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: VNQJ1

Calculation Name: 3JCI-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JCI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8B980

Base Structure: ElectronMicroscopy

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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2092331.19281
FMO2-HF: Nuclear repulsion 2016025.7552
FMO2-HF: Total energy -76305.43761
FMO2-MP2: Total energy -76530.829074


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:42:ASN)


Summations of interaction energy for fragment #1(A:42:ASN)
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.
79.75284.73.618-3.292-5.2730.025
Interaction energy analysis for fragmet #1(A:42:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.899 / q_NPA : 0.926
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].
3A44ILE0-0.072-0.0232.3060.9435.7453.612-3.217-5.1960.024
4A45PHE00.0580.0364.025-6.113-5.9670.006-0.075-0.0770.001
5A46ASN0-0.052-0.0276.0204.8214.8210.0000.0000.0000.000
6A47THR00.0410.0268.7520.2670.2670.0000.0000.0000.000
7A48ARG10.9500.97112.38415.47415.4740.0000.0000.0000.000
8A49LEU00.0030.01916.0340.0510.0510.0000.0000.0000.000
9A50SER0-0.010-0.02618.8470.1370.1370.0000.0000.0000.000
10A51ARG10.9080.97922.55310.73010.7300.0000.0000.0000.000
11A52THR0-0.052-0.06026.0390.0400.0400.0000.0000.0000.000
12A53PHE00.0180.02329.550-0.055-0.0550.0000.0000.0000.000
13A54GLY00.0500.03432.8290.0030.0030.0000.0000.0000.000
14A55TYR0-0.057-0.02636.099-0.033-0.0330.0000.0000.0000.000
15A56THR00.005-0.02737.8700.0110.0110.0000.0000.0000.000
16A57VAL0-0.058-0.01541.2160.0260.0260.0000.0000.0000.000
17A58LYS10.9420.96343.5066.8146.8140.0000.0000.0000.000
18A59ALA00.0110.02047.0420.0220.0220.0000.0000.0000.000
19A60THR0-0.075-0.04349.6480.0450.0450.0000.0000.0000.000
20A61THR0-0.006-0.02352.4160.0180.0180.0000.0000.0000.000
21A62VAL00.0120.01453.3860.1160.1160.0000.0000.0000.000
22A63ARG10.8950.94655.0205.3805.3800.0000.0000.0000.000
23A64THR00.0160.01154.6610.0080.0080.0000.0000.0000.000
24A65PRO00.0240.01050.066-0.026-0.0260.0000.0000.0000.000
25A66SER0-0.023-0.01549.1620.0840.0840.0000.0000.0000.000
26A67TRP0-0.050-0.03043.047-0.019-0.0190.0000.0000.0000.000
27A68ALA00.0130.02743.2610.0510.0510.0000.0000.0000.000
28A69VAL0-0.048-0.02240.057-0.190-0.1900.0000.0000.0000.000
29A70ASP-1-0.771-0.89437.310-7.934-7.9340.0000.0000.0000.000
30A71MET0-0.026-0.00133.973-0.119-0.1190.0000.0000.0000.000
31A72MET0-0.055-0.01829.687-0.188-0.1880.0000.0000.0000.000
32A73ARG10.8460.89128.2198.9688.9680.0000.0000.0000.000
33A74PHE0-0.023-0.02723.8880.0040.0040.0000.0000.0000.000
34A75ASN00.0460.01423.960-0.863-0.8630.0000.0000.0000.000
35A76ILE00.000-0.01217.141-0.054-0.0540.0000.0000.0000.000
36A77ASN00.0350.00921.646-0.767-0.7670.0000.0000.0000.000
37A78ASP-1-0.860-0.90924.054-10.873-10.8730.0000.0000.0000.000
38A79PHE0-0.082-0.06020.7500.1220.1220.0000.0000.0000.000
39A80VAL0-0.044-0.01918.055-0.629-0.6290.0000.0000.0000.000
