Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: K31G3

Calculation Name: 1HYQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HYQ

Chain ID: A

ChEMBL ID:

UniProt ID: O29562

Base Structure: X-ray

Registration Date: 2023-06-21

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2615417.494921
FMO2-HF: Nuclear repulsion 2531903.694771
FMO2-HF: Total energy -83513.80015
FMO2-MP2: Total energy -83760.895035


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-17.357-8.5893.634-5.103-7.3-0.048
Interaction energy analysis for fragmet #1(A:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.001
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].
3A4THR00.0380.0213.701-0.4081.461-0.013-0.765-1.0920.003
4A5ILE0-0.028-0.0196.267-0.551-0.5510.0000.0000.0000.000
5A6THR00.0140.0009.6710.0380.0380.0000.0000.0000.000
6A7VAL0-0.026-0.00912.887-0.068-0.0680.0000.0000.0000.000
7A8ALA00.0360.00715.6600.0000.0000.0000.0000.0000.000
8A9SER0-0.019-0.01418.995-0.020-0.0200.0000.0000.0000.000
9A10GLY00.0300.02022.6460.0050.0050.0000.0000.0000.000
10A11LYS10.8320.90326.037-0.066-0.0660.0000.0000.0000.000
11A12GLY00.0890.03326.5150.0070.0070.0000.0000.0000.000
12A13GLY0-0.0170.00727.2940.0010.0010.0000.0000.0000.000
13A14THR00.0430.02424.290-0.008-0.0080.0000.0000.0000.000
14A15GLY00.015-0.00124.995-0.008-0.0080.0000.0000.0000.000
15A16LYS10.8350.92519.300-0.190-0.1900.0000.0000.0000.000
16A17THR00.0610.02819.4350.0000.0000.0000.0000.0000.000
17A18THR0-0.027-0.01119.632-0.004-0.0040.0000.0000.0000.000
18A19ILE0-0.026-0.00917.685-0.013-0.0130.0000.0000.0000.000
19A20THR00.019-0.02614.121-0.013-0.0130.0000.0000.0000.000
20A21ALA00.0280.02315.161-0.007-0.0070.0000.0000.0000.000
21A22ASN0-0.060-0.05316.649-0.035-0.0350.0000.0000.0000.000
22A23LEU00.0230.03512.973-0.027-0.0270.0000.0000.0000.000
23A24GLY00.0870.03412.206-0.030-0.0300.0000.0000.0000.000
24A25VAL0-0.011-0.02113.194-0.055-0.0550.0000.0000.0000.000
25A26ALA0-0.069-0.04315.934-0.028-0.0280.0000.0000.0000.000
26A27LEU00.005-0.0059.289-0.019-0.0190.0000.0000.0000.000
27A28ALA00.0530.03711.975-0.058-0.0580.0000.0000.0000.000
28A29GLN0-0.082-0.03812.970-0.028-0.0280.0000.0000.0000.000
29A30LEU0-0.103-0.04013.0170.0070.0070.0000.0000.0000.000
30A31GLY0-0.042-0.02612.631-0.013-0.0130.0000.0000.0000.000
31A32HIS0-0.035-0.0057.736-0.149-0.1490.0000.0000.0000.000
32A33ASP-1-0.775-0.8636.874-0.679-0.6790.0000.0000.0000.000
33A34VAL0-0.036-0.0396.541-0.200-0.2000.0000.0000.0000.000
34A35THR00.0380.0037.665-0.058-0.0580.0000.0000.0000.000
35A36ILE0-0.048-0.0168.9720.2190.2190.0000.0000.0000.000
36A37VAL00.0280.01610.629-0.059-0.0590.0000.0000.0000.000
