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: 85JJY

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1933950.389023
FMO2-HF: Nuclear repulsion 1852590.961456
FMO2-HF: Total energy -81359.427567
FMO2-MP2: Total energy -81596.184681


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.
-1.5192.0330.639-1.535-2.6560.001
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 : 0.021 / 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-1-0.843-0.9143.6420.6512.806-0.011-0.890-1.2530.001
4A54MET00.0130.0032.516-2.225-1.1530.649-0.541-1.1810.000
5A55VAL0-0.018-0.0083.972-0.439-0.1140.001-0.104-0.2220.000
6A56GLU-1-0.954-1.0076.1530.8460.8460.0000.0000.0000.000
7A57ALA00.0120.0207.9260.0000.0000.0000.0000.0000.000
8A58VAL00.011-0.0038.555-0.039-0.0390.0000.0000.0000.000
9A59LYS10.9340.9819.5790.1790.1790.0000.0000.0000.000
10A60LYS10.9310.97212.386-0.206-0.2060.0000.0000.0000.000
11A61HIS00.0240.01413.6460.0340.0340.0000.0000.0000.000
12A62ILE00.0370.01013.790-0.006-0.0060.0000.0000.0000.000
13A63LEU0-0.062-0.03416.5500.0070.0070.0000.0000.0000.000
14A64ASN00.0140.00517.5880.0110.0110.0000.0000.0000.000
15A65MET0-0.015-0.00619.2280.0090.0090.0000.0000.0000.000
16A66LEU0-0.0190.00320.313-0.005-0.0050.0000.0000.0000.000
17A67HIS0-0.044-0.00623.0160.0040.0040.0000.0000.0000.000
18A68LEU00.0030.00721.9670.0040.0040.0000.0000.0000.000
19A69LYS10.9490.97821.406-0.149-0.1490.0000.0000.0000.000
20A70LYS10.8350.88919.650-0.031-0.0310.0000.0000.0000.000
21A71ARG10.9920.98816.6240.0680.0680.0000.0000.0000.000
22A72PRO00.0390.02919.4010.0240.0240.0000.0000.0000.000
23A73ASP-1-0.846-0.90821.2940.0430.0430.0000.0000.0000.000
24A74VAL0-0.047-0.02820.689-0.019-0.0190.0000.0000.0000.000
25A75THR00.0120.01123.3940.0100.0100.0000.0000.0000.000
26A76GLN0-0.008-0.00626.240-0.008-0.0080.0000.0000.0000.000
27A77PRO0-0.0140.00926.5520.0050.0050.0000.0000.0000.000
28A78VAL00.0450.01929.0850.0040.0040.0000.0000.0000.000
29A79PRO00.0440.01130.930-0.011-0.0110.0000.0000.0000.000
30A80LYS11.0301.00227.4710.1820.1820.0000.0000.0000.000
31A81ALA00.0280.01831.355-0.004-0.0040.0000.0000.0000.000
32A82ALA00.0070.00234.7410.0010.0010.0000.0000.0000.000
33A83LEU00.0150.00727.9990.0020.0020.0000.0000.0000.000
34A84LEU00.027-0.00229.4710.0000.0000.0000.0000.0000.000
35A85ASN0-0.047-0.01932.9150.0040.0040.0000.0000.0000.000
36A86ALA00.0450.01934.8670.0030.0030.0000.0000.0000.000
37A87ILE00.0280.00830.2420.0030.0030.0000.0000.0000.000
38A88ARG10.9851.00934.0080.1110.1110.0000.0000.0000.000
39A89LYS10.8490.91736.0870.0880.0880.0000.0000.0000.000
40A90LEU00.0130.00636.2160.0040.0040.0000.0000.0000.000
41A91HIS10.8650.95336.2970.1080.1080.0000.0000.0000.000
42A92VAL00.0850.05231.2750.0010.0010.0000.0000.0000.000
43A93GLY0-0.028-0.01330.650-0.011-0.0110.0000.0000.0000.000
44A94LYS10.9370.96830.5020.1960.1960.0000.0000.0000.000
45A95VAL00.003-0.00829.965-0.012-0.0120.0000.0000.0000.000
46A96GLY00.0010.00230.9370.0150.0150.0000.0000.0000.000
47A97GLU-1-0.905-0.95531.406-0.187-0.1870.0000.0000.0000.000
48A98ASN0-0.081-0.03431.831-0.006-0.0060.0000.0000.0000.000
