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: 4LNQN

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1638976.322561
FMO2-HF: Nuclear repulsion 1565050.472985
FMO2-HF: Total energy -73925.849576
FMO2-MP2: Total energy -74136.15586


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.
-10.044-2.3254.218-3.652-8.285-0.014
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 : -0.035 / q_NPA : -0.026
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].
3B5ALA0-0.019-0.0153.497-1.0970.7070.009-0.834-0.9790.000
4B6HIS00.0090.0045.7600.0030.0030.0000.0000.0000.000
5B7VAL00.006-0.0139.4700.0340.0340.0000.0000.0000.000
6B8GLU-1-0.968-0.96912.823-0.249-0.2490.0000.0000.0000.000
7B9SER0-0.014-0.01515.1470.0200.0200.0000.0000.0000.000
8B10THR0-0.022-0.00518.8990.0060.0060.0000.0000.0000.000
9B11CYS0-0.0070.00221.500-0.001-0.0010.0000.0000.0000.000
10B12LEU00.0290.03525.2830.0050.0050.0000.0000.0000.000
11B13LEU00.0030.00227.7420.0010.0010.0000.0000.0000.000
12B14ASP-1-0.766-0.85831.092-0.046-0.0460.0000.0000.0000.000
13B15ASP-1-0.871-0.94334.298-0.038-0.0380.0000.0000.0000.000
14B16ALA0-0.063-0.03136.5430.0010.0010.0000.0000.0000.000
15B17GLY0-0.0030.00334.1690.0000.0000.0000.0000.0000.000
16B18THR0-0.073-0.04034.625-0.003-0.0030.0000.0000.0000.000
17B19PRO0-0.060-0.02430.971-0.001-0.0010.0000.0000.0000.000
18B20LYS10.8090.85130.9220.0530.0530.0000.0000.0000.000
19B21ASP-1-0.844-0.92225.567-0.097-0.0970.0000.0000.0000.000
20B22PHE0-0.046-0.02322.729-0.003-0.0030.0000.0000.0000.000
21B23THR00.0160.01918.867-0.002-0.0020.0000.0000.0000.000
22B24TYR00.011-0.00716.865-0.013-0.0130.0000.0000.0000.000
23B25CYS00.0370.02314.782-0.020-0.0200.0000.0000.0000.000
24B26ILE0-0.023-0.01610.199-0.042-0.0420.0000.0000.0000.000
25B27SER00.0080.0038.8530.0920.0920.0000.0000.0000.000
26B28PHE0-0.005-0.0122.731-4.328-1.4842.935-1.259-4.5200.003
27B29ASN0-0.015-0.0092.510-4.746-1.8601.272-1.517-2.641-0.017
28B30LYS10.9250.9624.1310.3640.5490.002-0.042-0.1450.000
29B31ASP-1-0.882-0.9327.508-0.107-0.1070.0000.0000.0000.000
30B32LEU00.0200.0079.302-0.032-0.0320.0000.0000.0000.000
31B33LEU0-0.008-0.0058.4020.0510.0510.0000.0000.0000.000
32B34THR0-0.041-0.02212.2990.0330.0330.0000.0000.0000.000
33B36TRP00.0620.01517.8130.0060.0060.0000.0000.0000.000
34B37ASP-1-0.870-0.92320.977-0.091-0.0910.0000.0000.0000.000
35B38PRO0-0.004-0.02724.0590.0020.0020.0000.0000.0000.000
36B39GLU-1-0.905-0.94327.147-0.068-0.0680.0000.0000.0000.000
37B40GLU-1-0.931-0.95326.326-0.074-0.0740.0000.0000.0000.000
38B41ASN0-0.094-0.03426.876-0.003-0.0030.0000.0000.0000.000
39B42LYS10.8420.89923.6480.0910.0910.0000.0000.0000.000
40B43MET0-0.105-0.02816.546-0.001-0.0010.0000.0000.0000.000
41B44ALA00.0600.02320.0390.0080.0080.0000.0000.0000.000
