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: N933Q

Calculation Name: 5HLZ-A-Xray372

Preferred Name: Inhibin beta A chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5HLZ

Chain ID: A

ChEMBL ID: CHEMBL3588735

UniProt ID: P08476

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1935217.56776
FMO2-HF: Nuclear repulsion 1853856.721301
FMO2-HF: Total energy -81360.846459
FMO2-MP2: Total energy -81597.542327


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:51:GLN)


Summations of interaction energy for fragment #1(A:51: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.
-2.2871.1661.622-1.973-3.1030.001
Interaction energy analysis for fragmet #1(A:51:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : -0.006
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].
3A53GLU-1-0.885-0.9353.6480.3732.503-0.014-0.868-1.2470.001
4A54MET00.0210.0082.279-2.397-1.3941.636-1.006-1.6340.000
5A55VAL0-0.009-0.0064.059-0.409-0.0890.000-0.099-0.2220.000
6A56GLU-1-0.834-0.9316.1490.2880.2880.0000.0000.0000.000
7A57ALA0-0.0060.0127.8840.0220.0220.0000.0000.0000.000
8A58VAL00.013-0.0028.430-0.022-0.0220.0000.0000.0000.000
9A59LYS10.8350.9229.0360.2090.2090.0000.0000.0000.000
10A60LYS10.8850.93812.374-0.094-0.0940.0000.0000.0000.000
11A61HIS00.0260.01813.6180.0370.0370.0000.0000.0000.000
12A62ILE00.0380.00913.5320.0010.0010.0000.0000.0000.000
13A63LEU0-0.050-0.02816.4020.0150.0150.0000.0000.0000.000
14A64ASN00.0260.02217.7460.0260.0260.0000.0000.0000.000
15A65MET00.0030.00319.4120.0100.0100.0000.0000.0000.000
16A66LEU0-0.0260.00320.144-0.002-0.0020.0000.0000.0000.000
17A67HIS0-0.058-0.01922.9980.0080.0080.0000.0000.0000.000
18A68LEU00.0220.01921.9520.0080.0080.0000.0000.0000.000
19A69LYS10.9310.96621.387-0.121-0.1210.0000.0000.0000.000
20A70LYS10.7810.85719.657-0.029-0.0290.0000.0000.0000.000
21A71ARG10.9880.99016.7420.0620.0620.0000.0000.0000.000
22A72PRO00.0470.02019.4790.0240.0240.0000.0000.0000.000
23A73ASP-1-0.799-0.87021.3840.0450.0450.0000.0000.0000.000
24A74VAL0-0.026-0.01820.799-0.019-0.0190.0000.0000.0000.000
25A75THR00.0070.00723.4950.0090.0090.0000.0000.0000.000
26A76GLN00.0020.00526.322-0.005-0.0050.0000.0000.0000.000
27A77PRO0-0.0160.00426.5690.0030.0030.0000.0000.0000.000
28A78VAL00.0500.01829.1370.0040.0040.0000.0000.0000.000
29A79PRO00.0450.01230.960-0.010-0.0100.0000.0000.0000.000
30A80LYS11.0251.00227.2870.1640.1640.0000.0000.0000.000
31A81ALA00.0270.01831.362-0.005-0.0050.0000.0000.0000.000
32A82ALA0-0.001-0.00434.7640.0000.0000.0000.0000.0000.000
33A83LEU00.0090.00527.9240.0010.0010.0000.0000.0000.000
34A84LEU00.0280.00129.339-0.001-0.0010.0000.0000.0000.000
35A85ASN00.0190.01232.891-0.004-0.0040.0000.0000.0000.000
36A86ALA00.0140.01134.8450.0020.0020.0000.0000.0000.000
37A87ILE00.0310.00730.1220.0030.0030.0000.0000.0000.000
38A88ARG10.9560.98633.9750.1080.1080.0000.0000.0000.000
39A89LYS10.8690.93536.0390.0850.0850.0000.0000.0000.000
40A90LEU0-0.009-0.00836.0340.0040.0040.0000.0000.0000.000
41A91HIS10.7970.90636.2110.1170.1170.0000.0000.0000.000
42A92VAL00.0550.03331.8150.0000.0000.0000.0000.0000.000
43A93GLY0-0.035-0.01530.594-0.012-0.0120.0000.0000.0000.000
