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: 2NLKR

Calculation Name: 4E8E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E8E

Chain ID: A

ChEMBL ID:

UniProt ID: O61996

Base Structure: X-ray

Registration Date: 2023-09-21

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2754510.021671
FMO2-HF: Nuclear repulsion 2666151.612589
FMO2-HF: Total energy -88358.409082
FMO2-MP2: Total energy -88613.384786


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(A:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-21.976-16.7495.19-4.608-5.807-0.041
Interaction energy analysis for fragmet #1(A:0:HIS)
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 : -0.033
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].
3A2PRO00.0260.0363.8751.2852.928-0.015-0.815-0.8130.001
4A3VAL0-0.023-0.0256.3930.4440.4440.0000.0000.0000.000
5A4GLN0-0.046-0.0228.242-0.080-0.0800.0000.0000.0000.000
6A5PRO00.0310.02110.671-0.189-0.1890.0000.0000.0000.000
7A6ILE00.0080.0029.1680.0920.0920.0000.0000.0000.000
8A7LYS10.8330.90413.0590.1060.1060.0000.0000.0000.000
9A8LEU0-0.011-0.00916.736-0.068-0.0680.0000.0000.0000.000
10A9TYR00.0210.01819.1110.0450.0450.0000.0000.0000.000
11A10TYR00.043-0.01022.040-0.041-0.0410.0000.0000.0000.000
12A11LEU00.030-0.00124.1570.0450.0450.0000.0000.0000.000
13A12PRO00.0180.01125.550-0.022-0.0220.0000.0000.0000.000
14A13PRO00.0720.03026.615-0.026-0.0260.0000.0000.0000.000
15A14SER00.0100.01826.109-0.017-0.0170.0000.0000.0000.000
16A15PRO00.0420.01525.354-0.042-0.0420.0000.0000.0000.000
17A16PRO00.0050.00223.388-0.056-0.0560.0000.0000.0000.000
18A17CYS0-0.0120.00321.419-0.057-0.0570.0000.0000.0000.000
19A18ARG10.8080.88820.3040.4090.4090.0000.0000.0000.000
20A19ALA00.0420.04020.068-0.067-0.0670.0000.0000.0000.000
21A20VAL0-0.0250.00215.649-0.134-0.1340.0000.0000.0000.000
22A21MET0-0.015-0.00515.556-0.137-0.1370.0000.0000.0000.000
23A22MET00.0020.02115.980-0.069-0.0690.0000.0000.0000.000
24A23THR00.000-0.01112.644-0.106-0.1060.0000.0000.0000.000
25A24ALA0-0.0010.00011.279-0.321-0.3210.0000.0000.0000.000
26A25ARG10.8440.89211.0720.6080.6080.0000.0000.0000.000
27A26VAL0-0.036-0.01711.888-0.034-0.0340.0000.0000.0000.000
28A27LEU0-0.058-0.0237.012-0.207-0.2070.0000.0000.0000.000
29A28GLU-1-0.873-0.9197.445-2.796-2.7960.0000.0000.0000.000
30A29LEU0-0.058-0.0235.8570.2130.2130.0000.0000.0000.000
31A30ASP-1-0.871-0.9419.566-0.392-0.3920.0000.0000.0000.000
32A31LEU0-0.051-0.03112.375-0.073-0.0730.0000.0000.0000.000
33A32HIS00.0040.01115.1540.1380.1380.0000.0000.0000.000
34A33LEU0-0.021-0.02017.9640.0180.0180.0000.0000.0000.000
35A34ILE0-0.021-0.00820.5630.0610.0610.0000.0000.0000.000
