Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YYKN2

Calculation Name: 4TR4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TR4

Chain ID: A

ChEMBL ID:

UniProt ID: Q91ZI8

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017447.95465
FMO2-HF: Nuclear repulsion 1943157.866156
FMO2-HF: Total energy -74290.088494
FMO2-MP2: Total energy -74505.876725


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:114:GLY)


Summations of interaction energy for fragment #1(A:114: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.
1.6093.7851.717-1.703-2.1880.002
Interaction energy analysis for fragmet #1(A:114:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.022
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].
3A116ASP-1-0.776-0.8773.797-0.9700.431-0.011-0.643-0.7460.003
4A117PRO0-0.047-0.0186.5940.1790.1790.0000.0000.0000.000
5A118PHE0-0.029-0.0219.1030.1970.1970.0000.0000.0000.000
6A119THR0-0.019-0.0219.9760.1750.1750.0000.0000.0000.000
7A120GLY0-0.024-0.0049.0100.1400.1400.0000.0000.0000.000
8A121GLN0-0.020-0.0228.4730.0370.0370.0000.0000.0000.000
9A122LYS10.8270.9044.1141.6991.850-0.001-0.051-0.0990.000
10A123LEU00.0180.0132.2101.3691.7311.727-0.967-1.122-0.001
11A124ASP-1-0.861-0.9285.010-1.264-1.211-0.001-0.005-0.0460.000
12A125PHE0-0.009-0.0113.4110.1250.3340.003-0.037-0.1750.000
13A126PHE0-0.0360.0008.8030.2100.2100.0000.0000.0000.000
14A127LYS10.8870.94311.8950.0170.0170.0000.0000.0000.000
15A128GLN00.0180.00815.1690.0050.0050.0000.0000.0000.000
16A129ALA00.0700.04318.1070.0400.0400.0000.0000.0000.000
17A130HIS00.000-0.00919.5010.0240.0240.0000.0000.0000.000
18A131GLU-1-0.802-0.89623.642-0.050-0.0500.0000.0000.0000.000
19A132GLY0-0.025-0.01126.1820.0060.0060.0000.0000.0000.000
20A133GLY00.0020.01022.2220.0160.0160.0000.0000.0000.000
21A134PRO0-0.021-0.01818.875-0.003-0.0030.0000.0000.0000.000
22A135ALA00.007-0.00621.121-0.023-0.0230.0000.0000.0000.000
23A136PRO0-0.0090.00418.2810.0060.0060.0000.0000.0000.000
24A137ASN00.0580.03519.259-0.003-0.0030.0000.0000.0000.000
25A138SER00.001-0.02219.034-0.009-0.0090.0000.0000.0000.000
26A139GLU-1-0.861-0.89719.682-0.236-0.2360.0000.0000.0000.000
27A140VAL0-0.0020.00521.585-0.014-0.0140.0000.0000.0000.000
28A141VAL00.0070.00925.1180.0010.0010.0000.0000.0000.000
29A142ARG10.9180.96627.8510.0910.0910.0000.0000.0000.000
30A143PRO00.0510.01531.347-0.004-0.0040.0000.0000.0000.000
31A144ASP-1-0.873-0.93533.927-0.087-0.0870.0000.0000.0000.000
32A145GLY0-0.016-0.01234.4650.0040.0040.0000.0000.0000.000
33A146PHE0-0.053-0.02229.753-0.004-0.0040.0000.0000.0000.000
34A147GLN00.0310.01928.948-0.010-0.0100.0000.0000.0000.000
35A148SER0-0.047-0.04522.9850.0040.0040.0000.0000.0000.000
36A149GLN00.0510.03525.5390.0140.0140.0000.0000.0000.000
37A150ARG10.8280.90218.7210.1770.1770.0000.0000.0000.000
38A151ILE00.0000.00623.6540.0170.0170.0000.0000.0000.000
39A152LEU0-0.015-0.02722.8990.0130.0130.0000.0000.0000.000
