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: 66Q1Z

Calculation Name: 5E1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E1L

Chain ID: A

ChEMBL ID:

UniProt ID: P75862

Base Structure: X-ray

Registration Date: 2023-06-20

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1938652.810493
FMO2-HF: Nuclear repulsion 1865444.799745
FMO2-HF: Total energy -73208.010749
FMO2-MP2: Total energy -73413.007129


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:-8:SER)


Summations of interaction energy for fragment #1(A:-8:SER)
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.
-47.927-42.54320.108-11.802-13.691-0.034
Interaction energy analysis for fragmet #1(A:-8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.066 / 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].
3A-6LEU0-0.026-0.0103.5620.4783.081-0.041-1.315-1.247-0.002
4A-5VAL0-0.0090.0105.758-0.066-0.0660.0000.0000.0000.000
5A-4PRO00.0490.0278.3660.3290.3290.0000.0000.0000.000
6A-3ARG10.9150.9387.2843.5703.5700.0000.0000.0000.000
7A-2GLY00.0740.00511.4730.3210.3210.0000.0000.0000.000
8A-1SER0-0.083-0.04313.2380.1500.1500.0000.0000.0000.000
9A0HIS00.0320.02414.8310.1270.1270.0000.0000.0000.000
10A1MET0-0.039-0.03516.5530.1010.1010.0000.0000.0000.000
11A2ARG10.8840.95516.3751.0081.0080.0000.0000.0000.000
12A3ILE0-0.009-0.00811.6900.0250.0250.0000.0000.0000.000
13A4LYS10.9060.94915.9760.6230.6230.0000.0000.0000.000
14A5PRO00.0290.03317.7290.0090.0090.0000.0000.0000.000
15A6ASP-1-0.858-0.94418.802-0.497-0.4970.0000.0000.0000.000
16A7ASP-1-0.879-0.94420.150-0.306-0.3060.0000.0000.0000.000
17A8ASN0-0.073-0.02820.3020.0720.0720.0000.0000.0000.000
18A9TRP0-0.052-0.00214.696-0.078-0.0780.0000.0000.0000.000
19A10ARG10.8650.92214.8660.2410.2410.0000.0000.0000.000
20A11TRP00.009-0.00211.084-0.108-0.1080.0000.0000.0000.000
21A12TYR0-0.057-0.04510.508-0.050-0.0500.0000.0000.0000.000
22A13TYR00.033-0.02511.253-0.024-0.0240.0000.0000.0000.000
23A14ASP-1-0.826-0.9109.1440.7410.7410.0000.0000.0000.000
24A15GLU-1-0.807-0.93610.6621.1121.1120.0000.0000.0000.000
25A16GLU-1-1.005-0.97410.7160.8080.8080.0000.0000.0000.000
26A17HIS0-0.066-0.0505.5350.1170.1170.0000.0000.0000.000
27A18ASP-1-0.799-0.8627.4473.3123.3120.0000.0000.0000.000
28A19ARG10.8000.8821.814-22.239-27.40711.191-3.079-2.9440.035
29A20MET00.0200.0447.508-0.647-0.6470.0000.0000.0000.000
30A21MET0-0.046-0.0156.4370.2190.2190.0000.0000.0000.000
31A22LEU0-0.0080.0008.3860.0470.0470.0000.0000.0000.000
32A23ASP-1-0.832-0.90610.213-0.748-0.7480.0000.0000.0000.000
33A24LEU0-0.008-0.02110.5170.0010.0010.0000.0000.0000.000
34A25ALA00.0170.02614.1270.0210.0210.0000.0000.0000.000
35A26ASN0-0.043-0.03615.268-0.012-0.0120.0000.0000.0000.000
36A27GLY00.0270.01115.739-0.003-0.0030.0000.0000.0000.000
