Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K2RK3

Calculation Name: 1HDM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HDM

Chain ID: B

ChEMBL ID:

UniProt ID: P28067

Base Structure: X-ray

Registration Date: 2023-09-26

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1640258.099086
FMO2-HF: Nuclear repulsion 1566333.563838
FMO2-HF: Total energy -73924.535247
FMO2-MP2: Total energy -74135.001477


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:3:PHE)


Summations of interaction energy for fragment #1(B:3:PHE)
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.
-10.206-4.428.262-4.12-9.928-0.02
Interaction energy analysis for fragmet #1(B:3:PHE)
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 : -0.024
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].
3B5ALA0-0.021-0.0163.404-1.1520.7480.021-0.915-1.005-0.001
4B6HIS00.0150.0045.6490.0050.0050.0000.0000.0000.000
5B7VAL00.012-0.0099.3660.0470.0470.0000.0000.0000.000
6B8GLU-1-0.977-0.97412.720-0.308-0.3080.0000.0000.0000.000
7B9SER0-0.019-0.01815.0480.0280.0280.0000.0000.0000.000
8B10THR0-0.0150.00218.8020.0030.0030.0000.0000.0000.000
9B11CYS0-0.015-0.00421.4090.0000.0000.0000.0000.0000.000
10B12LEU00.0220.03225.1910.0040.0040.0000.0000.0000.000
11B13LEU0-0.001-0.00427.6580.0020.0020.0000.0000.0000.000
12B14ASP-1-0.858-0.92531.004-0.059-0.0590.0000.0000.0000.000
13B15ASP-1-0.849-0.93934.213-0.053-0.0530.0000.0000.0000.000
14B16ALA0-0.072-0.03436.4560.0010.0010.0000.0000.0000.000
15B17GLY0-0.019-0.00534.0740.0000.0000.0000.0000.0000.000
16B18THR0-0.077-0.03134.527-0.003-0.0030.0000.0000.0000.000
17B19PRO0-0.060-0.02530.971-0.001-0.0010.0000.0000.0000.000
18B20LYS10.9010.91630.8570.0670.0670.0000.0000.0000.000
19B21ASP-1-0.853-0.92625.764-0.111-0.1110.0000.0000.0000.000
20B22PHE0-0.053-0.02922.442-0.005-0.0050.0000.0000.0000.000
21B23THR00.0170.02118.7190.0010.0010.0000.0000.0000.000
22B24TYR0-0.008-0.01616.430-0.023-0.0230.0000.0000.0000.000
23B25CYS00.0300.02414.831-0.023-0.0230.0000.0000.0000.000
24B26ILE0-0.024-0.00910.130-0.053-0.0530.0000.0000.0000.000
25B27SER00.007-0.0038.7820.1110.1110.0000.0000.0000.000
26B28PHE0-0.001-0.0092.724-4.782-1.9583.461-1.307-4.9790.002
27B29ASN00.0040.0002.164-4.454-3.5854.778-1.858-3.789-0.021
28B30LYS10.9120.9554.0490.4430.6360.002-0.040-0.1550.000
29B31ASP-1-0.891-0.9327.485-0.065-0.0650.0000.0000.0000.000
30B32LEU00.0260.0079.261-0.042-0.0420.0000.0000.0000.000
31B33LEU0-0.017-0.0138.2740.0620.0620.0000.0000.0000.000
32B34THR00.002-0.00712.2800.0330.0330.0000.0000.0000.000
33B36TRP00.0440.01317.7590.0090.0090.0000.0000.0000.000
34B37ASP-1-0.872-0.93220.913-0.099-0.0990.0000.0000.0000.000
35B38PRO0-0.021-0.03324.0060.0020.0020.0000.0000.0000.000
36B39GLU-1-0.904-0.93827.084-0.075-0.0750.0000.0000.0000.000
