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: LN4N9

Calculation Name: 3HU5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HU5

Chain ID: A

ChEMBL ID:

UniProt ID: Q72G28

Base Structure: X-ray

Registration Date: 2023-09-23

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 190
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1919192.819524
FMO2-HF: Nuclear repulsion 1847257.380934
FMO2-HF: Total energy -71935.43859
FMO2-MP2: Total energy -72137.654695


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:ASN)


Summations of interaction energy for fragment #1(A:6: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.
-20.953-16.1690.838-2.99-2.631-0.02
Interaction energy analysis for fragmet #1(A:6:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.020
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].
3A8THR0-0.034-0.0202.470-11.739-7.0050.839-2.985-2.588-0.020
4A9VAL00.0260.0084.8111.7851.835-0.001-0.005-0.0430.000
5A10ALA00.0090.0047.6570.3120.3120.0000.0000.0000.000
6A11LEU0-0.027-0.00411.2630.0510.0510.0000.0000.0000.000
7A12ALA00.0150.01314.5780.0940.0940.0000.0000.0000.000
8A13ILE0-0.021-0.00617.9550.0320.0320.0000.0000.0000.000
9A14ILE00.000-0.01521.0230.0210.0210.0000.0000.0000.000
10A15ASP-1-0.735-0.86623.968-0.445-0.4450.0000.0000.0000.000
11A16MET0-0.0420.01625.4450.0390.0390.0000.0000.0000.000
12A17GLN0-0.023-0.03327.948-0.016-0.0160.0000.0000.0000.000
13A18ASN00.019-0.00531.0160.0060.0060.0000.0000.0000.000
14A19ASP-1-0.797-0.91434.518-0.263-0.2630.0000.0000.0000.000
15A20PHE0-0.040-0.02431.7480.0140.0140.0000.0000.0000.000
16A21VAL0-0.033-0.01830.377-0.003-0.0030.0000.0000.0000.000
17A22LEU00.0120.01633.7390.0100.0100.0000.0000.0000.000
18A23PRO00.013-0.02036.9530.0060.0060.0000.0000.0000.000
19A24GLY0-0.018-0.00339.6470.0070.0070.0000.0000.0000.000
20A25ALA0-0.0060.02438.2150.0070.0070.0000.0000.0000.000
21A26PRO00.009-0.00640.0590.0000.0000.0000.0000.0000.000
22A27ALA0-0.025-0.01336.6830.0040.0040.0000.0000.0000.000
23A28CYS0-0.076-0.02236.135-0.018-0.0180.0000.0000.0000.000
24A29VAL0-0.047-0.01331.9490.0060.0060.0000.0000.0000.000
25A30GLU-1-0.770-0.85834.035-0.256-0.2560.0000.0000.0000.000
26A31GLY0-0.0080.00332.3340.0050.0050.0000.0000.0000.000
27A32ALA00.001-0.01130.017-0.012-0.0120.0000.0000.0000.000
28A33MET0-0.012-0.00530.069-0.010-0.0100.0000.0000.0000.000
29A34GLY0-0.021-0.00731.4660.0040.0040.0000.0000.0000.000
30A35THR00.0220.00626.1450.0040.0040.0000.0000.0000.000
31A36VAL00.0200.02325.955-0.038-0.0380.0000.0000.0000.000
32A37PRO00.018-0.00125.716-0.033-0.0330.0000.0000.0000.000
33A38VAL00.0070.01621.730-0.023-0.0230.0000.0000.0000.000
34A39ILE00.0060.00021.523-0.066-0.0660.0000.0000.0000.000
35A40ALA00.0270.01720.937-0.070-0.0700.0000.0000.0000.000
36A41GLY0-0.017-0.00420.868-0.028-0.0280.0000.0000.0000.000
37A42LEU0-0.003-0.00815.618-0.052-0.0520.0000.0000.0000.000
38A43LEU0-0.027-0.00716.334-0.140-0.1400.0000.0000.0000.000
39A44ALA0-0.030-0.01817.118-0.065-0.0650.0000.0000.0000.000
