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: K23V3

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 OptHSide
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 -8026931.253837
FMO2-HF: Nuclear repulsion 7859351.234323
FMO2-HF: Total energy -167580.019514
FMO2-MP2: Total energy -168073.787453


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.
-48.518-44.97723.083-10.749-15.872-0.012
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 : 0.058 / q_NPA : 0.022
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].
3A8GLN0-0.023-0.0212.896-4.277-1.2320.026-1.376-1.6950.003
4A9LEU00.1040.0672.746-1.0330.0980.294-0.352-1.073-0.001
5A10ARG10.7660.8735.3341.7661.7660.0000.0000.0000.000
6A11ASN0-0.103-0.0567.8120.7910.7910.0000.0000.0000.000
7A12GLU-1-0.905-0.9507.025-2.602-2.6020.0000.0000.0000.000
8A13MET0-0.078-0.03510.499-0.015-0.0150.0000.0000.0000.000
9A14ILE00.0050.0069.8370.0180.0180.0000.0000.0000.000
10A15TYR00.007-0.03613.9130.1390.1390.0000.0000.0000.000
11A16SER0-0.040-0.00117.3500.0190.0190.0000.0000.0000.000
12A17VAL00.002-0.01518.8280.0960.0960.0000.0000.0000.000
13A18PHE00.0270.01122.116-0.026-0.0260.0000.0000.0000.000
14A19VAL0-0.009-0.01324.4470.0430.0430.0000.0000.0000.000
15A20ARG10.7800.88126.7980.4750.4750.0000.0000.0000.000
16A21ASN00.0360.01628.6950.0590.0590.0000.0000.0000.000
17A22TYR0-0.041-0.01925.2070.0010.0010.0000.0000.0000.000
18A23SER0-0.015-0.01728.7470.0270.0270.0000.0000.0000.000
19A24GLU-1-0.866-0.95432.075-0.319-0.3190.0000.0000.0000.000
20A25ALA0-0.046-0.02034.6290.0060.0060.0000.0000.0000.000
21A26GLY00.0000.01431.4060.0060.0060.0000.0000.0000.000
22A27ASN00.000-0.00130.917-0.018-0.0180.0000.0000.0000.000
23A28PHE00.0880.01125.203-0.023-0.0230.0000.0000.0000.000
24A29ALA0-0.0070.01328.269-0.014-0.0140.0000.0000.0000.000
25A30GLY0-0.0040.00330.5770.0060.0060.0000.0000.0000.000
26A31VAL00.0070.00023.987-0.009-0.0090.0000.0000.0000.000
27A32THR00.016-0.01926.199-0.020-0.0200.0000.0000.0000.000
28A33ALA0-0.062-0.02127.2180.0090.0090.0000.0000.0000.000
29A34ASP-1-0.808-0.87727.634-0.443-0.4430.0000.0000.0000.000
30A35LEU0-0.0070.00321.812-0.027-0.0270.0000.0000.0000.000
31A36GLN0-0.053-0.03423.304-0.015-0.0150.0000.0000.0000.000
32A37ARG10.8160.89324.5520.5290.5290.0000.0000.0000.000
33A38ILE00.0280.02019.901-0.023-0.0230.0000.0000.0000.000
34A39LYS10.8980.95216.4240.6800.6800.0000.0000.0000.000
35A40ASP-1-0.852-0.93320.227-0.433-0.4330.0000.0000.0000.000
36A41LEU0-0.066-0.01920.7750.0240.0240.0000.0000.0000.000
37A42GLY0-0.022-0.02418.342-0.006-0.0060.0000.0000.0000.000
38A43THR0-0.055-0.03616.052-0.113-0.1130.0000.0000.0000.000
