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: MN9MZ

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2739282.916131
FMO2-HF: Nuclear repulsion 2650925.623173
FMO2-HF: Total energy -88357.292958
FMO2-MP2: Total energy -88612.090602


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.
-6.446-1.6740.355-1.771-3.3580.002
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 : 0.006 / q_NPA : -0.014
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].
3A2PRO00.0260.0333.8261.0462.925-0.021-0.923-0.9350.001
4A3VAL0-0.031-0.0256.2720.2390.2390.0000.0000.0000.000
5A4GLN0-0.087-0.0378.364-0.144-0.1440.0000.0000.0000.000
6A5PRO00.0330.01310.645-0.104-0.1040.0000.0000.0000.000
7A6ILE00.0240.0138.9680.0840.0840.0000.0000.0000.000
8A7LYS10.9510.98812.907-0.047-0.0470.0000.0000.0000.000
9A8LEU0-0.0020.00716.577-0.009-0.0090.0000.0000.0000.000
10A9TYR0-0.025-0.00718.8050.0050.0050.0000.0000.0000.000
11A10TYR00.045-0.01422.200-0.004-0.0040.0000.0000.0000.000
12A11LEU00.022-0.01324.1330.0250.0250.0000.0000.0000.000
13A12PRO00.0030.00126.459-0.015-0.0150.0000.0000.0000.000
14A13PRO00.0880.04027.459-0.018-0.0180.0000.0000.0000.000
15A14SER0-0.0220.00326.976-0.006-0.0060.0000.0000.0000.000
16A15PRO00.0340.00826.481-0.023-0.0230.0000.0000.0000.000
17A16PRO00.0370.02024.106-0.032-0.0320.0000.0000.0000.000
18A17CYS0-0.0260.00522.278-0.025-0.0250.0000.0000.0000.000
19A18ARG10.8200.89421.5190.2590.2590.0000.0000.0000.000
20A19ALA00.0340.03521.418-0.047-0.0470.0000.0000.0000.000
21A20VAL0-0.0270.00716.454-0.075-0.0750.0000.0000.0000.000
22A21MET0-0.018-0.00916.804-0.078-0.0780.0000.0000.0000.000
23A22MET00.0180.02516.942-0.073-0.0730.0000.0000.0000.000
24A23THR0-0.013-0.02913.842-0.075-0.0750.0000.0000.0000.000
25A24ALA00.0000.00412.475-0.182-0.1820.0000.0000.0000.000
26A25ARG10.9150.97912.0080.5350.5350.0000.0000.0000.000
27A26VAL0-0.026-0.00512.220-0.089-0.0890.0000.0000.0000.000
28A27LEU0-0.066-0.0298.496-0.169-0.1690.0000.0000.0000.000
29A28GLU-1-0.918-0.9408.000-3.124-3.1240.0000.0000.0000.000
30A29LEU0-0.048-0.0317.090-0.088-0.0880.0000.0000.0000.000
31A30ASP-1-0.922-0.95910.197-0.381-0.3810.0000.0000.0000.000
32A31LEU0-0.030-0.02013.0760.0380.0380.0000.0000.0000.000
33A32HIS0-0.0020.00315.7030.0630.0630.0000.0000.0000.000
34A33LEU0-0.004-0.01418.0370.0270.0270.0000.0000.0000.000
35A34ILE0-0.0030.00420.6030.0320.0320.0000.0000.0000.000
36A35THR0-0.018-0.00823.324-0.010-0.0100.0000.0000.0000.000
37A36THR00.0100.00325.5570.0230.0230.0000.0000.0000.000
38A37ASN0-0.007-0.01227.956-0.015-0.0150.0000.0000.0000.000
39A38ILE00.0530.01729.0760.0120.0120.0000.0000.0000.000