40A153ASP-1-0.864-0.91926.105-0.078-0.0780.0000.0000.0000.000
41A154TYR0-0.065-0.06128.2220.0080.0080.0000.0000.0000.000
42A155ALA0-0.0320.00929.2980.0030.0030.0000.0000.0000.000
43A156GLN0-0.025-0.02431.0810.0050.0050.0000.0000.0000.000
44A157GLY0-0.007-0.01333.2100.0030.0030.0000.0000.0000.000
45A158THR0-0.014-0.01532.512-0.002-0.0020.0000.0000.0000.000
46A159ARG10.7690.86834.4950.0320.0320.0000.0000.0000.000
47A160PRO0-0.028-0.00833.299-0.003-0.0030.0000.0000.0000.000
48A161LEU0-0.0010.00729.3290.0000.0000.0000.0000.0000.000
49A162VAL0-0.020-0.01631.536-0.004-0.0040.0000.0000.0000.000
50A163LEU0-0.0170.00026.842-0.003-0.0030.0000.0000.0000.000
51A164ASN00.010-0.00430.968-0.004-0.0040.0000.0000.0000.000
52A165PHE00.0360.01725.224-0.001-0.0010.0000.0000.0000.000
53A166GLY00.046-0.00430.2430.0050.0050.0000.0000.0000.000
54A167SER0-0.028-0.02332.143-0.004-0.0040.0000.0000.0000.000
55A168CYS00.049-0.01134.1010.0080.0080.0000.0000.0000.000
56A169THR0-0.059-0.04235.3950.0040.0040.0000.0000.0000.000
57A170CYS0-0.0160.00433.2060.0000.0000.0000.0000.0000.000
58A171PRO00.0380.00736.2060.0050.0050.0000.0000.0000.000
59A172PRO00.0350.01736.5590.0060.0060.0000.0000.0000.000
60A173PHE00.0110.00634.1750.0060.0060.0000.0000.0000.000
61A174MET0-0.0180.01437.0980.0050.0050.0000.0000.0000.000
62A175ALA0-0.043-0.01040.3300.0060.0060.0000.0000.0000.000
63A176ARG10.7760.87233.5910.1100.1100.0000.0000.0000.000
64A177MET00.0440.04437.3110.0060.0060.0000.0000.0000.000
65A178SER00.0370.01141.2690.0040.0040.0000.0000.0000.000
66A179ALA0-0.024-0.02442.8830.0040.0040.0000.0000.0000.000
67A180PHE00.0320.01035.7290.0030.0030.0000.0000.0000.000
68A181GLN00.0540.01039.8400.0050.0050.0000.0000.0000.000
69A182ARG10.8960.94243.0130.0550.0550.0000.0000.0000.000
70A183LEU0-0.045-0.01839.9670.0040.0040.0000.0000.0000.000
71A184VAL00.0640.04739.7040.0030.0030.0000.0000.0000.000
72A185THR0-0.030-0.01642.1110.0040.0040.0000.0000.0000.000
73A186LYS10.8090.91445.1500.0370.0370.0000.0000.0000.000
74A187TYR00.003-0.02541.5840.0030.0030.0000.0000.0000.000
75A188GLN00.0500.04841.5450.0010.0010.0000.0000.0000.000
76A189ARG10.8910.96142.3780.0180.0180.0000.0000.0000.000
77A190ASP-1-0.833-0.91041.350-0.017-0.0170.0000.0000.0000.000
78A191VAL0-0.0160.00136.5640.0010.0010.0000.0000.0000.000
79A192ASP-1-0.775-0.83435.065-0.040-0.0400.0000.0000.0000.000
80A193PHE00.006-0.01835.184-0.002-0.0020.0000.0000.0000.000
81A194LEU0-0.0180.00029.5780.0010.0010.0000.0000.0000.000
82A195ILE0-0.006-0.01032.699-0.003-0.0030.0000.0000.0000.000
83A196ILE0-0.028-0.01326.708-0.001-0.0010.0000.0000.0000.000
84A197TYR0-0.002-0.02630.1830.0010.0010.0000.0000.0000.000
85A198ILE0-0.049-0.02726.988-0.012-0.0120.0000.0000.0000.000
86A199GLU-1-0.884-0.94526.050-0.265-0.2650.0000.0000.0000.000
87A200GLU-1-0.701-0.78828.831-0.136-0.1360.0000.0000.0000.000
88A201ALA0-0.032-0.01131.178-0.011-0.0110.0000.0000.0000.000
89A202HIS0-0.033-0.02632.789-0.004-0.0040.0000.0000.0000.000
