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: 7MGZK

Calculation Name: 3HD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W2Q0

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 OptH
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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1797420.627568
FMO2-HF: Nuclear repulsion 1726650.519675
FMO2-HF: Total energy -70770.107893
FMO2-MP2: Total energy -70975.78518


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:28:GLN)


Summations of interaction energy for fragment #1(A:28: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.
-4.160.940.718-2.358-3.460.011
Interaction energy analysis for fragmet #1(A:28:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / 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].
3A30ALA0-0.0070.0022.729-6.302-2.9180.640-1.815-2.2100.013
4A31GLN00.0350.0044.5061.0451.216-0.001-0.019-0.1510.000
5A32GLN0-0.029-0.0024.5002.1402.3270.000-0.011-0.1740.000
6A33TYR0-0.072-0.0318.009-0.568-0.5680.0000.0000.0000.000
7A34VAL00.0200.02811.7000.1040.1040.0000.0000.0000.000
8A35ASN00.010-0.01914.5590.0080.0080.0000.0000.0000.000
9A36ILE0-0.0180.01217.838-0.051-0.0510.0000.0000.0000.000
10A37ASN0-0.068-0.01821.0360.0340.0340.0000.0000.0000.000
11A38PRO00.007-0.02224.139-0.023-0.0230.0000.0000.0000.000
12A39PRO00.0050.01024.5560.0090.0090.0000.0000.0000.000
13A40MET0-0.012-0.00724.705-0.028-0.0280.0000.0000.0000.000
14A41PRO0-0.042-0.01926.8650.0270.0270.0000.0000.0000.000
15A42SER00.009-0.01028.264-0.014-0.0140.0000.0000.0000.000
16A43ASP-1-0.859-0.91129.5610.2840.2840.0000.0000.0000.000
17A44THR0-0.070-0.02830.963-0.030-0.0300.0000.0000.0000.000
18A45PRO00.018-0.00331.9690.0200.0200.0000.0000.0000.000
19A46GLY0-0.018-0.01732.774-0.007-0.0070.0000.0000.0000.000
20A47LYS10.8800.95729.245-0.340-0.3400.0000.0000.0000.000
21A48ILE00.0150.01922.9520.0010.0010.0000.0000.0000.000
22A49GLU-1-0.819-0.93325.6830.3820.3820.0000.0000.0000.000
23A50VAL00.0060.00720.3230.0530.0530.0000.0000.0000.000
24A51LEU0-0.033-0.02122.382-0.054-0.0540.0000.0000.0000.000
25A52GLU-1-0.811-0.91220.5650.4300.4300.0000.0000.0000.000
26A53PHE0-0.010-0.01221.344-0.058-0.0580.0000.0000.0000.000
27A54PHE00.048-0.00521.8780.0030.0030.0000.0000.0000.000
28A55ALA00.0520.00824.146-0.016-0.0160.0000.0000.0000.000
29A56TYR00.010-0.03326.121-0.007-0.0070.0000.0000.0000.000
30A57THR0-0.004-0.00428.465-0.004-0.0040.0000.0000.0000.000
31A58CYS0-0.0720.02322.006-0.013-0.0130.0000.0000.0000.000
32A59PRO00.0430.00722.3570.0130.0130.0000.0000.0000.000
33A60HIS00.0650.01318.2130.0130.0130.0000.0000.0000.000
34A61CYS0-0.0290.00220.2460.0400.0400.0000.0000.0000.000
35A62ALA00.0270.01522.1390.0110.0110.0000.0000.0000.000
36A63ALA0-0.039-0.02520.4250.0020.0020.0000.0000.0000.000
37A64ILE0-0.013-0.00216.5260.0090.0090.0000.0000.0000.000