40A39MET0-0.019-0.02532.5500.0120.0120.0000.0000.0000.000
41A40ASN0-0.044-0.01234.6310.0070.0070.0000.0000.0000.000
42A41GLY0-0.0070.00235.2660.0070.0070.0000.0000.0000.000
43A42GLU-1-0.838-0.92530.369-0.076-0.0760.0000.0000.0000.000
44A43HIS0-0.017-0.00329.2200.0040.0040.0000.0000.0000.000
45A44MET0-0.032-0.03130.2140.0040.0040.0000.0000.0000.000
46A45THR00.0090.02230.2980.0100.0100.0000.0000.0000.000
47A46PRO00.031-0.00530.758-0.001-0.0010.0000.0000.0000.000
48A47GLU-1-0.922-0.96527.0070.0290.0290.0000.0000.0000.000
49A48TYR0-0.0040.01224.971-0.001-0.0010.0000.0000.0000.000
50A49LEU00.0010.00126.446-0.004-0.0040.0000.0000.0000.000
51A50LYS10.8820.95525.596-0.079-0.0790.0000.0000.0000.000
52A51MET0-0.0350.00321.1020.0110.0110.0000.0000.0000.000
53A52ASN00.0430.00422.9140.0040.0040.0000.0000.0000.000
54A53PRO00.0400.03325.082-0.005-0.0050.0000.0000.0000.000
55A54GLN0-0.019-0.00726.680-0.001-0.0010.0000.0000.0000.000
56A55HIS10.8480.94328.1480.0530.0530.0000.0000.0000.000
57A56THR00.0150.00726.450-0.003-0.0030.0000.0000.0000.000
58A57ILE00.0020.02824.6630.0020.0020.0000.0000.0000.000
59A58PRO0-0.001-0.03320.724-0.002-0.0020.0000.0000.0000.000
60A59THR0-0.033-0.03220.1330.0130.0130.0000.0000.0000.000
61A60MET0-0.048-0.01312.864-0.053-0.0530.0000.0000.0000.000
62A61ASP-1-0.876-0.95415.8040.0760.0760.0000.0000.0000.000
63A62ASP-1-0.789-0.8638.833-0.264-0.2640.0000.0000.0000.000
64A63ASN00.0270.00310.5730.0450.0450.0000.0000.0000.000
65A64GLY0-0.0030.00512.5220.0850.0850.0000.0000.0000.000
66A65PHE0-0.053-0.01912.097-0.005-0.0050.0000.0000.0000.000
67A66ILE0-0.012-0.00314.217-0.062-0.0620.0000.0000.0000.000
68A67LEU0-0.0180.00114.4140.0050.0050.0000.0000.0000.000
69A68TRP00.042-0.00117.718-0.025-0.0250.0000.0000.0000.000
70A69GLU-1-0.913-0.95320.209-0.171-0.1710.0000.0000.0000.000
71A70SER00.0260.00320.027-0.009-0.0090.0000.0000.0000.000
72A71ARG10.8780.93018.7880.2430.2430.0000.0000.0000.000
73A72ALA00.0170.01317.818-0.041-0.0410.0000.0000.0000.000
74A73ILE00.0060.00314.876-0.027-0.0270.0000.0000.0000.000
75A74GLN0-0.033-0.02513.935-0.024-0.0240.0000.0000.0000.000
76A75THR0-0.009-0.00913.477-0.120-0.1200.0000.0000.0000.000
77A76TYR0-0.058-0.0418.786-0.049-0.0490.0000.0000.0000.000
78A77LEU00.0220.0049.546-0.061-0.0610.0000.0000.0000.000
79A78VAL0-0.0110.0008.273-0.318-0.3180.0000.0000.0000.000
80A79ASN0-0.048-0.0398.135-0.218-0.2180.0000.0000.0000.000
81A80ALA0-0.057-0.0115.9210.3580.3580.0000.0000.0000.000
82A81TYR0-0.061-0.0693.740-0.8010.3040.011-0.293-0.8240.000
83A82GLY00.0120.0234.910-0.862-0.750-0.001-0.011-0.1000.000
84A83LYS10.8190.9062.5102.4883.9020.366-0.526-1.2550.001
