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: 76MJK

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2743041.931359
FMO2-HF: Nuclear repulsion 2654683.738862
FMO2-HF: Total energy -88358.192497
FMO2-MP2: Total energy -88613.115179


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.
-8.015-3.9091.666-2.08-3.6930.003
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 : 0.005 / q_NPA : -0.016
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].
3A2PRO00.0240.0343.8261.3703.257-0.021-0.930-0.9360.001
4A3VAL0-0.023-0.0216.2840.3750.3750.0000.0000.0000.000
5A4GLN0-0.058-0.0258.374-0.070-0.0700.0000.0000.0000.000
6A5PRO00.0350.01410.657-0.168-0.1680.0000.0000.0000.000
7A6ILE00.0100.0049.0030.1100.1100.0000.0000.0000.000
8A7LYS10.8600.92712.9180.1040.1040.0000.0000.0000.000
9A8LEU0-0.0120.00216.586-0.030-0.0300.0000.0000.0000.000
10A9TYR0-0.017-0.00518.8140.0280.0280.0000.0000.0000.000
11A10TYR00.045-0.01122.069-0.019-0.0190.0000.0000.0000.000
12A11LEU00.024-0.00724.1420.0390.0390.0000.0000.0000.000
13A12PRO00.0210.00825.755-0.022-0.0220.0000.0000.0000.000
14A13PRO00.0850.03726.729-0.024-0.0240.0000.0000.0000.000
15A14SER0-0.0130.00826.369-0.009-0.0090.0000.0000.0000.000
16A15PRO00.0500.01525.738-0.035-0.0350.0000.0000.0000.000
17A16PRO00.0180.00923.906-0.046-0.0460.0000.0000.0000.000
18A17CYS0-0.021-0.00121.848-0.048-0.0480.0000.0000.0000.000
19A18ARG10.8170.88820.7350.3660.3660.0000.0000.0000.000
20A19ALA00.0310.03220.614-0.059-0.0590.0000.0000.0000.000
21A20VAL0-0.029-0.00516.082-0.108-0.1080.0000.0000.0000.000
22A21MET0-0.018-0.00615.933-0.120-0.1200.0000.0000.0000.000
23A22MET00.0210.02716.260-0.083-0.0830.0000.0000.0000.000
24A23THR0-0.008-0.01513.055-0.085-0.0850.0000.0000.0000.000
25A24ALA00.0010.00411.672-0.271-0.2710.0000.0000.0000.000
26A25ARG10.8540.90611.4060.6350.6350.0000.0000.0000.000
27A26VAL0-0.026-0.00811.727-0.071-0.0710.0000.0000.0000.000
28A27LEU0-0.063-0.0247.634-0.176-0.1760.0000.0000.0000.000
29A28GLU-1-0.891-0.9237.520-3.449-3.4490.0000.0000.0000.000
30A29LEU0-0.047-0.0266.060-0.076-0.0760.0000.0000.0000.000
31A30ASP-1-0.910-0.9579.701-0.478-0.4780.0000.0000.0000.000
32A31LEU0-0.036-0.01912.579-0.009-0.0090.0000.0000.0000.000
33A32HIS00.0000.00415.1400.1170.1170.0000.0000.0000.000
34A33LEU0-0.011-0.01517.9730.0210.0210.0000.0000.0000.000
35A34ILE00.0000.00720.7250.0500.0500.0000.0000.0000.000
36A35THR0-0.022-0.01123.335-0.018-0.0180.0000.0000.0000.000
37A36THR0-0.001-0.00225.5990.0270.0270.0000.0000.0000.000
38A37ASN0-0.023-0.02027.965-0.020-0.0200.0000.0000.0000.000
39A38ILE00.0480.01429.0730.0150.0150.0000.0000.0000.000