37B40GLU-1-0.980-0.99626.247-0.074-0.0740.0000.0000.0000.000
38B41ASN0-0.055-0.01626.842-0.005-0.0050.0000.0000.0000.000
39B42LYS10.8790.93423.5770.0960.0960.0000.0000.0000.000
40B43MET0-0.097-0.02616.441-0.003-0.0030.0000.0000.0000.000
41B44ALA00.0210.00419.9460.0110.0110.0000.0000.0000.000
42B45PRO0-0.026-0.02116.834-0.013-0.0130.0000.0000.0000.000
43B46CYS0-0.0180.00315.5460.0140.0140.0000.0000.0000.000
44B47ASN00.0890.03012.558-0.001-0.0010.0000.0000.0000.000
45B48SER00.0350.00913.124-0.009-0.0090.0000.0000.0000.000
46B49LEU00.0150.0137.550-0.023-0.0230.0000.0000.0000.000
47B50ALA00.0710.04012.261-0.040-0.0400.0000.0000.0000.000
48B51ASN00.0360.03913.656-0.028-0.0280.0000.0000.0000.000
49B52VAL0-0.013-0.00313.939-0.011-0.0110.0000.0000.0000.000
50B53LEU0-0.028-0.0259.576-0.024-0.0240.0000.0000.0000.000
51B54SER00.000-0.02514.207-0.023-0.0230.0000.0000.0000.000
52B55GLN0-0.049-0.01917.3640.0060.0060.0000.0000.0000.000
53B56HIS0-0.046-0.03115.826-0.020-0.0200.0000.0000.0000.000
54B57LEU0-0.024-0.02914.893-0.007-0.0070.0000.0000.0000.000
55B58ASN00.0740.02918.4680.0000.0000.0000.0000.0000.000
56B59GLN0-0.029-0.00621.3240.0140.0140.0000.0000.0000.000
57B60LYS10.8920.96118.4460.2190.2190.0000.0000.0000.000
58B61ASP-1-0.814-0.91623.017-0.115-0.1150.0000.0000.0000.000
59B62THR0-0.016-0.00923.9570.0010.0010.0000.0000.0000.000
60B63LEU0-0.046-0.01918.756-0.003-0.0030.0000.0000.0000.000
61B64MET00.0050.03221.4710.0030.0030.0000.0000.0000.000
62B65GLN00.0190.02225.1000.0020.0020.0000.0000.0000.000
63B66ARG10.9350.97819.2760.2330.2330.0000.0000.0000.000
64B67LEU00.0360.02520.4570.0040.0040.0000.0000.0000.000
65B68ASN0-0.039-0.02427.8910.0100.0100.0000.0000.0000.000
66B69GLY00.001-0.01026.0400.0010.0010.0000.0000.0000.000
67B70LEU00.0480.01026.683-0.001-0.0010.0000.0000.0000.000
68B71GLN00.0050.00629.4440.0050.0050.0000.0000.0000.000
69B72ASN0-0.025-0.01327.021-0.003-0.0030.0000.0000.0000.000
70B74ALA00.0620.04428.3250.0030.0030.0000.0000.0000.000
71B75THR00.017-0.01031.2460.0020.0020.0000.0000.0000.000
72B76HIS0-0.058-0.02625.6540.0060.0060.0000.0000.0000.000
73B77THR0-0.003-0.01828.2320.0040.0040.0000.0000.0000.000
74B78GLN0-0.0300.01230.6670.0050.0050.0000.0000.0000.000
75B79PRO0-0.029-0.00632.6060.0050.0050.0000.0000.0000.000
76B80PHE00.011-0.00228.1120.0040.0040.0000.0000.0000.000
77B81TRP00.0310.01328.3010.0010.0010.0000.0000.0000.000
78B82GLY00.0710.04333.5860.0020.0020.0000.0000.0000.000
79B83SER0-0.061-0.05935.6290.0040.0040.0000.0000.0000.000
80B84LEU0-0.100-0.05129.9320.0030.0030.0000.0000.0000.000
81B85THR00.0290.02033.5810.0020.0020.0000.0000.0000.000
82B86ASN00.0110.02035.5580.0020.0020.0000.0000.0000.000
83B87ARG10.8220.94033.9860.0470.0470.0000.0000.0000.000
84B88THR00.0090.00437.1520.0010.0010.0000.0000.0000.000
85B89ARG10.8920.93237.0560.0310.0310.0000.0000.0000.000
