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: ZYRKN

Calculation Name: 1OY5-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OY5

Chain ID: A

ChEMBL ID:

UniProt ID: O67463

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 222
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2408062.127923
FMO2-HF: Nuclear repulsion 2320865.471855
FMO2-HF: Total energy -87196.656068
FMO2-MP2: Total energy -87454.124805


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:3:ACE )


Summations of interaction energy for fragment #1(A:3:ACE )
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.
-0.2361.006-0.009-0.654-0.58-0.002
Interaction energy analysis for fragmet #1(A:3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.007
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].
3A5PRO 0-0.0050.0283.8660.0411.283-0.009-0.654-0.580-0.002
4A6LEU 00.0190.0046.9690.2030.2030.0000.0000.0000.000
5A7ARG 10.9110.9549.0230.7750.7750.0000.0000.0000.000
6A8PHE 00.016-0.00612.7010.0680.0680.0000.0000.0000.000
7A9PHE 00.0040.00415.440-0.018-0.0180.0000.0000.0000.000
8A10VAL 0-0.002-0.00419.4650.0200.0200.0000.0000.0000.000
9A11LEU 00.0290.02122.6160.0000.0000.0000.0000.0000.000
10A12THR 00.013-0.02325.9230.0080.0080.0000.0000.0000.000
11A13ILE 00.0580.03528.695-0.004-0.0040.0000.0000.0000.000
12A14PHE 0-0.072-0.04630.4190.0030.0030.0000.0000.0000.000
13A15PRO 00.0660.03126.987-0.005-0.0050.0000.0000.0000.000
14A16HIS 00.038-0.00326.596-0.010-0.0100.0000.0000.0000.000
15A17ILE 0-0.0060.02727.670-0.002-0.0020.0000.0000.0000.000
16A18ILE 00.0230.00022.124-0.003-0.0030.0000.0000.0000.000
17A19SER 0-0.007-0.00523.081-0.008-0.0080.0000.0000.0000.000
18A20CYS 00.012-0.01423.987-0.003-0.0030.0000.0000.0000.000
19A21TYR 0-0.085-0.05621.8860.0050.0050.0000.0000.0000.000
20A22SER 0-0.005-0.02019.590-0.009-0.0090.0000.0000.0000.000
21A23GLU -1-0.934-0.95320.239-0.166-0.1660.0000.0000.0000.000
22A24TYR 0-0.065-0.03522.6190.0080.0080.0000.0000.0000.000
23A25GLY 00.0080.00221.590-0.006-0.0060.0000.0000.0000.000
24A26ILE 00.023-0.00816.845-0.015-0.0150.0000.0000.0000.000
25A27VAL 00.0960.06816.687-0.026-0.0260.0000.0000.0000.000
26A28LYS 10.9891.01216.3930.1170.1170.0000.0000.0000.000
27A29GLN 0-0.110-0.04615.330-0.032-0.0320.0000.0000.0000.000
28A30ALA 00.022-0.00112.521-0.042-0.0420.0000.0000.0000.000
29A31ILE 00.0290.02611.754-0.113-0.1130.0000.0000.0000.000
30A32LYS 10.8770.93112.9280.2250.2250.0000.0000.0000.000
31A33LYS 10.7900.89710.4470.1350.1350.0000.0000.0000.000
32A34GLY 00.0250.0298.678-0.125-0.1250.0000.0000.0000.000
33A35LYS 10.8470.9225.4330.2180.2180.0000.0000.0000.000
34A36VAL 00.015-0.0058.4220.0400.0400.0000.0000.0000.000
35A37GLU -1-0.831-0.87611.049-0.765-0.7650.0000.0000.0000.000