42B45PRO0-0.013-0.01016.852-0.013-0.0130.0000.0000.0000.000
43B46CYS0-0.0250.00115.5640.0100.0100.0000.0000.0000.000
44B47ASN00.0940.02712.731-0.001-0.0010.0000.0000.0000.000
45B48SER00.0240.02113.011-0.002-0.0020.0000.0000.0000.000
46B49LEU00.0260.0137.726-0.014-0.0140.0000.0000.0000.000
47B50ALA00.0480.02512.245-0.032-0.0320.0000.0000.0000.000
48B51ASN00.004-0.00313.660-0.015-0.0150.0000.0000.0000.000
49B52VAL0-0.003-0.00614.094-0.008-0.0080.0000.0000.0000.000
50B53LEU0-0.015-0.0199.556-0.020-0.0200.0000.0000.0000.000
51B54SER0-0.004-0.00114.243-0.013-0.0130.0000.0000.0000.000
52B55GLN0-0.050-0.02817.4040.0040.0040.0000.0000.0000.000
53B56HIS00.0180.00315.796-0.014-0.0140.0000.0000.0000.000
54B57LEU0-0.011-0.02314.548-0.005-0.0050.0000.0000.0000.000
55B58ASN00.0650.03818.5340.0020.0020.0000.0000.0000.000
56B59GLN0-0.0140.00121.3440.0110.0110.0000.0000.0000.000
57B60LYS10.8090.91918.1860.2020.2020.0000.0000.0000.000
58B61ASP-1-0.839-0.92923.022-0.103-0.1030.0000.0000.0000.000
59B62THR0-0.001-0.00323.9360.0000.0000.0000.0000.0000.000
60B63LEU0-0.036-0.01718.890-0.001-0.0010.0000.0000.0000.000
61B64MET00.0070.02421.5970.0030.0030.0000.0000.0000.000
62B65GLN00.0100.01925.1810.0050.0050.0000.0000.0000.000
63B66ARG10.9250.97219.4060.1920.1920.0000.0000.0000.000
64B67LEU00.0040.01420.4830.0030.0030.0000.0000.0000.000
65B68ASN0-0.064-0.04627.8450.0060.0060.0000.0000.0000.000
66B69GLY00.0700.02626.1260.0020.0020.0000.0000.0000.000
67B70LEU00.0180.00126.7770.0000.0000.0000.0000.0000.000
68B71GLN00.0190.01029.5370.0050.0050.0000.0000.0000.000
69B72ASN0-0.034-0.01627.056-0.004-0.0040.0000.0000.0000.000
70B74ALA00.0630.04728.4280.0030.0030.0000.0000.0000.000
71B75THR00.010-0.01131.1950.0030.0030.0000.0000.0000.000
72B76HIS0-0.056-0.02526.0730.0030.0030.0000.0000.0000.000
73B77THR0-0.006-0.02528.3640.0040.0040.0000.0000.0000.000
74B78GLN0-0.0230.01930.7770.0050.0050.0000.0000.0000.000
75B79PRO0-0.032-0.01132.7430.0040.0040.0000.0000.0000.000
76B80PHE00.0120.00328.1300.0030.0030.0000.0000.0000.000
77B81TRP00.0160.00828.4720.0010.0010.0000.0000.0000.000
78B82GLY00.0700.04533.6900.0020.0020.0000.0000.0000.000
79B83SER0-0.074-0.06435.4370.0030.0030.0000.0000.0000.000
80B84LEU0-0.083-0.04430.0130.0030.0030.0000.0000.0000.000
81B85THR00.0340.01734.0150.0020.0020.0000.0000.0000.000
82B86ASN0-0.0160.00235.6510.0010.0010.0000.0000.0000.000
83B87ARG10.8120.93433.8250.0230.0230.0000.0000.0000.000
84B88THR00.0160.00037.1670.0000.0000.0000.0000.0000.000
85B89ARG10.8840.93337.1300.0130.0130.0000.0000.0000.000
86B90PRO00.0600.04339.3850.0000.0000.0000.0000.0000.000
87B91PRO0-0.0210.01240.4040.0010.0010.0000.0000.0000.000
88B92SER0-0.0260.00141.2480.0000.0000.0000.0000.0000.000
