2600.0000.0000.0000.000
110A112GLY00.0150.02416.013-0.452-0.4520.0000.0000.0000.000
111A113GLU-1-0.809-0.86213.274-40.659-40.6590.0000.0000.0000.000
112A114ILE0-0.042-0.03218.1201.3251.3250.0000.0000.0000.000
113A115GLN0-0.017-0.02015.5840.2230.2230.0000.0000.0000.000
114A116VAL00.000-0.00819.2021.5361.5360.0000.0000.0000.000
115A117GLU-1-0.761-0.88820.783-26.951-26.9510.0000.0000.0000.000
116A118LEU0-0.046-0.01220.0071.2121.2120.0000.0000.0000.000
117A119TYR0-0.023-0.04224.008-0.014-0.0140.0000.0000.0000.000
118A120GLY00.0290.00927.6500.2550.2550.0000.0000.0000.000
119A121ASP-1-0.931-0.95628.702-19.694-19.6940.0000.0000.0000.000
120A122TRP0-0.017-0.00621.618-0.136-0.1360.0000.0000.0000.000
121A123THR0-0.004-0.02027.156-0.474-0.4740.0000.0000.0000.000
122A124TYR00.043-0.01721.260-0.830-0.8300.0000.0000.0000.000
123A125ASP-1-0.867-0.92423.918-21.989-21.9890.0000.0000.0000.000
124A126GLN00.0210.01225.854-0.614-0.6140.0000.0000.0000.000
125A127ALA00.0150.00620.691-0.382-0.3820.0000.0000.0000.000
126A128GLN0-0.019-0.01920.551-1.539-1.5390.0000.0000.0000.000
127A129GLN0-0.004-0.01022.641-0.067-0.0670.0000.0000.0000.000
128A130TRP0-0.003-0.01021.056-0.066-0.0660.0000.0000.0000.000
129A131LEU00.0410.03616.332-0.302-0.3020.0000.0000.0000.000
130A132ASP-1-0.856-0.91319.762-25.070-25.0700.0000.0000.0000.000
131A133ALA0-0.123-0.07522.5760.9070.9070.0000.0000.0000.000
132A134GLY0-0.0070.00018.9880.5390.5390.0000.0000.0000.000
133A135ILE0-0.064-0.02817.987-1.032-1.0320.0000.0000.0000.000
134A136SER00.0770.04113.594-0.409-0.4090.0000.0000.0000.000
135A137GLN00.0060.01413.138-2.826-2.8260.0000.0000.0000.000
136A138ALA0-0.0080.00015.3592.3832.3830.0000.0000.0000.000
137A139ILE0-0.0010.00516.563-2.066-2.0660.0000.0000.0000.000
138A140TYR0-0.021-0.03518.4611.7151.7150.0000.0000.0000.000
139A141HIS10.8100.87920.04425.39725.3970.0000.0000.0000.000
140A142GLN0-0.0150.00022.0800.1170.1170.0000.0000.0000.000
141A143SER0-0.022-0.04623.1421.1521.1520.0000.0000.0000.000
142A144ARG10.9170.95626.44021.43421.4340.0000.0000.0000.000
143A145ASP-1-0.875-0.94029.118-18.708-18.7080.0000.0000.0000.000
144A146ALA00.0550.02926.9000.1790.1790.0000.0000.0000.000
145A147LEU0-0.067-0.02324.789-0.139-0.1390.0000.0000.0000.000
146A148LEU0-0.071-0.04827.3990.0920.0920.0000.0000.0000.000
147A149ALA0-0.0190.00630.6210.4660.4660.0000.0000.0000.000
148A150GLY0-0.036-0.00727.9130.1960.1960.0000.0000.0000.000
149A151GLU-1-0.951-0.97826.671-21.218-21.2180.0000.0000.0000.000
150A152THR00.006-0.00821.625-1.130-1.1300.0000.0000.0000.000
151A153TRP0-0.015-0.01918.8600.1840.1840.0000.0000.0000.000
152A154GLY00.0590.03421.259-0.028-0.0280.0000.0000.0000.000
153A155GLU-1-0.867-0.96120.022-30.104-30.1040.0000.0000.0000.000
154A156LYS10.8670.92421.37223.30723.3070.0000.0000.0000.000
155A157ASP-1-0.736-0.81620.933-25.590-25.5900.0000.0000.0000.000
156A158LEU00.0380.01715.949-1.107-1.1070.0000.0000.0000.000
157A159ASN0-0.047-0.01817.468-0.185-0.1850.0000.0000.0000.000
