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: JLMM9

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1937754.324757
FMO2-HF: Nuclear repulsion 1856392.806177
FMO2-HF: Total energy -81361.51858
FMO2-MP2: Total energy -81598.251824


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.
-0.9251.7081.47-1.574-2.530
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 : 0.028 / 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].
3A53GLU-1-0.887-0.9323.9210.4572.038-0.008-0.608-0.9650.001
4A54MET00.0340.0142.385-1.693-0.8601.478-0.918-1.394-0.001
5A55VAL0-0.003-0.0023.982-0.0840.1350.000-0.048-0.1710.000
6A56GLU-1-0.832-0.9316.6420.2860.2860.0000.0000.0000.000
7A57ALA00.0020.0168.3700.0410.0410.0000.0000.0000.000
8A58VAL00.0160.0028.7260.0380.0380.0000.0000.0000.000
9A59LYS10.8440.9258.8370.2750.2750.0000.0000.0000.000
10A60LYS10.8560.93412.7190.0590.0590.0000.0000.0000.000
11A61HIS00.0430.02713.8250.0590.0590.0000.0000.0000.000
12A62ILE00.0360.01113.7190.0190.0190.0000.0000.0000.000
13A63LEU0-0.039-0.02616.5040.0320.0320.0000.0000.0000.000
14A64ASN0-0.008-0.00217.7780.0430.0430.0000.0000.0000.000
15A65MET00.0020.00919.4980.0200.0200.0000.0000.0000.000
16A66LEU0-0.029-0.00420.1000.0060.0060.0000.0000.0000.000
17A67HIS0-0.054-0.02523.0660.0190.0190.0000.0000.0000.000
18A68LEU00.0090.01121.8000.0180.0180.0000.0000.0000.000
19A69LYS10.9480.96321.201-0.101-0.1010.0000.0000.0000.000
20A70LYS10.7830.86019.500-0.034-0.0340.0000.0000.0000.000
21A71ARG10.9850.98616.9530.0320.0320.0000.0000.0000.000
22A72PRO00.0610.03219.4870.0260.0260.0000.0000.0000.000
23A73ASP-1-0.796-0.87221.3040.0570.0570.0000.0000.0000.000
24A74VAL0-0.035-0.02320.889-0.020-0.0200.0000.0000.0000.000
25A75THR00.0090.01123.4800.0080.0080.0000.0000.0000.000
26A76GLN00.0140.00926.417-0.003-0.0030.0000.0000.0000.000
27A77PRO0-0.0170.00526.578-0.002-0.0020.0000.0000.0000.000
28A78VAL00.0470.01429.0550.0050.0050.0000.0000.0000.000
29A79PRO00.0380.00831.058-0.009-0.0090.0000.0000.0000.000
30A80LYS11.0060.99127.5000.1300.1300.0000.0000.0000.000
31A81ALA00.0430.02631.416-0.007-0.0070.0000.0000.0000.000
32A82ALA00.0050.00634.870-0.002-0.0020.0000.0000.0000.000
33A83LEU00.0210.01328.1400.0000.0000.0000.0000.0000.000
34A84LEU00.0340.00729.235-0.004-0.0040.0000.0000.0000.000
35A85ASN00.0080.01332.908-0.006-0.0060.0000.0000.0000.000
36A86ALA00.0070.00634.8550.0000.0000.0000.0000.0000.000
37A87ILE00.0180.00330.0470.0010.0010.0000.0000.0000.000
38A88ARG10.9650.99333.8790.1010.1010.0000.0000.0000.000
39A89LYS10.8610.92336.0480.0820.0820.0000.0000.0000.000
40A90LEU0-0.016-0.01835.8070.0040.0040.0000.0000.0000.000
41A91HIS10.7930.89136.2060.1210.1210.0000.0000.0000.000
42A92VAL00.0690.04131.935-0.001-0.0010.0000.0000.0000.000
43A93GLY0-0.026-0.01530.494-0.014-0.0140.0000.0000.0000.000
44A94LYS10.8260.90730.4990.2340.2340.0000.0000.0000.000
45A95VAL0-0.006-0.02530.028-0.010-0.0100.0000.0000.0000.000
46A96GLY00.0320.02131.4000.0120.0120.0000.0000.0000.000
47A97GLU-1-0.889-0.94931.573-0.165-0.1650.0000.0000.0000.000
48A98ASN0-0.108-0.04931.8360.0020.0020.0000.0000.0000.000