40A45LYS10.7800.87511.2431.1201.1200.0000.0000.0000.000
41A46ALA00.0110.00012.506-0.126-0.1260.0000.0000.0000.000
42A47ARG10.7550.83012.6170.5870.5870.0000.0000.0000.000
43A48ALA0-0.039-0.01214.271-0.008-0.0080.0000.0000.0000.000
44A49GLU-1-0.880-0.9299.129-1.335-1.3350.0000.0000.0000.000
45A50GLY0-0.0280.0018.668-0.536-0.5360.0000.0000.0000.000
46A51TRP00.0280.0037.641-0.105-0.1050.0000.0000.0000.000
47A52MET0-0.050-0.0139.8190.3130.3130.0000.0000.0000.000
48A53VAL00.0320.01012.168-0.025-0.0250.0000.0000.0000.000
49A54LEU0-0.015-0.01614.6960.0830.0830.0000.0000.0000.000
50A55HIS10.8350.91118.3120.7450.7450.0000.0000.0000.000
51A56VAL00.0220.01320.6870.0350.0350.0000.0000.0000.000
52A57VAL00.0040.00123.3240.0240.0240.0000.0000.0000.000
53A58ARG10.7760.83527.1090.3790.3790.0000.0000.0000.000
54A59ALA00.0390.00630.5530.0050.0050.0000.0000.0000.000
55A60HIS0-0.0470.00232.781-0.007-0.0070.0000.0000.0000.000
56A61ARG10.9150.93634.7000.2870.2870.0000.0000.0000.000
57A62ALA00.014-0.00938.6110.0030.0030.0000.0000.0000.000
58A63ASP-1-0.826-0.87741.726-0.212-0.2120.0000.0000.0000.000
59A64GLY00.0480.02140.9250.0070.0070.0000.0000.0000.000
60A65SER0-0.106-0.08340.739-0.009-0.0090.0000.0000.0000.000
61A66ASP-1-0.778-0.86935.404-0.296-0.2960.0000.0000.0000.000
62A67ALA00.0510.04335.824-0.021-0.0210.0000.0000.0000.000
63A68GLU-1-0.773-0.86933.391-0.329-0.3290.0000.0000.0000.000
64A69LYS10.9990.99237.5020.1960.1960.0000.0000.0000.000
65A70SER0-0.053-0.02438.7790.0080.0080.0000.0000.0000.000
66A71ARG10.8550.90233.6250.3070.3070.0000.0000.0000.000
67A72GLU-1-0.907-0.94840.970-0.197-0.1970.0000.0000.0000.000
68A73HIS00.008-0.00442.6290.0020.0020.0000.0000.0000.000
69A74LEU0-0.056-0.02640.6250.0060.0060.0000.0000.0000.000
70A75PHE0-0.0230.00738.407-0.004-0.0040.0000.0000.0000.000
71A76LEU0-0.027-0.00344.6610.0060.0060.0000.0000.0000.000
72A77GLU-1-0.969-0.98348.253-0.150-0.1500.0000.0000.0000.000
73A78GLY0-0.0080.01746.7720.0040.0040.0000.0000.0000.000
74A79GLY0-0.004-0.02043.861-0.001-0.0010.0000.0000.0000.000
75A80GLY00.0450.01041.080-0.003-0.0030.0000.0000.0000.000
76A81LEU0-0.074-0.03635.6530.0030.0030.0000.0000.0000.000
77A82CYS0-0.062-0.02633.228-0.013-0.0130.0000.0000.0000.000
78A83VAL0-0.0070.01934.884-0.012-0.0120.0000.0000.0000.000
79A84ALA00.0150.00234.772-0.005-0.0050.0000.0000.0000.000
80A85GLY0-0.023-0.00834.7260.0150.0150.0000.0000.0000.000
81A86THR0-0.044-0.02536.2030.0120.0120.0000.0000.0000.000
82A87PRO00.0710.01336.318-0.013-0.0130.0000.0000.0000.000
83A88GLY00.0320.03336.083-0.010-0.0100.0000.0000.0000.000
84A89ALA0-0.018-0.00933.209-0.015-0.0150.0000.0000.0000.000
85A90GLU-1-0.918-0.93831.758-0.315-0.3150.0000.0000.0000.000
86A91ILE0-0.046-0.03125.430-0.003-0.0030.0000.0000.0000.000
87A92VAL0-0.019-0.00728.7150.0170.0170.0000.0000.0000.000
88A93ALA00.0130.00028.889-0.024-0.0240.0000.0000.0000.000
89A94GLY0-0.035-0.01527.9220.0080.0080.0000.0000.0000.000
90A95LEU0-0.039-0.02323.419-0.040-0.0400.0000.0000.0000.000
91A96GLU-1-0.817-0.90724.452-0.452-0.4520.0000.0000.0000.000
