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: LZR39

Calculation Name: 3H0T-B-Xray372

Preferred Name: Hepcidin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3H0T

Chain ID: B

ChEMBL ID: CHEMBL3989381

UniProt ID: P81172

Base Structure: X-ray

Registration Date: 2023-06-26

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2245188.01821
FMO2-HF: Nuclear repulsion 2161666.944051
FMO2-HF: Total energy -83521.074159
FMO2-MP2: Total energy -83766.219657


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(B:1:GLN)


Summations of interaction energy for fragment #1(B:1: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.
-15.031-14.2118.37-4.246-4.9420.041
Interaction energy analysis for fragmet #1(B:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.029
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].
3B3GLN0-0.031-0.0151.874-12.749-12.1288.373-4.189-4.8050.041
4B4LEU0-0.017-0.0115.359-0.958-0.919-0.001-0.005-0.0320.000
5B5GLN00.0150.0048.5320.1540.1540.0000.0000.0000.000
6B6GLN0-0.005-0.01710.609-0.283-0.2830.0000.0000.0000.000
7B7SER00.0140.00814.0660.0590.0590.0000.0000.0000.000
8B8GLY00.0430.01517.123-0.069-0.0690.0000.0000.0000.000
9B9PRO0-0.021-0.00820.9190.0230.0230.0000.0000.0000.000
10B10GLY00.0890.04723.382-0.005-0.0050.0000.0000.0000.000
11B11LEU0-0.085-0.02823.966-0.017-0.0170.0000.0000.0000.000
12B12VAL0-0.012-0.00527.0140.0040.0040.0000.0000.0000.000
13B13LYS10.8710.93929.770-0.101-0.1010.0000.0000.0000.000
14B14PRO00.0480.01033.497-0.003-0.0030.0000.0000.0000.000
15B15SER0-0.076-0.03535.3000.0010.0010.0000.0000.0000.000
16B16GLN00.0190.01332.4640.0040.0040.0000.0000.0000.000
17B17THR00.009-0.01328.686-0.006-0.0060.0000.0000.0000.000
18B18LEU0-0.0140.01623.5490.0140.0140.0000.0000.0000.000
19B19SER00.025-0.00924.199-0.024-0.0240.0000.0000.0000.000
20B20LEU0-0.033-0.00319.1470.0280.0280.0000.0000.0000.000
21B21THR0-0.019-0.01516.805-0.063-0.0630.0000.0000.0000.000
22B22CYS0-0.074-0.00913.1060.0760.0760.0000.0000.0000.000
23B23ALA00.0260.01412.510-0.137-0.1370.0000.0000.0000.000
24B24ILE0-0.0160.0038.9140.2550.2550.0000.0000.0000.000
25B25SER0-0.0070.0066.031-0.214-0.2140.0000.0000.0000.000
26B26GLY00.0390.0084.016-0.770-0.742-0.001-0.0400.0130.000
27B27ASP-1-0.788-0.8804.598-2.079-1.947-0.001-0.012-0.1180.000
28B28SER0-0.038-0.0187.3710.3860.3860.0000.0000.0000.000
29B29VAL00.0630.02011.060-0.015-0.0150.0000.0000.0000.000
30B30SER0-0.041-0.02913.9640.0540.0540.0000.0000.0000.000
31B31SER0-0.0290.00011.2170.0860.0860.0000.0000.0000.000
32B32ASN00.015-0.00613.747-0.009-0.0090.0000.0000.0000.000
33B33SER0-0.017-0.01412.7690.0180.0180.0000.0000.0000.000
34B34ALA00.0010.02111.543-0.012-0.0120.0000.0000.0000.000