49A99GLY00.0190.02427.963-0.002-0.0020.0000.0000.0000.000
50A100TYR0-0.050-0.02724.1040.0100.0100.0000.0000.0000.000
51A101VAL0-0.016-0.01225.0200.0130.0130.0000.0000.0000.000
52A102GLU-1-0.768-0.86325.236-0.280-0.2800.0000.0000.0000.000
53A103ILE00.0210.01324.5590.0220.0220.0000.0000.0000.000
54A104GLU-1-0.887-0.92728.191-0.149-0.1490.0000.0000.0000.000
55A105ASP-1-0.834-0.89531.640-0.149-0.1490.0000.0000.0000.000
56A106ASP-1-0.857-0.91426.628-0.271-0.2710.0000.0000.0000.000
57A107ILE00.0300.00527.0190.0010.0010.0000.0000.0000.000
58A108GLY00.0020.00725.7090.0000.0000.0000.0000.0000.000
59A109ARG10.9020.93126.5250.2670.2670.0000.0000.0000.000
60A110ARG10.7910.86429.2200.1620.1620.0000.0000.0000.000
61A111ALA00.0130.00927.4010.0090.0090.0000.0000.0000.000
62A112GLU-1-0.922-0.95926.955-0.304-0.3040.0000.0000.0000.000
63A113MET0-0.040-0.02329.2630.0090.0090.0000.0000.0000.000
64A114ASN0-0.077-0.05332.2620.0120.0120.0000.0000.0000.000
65A115GLU-1-0.885-0.94527.122-0.287-0.2870.0000.0000.0000.000
66A116LEU0-0.041-0.00331.6360.0020.0020.0000.0000.0000.000
67A117MET0-0.042-0.03033.7830.0090.0090.0000.0000.0000.000
68A118GLU-1-0.908-0.95032.912-0.169-0.1690.0000.0000.0000.000
69A119GLN0-0.070-0.02630.9930.0020.0020.0000.0000.0000.000
70A120THR0-0.067-0.05036.061-0.001-0.0010.0000.0000.0000.000
71A121SER0-0.003-0.00339.6270.0030.0030.0000.0000.0000.000
72A122GLU-1-0.971-0.99542.829-0.107-0.1070.0000.0000.0000.000
73A123ILE0-0.041-0.02246.3900.0040.0040.0000.0000.0000.000
74A124ILE0-0.018-0.00949.5090.0010.0010.0000.0000.0000.000
75A125THR00.0150.00752.9900.0020.0020.0000.0000.0000.000
76A126PHE0-0.012-0.02855.2480.0010.0010.0000.0000.0000.000
77A127ALA0-0.033-0.00758.7960.0000.0000.0000.0000.0000.000
78A128GLU-1-0.911-0.95361.679-0.059-0.0590.0000.0000.0000.000
79A129SER0-0.054-0.03263.9980.0000.0000.0000.0000.0000.000
80A130GLY00.0430.02867.0300.0000.0000.0000.0000.0000.000
81A131THR00.0140.00067.7080.0010.0010.0000.0000.0000.000
82A132ALA0-0.0030.00869.6730.0020.0020.0000.0000.0000.000
83A133ARG10.9730.96371.0750.0450.0450.0000.0000.0000.000
84A134LYS10.9380.96770.4220.0480.0480.0000.0000.0000.000
85A135THR00.0160.00466.144-0.002-0.0020.0000.0000.0000.000
86A136LEU0-0.045-0.00163.2880.0020.0020.0000.0000.0000.000
87A137HIS10.8430.88760.9040.0650.0650.0000.0000.0000.000
88A138PHE0-0.014-0.01757.3950.0010.0010.0000.0000.0000.000
89A139GLU-1-0.744-0.83056.519-0.075-0.0750.0000.0000.0000.000
90A140ILE0-0.027-0.01150.2900.0000.0000.0000.0000.0000.000
91A141SER00.0280.01049.5490.0000.0000.0000.0000.0000.000
92A142LYS10.8510.90144.5180.1100.1100.0000.0000.0000.000
93A143GLU-1-0.813-0.87443.171-0.123-0.1230.0000.0000.0000.000
94A144GLY0-0.012-0.02144.569-0.006-0.0060.0000.0000.0000.000
95A145SER0-0.101-0.06145.313-0.002-0.0020.0000.0000.0000.000
96A146ASP-1-0.788-0.87140.913-0.125-0.1250.0000.0000.0000.000
97A147LEU0-0.0180.01640.074-0.010-0.0100.0000.0000.0000.000
98A148SER0-0.034-0.02839.0620.0000.0000.0000.0000.0000.000
99A149VAL0-0.039-0.00737.7910.0010.0010.0000.0000.0000.000
100A150VAL0-0.016-0.01441.0130.0020.0020.0000.0000.0000.000
