FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: K2GG3

Calculation Name: 1T72-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T72

Chain ID: A

ChEMBL ID:

UniProt ID: O67053

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2546755.938011
FMO2-HF: Nuclear repulsion 2459604.618343
FMO2-HF: Total energy -87151.319668
FMO2-MP2: Total energy -87401.249882


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.1911.018-0.016-0.678-0.5150.001
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.012
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].
3A3GLY00.0530.0143.8640.4041.613-0.016-0.678-0.5150.001
4A4GLY0-0.026-0.0087.167-0.091-0.0910.0000.0000.0000.000
5A5GLY00.0450.02610.534-0.015-0.0150.0000.0000.0000.000
6A6GLY00.0910.05210.8810.0110.0110.0000.0000.0000.000
7A7MET0-0.039-0.0279.3580.0530.0530.0000.0000.0000.000
8A8LYS10.7850.90213.6210.0780.0780.0000.0000.0000.000
9A9LEU00.0690.03415.0550.0080.0080.0000.0000.0000.000
10A10PHE00.0280.01516.1300.0040.0040.0000.0000.0000.000
11A11LYS10.8780.94316.8170.2250.2250.0000.0000.0000.000
12A12GLU-1-0.729-0.85920.166-0.035-0.0350.0000.0000.0000.000
13A13LEU00.0210.02120.3810.0150.0150.0000.0000.0000.000
14A14GLU-1-0.809-0.89421.489-0.148-0.1480.0000.0000.0000.000
15A15GLU-1-0.934-0.96823.385-0.080-0.0800.0000.0000.0000.000
16A16THR0-0.004-0.03025.1600.0150.0150.0000.0000.0000.000
17A17LYS10.8420.91023.8460.1470.1470.0000.0000.0000.000
18A18GLU-1-0.949-0.97628.085-0.085-0.0850.0000.0000.0000.000
19A19GLN0-0.076-0.03529.4130.0120.0120.0000.0000.0000.000
20A20VAL00.0770.04130.5340.0050.0050.0000.0000.0000.000
21A21ILE0-0.0010.00931.0970.0030.0030.0000.0000.0000.000
22A22LYS10.8300.90833.7640.0530.0530.0000.0000.0000.000
23A23MET00.0100.01135.7000.0020.0020.0000.0000.0000.000
24A24ALA00.0580.03136.8740.0030.0030.0000.0000.0000.000
25A25LYS10.9220.96238.5290.0500.0500.0000.0000.0000.000
26A26LEU0-0.005-0.00439.6060.0020.0020.0000.0000.0000.000
27A27VAL00.0720.04141.0940.0020.0020.0000.0000.0000.000
28A28GLN0-0.064-0.02740.5930.0020.0020.0000.0000.0000.000
29A29GLU-1-0.930-0.95844.570-0.030-0.0300.0000.0000.0000.000
30A30ALA00.0180.01246.1020.0020.0020.0000.0000.0000.000
31A31ILE00.0330.00945.7580.0020.0020.0000.0000.0000.000
32A32ASP-1-0.938-0.95348.812-0.030-0.0300.0000.0000.0000.000
33A33LYS10.8120.87849.0300.0270.0270.0000.0000.0000.000
34A34ALA00.0470.03451.8810.0010.0010.0000.0000.0000.000
35A35THR00.0170.00453.3160.0010.0010.0000.0000.0000.000
36A36GLU-1-0.793-0.87854.959-0.021-0.0210.0000.0000.0000.000
37A37ALA0-0.023-0.01056.3150.0010.0010.0000.0000.0000.000
38A38LEU00.0440.01857.8020.0010.0010.0000.0000.0000.000
