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: 94QV2

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2246873.594628
FMO2-HF: Nuclear repulsion 2163351.683852
FMO2-HF: Total energy -83521.910776
FMO2-MP2: Total energy -83766.912276


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.
-16.498-15.8919.386-4.78-5.2110.039
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 : 0.050 / q_NPA : 0.031
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].
3B3GLN0-0.046-0.0241.849-14.209-13.8439.389-4.715-5.0400.039
4B4LEU00.001-0.0105.251-1.023-0.988-0.001-0.004-0.0290.000
5B5GLN00.0080.0077.925-0.025-0.0250.0000.0000.0000.000
6B6GLN00.005-0.01210.281-0.310-0.3100.0000.0000.0000.000
7B7SER0-0.003-0.00113.7340.0660.0660.0000.0000.0000.000
8B8GLY00.0460.01616.895-0.072-0.0720.0000.0000.0000.000
9B9PRO0-0.008-0.00220.6880.0270.0270.0000.0000.0000.000
10B10GLY00.0700.03923.017-0.009-0.0090.0000.0000.0000.000
11B11LEU0-0.101-0.04523.612-0.021-0.0210.0000.0000.0000.000
12B12VAL00.0090.01526.9150.0050.0050.0000.0000.0000.000
13B13LYS10.8220.90529.627-0.143-0.1430.0000.0000.0000.000
14B14PRO00.0560.00633.434-0.002-0.0020.0000.0000.0000.000
15B15SER0-0.065-0.02635.398-0.001-0.0010.0000.0000.0000.000
16B16GLN00.0330.02632.4660.0050.0050.0000.0000.0000.000
17B17THR00.019-0.00628.880-0.007-0.0070.0000.0000.0000.000
18B18LEU0-0.0170.01723.7290.0140.0140.0000.0000.0000.000
19B19SER00.020-0.00624.000-0.027-0.0270.0000.0000.0000.000
20B20LEU0-0.050-0.01019.2490.0300.0300.0000.0000.0000.000
21B21THR00.0210.00716.790-0.074-0.0740.0000.0000.0000.000
22B22CYS0-0.0510.01012.8640.0840.0840.0000.0000.0000.000
23B23ALA00.0380.02612.089-0.163-0.1630.0000.0000.0000.000
24B24ILE0-0.033-0.0049.0810.2630.2630.0000.0000.0000.000
25B25SER0-0.021-0.0035.491-0.395-0.3950.0000.0000.0000.000
26B26GLY00.0500.0134.320-0.685-0.623-0.001-0.054-0.0060.000
27B27ASP-1-0.783-0.8825.113-1.613-1.469-0.001-0.007-0.1360.000
28B28SER0-0.029-0.0128.1180.3500.3500.0000.0000.0000.000
29B29VAL00.0520.02111.940-0.008-0.0080.0000.0000.0000.000
30B30SER0-0.027-0.02914.7120.0500.0500.0000.0000.0000.000
31B31SER0-0.043-0.01111.7760.0650.0650.0000.0000.0000.000
32B32ASN00.019-0.00114.522-0.001-0.0010.0000.0000.0000.000
33B33SER0-0.028-0.00813.5070.0140.0140.0000.0000.0000.000
34B34ALA00.0010.01111.4910.0380.0380.0000.0000.0000.000
35B35ALA0-0.026-0.00613.5610.0790.0790.0000.0000.0000.000
36B36TRP0-0.0030.0049.283-0.030-0.0300.0000.0000.0000.000
37B37ASN00.016-0.01015.0630.0640.0640.0000.0000.0000.000
38B38TRP00.0250.00916.1090.0560.0560.0000.0000.0000.000
39B39ILE0-0.019-0.00416.236-0.035-0.0350.0000.0000.0000.000
40B40ARG10.7470.86319.580-0.031-0.0310.0000.0000.0000.000