92A97PRO0-0.036-0.02622.466-0.047-0.0470.0000.0000.0000.000
93A98ALA00.0030.01520.2880.0540.0540.0000.0000.0000.000
94A99SER0-0.024-0.03021.519-0.034-0.0340.0000.0000.0000.000
95A100GLY00.0190.01018.869-0.027-0.0270.0000.0000.0000.000
96A101GLU-1-0.747-0.81917.393-0.943-0.9430.0000.0000.0000.000
97A102THR0-0.030-0.01117.8660.0650.0650.0000.0000.0000.000
98A103VAL0-0.014-0.01019.642-0.013-0.0130.0000.0000.0000.000
99A104LEU0-0.021-0.00220.9280.0050.0050.0000.0000.0000.000
100A105VAL00.0180.01223.8090.0070.0070.0000.0000.0000.000
101A106LYS10.7860.87025.3890.4730.4730.0000.0000.0000.000
102A107THR00.0080.00028.0220.0140.0140.0000.0000.0000.000
103A108ARG10.8320.89929.8650.3420.3420.0000.0000.0000.000
104A109PHE00.048-0.01528.946-0.015-0.0150.0000.0000.0000.000
105A110SER0-0.042-0.05324.721-0.042-0.0420.0000.0000.0000.000
106A111ALA00.033-0.00121.5960.0280.0280.0000.0000.0000.000
107A112PHE00.0180.02017.779-0.021-0.0210.0000.0000.0000.000
108A113MET0-0.032-0.00723.5660.0430.0430.0000.0000.0000.000
109A114GLY0-0.041-0.02027.1330.0280.0280.0000.0000.0000.000
110A115THR0-0.036-0.02423.7530.0040.0040.0000.0000.0000.000
111A116GLU-1-0.873-0.94722.099-0.561-0.5610.0000.0000.0000.000
112A117CYS00.010-0.00218.386-0.075-0.0750.0000.0000.0000.000
113A118ASP-1-0.759-0.84817.626-0.982-0.9820.0000.0000.0000.000
114A119MET0-0.035-0.01616.904-0.069-0.0690.0000.0000.0000.000
115A120LEU0-0.019-0.01217.226-0.040-0.0400.0000.0000.0000.000
116A121LEU00.0220.00713.414-0.123-0.1230.0000.0000.0000.000
117A122ARG10.9100.94112.3820.5430.5430.0000.0000.0000.000
118A123ARG10.8680.94512.8490.7280.7280.0000.0000.0000.000
119A124ARG10.8500.9299.1212.4302.4300.0000.0000.0000.000
120A125GLY0-0.005-0.0028.658-0.420-0.4200.0000.0000.0000.000
121A126VAL0-0.058-0.0327.814-0.500-0.5000.0000.0000.0000.000
122A127ASP-1-0.763-0.8445.504-6.581-6.5810.0000.0000.0000.000
123A128THR0-0.014-0.0097.4530.5430.5430.0000.0000.0000.000
124A129LEU0-0.026-0.0159.730-0.087-0.0870.0000.0000.0000.000
125A130LEU00.0140.00811.4370.2480.2480.0000.0000.0000.000
126A131VAL0-0.018-0.01414.5670.0590.0590.0000.0000.0000.000
127A132SER00.011-0.02118.3480.0550.0550.0000.0000.0000.000
128A133GLY00.0260.00520.979-0.008-0.0080.0000.0000.0000.000
129A134THR00.021-0.00224.4600.0360.0360.0000.0000.0000.000
130A135GLN00.0020.00027.4580.0030.0030.0000.0000.0000.000
131A136TYR00.024-0.02924.451-0.013-0.0130.0000.0000.0000.000
132A137PRO0-0.044-0.01827.974-0.016-0.0160.0000.0000.0000.000
133A138ASN0-0.022-0.00129.9690.0120.0120.0000.0000.0000.000
134A139CYM-1-0.849-0.85927.178-0.445-0.4450.0000.0000.0000.000
135A140ILE0-0.0250.02823.250-0.046-0.0460.0000.0000.0000.000
136A141ARG10.8570.89223.6710.3100.3100.0000.0000.0000.000
137A142GLY0-0.007-0.00224.864-0.015-0.0150.0000.0000.0000.000
138A143THR00.015-0.00620.257-0.013-0.0130.0000.0000.0000.000
139A144ALA0-0.0010.00320.043-0.063-0.0630.0000.0000.0000.000
140A145VAL0-0.004-0.01320.508-0.036-0.0360.0000.0000.0000.000