85A84ASP-1-0.876-0.9373.529-3.287-3.0250.000-0.018-0.2440.000
86A85ASP-1-0.895-0.9536.644-0.829-0.8290.0000.0000.0000.000
87A86SER00.0050.0029.4580.4050.4050.0000.0000.0000.000
88A87LEU00.0320.01211.4520.2390.2390.0000.0000.0000.000
89A88TYR0-0.096-0.10512.5190.2060.2060.0000.0000.0000.000
90A89PRO00.0850.06812.3860.0080.0080.0000.0000.0000.000
91A90LYS10.9490.9628.3870.3840.3840.0000.0000.0000.000
92A91ASN0-0.037-0.00713.5720.1030.1030.0000.0000.0000.000
93A92PRO00.0670.02716.778-0.018-0.0180.0000.0000.0000.000
94A93ARG10.9540.96719.6720.1700.1700.0000.0000.0000.000
95A94GLN00.0310.01217.345-0.046-0.0460.0000.0000.0000.000
96A95ARG10.8640.94212.3170.4500.4500.0000.0000.0000.000
97A96ALA00.0220.01318.7360.0050.0050.0000.0000.0000.000
98A97ILE0-0.018-0.00622.4260.0160.0160.0000.0000.0000.000
99A98ILE00.0480.02417.4050.0080.0080.0000.0000.0000.000
100A99ASP-1-0.775-0.86219.889-0.316-0.3160.0000.0000.0000.000
101A100GLN0-0.032-0.01122.3380.0160.0160.0000.0000.0000.000
102A101ARG10.8760.94123.9120.3100.3100.0000.0000.0000.000
103A102LEU00.0150.01119.1790.0080.0080.0000.0000.0000.000
104A103ASN0-0.051-0.03823.8480.0360.0360.0000.0000.0000.000
105A104PHE0-0.028-0.00526.5040.0170.0170.0000.0000.0000.000
106A105ASP-1-0.760-0.86725.752-0.295-0.2950.0000.0000.0000.000
107A106LEU0-0.028-0.01525.4130.0100.0100.0000.0000.0000.000
108A107GLY0-0.007-0.00727.9240.0150.0150.0000.0000.0000.000
109A108THR0-0.073-0.04330.9660.0180.0180.0000.0000.0000.000
110A109LEU0-0.0020.00729.3330.0080.0080.0000.0000.0000.000
111A110TYR00.0760.02129.0970.0090.0090.0000.0000.0000.000
112A111LEU00.0100.01531.2280.0100.0100.0000.0000.0000.000
113A112ARG10.7930.87633.6870.1530.1530.0000.0000.0000.000
114A113TYR00.0470.04732.7950.0040.0040.0000.0000.0000.000
115A114LEU0-0.033-0.00931.6070.0080.0080.0000.0000.0000.000
116A115ASN0-0.036-0.02335.6330.0110.0110.0000.0000.0000.000
117A116LEU00.0220.02538.6970.0080.0080.0000.0000.0000.000
118A117TYR00.0970.02437.2390.0030.0030.0000.0000.0000.000
119A118THR0-0.082-0.03936.7820.0000.0000.0000.0000.0000.000
120A119PRO0-0.044-0.04138.7570.0040.0040.0000.0000.0000.000
121A120ILE00.0140.02642.0930.0040.0040.0000.0000.0000.000
122A121LEU0-0.045-0.01236.6740.0020.0020.0000.0000.0000.000
123A122PHE0-0.042-0.02434.9890.0030.0030.0000.0000.0000.000
124A123ARG10.8810.94640.2800.1020.1020.0000.0000.0000.000
125A124GLY00.0320.04644.3400.0050.0050.0000.0000.0000.000
126A125GLU-1-0.954-0.98645.687-0.083-0.0830.0000.0000.0000.000
127A126ALA0-0.002-0.01346.678-0.005-0.0050.0000.0000.0000.000
128A127TYR00.019-0.00142.610-0.003-0.0030.0000.0000.0000.000