40A81PRO00.0380.03321.2280.3160.3160.0000.0000.0000.000
41A82PRO00.0340.02522.473-0.793-0.7930.0000.0000.0000.000
42A83GLY0-0.011-0.00821.818-0.042-0.0420.0000.0000.0000.000
43A84GLY00.0160.00622.5320.7220.7220.0000.0000.0000.000
44A85GLY00.0280.01922.723-0.550-0.5500.0000.0000.0000.000
45A86THR00.003-0.01120.3980.1200.1200.0000.0000.0000.000
46A87ASN0-0.034-0.01217.124-1.077-1.0770.0000.0000.0000.000
47A88LYS10.9930.98219.65813.76913.7690.0000.0000.0000.000
48A89ILE0-0.0130.00518.5590.7010.7010.0000.0000.0000.000
49A90SER00.000-0.01418.774-0.851-0.8510.0000.0000.0000.000
50A91ILE0-0.017-0.00313.986-0.767-0.7670.0000.0000.0000.000
51A92PRO00.0130.01812.3590.2600.2600.0000.0000.0000.000
52A93PHE0-0.018-0.0287.565-3.064-3.0640.0000.0000.0000.000
53A94GLU-1-0.843-0.89511.873-17.529-17.5290.0000.0000.0000.000
54A95TYR0-0.035-0.01710.1662.0852.0850.0000.0000.0000.000
55A96TYR00.015-0.00611.288-1.549-1.5490.0000.0000.0000.000
56A97ARG10.8250.9139.28921.39421.3940.0000.0000.0000.000
57A98ILE00.0610.03313.192-0.971-0.9710.0000.0000.0000.000
58A99ARG10.7660.8989.67220.83920.8390.0000.0000.0000.000
59A100LYS10.8110.89214.73314.09314.0930.0000.0000.0000.000
60A101VAL00.0320.02617.808-0.488-0.4880.0000.0000.0000.000
61A102LYS10.8380.91920.87011.72111.7210.0000.0000.0000.000
62A103VAL00.0220.02423.200-0.158-0.1580.0000.0000.0000.000
63A104GLU-1-0.852-0.93225.344-11.377-11.3770.0000.0000.0000.000
64A105PHE00.0450.01828.968-0.026-0.0260.0000.0000.0000.000
65A106TRP00.006-0.00828.6250.1190.1190.0000.0000.0000.000
66A107PRO0-0.0030.01134.2760.0080.0080.0000.0000.0000.000
67A108CYS0-0.026-0.01438.097-0.099-0.0990.0000.0000.0000.000
68A109SER00.0070.01040.5880.1560.1560.0000.0000.0000.000
69A110PRO00.0240.02442.571-0.119-0.1190.0000.0000.0000.000
70A111ILE00.027-0.01442.9360.0640.0640.0000.0000.0000.000
71A112THR0-0.025-0.00945.3810.0400.0400.0000.0000.0000.000
72A113GLN0-0.040-0.01546.4520.0670.0670.0000.0000.0000.000
73A114GLY00.005-0.00548.414-0.051-0.0510.0000.0000.0000.000
74A115ASP-1-0.871-0.93550.133-6.013-6.0130.0000.0000.0000.000
75A116ARG10.9300.98045.6866.3406.3400.0000.0000.0000.000
76A117GLY00.1000.06246.1060.1120.1120.0000.0000.0000.000
77A118VAL0-0.101-0.07041.952-0.158-0.1580.0000.0000.0000.000
78A119GLY00.0920.06540.5690.0950.0950.0000.0000.0000.000
79A120SER0-0.077-0.08237.859-0.121-0.1210.0000.0000.0000.000
80A121THR00.008-0.00231.8060.0210.0210.0000.0000.0000.000
81A122ALA0-0.019-0.01032.784-0.085-0.0850.0000.0000.0000.000
82A123VAL0-0.042-0.02226.520-0.158-0.1580.0000.0000.0000.000
83A124ILE00.0100.02029.4260.1880.1880.0000.0000.0000.000
84A125LEU0-0.073-0.05225.047-0.376-0.3760.0000.0000.0000.000
85A126ASP-1-0.839-0.93827.479-9.288-9.2880.0000.0000.0000.000
86A127ASP-1-0.764-0.85530.308-9.158-9.1580.0000.0000.0000.000
87A128ASN00.0290.03831.8680.3230.3230.0000.0000.0000.000
88A129PHE0-0.064-0.04630.689-0.003-0.0030.0000.0000.0000.000
89A130VAL0-0.0030.00336.1380.1850.1850.0000.0000.0000.000
90A131THR00.003-0.00839.290-0.149-0.1490.0000.0000.0000.000