38A65GLU-1-0.789-0.88120.3630.3060.3060.0000.0000.0000.000
39A66PRO0-0.004-0.00323.3650.0170.0170.0000.0000.0000.000
40A67MET0-0.015-0.00917.3490.0270.0270.0000.0000.0000.000
41A68VAL0-0.018-0.00319.9920.0520.0520.0000.0000.0000.000
42A69GLU-1-0.920-0.97721.8180.2540.2540.0000.0000.0000.000
43A70ASP-1-0.994-0.99823.2000.3360.3360.0000.0000.0000.000
44A71TRP00.0010.00318.6650.0050.0050.0000.0000.0000.000
45A72ALA0-0.005-0.01822.2220.0180.0180.0000.0000.0000.000
46A73LYS10.8780.95124.932-0.268-0.2680.0000.0000.0000.000
47A74THR0-0.063-0.02723.568-0.001-0.0010.0000.0000.0000.000
48A75ALA00.0060.02623.2030.0350.0350.0000.0000.0000.000
49A76PRO0-0.001-0.01122.174-0.032-0.0320.0000.0000.0000.000
50A77GLN00.0600.02425.237-0.034-0.0340.0000.0000.0000.000
51A78ASP-1-0.948-0.96726.3470.4940.4940.0000.0000.0000.000
52A79VAL0-0.030-0.01323.0210.0170.0170.0000.0000.0000.000
53A80VAL0-0.031-0.00326.198-0.030-0.0300.0000.0000.0000.000
54A81LEU00.0180.00422.8330.0300.0300.0000.0000.0000.000
55A82LYS10.8780.95125.583-0.368-0.3680.0000.0000.0000.000
56A83GLN0-0.052-0.02324.7700.0070.0070.0000.0000.0000.000
57A84VAL0-0.035-0.02425.946-0.026-0.0260.0000.0000.0000.000
58A85PRO0-0.0190.02626.4280.0090.0090.0000.0000.0000.000
59A86ILE00.0350.01824.492-0.006-0.0060.0000.0000.0000.000
60A87ALA0-0.017-0.03227.771-0.019-0.0190.0000.0000.0000.000
61A88PHE00.0210.00422.604-0.009-0.0090.0000.0000.0000.000
62A89ASN00.006-0.00328.491-0.015-0.0150.0000.0000.0000.000
63A90ALA00.0580.01432.0410.0060.0060.0000.0000.0000.000
64A91GLY00.0210.01635.0360.0030.0030.0000.0000.0000.000
65A92MET0-0.0150.02226.817-0.005-0.0050.0000.0000.0000.000
66A93LYS10.9760.99732.574-0.117-0.1170.0000.0000.0000.000
67A94PRO0-0.013-0.00634.7920.0080.0080.0000.0000.0000.000
68A95LEU00.0130.00031.7320.0020.0020.0000.0000.0000.000
69A96GLN0-0.028-0.02930.685-0.006-0.0060.0000.0000.0000.000
70A97GLN0-0.022-0.02433.1870.0030.0030.0000.0000.0000.000
71A98LEU0-0.006-0.00234.6650.0000.0000.0000.0000.0000.000
72A99TYR00.0210.02330.809-0.001-0.0010.0000.0000.0000.000
73A100TYR00.046-0.00331.6330.0030.0030.0000.0000.0000.000
74A101THR00.0080.01036.289-0.005-0.0050.0000.0000.0000.000
75A102LEU0-0.024-0.01535.200-0.006-0.0060.0000.0000.0000.000
76A103GLN00.0170.01233.288-0.005-0.0050.0000.0000.0000.000
77A104ALA00.0000.01437.629-0.002-0.0020.0000.0000.0000.000
78A105LEU0-0.129-0.07040.939-0.007-0.0070.0000.0000.0000.000
79A106GLU-1-0.938-0.95940.3100.1410.1410.0000.0000.0000.000
80A107ARG10.7820.86639.659-0.121-0.1210.0000.0000.0000.000
81A108PRO00.0320.02234.877-0.001-0.0010.0000.0000.0000.000
82A109ASP-1-0.786-0.87234.5000.1360.1360.0000.0000.0000.000
83A110LEU0-0.041-0.03935.493-0.004-0.0040.0000.0000.0000.000
84A111HIS00.0630.06228.194-0.028-0.0280.0000.0000.0000.000
85A112PRO00.0710.04429.776-0.006-0.0060.0000.0000.0000.000
86A113LYS10.9310.95430.860-0.124-0.1240.0000.0000.0000.000