35B35ALA0-0.047-0.02213.5100.0880.0880.0000.0000.0000.000
36B36TRP00.0060.0099.076-0.049-0.0490.0000.0000.0000.000
37B37ASN00.026-0.00615.1930.0940.0940.0000.0000.0000.000
38B38TRP00.0340.01816.4120.0330.0330.0000.0000.0000.000
39B39ILE0-0.014-0.00716.276-0.024-0.0240.0000.0000.0000.000
40B40ARG10.7620.87119.6060.0350.0350.0000.0000.0000.000
41B41GLN00.0430.02719.574-0.011-0.0110.0000.0000.0000.000
42B42SER00.0330.02022.6690.0220.0220.0000.0000.0000.000
43B43PRO00.0230.01725.636-0.017-0.0170.0000.0000.0000.000
44B44SER0-0.042-0.03127.4860.0060.0060.0000.0000.0000.000
45B45ARG10.8850.93827.9590.0110.0110.0000.0000.0000.000
46B46GLY0-0.0090.01025.552-0.012-0.0120.0000.0000.0000.000
47B47LEU0-0.036-0.02919.4690.0120.0120.0000.0000.0000.000
48B48GLU-1-0.737-0.84823.266-0.041-0.0410.0000.0000.0000.000
49B49TRP0-0.001-0.01119.8660.0220.0220.0000.0000.0000.000
50B50LEU0-0.004-0.00622.0240.0130.0130.0000.0000.0000.000
51B51GLY00.0540.01021.9180.0080.0080.0000.0000.0000.000
52B52ARG10.7310.88018.8280.2390.2390.0000.0000.0000.000
53B53THR0-0.012-0.00818.3520.0140.0140.0000.0000.0000.000
54B54TYR0-0.020-0.05118.096-0.059-0.0590.0000.0000.0000.000
55B55TYR00.0200.02418.4140.0440.0440.0000.0000.0000.000
56B56ARG10.8380.90116.4120.3550.3550.0000.0000.0000.000
57B57SER0-0.014-0.00422.2170.0130.0130.0000.0000.0000.000
58B58LYS10.9220.96123.7530.1500.1500.0000.0000.0000.000
59B59TRP00.0330.01817.582-0.018-0.0180.0000.0000.0000.000
60B60PHE0-0.022-0.00422.8390.0290.0290.0000.0000.0000.000
61B61ASN00.0410.02422.523-0.035-0.0350.0000.0000.0000.000
62B62ASP-1-0.759-0.82723.550-0.179-0.1790.0000.0000.0000.000
63B63TYR00.030-0.00824.347-0.001-0.0010.0000.0000.0000.000
64B64ALA00.0420.02926.392-0.003-0.0030.0000.0000.0000.000
65B65VAL00.0530.00627.9950.0100.0100.0000.0000.0000.000
66B66SER0-0.050-0.02029.7630.0050.0050.0000.0000.0000.000
67B67VAL00.0110.00127.1630.0090.0090.0000.0000.0000.000
68B68GLN0-0.0090.00430.1670.0040.0040.0000.0000.0000.000
69B69SER0-0.005-0.00931.1430.0020.0020.0000.0000.0000.000
70B70ARG10.7920.88031.359-0.006-0.0060.0000.0000.0000.000
71B71ILE0-0.0160.01224.5550.0100.0100.0000.0000.0000.000
72B72THR0-0.024-0.00326.371-0.005-0.0050.0000.0000.0000.000
73B73ILE0-0.0090.00820.8270.0120.0120.0000.0000.0000.000
74B74ASN00.0120.00622.678-0.028-0.0280.0000.0000.0000.000
75B75PRO00.0180.01019.2810.0180.0180.0000.0000.0000.000
76B76ASP-1-0.750-0.83418.8440.0380.0380.0000.0000.0000.000
77B77THR00.025-0.01417.464-0.006-0.0060.0000.0000.0000.000
78B78SER0-0.070-0.05017.581-0.005-0.0050.0000.0000.0000.000
79B79LYS10.8390.90217.298-0.051-0.0510.0000.0000.0000.000
80B80ASN0-0.036-0.00210.5460.0250.0250.0000.0000.0000.000
81B81GLN00.0260.01313.3020.0450.0450.0000.0000.0000.000
82B82PHE00.013-0.00113.593-0.052-0.0520.0000.0000.0000.000
