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: VN3L1

Calculation Name: 6J3D-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6J3D

Chain ID: A

ChEMBL ID:

UniProt ID: E0U503

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 233
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3039285.59204
FMO2-HF: Nuclear repulsion 2946981.334813
FMO2-HF: Total energy -92304.257227
FMO2-MP2: Total energy -92573.112694


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:20:SER)


Summations of interaction energy for fragment #1(A:20:SER)
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.
-179.798-172.8296.885-5.595-8.26-0.006
Interaction energy analysis for fragmet #1(A:20:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.912
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].
3A22ILE00.0780.0693.858-1.3901.213-0.028-1.308-1.266-0.005
200A219GLN00.003-0.0274.2862.7552.859-0.001-0.047-0.0550.000
201A220LYS10.7840.8912.33330.48233.2304.269-3.333-3.685-0.017
202A221MET0-0.0220.0002.2071.0611.6212.638-0.594-2.6050.016
203A222ASN0-0.041-0.0253.4387.1038.0570.007-0.313-0.6490.000
4A23TYR0-0.031-0.0067.114-0.275-0.2750.0000.0000.0000.000
5A24GLN00.0160.0219.5370.3640.3640.0000.0000.0000.000
6A25VAL0-0.001-0.00612.8950.1530.1530.0000.0000.0000.000
7A26SER00.0340.00616.2020.8080.8080.0000.0000.0000.000
8A27THR0-0.039-0.02118.016-0.916-0.9160.0000.0000.0000.000
9A28MET00.0180.01920.2070.3690.3690.0000.0000.0000.000
10A29THR00.0220.00221.8910.4170.4170.0000.0000.0000.000
11A30SER00.0030.00223.6020.7710.7710.0000.0000.0000.000
12A31LEU00.0180.00622.9720.4300.4300.0000.0000.0000.000
13A32LEU0-0.023-0.01625.7380.4690.4690.0000.0000.0000.000
14A33ASP-1-0.860-0.93228.223-9.693-9.6930.0000.0000.0000.000
15A34GLY00.0070.01729.5510.3020.3020.0000.0000.0000.000
16A35VAL0-0.029-0.01326.7490.2160.2160.0000.0000.0000.000
17A36TYR0-0.043-0.04526.682-0.597-0.5970.0000.0000.0000.000
18A37ASP-1-0.824-0.89827.682-10.444-10.4440.0000.0000.0000.000
19A38GLY00.005-0.00623.725-0.033-0.0330.0000.0000.0000.000
20A39ASP-1-0.835-0.92122.157-13.724-13.7240.0000.0000.0000.000
21A40PHE0-0.023-0.01515.041-0.525-0.5250.0000.0000.0000.000
22A41GLU-1-0.834-0.92920.288-12.854-12.8540.0000.0000.0000.000
23A42LEU00.0080.00718.507-1.060-1.0600.0000.0000.0000.000
24A43SER0-0.019-0.00918.841-0.684-0.6840.0000.0000.0000.000
25A44GLU-1-0.809-0.87215.662-18.832-18.8320.0000.0000.0000.000
26A45ILE00.0240.03114.155-1.456-1.4560.0000.0000.0000.000
27A46PRO00.017-0.00512.879-1.989-1.9890.0000.0000.0000.000
28A47LYS10.7980.89311.78817.77817.7780.0000.0000.0000.000
29A48TYR0-0.127-0.0938.739-3.035-3.0350.0000.0000.0000.000