39A44ASP-1-0.839-0.91211.401-1.163-1.1630.0000.0000.0000.000
40A45ILE0-0.019-0.0148.4730.0400.0400.0000.0000.0000.000
41A46LEU00.013-0.00113.1720.0220.0220.0000.0000.0000.000
42A47TRP0-0.017-0.01614.474-0.079-0.0790.0000.0000.0000.000
43A48LEU0-0.040-0.01916.4180.0990.0990.0000.0000.0000.000
44A49LEU00.007-0.00919.222-0.055-0.0550.0000.0000.0000.000
45A50PRO0-0.0160.00620.8500.0320.0320.0000.0000.0000.000
46A51ILE00.007-0.00422.6170.0480.0480.0000.0000.0000.000
47A52ASN0-0.050-0.00423.9530.0030.0030.0000.0000.0000.000
48A53PRO0-0.008-0.01027.102-0.004-0.0040.0000.0000.0000.000
49A54ILE00.0100.03128.803-0.012-0.0120.0000.0000.0000.000
50A55GLY00.0100.01330.9470.0260.0260.0000.0000.0000.000
51A56GLU-1-0.896-0.94032.977-0.269-0.2690.0000.0000.0000.000
52A57VAL0-0.038-0.02636.6200.0080.0080.0000.0000.0000.000
53A58ASN0-0.043-0.02935.161-0.014-0.0140.0000.0000.0000.000
54A59ARG10.8660.94234.1290.3080.3080.0000.0000.0000.000
55A60LYS10.8390.93829.7920.4390.4390.0000.0000.0000.000
56A61GLY00.0150.00533.932-0.016-0.0160.0000.0000.0000.000
57A62THR0-0.082-0.08636.2930.0070.0070.0000.0000.0000.000
58A63LEU0-0.057-0.03733.5230.0130.0130.0000.0000.0000.000
59A64GLY00.0520.03832.447-0.005-0.0050.0000.0000.0000.000
60A65SER00.0380.02426.625-0.027-0.0270.0000.0000.0000.000
61A66PRO0-0.003-0.01524.6830.0140.0140.0000.0000.0000.000
62A67TYR0-0.036-0.04419.6430.0070.0070.0000.0000.0000.000
63A68ALA0-0.0020.00424.6490.0030.0030.0000.0000.0000.000
64A69ILE0-0.0040.00023.2310.0300.0300.0000.0000.0000.000
65A70LYS10.8120.89027.5750.2850.2850.0000.0000.0000.000
66A71ASP-1-0.819-0.93029.173-0.314-0.3140.0000.0000.0000.000
67A72TYR00.014-0.00423.487-0.007-0.0070.0000.0000.0000.000
68A73ARG10.8480.92124.9230.2720.2720.0000.0000.0000.000
69A74GLY00.0390.04527.1080.0190.0190.0000.0000.0000.000
70A75ILE0-0.036-0.02826.501-0.039-0.0390.0000.0000.0000.000
71A76ASN00.001-0.01528.6770.0600.0600.0000.0000.0000.000
72A77PRO00.0370.01130.543-0.002-0.0020.0000.0000.0000.000
73A78GLU-1-0.804-0.87731.801-0.397-0.3970.0000.0000.0000.000
74A79TYR0-0.045-0.03026.0320.0060.0060.0000.0000.0000.000
75A80GLY00.0180.02230.946-0.002-0.0020.0000.0000.0000.000
76A81THR0-0.042-0.06232.4520.0060.0060.0000.0000.0000.000
77A82LEU00.0550.01627.197-0.018-0.0180.0000.0000.0000.000
78A83ALA00.0040.00628.738-0.017-0.0170.0000.0000.0000.000
79A84ASP-1-0.844-0.89429.763-0.314-0.3140.0000.0000.0000.000
80A85PHE00.0060.00621.192-0.017-0.0170.0000.0000.0000.000
81A86LYS10.8910.91824.8700.2980.2980.0000.0000.0000.000
82A87ALA0-0.005-0.00425.552-0.004-0.0040.0000.0000.0000.000
83A88LEU0-0.0220.00122.249-0.005-0.0050.0000.0000.0000.000
