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: 39GVL

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2244292.882204
FMO2-HF: Nuclear repulsion 2160773.243428
FMO2-HF: Total energy -83519.638776
FMO2-MP2: Total energy -83764.990926


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.
-16.891-19.82814.395-5.55-5.9090.043
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 : 0.011 / q_NPA : -0.003
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].
3B3GLN0-0.080-0.0451.745-16.052-19.23514.398-5.479-5.7360.043
4B4LEU00.0700.0114.546-0.570-0.490-0.001-0.021-0.0590.000
5B5GLN0-0.0040.0008.3020.2750.2750.0000.0000.0000.000
6B6GLN00.0740.02610.429-0.327-0.3270.0000.0000.0000.000
7B7SER0-0.014-0.00413.8430.0930.0930.0000.0000.0000.000
8B8GLY00.0360.00916.928-0.079-0.0790.0000.0000.0000.000
9B9PRO0-0.046-0.02420.7120.0200.0200.0000.0000.0000.000
10B10GLY00.1000.05623.101-0.013-0.0130.0000.0000.0000.000
11B11LEU0-0.083-0.03123.691-0.022-0.0220.0000.0000.0000.000
12B12VAL00.0000.00426.7200.0080.0080.0000.0000.0000.000
13B13LYS10.9400.98029.503-0.092-0.0920.0000.0000.0000.000
14B14PRO00.0500.01333.230-0.003-0.0030.0000.0000.0000.000
15B15SER0-0.089-0.04235.0230.0050.0050.0000.0000.0000.000
16B16GLN00.0180.00332.2870.0050.0050.0000.0000.0000.000
17B17THR00.0120.00328.322-0.010-0.0100.0000.0000.0000.000
18B18LEU0-0.0100.01623.3440.0170.0170.0000.0000.0000.000
19B19SER0-0.029-0.03224.308-0.021-0.0210.0000.0000.0000.000
20B20LEU00.0040.00918.9160.0260.0260.0000.0000.0000.000
21B21THR0-0.070-0.04216.165-0.040-0.0400.0000.0000.0000.000
22B22CYS-1-0.809-0.88912.2480.0350.0350.0000.0000.0000.000
23B23ALA0-0.008-0.01512.103-0.096-0.0960.0000.0000.0000.000
24B24ILE00.0080.0188.5650.1620.1620.0000.0000.0000.000
25B25SER0-0.043-0.0155.9850.3510.3510.0000.0000.0000.000
26B26GLY00.031-0.0013.861-1.142-1.112-0.001-0.0440.0150.000
27B27ASP-1-0.817-0.9084.718-0.0530.083-0.001-0.006-0.1290.000
28B28SER0-0.022-0.0067.8430.0770.0770.0000.0000.0000.000
29B29VAL00.0750.02811.493-0.064-0.0640.0000.0000.0000.000
30B30SER0-0.070-0.04914.2620.0040.0040.0000.0000.0000.000
31B31SER0-0.0140.01511.6120.0450.0450.0000.0000.0000.000
32B32ASN00.004-0.01714.107-0.033-0.0330.0000.0000.0000.000
33B33SER0-0.048-0.03012.328-0.013-0.0130.0000.0000.0000.000
34B34ALA00.0220.03211.593-0.057-0.0570.0000.0000.0000.000
35B35ALA0-0.069-0.04813.5120.1020.1020.0000.0000.0000.000
36B36TRP00.0180.0219.061-0.141-0.1410.0000.0000.0000.000
37B37ASN00.002-0.01615.2700.1400.1400.0000.0000.0000.000
38B38TRP00.0630.03516.284-0.021-0.0210.0000.0000.0000.000
39B39ILE0-0.028-0.01316.067-0.006-0.0060.0000.0000.0000.000
40B40ARG10.7830.89718.8550.1140.1140.0000.0000.0000.000