49A99GLY00.0360.02928.046-0.010-0.0100.0000.0000.0000.000
50A100TYR0-0.050-0.02523.9880.0100.0100.0000.0000.0000.000
51A101VAL0-0.024-0.02325.2210.0160.0160.0000.0000.0000.000
52A102GLU-1-0.912-0.95025.219-0.282-0.2820.0000.0000.0000.000
53A103ILE00.0100.00224.7640.0190.0190.0000.0000.0000.000
54A104GLU-1-0.970-1.00928.258-0.140-0.1400.0000.0000.0000.000
55A105ASP-1-0.957-0.97931.501-0.117-0.1170.0000.0000.0000.000
56A106ASP-1-0.882-0.92925.739-0.221-0.2210.0000.0000.0000.000
57A107ILE00.0280.00226.8550.0040.0040.0000.0000.0000.000
58A108GLY00.017-0.00225.3310.0070.0070.0000.0000.0000.000
59A109ARG10.9360.97626.2760.2190.2190.0000.0000.0000.000
60A110ARG10.9290.95728.8220.1200.1200.0000.0000.0000.000
61A111ALA0-0.0070.00227.2090.0080.0080.0000.0000.0000.000
62A112GLU-1-0.923-0.95425.992-0.255-0.2550.0000.0000.0000.000
63A113MET0-0.054-0.01528.8140.0030.0030.0000.0000.0000.000
64A114ASN0-0.037-0.05131.9900.0060.0060.0000.0000.0000.000
65A115GLU-1-0.865-0.91827.454-0.195-0.1950.0000.0000.0000.000
66A116LEU0-0.044-0.01231.5890.0010.0010.0000.0000.0000.000
67A117MET0-0.072-0.05333.7050.0060.0060.0000.0000.0000.000
68A118GLU-1-0.935-0.95932.139-0.106-0.1060.0000.0000.0000.000
69A119GLN0-0.037-0.01330.7580.0020.0020.0000.0000.0000.000
70A120THR0-0.060-0.02735.9360.0000.0000.0000.0000.0000.000
71A121SER00.0190.02039.2000.0060.0060.0000.0000.0000.000
72A122GLU-1-0.953-0.98842.354-0.080-0.0800.0000.0000.0000.000
73A123ILE0-0.032-0.01945.9000.0040.0040.0000.0000.0000.000
74A124ILE00.0020.00148.8750.0000.0000.0000.0000.0000.000
75A125THR00.005-0.00352.4400.0020.0020.0000.0000.0000.000
76A126PHE0-0.007-0.02054.9650.0000.0000.0000.0000.0000.000
77A127ALA0-0.026-0.00558.5960.0000.0000.0000.0000.0000.000
78A128GLU-1-0.906-0.95861.326-0.041-0.0410.0000.0000.0000.000
79A129SER0-0.036-0.02563.602-0.001-0.0010.0000.0000.0000.000
80A130GLY00.0190.02066.9530.0000.0000.0000.0000.0000.000
81A131THR00.0150.00067.6660.0010.0010.0000.0000.0000.000
82A132ALA00.0020.01169.9880.0010.0010.0000.0000.0000.000
83A133ARG10.9710.96071.2250.0340.0340.0000.0000.0000.000
84A134LYS10.9190.96670.5150.0380.0380.0000.0000.0000.000
85A135THR00.0310.00766.203-0.002-0.0020.0000.0000.0000.000
86A136LEU0-0.056-0.01263.1360.0010.0010.0000.0000.0000.000
87A137HIS10.8640.93260.6900.0470.0470.0000.0000.0000.000
88A138PHE0-0.014-0.00956.9570.0010.0010.0000.0000.0000.000
89A139GLU-1-0.854-0.93856.756-0.054-0.0540.0000.0000.0000.000
90A140ILE0-0.020-0.00550.4580.0010.0010.0000.0000.0000.000
91A141SER00.0360.02049.3150.0010.0010.0000.0000.0000.000
92A142LYS11.0211.00146.5270.0620.0620.0000.0000.0000.000
93A143GLU-1-0.899-0.93942.673-0.078-0.0780.0000.0000.0000.000
94A144GLY0-0.033-0.02444.508-0.004-0.0040.0000.0000.0000.000
95A145SER0-0.113-0.07045.178-0.003-0.0030.0000.0000.0000.000
96A146ASP-1-0.882-0.93240.395-0.089-0.0890.0000.0000.0000.000
97A147LEU0-0.073-0.01739.946-0.008-0.0080.0000.0000.0000.000
98A148SER0-0.026-0.01839.3090.0000.0000.0000.0000.0000.000
99A149VAL0-0.020-0.01338.5750.0010.0010.0000.0000.0000.000
100A150VAL0-0.026-0.02241.5270.0030.0030.0000.0000.0000.000