40A39MET0-0.020-0.02032.5580.0150.0150.0000.0000.0000.000
41A40ASN0-0.058-0.03434.6440.0140.0140.0000.0000.0000.000
42A41GLY0-0.0070.00035.2740.0100.0100.0000.0000.0000.000
43A42GLU-1-0.802-0.89130.421-0.158-0.1580.0000.0000.0000.000
44A43HIS0-0.016-0.00429.222-0.004-0.0040.0000.0000.0000.000
45A44MET0-0.029-0.03030.221-0.001-0.0010.0000.0000.0000.000
46A45THR0-0.0020.01930.2780.0130.0130.0000.0000.0000.000
47A46PRO00.021-0.00430.764-0.007-0.0070.0000.0000.0000.000
48A47GLU-1-0.902-0.96027.056-0.049-0.0490.0000.0000.0000.000
49A48TYR0-0.005-0.00324.966-0.012-0.0120.0000.0000.0000.000
50A49LEU00.0060.00526.451-0.012-0.0120.0000.0000.0000.000
51A50LYS10.8760.95225.4810.0080.0080.0000.0000.0000.000
52A51MET0-0.046-0.00221.1740.0030.0030.0000.0000.0000.000
53A52ASN00.021-0.01322.918-0.001-0.0010.0000.0000.0000.000
54A53PRO00.0530.03425.0860.0030.0030.0000.0000.0000.000
55A54GLN0-0.030-0.00926.7470.0140.0140.0000.0000.0000.000
56A55HIS10.8250.92628.0980.1530.1530.0000.0000.0000.000
57A56THR00.0320.02426.3430.0020.0020.0000.0000.0000.000
58A57ILE0-0.0030.03124.670-0.004-0.0040.0000.0000.0000.000
59A58PRO00.003-0.02920.7000.0040.0040.0000.0000.0000.000
60A59THR0-0.026-0.02119.9860.0140.0140.0000.0000.0000.000
61A60MET0-0.042-0.01012.720-0.073-0.0730.0000.0000.0000.000
62A61ASP-1-0.819-0.91915.797-0.109-0.1090.0000.0000.0000.000
63A62ASP-1-0.796-0.8538.855-0.823-0.8230.0000.0000.0000.000
64A63ASN00.0130.00210.5260.1230.1230.0000.0000.0000.000
65A64GLY00.0020.00512.5280.0980.0980.0000.0000.0000.000
66A65PHE0-0.051-0.01611.6320.0250.0250.0000.0000.0000.000
67A66ILE0-0.013-0.00914.220-0.079-0.0790.0000.0000.0000.000
68A67LEU0-0.0100.00814.6270.0050.0050.0000.0000.0000.000
69A68TRP00.029-0.00617.720-0.028-0.0280.0000.0000.0000.000
70A69GLU-1-0.858-0.93020.211-0.356-0.3560.0000.0000.0000.000
71A70SER00.0210.00220.030-0.035-0.0350.0000.0000.0000.000
72A71ARG10.8530.91118.7810.4100.4100.0000.0000.0000.000
73A72ALA00.0220.02117.808-0.074-0.0740.0000.0000.0000.000
74A73ILE00.0040.00414.881-0.075-0.0750.0000.0000.0000.000
75A74GLN0-0.041-0.03313.927-0.082-0.0820.0000.0000.0000.000
76A75THR0-0.006-0.01513.460-0.213-0.2130.0000.0000.0000.000
77A76TYR0-0.063-0.0478.711-0.156-0.1560.0000.0000.0000.000
78A77LEU00.0340.0099.525-0.204-0.2040.0000.0000.0000.000
79A78VAL0-0.016-0.0038.275-0.620-0.6200.0000.0000.0000.000
80A79ASN0-0.029-0.0207.732-0.464-0.4640.0000.0000.0000.000
81A80ALA0-0.049-0.0035.9730.2860.2860.0000.0000.0000.000
82A81TYR0-0.048-0.0663.697-0.8730.1430.014-0.234-0.796-0.001
83A82GLY00.0120.0254.256-1.714-1.4790.000-0.047-0.1880.000
