FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6Y58Z

Calculation Name: 4YPJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YPJ

Chain ID: A

ChEMBL ID:

UniProt ID: E5RWQ2

Base Structure: X-ray

Registration Date: 2023-09-23

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 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 810
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -22419938.298155
FMO2-HF: Nuclear repulsion 22104990.918322
FMO2-HF: Total energy -314947.379833
FMO2-MP2: Total energy -315883.602945


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:38:SER)


Summations of interaction energy for fragment #1(A:38: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.
-23.891-26.70622.941-10.007-10.1180.003
Interaction energy analysis for fragmet #1(A:38:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.018
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].
3A40SER0-0.011-0.0073.796-1.418-0.222-0.001-0.509-0.6860.002
4A41TYR0-0.069-0.0675.4890.7200.7200.0000.0000.0000.000
5A42ASP-1-0.914-0.9578.136-0.906-0.9060.0000.0000.0000.000
6A43GLY00.0170.02011.3020.1050.1050.0000.0000.0000.000
7A44GLU-1-0.884-0.92911.627-0.617-0.6170.0000.0000.0000.000
8A45ARG10.8340.87814.380-0.002-0.0020.0000.0000.0000.000
9A46ARG10.8810.94614.8610.0110.0110.0000.0000.0000.000
10A47VAL00.0360.0358.703-0.059-0.0590.0000.0000.0000.000
11A48ASN00.0100.00312.0280.2000.2000.0000.0000.0000.000
12A49PHE00.0530.0137.027-0.090-0.0900.0000.0000.0000.000
13A50ASN00.010-0.00711.0950.2400.2400.0000.0000.0000.000
14A51GLU-1-0.810-0.8819.538-0.506-0.5060.0000.0000.0000.000
15A52ASN0-0.020-0.0067.5090.2790.2790.0000.0000.0000.000
16A53TRP00.0280.0198.7910.4630.4630.0000.0000.0000.000
17A54ARG10.7450.87011.541-0.650-0.6500.0000.0000.0000.000
18A55PHE00.010-0.01213.9250.0270.0270.0000.0000.0000.000
19A56GLN00.0140.02117.585-0.045-0.0450.0000.0000.0000.000
20A57ARG10.9250.96020.851-0.127-0.1270.0000.0000.0000.000
21A58GLU-1-0.744-0.84124.4310.2630.2630.0000.0000.0000.000
22A59THR0-0.020-0.01626.960-0.013-0.0130.0000.0000.0000.000
23A60ASN0-0.023-0.01429.704-0.020-0.0200.0000.0000.0000.000
24A61GLY00.0490.04031.386-0.002-0.0020.0000.0000.0000.000
25A62SER0-0.093-0.07027.6910.0130.0130.0000.0000.0000.000
26A63ILE0-0.012-0.01322.337-0.007-0.0070.0000.0000.0000.000
27A64ALA0-0.003-0.01123.9370.0310.0310.0000.0000.0000.000
28A65GLY00.0200.00922.5980.0030.0030.0000.0000.0000.000
29A66ALA00.0280.02219.3080.0470.0470.0000.0000.0000.000
30A67GLN00.0170.00317.7700.0580.0580.0000.0000.0000.000
31A68ASN00.0070.01117.4500.0660.0660.0000.0000.0000.000
32A69PRO00.0420.01112.937-0.001-0.0010.0000.0000.0000.000
33A70GLY00.0050.00213.8030.0510.0510.0000.0000.0000.000
34A71PHE0-0.0390.00115.782-0.083-0.0830.0000.0000.0000.000