86B90PRO00.0530.04139.3750.0000.0000.0000.0000.0000.000
87B91PRO0-0.0320.00340.1540.0010.0010.0000.0000.0000.000
88B92SER0-0.0120.00841.2430.0010.0010.0000.0000.0000.000
89B93VAL00.046-0.00942.2410.0010.0010.0000.0000.0000.000
90B94GLN00.002-0.00344.4510.0000.0000.0000.0000.0000.000
91B95VAL0-0.0080.01645.2880.0010.0010.0000.0000.0000.000
92B96ALA0-0.0020.00946.3410.0000.0000.0000.0000.0000.000
93B97LYS10.9410.96947.177-0.014-0.0140.0000.0000.0000.000
94B98THR0-0.0010.00742.2800.0010.0010.0000.0000.0000.000
95B99THR00.011-0.00343.130-0.001-0.0010.0000.0000.0000.000
96B100PRO00.000-0.00343.6910.0010.0010.0000.0000.0000.000
97B101PHE00.0050.00439.4760.0020.0020.0000.0000.0000.000
98B102ASN0-0.0130.00041.503-0.001-0.0010.0000.0000.0000.000
99B103THR0-0.007-0.02743.657-0.003-0.0030.0000.0000.0000.000
100B104ARG10.9740.99647.318-0.014-0.0140.0000.0000.0000.000
101B105GLU-1-0.936-0.96650.4200.0120.0120.0000.0000.0000.000
102B106PRO0-0.0180.00550.7810.0010.0010.0000.0000.0000.000
103B107VAL0-0.015-0.01251.0760.0010.0010.0000.0000.0000.000
104B108MET0-0.0100.01344.7530.0000.0000.0000.0000.0000.000
105B109LEU0-0.041-0.00947.5660.0010.0010.0000.0000.0000.000
106B110ALA00.0500.01942.6790.0000.0000.0000.0000.0000.000
107B111CYS0-0.125-0.03743.838-0.001-0.0010.0000.0000.0000.000
108B112TYR00.000-0.01239.5090.0000.0000.0000.0000.0000.000
109B113VAL00.0620.02139.602-0.001-0.0010.0000.0000.0000.000
110B114TRP00.005-0.01136.9830.0010.0010.0000.0000.0000.000
111B115GLY00.0560.01336.270-0.001-0.0010.0000.0000.0000.000
112B116PHE0-0.0430.00735.382-0.001-0.0010.0000.0000.0000.000
113B117TYR00.022-0.01430.479-0.001-0.0010.0000.0000.0000.000
114B118PRO00.0890.03633.9850.0010.0010.0000.0000.0000.000
115B119ALA00.0230.00731.4850.0040.0040.0000.0000.0000.000
116B120GLU-1-0.914-0.94333.567-0.032-0.0320.0000.0000.0000.000
117B121VAL0-0.004-0.00136.3240.0010.0010.0000.0000.0000.000
118B122THR0-0.032-0.01339.2220.0010.0010.0000.0000.0000.000
119B123ILE0-0.002-0.02040.4110.0010.0010.0000.0000.0000.000
120B124THR0-0.019-0.00543.8660.0010.0010.0000.0000.0000.000
121B125TRP00.0390.01345.3870.0000.0000.0000.0000.0000.000
122B126ARG10.9480.96749.7990.0040.0040.0000.0000.0000.000
123B127LYS10.9631.01053.554-0.004-0.0040.0000.0000.0000.000
124B128ASN0-0.027-0.03256.0940.0000.0000.0000.0000.0000.000
125B129GLY00.0310.00957.6220.0000.0000.0000.0000.0000.000
126B130LYS10.9400.97857.385-0.002-0.0020.0000.0000.0000.000
127B131LEU00.0010.00149.9920.0010.0010.0000.0000.0000.000
128B132VAL0-0.0060.00150.0760.0010.0010.0000.0000.0000.000
129B133MET00.0450.01948.1980.0000.0000.0000.0000.0000.000
130B134HIS00.0160.01046.7190.0000.0000.0000.0000.0000.000
131B135SER0-0.044-0.02143.6190.0010.0010.0000.0000.0000.000
132B136SER00.0040.00439.369-0.002-0.0020.0000.0000.0000.000
133B137ALA00.0460.04141.0460.0010.0010.0000.0000.0000.000
