FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4L3YN

Calculation Name: 3DHU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DHU

Chain ID: A

ChEMBL ID:

UniProt ID: F9USZ1

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 422
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8041957.893793
FMO2-HF: Nuclear repulsion 7874377.267095
FMO2-HF: Total energy -167580.626698
FMO2-MP2: Total energy -168074.263201


3D Structure
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:6:GLN)


Summations of interaction energy for fragment #1(A:6:GLN)
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.
-53.382-50.39226.934-12.955-16.968-0.015
Interaction energy analysis for fragmet #1(A:6:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.031
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].
3A8GLN0-0.032-0.0233.002-3.625-0.5380.037-1.407-1.7170.000
4A9LEU00.1190.0692.829-0.6800.4240.303-0.369-1.038-0.001
5A10ARG10.7240.8535.3461.3081.3080.0000.0000.0000.000
6A11ASN0-0.088-0.0607.7990.7800.7800.0000.0000.0000.000
7A12GLU-1-0.885-0.9356.535-2.974-2.9740.0000.0000.0000.000
8A13MET0-0.035-0.01810.362-0.003-0.0030.0000.0000.0000.000
9A14ILE00.0080.0139.6010.0370.0370.0000.0000.0000.000
10A15TYR00.021-0.03013.5860.1400.1400.0000.0000.0000.000
11A16SER0-0.057-0.01716.974-0.037-0.0370.0000.0000.0000.000
12A17VAL00.002-0.00618.8560.0930.0930.0000.0000.0000.000
13A18PHE00.0230.01122.197-0.021-0.0210.0000.0000.0000.000
14A19VAL0-0.005-0.00724.3730.0490.0490.0000.0000.0000.000
15A20ARG10.7710.88226.7560.4800.4800.0000.0000.0000.000
16A21ASN00.0360.02228.8380.0630.0630.0000.0000.0000.000
17A22TYR0-0.040-0.03324.798-0.006-0.0060.0000.0000.0000.000
18A23SER0-0.007-0.01628.7270.0260.0260.0000.0000.0000.000
19A24GLU-1-0.819-0.93032.036-0.340-0.3400.0000.0000.0000.000
20A25ALA0-0.037-0.02234.0060.0070.0070.0000.0000.0000.000
21A26GLY00.0010.02131.3240.0060.0060.0000.0000.0000.000
22A27ASN0-0.023-0.01630.395-0.019-0.0190.0000.0000.0000.000
23A28PHE00.0760.01024.957-0.020-0.0200.0000.0000.0000.000
24A29ALA00.0200.01627.748-0.016-0.0160.0000.0000.0000.000
25A30GLY0-0.013-0.00230.1140.0060.0060.0000.0000.0000.000
26A31VAL0-0.0010.00123.495-0.012-0.0120.0000.0000.0000.000
27A32THR00.000-0.02725.841-0.021-0.0210.0000.0000.0000.000
28A33ALA0-0.042-0.01626.8660.0080.0080.0000.0000.0000.000
29A34ASP-1-0.793-0.86626.863-0.488-0.4880.0000.0000.0000.000
30A35LEU0-0.0040.00621.321-0.025-0.0250.0000.0000.0000.000
31A36GLN0-0.035-0.02522.667-0.016-0.0160.0000.0000.0000.000
32A37ARG10.8340.89423.8340.5450.5450.0000.0000.0000.000
33A38ILE0-0.0150.00819.469-0.028-0.0280.0000.0000.0000.000
34A39LYS10.8870.94915.5590.7930.7930.0000.0000.0000.000