36A35THR0-0.019-0.00923.518-0.019-0.0190.0000.0000.0000.000
37A36THR00.001-0.00225.9490.0280.0280.0000.0000.0000.000
38A37ASN0-0.023-0.02128.355-0.024-0.0240.0000.0000.0000.000
39A38ILE00.029-0.00229.2610.0180.0180.0000.0000.0000.000
40A39MET0-0.007-0.01232.8800.0150.0150.0000.0000.0000.000
41A40ASN0-0.075-0.03534.7620.0180.0180.0000.0000.0000.000
42A41GLY00.0160.01135.4030.0110.0110.0000.0000.0000.000
43A42GLU-1-0.790-0.88130.352-0.181-0.1810.0000.0000.0000.000
44A43HIS0-0.020-0.00929.325-0.002-0.0020.0000.0000.0000.000
45A44MET0-0.021-0.02530.349-0.006-0.0060.0000.0000.0000.000
46A45THR0-0.0090.01130.3890.0140.0140.0000.0000.0000.000
47A46PRO00.004-0.00531.126-0.010-0.0100.0000.0000.0000.000
48A47GLU-1-0.882-0.94627.404-0.073-0.0730.0000.0000.0000.000
49A48TYR00.006-0.00225.229-0.016-0.0160.0000.0000.0000.000
50A49LEU0-0.006-0.00526.896-0.016-0.0160.0000.0000.0000.000
51A50LYS10.8740.94225.7070.0400.0400.0000.0000.0000.000
52A51MET0-0.051-0.00321.5520.0040.0040.0000.0000.0000.000
53A52ASN00.030-0.01223.147-0.005-0.0050.0000.0000.0000.000
54A53PRO00.0360.03425.2770.0040.0040.0000.0000.0000.000
55A54GLN0-0.049-0.01827.1060.0170.0170.0000.0000.0000.000
56A55HIS10.8370.91828.1940.2010.2010.0000.0000.0000.000
57A56THR00.0190.02526.2080.0050.0050.0000.0000.0000.000
58A57ILE0-0.0070.02124.7560.0030.0030.0000.0000.0000.000
59A58PRO0-0.006-0.02620.5670.0030.0030.0000.0000.0000.000
60A59THR0-0.032-0.02120.2820.0020.0020.0000.0000.0000.000
61A60MET0-0.045-0.00413.020-0.075-0.0750.0000.0000.0000.000
62A61ASP-1-0.795-0.89815.828-0.115-0.1150.0000.0000.0000.000
63A62ASP-1-0.790-0.8448.988-0.874-0.8740.0000.0000.0000.000
64A63ASN0-0.005-0.00810.9190.1550.1550.0000.0000.0000.000
65A64GLY00.0220.01312.7900.1000.1000.0000.0000.0000.000
66A65PHE0-0.053-0.02011.8810.0200.0200.0000.0000.0000.000
67A66ILE0-0.012-0.01114.321-0.094-0.0940.0000.0000.0000.000
68A67LEU0-0.0210.00715.351-0.010-0.0100.0000.0000.0000.000
69A68TRP00.006-0.01918.103-0.003-0.0030.0000.0000.0000.000
70A69GLU-1-0.823-0.90920.603-0.474-0.4740.0000.0000.0000.000
71A70SER00.0130.00619.796-0.051-0.0510.0000.0000.0000.000
72A71ARG10.8520.91418.3570.5070.5070.0000.0000.0000.000
73A72ALA00.0110.01917.888-0.090-0.0900.0000.0000.0000.000
74A73ILE00.0060.00314.980-0.118-0.1180.0000.0000.0000.000
75A74GLN0-0.040-0.04013.863-0.110-0.1100.0000.0000.0000.000
76A75THR00.001-0.00712.736-0.287-0.2870.0000.0000.0000.000
77A76TYR0-0.070-0.0548.939-0.276-0.2760.0000.0000.0000.000
78A77LEU00.0350.0109.504-0.278-0.2780.0000.0000.0000.000
79A78VAL0-0.011-0.0037.771-0.820-0.8200.0000.0000.0000.000
80A79ASN0-0.031-0.0206.949-0.886-0.8860.0000.0000.0000.000