87A114VAL0-0.0020.01932.018-0.015-0.0150.0000.0000.0000.000
88A115PHE00.0000.00826.188-0.019-0.0190.0000.0000.0000.000
89A116THR0-0.007-0.00229.889-0.015-0.0150.0000.0000.0000.000
90A117ALA00.0410.01731.564-0.015-0.0150.0000.0000.0000.000
91A118ILE0-0.039-0.01230.558-0.013-0.0130.0000.0000.0000.000
92A119HIS0-0.064-0.05027.009-0.029-0.0290.0000.0000.0000.000
93A120THR0-0.037-0.01630.055-0.015-0.0150.0000.0000.0000.000
94A121GLU-1-0.924-0.95731.9570.0530.0530.0000.0000.0000.000
95A122ARG10.8600.94429.309-0.017-0.0170.0000.0000.0000.000
96A123LYS10.9270.96834.895-0.057-0.0570.0000.0000.0000.000
97A124ARG10.9460.96035.651-0.004-0.0040.0000.0000.0000.000
98A125LEU00.0070.01435.693-0.001-0.0010.0000.0000.0000.000
99A126PHE00.013-0.01232.8270.0060.0060.0000.0000.0000.000
100A127ASP-1-0.839-0.91636.6980.0580.0580.0000.0000.0000.000
101A128LYS10.8650.92740.002-0.082-0.0820.0000.0000.0000.000
102A129LYS10.9030.97442.182-0.044-0.0440.0000.0000.0000.000
103A130ALA00.0280.01340.5170.0000.0000.0000.0000.0000.000
104A131MET0-0.049-0.01336.4880.0030.0030.0000.0000.0000.000
105A132GLY00.0540.02140.6030.0030.0030.0000.0000.0000.000
106A133GLU-1-0.970-0.99244.0240.0460.0460.0000.0000.0000.000
107A134TRP00.0190.01236.575-0.001-0.0010.0000.0000.0000.000
108A135ALA00.0420.05541.7420.0010.0010.0000.0000.0000.000
109A136ALA00.0210.00242.5680.0010.0010.0000.0000.0000.000
110A137SER0-0.159-0.11042.867-0.001-0.0010.0000.0000.0000.000
111A138GLN0-0.017-0.01440.0490.0040.0040.0000.0000.0000.000
112A139GLY00.0100.00943.3190.0050.0050.0000.0000.0000.000
113A140VAL0-0.060-0.01742.5050.0040.0040.0000.0000.0000.000
114A141ASP-1-0.817-0.90645.9060.0700.0700.0000.0000.0000.000
115A142ARG10.9140.95847.167-0.060-0.0600.0000.0000.0000.000
116A143ALA00.0480.03248.4690.0020.0020.0000.0000.0000.000
117A144LYS10.9260.95547.017-0.102-0.1020.0000.0000.0000.000
118A145PHE00.012-0.00240.4760.0050.0050.0000.0000.0000.000
119A146ASP-1-0.859-0.95744.9810.0770.0770.0000.0000.0000.000
120A147SER0-0.029-0.00446.8340.0020.0020.0000.0000.0000.000
121A148VAL00.024-0.00442.6720.0030.0030.0000.0000.0000.000
122A149PHE00.0200.01639.0930.0060.0060.0000.0000.0000.000
123A150ASP-1-0.878-0.92642.2060.0940.0940.0000.0000.0000.000
124A151SER0-0.049-0.01843.2510.0020.0020.0000.0000.0000.000
125A152PHE00.0670.01543.3950.0050.0050.0000.0000.0000.000
126A153SER00.0030.02540.9600.0080.0080.0000.0000.0000.000
127A154VAL00.0270.02638.3890.0110.0110.0000.0000.0000.000
128A155GLN00.001-0.00438.4250.0050.0050.0000.0000.0000.000
129A156THR0-0.024-0.03538.8390.0050.0050.0000.0000.0000.000
130A157GLN00.002-0.01535.4550.0000.0000.0000.0000.0000.000
131A158VAL00.0060.01234.3310.0120.0120.0000.0000.0000.000
132A159GLN0-0.059-0.03133.8520.0000.0000.0000.0000.0000.000
133A160ARG10.8490.90432.272-0.274-0.2740.0000.0000.0000.000
134A161ALA00.0290.01930.1730.0190.0190.0000.0000.0000.000