84A83LYS10.7670.8731.9560.9842.0641.675-1.265-1.4900.004
85A84ASP-1-0.831-0.8913.029-1.593-1.705-0.0020.396-0.283-0.001
86A85ASP-1-0.830-0.9056.212-1.449-1.4490.0000.0000.0000.000
87A86SER0-0.038-0.0369.2120.5420.5420.0000.0000.0000.000
88A87LEU00.0370.01710.8120.3070.3070.0000.0000.0000.000
89A88TYR0-0.086-0.09211.7940.2600.2600.0000.0000.0000.000
90A89PRO00.0650.06112.156-0.064-0.0640.0000.0000.0000.000
91A90LYS10.8950.9128.5511.4661.4660.0000.0000.0000.000
92A91ASN0-0.037-0.00113.7800.1600.1600.0000.0000.0000.000
93A92PRO00.0730.02616.956-0.023-0.0230.0000.0000.0000.000
94A93ARG10.9530.97119.8750.2700.2700.0000.0000.0000.000
95A94GLN00.0190.00117.410-0.055-0.0550.0000.0000.0000.000
96A95ARG10.8170.90712.4210.9680.9680.0000.0000.0000.000
97A96ALA00.0250.01518.7430.0050.0050.0000.0000.0000.000
98A97ILE0-0.016-0.00222.4340.0240.0240.0000.0000.0000.000
99A98ILE00.0460.02416.7720.0150.0150.0000.0000.0000.000
100A99ASP-1-0.771-0.87119.593-0.607-0.6070.0000.0000.0000.000
101A100GLN0-0.0230.00421.9130.0280.0280.0000.0000.0000.000
102A101ARG10.8790.94323.0930.4630.4630.0000.0000.0000.000
103A102LEU00.0140.01118.6150.0170.0170.0000.0000.0000.000
104A103ASN0-0.061-0.04923.3300.0500.0500.0000.0000.0000.000
105A104PHE0-0.020-0.00126.3960.0270.0270.0000.0000.0000.000
106A105ASP-1-0.745-0.85725.081-0.464-0.4640.0000.0000.0000.000
107A106LEU0-0.028-0.01325.3410.0180.0180.0000.0000.0000.000
108A107GLY0-0.001-0.00527.9190.0240.0240.0000.0000.0000.000
109A108THR0-0.073-0.04630.7980.0300.0300.0000.0000.0000.000
110A109LEU00.0030.01228.5410.0140.0140.0000.0000.0000.000
111A110TYR00.0800.02228.7150.0090.0090.0000.0000.0000.000
112A111LEU00.0160.01930.8630.0170.0170.0000.0000.0000.000
113A112ARG10.8070.87233.6820.2440.2440.0000.0000.0000.000
114A113TYR00.0440.04232.0110.0090.0090.0000.0000.0000.000
115A114LEU0-0.034-0.00931.6610.0120.0120.0000.0000.0000.000
116A115ASN0-0.053-0.03035.4210.0260.0260.0000.0000.0000.000
117A116LEU00.0190.02638.4060.0120.0120.0000.0000.0000.000
118A117TYR00.1060.02836.6640.0080.0080.0000.0000.0000.000
119A118THR0-0.071-0.03736.5860.0010.0010.0000.0000.0000.000
120A119PRO0-0.036-0.03138.3950.0060.0060.0000.0000.0000.000
121A120ILE00.0020.01741.3860.0070.0070.0000.0000.0000.000
122A121LEU0-0.040-0.00835.9040.0040.0040.0000.0000.0000.000
123A122PHE0-0.043-0.02734.5160.0040.0040.0000.0000.0000.000
124A123ARG10.8150.91440.6450.1650.1650.0000.0000.0000.000
125A124GLY00.0260.04443.7790.0080.0080.0000.0000.0000.000
126A125GLU-1-0.893-0.95545.150-0.136-0.1360.0000.0000.0000.000
127A126ALA00.000-0.01346.037-0.006-0.0060.0000.0000.0000.000