41B41GLN00.0420.01918.979-0.030-0.0300.0000.0000.0000.000
42B42SER00.0270.01721.7650.0320.0320.0000.0000.0000.000
43B43PRO0-0.0010.01424.789-0.024-0.0240.0000.0000.0000.000
44B44SER0-0.047-0.04226.6780.0160.0160.0000.0000.0000.000
45B45ARG10.9530.98127.4370.0900.0900.0000.0000.0000.000
46B46GLY0-0.0090.01424.658-0.015-0.0150.0000.0000.0000.000
47B47LEU0-0.031-0.02818.6480.0130.0130.0000.0000.0000.000
48B48GLU-1-0.820-0.92122.464-0.124-0.1240.0000.0000.0000.000
49B49TRP0-0.016-0.00920.0010.0280.0280.0000.0000.0000.000
50B50LEU00.011-0.00321.9320.0300.0300.0000.0000.0000.000
51B51GLY00.0430.00222.0140.0260.0260.0000.0000.0000.000
52B52ARG10.7640.90518.8350.2850.2850.0000.0000.0000.000
53B53THR0-0.013-0.00918.2720.0390.0390.0000.0000.0000.000
54B54TYR0-0.005-0.02918.067-0.051-0.0510.0000.0000.0000.000
55B55TYR00.0270.02518.4190.0340.0340.0000.0000.0000.000
56B56ARG10.8500.92216.6850.2570.2570.0000.0000.0000.000
57B57SER0-0.016-0.00622.2870.0050.0050.0000.0000.0000.000
58B58LYS10.9530.98624.0110.0930.0930.0000.0000.0000.000
59B59TRP00.0310.01117.932-0.014-0.0140.0000.0000.0000.000
60B60PHE0-0.039-0.01522.8400.0190.0190.0000.0000.0000.000
61B61ASN00.0350.02622.523-0.027-0.0270.0000.0000.0000.000
62B62ASP-1-0.805-0.87723.563-0.197-0.1970.0000.0000.0000.000
63B63TYR00.019-0.02024.343-0.006-0.0060.0000.0000.0000.000
64B64ALA00.0420.03626.592-0.002-0.0020.0000.0000.0000.000
65B65VAL00.034-0.00728.1210.0150.0150.0000.0000.0000.000
66B66SER0-0.073-0.03329.4990.0110.0110.0000.0000.0000.000
67B67VAL00.0180.01126.9880.0120.0120.0000.0000.0000.000
68B68GLN00.0000.00329.9870.0040.0040.0000.0000.0000.000
69B69SER0-0.038-0.02530.9890.0070.0070.0000.0000.0000.000
70B70ARG10.8140.90330.4530.0370.0370.0000.0000.0000.000
71B71ILE0-0.0110.01224.2750.0100.0100.0000.0000.0000.000
72B72THR0-0.0200.00825.3870.0020.0020.0000.0000.0000.000
73B73ILE0-0.0050.01020.1970.0070.0070.0000.0000.0000.000
74B74ASN0-0.007-0.01021.920-0.020-0.0200.0000.0000.0000.000
75B75PRO00.0100.00118.9510.0160.0160.0000.0000.0000.000
76B76ASP-1-0.847-0.92018.4320.1320.1320.0000.0000.0000.000
77B77THR00.000-0.02417.5190.0030.0030.0000.0000.0000.000
78B78SER0-0.056-0.01417.5390.0180.0180.0000.0000.0000.000
79B79LYS10.9140.95616.967-0.185-0.1850.0000.0000.0000.000
80B80ASN0-0.0360.00310.6100.0340.0340.0000.0000.0000.000
81B81GLN00.0390.02412.8210.0370.0370.0000.0000.0000.000
82B82PHE00.023-0.00412.833-0.022-0.0220.0000.0000.0000.000
83B83SER00.0140.00317.0110.0560.0560.0000.0000.0000.000
84B84LEU00.0030.00919.746-0.042-0.0420.0000.0000.0000.000
85B85GLN0-0.044-0.03321.8980.0230.0230.0000.0000.0000.000
86B86LEU00.0350.01025.455-0.022-0.0220.0000.0000.0000.000