83B83SER0-0.002-0.01017.7600.0510.0510.0000.0000.0000.000
84B84LEU0-0.0070.00120.509-0.037-0.0370.0000.0000.0000.000
85B85GLN0-0.040-0.03022.6040.0160.0160.0000.0000.0000.000
86B86LEU00.0330.01426.053-0.018-0.0180.0000.0000.0000.000
87B87ASN00.0090.01828.5570.0210.0210.0000.0000.0000.000
88B88SER00.0150.00232.031-0.006-0.0060.0000.0000.0000.000
89B89VAL0-0.037-0.00129.304-0.005-0.0050.0000.0000.0000.000
90B90THR00.023-0.02232.5890.0020.0020.0000.0000.0000.000
91B91PRO00.0270.00432.3100.0050.0050.0000.0000.0000.000
92B92GLU-1-0.859-0.90731.9660.0220.0220.0000.0000.0000.000
93B93ASP-1-0.776-0.84928.6160.0140.0140.0000.0000.0000.000
94B94THR0-0.0030.02227.2230.0150.0150.0000.0000.0000.000
95B95ALA0-0.050-0.01824.080-0.016-0.0160.0000.0000.0000.000
96B96VAL0-0.0030.00518.1380.0270.0270.0000.0000.0000.000
97B97TYR00.008-0.02219.717-0.051-0.0510.0000.0000.0000.000
98B98TYR00.0180.00214.3260.0730.0730.0000.0000.0000.000
99B100ALA00.0590.00911.7840.0170.0170.0000.0000.0000.000
100B101ARG10.7650.8757.0721.5031.5030.0000.0000.0000.000
101B102GLY00.039-0.00611.639-0.002-0.0020.0000.0000.0000.000
102B103ILE00.0160.01913.726-0.037-0.0370.0000.0000.0000.000
103B104VAL00.000-0.01415.8090.0440.0440.0000.0000.0000.000
104B105PHE0-0.0050.00218.9900.0250.0250.0000.0000.0000.000
105B106SER00.0420.01718.6970.0180.0180.0000.0000.0000.000
106B107TYR0-0.067-0.03820.0770.0060.0060.0000.0000.0000.000
107B108ALA00.0160.03116.5610.0120.0120.0000.0000.0000.000
108B109MET0-0.017-0.01713.966-0.001-0.0010.0000.0000.0000.000
109B110ASP-1-0.870-0.9149.034-1.146-1.1460.0000.0000.0000.000
110B111VAL00.0140.0105.909-0.121-0.1210.0000.0000.0000.000
111B112TRP00.012-0.0038.7000.2170.2170.0000.0000.0000.000
112B113GLY00.0430.0209.2850.0940.0940.0000.0000.0000.000
113B114GLN0-0.043-0.02010.0390.0940.0940.0000.0000.0000.000
114B115GLY00.0190.00911.558-0.101-0.1010.0000.0000.0000.000
115B116THR0-0.045-0.02915.2390.0900.0900.0000.0000.0000.000
116B117THR0-0.002-0.00517.950-0.047-0.0470.0000.0000.0000.000
117B118VAL0-0.0170.00721.4700.0180.0180.0000.0000.0000.000
118B119THR0-0.008-0.01524.240-0.022-0.0220.0000.0000.0000.000
119B120VAL00.000-0.00427.7220.0070.0070.0000.0000.0000.000
120B121SER00.016-0.01330.796-0.009-0.0090.0000.0000.0000.000
121B122SER00.021-0.00133.7410.0070.0070.0000.0000.0000.000
122B123ALA00.0140.03035.3630.0000.0000.0000.0000.0000.000
123B124SER00.006-0.00835.2180.0060.0060.0000.0000.0000.000
124B125THR0-0.035-0.02835.438-0.003-0.0030.0000.0000.0000.000
125B126LYS10.8870.95036.747-0.073-0.0730.0000.0000.0000.000
126B127GLY00.0700.04437.9130.0040.0040.0000.0000.0000.000
127B128PRO0-0.043-0.01938.096-0.005-0.0050.0000.0000.0000.000
128B129SER0-0.022-0.00440.248-0.002-0.0020.0000.0000.0000.000