84A89THR00.0420.00920.698-0.022-0.0220.0000.0000.0000.000
85A90ASP-1-0.887-0.91321.210-0.369-0.3690.0000.0000.0000.000
86A91ARG10.9350.98223.2420.3750.3750.0000.0000.0000.000
87A92ALA00.028-0.00219.1240.0040.0040.0000.0000.0000.000
88A93HIS10.8260.89016.3770.6270.6270.0000.0000.0000.000
89A94GLU-1-0.976-0.96619.541-0.260-0.2600.0000.0000.0000.000
90A95LEU0-0.094-0.04921.1370.0310.0310.0000.0000.0000.000
91A96GLY0-0.0080.00217.207-0.011-0.0110.0000.0000.0000.000
92A97MET0-0.097-0.03015.277-0.085-0.0850.0000.0000.0000.000
93A98LYS10.8250.9089.7541.2291.2290.0000.0000.0000.000
94A99VAL00.0210.00114.100-0.042-0.0420.0000.0000.0000.000
95A100MET0-0.037-0.0019.497-0.037-0.0370.0000.0000.0000.000
96A101LEU00.0140.00514.7800.1050.1050.0000.0000.0000.000
97A102ASP-1-0.704-0.84115.913-1.335-1.3350.0000.0000.0000.000
98A103ILE0-0.033-0.01415.8880.1230.1230.0000.0000.0000.000
99A104VAL00.0100.00417.558-0.076-0.0760.0000.0000.0000.000
100A105TYR0-0.022-0.03318.1460.0620.0620.0000.0000.0000.000
101A106ASN00.0270.02620.4230.0600.0600.0000.0000.0000.000
102A107HIS00.0490.04621.7910.0660.0660.0000.0000.0000.000
103A108THR00.0230.03024.757-0.026-0.0260.0000.0000.0000.000
104A109SER0-0.020-0.02327.5550.0040.0040.0000.0000.0000.000
105A110PRO0-0.002-0.00530.7440.0080.0080.0000.0000.0000.000
106A111ASP-1-0.768-0.86033.815-0.284-0.2840.0000.0000.0000.000
107A112SER0-0.014-0.01130.2620.0150.0150.0000.0000.0000.000
108A113VAL00.0460.01731.1390.0170.0170.0000.0000.0000.000
109A114LEU00.0040.00226.5530.0190.0190.0000.0000.0000.000
110A115ALA00.0180.03131.0930.0180.0180.0000.0000.0000.000
111A116THR0-0.086-0.05133.2340.0210.0210.0000.0000.0000.000
112A117GLU-1-0.989-0.99733.959-0.188-0.1880.0000.0000.0000.000
113A118HIS10.7840.87831.4250.2030.2030.0000.0000.0000.000
114A119PRO00.0620.04132.238-0.013-0.0130.0000.0000.0000.000
115A120GLU-1-0.824-0.90432.726-0.179-0.1790.0000.0000.0000.000
116A121TRP0-0.025-0.01728.223-0.008-0.0080.0000.0000.0000.000
117A122PHE0-0.0180.00428.408-0.030-0.0300.0000.0000.0000.000
118A123TYR0-0.062-0.03325.6130.0110.0110.0000.0000.0000.000
119A124HIS0-0.041-0.04031.031-0.004-0.0040.0000.0000.0000.000
120A125ASP-1-0.887-0.95134.762-0.201-0.2010.0000.0000.0000.000
121A126ALA0-0.029-0.01936.6090.0100.0100.0000.0000.0000.000
122A127ASP-1-0.965-0.98440.219-0.144-0.1440.0000.0000.0000.000
123A128GLY0-0.041-0.01738.8640.0050.0050.0000.0000.0000.000
124A129GLN0-0.077-0.02338.283-0.008-0.0080.0000.0000.0000.000
125A130LEU00.0430.02932.767-0.006-0.0060.0000.0000.0000.000
126A131THR00.012-0.00531.339-0.004-0.0040.0000.0000.0000.000
127A132ASN0-0.030-0.01329.361-0.004-0.0040.0000.0000.0000.000