89B93VAL00.041-0.01442.2460.0010.0010.0000.0000.0000.000
90B94GLN0-0.012-0.00344.4540.0000.0000.0000.0000.0000.000
91B95VAL0-0.0150.01745.2910.0010.0010.0000.0000.0000.000
92B96ALA00.0000.01146.3290.0000.0000.0000.0000.0000.000
93B97LYS10.9430.97047.178-0.020-0.0200.0000.0000.0000.000
94B98THR0-0.0010.00142.2400.0020.0020.0000.0000.0000.000
95B99THR00.003-0.00443.134-0.002-0.0020.0000.0000.0000.000
96B100PRO00.0100.00043.6880.0010.0010.0000.0000.0000.000
97B101PHE00.0060.00039.1530.0020.0020.0000.0000.0000.000
98B102ASN0-0.020-0.00741.516-0.001-0.0010.0000.0000.0000.000
99B103THR00.019-0.00543.657-0.002-0.0020.0000.0000.0000.000
100B104ARG10.8870.93447.319-0.016-0.0160.0000.0000.0000.000
101B105GLU-1-0.882-0.91150.3150.0150.0150.0000.0000.0000.000
102B106PRO0-0.0010.00850.7800.0010.0010.0000.0000.0000.000
103B107VAL0-0.029-0.02251.0650.0010.0010.0000.0000.0000.000
104B108MET0-0.0060.01744.4610.0000.0000.0000.0000.0000.000
105B109LEU0-0.031-0.00347.5660.0010.0010.0000.0000.0000.000
106B110ALA00.0380.01542.6600.0000.0000.0000.0000.0000.000
107B111CYS0-0.110-0.04143.847-0.001-0.0010.0000.0000.0000.000
108B112TYR00.002-0.01239.5440.0010.0010.0000.0000.0000.000
109B113VAL00.0500.01439.618-0.001-0.0010.0000.0000.0000.000
110B114TRP00.016-0.00636.9980.0010.0010.0000.0000.0000.000
111B115GLY00.0570.01536.278-0.001-0.0010.0000.0000.0000.000
112B116PHE0-0.0320.00435.301-0.001-0.0010.0000.0000.0000.000
113B117TYR00.014-0.01430.6330.0010.0010.0000.0000.0000.000
114B118PRO00.0800.03033.9790.0000.0000.0000.0000.0000.000
115B119ALA00.0220.01231.4790.0030.0030.0000.0000.0000.000
116B120GLU-1-0.898-0.94433.317-0.015-0.0150.0000.0000.0000.000
117B121VAL0-0.016-0.00936.3380.0010.0010.0000.0000.0000.000
118B122THR0-0.027-0.01839.2350.0000.0000.0000.0000.0000.000
119B123ILE0-0.044-0.03340.4510.0010.0010.0000.0000.0000.000
120B124THR0-0.026-0.00743.8760.0000.0000.0000.0000.0000.000
121B125TRP00.0450.01545.4880.0000.0000.0000.0000.0000.000
122B126ARG10.9630.97549.808-0.003-0.0030.0000.0000.0000.000
123B127LYS10.8540.95053.562-0.009-0.0090.0000.0000.0000.000
124B128ASN0-0.008-0.03056.1010.0000.0000.0000.0000.0000.000
125B129GLY00.0160.00257.6310.0000.0000.0000.0000.0000.000
126B130LYS10.9390.98257.395-0.005-0.0050.0000.0000.0000.000
127B131LEU00.0120.00250.2450.0010.0010.0000.0000.0000.000
128B132VAL0-0.025-0.00750.2270.0000.0000.0000.0000.0000.000
129B133MET00.0260.01948.1800.0000.0000.0000.0000.0000.000
130B134HIS00.006-0.01046.7260.0000.0000.0000.0000.0000.000
131B135SER00.0010.01043.6320.0010.0010.0000.0000.0000.000
132B136SER0-0.005-0.00838.932-0.001-0.0010.0000.0000.0000.000
133B137ALA00.0410.03041.0570.0020.0020.0000.0000.0000.000
134B138HIS00.0660.04637.5130.0010.0010.0000.0000.0000.000