35A40ASP-1-0.840-0.91519.945-0.466-0.4660.0000.0000.0000.000
36A41LEU0-0.084-0.02920.7300.0280.0280.0000.0000.0000.000
37A42GLY0-0.017-0.02118.445-0.008-0.0080.0000.0000.0000.000
38A43THR0-0.042-0.03415.868-0.130-0.1300.0000.0000.0000.000
39A44ASP-1-0.888-0.95011.577-1.084-1.0840.0000.0000.0000.000
40A45ILE0-0.024-0.0098.075-0.005-0.0050.0000.0000.0000.000
41A46LEU00.0200.00812.7740.0340.0340.0000.0000.0000.000
42A47TRP0-0.021-0.02914.437-0.073-0.0730.0000.0000.0000.000
43A48LEU0-0.023-0.01716.3570.1000.1000.0000.0000.0000.000
44A49LEU0-0.0010.00019.205-0.052-0.0520.0000.0000.0000.000
45A50PRO0-0.024-0.00420.9930.0370.0370.0000.0000.0000.000
46A51ILE00.0180.00322.3890.0490.0490.0000.0000.0000.000
47A52ASN0-0.030-0.00424.0520.0000.0000.0000.0000.0000.000
48A53PRO0-0.001-0.00227.243-0.001-0.0010.0000.0000.0000.000
49A54ILE00.0130.03328.807-0.016-0.0160.0000.0000.0000.000
50A55GLY00.0420.02631.0530.0250.0250.0000.0000.0000.000
51A56GLU-1-0.892-0.93433.253-0.282-0.2820.0000.0000.0000.000
52A57VAL0-0.030-0.02136.7150.0070.0070.0000.0000.0000.000
53A58ASN0-0.037-0.02735.075-0.014-0.0140.0000.0000.0000.000
54A59ARG10.8310.92634.1460.3130.3130.0000.0000.0000.000
55A60LYS10.8060.91330.1120.4360.4360.0000.0000.0000.000
56A61GLY00.0130.00333.952-0.016-0.0160.0000.0000.0000.000
57A62THR0-0.071-0.07636.1240.0060.0060.0000.0000.0000.000
58A63LEU0-0.058-0.03433.7140.0140.0140.0000.0000.0000.000
59A64GLY00.0560.04132.398-0.005-0.0050.0000.0000.0000.000
60A65SER00.0440.02126.498-0.028-0.0280.0000.0000.0000.000
61A66PRO00.004-0.00724.7050.0110.0110.0000.0000.0000.000
62A67TYR0-0.058-0.05419.6580.0170.0170.0000.0000.0000.000
63A68ALA00.0150.00924.6420.0060.0060.0000.0000.0000.000
64A69ILE0-0.0010.00623.2010.0350.0350.0000.0000.0000.000
65A70LYS10.8040.88427.5270.2920.2920.0000.0000.0000.000
66A71ASP-1-0.815-0.93129.140-0.333-0.3330.0000.0000.0000.000
67A72TYR00.0160.00723.284-0.015-0.0150.0000.0000.0000.000
68A73ARG10.8260.91924.6200.2840.2840.0000.0000.0000.000
69A74GLY00.0260.02626.8910.0070.0070.0000.0000.0000.000
70A75ILE0-0.026-0.02526.319-0.039-0.0390.0000.0000.0000.000
71A76ASN0-0.005-0.00128.5680.0600.0600.0000.0000.0000.000
72A77PRO00.017-0.00530.3680.0000.0000.0000.0000.0000.000
73A78GLU-1-0.793-0.86631.670-0.409-0.4090.0000.0000.0000.000
74A79TYR0-0.042-0.03025.6230.0100.0100.0000.0000.0000.000
75A80GLY00.0180.02430.644-0.005-0.0050.0000.0000.0000.000
76A81THR0-0.039-0.05531.9170.0070.0070.0000.0000.0000.000
77A82LEU00.0620.01326.392-0.020-0.0200.0000.0000.0000.000
78A83ALA0-0.0030.01028.128-0.014-0.0140.0000.0000.0000.000
79A84ASP-1-0.851-0.90129.164-0.337-0.3370.0000.0000.0000.000
80A85PHE00.0060.00920.853-0.019-0.0190.0000.0000.0000.000