129A128ASP-1-0.912-0.96145.394-0.089-0.0890.0000.0000.0000.000
130A129GLN00.011-0.00845.822-0.006-0.0060.0000.0000.0000.000
131A130GLU-1-0.889-0.93945.372-0.103-0.1030.0000.0000.0000.000
132A131LYS10.9150.94442.0100.1000.1000.0000.0000.0000.000
133A132ALA0-0.0050.00141.703-0.009-0.0090.0000.0000.0000.000
134A133ASP-1-0.870-0.92642.606-0.115-0.1150.0000.0000.0000.000
135A134LYS10.9120.95840.2340.1030.1030.0000.0000.0000.000
136A135PHE00.0130.00234.391-0.010-0.0100.0000.0000.0000.000
137A136ASP-1-0.835-0.92037.753-0.166-0.1660.0000.0000.0000.000
138A137GLU-1-0.868-0.93339.452-0.133-0.1330.0000.0000.0000.000
139A138ALA0-0.061-0.04134.837-0.006-0.0060.0000.0000.0000.000
140A139LEU00.0090.00733.828-0.017-0.0170.0000.0000.0000.000
141A140GLY00.0660.03435.487-0.009-0.0090.0000.0000.0000.000
142A141TRP0-0.054-0.02934.739-0.006-0.0060.0000.0000.0000.000
143A142LEU00.0130.00828.802-0.009-0.0090.0000.0000.0000.000
144A143ASN00.0580.01931.748-0.025-0.0250.0000.0000.0000.000
145A144THR0-0.028-0.00433.963-0.002-0.0020.0000.0000.0000.000
146A145PHE0-0.063-0.03429.422-0.002-0.0020.0000.0000.0000.000
147A146LEU0-0.032-0.02327.306-0.018-0.0180.0000.0000.0000.000
148A147ASP-1-0.939-0.94630.444-0.214-0.2140.0000.0000.0000.000
149A148GLY0-0.027-0.01231.7330.0000.0000.0000.0000.0000.000
150A149ARG10.8670.94426.3470.2800.2800.0000.0000.0000.000
151A150PRO0-0.0320.01424.3300.0090.0090.0000.0000.0000.000
152A151PHE00.0470.01222.048-0.014-0.0140.0000.0000.0000.000
153A152VAL00.0270.01823.4750.0270.0270.0000.0000.0000.000
154A153ALA0-0.007-0.00721.2440.0360.0360.0000.0000.0000.000
155A154GLY0-0.044-0.02722.7730.0130.0130.0000.0000.0000.000
156A155GLU-1-0.887-0.95521.507-0.393-0.3930.0000.0000.0000.000
157A156ASN0-0.028-0.01217.250-0.023-0.0230.0000.0000.0000.000
158A157MET00.0000.02116.5880.0630.0630.0000.0000.0000.000
159A158THR0-0.015-0.01416.524-0.071-0.0710.0000.0000.0000.000
160A159VAL00.043-0.00414.9650.0280.0280.0000.0000.0000.000
161A160ALA0-0.011-0.00717.6430.0550.0550.0000.0000.0000.000
162A161ASP-1-0.734-0.87520.621-0.490-0.4900.0000.0000.0000.000
163A162ILE00.0150.01016.4470.0400.0400.0000.0000.0000.000
164A163THR0-0.042-0.03920.7690.0340.0340.0000.0000.0000.000
165A164ILE0-0.042-0.00723.0210.0350.0350.0000.0000.0000.000
166A165VAL0-0.001-0.00823.4370.0310.0310.0000.0000.0000.000
167A166VAL00.0000.02724.2030.0230.0230.0000.0000.0000.000
168A167THR0-0.037-0.02426.8490.0290.0290.0000.0000.0000.000
169A168ILE0-0.022-0.01429.2500.0190.0190.0000.0000.0000.000
170A169THR00.0420.00927.2120.0130.0130.0000.0000.0000.000
171A170ASN0-0.0020.00130.0080.0160.0160.0000.0000.0000.000
172A171ILE0-0.026-0.00432.6220.0120.0120.0000.0000.0000.000