135B139LYS10.8280.91237.282-0.008-0.0080.0000.0000.0000.000
136B140THR00.0470.03931.583-0.002-0.0020.0000.0000.0000.000
137B141ALA0-0.033-0.02632.0830.0030.0030.0000.0000.0000.000
138B142GLN0-0.022-0.01326.2740.0010.0010.0000.0000.0000.000
139B143PRO0-0.004-0.00625.860-0.001-0.0010.0000.0000.0000.000
140B144ASN00.007-0.00427.5960.0110.0110.0000.0000.0000.000
141B145GLY0-0.0150.00325.8240.0050.0050.0000.0000.0000.000
142B146ASP-1-0.838-0.89226.5220.0010.0010.0000.0000.0000.000
143B147TRP0-0.054-0.02527.069-0.002-0.0020.0000.0000.0000.000
144B148THR0-0.031-0.01630.6660.0000.0000.0000.0000.0000.000
145B149TYR00.0110.00628.2730.0010.0010.0000.0000.0000.000
146B150GLN0-0.042-0.03432.3250.0010.0010.0000.0000.0000.000
147B151THR0-0.022-0.01333.8390.0000.0000.0000.0000.0000.000
148B152LEU00.0280.00436.3510.0010.0010.0000.0000.0000.000
149B153SER0-0.0170.00838.9940.0000.0000.0000.0000.0000.000
150B154HIS00.0600.01539.042-0.001-0.0010.0000.0000.0000.000
151B155LEU0-0.0140.00143.711-0.001-0.0010.0000.0000.0000.000
152B156ALA0-0.027-0.00347.3390.0010.0010.0000.0000.0000.000
153B157LEU0-0.018-0.01348.938-0.001-0.0010.0000.0000.0000.000
154B158THR00.0750.01852.7240.0010.0010.0000.0000.0000.000
155B159PRO0-0.064-0.03155.386-0.001-0.0010.0000.0000.0000.000
156B160SER00.0430.01257.6280.0000.0000.0000.0000.0000.000
157B161TYR00.001-0.01860.7570.0000.0000.0000.0000.0000.000
158B162GLY00.0260.04062.3850.0000.0000.0000.0000.0000.000
159B163ASP-1-0.816-0.89458.3880.0090.0090.0000.0000.0000.000
160B164THR0-0.017-0.00657.1640.0010.0010.0000.0000.0000.000
161B165TYR0-0.046-0.02552.616-0.001-0.0010.0000.0000.0000.000
162B166THR0-0.005-0.02552.1390.0000.0000.0000.0000.0000.000
163B168VAL0-0.002-0.02148.3070.0000.0000.0000.0000.0000.000
164B169VAL00.000-0.00742.8150.0000.0000.0000.0000.0000.000
165B170GLU-1-0.875-0.93044.290-0.004-0.0040.0000.0000.0000.000
166B171HIS0-0.011-0.02037.5390.0000.0000.0000.0000.0000.000
167B172ILE00.0840.03538.6670.0000.0000.0000.0000.0000.000
168B173GLY0-0.023-0.01141.521-0.001-0.0010.0000.0000.0000.000
169B174ALA0-0.075-0.04642.3020.0010.0010.0000.0000.0000.000
170B175PRO0-0.0270.00145.8240.0000.0000.0000.0000.0000.000
171B176GLU-1-0.891-0.94449.009-0.005-0.0050.0000.0000.0000.000
172B177PRO0-0.028-0.00948.4210.0010.0010.0000.0000.0000.000
173B178ILE0-0.017-0.00745.5360.0010.0010.0000.0000.0000.000
174B179LEU0-0.015-0.00748.8050.0010.0010.0000.0000.0000.000
175B180ARG10.8680.92347.804-0.006-0.0060.0000.0000.0000.000
176B181ASP-1-0.832-0.89050.9500.0070.0070.0000.0000.0000.000
177B182TRP00.017-0.00451.9020.0010.0010.0000.0000.0000.000
178B183THR00.009-0.00954.032-0.001-0.0010.0000.0000.0000.000
179B184PRO0-0.041-0.01856.5570.0010.0010.0000.0000.0000.000
180B185GLY00.0010.01456.6700.0000.0000.0000.0000.0000.000