35A72ASP-1-0.767-0.86115.7710.4570.4570.0000.0000.0000.000
36A73ASP-1-0.803-0.88412.8510.7890.7890.0000.0000.0000.000
37A74SER0-0.055-0.06814.755-0.047-0.0470.0000.0000.0000.000
38A75SER00.0060.00415.772-0.035-0.0350.0000.0000.0000.000
39A76TRP0-0.030-0.01416.036-0.012-0.0120.0000.0000.0000.000
40A77ARG10.8480.88916.057-0.111-0.1110.0000.0000.0000.000
41A78LYS10.9270.94910.2400.0460.0460.0000.0000.0000.000
42A79LEU0-0.063-0.02513.728-0.071-0.0710.0000.0000.0000.000
43A80ASN0-0.015-0.01612.6460.1060.1060.0000.0000.0000.000
44A81LEU00.0090.02714.424-0.005-0.0050.0000.0000.0000.000
45A82PRO0-0.0080.00416.668-0.047-0.0470.0000.0000.0000.000
46A83HIS0-0.026-0.02518.9010.0090.0090.0000.0000.0000.000
47A84ASP-1-0.733-0.84620.7470.1170.1170.0000.0000.0000.000
48A85TRP00.001-0.01622.992-0.006-0.0060.0000.0000.0000.000
49A86SER0-0.050-0.03424.983-0.006-0.0060.0000.0000.0000.000
50A87ILE0-0.0100.01326.768-0.009-0.0090.0000.0000.0000.000
51A88GLU-1-0.770-0.83923.4270.0900.0900.0000.0000.0000.000
52A89LEU0-0.049-0.00527.870-0.005-0.0050.0000.0000.0000.000
53A90ASP-1-0.842-0.89730.5650.0370.0370.0000.0000.0000.000
54A91PHE0-0.012-0.01534.2240.0070.0070.0000.0000.0000.000
55A92ASN00.0120.00636.134-0.010-0.0100.0000.0000.0000.000
56A93LYS10.9550.97137.995-0.038-0.0380.0000.0000.0000.000
57A94ASN0-0.038-0.02640.738-0.003-0.0030.0000.0000.0000.000
58A95SER0-0.031-0.02635.9130.0050.0050.0000.0000.0000.000
59A96LEU00.0330.00836.066-0.004-0.0040.0000.0000.0000.000
60A97ALA0-0.0050.01435.4970.0000.0000.0000.0000.0000.000
61A98THR0-0.059-0.03137.400-0.006-0.0060.0000.0000.0000.000
62A99HIS00.0940.03739.8850.0000.0000.0000.0000.0000.000
63A100GLU-1-0.855-0.91540.9320.0610.0610.0000.0000.0000.000
64A101GLY00.0390.02337.001-0.001-0.0010.0000.0000.0000.000
65A102GLY00.0380.00435.9760.0020.0020.0000.0000.0000.000
66A103TYR0-0.084-0.04937.430-0.005-0.0050.0000.0000.0000.000
67A104LEU00.0100.01532.357-0.001-0.0010.0000.0000.0000.000
68A105ASP-1-0.783-0.85432.2020.1010.1010.0000.0000.0000.000
69A106GLY00.0380.04229.5080.0020.0020.0000.0000.0000.000
70A107GLY0-0.020-0.00929.3240.0030.0030.0000.0000.0000.000
71A108ILE0-0.003-0.00625.7020.0100.0100.0000.0000.0000.000
72A109GLY00.0120.00823.448-0.013-0.0130.0000.0000.0000.000
73A110TRP0-0.036-0.03319.0970.0280.0280.0000.0000.0000.000
74A111TYR0-0.003-0.01615.392-0.031-0.0310.0000.0000.0000.000
75A112ARG10.7790.86713.218-0.786-0.7860.0000.0000.0000.000
76A113LYS10.8470.9347.047-1.244-1.2440.0000.0000.0000.000
77A114THR00.0270.0196.5230.0200.0200.0000.0000.0000.000
78A115PHE0-0.039-0.0153.363-1.1830.1260.154-0.779-0.6830.006
79A116THR00.0480.0141.843-18.352-24.60919.427-6.569-6.6020.019
80A117ILE00.0100.0002.363-2.523-1.9273.360-2.119-1.837-0.024
81A118PRO00.0200.0213.7730.4480.7540.002-0.031-0.2770.000