81A86LYS10.8880.92324.0710.3420.3420.0000.0000.0000.000
82A87ALA0-0.018-0.01024.967-0.008-0.0080.0000.0000.0000.000
83A88LEU0-0.025-0.00221.779-0.006-0.0060.0000.0000.0000.000
84A89THR00.0420.00220.288-0.025-0.0250.0000.0000.0000.000
85A90ASP-1-0.875-0.90620.576-0.432-0.4320.0000.0000.0000.000
86A91ARG10.9190.96222.5490.4030.4030.0000.0000.0000.000
87A92ALA00.0260.00518.8430.0000.0000.0000.0000.0000.000
88A93HIS10.8320.89115.5440.7170.7170.0000.0000.0000.000
89A94GLU-1-0.972-0.97519.070-0.311-0.3110.0000.0000.0000.000
90A95LEU0-0.082-0.03020.6080.0370.0370.0000.0000.0000.000
91A96GLY00.0030.00616.579-0.016-0.0160.0000.0000.0000.000
92A97MET0-0.086-0.02714.988-0.096-0.0960.0000.0000.0000.000
93A98LYS10.8140.9029.2361.3891.3890.0000.0000.0000.000
94A99VAL0-0.010-0.01513.506-0.012-0.0120.0000.0000.0000.000
95A100MET0-0.033-0.0079.483-0.065-0.0650.0000.0000.0000.000
96A101LEU00.0120.00914.7360.1240.1240.0000.0000.0000.000
97A102ASP-1-0.680-0.82315.866-1.354-1.3540.0000.0000.0000.000
98A103ILE0-0.043-0.01115.8090.1180.1180.0000.0000.0000.000
99A104VAL0-0.003-0.00217.534-0.056-0.0560.0000.0000.0000.000
100A105TYR0-0.003-0.02818.2770.0600.0600.0000.0000.0000.000
101A106ASN00.0130.01620.3050.0650.0650.0000.0000.0000.000
102A107HIS00.0300.03421.6980.0670.0670.0000.0000.0000.000
103A108THR00.0230.03224.747-0.024-0.0240.0000.0000.0000.000
104A109SER0-0.024-0.03627.5440.0040.0040.0000.0000.0000.000
105A110PRO00.001-0.01130.7740.0080.0080.0000.0000.0000.000
106A111ASP-1-0.761-0.84633.860-0.284-0.2840.0000.0000.0000.000
107A112SER00.000-0.00530.2770.0150.0150.0000.0000.0000.000
108A113VAL00.0330.02331.3940.0180.0180.0000.0000.0000.000
109A114LEU0-0.0070.00226.7410.0180.0180.0000.0000.0000.000
110A115ALA00.0160.01631.2110.0180.0180.0000.0000.0000.000
111A116THR0-0.089-0.06333.3240.0210.0210.0000.0000.0000.000
112A117GLU-1-0.946-0.97534.259-0.193-0.1930.0000.0000.0000.000
113A118HIS10.7510.86931.8630.2100.2100.0000.0000.0000.000
114A119PRO00.0600.03632.503-0.012-0.0120.0000.0000.0000.000
115A120GLU-1-0.834-0.91132.799-0.179-0.1790.0000.0000.0000.000
116A121TRP0-0.016-0.00528.392-0.007-0.0070.0000.0000.0000.000
117A122PHE0-0.0040.00228.480-0.035-0.0350.0000.0000.0000.000
118A123TYR0-0.073-0.03425.6210.0130.0130.0000.0000.0000.000
119A124HIS0-0.034-0.03431.039-0.007-0.0070.0000.0000.0000.000
120A125ASP-1-0.848-0.91334.781-0.201-0.2010.0000.0000.0000.000
121A126ALA0-0.035-0.02736.9090.0090.0090.0000.0000.0000.000
122A127ASP-1-0.950-0.96840.506-0.139-0.1390.0000.0000.0000.000
123A128GLY0-0.054-0.01939.3530.0030.0030.0000.0000.0000.000
124A129GLN0-0.088-0.04038.449-0.008-0.0080.0000.0000.0000.000