141A146ASP-1-0.810-0.87022.401-0.526-0.5260.0000.0000.0000.000
142A147ALA0-0.021-0.01517.040-0.022-0.0220.0000.0000.0000.000
143A148PHE0-0.003-0.00817.019-0.050-0.0500.0000.0000.0000.000
144A149ALA0-0.053-0.01818.8900.0270.0270.0000.0000.0000.000
145A150LEU0-0.073-0.03918.3400.0600.0600.0000.0000.0000.000
146A151ASP-1-0.945-0.96014.964-0.741-0.7410.0000.0000.0000.000
147A152TYR0-0.096-0.05212.143-0.204-0.2040.0000.0000.0000.000
148A153ASP-1-0.825-0.8969.793-1.543-1.5430.0000.0000.0000.000
149A154VAL0-0.034-0.01112.380-0.199-0.1990.0000.0000.0000.000
150A155VAL0-0.034-0.02911.9400.1340.1340.0000.0000.0000.000
151A156VAL00.0180.00015.202-0.028-0.0280.0000.0000.0000.000
152A157VAL00.0520.01716.1940.0440.0440.0000.0000.0000.000
153A158THR0-0.004-0.00918.7950.0470.0470.0000.0000.0000.000
154A159ASP-1-0.834-0.91221.322-0.496-0.4960.0000.0000.0000.000
155A160ALA00.0070.00820.9190.0290.0290.0000.0000.0000.000
156A161CYS0-0.048-0.00221.956-0.041-0.0410.0000.0000.0000.000
157A162SER00.0140.01624.9050.0310.0310.0000.0000.0000.000
158A163ALA0-0.018-0.02328.761-0.010-0.0100.0000.0000.0000.000
159A164ARG10.8900.90031.8070.2440.2440.0000.0000.0000.000
160A165THR0-0.006-0.00234.7410.0120.0120.0000.0000.0000.000
161A166PRO00.0540.02532.534-0.015-0.0150.0000.0000.0000.000
162A167GLY00.0920.05632.190-0.013-0.0130.0000.0000.0000.000
163A168VAL0-0.0080.01332.456-0.005-0.0050.0000.0000.0000.000
164A169ALA00.0170.02028.462-0.020-0.0200.0000.0000.0000.000
165A170GLU-1-0.925-0.97428.505-0.252-0.2520.0000.0000.0000.000
166A171SER0-0.039-0.03728.925-0.009-0.0090.0000.0000.0000.000
167A172ASN00.0200.00127.603-0.013-0.0130.0000.0000.0000.000
168A173ILE0-0.0020.00723.644-0.027-0.0270.0000.0000.0000.000
169A174ASN0-0.009-0.01524.456-0.028-0.0280.0000.0000.0000.000
170A175ASP-1-0.796-0.87126.318-0.288-0.2880.0000.0000.0000.000
171A176MET0-0.023-0.01222.205-0.022-0.0220.0000.0000.0000.000
172A177ARG10.8620.92421.4260.3600.3600.0000.0000.0000.000
173A178ALA0-0.045-0.01622.4510.0060.0060.0000.0000.0000.000
174A179MET0-0.072-0.02822.9030.0080.0080.0000.0000.0000.000
175A180GLY00.0240.02219.498-0.004-0.0040.0000.0000.0000.000
176A181ILE0-0.0070.01017.769-0.066-0.0660.0000.0000.0000.000
177A182THR00.0120.02214.6060.1050.1050.0000.0000.0000.000
178A183CYS0-0.027-0.00817.076-0.063-0.0630.0000.0000.0000.000
179A184VAL0-0.014-0.00815.7390.0930.0930.0000.0000.0000.000
180A185PRO00.0160.01118.957-0.054-0.0540.0000.0000.0000.000
181A186LEU00.0510.01616.533-0.043-0.0430.0000.0000.0000.000
182A187THR0-0.054-0.03816.719-0.049-0.0490.0000.0000.0000.000
183A188ALA00.0130.01116.1390.0580.0580.0000.0000.0000.000
184A189LEU00.0010.00712.094-0.017-0.0170.0000.0000.0000.000
185A190ASP-1-0.799-0.90210.238-1.215-1.2150.0000.0000.0000.000
186A191ASP-1-0.905-0.9489.595-0.258-0.2580.0000.0000.0000.000
187A192VAL0-0.088-0.04810.9820.0810.0810.0000.0000.0000.000
188A193LEU0-0.010-0.0106.733-0.150-0.1500.0000.0000.0000.000
189A194ALA0-0.0130.0005.638-0.459-0.4590.0000.0000.0000.000
190A195ARG10.8820.9616.2270.8070.8070.0000.0000.0000.000