128A127TYR00.017-0.00141.556-0.001-0.0010.0000.0000.0000.000
129A128ASP-1-0.873-0.93944.885-0.146-0.1460.0000.0000.0000.000
130A129GLN0-0.001-0.01745.224-0.003-0.0030.0000.0000.0000.000
131A130GLU-1-0.904-0.94544.758-0.169-0.1690.0000.0000.0000.000
132A131LYS10.8930.93541.6600.1610.1610.0000.0000.0000.000
133A132ALA0-0.009-0.00241.075-0.013-0.0130.0000.0000.0000.000
134A133ASP-1-0.879-0.93441.798-0.171-0.1710.0000.0000.0000.000
135A134LYS10.8040.89839.6990.1730.1730.0000.0000.0000.000
136A135PHE00.0150.00333.588-0.016-0.0160.0000.0000.0000.000
137A136ASP-1-0.779-0.88936.945-0.240-0.2400.0000.0000.0000.000
138A137GLU-1-0.795-0.86838.666-0.203-0.2030.0000.0000.0000.000
139A138ALA0-0.056-0.03633.978-0.008-0.0080.0000.0000.0000.000
140A139LEU00.0050.00833.033-0.024-0.0240.0000.0000.0000.000
141A140GLY00.0570.02934.735-0.009-0.0090.0000.0000.0000.000
142A141TRP0-0.054-0.03234.019-0.006-0.0060.0000.0000.0000.000
143A142LEU00.0200.01628.030-0.012-0.0120.0000.0000.0000.000
144A143ASN00.0570.01631.017-0.029-0.0290.0000.0000.0000.000
145A144THR0-0.029-0.01333.2800.0020.0020.0000.0000.0000.000
146A145PHE0-0.059-0.03628.653-0.001-0.0010.0000.0000.0000.000
147A146LEU0-0.027-0.01226.638-0.022-0.0220.0000.0000.0000.000
148A147ASP-1-0.921-0.93929.783-0.276-0.2760.0000.0000.0000.000
149A148GLY0-0.034-0.01831.182-0.002-0.0020.0000.0000.0000.000
150A149ARG10.8660.94025.6910.3770.3770.0000.0000.0000.000
151A150PRO0-0.0410.01323.7440.0110.0110.0000.0000.0000.000
152A151PHE00.0510.01221.745-0.016-0.0160.0000.0000.0000.000
153A152VAL00.0160.00922.7040.0340.0340.0000.0000.0000.000
154A153ALA0-0.010-0.01420.5170.0430.0430.0000.0000.0000.000
155A154GLY0-0.032-0.01722.2650.0120.0120.0000.0000.0000.000
156A155GLU-1-0.876-0.95321.075-0.493-0.4930.0000.0000.0000.000
157A156ASN0-0.025-0.00916.7300.0190.0190.0000.0000.0000.000
158A157MET0-0.0040.01616.2300.0670.0670.0000.0000.0000.000
159A158THR0-0.011-0.01515.810-0.112-0.1120.0000.0000.0000.000
160A159VAL00.0510.00014.1430.0460.0460.0000.0000.0000.000
161A160ALA0-0.007-0.00516.8250.0760.0760.0000.0000.0000.000
162A161ASP-1-0.741-0.87519.950-0.662-0.6620.0000.0000.0000.000
163A162ILE00.0110.00915.7300.0580.0580.0000.0000.0000.000
164A163THR0-0.033-0.03320.0550.0480.0480.0000.0000.0000.000
165A164ILE0-0.050-0.01022.2230.0530.0530.0000.0000.0000.000
166A165VAL0-0.007-0.01122.9180.0470.0470.0000.0000.0000.000
167A166VAL00.0040.02823.4410.0350.0350.0000.0000.0000.000
168A167THR0-0.038-0.02326.1540.0400.0400.0000.0000.0000.000
169A168ILE0-0.021-0.01228.6320.0280.0280.0000.0000.0000.000
170A169THR00.029-0.00126.6690.0250.0250.0000.0000.0000.000