30A49GLY0-0.019-0.0168.347-3.901-3.9010.0000.0000.0000.000
31A50ASP-1-0.851-0.9169.852-26.403-26.4030.0000.0000.0000.000
32A51PHE00.008-0.00210.2211.7651.7650.0000.0000.0000.000
33A52GLY00.008-0.01711.317-2.064-2.0640.0000.0000.0000.000
34A53ILE0-0.0310.00113.5590.9870.9870.0000.0000.0000.000
35A54GLY00.0180.00116.510-0.791-0.7910.0000.0000.0000.000
36A55THR00.0290.02619.2710.7360.7360.0000.0000.0000.000
37A56PHE0-0.0020.01821.975-0.717-0.7170.0000.0000.0000.000
38A57ASN0-0.014-0.02724.588-0.138-0.1380.0000.0000.0000.000
39A58LYS10.8560.92627.1179.5039.5030.0000.0000.0000.000
40A59LEU00.0350.03326.5840.2890.2890.0000.0000.0000.000
41A60ASP-1-0.838-0.87728.331-10.035-10.0350.0000.0000.0000.000
42A61GLY00.0810.04127.327-0.188-0.1880.0000.0000.0000.000
43A62GLU-1-0.820-0.90223.411-12.794-12.7940.0000.0000.0000.000
44A63LEU0-0.040-0.01717.6240.0720.0720.0000.0000.0000.000
45A64ILE0-0.033-0.02218.414-0.453-0.4530.0000.0000.0000.000
46A65GLY00.0730.02916.9380.6860.6860.0000.0000.0000.000
47A66PHE0-0.022-0.01614.329-1.220-1.2200.0000.0000.0000.000
48A67ASP-1-0.818-0.87714.371-17.186-17.1860.0000.0000.0000.000
49A68GLY0-0.023-0.01414.8330.4190.4190.0000.0000.0000.000
50A69GLU-1-0.924-0.91815.912-12.862-12.8620.0000.0000.0000.000
51A70PHE0-0.009-0.01713.562-0.575-0.5750.0000.0000.0000.000
52A71TYR0-0.047-0.05919.7060.5670.5670.0000.0000.0000.000
53A72ARG10.8280.89722.29111.00811.0080.0000.0000.0000.000
54A73LEU0-0.023-0.00824.1860.4130.4130.0000.0000.0000.000
55A74ARG10.8360.88026.8859.9969.9960.0000.0000.0000.000
56A75SER0-0.020-0.03530.326-0.013-0.0130.0000.0000.0000.000
57A76ASP-1-0.876-0.92033.214-9.140-9.1400.0000.0000.0000.000
58A77GLY0-0.026-0.01032.7200.1990.1990.0000.0000.0000.000
59A78THR0-0.107-0.07131.827-0.131-0.1310.0000.0000.0000.000
60A79ALA00.0560.03426.655-0.299-0.2990.0000.0000.0000.000
61A80THR0-0.078-0.03627.8660.4150.4150.0000.0000.0000.000
62A81PRO00.019-0.00124.855-0.428-0.4280.0000.0000.0000.000
63A82VAL00.0200.01820.4390.2440.2440.0000.0000.0000.000
64A83GLN0-0.082-0.04123.3910.1660.1660.0000.0000.0000.000
65A84ASN0-0.007-0.02923.403-0.653-0.6530.0000.0000.0000.000
66A85GLY00.0080.01224.6930.5190.5190.0000.0000.0000.000
67A86ASP-1-0.794-0.86823.672-11.962-11.9620.0000.0000.0000.000
68A87LEU0-0.043-0.01223.131-0.558-0.5580.0000.0000.0000.000
69A88SER0-0.008-0.01920.2620.0300.0300.0000.0000.0000.000
70A89PRO0-0.0010.01421.954-0.376-0.3760.0000.0000.0000.000
71A90PHE0-0.013-0.02318.559-0.313-0.3130.0000.0000.0000.000
72A91CYS0-0.051-0.01316.4960.2240.2240.0000.0000.0000.000
73A92SER0-0.011-0.00612.404-0.350-0.3500.0000.0000.0000.000
74A93PHE00.0300.00710.6740.6740.6740.0000.0000.0000.000