128A133LYS10.8800.94423.1050.4840.4840.0000.0000.0000.000
129A134VAL0-0.0290.00624.9710.0070.0070.0000.0000.0000.000
130A135GLY00.0170.00428.3310.0090.0090.0000.0000.0000.000
131A136ASP-1-0.883-0.95928.997-0.413-0.4130.0000.0000.0000.000
132A137TRP00.0180.01922.056-0.002-0.0020.0000.0000.0000.000
133A138SER00.0460.01629.4990.0060.0060.0000.0000.0000.000
134A139ASP-1-0.893-0.95529.963-0.417-0.4170.0000.0000.0000.000
135A140VAL0-0.043-0.01926.5970.0010.0010.0000.0000.0000.000
136A141LYS10.7880.88529.2690.3420.3420.0000.0000.0000.000
137A142ASP-1-0.750-0.88126.161-0.449-0.4490.0000.0000.0000.000
138A143LEU0-0.033-0.01423.9210.0320.0320.0000.0000.0000.000
139A144ASP-1-0.804-0.90925.156-0.261-0.2610.0000.0000.0000.000
140A145TYR0-0.063-0.06020.5690.0160.0160.0000.0000.0000.000
141A146GLY00.0100.01423.5460.0230.0230.0000.0000.0000.000
142A147HIS0-0.057-0.01625.9570.0430.0430.0000.0000.0000.000
143A148HIS0-0.013-0.01721.9480.0000.0000.0000.0000.0000.000
144A149GLU-1-0.926-0.97325.082-0.120-0.1200.0000.0000.0000.000
145A150LEU00.0040.02223.878-0.010-0.0100.0000.0000.0000.000
146A151TRP0-0.025-0.02719.108-0.036-0.0360.0000.0000.0000.000
147A152GLN0-0.005-0.01621.934-0.012-0.0120.0000.0000.0000.000
148A153TYR00.0750.04623.9080.0020.0020.0000.0000.0000.000
149A154GLN00.0280.00020.530-0.002-0.0020.0000.0000.0000.000
150A155ILE00.0190.01418.137-0.066-0.0660.0000.0000.0000.000
151A156ASP-1-0.877-0.93220.312-0.211-0.2110.0000.0000.0000.000
152A157THR0-0.059-0.02622.1870.0100.0100.0000.0000.0000.000
153A158LEU0-0.0120.00716.450-0.017-0.0170.0000.0000.0000.000
154A159LEU0-0.024-0.00318.393-0.011-0.0110.0000.0000.0000.000
155A160TYR0-0.010-0.00220.2420.0260.0260.0000.0000.0000.000
156A161TRP00.0340.00719.7290.0160.0160.0000.0000.0000.000
157A162SER00.0320.02415.742-0.040-0.0400.0000.0000.0000.000
158A163GLN0-0.127-0.04218.2440.0520.0520.0000.0000.0000.000
159A164PHE0-0.083-0.04520.4050.0370.0370.0000.0000.0000.000
160A165VAL0-0.045-0.03016.548-0.018-0.0180.0000.0000.0000.000
161A166ASP-1-0.732-0.83312.252-0.838-0.8380.0000.0000.0000.000
162A167GLY00.0240.00311.270-0.200-0.2000.0000.0000.0000.000
163A168TYR0-0.044-0.03211.3550.2010.2010.0000.0000.0000.000
164A169ARG10.7800.85011.2480.9370.9370.0000.0000.0000.000
165A170CYS0-0.082-0.01512.2980.2550.2550.0000.0000.0000.000
166A171ASP-1-0.787-0.91114.074-1.066-1.0660.0000.0000.0000.000
167A172VAL0-0.014-0.01416.8710.0590.0590.0000.0000.0000.000
168A173ALA00.0360.02512.7980.0890.0890.0000.0000.0000.000
169A174PRO0-0.048-0.02514.0000.0980.0980.0000.0000.0000.000
170A175LEU0-0.0050.00815.4950.1160.1160.0000.0000.0000.000