87B87ASN00.0010.01428.0730.0220.0220.0000.0000.0000.000
88B88SER0-0.016-0.01731.576-0.009-0.0090.0000.0000.0000.000
89B89VAL0-0.0230.00328.952-0.008-0.0080.0000.0000.0000.000
90B90THR00.024-0.00932.2690.0050.0050.0000.0000.0000.000
91B91PRO00.0300.00031.7240.0010.0010.0000.0000.0000.000
92B92GLU-1-0.886-0.93631.151-0.022-0.0220.0000.0000.0000.000
93B93ASP-1-0.768-0.85228.158-0.041-0.0410.0000.0000.0000.000
94B94THR0-0.0130.02526.5430.0120.0120.0000.0000.0000.000
95B95ALA0-0.049-0.02223.162-0.021-0.0210.0000.0000.0000.000
96B96VAL0-0.009-0.00317.2780.0400.0400.0000.0000.0000.000
97B97TYR0-0.001-0.03118.992-0.064-0.0640.0000.0000.0000.000
98B98TYR0-0.020-0.01713.5110.0690.0690.0000.0000.0000.000
99B99CYS-1-0.890-0.91212.793-0.091-0.0910.0000.0000.0000.000
100B100ALA00.054-0.00411.946-0.113-0.1130.0000.0000.0000.000
101B101ARG10.7770.8886.6801.3871.3870.0000.0000.0000.000
102B102GLY00.041-0.00811.633-0.106-0.1060.0000.0000.0000.000
103B103ILE00.0080.01813.7240.0470.0470.0000.0000.0000.000
104B104VAL0-0.006-0.01815.8070.0360.0360.0000.0000.0000.000
105B105PHE0-0.016-0.00418.9890.0150.0150.0000.0000.0000.000
106B106SER00.0300.00718.7420.0220.0220.0000.0000.0000.000
107B107TYR0-0.037-0.01720.094-0.006-0.0060.0000.0000.0000.000
108B108ALA00.0130.02816.444-0.003-0.0030.0000.0000.0000.000
109B109MET0-0.015-0.00813.9420.0460.0460.0000.0000.0000.000
110B110ASP-1-0.881-0.8999.861-1.321-1.3210.0000.0000.0000.000
111B111VAL0-0.012-0.0126.179-0.389-0.3890.0000.0000.0000.000
112B112TRP0-0.009-0.0148.7520.4800.4800.0000.0000.0000.000
113B113GLY00.1010.0588.304-0.170-0.1700.0000.0000.0000.000
114B114GLN0-0.069-0.0399.3990.1930.1930.0000.0000.0000.000
115B115GLY0-0.0060.00210.822-0.067-0.0670.0000.0000.0000.000
116B116THR0-0.025-0.01014.5200.1280.1280.0000.0000.0000.000
117B117THR0-0.019-0.01617.591-0.059-0.0590.0000.0000.0000.000
118B118VAL0-0.0060.01120.9300.0310.0310.0000.0000.0000.000
119B119THR0-0.018-0.02423.886-0.029-0.0290.0000.0000.0000.000
120B120VAL00.0080.00627.2870.0120.0120.0000.0000.0000.000
121B121SER00.010-0.01830.420-0.010-0.0100.0000.0000.0000.000
122B122SER0-0.023-0.02033.4070.0080.0080.0000.0000.0000.000
123B123ALA0-0.0140.00835.1030.0030.0030.0000.0000.0000.000
124B124SER0-0.034-0.02034.9370.0080.0080.0000.0000.0000.000
125B125THR0-0.010-0.02935.145-0.005-0.0050.0000.0000.0000.000
126B126LYS10.9100.97636.474-0.057-0.0570.0000.0000.0000.000
127B127GLY00.0630.03837.6140.0030.0030.0000.0000.0000.000
128B128PRO0-0.061-0.02137.933-0.006-0.0060.0000.0000.0000.000
129B129SER0-0.015-0.00739.874-0.001-0.0010.0000.0000.0000.000
130B130VAL0-0.0020.00240.782-0.002-0.0020.0000.0000.0000.000
