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: 43MJN

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2619745.662216
FMO2-HF: Nuclear repulsion 2536231.077977
FMO2-HF: Total energy -83514.584239
FMO2-MP2: Total energy -83761.562122


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.
-21.308-18.00315.86-8.488-10.677-0.081
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 : -0.012 / q_NPA : -0.007
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].
3A4THR00.0390.0043.8700.0771.827-0.012-0.797-0.9410.002
4A5ILE0-0.038-0.0186.359-0.590-0.5900.0000.0000.0000.000
5A6THR00.003-0.0139.6380.0040.0040.0000.0000.0000.000
6A7VAL0-0.036-0.01012.787-0.069-0.0690.0000.0000.0000.000
7A8ALA00.0260.00915.567-0.007-0.0070.0000.0000.0000.000
8A9SER00.0160.00419.035-0.015-0.0150.0000.0000.0000.000
9A10GLY00.0070.01822.7210.0060.0060.0000.0000.0000.000
10A11LYS10.8050.87726.054-0.074-0.0740.0000.0000.0000.000
11A12GLY00.0780.02726.2920.0050.0050.0000.0000.0000.000
12A13GLY00.0040.01126.9040.0000.0000.0000.0000.0000.000
13A14THR00.0050.00924.073-0.007-0.0070.0000.0000.0000.000
14A15GLY00.0320.01124.610-0.008-0.0080.0000.0000.0000.000
15A16LYS10.8040.91219.108-0.207-0.2070.0000.0000.0000.000
16A17THR00.0530.01519.0020.0000.0000.0000.0000.0000.000
17A18THR0-0.012-0.01119.380-0.004-0.0040.0000.0000.0000.000
18A19ILE0-0.021-0.00117.585-0.015-0.0150.0000.0000.0000.000
19A20THR00.015-0.02513.846-0.013-0.0130.0000.0000.0000.000
20A21ALA00.0290.02414.9600.0000.0000.0000.0000.0000.000
21A22ASN0-0.067-0.05216.560-0.035-0.0350.0000.0000.0000.000
22A23LEU00.0330.02312.876-0.028-0.0280.0000.0000.0000.000
23A24GLY00.0680.02711.977-0.023-0.0230.0000.0000.0000.000
24A25VAL0-0.021-0.01712.926-0.058-0.0580.0000.0000.0000.000
25A26ALA0-0.038-0.02715.657-0.034-0.0340.0000.0000.0000.000
26A27LEU00.0030.0038.795-0.016-0.0160.0000.0000.0000.000
27A28ALA00.0460.03511.866-0.069-0.0690.0000.0000.0000.000
28A29GLN0-0.068-0.04512.716-0.031-0.0310.0000.0000.0000.000
29A30LEU0-0.091-0.03613.4640.0040.0040.0000.0000.0000.000
30A31GLY0-0.043-0.01912.891-0.009-0.0090.0000.0000.0000.000
31A32HIS0-0.024-0.0037.731-0.133-0.1330.0000.0000.0000.000
32A33ASP-1-0.790-0.8806.589-0.900-0.9000.0000.0000.0000.000
33A34VAL0-0.033-0.0306.336-0.128-0.1280.0000.0000.0000.000
34A35THR00.0150.0017.272-0.123-0.1230.0000.0000.0000.000
35A36ILE0-0.046-0.0228.8770.2280.2280.0000.0000.0000.000
36A37VAL00.0200.01610.708-0.082-0.0820.0000.0000.0000.000
37A38ASP-1-0.825-0.92512.7520.1990.1990.0000.0000.0000.000
38A39ALA00.011-0.00416.136-0.012-0.0120.0000.0000.0000.000
39A40ASP-1-0.851-0.92117.8550.1430.1430.0000.0000.0000.000