82A119GLU-1-0.789-0.9055.3850.5170.552-0.0010.000-0.0330.000
83A120SER0-0.027-0.0088.3510.0680.0680.0000.0000.0000.000
84A121MET0-0.0150.0067.4490.1370.1370.0000.0000.0000.000
85A122LYS10.8240.9068.720-0.867-0.8670.0000.0000.0000.000
86A123GLY0-0.032-0.01112.235-0.100-0.1000.0000.0000.0000.000
87A124LYS10.8530.93013.064-0.078-0.0780.0000.0000.0000.000
88A125ARG10.7790.87714.341-0.262-0.2620.0000.0000.0000.000
89A126ILE00.030-0.0109.594-0.022-0.0220.0000.0000.0000.000
90A127SER0-0.015-0.01913.6700.0500.0500.0000.0000.0000.000
91A128LEU0-0.0250.00012.356-0.009-0.0090.0000.0000.0000.000
92A129ASP-1-0.781-0.83714.5240.2320.2320.0000.0000.0000.000
93A130PHE00.016-0.00816.3790.0090.0090.0000.0000.0000.000
94A131ASP-1-0.744-0.88219.1590.0770.0770.0000.0000.0000.000
95A132GLY00.005-0.00221.601-0.023-0.0230.0000.0000.0000.000
96A133VAL0-0.044-0.02120.4110.0080.0080.0000.0000.0000.000
97A134TYR00.0210.02223.358-0.009-0.0090.0000.0000.0000.000
98A135MET00.004-0.01226.021-0.002-0.0020.0000.0000.0000.000
99A136ASN0-0.061-0.02326.5840.0150.0150.0000.0000.0000.000
100A137SER0-0.0050.02322.0010.0040.0040.0000.0000.0000.000
101A138THR00.0080.00822.284-0.017-0.0170.0000.0000.0000.000
102A139THR0-0.0110.00516.7680.0300.0300.0000.0000.0000.000
103A140TYR00.019-0.00517.385-0.056-0.0560.0000.0000.0000.000
104A141LEU0-0.003-0.00510.9500.0970.0970.0000.0000.0000.000
105A142ASN0-0.038-0.03711.3650.0860.0860.0000.0000.0000.000
106A143GLY00.000-0.00414.227-0.069-0.0690.0000.0000.0000.000
107A144GLU-1-0.917-0.93217.6790.4330.4330.0000.0000.0000.000
108A145VAL0-0.039-0.02818.6310.0530.0530.0000.0000.0000.000
109A146LEU0-0.049-0.02815.207-0.011-0.0110.0000.0000.0000.000
110A147GLY00.0240.00619.899-0.041-0.0410.0000.0000.0000.000
111A148THR0-0.027-0.03322.6000.0290.0290.0000.0000.0000.000
112A149TYR0-0.029-0.03224.324-0.013-0.0130.0000.0000.0000.000
113A150PRO00.0090.01026.149-0.002-0.0020.0000.0000.0000.000
114A151PHE00.0160.00729.300-0.008-0.0080.0000.0000.0000.000
115A152GLY00.0230.00227.7870.0100.0100.0000.0000.0000.000
116A153TYR0-0.0250.00128.067-0.003-0.0030.0000.0000.0000.000
117A154ASN0-0.031-0.02327.666-0.021-0.0210.0000.0000.0000.000
118A155ALA0-0.0080.01523.2380.0160.0160.0000.0000.0000.000
119A156PHE0-0.023-0.01520.3600.0030.0030.0000.0000.0000.000
120A157SER0-0.056-0.06718.7270.0110.0110.0000.0000.0000.000
121A158TYR00.0230.01717.190-0.012-0.0120.0000.0000.0000.000
122A159ASP-1-0.784-0.86316.5360.5160.5160.0000.0000.0000.000
123A160ILE0-0.037-0.04010.9550.0420.0420.0000.0000.0000.000
124A161SER00.0230.00813.3940.1140.1140.0000.0000.0000.000
125A162ASP-1-0.850-0.92413.8700.5430.5430.0000.0000.0000.000
126A163LYS10.8800.95214.472-0.540-0.5400.0000.0000.0000.000
127A164LEU00.0090.0178.2280.1190.1190.0000.0000.0000.000