131B131PHE00.000-0.00943.151-0.001-0.0010.0000.0000.0000.000
132B132PRO00.0070.00644.0440.0010.0010.0000.0000.0000.000
133B133LEU0-0.035-0.01741.038-0.003-0.0030.0000.0000.0000.000
134B134ALA00.0370.01645.3640.0000.0000.0000.0000.0000.000
135B135PRO00.0530.04647.867-0.003-0.0030.0000.0000.0000.000
136B136SER0-0.031-0.02348.8730.0000.0000.0000.0000.0000.000
137B137SER00.0570.02550.690-0.001-0.0010.0000.0000.0000.000
138B138LYS10.9230.94249.3040.0080.0080.0000.0000.0000.000
139B139SER0-0.0280.00745.703-0.002-0.0020.0000.0000.0000.000
140B140THR00.001-0.02046.4930.0020.0020.0000.0000.0000.000
141B141SER0-0.021-0.00646.100-0.002-0.0020.0000.0000.0000.000
142B142GLY00.0330.02247.9040.0010.0010.0000.0000.0000.000
143B143GLY00.017-0.00149.5320.0020.0020.0000.0000.0000.000
144B144THR0-0.024-0.00543.8660.0030.0030.0000.0000.0000.000
145B145ALA0-0.0010.00446.859-0.003-0.0030.0000.0000.0000.000
146B146ALA00.0350.03142.5060.0020.0020.0000.0000.0000.000
147B147LEU00.0070.00743.1540.0000.0000.0000.0000.0000.000
148B148GLY00.026-0.01841.4720.0000.0000.0000.0000.0000.000
149B149CYS0-0.085-0.01140.3870.0050.0050.0000.0000.0000.000
150B150LEU00.0290.02439.0720.0000.0000.0000.0000.0000.000
151B151VAL0-0.023-0.01936.6150.0030.0030.0000.0000.0000.000
152B152LYS10.9520.96037.668-0.016-0.0160.0000.0000.0000.000
153B153ASP-1-0.839-0.91538.2820.0330.0330.0000.0000.0000.000
154B154TYR00.0340.01431.9140.0040.0040.0000.0000.0000.000
155B155PHE00.0100.00531.095-0.002-0.0020.0000.0000.0000.000
156B156PRO00.0250.02629.479-0.002-0.0020.0000.0000.0000.000
157B157GLU-1-0.877-0.94326.9850.0860.0860.0000.0000.0000.000
158B158PRO0-0.003-0.00627.4650.0130.0130.0000.0000.0000.000
159B159VAL00.024-0.00129.4850.0010.0010.0000.0000.0000.000
160B160THR0-0.025-0.01129.9470.0040.0040.0000.0000.0000.000
161B161VAL0-0.022-0.02232.625-0.003-0.0030.0000.0000.0000.000
162B162SER0-0.0290.00034.6370.0030.0030.0000.0000.0000.000
163B163TRP00.0250.00537.104-0.004-0.0040.0000.0000.0000.000
164B164ASN00.012-0.01740.3430.0020.0020.0000.0000.0000.000
165B165SER0-0.024-0.02040.8070.0010.0010.0000.0000.0000.000
166B166GLY0-0.013-0.00738.1710.0060.0060.0000.0000.0000.000
167B167ALA0-0.0060.01538.948-0.001-0.0010.0000.0000.0000.000
168B168LEU0-0.044-0.00740.875-0.004-0.0040.0000.0000.0000.000
169B169THR00.010-0.01035.5030.0000.0000.0000.0000.0000.000
170B170SER00.005-0.00636.420-0.005-0.0050.0000.0000.0000.000
171B171GLY00.0570.02736.9080.0000.0000.0000.0000.0000.000
172B172VAL0-0.044-0.01934.684-0.002-0.0020.0000.0000.0000.000
173B173HIS0-0.0070.00330.601-0.003-0.0030.0000.0000.0000.000
174B174THR0-0.009-0.00531.683-0.003-0.0030.0000.0000.0000.000
175B175PHE0-0.0220.00130.686-0.001-0.0010.0000.0000.0000.000