90A203PRO00.0220.02532.2340.0090.0090.0000.0000.0000.000
91A204SER00.005-0.01935.3650.0020.0020.0000.0000.0000.000
92A205ASP-1-0.866-0.93035.184-0.158-0.1580.0000.0000.0000.000
93A206GLY00.0070.02134.328-0.008-0.0080.0000.0000.0000.000
94A207TRP0-0.029-0.02132.0680.0100.0100.0000.0000.0000.000
95A208VAL0-0.034-0.02035.8280.0080.0080.0000.0000.0000.000
96A209THR00.0010.00338.029-0.001-0.0010.0000.0000.0000.000
97A210THR0-0.0040.00739.1670.0040.0040.0000.0000.0000.000
98A211ASP-1-0.930-0.96441.257-0.091-0.0910.0000.0000.0000.000
99A212SER0-0.020-0.01440.4190.0050.0050.0000.0000.0000.000
100A213PRO0-0.021-0.01642.5510.0010.0010.0000.0000.0000.000
101A214TYR0-0.047-0.01840.4550.0020.0020.0000.0000.0000.000
102A215VAL00.0520.01541.117-0.004-0.0040.0000.0000.0000.000
103A216ILE0-0.014-0.00835.9550.0020.0020.0000.0000.0000.000
104A217PRO0-0.0100.01035.997-0.005-0.0050.0000.0000.0000.000
105A218GLN00.001-0.00427.4490.0060.0060.0000.0000.0000.000
106A219HIS0-0.064-0.03629.683-0.011-0.0110.0000.0000.0000.000
107A220ARG10.8950.94229.2940.1540.1540.0000.0000.0000.000
108A221SER0-0.044-0.04828.676-0.010-0.0100.0000.0000.0000.000
109A222LEU00.0690.01526.6450.0030.0030.0000.0000.0000.000
110A223GLU-1-0.841-0.89730.145-0.150-0.1500.0000.0000.0000.000
111A224ASP-1-0.826-0.89732.521-0.150-0.1500.0000.0000.0000.000
112A225ARG10.7820.87725.3540.2350.2350.0000.0000.0000.000
113A226VAL0-0.032-0.02032.4410.0090.0090.0000.0000.0000.000
114A227SER0-0.041-0.01234.5460.0110.0110.0000.0000.0000.000
115A228ALA00.0100.00734.8020.0070.0070.0000.0000.0000.000
116A229ALA00.009-0.00734.2150.0060.0060.0000.0000.0000.000
117A230ARG10.8770.93336.2890.1050.1050.0000.0000.0000.000
118A231VAL00.0080.02139.6360.0060.0060.0000.0000.0000.000
119A232LEU0-0.018-0.01736.5870.0050.0050.0000.0000.0000.000
120A233GLN0-0.067-0.04237.9890.0020.0020.0000.0000.0000.000
121A234GLN00.0010.02541.1450.0040.0040.0000.0000.0000.000
122A235GLY0-0.052-0.01843.6480.0050.0050.0000.0000.0000.000
123A236ALA0-0.048-0.04341.540-0.002-0.0020.0000.0000.0000.000
124A237PRO00.0200.01142.617-0.002-0.0020.0000.0000.0000.000
125A238GLY00.0120.00041.5600.0020.0020.0000.0000.0000.000
126A239CYS0-0.0340.00637.0780.0030.0030.0000.0000.0000.000
127A240ALA00.0180.02035.133-0.002-0.0020.0000.0000.0000.000
128A241LEU0-0.002-0.00433.777-0.003-0.0030.0000.0000.0000.000
129A242VAL0-0.0090.00028.7410.0020.0020.0000.0000.0000.000
130A243LEU0-0.026-0.01129.019-0.001-0.0010.0000.0000.0000.000
131A244ASP-1-0.704-0.82023.298-0.266-0.2660.0000.0000.0000.000
132A245THR00.005-0.01320.7760.0030.0030.0000.0000.0000.000
133A246MET00.0350.01723.771-0.002-0.0020.0000.0000.0000.000
134A247ALA0-0.0270.00418.304-0.011-0.0110.0000.0000.0000.000
135A248ASN00.0300.01519.561-0.008-0.0080.0000.0000.0000.000
136A249SER00.0160.02318.528-0.023-0.0230.0000.0000.0000.000
137A250SER00.019-0.02019.188-0.004-0.0040.0000.0000.0000.000
138A251SER0-0.018-0.02621.8670.0200.0200.0000.0000.0000.000
139A252SER0-0.035-0.01917.5840.0020.0020.0000.0000.0000.000