91A132LYS10.8560.92939.1127.7287.7280.0000.0000.0000.000
92A133ALA00.0100.00541.7340.1620.1620.0000.0000.0000.000
93A134THR0-0.005-0.00844.242-0.101-0.1010.0000.0000.0000.000
94A135ALA00.0420.01746.642-0.019-0.0190.0000.0000.0000.000
95A136LEU0-0.0230.01344.9560.0960.0960.0000.0000.0000.000
96A137THR00.021-0.01348.172-0.054-0.0540.0000.0000.0000.000
97A138TYR00.0100.00845.0900.0990.0990.0000.0000.0000.000
98A139ASP-1-0.705-0.83241.511-7.320-7.3200.0000.0000.0000.000
99A140PRO0-0.041-0.02240.9170.0040.0040.0000.0000.0000.000
100A141TYR00.007-0.01935.870-0.166-0.1660.0000.0000.0000.000
101A142VAL00.0150.01838.408-0.166-0.1660.0000.0000.0000.000
102A143ASN00.0180.00240.294-0.068-0.0680.0000.0000.0000.000
103A144TYR00.0310.04135.002-0.076-0.0760.0000.0000.0000.000
104A145SER00.012-0.00733.800-0.048-0.0480.0000.0000.0000.000
105A146SER0-0.033-0.01430.432-0.077-0.0770.0000.0000.0000.000
106A147ARG10.9080.96531.6697.2307.2300.0000.0000.0000.000
107A148HIS0-0.084-0.04930.114-0.377-0.3770.0000.0000.0000.000
108A149THR00.0580.01534.236-0.026-0.0260.0000.0000.0000.000
109A150ILE0-0.027-0.00135.488-0.201-0.2010.0000.0000.0000.000
110A151PRO00.0120.00737.7740.1690.1690.0000.0000.0000.000
111A152GLN0-0.0390.00640.255-0.257-0.2570.0000.0000.0000.000
112A153PRO00.0230.00142.5540.1070.1070.0000.0000.0000.000
113A154PHE00.027-0.00541.136-0.174-0.1740.0000.0000.0000.000
114A155SER0-0.036-0.01738.540-0.061-0.0610.0000.0000.0000.000
115A156TYR00.0010.00328.525-0.176-0.1760.0000.0000.0000.000
116A157HIS00.0160.01232.608-0.095-0.0950.0000.0000.0000.000
117A158SER0-0.032-0.01627.631-0.317-0.3170.0000.0000.0000.000
118A159ARG10.8180.93327.5779.5169.5160.0000.0000.0000.000
119A160TYR00.031-0.00217.706-0.412-0.4120.0000.0000.0000.000
120A161PHE00.0160.02322.7390.0300.0300.0000.0000.0000.000
121A162THR0-0.042-0.03618.192-0.542-0.5420.0000.0000.0000.000
122A163PRO00.0240.03219.6660.3280.3280.0000.0000.0000.000
123A164LYS10.8180.90020.54411.90811.9080.0000.0000.0000.000
124A165PRO0-0.0390.00120.0340.2640.2640.0000.0000.0000.000
125A166VAL00.0710.02623.0310.0400.0400.0000.0000.0000.000
126A167LEU0-0.075-0.04121.918-0.183-0.1830.0000.0000.0000.000
127A168ASP-1-0.802-0.92125.886-9.177-9.1770.0000.0000.0000.000
128A169SER0-0.0060.00929.651-0.026-0.0260.0000.0000.0000.000
129A170THR0-0.064-0.00932.4390.3340.3340.0000.0000.0000.000
130A171ILE0-0.073-0.04531.6160.1590.1590.0000.0000.0000.000
131A172ASP-1-0.869-0.91830.378-9.134-9.1340.0000.0000.0000.000
132A173TYR0-0.030-0.00825.081-0.076-0.0760.0000.0000.0000.000
133A174PHE00.014-0.00924.731-0.471-0.4710.0000.0000.0000.000
134A175GLN00.0070.00018.367-0.297-0.2970.0000.0000.0000.000
135A176PRO00.0900.03722.146-0.056-0.0560.0000.0000.0000.000
136A177ASN00.0050.00619.593-0.722-0.7220.0000.0000.0000.000
137A178ASN00.0550.02216.139-0.694-0.6940.0000.0000.0000.000
138A179LYS10.9760.97711.99316.64216.6420.0000.0000.0000.000
139A180ARG10.9660.99611.82616.02616.0260.0000.0000.0000.000
140A181ASN00.021-0.01012.937-0.752-0.7520.0000.0000.0000.000