125A130LEU00.0440.02732.778-0.005-0.0050.0000.0000.0000.000
126A131THR0-0.005-0.01831.706-0.007-0.0070.0000.0000.0000.000
127A132ASN0-0.029-0.02629.378-0.006-0.0060.0000.0000.0000.000
128A133LYS10.8590.94223.0830.4720.4720.0000.0000.0000.000
129A134VAL0-0.0210.00525.1020.0030.0030.0000.0000.0000.000
130A135GLY00.0190.00528.4650.0040.0040.0000.0000.0000.000
131A136ASP-1-0.857-0.94429.242-0.417-0.4170.0000.0000.0000.000
132A137TRP0-0.0140.01222.061-0.003-0.0030.0000.0000.0000.000
133A138SER00.0390.00929.5880.0050.0050.0000.0000.0000.000
134A139ASP-1-0.873-0.94329.946-0.418-0.4180.0000.0000.0000.000
135A140VAL0-0.045-0.01426.545-0.003-0.0030.0000.0000.0000.000
136A141LYS10.8070.89429.0450.3410.3410.0000.0000.0000.000
137A142ASP-1-0.763-0.87926.216-0.444-0.4440.0000.0000.0000.000
138A143LEU0-0.014-0.00623.8200.0330.0330.0000.0000.0000.000
139A144ASP-1-0.824-0.91725.199-0.243-0.2430.0000.0000.0000.000
140A145TYR0-0.047-0.05920.9550.0170.0170.0000.0000.0000.000
141A146GLY0-0.0060.01423.7980.0210.0210.0000.0000.0000.000
142A147HIS0-0.043-0.00726.1370.0400.0400.0000.0000.0000.000
143A148HIS0-0.031-0.01922.2000.0000.0000.0000.0000.0000.000
144A149GLU-1-0.914-0.97425.328-0.125-0.1250.0000.0000.0000.000
145A150LEU00.0010.02124.284-0.010-0.0100.0000.0000.0000.000
146A151TRP0-0.039-0.03619.526-0.037-0.0370.0000.0000.0000.000
147A152GLN0-0.004-0.01522.228-0.014-0.0140.0000.0000.0000.000
148A153TYR00.0620.04224.104-0.011-0.0110.0000.0000.0000.000
149A154GLN00.0610.02720.938-0.005-0.0050.0000.0000.0000.000
150A155ILE00.0180.02118.480-0.074-0.0740.0000.0000.0000.000
151A156ASP-1-0.860-0.93120.367-0.249-0.2490.0000.0000.0000.000
152A157THR0-0.045-0.02222.1920.0070.0070.0000.0000.0000.000
153A158LEU0-0.0040.01016.112-0.030-0.0300.0000.0000.0000.000
154A159LEU0-0.045-0.01518.367-0.010-0.0100.0000.0000.0000.000
155A160TYR0-0.051-0.01320.2100.0320.0320.0000.0000.0000.000
156A161TRP00.025-0.00319.5380.0110.0110.0000.0000.0000.000
157A162SER00.0490.02715.174-0.038-0.0380.0000.0000.0000.000
158A163GLN0-0.127-0.04417.7830.0600.0600.0000.0000.0000.000
159A164PHE0-0.081-0.04019.7740.0430.0430.0000.0000.0000.000
160A165VAL0-0.038-0.02616.161-0.019-0.0190.0000.0000.0000.000
161A166ASP-1-0.719-0.82711.673-0.954-0.9540.0000.0000.0000.000
162A167GLY00.0280.00510.856-0.263-0.2630.0000.0000.0000.000
163A168TYR0-0.026-0.03011.2860.2380.2380.0000.0000.0000.000
164A169ARG10.7980.86811.2940.9840.9840.0000.0000.0000.000
165A170CYS0-0.077-0.01812.1370.2500.2500.0000.0000.0000.000
166A171ASP-1-0.809-0.92713.917-1.066-1.0660.0000.0000.0000.000
167A172VAL0-0.022-0.01316.7470.0610.0610.0000.0000.0000.000
168A173ALA00.0390.02612.8660.0880.0880.0000.0000.0000.000
