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: G6VK1

Calculation Name: 1DEE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DEE

Chain ID: B

ChEMBL ID:

UniProt ID: P02976

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 -2299212.6967
FMO2-HF: Nuclear repulsion 2214189.118083
FMO2-HF: Total energy -85023.578617
FMO2-MP2: Total energy -85271.130978


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:501:GLN)


Summations of interaction energy for fragment #1(B:501: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.
-0.271.615-0.006-0.644-1.2340.002
Interaction energy analysis for fragmet #1(B:501:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.015
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].
3B503GLN0-0.015-0.0063.794-0.4710.977-0.005-0.540-0.9030.002
4B504LEU0-0.016-0.0135.8380.2550.2550.0000.0000.0000.000
5B505VAL00.0110.0019.5050.0310.0310.0000.0000.0000.000
6B506GLU-1-0.768-0.87211.932-0.503-0.5030.0000.0000.0000.000
7B507SER0-0.003-0.02315.5100.0430.0430.0000.0000.0000.000
8B508GLY00.0480.01718.491-0.008-0.0080.0000.0000.0000.000
9B509GLY0-0.015-0.00321.3860.0060.0060.0000.0000.0000.000
10B510GLY00.0260.00623.1450.0150.0150.0000.0000.0000.000
11B511VAL0-0.021-0.00826.408-0.009-0.0090.0000.0000.0000.000
12B512VAL0-0.025-0.01429.8730.0100.0100.0000.0000.0000.000
13B513GLN0-0.024-0.00532.215-0.002-0.0020.0000.0000.0000.000
14B514PRO00.0380.00035.050-0.002-0.0020.0000.0000.0000.000
15B515GLY0-0.041-0.00236.2630.0060.0060.0000.0000.0000.000
16B516LYS10.9230.96133.5810.0730.0730.0000.0000.0000.000
17B517SER00.000-0.01431.425-0.005-0.0050.0000.0000.0000.000
18B518LEU0-0.037-0.01325.9710.0060.0060.0000.0000.0000.000
19B519ARG10.8900.95223.1430.1150.1150.0000.0000.0000.000
20B520LEU0-0.0060.01620.3000.0080.0080.0000.0000.0000.000
21B521SER00.002-0.01518.0290.0150.0150.0000.0000.0000.000
22B522CYS0-0.077-0.01913.930-0.010-0.0100.0000.0000.0000.000
23B523ALA00.0080.02212.2000.0140.0140.0000.0000.0000.000
24B524ALA00.0190.0059.652-0.107-0.1070.0000.0000.0000.000
25B525SER0-0.006-0.0056.2430.2010.2010.0000.0000.0000.000
26B526GLY00.0520.0233.644-0.996-0.8720.001-0.083-0.0420.000
27B527PHE0-0.009-0.0114.3850.7790.951-0.001-0.014-0.1570.000
28B528THR00.0300.0167.4460.0330.0330.0000.0000.0000.000
29B529PHE00.0210.02311.057-0.018-0.0180.0000.0000.0000.000
30B530SER00.022-0.00612.545-0.010-0.0100.0000.0000.0000.000
31B531GLY0-0.0050.00814.4010.0210.0210.0000.0000.0000.000
32B532TYR0-0.046-0.01511.076-0.012-0.0120.0000.0000.0000.000
33B533GLY00.0460.03115.3790.0280.0280.0000.0000.0000.000
34B534MET0-0.059-0.02112.432-0.079-0.0790.0000.0000.0000.000
35B535HIS00.0780.02016.4190.0720.0720.0000.0000.0000.000
36B536TRP00.0010.00417.165-0.054-0.0540.0000.0000.0000.000