158A160LYS10.9190.98119.48524.00524.0050.0000.0000.0000.000
159A161VAL00.0260.01514.377-0.450-0.4500.0000.0000.0000.000
160A162LYS10.9740.98814.38533.16633.1660.0000.0000.0000.000
161A163LYS10.8940.95715.50427.30427.3040.0000.0000.0000.000
162A164LEU0-0.014-0.00916.5220.5800.5800.0000.0000.0000.000
163A165ILE00.0250.01910.5650.3050.3050.0000.0000.0000.000
164A166GLU-1-0.929-0.96312.773-44.230-44.2300.0000.0000.0000.000
165A167MET0-0.140-0.05814.8021.9311.9310.0000.0000.0000.000
166A168GLY00.0230.01812.3191.0761.0760.0000.0000.0000.000
167A169PHE0-0.081-0.04512.636-0.345-0.3450.0000.0000.0000.000
168A170ARG10.7920.8618.49043.28643.2860.0000.0000.0000.000
169A171VAL0-0.022-0.01311.1002.9302.9300.0000.0000.0000.000
170A172SER00.0110.00812.616-3.330-3.3300.0000.0000.0000.000
171A173VAL0-0.033-0.00614.4902.3122.3120.0000.0000.0000.000
172A174THR00.002-0.01517.0650.3470.3470.0000.0000.0000.000
173A175GLY00.0260.01620.0250.9050.9050.0000.0000.0000.000
174A176GLY00.1010.04720.773-1.120-1.1200.0000.0000.0000.000
175A177LEU0-0.091-0.00716.552-0.821-0.8210.0000.0000.0000.000
176A178SER0-0.006-0.01918.5861.4511.4510.0000.0000.0000.000
177A179VAL00.0660.01815.739-1.303-1.3030.0000.0000.0000.000
178A180ASP-1-0.901-0.94916.086-29.531-29.5310.0000.0000.0000.000
179A181THR0-0.040-0.04217.501-0.948-0.9480.0000.0000.0000.000
180A182LEU00.0210.02912.078-0.555-0.5550.0000.0000.0000.000
181A183LYS10.9070.94512.65331.33931.3390.0000.0000.0000.000
182A184LEU0-0.049-0.01513.7170.4000.4000.0000.0000.0000.000
183A185PHE0-0.049-0.02811.7920.8330.8330.0000.0000.0000.000
184A186GLU-1-0.864-0.9288.983-56.308-56.3080.0000.0000.0000.000
185A187GLY0-0.014-0.0028.8962.8782.8780.0000.0000.0000.000
186A188VAL0-0.090-0.0449.6521.8221.8220.0000.0000.0000.000
187A189ASP-1-0.924-0.9525.218-84.798-84.7980.0000.0000.0000.000
188A190VAL0-0.046-0.0207.8113.8573.8570.0000.0000.0000.000
189A191PHE00.0160.0127.484-5.052-5.0520.0000.0000.0000.000
190A192THR0-0.005-0.0129.448-2.898-2.8980.0000.0000.0000.000
191A193PHE00.0410.0179.8292.9592.9590.0000.0000.0000.000
192A194ILE00.0220.01214.3790.1910.1910.0000.0000.0000.000
193A195ALA00.0270.02717.9351.4091.4090.0000.0000.0000.000
194A196GLY00.1160.03919.8870.3300.3300.0000.0000.0000.000
195A197ARG10.8050.89423.48119.85019.8500.0000.0000.0000.000
196A198GLY00.0030.00424.3760.3090.3090.0000.0000.0000.000
197A199ILE00.0010.01218.745-0.168-0.1680.0000.0000.0000.000
198A200THR0-0.015-0.03723.2310.8530.8530.0000.0000.0000.000
199A201GLU-1-0.845-0.89125.888-19.305-19.3050.0000.0000.0000.000
200A202ALA0-0.0060.01325.4240.6300.6300.0000.0000.0000.000
201A203LYS10.9390.94927.38718.51318.5130.0000.0000.0000.000
202A204ASN0-0.001-0.00625.6110.1150.1150.0000.0000.0000.000
203A205PRO00.0330.03724.418-0.909-0.9090.0000.0000.0000.000
204A206ALA00.0780.04521.943-1.229-1.2290.0000.0000.0000.000
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206A208ALA0-0.009-0.01020.427-1.069-1.0690.0000.0000.0000.000
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