36A38VAL 0-0.0030.00213.5040.0350.0350.0000.0000.0000.000
37A39TYR 0-0.044-0.05413.7440.0220.0220.0000.0000.0000.000
38A40PRO 0-0.020-0.00819.2760.0190.0190.0000.0000.0000.000
39A41ILE 0-0.013-0.00621.200-0.004-0.0040.0000.0000.0000.000
40A42ASP -1-0.757-0.88624.868-0.085-0.0850.0000.0000.0000.000
41A43LEU 00.027-0.00628.5320.0020.0020.0000.0000.0000.000
42A44ARG 10.8370.89730.6450.0870.0870.0000.0000.0000.000
43A45GLU -1-0.966-0.96029.406-0.095-0.0950.0000.0000.0000.000
44A46PHE 0-0.018-0.01925.733-0.002-0.0020.0000.0000.0000.000
45A47ALA 00.0020.00531.4710.0040.0040.0000.0000.0000.000
46A48PRO 00.0380.01134.3380.0020.0020.0000.0000.0000.000
47A49LYS 10.9110.96036.7640.0410.0410.0000.0000.0000.000
48A50GLY 00.008-0.00338.0900.0020.0020.0000.0000.0000.000
49A51GLN 0-0.034-0.00239.105-0.001-0.0010.0000.0000.0000.000
50A52VAL 00.0230.00134.667-0.001-0.0010.0000.0000.0000.000
51A53ASP -1-0.919-0.95537.017-0.047-0.0470.0000.0000.0000.000
52A54ASP -1-0.865-0.92339.320-0.035-0.0350.0000.0000.0000.000
53A55VAL 0-0.019-0.02642.7300.0000.0000.0000.0000.0000.000
54A56PRO 0-0.0280.01343.3330.0000.0000.0000.0000.0000.000
55A57TYR 00.007-0.01044.6570.0010.0010.0000.0000.0000.000
56A58GLY 0-0.022-0.02447.3310.0000.0000.0000.0000.0000.000
57A59GLY 0-0.028-0.01049.7900.0010.0010.0000.0000.0000.000
58A60LEU 00.0220.01246.0220.0010.0010.0000.0000.0000.000
59A61PRO 0-0.039-0.02247.185-0.001-0.0010.0000.0000.0000.000
60A62GLY 00.0360.02144.889-0.001-0.0010.0000.0000.0000.000
61A63MET 0-0.074-0.02840.8440.0000.0000.0000.0000.0000.000
62A64VAL 00.0230.01338.3650.0000.0000.0000.0000.0000.000
63A65LEU 0-0.019-0.01832.941-0.002-0.0020.0000.0000.0000.000
64A66LYS 10.8480.91736.6830.0490.0490.0000.0000.0000.000
65A67PRO 0-0.011-0.01834.350-0.003-0.0030.0000.0000.0000.000
66A68GLU -1-0.828-0.91533.277-0.050-0.0500.0000.0000.0000.000
67A69PRO 00.0430.02932.587-0.003-0.0030.0000.0000.0000.000
68A70ILE 00.0060.00428.449-0.007-0.0070.0000.0000.0000.000
69A71TYR 0-0.060-0.05028.410-0.004-0.0040.0000.0000.0000.000
70A72GLU -1-0.858-0.92228.470-0.073-0.0730.0000.0000.0000.000
71A73ALA 0-0.023-0.01026.136-0.008-0.0080.0000.0000.0000.000
72A74TYR 0-0.050-0.04423.348-0.014-0.0140.0000.0000.0000.000
73A75ASP -1-0.868-0.93523.581-0.082-0.0820.0000.0000.0000.000
74A76TYR 00.0420.01821.984-0.016-0.0160.0000.0000.0000.000
75A77VAL 0-0.052-0.02818.965-0.016-0.0160.0000.0000.0000.000
76A78VAL 0-0.050-0.03619.260-0.019-0.0190.0000.0000.0000.000
77A79GLU -1-0.986-0.98619.792-0.103-0.1030.0000.0000.0000.000
78A80ASN 0-0.082-0.04519.397-0.012-0.0120.0000.0000.0000.000
79A81TYR 0-0.052-0.02214.730-0.049-0.0490.0000.0000.0000.000
80A82GLY 00.0090.01814.630-0.025-0.0250.0000.0000.0000.000
81A83LYS 10.9430.96516.5790.0440.0440.0000.0000.0000.000
82A84PRO 0-0.0010.00717.209-0.005-0.0050.0000.0000.0000.000