101A151GLU-1-0.813-0.86439.136-0.167-0.1670.0000.0000.0000.000
102A152ARG10.8060.87443.4020.1080.1080.0000.0000.0000.000
103A153ALA00.0470.03147.1030.0010.0010.0000.0000.0000.000
104A154GLU-1-0.821-0.89050.337-0.092-0.0920.0000.0000.0000.000
105A155VAL00.0240.01953.8470.0010.0010.0000.0000.0000.000
106A156TRP0-0.032-0.02454.7310.0030.0030.0000.0000.0000.000
107A157LEU00.0070.00159.4020.0020.0020.0000.0000.0000.000
108A158PHE00.0280.00963.2260.0000.0000.0000.0000.0000.000
109A159LEU0-0.0030.00965.8670.0020.0020.0000.0000.0000.000
110A160LYS10.8280.90468.6050.0470.0470.0000.0000.0000.000
111A161VAL00.0360.01171.4340.0010.0010.0000.0000.0000.000
112A162PRO00.0260.01774.0470.0000.0000.0000.0000.0000.000
113A163LYS10.9360.95976.9760.0380.0380.0000.0000.0000.000
114A164ALA00.0370.02475.655-0.001-0.0010.0000.0000.0000.000
115A165ASN0-0.0060.00376.3970.0020.0020.0000.0000.0000.000
116A166ARG10.9920.98675.5940.0390.0390.0000.0000.0000.000
117A167THR00.0090.00676.685-0.001-0.0010.0000.0000.0000.000
118A168ARG10.8510.89075.1710.0450.0450.0000.0000.0000.000
119A169THR00.0110.01571.563-0.001-0.0010.0000.0000.0000.000
120A170LYS10.8150.89567.3430.0540.0540.0000.0000.0000.000
121A171VAL00.0030.01669.5010.0020.0020.0000.0000.0000.000
122A172THR00.006-0.00666.935-0.002-0.0020.0000.0000.0000.000
123A173ILE0-0.032-0.02065.0900.0020.0020.0000.0000.0000.000
124A174ARG10.8160.90064.3100.0570.0570.0000.0000.0000.000
125A175LEU00.0170.01259.9190.0020.0020.0000.0000.0000.000
126A176PHE00.011-0.00661.902-0.002-0.0020.0000.0000.0000.000
127A177GLN00.0750.05456.988-0.001-0.0010.0000.0000.0000.000
128A178GLN0-0.050-0.03661.1410.0010.0010.0000.0000.0000.000
129A179GLN00.0260.00357.248-0.004-0.0040.0000.0000.0000.000
130A180LYS10.9891.00260.7720.0630.0630.0000.0000.0000.000
131A202SER0-0.009-0.00763.1000.0010.0010.0000.0000.0000.000
132A203GLU-1-0.830-0.90263.416-0.061-0.0610.0000.0000.0000.000
133A204LEU0-0.0210.00457.2550.0000.0000.0000.0000.0000.000
134A205LEU0-0.019-0.00860.6560.0010.0010.0000.0000.0000.000
135A206LEU0-0.028-0.01156.252-0.003-0.0030.0000.0000.0000.000
136A207SER00.032-0.00157.109-0.002-0.0020.0000.0000.0000.000
137A208GLU-1-0.864-0.91259.474-0.061-0.0610.0000.0000.0000.000
138A209LYS10.8340.92559.9550.0700.0700.0000.0000.0000.000
139A210VAL00.0190.01762.9900.0020.0020.0000.0000.0000.000
140A211VAL0-0.020-0.01063.721-0.002-0.0020.0000.0000.0000.000
141A212ASP-1-0.794-0.87865.945-0.052-0.0520.0000.0000.0000.000
142A213ALA00.0320.01167.933-0.001-0.0010.0000.0000.0000.000
143A214ARG10.8520.90068.9910.0540.0540.0000.0000.0000.000
144A215LYS10.8390.91070.5560.0470.0470.0000.0000.0000.000
145A216SER0-0.040-0.02069.697-0.001-0.0010.0000.0000.0000.000
146A217THR00.0120.02764.7650.0000.0000.0000.0000.0000.000
147A218TRP00.0370.01861.2280.0010.0010.0000.0000.0000.000
148A219HIS0-0.035-0.02261.575-0.002-0.0020.0000.0000.0000.000
149A220VAL00.0620.04855.0340.0010.0010.0000.0000.0000.000
150A221PHE00.014-0.00857.6500.0020.0020.0000.0000.0000.000
151A222PRO00.0420.01752.634-0.001-0.0010.0000.0000.0000.000
152A223VAL0-0.023-0.01052.9390.0020.0020.0000.0000.0000.000