40A41ILE0-0.0140.00220.706-0.015-0.0150.0000.0000.0000.000
41A42THR0-0.042-0.01523.483-0.015-0.0150.0000.0000.0000.000
42A43MET00.005-0.00625.704-0.003-0.0030.0000.0000.0000.000
43A44ALA0-0.053-0.03726.5030.0010.0010.0000.0000.0000.000
44A45ASN0-0.027-0.01621.089-0.010-0.0100.0000.0000.0000.000
45A46LEU00.011-0.01415.923-0.015-0.0150.0000.0000.0000.000
46A47GLU-1-0.819-0.90020.1330.0710.0710.0000.0000.0000.000
47A48LEU00.0000.01922.178-0.014-0.0140.0000.0000.0000.000
48A49ILE0-0.068-0.03421.474-0.012-0.0120.0000.0000.0000.000
49A50LEU0-0.045-0.03416.626-0.010-0.0100.0000.0000.0000.000
50A51GLY0-0.017-0.01221.361-0.012-0.0120.0000.0000.0000.000
51A52MET0-0.084-0.02418.644-0.013-0.0130.0000.0000.0000.000
52A53GLU-1-0.950-0.97323.8070.0080.0080.0000.0000.0000.000
53A54GLY0-0.023-0.00824.1830.0040.0040.0000.0000.0000.000
54A55LEU0-0.011-0.01118.907-0.007-0.0070.0000.0000.0000.000
55A56PRO0-0.052-0.02522.8380.0090.0090.0000.0000.0000.000
56A57VAL0-0.0200.01420.1130.0030.0030.0000.0000.0000.000
57A58THR00.016-0.00319.1810.0100.0100.0000.0000.0000.000
58A59LEU00.0410.00613.913-0.007-0.0070.0000.0000.0000.000
59A60GLN0-0.029-0.01218.015-0.005-0.0050.0000.0000.0000.000
60A61ASN00.002-0.00221.5930.0000.0000.0000.0000.0000.000
61A62VAL0-0.0240.00215.934-0.006-0.0060.0000.0000.0000.000
62A63LEU0-0.079-0.03218.206-0.004-0.0040.0000.0000.0000.000
63A64ALA0-0.049-0.02420.247-0.007-0.0070.0000.0000.0000.000
64A65GLY0-0.0170.00222.102-0.009-0.0090.0000.0000.0000.000
65A66GLU-1-0.936-0.96223.1290.0480.0480.0000.0000.0000.000
66A67ALA0-0.016-0.00321.045-0.009-0.0090.0000.0000.0000.000
67A68ARG10.7660.84817.7100.0690.0690.0000.0000.0000.000
68A69ILE00.0570.01411.2300.0070.0070.0000.0000.0000.000
69A70ASP-1-0.846-0.92414.554-0.089-0.0890.0000.0000.0000.000
70A71GLU-1-0.866-0.90615.496-0.020-0.0200.0000.0000.0000.000
71A72ALA0-0.0080.00116.0100.0080.0080.0000.0000.0000.000
72A73ILE0-0.023-0.01110.7930.0410.0410.0000.0000.0000.000
73A74TYR0-0.008-0.00614.272-0.053-0.0530.0000.0000.0000.000
74A75VAL0-0.001-0.01014.761-0.006-0.0060.0000.0000.0000.000
75A76GLY00.0350.02116.4570.0160.0160.0000.0000.0000.000
76A77PRO0-0.059-0.04217.970-0.025-0.0250.0000.0000.0000.000
77A78GLY00.006-0.00817.1570.0060.0060.0000.0000.0000.000
78A79GLY0-0.0160.01015.380-0.027-0.0270.0000.0000.0000.000
79A80VAL0-0.0330.00212.387-0.036-0.0360.0000.0000.0000.000
80A81LYS10.8630.9148.0150.7190.7190.0000.0000.0000.000
81A82VAL0-0.050-0.03512.3520.0830.0830.0000.0000.0000.000
82A83VAL00.0410.02611.351-0.029-0.0290.0000.0000.0000.000
83A84PRO00.0120.02314.4220.0520.0520.0000.0000.0000.000
84A85ALA00.0640.01817.098-0.007-0.0070.0000.0000.0000.000