81A80ALA0-0.0420.0006.1980.2440.2440.0000.0000.0000.000
82A81TYR0-0.055-0.0633.645-0.4780.5350.015-0.229-0.7980.000
83A82GLY00.0310.0353.923-1.435-0.8650.003-0.240-0.333-0.001
84A83LYS10.7930.8822.063-12.613-10.8225.187-3.496-3.481-0.040
85A84ASP-1-0.841-0.8993.087-2.824-2.6140.0000.172-0.382-0.001
86A85ASP-1-0.805-0.8985.441-2.928-2.9280.0000.0000.0000.000
87A86SER0-0.025-0.0298.1360.7760.7760.0000.0000.0000.000
88A87LEU00.0230.01310.3620.3990.3990.0000.0000.0000.000
89A88TYR0-0.093-0.09511.3860.3240.3240.0000.0000.0000.000
90A89PRO00.0660.05711.463-0.111-0.1110.0000.0000.0000.000
91A90LYS10.8950.9187.9102.5702.5700.0000.0000.0000.000
92A91ASN0-0.0320.00313.0400.2490.2490.0000.0000.0000.000
93A92PRO00.0600.01416.394-0.020-0.0200.0000.0000.0000.000
94A93ARG10.9450.97519.1120.4160.4160.0000.0000.0000.000
95A94GLN00.0290.00616.759-0.064-0.0640.0000.0000.0000.000
96A95ARG10.8140.90711.4791.5071.5070.0000.0000.0000.000
97A96ALA00.0610.02817.6460.0120.0120.0000.0000.0000.000
98A97ILE0-0.036-0.00721.3040.0440.0440.0000.0000.0000.000
99A98ILE00.0320.01915.9060.0240.0240.0000.0000.0000.000
100A99ASP-1-0.786-0.88218.679-0.858-0.8580.0000.0000.0000.000
101A100GLN0-0.0230.00420.9610.0490.0490.0000.0000.0000.000
102A101ARG10.8450.92122.2190.6050.6050.0000.0000.0000.000
103A102LEU00.0200.01317.8150.0340.0340.0000.0000.0000.000
104A103ASN0-0.049-0.04122.5230.0680.0680.0000.0000.0000.000
105A104PHE0-0.0020.01125.6380.0360.0360.0000.0000.0000.000
106A105ASP-1-0.726-0.85024.614-0.565-0.5650.0000.0000.0000.000
107A106LEU0-0.028-0.01624.9550.0280.0280.0000.0000.0000.000
108A107GLY00.0250.00827.1680.0310.0310.0000.0000.0000.000
109A108THR0-0.076-0.04830.1190.0370.0370.0000.0000.0000.000
110A109LEU00.0030.01928.1610.0180.0180.0000.0000.0000.000
111A110TYR00.0690.01927.9760.0160.0160.0000.0000.0000.000
112A111LEU00.0040.01230.1150.0230.0230.0000.0000.0000.000
113A112ARG10.8050.87732.8360.3120.3120.0000.0000.0000.000
114A113TYR00.0460.03031.6700.0140.0140.0000.0000.0000.000
115A114LEU0-0.035-0.01031.2460.0160.0160.0000.0000.0000.000
116A115ASN0-0.065-0.03734.9680.0320.0320.0000.0000.0000.000
117A116LEU00.0030.02037.7410.0150.0150.0000.0000.0000.000
118A117TYR00.0910.02336.3310.0110.0110.0000.0000.0000.000
119A118THR0-0.078-0.04036.2510.0010.0010.0000.0000.0000.000
120A119PRO0-0.009-0.01638.0280.0080.0080.0000.0000.0000.000
121A120ILE0-0.0050.01540.8770.0070.0070.0000.0000.0000.000
122A121LEU0-0.018-0.00835.4500.0070.0070.0000.0000.0000.000
123A122PHE0-0.042-0.02834.2080.0040.0040.0000.0000.0000.000
124A123ARG10.7920.89040.2960.1960.1960.0000.0000.0000.000
125A124GLY00.0290.04043.6790.0090.0090.0000.0000.0000.000