44A94LYS10.8370.90630.4450.2210.2210.0000.0000.0000.000
45A95VAL0-0.016-0.02429.895-0.012-0.0120.0000.0000.0000.000
46A96GLY00.0100.00830.8670.0140.0140.0000.0000.0000.000
47A97GLU-1-0.906-0.95631.332-0.178-0.1780.0000.0000.0000.000
48A98ASN0-0.085-0.03631.606-0.004-0.0040.0000.0000.0000.000
49A99GLY00.0420.03227.989-0.008-0.0080.0000.0000.0000.000
50A100TYR0-0.057-0.02923.9490.0090.0090.0000.0000.0000.000
51A101VAL0-0.006-0.01425.2280.0150.0150.0000.0000.0000.000
52A102GLU-1-0.782-0.86725.148-0.263-0.2630.0000.0000.0000.000
53A103ILE00.0190.00924.6500.0190.0190.0000.0000.0000.000
54A104GLU-1-0.877-0.93428.180-0.144-0.1440.0000.0000.0000.000
55A105ASP-1-0.851-0.90531.498-0.130-0.1300.0000.0000.0000.000
56A106ASP-1-0.862-0.92526.304-0.238-0.2380.0000.0000.0000.000
57A107ILE00.018-0.00226.9010.0040.0040.0000.0000.0000.000
58A108GLY00.006-0.00525.3440.0050.0050.0000.0000.0000.000
59A109ARG10.9190.95326.2830.2390.2390.0000.0000.0000.000
60A110ARG10.8120.87828.8350.1380.1380.0000.0000.0000.000
61A111ALA0-0.0030.00427.2070.0080.0080.0000.0000.0000.000
62A112GLU-1-0.911-0.95226.425-0.274-0.2740.0000.0000.0000.000
63A113MET0-0.045-0.01728.8200.0040.0040.0000.0000.0000.000
64A114ASN0-0.040-0.04731.9630.0060.0060.0000.0000.0000.000
65A115GLU-1-0.886-0.92927.115-0.226-0.2260.0000.0000.0000.000
66A116LEU0-0.046-0.01731.5850.0010.0010.0000.0000.0000.000
67A117MET0-0.059-0.04233.7080.0060.0060.0000.0000.0000.000
68A118GLU-1-0.952-0.96832.408-0.128-0.1280.0000.0000.0000.000
69A119GLN0-0.051-0.01530.6710.0040.0040.0000.0000.0000.000
70A120THR0-0.058-0.03435.932-0.001-0.0010.0000.0000.0000.000
71A121SER00.0390.02739.1990.0030.0030.0000.0000.0000.000
72A122GLU-1-0.963-0.99042.350-0.090-0.0900.0000.0000.0000.000
73A123ILE0-0.037-0.02445.8970.0040.0040.0000.0000.0000.000
74A124ILE0-0.0040.00048.8710.0000.0000.0000.0000.0000.000
75A125THR0-0.005-0.00552.4360.0020.0020.0000.0000.0000.000
76A126PHE0-0.009-0.01954.9610.0000.0000.0000.0000.0000.000
77A127ALA0-0.033-0.00558.5910.0000.0000.0000.0000.0000.000
78A128GLU-1-0.910-0.95961.323-0.048-0.0480.0000.0000.0000.000
79A129SER0-0.028-0.02163.597-0.001-0.0010.0000.0000.0000.000
80A130GLY00.0290.02466.9500.0000.0000.0000.0000.0000.000
81A131THR00.0150.00067.6640.0010.0010.0000.0000.0000.000
82A132ALA0-0.0080.00669.9860.0020.0020.0000.0000.0000.000
83A133ARG10.9730.96371.2260.0380.0380.0000.0000.0000.000
84A134LYS10.9290.97170.5100.0420.0420.0000.0000.0000.000
85A135THR00.028-0.00166.318-0.002-0.0020.0000.0000.0000.000
86A136LEU0-0.057-0.00863.1130.0010.0010.0000.0000.0000.000
87A137HIS10.8190.87160.9230.0540.0540.0000.0000.0000.000
88A138PHE0-0.010-0.01257.0220.0010.0010.0000.0000.0000.000
89A139GLU-1-0.739-0.83656.723-0.062-0.0620.0000.0000.0000.000
90A140ILE0-0.037-0.02050.4660.0000.0000.0000.0000.0000.000
91A141SER00.0410.02249.3950.0010.0010.0000.0000.0000.000
92A142LYS10.9900.98644.9600.0820.0820.0000.0000.0000.000
93A143GLU-1-0.913-0.94742.847-0.095-0.0950.0000.0000.0000.000
94A144GLY0-0.024-0.02344.501-0.005-0.0050.0000.0000.0000.000
95A145SER0-0.090-0.05345.172-0.002-0.0020.0000.0000.0000.000
96A146ASP-1-0.889-0.94340.458-0.104-0.1040.0000.0000.0000.000
97A147LEU0-0.0370.00439.942-0.008-0.0080.0000.0000.0000.000