135A162SER00.0380.00629.1760.0180.0180.0000.0000.0000.000
136A163GLN0-0.0040.01929.5590.0120.0120.0000.0000.0000.000
137A164LEU0-0.038-0.02327.4240.0150.0150.0000.0000.0000.000
138A165ALA00.008-0.00525.1340.0290.0290.0000.0000.0000.000
139A166GLU-1-0.952-0.98424.8790.2830.2830.0000.0000.0000.000
140A167ALA0-0.029-0.00126.0470.0160.0160.0000.0000.0000.000
141A168ALA0-0.049-0.02721.8500.0280.0280.0000.0000.0000.000
142A169HIS0-0.029-0.01121.2670.0430.0430.0000.0000.0000.000
143A170ILE0-0.044-0.01419.9460.0370.0370.0000.0000.0000.000
144A171ASP-1-0.907-0.95518.1830.3820.3820.0000.0000.0000.000
145A172GLY0-0.010-0.01618.841-0.053-0.0530.0000.0000.0000.000
146A173THR0-0.095-0.01219.5000.0350.0350.0000.0000.0000.000
147A174PRO00.033-0.03917.073-0.044-0.0440.0000.0000.0000.000
148A175ALA00.009-0.00717.0860.0450.0450.0000.0000.0000.000
149A176PHE00.0000.00416.074-0.051-0.0510.0000.0000.0000.000
150A177ALA00.0310.03217.6780.0800.0800.0000.0000.0000.000
151A178VAL0-0.007-0.01917.254-0.042-0.0420.0000.0000.0000.000
152A179GLY00.0350.00720.0940.0320.0320.0000.0000.0000.000
153A180GLY0-0.031-0.00722.809-0.015-0.0150.0000.0000.0000.000
154A181ARG10.9320.97120.327-0.734-0.7340.0000.0000.0000.000
155A182TYR00.0040.00615.8540.0330.0330.0000.0000.0000.000
156A183MET00.0610.05016.242-0.055-0.0550.0000.0000.0000.000
157A184THR00.008-0.02111.3270.1290.1290.0000.0000.0000.000
158A185SER00.0650.02612.239-0.155-0.1550.0000.0000.0000.000
159A186PRO00.0610.02411.2460.1940.1940.0000.0000.0000.000
160A187VAL00.0350.0149.7230.1100.1100.0000.0000.0000.000
161A188LEU00.0090.0148.9410.0520.0520.0000.0000.0000.000
162A189ALA0-0.027-0.0067.1480.8730.8730.0000.0000.0000.000
163A190GLY00.0270.0205.0830.3050.3050.0000.0000.0000.000
164A191ASN0-0.026-0.0206.053-0.532-0.5320.0000.0000.0000.000
165A192ASP-1-0.881-0.9539.218-0.346-0.3460.0000.0000.0000.000
166A193TYR0-0.058-0.0323.151-1.479-0.1210.079-0.513-0.925-0.002
167A194ALA0-0.065-0.0297.860-0.072-0.0720.0000.0000.0000.000
168A195GLY00.0090.00711.0680.0650.0650.0000.0000.0000.000
169A196ALA00.0480.01713.155-0.111-0.1110.0000.0000.0000.000
170A197LEU00.0440.0197.357-0.041-0.0410.0000.0000.0000.000
171A198LYS10.9721.00610.7510.4200.4200.0000.0000.0000.000
172A199VAL0-0.002-0.01211.7120.0180.0180.0000.0000.0000.000
173A200VAL0-0.010-0.00512.7090.0520.0520.0000.0000.0000.000
174A201ASP-1-0.897-0.9469.785-2.184-2.1840.0000.0000.0000.000
175A202GLN0-0.058-0.04513.3180.0940.0940.0000.0000.0000.000
176A203LEU0-0.011-0.00516.5030.0760.0760.0000.0000.0000.000
177A204ILE0-0.030-0.00513.7580.0530.0530.0000.0000.0000.000
178A205VAL0-0.064-0.03516.3210.0380.0380.0000.0000.0000.000
179A206GLN00.0490.02418.8760.0460.0460.0000.0000.0000.000
180A207SER0-0.083-0.03020.6220.0400.0400.0000.0000.0000.000
181A208ARG10.9010.95916.1751.0391.0390.0000.0000.0000.000
182A209GLU-1-1.002-0.98922.811-0.460-0.4600.0000.0000.0000.000