37A28MET0-0.093-0.02011.577-0.011-0.0110.0000.0000.0000.000
38A29LEU00.0450.0279.0820.1780.1780.0000.0000.0000.000
39A30PHE00.005-0.0095.308-0.756-0.7560.0000.0000.0000.000
40A31ARG10.9070.9732.2701.5172.4903.341-1.289-3.025-0.007
41A32SER0-0.001-0.0102.555-5.909-3.8211.022-1.766-1.345-0.025
42A33ARG10.8290.8732.496-4.751-1.6310.880-1.500-2.5000.008
43A34PHE0-0.026-0.0224.7820.4720.554-0.001-0.003-0.0780.000
44A35ALA00.0380.0257.868-0.202-0.2020.0000.0000.0000.000
45A36ARG10.9570.9719.268-1.522-1.5220.0000.0000.0000.000
46A37LYS10.8590.91511.305-2.295-2.2950.0000.0000.0000.000
47A38MET0-0.081-0.0369.087-0.261-0.2610.0000.0000.0000.000
48A39LEU00.0310.03810.811-0.144-0.1440.0000.0000.0000.000
49A40THR0-0.046-0.04814.7810.0110.0110.0000.0000.0000.000
50A41PRO00.015-0.01717.5350.0390.0390.0000.0000.0000.000
51A42ASP-1-0.831-0.89918.7540.2870.2870.0000.0000.0000.000
52A43ALA0-0.030-0.01914.051-0.039-0.0390.0000.0000.0000.000
53A44PHE0-0.078-0.03514.3410.0360.0360.0000.0000.0000.000
54A45SER0-0.0230.00417.374-0.020-0.0200.0000.0000.0000.000
55A46PRO0-0.034-0.02217.044-0.022-0.0220.0000.0000.0000.000
56A47ALA00.0200.02317.335-0.003-0.0030.0000.0000.0000.000
57A48GLY00.0140.01117.723-0.042-0.0420.0000.0000.0000.000
58A49PHE0-0.0250.00214.9200.0050.0050.0000.0000.0000.000
59A50CYS0-0.0190.00218.5740.0040.0040.0000.0000.0000.000
60A51VAL00.0710.00821.202-0.041-0.0410.0000.0000.0000.000
61A52ASP-1-0.887-0.93922.712-0.179-0.1790.0000.0000.0000.000
62A53ASP-1-0.730-0.86917.408-0.222-0.2220.0000.0000.0000.000
63A54ALA00.001-0.00218.451-0.083-0.0830.0000.0000.0000.000
64A55ALA0-0.018-0.00820.306-0.052-0.0520.0000.0000.0000.000
65A56LEU0-0.009-0.00617.910-0.023-0.0230.0000.0000.0000.000
66A57TYR0-0.049-0.04213.348-0.113-0.1130.0000.0000.0000.000
67A58PHE00.017-0.01817.064-0.076-0.0760.0000.0000.0000.000
68A59SER0-0.0380.00419.851-0.011-0.0110.0000.0000.0000.000
69A60PHE00.032-0.00115.3030.0000.0000.0000.0000.0000.000
70A61GLU-1-0.857-0.89915.876-0.969-0.9690.0000.0000.0000.000
71A62GLU-1-0.892-0.93716.897-0.521-0.5210.0000.0000.0000.000
72A63LYS10.8260.93318.5410.3340.3340.0000.0000.0000.000
73A64CYS0-0.020-0.01214.5830.0000.0000.0000.0000.0000.000
74A65ARG10.7960.88516.5030.5490.5490.0000.0000.0000.000
75A66ASP-1-0.875-0.91818.499-0.576-0.5760.0000.0000.0000.000
76A67PHE0-0.041-0.01614.0700.0070.0070.0000.0000.0000.000
77A68ASN00.0060.00116.681-0.061-0.0610.0000.0000.0000.000
78A69LEU0-0.033-0.01610.541-0.096-0.0960.0000.0000.0000.000
79A70SER00.011-0.01210.5740.0000.0000.0000.0000.0000.000
80A71LYS10.9750.96512.4831.0881.0880.0000.0000.0000.000
81A72GLU-1-0.853-0.9077.021-4.619-4.6190.0000.0000.0000.000
82A73GLN00.0640.0397.458-0.125-0.1250.0000.0000.0000.000
83A74LYS10.8380.9258.7620.9690.9690.0000.0000.0000.000
84A75ALA00.0200.02010.0790.1460.1460.0000.0000.0000.000