129B130VAL00.0050.00341.1180.0000.0000.0000.0000.0000.000
130B131PHE0-0.015-0.01843.502-0.002-0.0020.0000.0000.0000.000
131B132PRO00.0160.01144.4080.0020.0020.0000.0000.0000.000
132B133LEU0-0.032-0.01141.520-0.002-0.0020.0000.0000.0000.000
133B134ALA00.0320.01345.7380.0000.0000.0000.0000.0000.000
134B135PRO00.0450.03848.137-0.002-0.0020.0000.0000.0000.000
135B136SER0-0.036-0.03549.192-0.001-0.0010.0000.0000.0000.000
136B137SER00.0510.03051.0330.0000.0000.0000.0000.0000.000
137B138LYS10.9450.96149.469-0.015-0.0150.0000.0000.0000.000
138B139SER0-0.039-0.00446.111-0.001-0.0010.0000.0000.0000.000
139B140THR0-0.011-0.02046.8200.0020.0020.0000.0000.0000.000
140B141SER0-0.011-0.00246.397-0.002-0.0020.0000.0000.0000.000
141B142GLY00.0240.01748.1580.0010.0010.0000.0000.0000.000
142B143GLY00.011-0.00249.7060.0010.0010.0000.0000.0000.000
143B144THR0-0.0010.00144.0800.0020.0020.0000.0000.0000.000
144B145ALA00.0000.01147.082-0.002-0.0020.0000.0000.0000.000
145B146ALA00.0030.00742.7030.0020.0020.0000.0000.0000.000
146B147LEU00.0150.01443.430-0.001-0.0010.0000.0000.0000.000
147B148GLY00.034-0.00941.7950.0010.0010.0000.0000.0000.000
148B149CYS0-0.092-0.01340.6060.0030.0030.0000.0000.0000.000
149B150LEU00.0270.02039.5100.0020.0020.0000.0000.0000.000
150B151VAL0-0.004-0.00836.7460.0000.0000.0000.0000.0000.000
151B152LYS10.8750.89938.110-0.044-0.0440.0000.0000.0000.000
152B153ASP-1-0.819-0.89138.7650.0520.0520.0000.0000.0000.000
153B154TYR0-0.011-0.01631.673-0.004-0.0040.0000.0000.0000.000
154B155PHE00.0200.00531.4590.0010.0010.0000.0000.0000.000
155B156PRO00.0300.02529.800-0.004-0.0040.0000.0000.0000.000
156B157GLU-1-0.788-0.88327.9940.1160.1160.0000.0000.0000.000
157B158PRO0-0.029-0.00927.6850.0100.0100.0000.0000.0000.000
158B159VAL00.020-0.00329.789-0.003-0.0030.0000.0000.0000.000
159B160THR0-0.045-0.01630.1750.0060.0060.0000.0000.0000.000
160B161VAL0-0.013-0.02132.806-0.004-0.0040.0000.0000.0000.000
161B162SER0-0.037-0.00734.7650.0040.0040.0000.0000.0000.000
162B163TRP00.0390.00437.190-0.005-0.0050.0000.0000.0000.000
163B164ASN00.002-0.01740.4290.0020.0020.0000.0000.0000.000
164B165SER0-0.026-0.02240.7780.0000.0000.0000.0000.0000.000
165B166GLY0-0.003-0.00338.1410.0040.0040.0000.0000.0000.000
166B167ALA0-0.0070.01538.8990.0000.0000.0000.0000.0000.000
167B168LEU0-0.040-0.00540.802-0.003-0.0030.0000.0000.0000.000
168B169THR00.008-0.01135.4920.0010.0010.0000.0000.0000.000
169B170SER00.012-0.00136.461-0.002-0.0020.0000.0000.0000.000
170B171GLY00.0510.02336.967-0.001-0.0010.0000.0000.0000.000
171B172VAL0-0.046-0.02035.047-0.002-0.0020.0000.0000.0000.000
172B173HIS0-0.021-0.00431.0320.0010.0010.0000.0000.0000.000
173B174THR0-0.004-0.00431.961-0.005-0.0050.0000.0000.0000.000