39A39ASN0-0.066-0.03958.3780.0010.0010.0000.0000.0000.000
40A40LYS10.6810.81960.1510.0220.0220.0000.0000.0000.000
41A41GLN0-0.071-0.03962.6990.0010.0010.0000.0000.0000.000
42A42ASN0-0.0240.00460.0400.0010.0010.0000.0000.0000.000
43A43VAL00.0840.01959.6700.0000.0000.0000.0000.0000.000
44A44GLU-1-0.963-0.96558.057-0.016-0.0160.0000.0000.0000.000
45A45LEU0-0.026-0.02854.1580.0000.0000.0000.0000.0000.000
46A46ALA00.0380.02054.839-0.001-0.0010.0000.0000.0000.000
47A47GLU-1-0.838-0.91054.650-0.013-0.0130.0000.0000.0000.000
48A48GLU-1-0.917-0.94351.439-0.022-0.0220.0000.0000.0000.000
49A49VAL0-0.0020.00949.733-0.001-0.0010.0000.0000.0000.000
50A50ILE0-0.0130.00449.8050.0000.0000.0000.0000.0000.000
51A51LYS10.7220.83850.5270.0150.0150.0000.0000.0000.000
52A52GLY0-0.0020.00647.2330.0000.0000.0000.0000.0000.000
53A53ASP-1-0.799-0.91245.410-0.023-0.0230.0000.0000.0000.000
54A54ASP-1-0.895-0.94144.325-0.013-0.0130.0000.0000.0000.000
55A55THR0-0.134-0.08340.7710.0000.0000.0000.0000.0000.000
56A56ILE0-0.062-0.02840.225-0.003-0.0030.0000.0000.0000.000
57A57ASP-1-0.853-0.92139.588-0.014-0.0140.0000.0000.0000.000
58A58LEU0-0.021-0.02639.1240.0000.0000.0000.0000.0000.000
59A59LEU0-0.081-0.03334.386-0.001-0.0010.0000.0000.0000.000
60A60GLU-1-0.734-0.86034.829-0.025-0.0250.0000.0000.0000.000
61A61VAL00.0100.01334.2130.0000.0000.0000.0000.0000.000
62A62ASP-1-0.884-0.92231.332-0.033-0.0330.0000.0000.0000.000
63A63ILE00.0240.00830.075-0.002-0.0020.0000.0000.0000.000
64A64GLU-1-0.800-0.87429.405-0.015-0.0150.0000.0000.0000.000
65A65ARG10.8830.93929.1950.0010.0010.0000.0000.0000.000
66A66ARG10.7720.85926.2380.0510.0510.0000.0000.0000.000
67A67CYS00.0270.01825.030-0.003-0.0030.0000.0000.0000.000
68A68ILE00.0100.00224.4930.0030.0030.0000.0000.0000.000
69A69ARG10.8840.94223.8780.0040.0040.0000.0000.0000.000
70A70MET0-0.0140.01020.6920.0090.0090.0000.0000.0000.000
71A71ILE00.0250.00419.521-0.003-0.0030.0000.0000.0000.000
72A72ALA0-0.052-0.03019.8270.0110.0110.0000.0000.0000.000
73A73LEU0-0.078-0.03518.8600.0230.0230.0000.0000.0000.000
74A74TYR0-0.096-0.07015.2230.0200.0200.0000.0000.0000.000
75A75GLN0-0.070-0.01713.5010.0220.0220.0000.0000.0000.000
76A76PRO00.0010.01915.482-0.009-0.0090.0000.0000.0000.000
77A77GLU-1-0.907-0.95911.980-0.140-0.1400.0000.0000.0000.000
78A78ALA0-0.019-0.02116.480-0.003-0.0030.0000.0000.0000.000
79A79GLY00.0510.03418.4870.0100.0100.0000.0000.0000.000
80A80ASP-1-0.895-0.95216.700-0.200-0.2000.0000.0000.0000.000
81A81LEU0-0.022-0.01219.7400.0160.0160.0000.0000.0000.000
82A82ARG10.8150.89221.5900.1140.1140.0000.0000.0000.000
83A83MET00.0380.02623.1100.0040.0040.0000.0000.0000.000
84A84ILE0-0.022-0.01920.7680.0080.0080.0000.0000.0000.000