83A85PHE 0-0.007-0.01117.5630.0240.0240.0000.0000.0000.000
84A86VAL 00.011-0.01519.238-0.016-0.0160.0000.0000.0000.000
85A87LEU 0-0.025-0.01321.1730.0130.0130.0000.0000.0000.000
86A88ILE 00.0090.02623.583-0.010-0.0100.0000.0000.0000.000
87A89THR 0-0.024-0.03225.8560.0040.0040.0000.0000.0000.000
88A90GLU -1-0.782-0.87428.512-0.036-0.0360.0000.0000.0000.000
89A91PRO 0-0.066-0.00932.2810.0010.0010.0000.0000.0000.000
90A92TRP 0-0.034-0.01534.6610.0000.0000.0000.0000.0000.000
91A93GLY 00.0820.05031.9890.0040.0040.0000.0000.0000.000
92A94GLU -1-0.895-0.97729.750-0.040-0.0400.0000.0000.0000.000
93A95LYS 10.9330.97830.0130.0130.0130.0000.0000.0000.000
94A96LEU 00.0390.03223.4460.0040.0040.0000.0000.0000.000
95A97ASN 00.007-0.03924.9150.0090.0090.0000.0000.0000.000
96A98GLN 00.0440.00419.970-0.009-0.0090.0000.0000.0000.000
97A99LYS 10.9100.98821.138-0.016-0.0160.0000.0000.0000.000
98A100LEU 00.0880.04020.5860.0060.0060.0000.0000.0000.000
99A101VAL 0-0.0030.02617.889-0.001-0.0010.0000.0000.0000.000
100A102ASN 0-0.001-0.01016.4770.0000.0000.0000.0000.0000.000
101A103GLU -1-0.900-0.91115.4970.0370.0370.0000.0000.0000.000
102A104LEU 0-0.044-0.03615.7130.0050.0050.0000.0000.0000.000
103A105SER 0-0.046-0.06212.616-0.015-0.0150.0000.0000.0000.000
104A106LYS 10.8940.94711.048-0.214-0.2140.0000.0000.0000.000
105A107LYS 10.8600.95711.4790.0410.0410.0000.0000.0000.000
106A108GLU -1-0.867-0.9368.546-0.069-0.0690.0000.0000.0000.000
107A109ARG 10.8560.92310.8520.1060.1060.0000.0000.0000.000
108A110ILE 0-0.0360.00214.1130.0490.0490.0000.0000.0000.000
109A111MET 00.0370.05017.054-0.021-0.0210.0000.0000.0000.000
110A112ILE 0-0.034-0.02820.0380.0160.0160.0000.0000.0000.000
111A113ILE 00.0130.00122.915-0.006-0.0060.0000.0000.0000.000
112A114CYS 0-0.057-0.02126.1290.0050.0050.0000.0000.0000.000
113A115GLY 00.0620.01528.5370.0020.0020.0000.0000.0000.000
114A116ARG 10.8700.91432.0530.0570.0570.0000.0000.0000.000
115A117TYR 0-0.022-0.00335.2870.0010.0010.0000.0000.0000.000
116A118GLU -1-0.861-0.93338.964-0.032-0.0320.0000.0000.0000.000
117A119GLY 00.0010.00736.2540.0020.0020.0000.0000.0000.000
118A120VAL 0-0.055-0.02332.133-0.003-0.0030.0000.0000.0000.000
119A121ASP -1-0.712-0.80335.360-0.031-0.0310.0000.0000.0000.000
120A122GLU -1-0.785-0.91135.250-0.029-0.0290.0000.0000.0000.000
121A123ARG 10.7630.83534.9430.0340.0340.0000.0000.0000.000
122A124VAL 00.0360.03530.049-0.001-0.0010.0000.0000.0000.000
123A125LYS 10.8470.90830.3720.0300.0300.0000.0000.0000.000
124A126LYS 10.8420.93630.4890.0280.0280.0000.0000.0000.000
125A127ILE 00.0050.01326.4660.0020.0020.0000.0000.0000.000
126A128VAL 0-0.030-0.00625.741-0.007-0.0070.0000.0000.0000.000
127A129ASP -1-0.899-0.92122.457-0.036-0.0360.0000.0000.0000.000