174B175PHE0-0.0150.00030.9940.0020.0020.0000.0000.0000.000
175B176PRO00.0490.01727.3310.0080.0080.0000.0000.0000.000
176B177ALA0-0.0170.00429.382-0.010-0.0100.0000.0000.0000.000
177B178VAL0-0.030-0.01230.132-0.002-0.0020.0000.0000.0000.000
178B179LEU0-0.0140.00430.4220.0060.0060.0000.0000.0000.000
179B180GLN0-0.040-0.03233.010-0.012-0.0120.0000.0000.0000.000
180B181SER00.0490.01536.1660.0050.0050.0000.0000.0000.000
181B182SER00.008-0.00138.1560.0010.0010.0000.0000.0000.000
182B183GLY00.0050.01635.2420.0020.0020.0000.0000.0000.000
183B184LEU0-0.027-0.00535.1570.0090.0090.0000.0000.0000.000
184B185TYR00.0390.02028.546-0.004-0.0040.0000.0000.0000.000
185B186SER00.000-0.00734.591-0.002-0.0020.0000.0000.0000.000
186B187LEU00.0340.04232.1440.0000.0000.0000.0000.0000.000
187B188SER00.001-0.00635.204-0.005-0.0050.0000.0000.0000.000
188B189SER0-0.016-0.01335.2840.0020.0020.0000.0000.0000.000
189B190VAL0-0.004-0.00436.887-0.003-0.0030.0000.0000.0000.000
190B191VAL00.0300.02637.9930.0030.0030.0000.0000.0000.000
191B192THR0-0.003-0.00740.370-0.004-0.0040.0000.0000.0000.000
192B193VAL00.0130.00642.4420.0020.0020.0000.0000.0000.000
193B194PRO00.0710.04045.421-0.002-0.0020.0000.0000.0000.000
194B195SER00.0240.01748.6600.0020.0020.0000.0000.0000.000
195B196SER00.007-0.00651.0420.0010.0010.0000.0000.0000.000
196B197SER00.0000.00149.8230.0010.0010.0000.0000.0000.000
197B198LEU0-0.008-0.00549.1360.0020.0020.0000.0000.0000.000
198B199GLY0-0.045-0.01652.5570.0010.0010.0000.0000.0000.000
199B200THR0-0.008-0.00854.4160.0000.0000.0000.0000.0000.000
200B201GLN0-0.0180.00648.5850.0010.0010.0000.0000.0000.000
201B202THR0-0.033-0.01649.0540.0000.0000.0000.0000.0000.000
202B203TYR00.0280.00045.2780.0030.0030.0000.0000.0000.000
203B204ILE00.0270.00744.517-0.001-0.0010.0000.0000.0000.000
204B206ASN00.0170.00739.4150.0000.0000.0000.0000.0000.000
205B207VAL00.0330.00937.5410.0040.0040.0000.0000.0000.000
206B208ASN0-0.022-0.02735.287-0.004-0.0040.0000.0000.0000.000
207B209HIS00.0690.04533.643-0.001-0.0010.0000.0000.0000.000
208B210LYS10.9990.98230.774-0.167-0.1670.0000.0000.0000.000
209B211PRO00.0160.02631.140-0.002-0.0020.0000.0000.0000.000
210B212SER0-0.012-0.03533.806-0.004-0.0040.0000.0000.0000.000
211B213ASN0-0.052-0.01636.857-0.002-0.0020.0000.0000.0000.000
212B214THR00.0130.01638.410-0.009-0.0090.0000.0000.0000.000
213B215LYS10.8240.89738.972-0.076-0.0760.0000.0000.0000.000
214B216VAL00.0120.01141.080-0.004-0.0040.0000.0000.0000.000
215B217ASP-1-0.796-0.87942.2370.0740.0740.0000.0000.0000.000
216B218LYS10.9150.96244.627-0.050-0.0500.0000.0000.0000.000
217B219LYS10.8840.92945.902-0.035-0.0350.0000.0000.0000.000
218B220VAL0-0.053-0.02844.994-0.001-0.0010.0000.0000.0000.000
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