41B41GLN00.0440.03619.850-0.003-0.0030.0000.0000.0000.000
42B42SER00.0280.01222.8880.0220.0220.0000.0000.0000.000
43B43PRO00.0170.00025.808-0.017-0.0170.0000.0000.0000.000
44B44SER0-0.027-0.00928.2860.0030.0030.0000.0000.0000.000
45B45ARG10.8550.91727.726-0.057-0.0570.0000.0000.0000.000
46B46GLY0-0.0050.01726.400-0.012-0.0120.0000.0000.0000.000
47B47LEU0-0.015-0.03019.9020.0170.0170.0000.0000.0000.000
48B48GLU-1-0.730-0.83223.3720.0200.0200.0000.0000.0000.000
49B49TRP00.015-0.00919.4750.0280.0280.0000.0000.0000.000
50B50LEU0-0.014-0.01421.8250.0020.0020.0000.0000.0000.000
51B51GLY00.0610.01421.8760.0000.0000.0000.0000.0000.000
52B52ARG10.7190.87718.9930.1880.1880.0000.0000.0000.000
53B53THR0-0.002-0.00518.8330.0040.0040.0000.0000.0000.000
54B54TYR0-0.021-0.05018.264-0.051-0.0510.0000.0000.0000.000
55B55TYR00.0180.02118.6870.0410.0410.0000.0000.0000.000
56B56ARG10.8150.88716.7950.3220.3220.0000.0000.0000.000
57B57SER0-0.0010.00222.5540.0120.0120.0000.0000.0000.000
58B58LYS10.9070.95824.4280.1280.1280.0000.0000.0000.000
59B59TRP00.0310.02218.321-0.021-0.0210.0000.0000.0000.000
60B60PHE0-0.0100.00123.1600.0230.0230.0000.0000.0000.000
61B61ASN00.0360.02022.851-0.027-0.0270.0000.0000.0000.000
62B62ASP-1-0.738-0.80823.856-0.136-0.1360.0000.0000.0000.000
63B63TYR00.026-0.00924.3570.0070.0070.0000.0000.0000.000
64B64ALA00.0420.03226.184-0.008-0.0080.0000.0000.0000.000
65B65VAL00.0440.00427.7770.0100.0100.0000.0000.0000.000
66B66SER0-0.065-0.02929.2500.0030.0030.0000.0000.0000.000
67B67VAL00.007-0.00426.8440.0090.0090.0000.0000.0000.000
68B68GLN0-0.0060.00030.0140.0040.0040.0000.0000.0000.000
69B69SER0-0.009-0.00330.9510.0010.0010.0000.0000.0000.000
70B70ARG10.8180.88931.397-0.056-0.0560.0000.0000.0000.000
71B71ILE0-0.0270.01524.4210.0120.0120.0000.0000.0000.000
72B72THR0-0.025-0.01026.103-0.009-0.0090.0000.0000.0000.000
73B73ILE0-0.0160.00120.4920.0180.0180.0000.0000.0000.000
74B74ASN00.0130.01622.287-0.037-0.0370.0000.0000.0000.000
75B75PRO00.0260.01719.2770.0290.0290.0000.0000.0000.000
76B76ASP-1-0.741-0.83518.6310.0950.0950.0000.0000.0000.000
77B77THR00.0490.00217.8180.0180.0180.0000.0000.0000.000
78B78SER0-0.082-0.04318.063-0.004-0.0040.0000.0000.0000.000
79B79LYS10.8310.88717.043-0.105-0.1050.0000.0000.0000.000
80B80ASN0-0.038-0.01911.1340.0450.0450.0000.0000.0000.000
81B81GLN00.0050.00313.0430.0900.0900.0000.0000.0000.000
82B82PHE00.002-0.01313.343-0.084-0.0840.0000.0000.0000.000
83B83SER00.002-0.01317.2890.0660.0660.0000.0000.0000.000
84B84LEU0-0.018-0.00220.068-0.044-0.0440.0000.0000.0000.000
85B85GLN0-0.040-0.03022.2090.0150.0150.0000.0000.0000.000
86B86LEU00.0140.00125.862-0.019-0.0190.0000.0000.0000.000