173A172ASP-1-0.894-0.94533.524-0.228-0.2280.0000.0000.0000.000
174A173ALA0-0.033-0.00233.9630.0090.0090.0000.0000.0000.000
175A174PHE0-0.081-0.05435.0850.0100.0100.0000.0000.0000.000
176A175GLY0-0.0170.01038.4840.0110.0110.0000.0000.0000.000
177A176TYR0-0.062-0.03537.6140.0100.0100.0000.0000.0000.000
178A177ASP-1-0.840-0.90638.299-0.184-0.1840.0000.0000.0000.000
179A178PHE0-0.004-0.02233.5050.0040.0040.0000.0000.0000.000
180A179SER0-0.057-0.04837.358-0.007-0.0070.0000.0000.0000.000
181A180SER00.0180.00838.999-0.002-0.0020.0000.0000.0000.000
182A181HIS0-0.0380.00136.289-0.001-0.0010.0000.0000.0000.000
183A182GLU-1-0.898-0.95836.033-0.204-0.2040.0000.0000.0000.000
184A183ASN0-0.064-0.04332.476-0.015-0.0150.0000.0000.0000.000
185A184ILE00.0180.01131.436-0.025-0.0250.0000.0000.0000.000
186A185ALA00.0200.02231.519-0.020-0.0200.0000.0000.0000.000
187A186LYS10.9310.95331.7280.2240.2240.0000.0000.0000.000
188A187TRP0-0.059-0.03324.498-0.008-0.0080.0000.0000.0000.000
189A188PHE00.0340.02727.183-0.038-0.0380.0000.0000.0000.000
190A189GLU-1-0.879-0.95427.819-0.320-0.3200.0000.0000.0000.000
191A190ARG10.8390.93224.5600.3660.3660.0000.0000.0000.000
192A191THR00.009-0.02422.312-0.049-0.0490.0000.0000.0000.000
193A192LYS10.8850.96123.0300.2730.2730.0000.0000.0000.000
194A193LYS10.9290.96724.0650.3410.3410.0000.0000.0000.000
195A194MET0-0.068-0.02718.516-0.024-0.0240.0000.0000.0000.000
196A195LEU00.031-0.00318.276-0.084-0.0840.0000.0000.0000.000
197A196GLU-1-0.941-0.95820.348-0.437-0.4370.0000.0000.0000.000
198A197PRO0-0.059-0.02018.3610.0210.0210.0000.0000.0000.000
199A198TYR0-0.049-0.02813.474-0.100-0.1000.0000.0000.0000.000
200A199GLY00.0260.01218.0110.0060.0060.0000.0000.0000.000
201A200TYR0-0.013-0.03420.9090.0350.0350.0000.0000.0000.000
202A201ASP-1-0.918-0.97123.329-0.294-0.2940.0000.0000.0000.000
203A202GLU-1-0.850-0.92621.889-0.463-0.4630.0000.0000.0000.000
204A203ILE0-0.044-0.00819.5540.0200.0200.0000.0000.0000.000
205A204ASP-1-0.721-0.86524.080-0.340-0.3400.0000.0000.0000.000
206A205VAL0-0.0050.00726.0630.0340.0340.0000.0000.0000.000
207A206THR0-0.039-0.03827.7280.0320.0320.0000.0000.0000.000
208A207GLY00.0170.00428.1000.0220.0220.0000.0000.0000.000
209A208ALA00.008-0.00829.2790.0220.0220.0000.0000.0000.000
210A209LYS10.9670.98131.7810.2500.2500.0000.0000.0000.000
211A210MET0-0.046-0.01230.3070.0130.0130.0000.0000.0000.000
212A211LEU0-0.021-0.00632.0810.0140.0140.0000.0000.0000.000
213A212ALA00.0290.01035.4560.0110.0110.0000.0000.0000.000
214A213SER0-0.095-0.04337.6260.0100.0100.0000.0000.0000.000
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