85A86GLY00.0130.00918.185-0.017-0.0170.0000.0000.0000.000
86A87VAL0-0.055-0.03221.414-0.015-0.0150.0000.0000.0000.000
87A88SER00.0370.01820.9450.0200.0200.0000.0000.0000.000
88A89LEU00.1200.03215.216-0.011-0.0110.0000.0000.0000.000
89A90GLU-1-0.860-0.91819.5500.1380.1380.0000.0000.0000.000
90A91GLY0-0.028-0.01422.474-0.010-0.0100.0000.0000.0000.000
91A92LEU00.0440.03518.327-0.014-0.0140.0000.0000.0000.000
92A93ARG11.0050.99919.005-0.225-0.2250.0000.0000.0000.000
93A94LYS10.8110.89020.580-0.126-0.1260.0000.0000.0000.000
94A95ALA0-0.056-0.01323.228-0.013-0.0130.0000.0000.0000.000
95A96ASN00.015-0.00420.859-0.002-0.0020.0000.0000.0000.000
96A97PRO0-0.019-0.00919.0510.0180.0180.0000.0000.0000.000
97A98GLU-1-0.841-0.90517.1390.1440.1440.0000.0000.0000.000
98A99LYS10.8930.93316.097-0.084-0.0840.0000.0000.0000.000
99A100LEU00.005-0.00415.1930.0100.0100.0000.0000.0000.000
100A101GLU-1-0.947-0.97012.1650.3680.3680.0000.0000.0000.000
101A102ASP-1-0.855-0.90511.2160.2190.2190.0000.0000.0000.000
102A103VAL00.007-0.00411.5920.0040.0040.0000.0000.0000.000
103A104LEU00.007-0.0219.3650.0230.0230.0000.0000.0000.000
104A105THR0-0.041-0.0227.2050.3470.3470.0000.0000.0000.000
105A106GLN00.0180.0147.0310.0110.0110.0000.0000.0000.000
106A107ILE0-0.033-0.0157.115-0.210-0.2100.0000.0000.0000.000
107A108MET0-0.0330.0063.120-0.767-0.1260.048-0.183-0.5060.000
108A109GLU-1-0.936-0.9672.725-5.530-3.7000.305-0.832-1.303-0.010
109A110SER0-0.112-0.0515.298-0.622-0.6220.0000.0000.0000.000
110A111THR0-0.035-0.0123.9460.8581.0860.000-0.060-0.1680.000
111A112ASP-1-0.833-0.8942.214-11.799-9.5314.085-2.630-3.723-0.024
112A113ILE0-0.043-0.0261.909-2.631-6.47911.436-3.835-3.753-0.049
113A114LEU00.0080.0094.052-0.485-0.236-0.001-0.031-0.2170.000
114A115LEU0-0.007-0.0036.191-0.172-0.1720.0000.0000.0000.000
115A116LEU00.0390.0129.708-0.038-0.0380.0000.0000.0000.000
116A117ASP-1-0.734-0.83112.0920.1550.1550.0000.0000.0000.000
117A118ALA00.0100.00415.738-0.024-0.0240.0000.0000.0000.000
118A119PRO00.0060.00017.804-0.024-0.0240.0000.0000.0000.000
119A120ALA00.0200.00221.478-0.007-0.0070.0000.0000.0000.000
120A121GLY0-0.066-0.02823.948-0.008-0.0080.0000.0000.0000.000
121A122LEU0-0.006-0.01222.8370.0160.0160.0000.0000.0000.000
122A123GLU-1-0.819-0.88923.6610.1580.1580.0000.0000.0000.000
123A124ARG10.9080.93123.286-0.120-0.1200.0000.0000.0000.000
124A125SER0-0.014-0.03120.8020.0150.0150.0000.0000.0000.000
125A126ALA00.0090.02719.1420.0350.0350.0000.0000.0000.000
126A127VAL0-0.014-0.01718.7190.0260.0260.0000.0000.0000.000
127A128ILE0-0.041-0.01616.7850.0120.0120.0000.0000.0000.000