85A85MET0-0.024-0.02525.0030.0090.0090.0000.0000.0000.000
86A86GLY00.0230.01927.4080.0050.0050.0000.0000.0000.000
87A87ILE0-0.027-0.02726.0240.0030.0030.0000.0000.0000.000
88A88TYR0-0.105-0.08629.0380.0050.0050.0000.0000.0000.000
89A89LYS10.7620.88030.8390.0390.0390.0000.0000.0000.000
90A90ILE00.003-0.00231.9310.0020.0020.0000.0000.0000.000
91A91VAL0-0.056-0.01433.1060.0000.0000.0000.0000.0000.000
92A92SER00.0470.00035.1380.0010.0010.0000.0000.0000.000
93A93ASP-1-0.838-0.88537.733-0.031-0.0310.0000.0000.0000.000
94A94LEU0-0.001-0.02836.0140.0000.0000.0000.0000.0000.000
95A95GLU-1-0.799-0.86339.470-0.017-0.0170.0000.0000.0000.000
96A96ARG10.7000.80541.2420.0190.0190.0000.0000.0000.000
97A97MET0-0.069-0.02841.7750.0000.0000.0000.0000.0000.000
98A98GLY0-0.0130.01543.943-0.001-0.0010.0000.0000.0000.000
99A99ASP-1-0.759-0.85345.330-0.014-0.0140.0000.0000.0000.000
100A100GLU-1-0.829-0.91647.586-0.017-0.0170.0000.0000.0000.000
101A101ALA0-0.021-0.02348.3270.0000.0000.0000.0000.0000.000
102A102GLU-1-0.924-0.95949.530-0.014-0.0140.0000.0000.0000.000
103A103ASN00.005-0.01251.2730.0020.0020.0000.0000.0000.000
104A104ILE0-0.059-0.03151.8680.0010.0010.0000.0000.0000.000
105A105ALA00.0000.00953.6780.0000.0000.0000.0000.0000.000
106A106GLU-1-0.866-0.94855.493-0.011-0.0110.0000.0000.0000.000
107A107ARG10.8030.89557.5130.0130.0130.0000.0000.0000.000
108A108ALA0-0.002-0.00158.3360.0000.0000.0000.0000.0000.000
109A109ILE0-0.0160.00458.4390.0000.0000.0000.0000.0000.000
110A110LEU0-0.025-0.01461.6370.0010.0010.0000.0000.0000.000
111A111LEU0-0.081-0.03861.5200.0010.0010.0000.0000.0000.000
112A112ALA00.0080.01664.0150.0000.0000.0000.0000.0000.000
113A113GLU-1-1.003-0.98865.862-0.009-0.0090.0000.0000.0000.000
114A114GLU-1-0.860-0.91268.908-0.010-0.0100.0000.0000.0000.000
115A115PRO00.0100.00169.382-0.001-0.0010.0000.0000.0000.000
116A116PRO00.0800.04366.8180.0000.0000.0000.0000.0000.000
117A117LEU0-0.078-0.01767.2940.0000.0000.0000.0000.0000.000
118A118LYS10.8320.90663.6430.0170.0170.0000.0000.0000.000
119A119PRO00.003-0.01166.4070.0000.0000.0000.0000.0000.000
120A120TYR0-0.005-0.01261.220-0.001-0.0010.0000.0000.0000.000
121A121VAL00.0170.02660.876-0.001-0.0010.0000.0000.0000.000
122A122ASN00.006-0.01459.792-0.002-0.0020.0000.0000.0000.000
123A123ILE00.0300.02357.121-0.001-0.0010.0000.0000.0000.000
124A124ASN0-0.017-0.00856.139-0.001-0.0010.0000.0000.0000.000
125A125PHE0-0.043-0.02855.098-0.001-0.0010.0000.0000.0000.000
126A126MET0-0.0040.01253.438-0.001-0.0010.0000.0000.0000.000
127A127SER00.0620.02751.854-0.001-0.0010.0000.0000.0000.000
128A128GLU-1-0.884-0.92450.454-0.034-0.0340.0000.0000.0000.000