134B138HIS00.0650.04837.4870.0000.0000.0000.0000.0000.000
135B139LYS10.8170.88637.1820.0020.0020.0000.0000.0000.000
136B140THR00.0090.02731.777-0.002-0.0020.0000.0000.0000.000
137B141ALA00.027-0.00732.0380.0030.0030.0000.0000.0000.000
138B142GLN00.0050.00526.2920.0020.0020.0000.0000.0000.000
139B143PRO0-0.032-0.02225.863-0.001-0.0010.0000.0000.0000.000
140B144ASN00.019-0.00827.5920.0100.0100.0000.0000.0000.000
141B145GLY0-0.0190.00125.8190.0030.0030.0000.0000.0000.000
142B146ASP-1-0.844-0.89226.517-0.027-0.0270.0000.0000.0000.000
143B147TRP0-0.056-0.02827.2000.0010.0010.0000.0000.0000.000
144B148THR0-0.041-0.02730.6570.0030.0030.0000.0000.0000.000
145B149TYR00.0050.00327.867-0.001-0.0010.0000.0000.0000.000
146B150GLN0-0.063-0.04932.5510.0030.0030.0000.0000.0000.000
147B151THR0-0.0010.00233.8330.0000.0000.0000.0000.0000.000
148B152LEU00.006-0.00336.3450.0010.0010.0000.0000.0000.000
149B153SER0-0.0390.00438.9880.0000.0000.0000.0000.0000.000
150B154HIS00.0690.01639.360-0.001-0.0010.0000.0000.0000.000
151B155LEU0-0.0110.00343.707-0.001-0.0010.0000.0000.0000.000
152B156ALA0-0.024-0.01447.3350.0010.0010.0000.0000.0000.000
153B157LEU0-0.030-0.01348.936-0.001-0.0010.0000.0000.0000.000
154B158THR00.0920.03652.7210.0010.0010.0000.0000.0000.000
155B159PRO0-0.094-0.05055.197-0.001-0.0010.0000.0000.0000.000
156B160SER00.0840.02957.6270.0000.0000.0000.0000.0000.000
157B161TYR0-0.039-0.02860.7070.0000.0000.0000.0000.0000.000
158B162GLY00.0200.03662.3840.0000.0000.0000.0000.0000.000
159B163ASP-1-0.905-0.95258.5190.0050.0050.0000.0000.0000.000
160B164THR00.0200.02356.9980.0000.0000.0000.0000.0000.000
161B165TYR0-0.055-0.02952.632-0.001-0.0010.0000.0000.0000.000
162B166THR0-0.009-0.05552.0540.0000.0000.0000.0000.0000.000
163B168VAL00.001-0.02248.2940.0000.0000.0000.0000.0000.000
164B169VAL00.001-0.00442.9320.0000.0000.0000.0000.0000.000
165B170GLU-1-0.922-0.95244.290-0.012-0.0120.0000.0000.0000.000
166B171HIS0-0.006-0.01237.5330.0010.0010.0000.0000.0000.000
167B172ILE00.0900.04338.7670.0010.0010.0000.0000.0000.000
168B173GLY0-0.038-0.03041.526-0.001-0.0010.0000.0000.0000.000
169B174ALA0-0.083-0.05142.2890.0010.0010.0000.0000.0000.000
170B175PRO0-0.0280.00145.8110.0000.0000.0000.0000.0000.000
171B176GLU-1-0.884-0.94148.995-0.013-0.0130.0000.0000.0000.000
172B177PRO0-0.018-0.00148.4090.0000.0000.0000.0000.0000.000
173B178ILE0-0.020-0.00745.3970.0010.0010.0000.0000.0000.000
174B179LEU0-0.012-0.01548.7960.0010.0010.0000.0000.0000.000
175B180ARG10.8470.91947.7390.0030.0030.0000.0000.0000.000
176B181ASP-1-0.799-0.85050.9440.0000.0000.0000.0000.0000.000
177B182TRP00.011-0.00851.8210.0010.0010.0000.0000.0000.000
178B183THR0-0.003-0.02454.0290.0000.0000.0000.0000.0000.000
179B184PRO0-0.053-0.01856.5560.0010.0010.0000.0000.0000.000
180B185GLY00.0090.01456.6470.0000.0000.0000.0000.0000.000