87B87ASN00.0170.00228.4450.0180.0180.0000.0000.0000.000
88B88SER0-0.004-0.00232.014-0.006-0.0060.0000.0000.0000.000
89B89VAL0-0.042-0.00229.378-0.006-0.0060.0000.0000.0000.000
90B90THR00.006-0.02232.7140.0000.0000.0000.0000.0000.000
91B91PRO00.0290.01032.3490.0070.0070.0000.0000.0000.000
92B92GLU-1-0.804-0.88031.7280.0720.0720.0000.0000.0000.000
93B93ASP-1-0.757-0.84328.7450.0700.0700.0000.0000.0000.000
94B94THR0-0.044-0.01427.3700.0200.0200.0000.0000.0000.000
95B95ALA0-0.052-0.02124.102-0.016-0.0160.0000.0000.0000.000
96B96VAL0-0.0080.00418.4360.0270.0270.0000.0000.0000.000
97B97TYR00.022-0.01219.750-0.048-0.0480.0000.0000.0000.000
98B98TYR00.008-0.00914.5210.0820.0820.0000.0000.0000.000
99B100ALA00.0400.00311.6580.0590.0590.0000.0000.0000.000
100B101ARG10.8000.8777.6451.2771.2770.0000.0000.0000.000
101B102GLY00.0330.00511.6690.0380.0380.0000.0000.0000.000
102B103ILE0-0.0080.01014.023-0.044-0.0440.0000.0000.0000.000
103B104VAL00.018-0.00416.3370.0420.0420.0000.0000.0000.000
104B105PHE0-0.003-0.00519.5870.0250.0250.0000.0000.0000.000
105B106SER00.0350.01519.0200.0140.0140.0000.0000.0000.000
106B107TYR0-0.069-0.04620.1570.0090.0090.0000.0000.0000.000
107B108ALA00.0210.03216.7740.0170.0170.0000.0000.0000.000
108B109MET0-0.009-0.01813.864-0.010-0.0100.0000.0000.0000.000
109B110ASP-1-0.836-0.8979.687-0.918-0.9180.0000.0000.0000.000
110B111VAL0-0.0090.0105.568-0.122-0.1220.0000.0000.0000.000
111B112TRP00.015-0.0048.5170.1450.1450.0000.0000.0000.000
112B113GLY00.0510.0178.8720.1900.1900.0000.0000.0000.000
113B114GLN0-0.051-0.0289.9500.0950.0950.0000.0000.0000.000
114B115GLY00.0450.03111.392-0.131-0.1310.0000.0000.0000.000
115B116THR0-0.071-0.05215.1140.1020.1020.0000.0000.0000.000
116B117THR00.0010.00517.927-0.052-0.0520.0000.0000.0000.000
117B118VAL0-0.0210.00521.3590.0190.0190.0000.0000.0000.000
118B119THR0-0.009-0.00924.192-0.030-0.0300.0000.0000.0000.000
119B120VAL00.0200.01027.7210.0060.0060.0000.0000.0000.000
120B121SER00.001-0.02230.686-0.014-0.0140.0000.0000.0000.000
121B122SER00.0470.00733.5910.0080.0080.0000.0000.0000.000
122B123ALA0-0.0030.03235.2920.0000.0000.0000.0000.0000.000
123B124SER00.029-0.00135.2720.0070.0070.0000.0000.0000.000
124B125THR0-0.025-0.01735.385-0.002-0.0020.0000.0000.0000.000
125B126LYS10.8350.92436.768-0.104-0.1040.0000.0000.0000.000
126B127GLY00.0810.04637.8830.0060.0060.0000.0000.0000.000
127B128PRO0-0.027-0.01437.979-0.006-0.0060.0000.0000.0000.000
128B129SER0-0.032-0.01240.157-0.004-0.0040.0000.0000.0000.000
129B130VAL00.0180.01341.1860.0000.0000.0000.0000.0000.000
130B131PHE0-0.008-0.01143.658-0.004-0.0040.0000.0000.0000.000