75A94THR0-0.038-0.0474.918-4.556-4.5560.0000.0000.0000.000
76A95PHE0-0.0130.0255.7802.5542.5540.0000.0000.0000.000
77A96PHE0-0.069-0.0435.798-6.079-6.0790.0000.0000.0000.000
78A97THR0-0.048-0.0516.199-0.426-0.4260.0000.0000.0000.000
79A98PRO00.0090.0068.353-0.501-0.5010.0000.0000.0000.000
80A99ASP-1-0.807-0.8795.503-38.670-38.6700.0000.0000.0000.000
81A100MET0-0.046-0.0148.7672.0512.0510.0000.0000.0000.000
82A101THR0-0.012-0.02111.918-0.200-0.2000.0000.0000.0000.000
83A102HIS0-0.045-0.02415.2860.2070.2070.0000.0000.0000.000
84A103LYS10.8700.93018.47513.04013.0400.0000.0000.0000.000
85A104ILE00.0200.00420.8390.0810.0810.0000.0000.0000.000
86A105ASP-1-0.901-0.94224.326-11.310-11.3100.0000.0000.0000.000
87A106ALA00.010-0.00427.7810.4810.4810.0000.0000.0000.000
88A107LYS10.9100.96428.3078.6098.6090.0000.0000.0000.000
89A108MET00.0050.02624.003-0.091-0.0910.0000.0000.0000.000
90A109THR0-0.052-0.04327.317-0.221-0.2210.0000.0000.0000.000
91A110ARG10.9270.95723.19511.23711.2370.0000.0000.0000.000
92A111GLU-1-0.842-0.90623.877-10.473-10.4730.0000.0000.0000.000
93A112GLU-1-0.881-0.93624.916-10.219-10.2190.0000.0000.0000.000
94A113PHE00.0670.02217.917-0.336-0.3360.0000.0000.0000.000
95A114GLU-1-0.862-0.92719.931-13.674-13.6740.0000.0000.0000.000
96A115LYS10.7640.86720.11310.04610.0460.0000.0000.0000.000
97A116GLU-1-0.843-0.90520.236-13.195-13.1950.0000.0000.0000.000
98A117ILE00.0070.00815.142-0.570-0.5700.0000.0000.0000.000
99A118ASN0-0.012-0.01016.211-1.582-1.5820.0000.0000.0000.000
100A119SER0-0.091-0.04417.521-0.168-0.1680.0000.0000.0000.000
101A120ILE00.0150.01115.057-0.092-0.0920.0000.0000.0000.000
102A121LEU0-0.0240.00010.988-1.121-1.1210.0000.0000.0000.000
103A122PRO0-0.0090.0039.6080.9250.9250.0000.0000.0000.000
104A123SER00.001-0.01211.2440.6930.6930.0000.0000.0000.000
105A124LYS10.9020.96011.93815.62315.6230.0000.0000.0000.000
106A125ASN00.0060.00313.1780.6360.6360.0000.0000.0000.000
107A126LEU0-0.0220.0017.132-0.772-0.7720.0000.0000.0000.000
108A127PHE00.0660.0326.9971.8871.8870.0000.0000.0000.000
109A128TYR0-0.024-0.0396.616-3.596-3.5960.0000.0000.0000.000
110A129ALA00.0020.0227.6711.3271.3270.0000.0000.0000.000
111A130ILE0-0.045-0.0289.503-0.464-0.4640.0000.0000.0000.000
112A131ARG10.8220.86312.51718.04718.0470.0000.0000.0000.000
113A132ILE0-0.020-0.00815.2790.1120.1120.0000.0000.0000.000
114A133ASP-1-0.782-0.85318.791-15.515-15.5150.0000.0000.0000.000
115A134GLY0-0.006-0.02721.3640.1100.1100.0000.0000.0000.000
116A135LEU0-0.059-0.01324.9430.1080.1080.0000.0000.0000.000
117A136PHE00.0340.00122.391-0.168-0.1680.0000.0000.0000.000
118A137LYS10.9591.00228.4288.8408.8400.0000.0000.0000.000