141A182GLN00.0290.04413.963-0.445-0.4450.0000.0000.0000.000
142A183LEU00.0680.03614.298-1.102-1.1020.0000.0000.0000.000
143A184TRP0-0.060-0.0427.733-1.253-1.2530.0000.0000.0000.000
144A185LEU00.0220.02513.9860.8140.8140.0000.0000.0000.000
145A186ARG10.9530.96414.73613.97513.9750.0000.0000.0000.000
146A187LEU0-0.022-0.01014.7450.8700.8700.0000.0000.0000.000
147A188GLN0-0.056-0.02717.307-0.053-0.0530.0000.0000.0000.000
148A189THR00.0270.00821.029-0.195-0.1950.0000.0000.0000.000
149A190SER00.0430.01223.4070.0630.0630.0000.0000.0000.000
150A191ALA00.0200.02524.8310.3560.3560.0000.0000.0000.000
151A192ASN0-0.039-0.02120.288-0.705-0.7050.0000.0000.0000.000
152A193VAL00.0360.03421.4320.3830.3830.0000.0000.0000.000
153A194ASP-1-0.804-0.89523.239-10.978-10.9780.0000.0000.0000.000
154A195HIS0-0.072-0.05819.592-0.629-0.6290.0000.0000.0000.000
155A196VAL00.0440.03323.9870.1170.1170.0000.0000.0000.000
156A197GLY0-0.020-0.04225.642-0.380-0.3800.0000.0000.0000.000
157A198LEU0-0.004-0.01026.9100.0670.0670.0000.0000.0000.000
158A199GLY00.0610.05029.9670.0780.0780.0000.0000.0000.000
159A200THR0-0.075-0.03733.694-0.127-0.1270.0000.0000.0000.000
160A201ALA00.0250.01136.1530.1090.1090.0000.0000.0000.000
161A202PHE00.0130.01136.244-0.052-0.0520.0000.0000.0000.000
162A203GLU-1-0.852-0.91041.328-6.274-6.2740.0000.0000.0000.000
163A204ASN00.006-0.01244.931-0.085-0.0850.0000.0000.0000.000
164A205SER00.0490.01847.3890.0100.0100.0000.0000.0000.000
165A206LYS10.8810.95149.4775.6605.6600.0000.0000.0000.000
166A207TYR0-0.032-0.03449.2450.1740.1740.0000.0000.0000.000
167A208ASP-1-0.793-0.88846.088-6.480-6.4800.0000.0000.0000.000
168A209GLN0-0.034-0.02842.867-0.009-0.0090.0000.0000.0000.000
169A210ASP-1-0.808-0.86740.765-7.297-7.2970.0000.0000.0000.000
170A211TYR0-0.014-0.02335.739-0.048-0.0480.0000.0000.0000.000
171A212ASN00.0050.00133.690-0.051-0.0510.0000.0000.0000.000
172A213ILE00.003-0.00130.124-0.173-0.1730.0000.0000.0000.000
173A214ARG10.9060.96725.43910.70110.7010.0000.0000.0000.000
174A215VAL0-0.0050.00523.5640.0380.0380.0000.0000.0000.000
175A216THR0-0.021-0.02420.167-0.331-0.3310.0000.0000.0000.000
176A217MET0-0.0010.01918.4970.1220.1220.0000.0000.0000.000
177A218TYR0-0.009-0.01214.506-0.592-0.5920.0000.0000.0000.000
178A219VAL00.002-0.00113.1500.3610.3610.0000.0000.0000.000
179A220GLN00.0340.0295.8630.9270.9270.0000.0000.0000.000
180A221PHE00.0670.0199.4371.3361.3360.0000.0000.0000.000
181A222ARG10.9060.9426.10424.21924.2190.0000.0000.0000.000
182A223GLU-1-0.915-0.9516.716-31.076-31.0760.0000.0000.0000.000
183A224PHE00.0050.0026.9042.5582.5580.0000.0000.0000.000
184A225ASN0-0.034-0.0408.602-0.845-0.8450.0000.0000.0000.000
185A226LEU00.0050.01311.5701.7361.7360.0000.0000.0000.000
186A227LYS10.8360.91313.48019.42019.4200.0000.0000.0000.000
187A228ASP-1-0.886-0.93816.363-17.036-17.0360.0000.0000.0000.000
188A229PRO0-0.069-0.02418.1710.1790.1790.0000.0000.0000.000
189A230PRO0-0.003-0.01721.8470.0220.0220.0000.0000.0000.000
190A231LEU-1-0.930-0.94223.931-11.838-11.8380.0000.0000.0000.000