129A129ILE0-0.041-0.02149.142-0.002-0.0020.0000.0000.0000.000
130A130VAL00.0530.01847.491-0.002-0.0020.0000.0000.0000.000
131A131LYS10.7800.88346.0860.0320.0320.0000.0000.0000.000
132A132GLU-1-0.894-0.95443.960-0.049-0.0490.0000.0000.0000.000
133A133MET0-0.087-0.01543.062-0.003-0.0030.0000.0000.0000.000
134A134VAL00.0380.03440.724-0.002-0.0020.0000.0000.0000.000
135A135ASN0-0.067-0.02839.700-0.005-0.0050.0000.0000.0000.000
136A136ASP-1-0.817-0.90438.375-0.056-0.0560.0000.0000.0000.000
137A137SER0-0.010-0.00937.536-0.005-0.0050.0000.0000.0000.000
138A138VAL00.0530.03134.210-0.005-0.0050.0000.0000.0000.000
139A139ILE0-0.033-0.01533.597-0.007-0.0070.0000.0000.0000.000
140A140SER0-0.081-0.05132.839-0.006-0.0060.0000.0000.0000.000
141A141PHE00.0540.01228.656-0.006-0.0060.0000.0000.0000.000
142A142ILE0-0.062-0.02729.031-0.008-0.0080.0000.0000.0000.000
143A143GLN0-0.076-0.04127.621-0.014-0.0140.0000.0000.0000.000
144A144GLN0-0.033-0.01124.710-0.007-0.0070.0000.0000.0000.000
145A145ASP-1-0.864-0.90329.799-0.080-0.0800.0000.0000.0000.000
146A146THR00.040-0.01932.5220.0050.0050.0000.0000.0000.000
147A147LEU0-0.036-0.01734.7380.0060.0060.0000.0000.0000.000
148A148LEU0-0.086-0.03036.1040.0040.0040.0000.0000.0000.000
149A149ALA00.0670.03435.8360.0040.0040.0000.0000.0000.000
150A150LYS10.8470.91436.9150.0590.0590.0000.0000.0000.000
151A151LYS10.8980.94940.0620.0610.0610.0000.0000.0000.000
152A152VAL0-0.027-0.00840.1520.0020.0020.0000.0000.0000.000
153A153ILE00.0480.02240.4430.0020.0020.0000.0000.0000.000
154A154GLU-1-0.941-0.97344.183-0.041-0.0410.0000.0000.0000.000
155A155LYS10.7920.87344.1750.0470.0470.0000.0000.0000.000
156A156ASP-1-0.808-0.91946.126-0.028-0.0280.0000.0000.0000.000
157A157ASP-1-0.890-0.93348.183-0.028-0.0280.0000.0000.0000.000
158A158THR0-0.090-0.04850.7360.0020.0020.0000.0000.0000.000
159A159VAL0-0.024-0.01649.7490.0010.0010.0000.0000.0000.000
160A160ASP-1-0.812-0.89252.390-0.020-0.0200.0000.0000.0000.000
161A161GLU-1-0.954-0.98754.133-0.023-0.0230.0000.0000.0000.000
162A162LEU0-0.087-0.02955.2810.0010.0010.0000.0000.0000.000
163A163TYR0-0.013-0.03255.7200.0010.0010.0000.0000.0000.000
164A164HIS0-0.048-0.04156.3110.0020.0020.0000.0000.0000.000
165A165GLN0-0.115-0.06059.6650.0010.0010.0000.0000.0000.000
166A166LEU00.0240.02259.5640.0010.0010.0000.0000.0000.000
167A167GLU-1-0.681-0.77760.854-0.014-0.0140.0000.0000.0000.000
168A168ARG10.9030.95363.5000.0170.0170.0000.0000.0000.000
169A169GLU-1-0.798-0.87264.361-0.017-0.0170.0000.0000.0000.000
170A170LEU0-0.018-0.01163.4490.0010.0010.0000.0000.0000.000
171A171MET0-0.029-0.01467.3980.0010.0010.0000.0000.0000.000