171A176VAL0-0.0170.01116.7520.0940.0940.0000.0000.0000.000
172A177PRO00.0180.01116.177-0.076-0.0760.0000.0000.0000.000
173A178LEU00.0250.00510.582-0.038-0.0380.0000.0000.0000.000
174A179ASP-1-0.868-0.95113.928-0.202-0.2020.0000.0000.0000.000
175A180PHE00.0120.02416.3700.0450.0450.0000.0000.0000.000
176A181TRP00.050-0.00511.634-0.059-0.0590.0000.0000.0000.000
177A182LEU0-0.034-0.01510.2670.0060.0060.0000.0000.0000.000
178A183GLU-1-0.780-0.85912.7440.2290.2290.0000.0000.0000.000
179A184ALA00.013-0.00114.4210.0380.0380.0000.0000.0000.000
180A185ARG10.8240.8865.3801.9561.9560.0000.0000.0000.000
181A186LYS10.7920.88912.401-0.090-0.0900.0000.0000.0000.000
182A187GLN0-0.070-0.04914.2280.0350.0350.0000.0000.0000.000
183A188VAL00.0460.01513.8120.0410.0410.0000.0000.0000.000
184A189ASN00.0000.0029.315-0.088-0.0880.0000.0000.0000.000
185A190ALA0-0.052-0.01212.9580.1340.1340.0000.0000.0000.000
186A191LYS10.8290.92115.6600.0670.0670.0000.0000.0000.000
187A192TYR0-0.014-0.00814.6670.0390.0390.0000.0000.0000.000
188A193PRO00.0160.00910.717-0.121-0.1210.0000.0000.0000.000
189A194GLU-1-0.902-0.9568.708-0.859-0.8590.0000.0000.0000.000
190A195THR0-0.034-0.0018.525-0.354-0.3540.0000.0000.0000.000
191A196LEU0-0.018-0.0035.471-0.236-0.2360.0000.0000.0000.000
192A197TRP00.003-0.0026.6880.5900.5900.0000.0000.0000.000
193A198LEU0-0.043-0.0226.373-1.531-1.5310.0000.0000.0000.000
194A199ALA00.0440.0208.1630.6990.6990.0000.0000.0000.000
195A200GLU-1-0.865-0.92710.144-1.470-1.4700.0000.0000.0000.000
196A201SER0-0.026-0.03310.9860.1670.1670.0000.0000.0000.000
197A202ALA00.0180.01012.9380.1010.1010.0000.0000.0000.000
198A203GLY00.0350.02315.771-0.053-0.0530.0000.0000.0000.000
199A204SER00.019-0.01518.3970.0200.0200.0000.0000.0000.000
200A205GLY00.0040.00519.9330.0480.0480.0000.0000.0000.000
201A206PHE00.0280.01019.8950.0340.0340.0000.0000.0000.000
202A207ILE00.0070.00715.8840.0330.0330.0000.0000.0000.000
203A208GLU-1-0.919-0.96820.282-0.324-0.3240.0000.0000.0000.000
204A209GLU-1-0.915-0.94223.424-0.297-0.2970.0000.0000.0000.000
205A210LEU0-0.013-0.01120.7780.0290.0290.0000.0000.0000.000
206A211ARG10.8340.90416.8070.5040.5040.0000.0000.0000.000
207A212SER0-0.094-0.03323.9110.0460.0460.0000.0000.0000.000
208A213GLN0-0.068-0.04027.0770.0470.0470.0000.0000.0000.000
209A214GLY0-0.047-0.01726.8890.0130.0130.0000.0000.0000.000
210A215TYR0-0.010-0.00224.1410.0050.0050.0000.0000.0000.000
211A216THR0-0.015-0.01018.3630.0240.0240.0000.0000.0000.000
212A217GLY00.0780.02918.663-0.035-0.0350.0000.0000.0000.000
213A218LEU0-0.108-0.02113.0060.0320.0320.0000.0000.0000.000
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