98A148SER0-0.006-0.00739.1820.0010.0010.0000.0000.0000.000
99A149VAL0-0.014-0.00838.3610.0020.0020.0000.0000.0000.000
100A150VAL0-0.018-0.01841.3980.0030.0030.0000.0000.0000.000
101A151GLU-1-0.823-0.88139.148-0.146-0.1460.0000.0000.0000.000
102A152ARG10.7970.87043.6710.0950.0950.0000.0000.0000.000
103A153ALA00.0430.01947.1310.0020.0020.0000.0000.0000.000
104A154GLU-1-0.835-0.88650.398-0.081-0.0810.0000.0000.0000.000
105A155VAL00.0140.00753.7110.0020.0020.0000.0000.0000.000
106A156TRP0-0.008-0.01254.3800.0030.0030.0000.0000.0000.000
107A157LEU0-0.002-0.00859.1200.0020.0020.0000.0000.0000.000
108A158PHE00.0230.00562.9070.0000.0000.0000.0000.0000.000
109A159LEU0-0.0060.00765.3410.0010.0010.0000.0000.0000.000
110A160LYS10.8240.90168.3020.0400.0400.0000.0000.0000.000
111A161VAL00.0450.00671.1280.0010.0010.0000.0000.0000.000
112A162PRO00.0050.00673.6350.0000.0000.0000.0000.0000.000
113A163LYS10.9470.96576.4110.0330.0330.0000.0000.0000.000
114A164ALA00.0290.01975.204-0.001-0.0010.0000.0000.0000.000
115A165ASN00.0100.02076.0520.0020.0020.0000.0000.0000.000
116A166ARG10.9650.96975.8280.0360.0360.0000.0000.0000.000
117A167THR0-0.023-0.00977.453-0.001-0.0010.0000.0000.0000.000
118A168ARG10.8600.90675.6280.0410.0410.0000.0000.0000.000
119A169THR00.0210.01171.2470.0000.0000.0000.0000.0000.000
120A170LYS10.8710.93067.5770.0510.0510.0000.0000.0000.000
121A171VAL00.0150.01969.6290.0010.0010.0000.0000.0000.000
122A172THR0-0.011-0.00967.198-0.002-0.0020.0000.0000.0000.000
123A173ILE0-0.023-0.00765.4510.0010.0010.0000.0000.0000.000
124A174ARG10.8370.91564.8000.0520.0520.0000.0000.0000.000
125A175LEU00.0020.00560.3940.0020.0020.0000.0000.0000.000
126A176PHE00.007-0.00862.567-0.002-0.0020.0000.0000.0000.000
127A177GLN00.1030.07057.000-0.001-0.0010.0000.0000.0000.000
128A178GLN0-0.073-0.04161.3180.0000.0000.0000.0000.0000.000
129A179GLN00.004-0.00657.598-0.003-0.0030.0000.0000.0000.000
130A180LYS10.9880.99661.7770.0550.0550.0000.0000.0000.000
131A202SER00.0010.00663.3160.0000.0000.0000.0000.0000.000
132A203GLU-1-0.819-0.90863.808-0.054-0.0540.0000.0000.0000.000
133A204LEU0-0.0120.01557.6470.0000.0000.0000.0000.0000.000
134A205LEU0-0.018-0.02161.3590.0010.0010.0000.0000.0000.000
135A206LEU0-0.045-0.01556.918-0.003-0.0030.0000.0000.0000.000
136A207SER00.0220.00057.809-0.002-0.0020.0000.0000.0000.000
137A208GLU-1-0.827-0.89660.033-0.057-0.0570.0000.0000.0000.000
138A209LYS10.8640.93859.6530.0650.0650.0000.0000.0000.000
139A210VAL00.0140.00963.2570.0020.0020.0000.0000.0000.000
140A211VAL0-0.031-0.01363.800-0.002-0.0020.0000.0000.0000.000
141A212ASP-1-0.823-0.91966.134-0.049-0.0490.0000.0000.0000.000
142A213ALA0-0.003-0.00168.0610.0000.0000.0000.0000.0000.000
143A214ARG10.8950.95169.5660.0490.0490.0000.0000.0000.000
144A215LYS10.8840.92969.8760.0410.0410.0000.0000.0000.000
145A216SER0-0.028-0.01169.424-0.001-0.0010.0000.0000.0000.000
146A217THR0-0.0160.00964.2430.0000.0000.0000.0000.0000.000
147A218TRP00.0290.01860.8510.0000.0000.0000.0000.0000.000
148A219HIS0-0.001-0.00361.408-0.002-0.0020.0000.0000.0000.000
149A220VAL00.0320.03455.0010.0010.0010.0000.0000.0000.000
150A221PHE00.007-0.00757.8640.0000.0000.0000.0000.0000.000