37B537VAL0-0.028-0.01418.3530.0320.0320.0000.0000.0000.000
38B538ARG10.7960.87319.5960.1970.1970.0000.0000.0000.000
39B539GLN00.0260.02220.499-0.028-0.0280.0000.0000.0000.000
40B540ALA00.0110.01223.1560.0090.0090.0000.0000.0000.000
41B541PRO00.027-0.01025.953-0.014-0.0140.0000.0000.0000.000
42B542GLY00.0070.01825.9760.0130.0130.0000.0000.0000.000
43B543LYS10.9080.95226.4700.2030.2030.0000.0000.0000.000
44B544GLY00.0310.01524.780-0.020-0.0200.0000.0000.0000.000
45B545LEU0-0.009-0.00318.9180.0100.0100.0000.0000.0000.000
46B546GLU-1-0.814-0.88722.848-0.201-0.2010.0000.0000.0000.000
47B547TRP0-0.013-0.01121.210-0.001-0.0010.0000.0000.0000.000
48B548VAL0-0.010-0.00822.6670.0280.0280.0000.0000.0000.000
49B549ALA00.012-0.00622.5870.0290.0290.0000.0000.0000.000
50B550LEU0-0.0180.01720.945-0.035-0.0350.0000.0000.0000.000
51B551ILE0-0.021-0.00819.9570.0360.0360.0000.0000.0000.000
52B552SER0-0.003-0.02520.202-0.036-0.0360.0000.0000.0000.000
53B553TYR0-0.019-0.02218.0750.0020.0020.0000.0000.0000.000
54B554ASP-1-0.754-0.83219.427-0.120-0.1200.0000.0000.0000.000
55B555GLU-1-0.924-0.97122.045-0.103-0.1030.0000.0000.0000.000
56B556SER0-0.022-0.01524.0180.0030.0030.0000.0000.0000.000
57B557ASN0-0.0200.00025.6110.0040.0040.0000.0000.0000.000
58B558LYS10.8810.92924.8560.1290.1290.0000.0000.0000.000
59B559TYR0-0.026-0.00825.6140.0120.0120.0000.0000.0000.000
60B560TYR00.0240.01125.855-0.018-0.0180.0000.0000.0000.000
61B561ALA00.0520.03627.1030.0080.0080.0000.0000.0000.000
62B562ASP-1-0.826-0.91728.849-0.141-0.1410.0000.0000.0000.000
63B563SER0-0.027-0.00730.1000.0100.0100.0000.0000.0000.000
64B564VAL00.012-0.00527.3610.0080.0080.0000.0000.0000.000
65B565LYS10.8670.93930.7670.1350.1350.0000.0000.0000.000
66B566GLY00.0020.00732.4180.0070.0070.0000.0000.0000.000
67B567ARG10.7140.83031.4980.1480.1480.0000.0000.0000.000
68B568PHE00.021-0.02026.3080.0020.0020.0000.0000.0000.000
69B569THR0-0.026-0.01727.6700.0110.0110.0000.0000.0000.000
70B570ILE0-0.0070.01420.696-0.003-0.0030.0000.0000.0000.000
71B571SER0-0.023-0.02522.7420.0210.0210.0000.0000.0000.000
72B572ARG10.8030.89916.0750.2250.2250.0000.0000.0000.000
73B573ASP-1-0.761-0.85418.746-0.041-0.0410.0000.0000.0000.000
74B574ASN00.007-0.02916.965-0.041-0.0410.0000.0000.0000.000
75B575SER0-0.017-0.00716.4210.0100.0100.0000.0000.0000.000
76B576LYS10.8790.94416.3310.0450.0450.0000.0000.0000.000
77B577ASN0-0.0170.00011.961-0.031-0.0310.0000.0000.0000.000
78B578THR0-0.017-0.00813.161-0.064-0.0640.0000.0000.0000.000
79B579LEU0-0.0120.00515.7750.0280.0280.0000.0000.0000.000
80B580TYR0-0.003-0.03017.7190.0060.0060.0000.0000.0000.000
81B581LEU00.0310.01220.963-0.008-0.0080.0000.0000.0000.000
82B582GLN0-0.028-0.00523.5460.0080.0080.0000.0000.0000.000