128A129ALA00.0350.01414.8900.0380.0380.0000.0000.0000.000
129A130ILE0-0.026-0.00113.9620.0660.0660.0000.0000.0000.000
130A131ALA0-0.0080.00414.4500.0150.0150.0000.0000.0000.000
131A132ALA0-0.043-0.00211.7430.0010.0010.0000.0000.0000.000
132A133ALA00.0190.0158.9720.2010.2010.0000.0000.0000.000
133A134GLN00.0170.0144.2880.1200.307-0.001-0.120-0.0660.000
134A135GLU-1-0.861-0.9218.4000.1680.1680.0000.0000.0000.000
135A136LEU0-0.019-0.01111.4360.0680.0680.0000.0000.0000.000
136A137LEU00.0000.00414.022-0.050-0.0500.0000.0000.0000.000
137A138LEU0-0.012-0.00315.7270.0040.0040.0000.0000.0000.000
138A139VAL0-0.005-0.00818.905-0.019-0.0190.0000.0000.0000.000
139A140VAL0-0.012-0.01221.5280.0010.0010.0000.0000.0000.000
140A141ASN0-0.047-0.03125.366-0.003-0.0030.0000.0000.0000.000
141A142PRO00.0460.00628.5450.0020.0020.0000.0000.0000.000
142A143GLU-1-0.824-0.87931.2800.0630.0630.0000.0000.0000.000
143A144ILE00.1080.03232.0080.0050.0050.0000.0000.0000.000
144A145SER0-0.0290.01533.0630.0030.0030.0000.0000.0000.000
145A146SER00.0360.00327.7680.0060.0060.0000.0000.0000.000
146A147ILE00.0020.02228.0420.0090.0090.0000.0000.0000.000
147A148THR0-0.013-0.02428.6120.0060.0060.0000.0000.0000.000
148A149ASP-1-0.855-0.92828.8390.0900.0900.0000.0000.0000.000
149A150GLY00.0200.00825.1760.0090.0090.0000.0000.0000.000
150A151LEU00.0280.01324.6950.0120.0120.0000.0000.0000.000
151A152LYS10.8310.91226.057-0.086-0.0860.0000.0000.0000.000
152A153THR00.015-0.00820.6510.0000.0000.0000.0000.0000.000
153A154LYS10.7540.87521.463-0.094-0.0940.0000.0000.0000.000
154A155ILE00.0350.01321.7860.0080.0080.0000.0000.0000.000
155A156VAL0-0.071-0.04120.6730.0010.0010.0000.0000.0000.000
156A157ALA00.0540.01817.5120.0110.0110.0000.0000.0000.000
157A158GLU-1-0.830-0.90318.4160.1350.1350.0000.0000.0000.000
158A159ARG10.8490.91920.552-0.129-0.1290.0000.0000.0000.000
159A160LEU0-0.051-0.01617.242-0.010-0.0100.0000.0000.0000.000
160A161GLY0-0.0010.02116.8710.0120.0120.0000.0000.0000.000
161A162THR0-0.001-0.00612.973-0.025-0.0250.0000.0000.0000.000
162A163LYS10.8390.92013.173-0.231-0.2310.0000.0000.0000.000
163A164VAL00.0310.00814.2330.0300.0300.0000.0000.0000.000
164A165LEU0-0.0060.01710.885-0.031-0.0310.0000.0000.0000.000
165A166GLY00.011-0.01214.361-0.032-0.0320.0000.0000.0000.000
166A167VAL0-0.022-0.00617.7870.0210.0210.0000.0000.0000.000
167A168VAL0-0.009-0.00218.631-0.016-0.0160.0000.0000.0000.000
168A169VAL00.0010.00121.6810.0050.0050.0000.0000.0000.000
169A170ASN00.010-0.02123.993-0.015-0.0150.0000.0000.0000.000
170A171ARG10.8320.92525.854-0.066-0.0660.0000.0000.0000.000
171A172ILE0-0.0060.01528.366-0.002-0.0020.0000.0000.0000.000