85A76GLU-1-0.852-0.9462.119-23.745-22.1213.717-2.849-2.493-0.043
86A77LEU0-0.039-0.0146.9070.2720.2720.0000.0000.0000.000
87A78VAL00.0200.0138.6840.3990.3990.0000.0000.0000.000
88A79LEU00.0130.0058.4690.2930.2930.0000.0000.0000.000
89A80ASN0-0.001-0.0114.2391.7201.782-0.001-0.001-0.0590.000
90A81ALA00.0240.0168.5180.4410.4410.0000.0000.0000.000
91A82LEU0-0.0110.00112.1000.1760.1760.0000.0000.0000.000
92A83VAL0-0.0060.0018.8900.1610.1610.0000.0000.0000.000
93A84ALA0-0.053-0.03711.7840.1770.1770.0000.0000.0000.000
94A85ILE0-0.019-0.01613.3590.0600.0600.0000.0000.0000.000
95A86ARG10.8370.92315.2030.1110.1110.0000.0000.0000.000
96A87TYR00.0640.02213.2840.0250.0250.0000.0000.0000.000
97A88LEU0-0.0520.01112.0960.1760.1760.0000.0000.0000.000
98A89LYS10.8590.93215.258-0.988-0.9880.0000.0000.0000.000
99A90PRO00.0490.03017.5430.0250.0250.0000.0000.0000.000
100A91GLN0-0.046-0.03115.7520.1200.1200.0000.0000.0000.000
101A92MET0-0.010-0.00518.997-0.066-0.0660.0000.0000.0000.000
102A93PRO00.018-0.01220.3040.0350.0350.0000.0000.0000.000
103A94LYS10.8880.95617.267-0.613-0.6130.0000.0000.0000.000
104A95SER00.050-0.00322.057-0.027-0.0270.0000.0000.0000.000
105A96TRP00.0160.01124.638-0.019-0.0190.0000.0000.0000.000
106A97HIS00.0090.00821.289-0.031-0.0310.0000.0000.0000.000
107A98PHE0-0.0190.00218.603-0.008-0.0080.0000.0000.0000.000
108A99VAL00.0700.03324.5590.0090.0090.0000.0000.0000.000
109A100SER0-0.087-0.05527.057-0.008-0.0080.0000.0000.0000.000
110A101HIS00.003-0.01526.232-0.015-0.0150.0000.0000.0000.000
111A102GLY0-0.0220.01131.274-0.010-0.0100.0000.0000.0000.000
112A103GLU-1-0.861-0.91731.988-0.014-0.0140.0000.0000.0000.000
113A104MET0-0.029-0.02129.8140.0070.0070.0000.0000.0000.000
114A105TRP00.0350.02223.161-0.006-0.0060.0000.0000.0000.000
115A106VAL0-0.021-0.02427.7280.0140.0140.0000.0000.0000.000
116A107PRO0-0.0180.01522.784-0.018-0.0180.0000.0000.0000.000
117A108MET00.0230.01424.3190.0230.0230.0000.0000.0000.000
118A109PRO00.0170.00320.453-0.024-0.0240.0000.0000.0000.000
119A110GLY0-0.011-0.01818.672-0.012-0.0120.0000.0000.0000.000
120A111ASP-1-0.858-0.93319.656-0.269-0.2690.0000.0000.0000.000
121A112ALA00.0030.00818.690-0.016-0.0160.0000.0000.0000.000
122A113ALA00.004-0.00518.8390.0480.0480.0000.0000.0000.000
123A114CYS0-0.056-0.00719.172-0.051-0.0510.0000.0000.0000.000
124A115VAL0-0.0070.00619.1620.0380.0380.0000.0000.0000.000
125A116TRP00.0460.01621.449-0.021-0.0210.0000.0000.0000.000
126A117LEU0-0.021-0.00619.1950.0370.0370.0000.0000.0000.000
127A118SER0-0.020-0.01723.226-0.012-0.0120.0000.0000.0000.000
128A119ASP-1-0.931-0.97024.6210.1560.1560.0000.0000.0000.000
129A120THR00.0150.00222.525-0.019-0.0190.0000.0000.0000.000
130A121HIS0-0.021-0.00225.718-0.031-0.0310.0000.0000.0000.000
131A122GLU-1-0.947-0.97218.206-0.019-0.0190.0000.0000.0000.000