171A170ASN0-0.0010.01029.1780.0240.0240.0000.0000.0000.000
172A171ILE0-0.016-0.00331.9700.0180.0180.0000.0000.0000.000
173A172ASP-1-0.896-0.94332.888-0.301-0.3010.0000.0000.0000.000
174A173ALA0-0.021-0.00233.3620.0140.0140.0000.0000.0000.000
175A174PHE0-0.083-0.05634.1990.0140.0140.0000.0000.0000.000
176A175GLY0-0.0110.01637.8950.0150.0150.0000.0000.0000.000
177A176TYR0-0.089-0.05236.9910.0110.0110.0000.0000.0000.000
178A177ASP-1-0.822-0.88037.693-0.242-0.2420.0000.0000.0000.000
179A178PHE00.004-0.02532.6830.0020.0020.0000.0000.0000.000
180A179SER0-0.078-0.06936.745-0.009-0.0090.0000.0000.0000.000
181A180SER0-0.008-0.00538.433-0.004-0.0040.0000.0000.0000.000
182A181HIS0-0.0200.00735.613-0.003-0.0030.0000.0000.0000.000
183A182GLU-1-0.811-0.90635.427-0.262-0.2620.0000.0000.0000.000
184A183ASN0-0.068-0.03731.885-0.012-0.0120.0000.0000.0000.000
185A184ILE00.0280.01730.807-0.031-0.0310.0000.0000.0000.000
186A185ALA00.0130.01930.940-0.024-0.0240.0000.0000.0000.000
187A186LYS10.8400.89931.3580.2680.2680.0000.0000.0000.000
188A187TRP0-0.058-0.03423.984-0.009-0.0090.0000.0000.0000.000
189A188PHE00.0320.02126.659-0.045-0.0450.0000.0000.0000.000
190A189GLU-1-0.827-0.90927.335-0.403-0.4030.0000.0000.0000.000
191A190ARG10.8460.93524.1530.4570.4570.0000.0000.0000.000
192A191THR00.018-0.01421.749-0.059-0.0590.0000.0000.0000.000
193A192LYS10.8530.93922.5790.3390.3390.0000.0000.0000.000
194A193LYS10.8710.93523.7110.4020.4020.0000.0000.0000.000
195A194MET0-0.073-0.02918.271-0.018-0.0180.0000.0000.0000.000
196A195LEU00.034-0.00217.736-0.103-0.1030.0000.0000.0000.000
197A196GLU-1-0.939-0.95719.965-0.507-0.5070.0000.0000.0000.000
198A197PRO0-0.056-0.02418.1350.0270.0270.0000.0000.0000.000
199A198TYR0-0.051-0.02812.768-0.014-0.0140.0000.0000.0000.000
200A199GLY00.0420.01717.750-0.016-0.0160.0000.0000.0000.000
201A200TYR0-0.006-0.03120.5430.0310.0310.0000.0000.0000.000
202A201ASP-1-0.881-0.96222.941-0.359-0.3590.0000.0000.0000.000
203A202GLU-1-0.815-0.86721.287-0.602-0.6020.0000.0000.0000.000
204A203ILE0-0.027-0.00319.0080.0190.0190.0000.0000.0000.000
205A204ASP-1-0.718-0.85323.508-0.476-0.4760.0000.0000.0000.000
206A205VAL0-0.0190.00025.4100.0410.0410.0000.0000.0000.000
207A206THR0-0.032-0.02827.1180.0440.0440.0000.0000.0000.000
208A207GLY00.0270.01027.4740.0270.0270.0000.0000.0000.000
209A208ALA00.007-0.00728.6000.0260.0260.0000.0000.0000.000
210A209LYS10.9380.97430.8020.3540.3540.0000.0000.0000.000
211A210MET0-0.049-0.01829.9370.0170.0170.0000.0000.0000.000
212A211LEU0-0.023-0.00631.2320.0170.0170.0000.0000.0000.000
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