172A172THR0-0.049-0.03369.4290.0010.0010.0000.0000.0000.000
173A173TYR00.0460.01368.9130.0000.0000.0000.0000.0000.000
174A174VAL0-0.044-0.01769.8720.0010.0010.0000.0000.0000.000
175A175LEU0-0.064-0.03072.7290.0010.0010.0000.0000.0000.000
176A176GLU-1-0.985-0.97774.788-0.012-0.0120.0000.0000.0000.000
177A177ASP-1-0.812-0.89576.128-0.009-0.0090.0000.0000.0000.000
178A178PRO00.0290.01175.2380.0000.0000.0000.0000.0000.000
179A179ARG10.8180.88674.7140.0090.0090.0000.0000.0000.000
180A180ASN00.0080.00171.6290.0000.0000.0000.0000.0000.000
181A181ILE0-0.0150.00770.0820.0000.0000.0000.0000.0000.000
182A182LYS10.8790.93367.9940.0090.0090.0000.0000.0000.000
183A183ARG10.8850.92266.8450.0110.0110.0000.0000.0000.000
184A184ALA00.0230.00665.638-0.001-0.0010.0000.0000.0000.000
185A185MET0-0.025-0.00863.8520.0000.0000.0000.0000.0000.000
186A186HIS00.0760.03762.166-0.001-0.0010.0000.0000.0000.000
187A187LEU00.0190.01060.842-0.001-0.0010.0000.0000.0000.000
188A188SER0-0.070-0.06060.426-0.001-0.0010.0000.0000.0000.000
189A189PHE0-0.053-0.04157.2860.0000.0000.0000.0000.0000.000
190A190VAL00.0260.02356.612-0.001-0.0010.0000.0000.0000.000
191A191ALA0-0.001-0.00655.500-0.001-0.0010.0000.0000.0000.000
192A192ARG10.8320.90254.9100.0130.0130.0000.0000.0000.000
193A193HIS00.001-0.00152.2840.0000.0000.0000.0000.0000.000
194A194TYR0-0.003-0.03850.818-0.001-0.0010.0000.0000.0000.000
195A195GLU-1-0.861-0.91450.218-0.021-0.0210.0000.0000.0000.000
196A196ARG10.8930.93548.6390.0170.0170.0000.0000.0000.000
197A197ILE0-0.025-0.01245.795-0.001-0.0010.0000.0000.0000.000
198A198ALA0-0.037-0.01745.263-0.002-0.0020.0000.0000.0000.000
199A199ASP-1-0.875-0.93045.080-0.026-0.0260.0000.0000.0000.000
200A200HIS0-0.010-0.03041.6180.0000.0000.0000.0000.0000.000
201A201ALA00.000-0.00840.947-0.003-0.0030.0000.0000.0000.000
202A202GLU-1-0.886-0.94240.515-0.036-0.0360.0000.0000.0000.000
203A203ASN00.0390.02039.815-0.002-0.0020.0000.0000.0000.000
204A204VAL0-0.045-0.01335.494-0.002-0.0020.0000.0000.0000.000
205A205ALA00.001-0.00435.627-0.005-0.0050.0000.0000.0000.000
206A206GLU-1-0.890-0.95236.193-0.047-0.0470.0000.0000.0000.000
207A207ALA0-0.041-0.02232.858-0.002-0.0020.0000.0000.0000.000
208A208ALA0-0.013-0.00831.829-0.006-0.0060.0000.0000.0000.000
209A209ILE0-0.014-0.00531.715-0.008-0.0080.0000.0000.0000.000
210A210TYR0-0.038-0.00928.428-0.005-0.0050.0000.0000.0000.000
211A211LEU0-0.012-0.01426.641-0.004-0.0040.0000.0000.0000.000
212A212SER0-0.060-0.01427.268-0.008-0.0080.0000.0000.0000.000
213A213GLU-1-0.872-0.95128.499-0.064-0.0640.0000.0000.0000.000
214A214GLY0-0.032-0.00227.2480.0020.0020.0000.0000.0000.000
215A215GLU-1-0.941-0.93422.356-0.147-0.1470.0000.0000.0000.000