37A38ASP-1-0.825-0.93013.1900.1820.1820.0000.0000.0000.000
38A39ALA0-0.007-0.01516.087-0.017-0.0170.0000.0000.0000.000
39A40ASP-1-0.893-0.95117.8570.1410.1410.0000.0000.0000.000
40A41ILE0-0.0290.00121.030-0.015-0.0150.0000.0000.0000.000
41A42THR0-0.025-0.01223.783-0.014-0.0140.0000.0000.0000.000
42A43MET00.0090.00125.731-0.003-0.0030.0000.0000.0000.000
43A44ALA0-0.080-0.04326.9020.0010.0010.0000.0000.0000.000
44A45ASN0-0.001-0.00821.513-0.009-0.0090.0000.0000.0000.000
45A46LEU00.020-0.00716.139-0.016-0.0160.0000.0000.0000.000
46A47GLU-1-0.847-0.92320.4130.0610.0610.0000.0000.0000.000
47A48LEU0-0.0050.01522.574-0.012-0.0120.0000.0000.0000.000
48A49ILE0-0.043-0.03321.839-0.012-0.0120.0000.0000.0000.000
49A50LEU0-0.075-0.03916.852-0.011-0.0110.0000.0000.0000.000
50A51GLY0-0.007-0.01021.567-0.012-0.0120.0000.0000.0000.000
51A52MET0-0.090-0.03218.687-0.013-0.0130.0000.0000.0000.000
52A53GLU-1-0.961-0.97623.7310.0060.0060.0000.0000.0000.000
53A54GLY0-0.002-0.00624.5090.0040.0040.0000.0000.0000.000
54A55LEU00.0010.00719.555-0.006-0.0060.0000.0000.0000.000
55A56PRO0-0.061-0.03123.5010.0090.0090.0000.0000.0000.000
56A57VAL0-0.0080.01920.3500.0070.0070.0000.0000.0000.000
57A58THR00.0220.00319.5540.0100.0100.0000.0000.0000.000
58A59LEU00.0580.01014.314-0.008-0.0080.0000.0000.0000.000
59A60GLN0-0.023-0.00518.382-0.005-0.0050.0000.0000.0000.000
60A61ASN0-0.004-0.00521.804-0.001-0.0010.0000.0000.0000.000
61A62VAL0-0.0090.00716.392-0.005-0.0050.0000.0000.0000.000
62A63LEU0-0.095-0.04318.280-0.002-0.0020.0000.0000.0000.000
63A64ALA0-0.056-0.02020.545-0.006-0.0060.0000.0000.0000.000
64A65GLY0-0.030-0.00722.424-0.010-0.0100.0000.0000.0000.000
65A66GLU-1-0.929-0.95923.5070.0520.0520.0000.0000.0000.000
66A67ALA0-0.013-0.00921.342-0.009-0.0090.0000.0000.0000.000
67A68ARG10.8480.92118.0300.0520.0520.0000.0000.0000.000
68A69ILE00.0660.02911.555-0.002-0.0020.0000.0000.0000.000
69A70ASP-1-0.871-0.93514.691-0.074-0.0740.0000.0000.0000.000
70A71GLU-1-0.920-0.97115.660-0.010-0.0100.0000.0000.0000.000
71A72ALA0-0.040-0.00916.2360.0050.0050.0000.0000.0000.000
72A73ILE0-0.011-0.00811.2680.0350.0350.0000.0000.0000.000
73A74TYR0-0.021-0.01014.981-0.044-0.0440.0000.0000.0000.000
74A75VAL00.002-0.00315.546-0.001-0.0010.0000.0000.0000.000
75A76GLY00.0450.01616.4380.0190.0190.0000.0000.0000.000
76A77PRO0-0.040-0.03818.255-0.024-0.0240.0000.0000.0000.000
77A78GLY0-0.032-0.03117.5830.0000.0000.0000.0000.0000.000
78A79GLY00.0040.02015.659-0.023-0.0230.0000.0000.0000.000
79A80VAL0-0.0350.01612.580-0.036-0.0360.0000.0000.0000.000
80A81LYS10.8510.9268.9700.6030.6030.0000.0000.0000.000
81A82VAL0-0.033-0.03012.6690.0630.0630.0000.0000.0000.000
82A83VAL00.0310.01811.834-0.024-0.0240.0000.0000.0000.000