169A174PRO0-0.055-0.02913.9800.1050.1050.0000.0000.0000.000
170A175LEU0-0.0070.01115.8740.1070.1070.0000.0000.0000.000
171A176VAL0-0.0250.00117.0880.0880.0880.0000.0000.0000.000
172A177PRO00.0250.01316.506-0.067-0.0670.0000.0000.0000.000
173A178LEU00.0240.00810.528-0.057-0.0570.0000.0000.0000.000
174A179ASP-1-0.857-0.94013.907-0.171-0.1710.0000.0000.0000.000
175A180PHE00.0140.02216.4570.0390.0390.0000.0000.0000.000
176A181TRP00.0470.00111.930-0.080-0.0800.0000.0000.0000.000
177A182LEU0-0.041-0.01410.473-0.011-0.0110.0000.0000.0000.000
178A183GLU-1-0.781-0.86713.0450.1530.1530.0000.0000.0000.000
179A184ALA00.0290.00614.8630.0290.0290.0000.0000.0000.000
180A185ARG10.8080.8805.4302.3732.3730.0000.0000.0000.000
181A186LYS10.7850.88012.901-0.056-0.0560.0000.0000.0000.000
182A187GLN0-0.064-0.04414.5140.0300.0300.0000.0000.0000.000
183A188VAL00.0470.02713.7470.0420.0420.0000.0000.0000.000
184A189ASN0-0.014-0.0169.103-0.031-0.0310.0000.0000.0000.000
185A190ALA0-0.038-0.01512.6720.1230.1230.0000.0000.0000.000
186A191LYS10.7940.89315.4050.0930.0930.0000.0000.0000.000
187A192TYR0-0.025-0.01214.0840.0420.0420.0000.0000.0000.000
188A193PRO00.0070.00210.263-0.138-0.1380.0000.0000.0000.000
189A194GLU-1-0.868-0.9397.862-0.973-0.9730.0000.0000.0000.000
190A195THR0-0.042-0.0077.912-0.445-0.4450.0000.0000.0000.000
191A196LEU0-0.022-0.0044.882-0.151-0.1510.0000.0000.0000.000
192A197TRP0-0.007-0.0146.6830.6030.6030.0000.0000.0000.000
193A198LEU0-0.042-0.0246.453-1.420-1.4200.0000.0000.0000.000
194A199ALA00.0320.0128.0180.7190.7190.0000.0000.0000.000
195A200GLU-1-0.827-0.90610.036-1.449-1.4490.0000.0000.0000.000
196A201SER0-0.012-0.03311.1310.1710.1710.0000.0000.0000.000
197A202ALA00.012-0.00312.9900.0880.0880.0000.0000.0000.000
198A203GLY00.0420.02516.029-0.015-0.0150.0000.0000.0000.000
199A204SER00.004-0.01418.4020.0330.0330.0000.0000.0000.000
200A205GLY00.0210.01319.6250.0390.0390.0000.0000.0000.000
201A206PHE00.0180.01120.1050.0320.0320.0000.0000.0000.000
202A207ILE0-0.0020.00215.7390.0250.0250.0000.0000.0000.000
203A208GLU-1-0.907-0.97020.100-0.286-0.2860.0000.0000.0000.000
204A209GLU-1-0.904-0.92523.102-0.280-0.2800.0000.0000.0000.000
205A210LEU0-0.020-0.01120.7320.0310.0310.0000.0000.0000.000
206A211ARG10.8260.90516.5980.4610.4610.0000.0000.0000.000
207A212SER0-0.105-0.05123.9250.0430.0430.0000.0000.0000.000
208A213GLN0-0.074-0.04627.3200.0440.0440.0000.0000.0000.000
209A214GLY0-0.034-0.00726.7150.0110.0110.0000.0000.0000.000
210A215TYR0-0.018-0.01124.0950.0050.0050.0000.0000.0000.000
211A216THR0-0.025-0.01718.4010.0220.0220.0000.0000.0000.000
212A217GLY00.1000.03518.538-0.036-0.0360.0000.0000.0000.000
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