132A123GLN0-0.005-0.01721.0060.0380.0380.0000.0000.0000.000
133A124VAL0-0.018-0.01115.691-0.021-0.0210.0000.0000.0000.000
134A125ASN0-0.028-0.04215.9190.0280.0280.0000.0000.0000.000
135A126LEU0-0.011-0.01714.773-0.012-0.0120.0000.0000.0000.000
136A127LEU00.0240.02212.806-0.056-0.0560.0000.0000.0000.000
137A128VAL00.0250.01115.3990.0820.0820.0000.0000.0000.000
138A129VAL0-0.035-0.02713.704-0.067-0.0670.0000.0000.0000.000
139A130GLU-1-0.814-0.90617.1430.1650.1650.0000.0000.0000.000
140A131SER0-0.022-0.04220.3250.0270.0270.0000.0000.0000.000
141A132GLY00.0360.02823.3970.0040.0040.0000.0000.0000.000
142A133GLU-1-0.914-0.96026.1520.0580.0580.0000.0000.0000.000
143A134ASN0-0.024-0.02228.258-0.013-0.0130.0000.0000.0000.000
144A135ALA0-0.010-0.00323.4400.0100.0100.0000.0000.0000.000
145A136ALA00.0620.05221.099-0.010-0.0100.0000.0000.0000.000
146A137LEU0-0.032-0.01715.5640.0630.0630.0000.0000.0000.000
147A138CYS0-0.028-0.00915.846-0.090-0.0900.0000.0000.0000.000
148A139LEU0-0.008-0.0019.4330.1470.1470.0000.0000.0000.000
149A140LEU0-0.0330.0009.632-0.091-0.0910.0000.0000.0000.000
150A141ALA00.0250.00810.108-0.299-0.2990.0000.0000.0000.000
151A142GLN00.0750.04911.295-0.038-0.0380.0000.0000.0000.000
152A143PRO00.002-0.0108.380-0.078-0.0780.0000.0000.0000.000
153A144CYS0-0.012-0.0228.0670.0010.0010.0000.0000.0000.000
154A145VAL00.0370.03510.482-0.070-0.0700.0000.0000.0000.000
155A146VAL00.0000.00513.0470.1890.1890.0000.0000.0000.000
156A147ILE00.0550.02315.667-0.080-0.0800.0000.0000.0000.000
157A148ALA0-0.004-0.00817.5150.0970.0970.0000.0000.0000.000
158A149GLY00.0000.00619.0340.0390.0390.0000.0000.0000.000
159A150ARG10.9140.96713.226-1.020-1.0200.0000.0000.0000.000
160A151ALA00.0280.01511.552-0.132-0.1320.0000.0000.0000.000
161A152MET0-0.053-0.0259.7480.3120.3120.0000.0000.0000.000
162A153GLN0-0.001-0.0145.2781.0081.0080.0000.0000.0000.000
163A154LEU0-0.009-0.0015.6970.2800.2800.0000.0000.0000.000
164A155GLY0-0.025-0.0115.259-0.547-0.5470.0000.0000.0000.000
165A156ASP-1-0.793-0.8636.7813.7123.7120.0000.0000.0000.000
166A157ALA00.0250.0128.684-0.411-0.4110.0000.0000.0000.000
167A158ILE0-0.066-0.03812.0260.1910.1910.0000.0000.0000.000
168A159LYS10.8490.93815.392-0.341-0.3410.0000.0000.0000.000
169A160ILE0-0.038-0.01717.8410.0430.0430.0000.0000.0000.000
170A161MET00.0190.01621.383-0.028-0.0280.0000.0000.0000.000
171A162ASN00.0730.00324.952-0.011-0.0110.0000.0000.0000.000
172A163ASP-1-0.787-0.85626.4190.0840.0840.0000.0000.0000.000
173A164ARG10.7570.86924.019-0.128-0.1280.0000.0000.0000.000
174A165LEU0-0.041-0.00920.537-0.015-0.0150.0000.0000.0000.000
175A166LYS10.8330.91023.9980.0380.0380.0000.0000.0000.000
176A167PRO00.0160.02223.590-0.017-0.0170.0000.0000.0000.000
177A168GLN0-0.004-0.00818.771-0.001-0.0010.0000.0000.0000.000