128A130MET 0-0.082-0.05121.8140.0070.0070.0000.0000.0000.000
129A131GLU -1-0.855-0.94425.682-0.038-0.0380.0000.0000.0000.000
130A132ILE 0-0.092-0.04224.5690.0050.0050.0000.0000.0000.000
131A133SER 0-0.020-0.00728.3610.0010.0010.0000.0000.0000.000
132A134LEU 00.0700.01331.733-0.001-0.0010.0000.0000.0000.000
133A135GLY 0-0.048-0.02534.0180.0020.0020.0000.0000.0000.000
134A136ASP -1-0.935-0.94934.753-0.012-0.0120.0000.0000.0000.000
135A137PHE 0-0.084-0.04433.0350.0000.0000.0000.0000.0000.000
136A138ILE 00.0290.02537.063-0.001-0.0010.0000.0000.0000.000
137A139LEU 0-0.025-0.00232.329-0.001-0.0010.0000.0000.0000.000
138A140SER 0-0.013-0.01736.2280.0000.0000.0000.0000.0000.000
139A141GLY 0-0.011-0.03033.414-0.001-0.0010.0000.0000.0000.000
140A142GLY 00.0220.02429.6660.0020.0020.0000.0000.0000.000
141A143GLU -1-0.757-0.86527.569-0.079-0.0790.0000.0000.0000.000
142A144ILE 00.0230.00426.762-0.007-0.0070.0000.0000.0000.000
143A145VAL 00.0190.01826.112-0.001-0.0010.0000.0000.0000.000
144A146ALA 00.0250.01323.521-0.002-0.0020.0000.0000.0000.000
145A147LEU 0-0.014-0.00622.249-0.011-0.0110.0000.0000.0000.000
146A148ALA 00.0040.02022.133-0.005-0.0050.0000.0000.0000.000
147A149VAL 0-0.006-0.00119.5600.0010.0010.0000.0000.0000.000
148A150ILE 0-0.006-0.00317.351-0.005-0.0050.0000.0000.0000.000
149A151ASP -1-0.916-0.92517.535-0.105-0.1050.0000.0000.0000.000
150A152ALA 00.000-0.01718.7030.0030.0030.0000.0000.0000.000
151A153VAL 0-0.009-0.01514.1300.0140.0140.0000.0000.0000.000
152A154SER 0-0.003-0.01113.789-0.014-0.0140.0000.0000.0000.000
153A155ARG 10.9360.96214.0700.0250.0250.0000.0000.0000.000
154A156VAL 0-0.051-0.01614.4650.0190.0190.0000.0000.0000.000
155A157LEU 0-0.0020.0199.3910.0370.0370.0000.0000.0000.000
156A158PRO 00.0280.0177.776-0.008-0.0080.0000.0000.0000.000
157A159GLY 0-0.001-0.0118.754-0.057-0.0570.0000.0000.0000.000
158A160VAL 0-0.032-0.00910.441-0.068-0.0680.0000.0000.0000.000
159A161LEU 00.0450.01813.146-0.005-0.0050.0000.0000.0000.000
160A162SER 0-0.072-0.04615.6790.0170.0170.0000.0000.0000.000
161A163GLU -1-0.910-0.93316.5810.0970.0970.0000.0000.0000.000
162A164PRO 0-0.072-0.05017.928-0.004-0.0040.0000.0000.0000.000
163A165NME 00.0440.03817.2390.0120.0120.0000.0000.0000.000
164A178ACE 0-0.014-0.01933.9010.0000.0000.0000.0000.0000.000
165A179TYR 0-0.007-0.00433.114-0.001-0.0010.0000.0000.0000.000
166A180PRO 0-0.0020.00435.795-0.001-0.0010.0000.0000.0000.000
167A181VAL 00.0350.03033.2410.0020.0020.0000.0000.0000.000
168A182TYR 00.0420.00936.450-0.002-0.0020.0000.0000.0000.000
169A183THR 00.003-0.01734.8150.0010.0010.0000.0000.0000.000
170A184ARG 10.9400.96436.0490.0020.0020.0000.0000.0000.000
171A185PRO 00.0320.01138.8070.0010.0010.0000.0000.0000.000
172A186ARG 10.9841.01942.0180.0020.0020.0000.0000.0000.000
173A187GLU -1-0.900-0.97144.017-0.004-0.0040.0000.0000.0000.000