83A84PRO00.0080.02114.8620.0490.0490.0000.0000.0000.000
84A85ALA00.0840.03017.3270.0010.0010.0000.0000.0000.000
85A86GLY00.0070.01418.453-0.012-0.0120.0000.0000.0000.000
86A87VAL0-0.055-0.03321.620-0.015-0.0150.0000.0000.0000.000
87A88SER00.0300.01521.2260.0200.0200.0000.0000.0000.000
88A89LEU00.1240.03515.600-0.008-0.0080.0000.0000.0000.000
89A90GLU-1-0.879-0.92019.8370.1480.1480.0000.0000.0000.000
90A91GLY0-0.029-0.01722.773-0.009-0.0090.0000.0000.0000.000
91A92LEU00.0420.02018.262-0.010-0.0100.0000.0000.0000.000
92A93ARG10.9960.98719.433-0.237-0.2370.0000.0000.0000.000
93A94LYS10.8500.92520.856-0.133-0.1330.0000.0000.0000.000
94A95ALA0-0.059-0.02523.381-0.012-0.0120.0000.0000.0000.000
95A96ASN00.0320.01421.626-0.004-0.0040.0000.0000.0000.000
96A97PRO0-0.016-0.00819.4800.0170.0170.0000.0000.0000.000
97A98GLU-1-0.903-0.93717.6710.1650.1650.0000.0000.0000.000
98A99LYS10.9931.00016.707-0.099-0.0990.0000.0000.0000.000
99A100LEU0-0.013-0.01615.5530.0180.0180.0000.0000.0000.000
100A101GLU-1-0.929-0.96212.4110.4480.4480.0000.0000.0000.000
101A102ASP-1-0.877-0.92811.7440.3120.3120.0000.0000.0000.000
102A103VAL0-0.054-0.03411.6660.0040.0040.0000.0000.0000.000
103A104LEU00.003-0.0139.4930.0170.0170.0000.0000.0000.000
104A105THR0-0.029-0.0107.7430.3870.3870.0000.0000.0000.000
105A106GLN00.000-0.0037.111-0.029-0.0290.0000.0000.0000.000
106A107ILE0-0.033-0.0137.339-0.210-0.2100.0000.0000.0000.000
107A108MET0-0.046-0.0203.548-0.585-0.1340.012-0.117-0.3460.000
108A109GLU-1-0.936-0.9632.901-4.380-2.9580.152-0.695-0.880-0.008
109A110SER0-0.131-0.0635.251-0.721-0.661-0.001-0.001-0.0580.000
110A111THR0-0.029-0.0114.4080.7480.850-0.001-0.009-0.0910.000
111A112ASP-1-0.865-0.9072.323-8.780-5.9361.322-1.743-2.423-0.013
112A113ILE0-0.048-0.0462.530-2.609-0.9712.165-1.647-2.156-0.030
113A114LEU00.0240.0214.558-0.299-0.095-0.001-0.012-0.1910.000
114A115LEU0-0.035-0.0236.240-0.093-0.0930.0000.0000.0000.000
115A116LEU00.0530.0179.788-0.064-0.0640.0000.0000.0000.000
116A117ASP-1-0.770-0.83512.3950.1360.1360.0000.0000.0000.000
117A118ALA0-0.009-0.00815.876-0.006-0.0060.0000.0000.0000.000
118A119PRO00.022-0.00417.780-0.025-0.0250.0000.0000.0000.000
119A120ALA0-0.046-0.01621.4840.0020.0020.0000.0000.0000.000
120A121GLY00.0420.02723.7350.0000.0000.0000.0000.0000.000
121A122LEU0-0.040-0.03423.1130.0140.0140.0000.0000.0000.000
122A123GLU-1-0.877-0.90723.7160.1550.1550.0000.0000.0000.000
123A124ARG10.9120.92623.526-0.134-0.1340.0000.0000.0000.000
124A125SER00.014-0.02921.0220.0200.0200.0000.0000.0000.000
125A126ALA00.0350.03619.3310.0330.0330.0000.0000.0000.000
126A127VAL0-0.005-0.01318.6830.0300.0300.0000.0000.0000.000