172A173THR00.022-0.00130.762-0.003-0.0030.0000.0000.0000.000
173A174THR00.021-0.02231.4280.0010.0010.0000.0000.0000.000
174A175LEU0-0.034-0.01033.566-0.001-0.0010.0000.0000.0000.000
175A176GLY00.0580.03035.278-0.001-0.0010.0000.0000.0000.000
176A177ILE0-0.0080.00529.9230.0030.0030.0000.0000.0000.000
177A178GLU-1-0.887-0.94431.1290.0250.0250.0000.0000.0000.000
178A179MET0-0.039-0.01632.3020.0020.0020.0000.0000.0000.000
179A180ALA00.0640.03232.1080.0020.0020.0000.0000.0000.000
180A181LYS10.8240.90525.317-0.040-0.0400.0000.0000.0000.000
181A182ASN0-0.002-0.00929.0010.0050.0050.0000.0000.0000.000
182A183GLU-1-0.957-0.96930.9790.0440.0440.0000.0000.0000.000
183A184ILE00.004-0.01426.9260.0040.0040.0000.0000.0000.000
184A185GLU-1-0.786-0.88424.8730.0590.0590.0000.0000.0000.000
185A186ALA0-0.025-0.00427.5720.0030.0030.0000.0000.0000.000
186A187ILE0-0.061-0.02030.6460.0020.0020.0000.0000.0000.000
187A188LEU0-0.056-0.04124.8860.0030.0030.0000.0000.0000.000
188A189GLU-1-0.870-0.91525.5540.0950.0950.0000.0000.0000.000
189A190ALA00.0040.00121.3650.0070.0070.0000.0000.0000.000
190A191LYS10.8860.95118.149-0.072-0.0720.0000.0000.0000.000
191A192VAL0-0.016-0.02320.7520.0110.0110.0000.0000.0000.000
192A193ILE0-0.087-0.04515.793-0.009-0.0090.0000.0000.0000.000
193A194GLY00.0400.02619.482-0.007-0.0070.0000.0000.0000.000
194A195LEU0-0.014-0.00621.4940.0070.0070.0000.0000.0000.000
195A196ILE00.0250.02021.234-0.008-0.0080.0000.0000.0000.000
196A197PRO0-0.002-0.00725.3570.0030.0030.0000.0000.0000.000
197A198GLU-1-0.878-0.95128.6090.0440.0440.0000.0000.0000.000
198A199ASP-1-0.768-0.86229.0550.0120.0120.0000.0000.0000.000
199A200PRO0-0.018-0.02030.3600.0020.0020.0000.0000.0000.000
200A201GLU-1-0.764-0.82429.4020.0070.0070.0000.0000.0000.000
201A202VAL00.0400.01325.917-0.001-0.0010.0000.0000.0000.000
202A203ARG10.9700.99527.352-0.025-0.0250.0000.0000.0000.000
203A204ARG10.8420.89330.033-0.013-0.0130.0000.0000.0000.000
204A205ALA0-0.008-0.00825.706-0.002-0.0020.0000.0000.0000.000
205A206ALA00.0110.01326.459-0.001-0.0010.0000.0000.0000.000
206A207ALA0-0.048-0.02627.3610.0000.0000.0000.0000.0000.000
207A208TYR0-0.075-0.04029.833-0.002-0.0020.0000.0000.0000.000
208A209GLY00.0500.05626.391-0.005-0.0050.0000.0000.0000.000
209A210LYS10.9190.94724.7690.0190.0190.0000.0000.0000.000
210A211PRO00.0640.04520.4190.0020.0020.0000.0000.0000.000
211A212VAL00.0320.00023.001-0.011-0.0110.0000.0000.0000.000
212A213VAL0-0.0040.00318.994-0.006-0.0060.0000.0000.0000.000
213A214LEU00.0150.01619.874-0.011-0.0110.0000.0000.0000.000
214A215ARG10.7270.86123.703-0.009-0.0090.0000.0000.0000.000
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