83B583MET0-0.0160.00424.807-0.008-0.0080.0000.0000.0000.000
84B584ASN00.0600.02328.6910.0130.0130.0000.0000.0000.000
85B585SER00.0090.00032.450-0.003-0.0030.0000.0000.0000.000
86B586LEU0-0.0210.00728.767-0.005-0.0050.0000.0000.0000.000
87B587ARG10.8680.89132.8950.1400.1400.0000.0000.0000.000
88B588ALA00.0400.00732.757-0.007-0.0070.0000.0000.0000.000
89B589GLU-1-0.830-0.89232.280-0.138-0.1380.0000.0000.0000.000
90B590ASP-1-0.765-0.81628.765-0.166-0.1660.0000.0000.0000.000
91B591THR00.0360.02827.583-0.009-0.0090.0000.0000.0000.000
92B592ALA0-0.019-0.01424.320-0.004-0.0040.0000.0000.0000.000
93B593VAL0-0.0030.01718.7250.0170.0170.0000.0000.0000.000
94B594TYR0-0.053-0.05120.056-0.012-0.0120.0000.0000.0000.000
95B595TYR00.0260.01215.221-0.004-0.0040.0000.0000.0000.000
96B597ALA0-0.006-0.01812.781-0.097-0.0970.0000.0000.0000.000
97B598LYS10.8480.9118.6801.0161.0160.0000.0000.0000.000
98B599VAL00.0140.01612.590-0.042-0.0420.0000.0000.0000.000
99B600LYS10.8850.94310.0381.0581.0580.0000.0000.0000.000
100B601PHE00.006-0.01913.5750.0140.0140.0000.0000.0000.000
101B602TYR0-0.010-0.00216.174-0.007-0.0070.0000.0000.0000.000
102B603ASP-1-0.787-0.87919.131-0.226-0.2260.0000.0000.0000.000
103B604PRO0-0.011-0.00820.767-0.032-0.0320.0000.0000.0000.000
104B605THR0-0.080-0.05222.550-0.016-0.0160.0000.0000.0000.000
105B606ALA0-0.049-0.00517.119-0.032-0.0320.0000.0000.0000.000
106B607PRO00.0020.00815.465-0.008-0.0080.0000.0000.0000.000
107B608ASN00.026-0.01214.343-0.043-0.0430.0000.0000.0000.000
108B609ASP-1-0.794-0.89310.318-1.135-1.1350.0000.0000.0000.000
109B610TYR0-0.0100.0054.429-0.698-0.557-0.001-0.007-0.1320.000
110B611TRP0-0.003-0.0209.0650.2550.2550.0000.0000.0000.000
111B612GLY00.0570.0359.607-0.161-0.1610.0000.0000.0000.000
112B613GLN0-0.042-0.02710.672-0.056-0.0560.0000.0000.0000.000
113B614GLY00.006-0.00212.9180.0370.0370.0000.0000.0000.000
114B615THR0-0.065-0.02416.2800.0470.0470.0000.0000.0000.000
115B616LEU0-0.0130.00019.306-0.007-0.0070.0000.0000.0000.000
116B617VAL0-0.0060.01122.6600.0180.0180.0000.0000.0000.000
117B618THR0-0.021-0.01425.501-0.003-0.0030.0000.0000.0000.000
118B619VAL00.0070.00528.7390.0100.0100.0000.0000.0000.000
119B620SER0-0.033-0.03831.7820.0010.0010.0000.0000.0000.000
120B621SER00.0470.01334.9790.0010.0010.0000.0000.0000.000
121B622GLY0-0.0060.01537.7040.0060.0060.0000.0000.0000.000
122B623SER00.007-0.00236.889-0.002-0.0020.0000.0000.0000.000
123B624ALA0-0.013-0.01132.790-0.002-0.0020.0000.0000.0000.000
124B625SER00.0150.00534.6360.0050.0050.0000.0000.0000.000
125B626ALA00.0110.00534.793-0.005-0.0050.0000.0000.0000.000
126B627PRO0-0.028-0.00534.2810.0010.0010.0000.0000.0000.000
127B628THR0-0.016-0.01437.1710.0070.0070.0000.0000.0000.000