119A138LYS10.8480.90330.1739.2029.2020.0000.0000.0000.000
120A139VAL00.0260.02425.958-0.361-0.3610.0000.0000.0000.000
121A140GLN0-0.058-0.03228.4050.3060.3060.0000.0000.0000.000
122A141THR0-0.017-0.03526.280-0.303-0.3030.0000.0000.0000.000
123A142ARG10.7990.89524.73412.18112.1810.0000.0000.0000.000
124A143THR0-0.007-0.03027.473-0.409-0.4090.0000.0000.0000.000
125A144VAL0-0.044-0.01726.5220.4170.4170.0000.0000.0000.000
126A145GLU-1-0.835-0.89629.302-8.985-8.9850.0000.0000.0000.000
127A146LEU0-0.0240.00032.043-0.072-0.0720.0000.0000.0000.000
128A147GLN0-0.029-0.01231.9810.4630.4630.0000.0000.0000.000
129A148GLU-1-0.867-0.95234.311-8.665-8.6650.0000.0000.0000.000
130A149LYS10.8160.93332.6729.5499.5490.0000.0000.0000.000
131A150PRO0-0.068-0.04437.5540.2030.2030.0000.0000.0000.000
132A151TYR0-0.029-0.05031.8390.1780.1780.0000.0000.0000.000
133A152VAL00.0140.01835.0900.1260.1260.0000.0000.0000.000
134A153PRO00.0730.03332.448-0.227-0.2270.0000.0000.0000.000
135A154MET00.0030.02225.3310.0970.0970.0000.0000.0000.000
136A155VAL00.0270.00630.6940.0640.0640.0000.0000.0000.000
137A156GLU-1-0.876-0.92532.610-8.050-8.0500.0000.0000.0000.000
138A157ALA0-0.0100.00031.8490.1560.1560.0000.0000.0000.000
139A158VAL0-0.004-0.00129.5050.0440.0440.0000.0000.0000.000
140A159LYS10.7510.86832.7688.4158.4150.0000.0000.0000.000
141A160THR0-0.049-0.02936.3670.2090.2090.0000.0000.0000.000
142A161GLN00.0470.04630.377-0.260-0.2600.0000.0000.0000.000
143A162PRO0-0.0260.00132.8900.1390.1390.0000.0000.0000.000
144A163ILE0-0.002-0.00732.144-0.323-0.3230.0000.0000.0000.000
145A164PHE0-0.046-0.00631.2230.3860.3860.0000.0000.0000.000
146A165ASN0-0.022-0.02231.918-0.339-0.3390.0000.0000.0000.000
147A166PHE00.0130.01129.7850.2300.2300.0000.0000.0000.000
148A167ASP-1-0.868-0.93632.112-8.805-8.8050.0000.0000.0000.000
149A168ASN0-0.051-0.03932.960-0.009-0.0090.0000.0000.0000.000
150A169VAL00.0070.03128.5860.0590.0590.0000.0000.0000.000
151A170ARG10.9340.96227.49310.41510.4150.0000.0000.0000.000
152A171GLY0-0.006-0.01125.4860.1810.1810.0000.0000.0000.000
153A172THR0-0.034-0.02719.0110.1130.1130.0000.0000.0000.000
154A173ILE0-0.0130.00118.7700.1880.1880.0000.0000.0000.000
155A174VAL0-0.016-0.00715.019-0.683-0.6830.0000.0000.0000.000
156A175GLY00.0410.02314.5870.9600.9600.0000.0000.0000.000
157A176PHE0-0.032-0.0238.916-2.155-2.1550.0000.0000.0000.000
158A177LEU0-0.0280.00911.4721.5471.5470.0000.0000.0000.000
159A178THR00.0020.00711.259-2.665-2.6650.0000.0000.0000.000
160A179PRO00.0000.01011.5791.6451.6450.0000.0000.0000.000
161A180ALA00.0610.00214.5180.1450.1450.0000.0000.0000.000
162A181TYR0-0.075-0.04911.5450.2830.2830.0000.0000.0000.000