153A224SER00.0520.02247.6790.0010.0010.0000.0000.0000.000
154A225SER00.0550.02448.542-0.003-0.0030.0000.0000.0000.000
155A226SER0-0.024-0.00949.601-0.001-0.0010.0000.0000.0000.000
156A227ILE00.0000.00149.2540.0020.0020.0000.0000.0000.000
157A228GLN00.0120.00343.191-0.002-0.0020.0000.0000.0000.000
158A229ARG10.8990.94547.4090.0940.0940.0000.0000.0000.000
159A230LEU0-0.106-0.04949.5710.0020.0020.0000.0000.0000.000
160A231LEU00.0440.02345.9250.0020.0020.0000.0000.0000.000
161A232ASP-1-0.824-0.90044.910-0.132-0.1320.0000.0000.0000.000
162A233GLN0-0.093-0.03946.7550.0040.0040.0000.0000.0000.000
163A234GLY00.0400.01648.4830.0050.0050.0000.0000.0000.000
164A235LYS10.7870.89949.4010.0960.0960.0000.0000.0000.000
165A236SER00.0650.02150.550-0.003-0.0030.0000.0000.0000.000
166A237SER0-0.029-0.02752.8970.0010.0010.0000.0000.0000.000
167A238LEU0-0.075-0.03855.652-0.002-0.0020.0000.0000.0000.000
168A239ASP-1-0.829-0.89158.210-0.064-0.0640.0000.0000.0000.000
169A240VAL0-0.004-0.01759.814-0.001-0.0010.0000.0000.0000.000
170A241ARG10.8550.93062.9160.0600.0600.0000.0000.0000.000
171A242ILE00.006-0.00263.697-0.002-0.0020.0000.0000.0000.000
172A243ALA0-0.049-0.02267.0100.0020.0020.0000.0000.0000.000
173A244CYS00.0040.01068.514-0.001-0.0010.0000.0000.0000.000
174A245GLU-1-0.872-0.92771.030-0.053-0.0530.0000.0000.0000.000
175A246GLN00.0690.03372.1110.0000.0000.0000.0000.0000.000
176A248GLN00.0210.01174.1190.0010.0010.0000.0000.0000.000
177A249GLU-1-0.770-0.86077.619-0.043-0.0430.0000.0000.0000.000
178A250SER0-0.029-0.02375.1740.0010.0010.0000.0000.0000.000
179A251GLY0-0.041-0.01276.7940.0000.0000.0000.0000.0000.000
180A252ALA0-0.025-0.01872.8380.0000.0000.0000.0000.0000.000
181A253SER0-0.024-0.02673.1950.0010.0010.0000.0000.0000.000
182A254LEU00.0100.00066.5580.0000.0000.0000.0000.0000.000
183A255VAL0-0.023-0.01167.7770.0010.0010.0000.0000.0000.000
184A256LEU0-0.040-0.01766.818-0.002-0.0020.0000.0000.0000.000
185A257LEU00.0330.02068.3950.0000.0000.0000.0000.0000.000
186A258GLY00.024-0.00667.964-0.002-0.0020.0000.0000.0000.000
187A283GLU-1-0.806-0.90569.046-0.047-0.0470.0000.0000.0000.000
188A284GLU-1-0.858-0.93071.508-0.041-0.0410.0000.0000.0000.000
189A285LYS10.9180.96070.8300.0440.0440.0000.0000.0000.000
190A286GLU-1-0.818-0.88070.028-0.049-0.0490.0000.0000.0000.000
191A287GLN00.0290.01567.228-0.003-0.0030.0000.0000.0000.000
192A288SER0-0.035-0.01264.440-0.001-0.0010.0000.0000.0000.000
193A289HIS10.7880.86964.1030.0520.0520.0000.0000.0000.000
194A290ARG10.9640.99263.3500.0550.0550.0000.0000.0000.000
195A291PRO0-0.0080.00162.380-0.002-0.0020.0000.0000.0000.000
196A292PHE0-0.003-0.00255.5450.0010.0010.0000.0000.0000.000
197A293LEU0-0.0030.00153.4300.0000.0000.0000.0000.0000.000
198A294MET0-0.0030.01448.7630.0000.0000.0000.0000.0000.000
199A295LEU0-0.001-0.01847.2940.0000.0000.0000.0000.0000.000
200A296GLN00.0270.02141.9170.0060.0060.0000.0000.0000.000
201A297ALA0-0.013-0.02442.894-0.001-0.0010.0000.0000.0000.000
202A298ARG10.8990.95235.3170.1900.1900.0000.0000.0000.000
203A299GLN00.0070.00134.307-0.002-0.0020.0000.0000.0000.000