140A253ALA0-0.046-0.00817.792-0.001-0.0010.0000.0000.0000.000
141A254TYR00.006-0.02318.7410.0300.0300.0000.0000.0000.000
142A255GLY00.0100.03921.1320.0230.0230.0000.0000.0000.000
143A256ALA0-0.067-0.05122.5130.0210.0210.0000.0000.0000.000
144A257TYR00.0570.01420.3180.0170.0170.0000.0000.0000.000
145A258PHE00.0230.01426.3440.0110.0110.0000.0000.0000.000
146A259GLU-1-0.733-0.85730.050-0.111-0.1110.0000.0000.0000.000
147A260ARG10.7970.92424.6790.1470.1470.0000.0000.0000.000
148A261LEU0-0.0280.01030.2910.0020.0020.0000.0000.0000.000
149A262TYR0-0.007-0.03224.3710.0000.0000.0000.0000.0000.000
150A263VAL0-0.0120.00530.0740.0030.0030.0000.0000.0000.000
151A264ILE0-0.0010.01026.2310.0010.0010.0000.0000.0000.000
152A265GLN00.025-0.00729.0280.0010.0010.0000.0000.0000.000
153A266SER00.0220.00329.2790.0020.0020.0000.0000.0000.000
154A267GLY00.0120.01525.3610.0090.0090.0000.0000.0000.000
155A268THR0-0.0170.01424.1090.0000.0000.0000.0000.0000.000
156A269ILE0-0.036-0.01922.757-0.007-0.0070.0000.0000.0000.000
157A270MET0-0.051-0.02526.7030.0090.0090.0000.0000.0000.000
158A271TYR0-0.022-0.03729.9860.0010.0010.0000.0000.0000.000
159A272GLN0-0.070-0.06223.9070.0000.0000.0000.0000.0000.000
160A273GLY00.0210.02829.0870.0050.0050.0000.0000.0000.000
161A274GLY00.0260.01829.687-0.012-0.0120.0000.0000.0000.000
162A275ARG10.8220.89227.4430.1530.1530.0000.0000.0000.000
163A276GLY00.0280.00631.5660.0070.0070.0000.0000.0000.000
164A277PRO0-0.0270.00034.985-0.004-0.0040.0000.0000.0000.000
165A278ASP-1-0.857-0.93537.309-0.101-0.1010.0000.0000.0000.000
166A279GLY0-0.006-0.01538.8480.0050.0050.0000.0000.0000.000
167A280TYR00.017-0.00138.1810.0040.0040.0000.0000.0000.000
168A281GLN00.0900.05832.3070.0020.0020.0000.0000.0000.000
169A282VAL00.0100.00536.4700.0030.0030.0000.0000.0000.000
170A283SER0-0.084-0.04839.0110.0050.0050.0000.0000.0000.000
171A284GLU-1-0.824-0.90335.344-0.065-0.0650.0000.0000.0000.000
172A285LEU00.0310.02435.0400.0040.0040.0000.0000.0000.000
173A286ARG10.9030.95537.4970.0530.0530.0000.0000.0000.000
174A287THR00.002-0.00540.0370.0050.0050.0000.0000.0000.000
175A288TRP00.0120.01334.0220.0030.0030.0000.0000.0000.000
176A289LEU0-0.016-0.01837.6270.0040.0040.0000.0000.0000.000
177A290GLU-1-0.887-0.95940.215-0.031-0.0310.0000.0000.0000.000
178A291ARG10.8610.92840.6440.0200.0200.0000.0000.0000.000
179A292TYR00.0610.03938.0020.0040.0040.0000.0000.0000.000
180A293ASP-1-0.799-0.89140.901-0.020-0.0200.0000.0000.0000.000
181A294GLU-1-0.805-0.88344.051-0.012-0.0120.0000.0000.0000.000
182A295GLN0-0.064-0.03339.9100.0000.0000.0000.0000.0000.000
183A296LEU0-0.052-0.01141.2790.0030.0030.0000.0000.0000.000
184A297HIS10.6920.82545.0510.0160.0160.0000.0000.0000.000
185A298GLY00.0420.04348.2990.0010.0010.0000.0000.0000.000
186A299THR0-0.034-0.03449.645-0.001-0.0010.0000.0000.0000.000
187A300ARG10.7740.86246.9890.0250.0250.0000.0000.0000.000
188A301PRO00.0220.01652.391-0.001-0.0010.0000.0000.0000.000