128A165TYR0-0.007-0.0109.883-0.260-0.2600.0000.0000.0000.000
129A166LYS10.8540.9109.260-0.581-0.5810.0000.0000.0000.000
130A167ASP-1-0.842-0.93310.6791.1971.1970.0000.0000.0000.000
131A168GLY00.0390.0196.957-0.165-0.1650.0000.0000.0000.000
132A169ARG10.8400.9426.836-0.544-0.5440.0000.0000.0000.000
133A170ALA0-0.007-0.0125.8760.4600.4600.0000.0000.0000.000
134A171ASN00.0130.0356.417-1.213-1.2130.0000.0000.0000.000
135A172VAL0-0.014-0.0107.6590.4630.4630.0000.0000.0000.000
136A173LEU00.0150.02310.325-0.248-0.2480.0000.0000.0000.000
137A174VAL0-0.035-0.02012.139-0.017-0.0170.0000.0000.0000.000
138A175VAL00.0290.01015.328-0.038-0.0380.0000.0000.0000.000
139A176LYS10.8280.94218.034-0.329-0.3290.0000.0000.0000.000
140A177VAL00.009-0.01121.092-0.006-0.0060.0000.0000.0000.000
141A178ASN00.0090.00923.771-0.025-0.0250.0000.0000.0000.000
142A179ASN00.0420.02327.573-0.012-0.0120.0000.0000.0000.000
143A180THR0-0.006-0.01629.923-0.010-0.0100.0000.0000.0000.000
144A181GLN00.0010.02532.882-0.003-0.0030.0000.0000.0000.000
145A182PRO00.0350.00435.8170.0000.0000.0000.0000.0000.000
146A183SER00.000-0.03433.269-0.003-0.0030.0000.0000.0000.000
147A184SER0-0.022-0.01835.2110.0010.0010.0000.0000.0000.000
148A185ARG10.8010.88337.327-0.058-0.0580.0000.0000.0000.000
149A186TRP0-0.0110.00634.612-0.007-0.0070.0000.0000.0000.000
150A187TYR0-0.047-0.05029.0490.0090.0090.0000.0000.0000.000
151A188SER0-0.009-0.02230.755-0.005-0.0050.0000.0000.0000.000
152A189GLY00.0460.03228.5220.0000.0000.0000.0000.0000.000
153A190SER0-0.048-0.02426.7000.0060.0060.0000.0000.0000.000
154A191GLY00.0390.02622.570-0.002-0.0020.0000.0000.0000.000
155A192ILE0-0.0120.00916.791-0.007-0.0070.0000.0000.0000.000
156A193TYR0-0.023-0.02520.110-0.020-0.0200.0000.0000.0000.000
157A194ARG10.8220.90021.418-0.149-0.1490.0000.0000.0000.000
158A195ASN00.0170.02018.2400.0210.0210.0000.0000.0000.000
159A196VAL00.0200.00614.0850.0320.0320.0000.0000.0000.000
160A197TYR0-0.091-0.07113.341-0.067-0.0670.0000.0000.0000.000
161A198LEU0-0.0150.0067.9350.1480.1480.0000.0000.0000.000
162A199THR0-0.028-0.03712.216-0.161-0.1610.0000.0000.0000.000
163A200VAL0-0.044-0.01710.9730.0950.0950.0000.0000.0000.000
164A201THR0-0.010-0.01614.346-0.062-0.0620.0000.0000.0000.000
165A202ASP-1-0.801-0.89516.8100.1070.1070.0000.0000.0000.000
166A203PRO00.0170.00118.4220.0140.0140.0000.0000.0000.000
167A204ILE0-0.0340.01021.0250.0040.0040.0000.0000.0000.000
168A205HIS10.8050.87921.427-0.175-0.1750.0000.0000.0000.000
169A206VAL00.0080.00723.5100.0090.0090.0000.0000.0000.000
170A207ALA00.0000.01423.3910.0150.0150.0000.0000.0000.000
171A208ARG10.8610.90521.556-0.191-0.1910.0000.0000.0000.000
172A209TYR0-0.040-0.03424.415-0.007-0.0070.0000.0000.0000.000
173A210GLY00.0120.03426.405-0.007-0.0070.0000.0000.0000.000