174A188TYR 00.004-0.00944.877-0.001-0.0010.0000.0000.0000.000
175A189ARG 10.9510.98446.9350.0160.0160.0000.0000.0000.000
176A190GLY 00.0540.03249.7900.0000.0000.0000.0000.0000.000
177A191MET 0-0.037-0.01546.8760.0010.0010.0000.0000.0000.000
178A192LYS 10.9370.97447.0080.0010.0010.0000.0000.0000.000
179A193VAL 0-0.018-0.00541.6070.0000.0000.0000.0000.0000.000
180A194PRO 00.0190.00443.2540.0010.0010.0000.0000.0000.000
181A195GLU -1-0.838-0.92144.1460.0040.0040.0000.0000.0000.000
182A196GLU -1-0.887-0.91945.2190.0060.0060.0000.0000.0000.000
183A197LEU 0-0.106-0.10139.0920.0020.0020.0000.0000.0000.000
184A198LEU 0-0.001-0.04840.7000.0000.0000.0000.0000.0000.000
185A199SER 0-0.0460.00642.1270.0000.0000.0000.0000.0000.000
186A200GLY 0-0.019-0.11741.9170.0000.0000.0000.0000.0000.000
187A201HIS 00.0820.01739.9970.0020.0020.0000.0000.0000.000
188A202HIS 0-0.009-0.02842.5440.0010.0010.0000.0000.0000.000
189A203LYS 10.9151.06542.251-0.010-0.0100.0000.0000.0000.000
190A204LEU 0-0.0020.03837.8840.0000.0000.0000.0000.0000.000
191A205ILE 00.0270.02639.3350.0010.0010.0000.0000.0000.000
192A206GLU -1-0.877-0.95541.7680.0110.0110.0000.0000.0000.000
193A207LEU 0-0.0140.04238.370-0.001-0.0010.0000.0000.0000.000
194A208TRP 00.035-0.00833.365-0.001-0.0010.0000.0000.0000.000
195A209LYN 0-0.0210.00139.4640.0000.0000.0000.0000.0000.000
196A210LEU 00.0460.03440.0380.0000.0000.0000.0000.0000.000
197A211TRP 00.0180.01231.7010.0000.0000.0000.0000.0000.000
198A212HIS 10.8880.93836.549-0.021-0.0210.0000.0000.0000.000
199A213ARG 10.8730.93340.299-0.014-0.0140.0000.0000.0000.000
200A214ILE 00.0270.00741.191-0.001-0.0010.0000.0000.0000.000
201A215GLU -1-0.904-0.93634.4400.0160.0160.0000.0000.0000.000
202A216ASN 00.006-0.01638.4280.0000.0000.0000.0000.0000.000
203A217THR 0-0.064-0.04740.956-0.002-0.0020.0000.0000.0000.000
204A218VAL 00.0290.00238.122-0.001-0.0010.0000.0000.0000.000
205A219LYS 10.9190.98333.700-0.012-0.0120.0000.0000.0000.000
206A220LYS 10.9160.95839.181-0.009-0.0090.0000.0000.0000.000
207A221ARG 10.9260.98841.878-0.002-0.0020.0000.0000.0000.000
208A222PRO 0-0.0100.00039.231-0.001-0.0010.0000.0000.0000.000
209A223ASP -1-0.833-0.91240.763-0.011-0.0110.0000.0000.0000.000
210A224LEU 0-0.072-0.06843.6690.0000.0000.0000.0000.0000.000
211A225ILE 00.0100.02147.3330.0010.0010.0000.0000.0000.000
212A226PRO 0-0.047-0.03747.8120.0000.0000.0000.0000.0000.000
213A227LYS 10.9891.01542.0310.0070.0070.0000.0000.0000.000
214A228ASP -1-0.842-0.93746.961-0.003-0.0030.0000.0000.0000.000
215A229LEU 00.0470.02548.8580.0010.0010.0000.0000.0000.000
216A230THR 0-0.078-0.04350.5460.0000.0000.0000.0000.0000.000
217A231GLU -1-0.942-1.01645.402-0.002-0.0020.0000.0000.0000.000
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