127A128ILE0-0.052-0.01616.9470.0160.0160.0000.0000.0000.000
128A129ALA00.0540.02514.9570.0470.0470.0000.0000.0000.000
129A130ILE0-0.029-0.00913.8920.0750.0750.0000.0000.0000.000
130A131ALA0-0.024-0.00514.0860.0280.0280.0000.0000.0000.000
131A132ALA0-0.0220.00311.7460.0120.0120.0000.0000.0000.000
132A133ALA0-0.0200.0129.3010.2030.2030.0000.0000.0000.000
133A134GLN00.0160.0114.013-0.228-0.050-0.001-0.114-0.0630.000
134A135GLU-1-0.851-0.9238.0190.0880.0880.0000.0000.0000.000
135A136LEU0-0.0020.00211.5280.0610.0610.0000.0000.0000.000
136A137LEU0-0.0090.00514.003-0.049-0.0490.0000.0000.0000.000
137A138LEU0-0.014-0.00315.8130.0060.0060.0000.0000.0000.000
138A139VAL00.0020.00519.262-0.021-0.0210.0000.0000.0000.000
139A140VAL00.000-0.00721.7890.0020.0020.0000.0000.0000.000
140A141ASN0-0.049-0.02625.549-0.004-0.0040.0000.0000.0000.000
141A142PRO00.0300.00328.6920.0020.0020.0000.0000.0000.000
142A143GLU-1-0.833-0.89231.0630.0570.0570.0000.0000.0000.000
143A144ILE00.1040.02732.0330.0050.0050.0000.0000.0000.000
144A145SER00.0040.02132.7720.0040.0040.0000.0000.0000.000
145A146SER00.031-0.00128.0910.0060.0060.0000.0000.0000.000
146A147ILE00.0080.01228.3870.0090.0090.0000.0000.0000.000
147A148THR0-0.012-0.00328.6500.0030.0030.0000.0000.0000.000
148A149ASP-1-0.907-0.94628.6000.0930.0930.0000.0000.0000.000
149A150GLY00.0330.01425.2640.0100.0100.0000.0000.0000.000
150A151LEU00.0300.01824.6820.0120.0120.0000.0000.0000.000
151A152LYS10.8340.90525.993-0.085-0.0850.0000.0000.0000.000
152A153THR00.0200.00620.8020.0020.0020.0000.0000.0000.000
153A154LYS10.8210.92521.288-0.091-0.0910.0000.0000.0000.000
154A155ILE00.0250.00321.6320.0100.0100.0000.0000.0000.000
155A156VAL0-0.048-0.02520.6230.0040.0040.0000.0000.0000.000
156A157ALA00.0590.02517.5520.0120.0120.0000.0000.0000.000
157A158GLU-1-0.845-0.91518.3320.1410.1410.0000.0000.0000.000
158A159ARG10.8140.90920.545-0.136-0.1360.0000.0000.0000.000
159A160LEU0-0.057-0.03417.386-0.010-0.0100.0000.0000.0000.000
160A161GLY0-0.0080.01816.7320.0110.0110.0000.0000.0000.000
161A162THR0-0.041-0.01013.010-0.002-0.0020.0000.0000.0000.000
162A163LYS10.9270.95712.924-0.218-0.2180.0000.0000.0000.000
163A164VAL00.006-0.00214.0470.0280.0280.0000.0000.0000.000
164A165LEU0-0.0050.01210.844-0.027-0.0270.0000.0000.0000.000
165A166GLY00.008-0.00614.206-0.033-0.0330.0000.0000.0000.000
166A167VAL0-0.050-0.04417.5860.0180.0180.0000.0000.0000.000
167A168VAL0-0.0050.00218.233-0.016-0.0160.0000.0000.0000.000
168A169VAL00.010-0.00221.1040.0060.0060.0000.0000.0000.000
169A170ASN0-0.008-0.03524.032-0.015-0.0150.0000.0000.0000.000
170A171ARG10.8580.94025.818-0.055-0.0550.0000.0000.0000.000
171A172ILE00.0100.02627.8990.0000.0000.0000.0000.0000.000