101A151GLU-1-0.886-0.92939.048-0.131-0.1310.0000.0000.0000.000
102A152ARG10.8110.88643.6590.0880.0880.0000.0000.0000.000
103A153ALA00.0250.00947.1200.0020.0020.0000.0000.0000.000
104A154GLU-1-0.848-0.91050.389-0.076-0.0760.0000.0000.0000.000
105A155VAL00.0220.01453.7020.0020.0020.0000.0000.0000.000
106A156TRP0-0.001-0.00254.3380.0020.0020.0000.0000.0000.000
107A157LEU0-0.002-0.01159.1140.0020.0020.0000.0000.0000.000
108A158PHE00.0220.00662.9010.0000.0000.0000.0000.0000.000
109A159LEU00.0050.01065.3360.0010.0010.0000.0000.0000.000
110A160LYS10.9620.98368.2940.0350.0350.0000.0000.0000.000
111A161VAL00.011-0.01671.1740.0000.0000.0000.0000.0000.000
112A162PRO0-0.025-0.01573.6270.0000.0000.0000.0000.0000.000
113A163LYS10.9470.96776.4050.0310.0310.0000.0000.0000.000
114A164ALA00.0440.03075.199-0.001-0.0010.0000.0000.0000.000
115A165ASN0-0.0150.00776.0160.0010.0010.0000.0000.0000.000
116A166ARG10.9640.96775.8120.0340.0340.0000.0000.0000.000
117A167THR0-0.024-0.00877.433-0.001-0.0010.0000.0000.0000.000
118A168ARG10.9470.98575.3490.0390.0390.0000.0000.0000.000
119A169THR00.0280.01170.8690.0000.0000.0000.0000.0000.000
120A170LYS10.9160.96768.1500.0480.0480.0000.0000.0000.000
121A171VAL00.0320.02669.5990.0010.0010.0000.0000.0000.000
122A172THR00.0080.00367.335-0.002-0.0020.0000.0000.0000.000
123A173ILE0-0.016-0.00565.4320.0010.0010.0000.0000.0000.000
124A174ARG10.8670.92664.9480.0510.0510.0000.0000.0000.000
125A175LEU00.0100.01060.2900.0020.0020.0000.0000.0000.000
126A176PHE00.005-0.01062.727-0.002-0.0020.0000.0000.0000.000
127A177GLN00.1000.07756.959-0.001-0.0010.0000.0000.0000.000
128A178GLN0-0.033-0.01561.4840.0000.0000.0000.0000.0000.000
129A179GLN00.011-0.00157.807-0.003-0.0030.0000.0000.0000.000
130A180LYS10.9800.98961.9320.0510.0510.0000.0000.0000.000
131A202SER0-0.035-0.02763.5410.0000.0000.0000.0000.0000.000
132A203GLU-1-0.804-0.88664.025-0.050-0.0500.0000.0000.0000.000
133A204LEU0-0.0060.02257.7500.0000.0000.0000.0000.0000.000
134A205LEU0-0.023-0.02661.6380.0010.0010.0000.0000.0000.000
135A206LEU0-0.038-0.01357.162-0.003-0.0030.0000.0000.0000.000
136A207SER00.0630.01458.014-0.003-0.0030.0000.0000.0000.000
137A208GLU-1-0.867-0.91760.223-0.055-0.0550.0000.0000.0000.000
138A209LYS10.8690.92959.1360.0610.0610.0000.0000.0000.000
139A210VAL00.0100.01063.4350.0020.0020.0000.0000.0000.000
140A211VAL0-0.031-0.01263.800-0.001-0.0010.0000.0000.0000.000
141A212ASP-1-0.876-0.96966.119-0.045-0.0450.0000.0000.0000.000
142A213ALA0-0.002-0.00268.0440.0000.0000.0000.0000.0000.000
143A214ARG10.9040.96569.5380.0460.0460.0000.0000.0000.000
144A215LYS10.9690.97369.7800.0380.0380.0000.0000.0000.000
145A216SER0-0.038-0.01269.414-0.001-0.0010.0000.0000.0000.000
146A217THR0-0.0070.01663.8950.0000.0000.0000.0000.0000.000
147A218TRP00.0170.01760.8560.0000.0000.0000.0000.0000.000
148A219HIS0-0.022-0.01261.393-0.002-0.0020.0000.0000.0000.000
149A220VAL00.0390.03854.9940.0010.0010.0000.0000.0000.000
150A221PHE0-0.024-0.01257.8790.0000.0000.0000.0000.0000.000
151A222PRO00.0270.01553.470-0.001-0.0010.0000.0000.0000.000
152A223VAL00.0110.00353.4930.0010.0010.0000.0000.0000.000