128B629LEU0-0.028-0.01237.308-0.003-0.0030.0000.0000.0000.000
129B630PHE0-0.006-0.00541.0820.0050.0050.0000.0000.0000.000
130B631PRO00.0180.01642.877-0.004-0.0040.0000.0000.0000.000
131B632LEU0-0.033-0.01241.8770.0000.0000.0000.0000.0000.000
132B633VAL00.0460.02145.436-0.001-0.0010.0000.0000.0000.000
133B634SER00.0140.01148.0090.0010.0010.0000.0000.0000.000
134B635CYS0-0.017-0.01049.5590.0030.0030.0000.0000.0000.000
135B636GLU-1-0.900-0.95153.112-0.041-0.0410.0000.0000.0000.000
136B637ASN0-0.024-0.00850.620-0.001-0.0010.0000.0000.0000.000
137B638SER0-0.033-0.01348.865-0.002-0.0020.0000.0000.0000.000
138B639ASN00.0470.01350.954-0.001-0.0010.0000.0000.0000.000
139B640PRO0-0.0350.00152.7190.0010.0010.0000.0000.0000.000
140B641SER00.0350.00347.267-0.003-0.0030.0000.0000.0000.000
141B642SER0-0.008-0.00447.3800.0030.0030.0000.0000.0000.000
142B643THR0-0.083-0.04143.2660.0000.0000.0000.0000.0000.000
143B644VAL00.0540.04346.324-0.002-0.0020.0000.0000.0000.000
144B645ALA0-0.023-0.01543.490-0.002-0.0020.0000.0000.0000.000
145B646VAL00.0100.02242.7660.0010.0010.0000.0000.0000.000
146B647GLY00.017-0.01740.933-0.005-0.0050.0000.0000.0000.000
147B648CYS0-0.107-0.02538.1080.0010.0010.0000.0000.0000.000
148B649LEU00.0140.01138.971-0.006-0.0060.0000.0000.0000.000
149B650ALA00.0330.02235.9810.0050.0050.0000.0000.0000.000
150B651GLN00.004-0.02137.703-0.004-0.0040.0000.0000.0000.000
151B652ASP-1-0.779-0.88538.901-0.069-0.0690.0000.0000.0000.000
152B653PHE0-0.0230.02231.4210.0050.0050.0000.0000.0000.000
153B654LEU0-0.0350.00732.411-0.008-0.0080.0000.0000.0000.000
154B655PRO00.0510.00428.0470.0090.0090.0000.0000.0000.000
155B656ASP-1-0.810-0.89128.234-0.144-0.1440.0000.0000.0000.000
156B657SER0-0.053-0.03625.892-0.014-0.0140.0000.0000.0000.000
157B658ILE00.0250.01627.3970.0130.0130.0000.0000.0000.000
158B659THR0-0.049-0.02326.707-0.010-0.0100.0000.0000.0000.000
159B660PHE00.0380.00629.1100.0100.0100.0000.0000.0000.000
160B661SER0-0.027-0.00231.064-0.001-0.0010.0000.0000.0000.000
161B662TRP00.0480.00233.1590.0040.0040.0000.0000.0000.000
162B663LYS10.8260.90133.6270.0370.0370.0000.0000.0000.000
163B664TYR00.0350.01438.504-0.002-0.0020.0000.0000.0000.000
164B665LYS10.9090.96141.9080.0270.0270.0000.0000.0000.000
165B666ASN0-0.056-0.01242.6690.0000.0000.0000.0000.0000.000
166B667ASN0-0.024-0.01738.5020.0000.0000.0000.0000.0000.000
167B668SER00.012-0.00637.8740.0020.0020.0000.0000.0000.000
168B669ASP-1-0.832-0.90733.458-0.045-0.0450.0000.0000.0000.000
169B670ILE00.0050.01635.9090.0010.0010.0000.0000.0000.000
170B671SER0-0.001-0.00534.043-0.003-0.0030.0000.0000.0000.000
171B672SER0-0.037-0.03034.285-0.008-0.0080.0000.0000.0000.000
172B673THR00.0090.01333.1690.0010.0010.0000.0000.0000.000