126A125GLU-1-0.900-0.94044.964-0.167-0.1670.0000.0000.0000.000
127A126ALA00.001-0.01045.665-0.006-0.0060.0000.0000.0000.000
128A127TYR00.006-0.01341.078-0.001-0.0010.0000.0000.0000.000
129A128ASP-1-0.843-0.91843.902-0.183-0.1830.0000.0000.0000.000
130A129GLN0-0.040-0.03944.339-0.003-0.0030.0000.0000.0000.000
131A130GLU-1-0.860-0.91143.322-0.216-0.2160.0000.0000.0000.000
132A131LYS10.8590.91540.6530.1970.1970.0000.0000.0000.000
133A132ALA00.0230.01640.136-0.016-0.0160.0000.0000.0000.000
134A133ASP-1-0.863-0.92140.880-0.208-0.2080.0000.0000.0000.000
135A134LYS10.7860.88138.8520.2190.2190.0000.0000.0000.000
136A135PHE00.0220.01032.978-0.021-0.0210.0000.0000.0000.000
137A136ASP-1-0.752-0.86036.280-0.292-0.2920.0000.0000.0000.000
138A137GLU-1-0.803-0.86837.763-0.256-0.2560.0000.0000.0000.000
139A138ALA0-0.039-0.02433.227-0.011-0.0110.0000.0000.0000.000
140A139LEU0-0.0080.00932.556-0.031-0.0310.0000.0000.0000.000
141A140GLY00.0680.03133.921-0.013-0.0130.0000.0000.0000.000
142A141TRP0-0.056-0.02233.056-0.010-0.0100.0000.0000.0000.000
143A142LEU00.0260.01827.156-0.018-0.0180.0000.0000.0000.000
144A143ASN00.0520.01230.222-0.032-0.0320.0000.0000.0000.000
145A144THR0-0.022-0.01932.6800.0060.0060.0000.0000.0000.000
146A145PHE0-0.063-0.04327.704-0.006-0.0060.0000.0000.0000.000
147A146LEU0-0.010-0.00125.862-0.029-0.0290.0000.0000.0000.000
148A147ASP-1-0.910-0.93428.856-0.335-0.3350.0000.0000.0000.000
149A148GLY0-0.024-0.01830.478-0.008-0.0080.0000.0000.0000.000
150A149ARG10.8480.93224.9090.4720.4720.0000.0000.0000.000
151A150PRO0-0.0410.01322.8750.0180.0180.0000.0000.0000.000
152A151PHE00.0520.01421.046-0.015-0.0150.0000.0000.0000.000
153A152VAL00.004-0.00121.8720.0350.0350.0000.0000.0000.000
154A153ALA0-0.003-0.01419.9810.0510.0510.0000.0000.0000.000
155A154GLY0-0.016-0.00421.4080.0070.0070.0000.0000.0000.000
156A155GLU-1-0.882-0.97020.446-0.620-0.6200.0000.0000.0000.000
157A156ASN0-0.040-0.01516.1600.0260.0260.0000.0000.0000.000
158A157MET0-0.0070.01715.9290.0670.0670.0000.0000.0000.000
159A158THR0-0.016-0.03015.325-0.144-0.1440.0000.0000.0000.000
160A159VAL00.041-0.00413.4280.0770.0770.0000.0000.0000.000
161A160ALA0-0.0010.00116.1450.1030.1030.0000.0000.0000.000
162A161ASP-1-0.747-0.85219.365-0.806-0.8060.0000.0000.0000.000
163A162ILE00.0270.01315.2820.0770.0770.0000.0000.0000.000
164A163THR0-0.048-0.03619.4910.0540.0540.0000.0000.0000.000
165A164ILE0-0.043-0.02221.8150.0650.0650.0000.0000.0000.000
166A165VAL0-0.001-0.00822.1350.0550.0550.0000.0000.0000.000
167A166VAL0-0.0080.02322.8780.0490.0490.0000.0000.0000.000
168A167THR0-0.054-0.03125.6340.0510.0510.0000.0000.0000.000
169A168ILE0-0.019-0.00328.0260.0360.0360.0000.0000.0000.000