131B132PRO00.0210.01744.5710.0020.0020.0000.0000.0000.000
132B133LEU0-0.036-0.01641.567-0.003-0.0030.0000.0000.0000.000
133B134ALA00.0290.00845.8580.0000.0000.0000.0000.0000.000
134B135PRO00.0230.02948.365-0.002-0.0020.0000.0000.0000.000
135B136SER0-0.031-0.03349.480-0.002-0.0020.0000.0000.0000.000
136B137SER00.0560.03650.9940.0010.0010.0000.0000.0000.000
137B138LYS10.9450.96449.187-0.035-0.0350.0000.0000.0000.000
138B139SER0-0.044-0.01646.2790.0000.0000.0000.0000.0000.000
139B140THR0-0.017-0.02547.2280.0020.0020.0000.0000.0000.000
140B141SER0-0.006-0.00246.886-0.003-0.0030.0000.0000.0000.000
141B142GLY00.0570.03248.5570.0010.0010.0000.0000.0000.000
142B143GLY00.0110.00150.4000.0010.0010.0000.0000.0000.000
143B144THR0-0.0150.00744.3930.0020.0020.0000.0000.0000.000
144B145ALA00.0250.01047.067-0.002-0.0020.0000.0000.0000.000
145B146ALA0-0.0050.02142.9330.0020.0020.0000.0000.0000.000
146B147LEU00.0070.01643.812-0.002-0.0020.0000.0000.0000.000
147B148GLY00.0700.01341.9910.0030.0030.0000.0000.0000.000
148B149CYS0-0.091-0.01040.6680.0030.0030.0000.0000.0000.000
149B150LEU00.0400.03939.8110.0040.0040.0000.0000.0000.000
150B151VAL0-0.030-0.02937.298-0.001-0.0010.0000.0000.0000.000
151B152LYS10.8790.90238.110-0.070-0.0700.0000.0000.0000.000
152B153ASP-1-0.815-0.88339.0730.0830.0830.0000.0000.0000.000
153B154TYR0-0.017-0.01831.936-0.007-0.0070.0000.0000.0000.000
154B155PHE00.0220.01431.6360.0040.0040.0000.0000.0000.000
155B156PRO00.0290.02329.728-0.007-0.0070.0000.0000.0000.000
156B157GLU-1-0.760-0.87028.0110.1660.1660.0000.0000.0000.000
157B158PRO0-0.033-0.01027.4430.0100.0100.0000.0000.0000.000
158B159VAL0-0.002-0.01029.542-0.006-0.0060.0000.0000.0000.000
159B160THR0-0.053-0.02130.0950.0100.0100.0000.0000.0000.000
160B161VAL0-0.008-0.02332.665-0.006-0.0060.0000.0000.0000.000
161B162SER0-0.0020.01334.6020.0040.0040.0000.0000.0000.000
162B163TRP00.0310.00236.914-0.006-0.0060.0000.0000.0000.000
163B164ASN00.010-0.00840.2720.0020.0020.0000.0000.0000.000
164B165SER0-0.024-0.02040.966-0.001-0.0010.0000.0000.0000.000
165B166GLY00.0120.01437.9700.0050.0050.0000.0000.0000.000
166B167ALA0-0.035-0.00938.755-0.001-0.0010.0000.0000.0000.000
167B168LEU0-0.035-0.00940.366-0.005-0.0050.0000.0000.0000.000
168B169THR00.017-0.00335.1920.0030.0030.0000.0000.0000.000
169B170SER00.0320.00936.1840.0000.0000.0000.0000.0000.000
170B171GLY00.0490.02437.3590.0000.0000.0000.0000.0000.000
171B172VAL0-0.043-0.01435.170-0.001-0.0010.0000.0000.0000.000
172B173HIS0-0.021-0.00731.2340.0030.0030.0000.0000.0000.000
173B174THR0-0.013-0.00432.202-0.007-0.0070.0000.0000.0000.000
174B175PHE00.0020.00831.1550.0050.0050.0000.0000.0000.000
175B176PRO00.0400.00627.4790.0070.0070.0000.0000.0000.000