172A173THR00.001-0.00830.701-0.003-0.0030.0000.0000.0000.000
173A174THR00.017-0.02930.7880.0020.0020.0000.0000.0000.000
174A175LEU0-0.021-0.00232.962-0.001-0.0010.0000.0000.0000.000
175A176GLY00.0530.02735.691-0.001-0.0010.0000.0000.0000.000
176A177ILE0-0.0010.00530.0720.0010.0010.0000.0000.0000.000
177A178GLU-1-0.865-0.91831.0420.0170.0170.0000.0000.0000.000
178A179MET0-0.028-0.02131.6820.0020.0020.0000.0000.0000.000
179A180ALA00.0470.03031.6350.0030.0030.0000.0000.0000.000
180A181LYS10.8290.90424.407-0.031-0.0310.0000.0000.0000.000
181A182ASN0-0.005-0.00628.4840.0050.0050.0000.0000.0000.000
182A183GLU-1-0.948-0.96730.4010.0400.0400.0000.0000.0000.000
183A184ILE0-0.009-0.02426.5580.0040.0040.0000.0000.0000.000
184A185GLU-1-0.795-0.88924.3270.0500.0500.0000.0000.0000.000
185A186ALA0-0.020-0.00127.0930.0030.0030.0000.0000.0000.000
186A187ILE0-0.053-0.01630.1330.0020.0020.0000.0000.0000.000
187A188LEU0-0.060-0.03624.5660.0040.0040.0000.0000.0000.000
188A189GLU-1-0.922-0.95925.0950.0910.0910.0000.0000.0000.000
189A190ALA00.0020.00321.2070.0090.0090.0000.0000.0000.000
190A191LYS10.9030.95417.885-0.054-0.0540.0000.0000.0000.000
191A192VAL0-0.021-0.01120.3710.0100.0100.0000.0000.0000.000
192A193ILE0-0.072-0.03915.425-0.011-0.0110.0000.0000.0000.000
193A194GLY00.0490.02319.194-0.009-0.0090.0000.0000.0000.000
194A195LEU0-0.0200.00321.0610.0090.0090.0000.0000.0000.000
195A196ILE00.0180.00521.191-0.008-0.0080.0000.0000.0000.000
196A197PRO0-0.003-0.00325.3480.0040.0040.0000.0000.0000.000
197A198GLU-1-0.878-0.95028.9280.0360.0360.0000.0000.0000.000
198A199ASP-1-0.770-0.87529.2290.0020.0020.0000.0000.0000.000
199A200PRO0-0.033-0.02330.7370.0020.0020.0000.0000.0000.000
200A201GLU-1-0.739-0.83029.9610.0000.0000.0000.0000.0000.000
201A202VAL00.0420.02126.047-0.002-0.0020.0000.0000.0000.000
202A203ARG10.9520.98227.714-0.018-0.0180.0000.0000.0000.000
203A204ARG10.8450.89730.362-0.006-0.0060.0000.0000.0000.000
204A205ALA0-0.0010.00626.142-0.002-0.0020.0000.0000.0000.000
205A206ALA00.0030.00426.737-0.001-0.0010.0000.0000.0000.000
206A207ALA0-0.051-0.02927.6970.0000.0000.0000.0000.0000.000
207A208TYR0-0.075-0.05130.115-0.001-0.0010.0000.0000.0000.000
208A209GLY00.0590.06926.465-0.004-0.0040.0000.0000.0000.000
209A210LYS10.9560.98324.9240.0270.0270.0000.0000.0000.000
210A211PRO00.0700.03720.5900.0020.0020.0000.0000.0000.000
211A212VAL00.0300.00823.169-0.009-0.0090.0000.0000.0000.000
212A213VAL00.0100.01519.377-0.004-0.0040.0000.0000.0000.000
213A214LEU00.0020.00620.467-0.009-0.0090.0000.0000.0000.000
214A215ARG10.7190.84724.0380.0010.0010.0000.0000.0000.000
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