173B674ARG10.9320.96432.5280.1160.1160.0000.0000.0000.000
174B675GLY00.0280.01631.3610.0070.0070.0000.0000.0000.000
175B676PHE0-0.048-0.02431.627-0.010-0.0100.0000.0000.0000.000
176B677PRO00.021-0.00229.6780.0020.0020.0000.0000.0000.000
177B678SER0-0.027-0.04030.5650.0120.0120.0000.0000.0000.000
178B679VAL0-0.032-0.00632.535-0.008-0.0080.0000.0000.0000.000
179B680LEU0-0.006-0.00934.0150.0050.0050.0000.0000.0000.000
180B681ARG10.9520.97736.0200.0820.0820.0000.0000.0000.000
181B682GLY00.017-0.00139.5530.0040.0040.0000.0000.0000.000
182B683GLY00.0060.01837.1450.0040.0040.0000.0000.0000.000
183B684LYS10.7980.90135.9740.0700.0700.0000.0000.0000.000
184B685TYR00.0230.00331.035-0.007-0.0070.0000.0000.0000.000
185B686ALA0-0.014-0.00935.2530.0080.0080.0000.0000.0000.000
186B687ALA00.0280.02333.332-0.008-0.0080.0000.0000.0000.000
187B688THR00.003-0.00135.3330.0090.0090.0000.0000.0000.000
188B689SER0-0.0230.00934.657-0.005-0.0050.0000.0000.0000.000
189B690GLN00.001-0.01736.3850.0010.0010.0000.0000.0000.000
190B691VAL00.0530.03037.391-0.005-0.0050.0000.0000.0000.000
191B692LEU0-0.055-0.01739.4330.0020.0020.0000.0000.0000.000
192B693LEU00.0540.03241.4500.0000.0000.0000.0000.0000.000
193B694PRO00.0080.00243.2570.0000.0000.0000.0000.0000.000
194B695SER00.047-0.00346.0960.0020.0020.0000.0000.0000.000
195B696LYS10.9280.96549.0740.0480.0480.0000.0000.0000.000
196B697ASP-1-0.845-0.89251.077-0.033-0.0330.0000.0000.0000.000
197B698VAL0-0.115-0.07147.4970.0010.0010.0000.0000.0000.000
198B699ALA00.0040.00548.556-0.001-0.0010.0000.0000.0000.000
199B700GLN00.001-0.01449.383-0.002-0.0020.0000.0000.0000.000
200B701GLY0-0.0080.00851.0000.0010.0010.0000.0000.0000.000
201B702THR0-0.012-0.00451.0510.0000.0000.0000.0000.0000.000
202B703ASN0-0.006-0.00746.7630.0010.0010.0000.0000.0000.000
203B704GLU-1-0.819-0.90849.295-0.026-0.0260.0000.0000.0000.000
204B705HIS0-0.033-0.03145.456-0.001-0.0010.0000.0000.0000.000
205B706VAL0-0.0160.00041.8680.0010.0010.0000.0000.0000.000
206B707VAL00.0160.00839.9580.0000.0000.0000.0000.0000.000
207B709LYS10.8360.88934.8180.0370.0370.0000.0000.0000.000
208B710VAL0-0.008-0.00932.983-0.007-0.0070.0000.0000.0000.000
209B711GLN00.0090.00028.1940.0090.0090.0000.0000.0000.000
210B712HIS00.028-0.01529.663-0.003-0.0030.0000.0000.0000.000
211B713PRO00.0040.01126.7770.0090.0090.0000.0000.0000.000
212B714ASN0-0.046-0.01829.3270.0100.0100.0000.0000.0000.000
213B715GLY0-0.008-0.00732.5010.0050.0050.0000.0000.0000.000
214B716ASN00.0260.02230.731-0.011-0.0110.0000.0000.0000.000
215B717LYS10.9000.96034.2970.0530.0530.0000.0000.0000.000
216B718GLU-1-0.766-0.88836.848-0.037-0.0370.0000.0000.0000.000
217B719LYS10.8790.94539.3670.0460.0460.0000.0000.0000.000
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