174A211THR0-0.029-0.05128.262-0.003-0.0030.0000.0000.0000.000
175A212PHE00.0170.01130.8460.0040.0040.0000.0000.0000.000
176A213VAL0-0.0170.00533.511-0.002-0.0020.0000.0000.0000.000
177A214THR00.0130.01136.0620.0020.0020.0000.0000.0000.000
178A215THR00.032-0.00339.701-0.004-0.0040.0000.0000.0000.000
179A216PRO00.0280.01242.8130.0000.0000.0000.0000.0000.000
180A217ASN0-0.008-0.01145.804-0.002-0.0020.0000.0000.0000.000
181A218LEU00.0430.04944.769-0.001-0.0010.0000.0000.0000.000
182A219GLU-1-0.835-0.91048.3100.0000.0000.0000.0000.0000.000
183A220LYS10.9040.94151.376-0.009-0.0090.0000.0000.0000.000
184A221SER00.0430.00449.010-0.001-0.0010.0000.0000.0000.000
185A222ILE00.0080.00548.509-0.002-0.0020.0000.0000.0000.000
186A223LYS10.7850.88851.263-0.001-0.0010.0000.0000.0000.000
187A224GLU-1-0.853-0.89853.389-0.006-0.0060.0000.0000.0000.000
188A225ASP-1-0.817-0.90751.258-0.024-0.0240.0000.0000.0000.000
189A226ARG10.7000.80548.4500.0030.0030.0000.0000.0000.000
190A227ALA00.0110.02144.3980.0020.0020.0000.0000.0000.000
191A228ASP-1-0.784-0.85445.148-0.006-0.0060.0000.0000.0000.000
192A229VAL0-0.026-0.02339.2140.0020.0020.0000.0000.0000.000
193A230ASN0-0.078-0.04940.7390.0030.0030.0000.0000.0000.000
194A231ILE00.0290.01634.6390.0010.0010.0000.0000.0000.000
195A232LYS10.8340.89535.908-0.028-0.0280.0000.0000.0000.000
196A233THR00.0350.00830.0990.0020.0020.0000.0000.0000.000
197A234LYS10.8620.93329.712-0.054-0.0540.0000.0000.0000.000
198A235ILE00.0280.02027.2420.0020.0020.0000.0000.0000.000
199A236SER00.0170.01824.3760.0000.0000.0000.0000.0000.000
200A237ASN0-0.028-0.01625.6370.0000.0000.0000.0000.0000.000
201A238ASP-1-0.797-0.88421.0900.2230.2230.0000.0000.0000.000
202A239ALA0-0.016-0.00522.8760.0240.0240.0000.0000.0000.000
203A240ALA0-0.001-0.00824.305-0.004-0.0040.0000.0000.0000.000
204A241GLU-1-0.840-0.90226.5900.0840.0840.0000.0000.0000.000
205A242ALA0-0.021-0.01228.685-0.001-0.0010.0000.0000.0000.000
206A243LYS10.8080.88027.272-0.086-0.0860.0000.0000.0000.000
207A244GLN00.0140.02431.0940.0080.0080.0000.0000.0000.000
208A245VAL0-0.025-0.02029.346-0.002-0.0020.0000.0000.0000.000
209A246LYS10.8740.93631.5840.0130.0130.0000.0000.0000.000
210A247ILE0-0.010-0.00930.0050.0010.0010.0000.0000.0000.000
211A248LYS10.8410.91030.9030.0510.0510.0000.0000.0000.000
212A249SER0-0.014-0.00631.585-0.003-0.0030.0000.0000.0000.000
213A250THR00.004-0.00732.0170.0030.0030.0000.0000.0000.000
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215A252TYR00.0380.01130.987-0.002-0.0020.0000.0000.0000.000
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480A517ASP-1-0.779-0.86759.3830.0140.0140.0000.0000.0000.000
481A518GLY00.0310.01762.5820.0000.0000.0000.0000.0000.000
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