151A222PRO00.0200.01053.189-0.001-0.0010.0000.0000.0000.000
152A223VAL00.004-0.00153.4440.0010.0010.0000.0000.0000.000
153A224SER00.0800.02848.2020.0010.0010.0000.0000.0000.000
154A225SER00.0480.02349.248-0.003-0.0030.0000.0000.0000.000
155A226SER0-0.032-0.01650.308-0.001-0.0010.0000.0000.0000.000
156A227ILE00.0080.00249.4290.0010.0010.0000.0000.0000.000
157A228GLN00.0310.02343.985-0.002-0.0020.0000.0000.0000.000
158A229ARG10.9430.96847.9100.0840.0840.0000.0000.0000.000
159A230LEU0-0.136-0.07449.9400.0010.0010.0000.0000.0000.000
160A231LEU00.0530.02446.3210.0030.0030.0000.0000.0000.000
161A232ASP-1-0.824-0.89245.243-0.117-0.1170.0000.0000.0000.000
162A233GLN0-0.116-0.05447.1600.0040.0040.0000.0000.0000.000
163A234GLY00.0350.02048.6380.0040.0040.0000.0000.0000.000
164A235LYS10.8260.91849.5470.0820.0820.0000.0000.0000.000
165A236SER00.0490.01450.923-0.003-0.0030.0000.0000.0000.000
166A237SER0-0.028-0.02353.1350.0010.0010.0000.0000.0000.000
167A238LEU0-0.058-0.02655.924-0.001-0.0010.0000.0000.0000.000
168A239ASP-1-0.832-0.88458.382-0.055-0.0550.0000.0000.0000.000
169A240VAL0-0.012-0.02460.215-0.001-0.0010.0000.0000.0000.000
170A241ARG10.8750.94363.1740.0540.0540.0000.0000.0000.000
171A242ILE00.002-0.00464.129-0.002-0.0020.0000.0000.0000.000
172A243ALA0-0.048-0.02367.4010.0020.0020.0000.0000.0000.000
173A244CYS0-0.020-0.00969.209-0.001-0.0010.0000.0000.0000.000
174A245GLU-1-0.871-0.93771.607-0.047-0.0470.0000.0000.0000.000
175A246GLN00.0590.02672.6380.0000.0000.0000.0000.0000.000
176A248GLN00.0650.03874.4710.0000.0000.0000.0000.0000.000
177A249GLU-1-0.801-0.86877.864-0.040-0.0400.0000.0000.0000.000
178A250SER0-0.021-0.02475.3590.0000.0000.0000.0000.0000.000
179A251GLY0-0.073-0.03077.2210.0000.0000.0000.0000.0000.000
180A252ALA0-0.042-0.03272.6770.0000.0000.0000.0000.0000.000
181A253SER0-0.011-0.01873.0900.0010.0010.0000.0000.0000.000
182A254LEU0-0.006-0.00566.5510.0000.0000.0000.0000.0000.000
183A255VAL0-0.0130.00067.5670.0010.0010.0000.0000.0000.000
184A256LEU0-0.034-0.01766.811-0.002-0.0020.0000.0000.0000.000
185A257LEU00.0490.02167.9060.0000.0000.0000.0000.0000.000
186A258GLY0-0.006-0.00768.1860.0000.0000.0000.0000.0000.000
187A283GLU-1-0.807-0.91068.751-0.039-0.0390.0000.0000.0000.000
188A284GLU-1-0.817-0.91570.966-0.033-0.0330.0000.0000.0000.000
189A285LYS10.8820.93670.3990.0360.0360.0000.0000.0000.000
190A286GLU-1-0.796-0.87969.929-0.041-0.0410.0000.0000.0000.000
191A287GLN0-0.0120.00766.929-0.002-0.0020.0000.0000.0000.000
192A288SER0-0.059-0.02964.036-0.001-0.0010.0000.0000.0000.000
193A289HIS10.7700.86563.7620.0430.0430.0000.0000.0000.000
194A290ARG10.9951.01162.7210.0450.0450.0000.0000.0000.000
195A291PRO00.0140.01362.027-0.001-0.0010.0000.0000.0000.000
196A292PHE0-0.014-0.00855.1280.0010.0010.0000.0000.0000.000
197A293LEU00.0070.00553.449-0.001-0.0010.0000.0000.0000.000
198A294MET0-0.029-0.00848.6210.0010.0010.0000.0000.0000.000
199A295LEU00.010-0.01247.359-0.001-0.0010.0000.0000.0000.000
200A296GLN00.0240.02942.0730.0060.0060.0000.0000.0000.000
201A297ALA0-0.010-0.01542.755-0.003-0.0030.0000.0000.0000.000
202A298ARG10.9120.96035.2260.1670.1670.0000.0000.0000.000
203A299GLN0-0.0340.00034.580-0.005-0.0050.0000.0000.0000.000