163A182ALA00.0040.00214.025-0.147-0.1470.0000.0000.0000.000
164A183ASN00.0650.03216.076-0.473-0.4730.0000.0000.0000.000
165A184GLY00.0200.02419.1060.2450.2450.0000.0000.0000.000
166A185ILE0-0.040-0.01415.9450.0780.0780.0000.0000.0000.000
167A186ALA00.0490.01014.863-0.144-0.1440.0000.0000.0000.000
168A187VAL00.0440.02816.8980.7450.7450.0000.0000.0000.000
169A188SER0-0.068-0.04516.761-0.734-0.7340.0000.0000.0000.000
170A189GLY0-0.013-0.00116.7520.8930.8930.0000.0000.0000.000
171A190TYR00.005-0.02716.130-1.379-1.3790.0000.0000.0000.000
172A191HIS00.0400.03316.3810.9240.9240.0000.0000.0000.000
173A192LEU00.0170.00016.555-1.118-1.1180.0000.0000.0000.000
174A193HIS00.0410.02018.9260.7030.7030.0000.0000.0000.000
175A194PHE0-0.001-0.01120.184-0.462-0.4620.0000.0000.0000.000
176A195ILE0-0.0060.00921.9870.1750.1750.0000.0000.0000.000
177A196ASP-1-0.737-0.85924.325-10.799-10.7990.0000.0000.0000.000
178A197GLU-1-0.890-0.97026.157-10.695-10.6950.0000.0000.0000.000
179A198GLY0-0.060-0.02327.369-0.029-0.0290.0000.0000.0000.000
180A199ARG10.8210.91722.22413.20013.2000.0000.0000.0000.000
181A200ASN0-0.043-0.01927.2200.1780.1780.0000.0000.0000.000
182A201SER00.0450.00929.2670.0990.0990.0000.0000.0000.000
183A202GLY00.009-0.01126.163-0.326-0.3260.0000.0000.0000.000
184A203GLY0-0.0010.02824.8860.4070.4070.0000.0000.0000.000
185A204HIS10.7990.90821.92312.75012.7500.0000.0000.0000.000
186A205VAL0-0.030-0.03422.6320.5770.5770.0000.0000.0000.000
187A206PHE0-0.0040.01524.269-0.131-0.1310.0000.0000.0000.000
188A207ASP-1-0.877-0.94226.268-10.538-10.5380.0000.0000.0000.000
189A208TYR0-0.016-0.02120.665-0.099-0.0990.0000.0000.0000.000
190A209VAL0-0.082-0.04227.0100.1290.1290.0000.0000.0000.000
191A210LEU00.0100.00122.0150.0360.0360.0000.0000.0000.000
192A211GLU-1-0.956-0.99726.700-8.886-8.8860.0000.0000.0000.000
193A212ASP-1-0.870-0.93227.529-9.917-9.9170.0000.0000.0000.000
194A213CYS0-0.058-0.01522.351-0.122-0.1220.0000.0000.0000.000
195A214THR0-0.0170.00418.5430.1170.1170.0000.0000.0000.000
196A215VAL00.0180.01515.380-0.201-0.2010.0000.0000.0000.000
197A216THR0-0.022-0.01812.808-0.479-0.4790.0000.0000.0000.000
198A217ILE00.0240.0039.2720.0030.0030.0000.0000.0000.000
199A218SER00.0080.0276.309-2.462-2.4620.0000.0000.0000.000
204A223MET0-0.0060.0086.088-2.177-2.1770.0000.0000.0000.000
205A224ASN0-0.056-0.0327.5704.5624.5620.0000.0000.0000.000
206A225LEU00.0420.0229.8520.3930.3930.0000.0000.0000.000
207A226ARG10.8450.92313.60218.91418.9140.0000.0000.0000.000
208A227LEU00.003-0.00515.4620.4460.4460.0000.0000.0000.000
209A228PRO00.0350.02019.167-0.164-0.1640.0000.0000.0000.000
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