153A224SER00.0500.01248.343-0.001-0.0010.0000.0000.0000.000
154A225SER00.0650.02949.440-0.002-0.0020.0000.0000.0000.000
155A226SER0-0.032-0.01650.542-0.001-0.0010.0000.0000.0000.000
156A227ILE00.0110.00349.3560.0010.0010.0000.0000.0000.000
157A228GLN00.0650.04844.326-0.001-0.0010.0000.0000.0000.000
158A229ARG10.9260.96348.0850.0770.0770.0000.0000.0000.000
159A230LEU0-0.116-0.07150.1570.0010.0010.0000.0000.0000.000
160A231LEU00.0460.02346.2730.0030.0030.0000.0000.0000.000
161A232ASP-1-0.845-0.90445.397-0.109-0.1090.0000.0000.0000.000
162A233GLN0-0.144-0.08447.3570.0040.0040.0000.0000.0000.000
163A234GLY00.0390.02148.8630.0030.0030.0000.0000.0000.000
164A235LYS10.8470.93849.7760.0740.0740.0000.0000.0000.000
165A236SER00.0550.02351.481-0.003-0.0030.0000.0000.0000.000
166A237SER0-0.0040.00653.1370.0010.0010.0000.0000.0000.000
167A238LEU0-0.040-0.01856.002-0.002-0.0020.0000.0000.0000.000
168A239ASP-1-0.858-0.91258.392-0.049-0.0490.0000.0000.0000.000
169A240VAL0-0.015-0.02660.231-0.001-0.0010.0000.0000.0000.000
170A241ARG10.8890.93963.1880.0500.0500.0000.0000.0000.000
171A242ILE0-0.011-0.01264.401-0.002-0.0020.0000.0000.0000.000
172A243ALA0-0.048-0.02267.3980.0020.0020.0000.0000.0000.000
173A244CYS0-0.024-0.00869.259-0.001-0.0010.0000.0000.0000.000
174A245GLU-1-0.874-0.92971.614-0.044-0.0440.0000.0000.0000.000
175A246GLN00.019-0.00373.1000.0000.0000.0000.0000.0000.000
176A248GLN00.0750.04174.4580.0000.0000.0000.0000.0000.000
177A249GLU-1-0.906-0.94877.853-0.037-0.0370.0000.0000.0000.000
178A250SER0-0.032-0.03475.3460.0000.0000.0000.0000.0000.000
179A251GLY0-0.060-0.02077.2080.0000.0000.0000.0000.0000.000
180A252ALA0-0.044-0.03572.6560.0000.0000.0000.0000.0000.000
181A253SER0-0.014-0.02073.1250.0010.0010.0000.0000.0000.000
182A254LEU0-0.002-0.00466.5200.0000.0000.0000.0000.0000.000
183A255VAL0-0.0080.00467.5680.0010.0010.0000.0000.0000.000
184A256LEU0-0.037-0.02166.875-0.002-0.0020.0000.0000.0000.000
185A257LEU00.0300.01067.9070.0000.0000.0000.0000.0000.000
186A258GLY0-0.022-0.00868.1910.0000.0000.0000.0000.0000.000
187A283GLU-1-0.859-0.93368.757-0.034-0.0340.0000.0000.0000.000
188A284GLU-1-0.827-0.91870.973-0.028-0.0280.0000.0000.0000.000
189A285LYS10.8820.93870.1510.0310.0310.0000.0000.0000.000
190A286GLU-1-0.896-0.97369.802-0.036-0.0360.0000.0000.0000.000
191A287GLN0-0.0150.00766.853-0.001-0.0010.0000.0000.0000.000
192A288SER0-0.075-0.04064.052-0.001-0.0010.0000.0000.0000.000
193A289HIS10.8380.92263.7650.0380.0380.0000.0000.0000.000
194A290ARG11.0021.01562.5590.0390.0390.0000.0000.0000.000
195A291PRO00.0110.01662.049-0.001-0.0010.0000.0000.0000.000
196A292PHE0-0.009-0.00955.5460.0010.0010.0000.0000.0000.000
197A293LEU00.0060.00153.479-0.001-0.0010.0000.0000.0000.000
198A294MET0-0.034-0.00348.4580.0010.0010.0000.0000.0000.000
199A295LEU00.005-0.01647.250-0.002-0.0020.0000.0000.0000.000
200A296GLN00.0400.03842.5080.0060.0060.0000.0000.0000.000
201A297ALA00.006-0.00642.751-0.003-0.0030.0000.0000.0000.000
202A298ARG10.9730.99435.0170.1560.1560.0000.0000.0000.000
203A299GLN0-0.0220.00834.972-0.007-0.0070.0000.0000.0000.000