176B177ALA0-0.0160.00929.493-0.012-0.0120.0000.0000.0000.000
177B178VAL0-0.016-0.01030.2840.0000.0000.0000.0000.0000.000
178B179LEU0-0.020-0.00830.4590.0010.0010.0000.0000.0000.000
179B180GLN0-0.027-0.01833.049-0.014-0.0140.0000.0000.0000.000
180B181SER00.0450.00936.2990.0060.0060.0000.0000.0000.000
181B182SER0-0.0040.00138.2770.0010.0010.0000.0000.0000.000
182B183GLY00.0240.02235.4480.0020.0020.0000.0000.0000.000
183B184LEU0-0.028-0.00435.0760.0110.0110.0000.0000.0000.000
184B185TYR00.0450.02128.596-0.003-0.0030.0000.0000.0000.000
185B186SER0-0.020-0.01634.541-0.010-0.0100.0000.0000.0000.000
186B187LEU00.0570.04632.1830.0010.0010.0000.0000.0000.000
187B188SER0-0.009-0.02235.188-0.010-0.0100.0000.0000.0000.000
188B189SER0-0.0020.00335.4440.0030.0030.0000.0000.0000.000
189B190VAL0-0.013-0.01137.110-0.005-0.0050.0000.0000.0000.000
190B191VAL00.0280.01638.1570.0040.0040.0000.0000.0000.000
191B192THR0-0.055-0.03440.290-0.005-0.0050.0000.0000.0000.000
192B193VAL00.0290.01042.4280.0020.0020.0000.0000.0000.000
193B194PRO00.0750.03145.308-0.002-0.0020.0000.0000.0000.000
194B195SER0-0.0100.00848.6270.0020.0020.0000.0000.0000.000
195B196SER00.0230.00450.9720.0010.0010.0000.0000.0000.000
196B197SER0-0.012-0.01049.7190.0010.0010.0000.0000.0000.000
197B198LEU0-0.008-0.01249.0520.0020.0020.0000.0000.0000.000
198B199GLY0-0.0100.01152.5000.0010.0010.0000.0000.0000.000
199B200THR0-0.038-0.02354.3720.0000.0000.0000.0000.0000.000
200B201GLN0-0.033-0.01148.6020.0000.0000.0000.0000.0000.000
201B202THR00.0010.00249.3600.0000.0000.0000.0000.0000.000
202B203TYR00.023-0.00245.3020.0030.0030.0000.0000.0000.000
203B204ILE00.009-0.01344.410-0.001-0.0010.0000.0000.0000.000
204B206ASN0-0.007-0.01939.184-0.002-0.0020.0000.0000.0000.000
205B207VAL00.0390.01837.4460.0070.0070.0000.0000.0000.000
206B208ASN0-0.012-0.01835.368-0.005-0.0050.0000.0000.0000.000
207B209HIS00.0090.00933.488-0.002-0.0020.0000.0000.0000.000
208B210LYS11.0140.99930.540-0.203-0.2030.0000.0000.0000.000
209B211PRO00.0050.01730.743-0.002-0.0020.0000.0000.0000.000
210B212SER0-0.004-0.03233.312-0.005-0.0050.0000.0000.0000.000
211B213ASN0-0.055-0.02336.403-0.004-0.0040.0000.0000.0000.000
212B214THR00.0270.02838.025-0.010-0.0100.0000.0000.0000.000
213B215LYS10.8410.90438.549-0.096-0.0960.0000.0000.0000.000
214B216VAL0-0.015-0.00740.933-0.005-0.0050.0000.0000.0000.000
215B217ASP-1-0.788-0.87142.2480.0950.0950.0000.0000.0000.000
216B218LYS10.8860.93744.320-0.072-0.0720.0000.0000.0000.000
217B219LYS10.8560.92545.676-0.049-0.0490.0000.0000.0000.000
218B220VAL0-0.058-0.02745.051-0.001-0.0010.0000.0000.0000.000
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