170A169THR00.019-0.01426.3170.0330.0330.0000.0000.0000.000
171A170ASN0-0.0060.01528.8760.0290.0290.0000.0000.0000.000
172A171ILE0-0.0030.00331.7090.0210.0210.0000.0000.0000.000
173A172ASP-1-0.877-0.93932.301-0.345-0.3450.0000.0000.0000.000
174A173ALA0-0.016-0.00432.8700.0200.0200.0000.0000.0000.000
175A174PHE0-0.063-0.04433.9660.0150.0150.0000.0000.0000.000
176A175GLY0-0.0090.00737.5880.0150.0150.0000.0000.0000.000
177A176TYR0-0.087-0.06336.8450.0130.0130.0000.0000.0000.000
178A177ASP-1-0.820-0.88237.354-0.279-0.2790.0000.0000.0000.000
179A178PHE00.000-0.02032.376-0.001-0.0010.0000.0000.0000.000
180A179SER0-0.079-0.06936.479-0.011-0.0110.0000.0000.0000.000
181A180SER0-0.003-0.00638.159-0.007-0.0070.0000.0000.0000.000
182A181HIS0-0.021-0.00734.851-0.009-0.0090.0000.0000.0000.000
183A182GLU-1-0.803-0.91234.564-0.309-0.3090.0000.0000.0000.000
184A183ASN0-0.089-0.04131.260-0.011-0.0110.0000.0000.0000.000
185A184ILE00.0120.00830.126-0.036-0.0360.0000.0000.0000.000
186A185ALA00.0110.01330.344-0.025-0.0250.0000.0000.0000.000
187A186LYS10.8180.89131.1160.3030.3030.0000.0000.0000.000
188A187TRP0-0.089-0.04123.267-0.008-0.0080.0000.0000.0000.000
189A188PHE00.0110.01426.265-0.045-0.0450.0000.0000.0000.000
190A189GLU-1-0.825-0.92027.059-0.440-0.4400.0000.0000.0000.000
191A190ARG10.8460.95023.7250.5450.5450.0000.0000.0000.000
192A191THR00.048-0.01221.256-0.052-0.0520.0000.0000.0000.000
193A192LYS10.8610.95422.2770.3770.3770.0000.0000.0000.000
194A193LYS10.8790.92623.4990.4330.4330.0000.0000.0000.000
195A194MET0-0.072-0.02817.827-0.003-0.0030.0000.0000.0000.000
196A195LEU00.0380.00017.612-0.118-0.1180.0000.0000.0000.000
197A196GLU-1-0.967-0.97119.968-0.518-0.5180.0000.0000.0000.000
198A197PRO0-0.039-0.01518.5250.0320.0320.0000.0000.0000.000
199A198TYR0-0.019-0.01212.7290.0070.0070.0000.0000.0000.000
200A199GLY00.0300.01317.700-0.033-0.0330.0000.0000.0000.000
201A200TYR0-0.024-0.05220.4990.0420.0420.0000.0000.0000.000
202A201ASP-1-0.821-0.91122.827-0.368-0.3680.0000.0000.0000.000
203A202GLU-1-0.803-0.84621.173-0.594-0.5940.0000.0000.0000.000
204A203ILE0-0.0130.00718.9760.0160.0160.0000.0000.0000.000
205A204ASP-1-0.711-0.84023.248-0.543-0.5430.0000.0000.0000.000
206A205VAL00.0170.00824.9170.0410.0410.0000.0000.0000.000
207A206THR0-0.043-0.03426.7630.0500.0500.0000.0000.0000.000
208A207GLY00.0250.00827.1190.0310.0310.0000.0000.0000.000
209A208ALA0-0.002-0.00628.4370.0270.0270.0000.0000.0000.000
210A209LYS10.8540.91729.9380.3860.3860.0000.0000.0000.000
211A210MET0-0.050-0.02029.7530.0180.0180.0000.0000.0000.000
212A211LEU0-0.025-0.00130.8200.0190.0190.0000.0000.0000.000
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