176B176PRO00.0570.02526.8720.0120.0120.0000.0000.0000.000
177B177ALA0-0.0200.00228.938-0.009-0.0090.0000.0000.0000.000
178B178VAL0-0.017-0.01429.572-0.008-0.0080.0000.0000.0000.000
179B179LEU0-0.0070.01129.7080.0100.0100.0000.0000.0000.000
180B180GLN0-0.071-0.06332.370-0.014-0.0140.0000.0000.0000.000
181B181SER00.0400.01035.4750.0050.0050.0000.0000.0000.000
182B182SER00.007-0.00437.4260.0020.0020.0000.0000.0000.000
183B183GLY00.0200.02734.6160.0050.0050.0000.0000.0000.000
184B184LEU0-0.033-0.00134.6680.0110.0110.0000.0000.0000.000
185B185TYR00.0570.02327.893-0.005-0.0050.0000.0000.0000.000
186B186SER0-0.004-0.01034.0540.0020.0020.0000.0000.0000.000
187B187LEU00.0110.03231.668-0.003-0.0030.0000.0000.0000.000
188B188SER0-0.0030.00234.757-0.001-0.0010.0000.0000.0000.000
189B189SER0-0.014-0.03234.9220.0000.0000.0000.0000.0000.000
190B190VAL0-0.002-0.00336.627-0.001-0.0010.0000.0000.0000.000
191B191VAL00.0140.02337.7620.0030.0030.0000.0000.0000.000
192B192THR00.0100.00440.164-0.003-0.0030.0000.0000.0000.000
193B193VAL00.0070.00742.2430.0020.0020.0000.0000.0000.000
194B194PRO00.0670.03345.279-0.003-0.0030.0000.0000.0000.000
195B195SER00.012-0.00148.5330.0030.0030.0000.0000.0000.000
196B196SER00.013-0.00550.8540.0010.0010.0000.0000.0000.000
197B197SER00.0070.01549.7200.0020.0020.0000.0000.0000.000
198B198LEU0-0.004-0.00148.8620.0020.0020.0000.0000.0000.000
199B199GLY0-0.044-0.01552.3860.0010.0010.0000.0000.0000.000
200B200THR0-0.014-0.01054.3120.0010.0010.0000.0000.0000.000
201B201GLN0-0.0030.01648.5270.0010.0010.0000.0000.0000.000
202B202THR0-0.039-0.00848.932-0.001-0.0010.0000.0000.0000.000
203B203TYR00.029-0.01245.1260.0020.0020.0000.0000.0000.000
204B204ILE00.0130.00044.324-0.002-0.0020.0000.0000.0000.000
205B206ASN00.005-0.00139.3400.0000.0000.0000.0000.0000.000
206B207VAL00.0460.01337.2240.0030.0030.0000.0000.0000.000
207B208ASN0-0.042-0.02834.918-0.003-0.0030.0000.0000.0000.000
208B209HIS00.0610.05733.457-0.001-0.0010.0000.0000.0000.000
209B210LYS11.0020.98431.137-0.166-0.1660.0000.0000.0000.000
210B211PRO00.0040.01930.8960.0000.0000.0000.0000.0000.000
211B212SER0-0.017-0.03233.548-0.003-0.0030.0000.0000.0000.000
212B213ASN0-0.047-0.00736.6060.0000.0000.0000.0000.0000.000
213B214THR00.0270.00938.148-0.009-0.0090.0000.0000.0000.000
214B215LYS10.8310.88938.698-0.071-0.0710.0000.0000.0000.000
215B216VAL00.0120.01240.884-0.004-0.0040.0000.0000.0000.000
216B217ASP-1-0.798-0.87442.0520.0650.0650.0000.0000.0000.000
217B218LYS10.9060.95144.361-0.035-0.0350.0000.0000.0000.000
218B219LYS10.8950.93945.700-0.024-0.0240.0000.0000.0000.000
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