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: 6N5NZ

Calculation Name: 1OYS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OYS

Chain ID: A

ChEMBL ID:

UniProt ID: P28619

Base Structure: X-ray

Registration Date: 2023-06-26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2476667.996018
FMO2-HF: Nuclear repulsion 2392886.957191
FMO2-HF: Total energy -83781.038826
FMO2-MP2: Total energy -84023.870316


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.45-2.4132.522-1.569-3.99-0.003
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.035
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].
3A3HIS0-0.103-0.0723.687-0.2991.015-0.005-0.554-0.7550.001
4A4ASP-1-0.862-0.9226.1320.0550.0550.0000.0000.0000.000
5A5GLY0-0.047-0.0114.224-0.0170.105-0.001-0.010-0.1110.000
6A6ARG10.6950.8435.0710.8260.983-0.001-0.008-0.1480.000
7A7GLN00.0210.0034.2662.7222.9570.003-0.059-0.1790.000
8A8HIS00.0390.0094.726-0.633-0.507-0.001-0.009-0.1160.000
9A9ASP-1-0.899-0.9665.7380.4130.4130.0000.0000.0000.000
10A10GLU-1-0.883-0.9278.3351.0381.0380.0000.0000.0000.000
11A11LEU0-0.0330.00410.026-0.117-0.1170.0000.0000.0000.000
12A12ARG10.8010.87612.2870.3630.3630.0000.0000.0000.000
13A13PRO0-0.002-0.01813.3640.0130.0130.0000.0000.0000.000
14A14ILE00.0250.01616.421-0.042-0.0420.0000.0000.0000.000
15A15THR0-0.091-0.04419.6570.0160.0160.0000.0000.0000.000
16A16PHE0-0.008-0.02323.087-0.014-0.0140.0000.0000.0000.000
17A17ASP-1-0.833-0.92026.494-0.039-0.0390.0000.0000.0000.000
18A18LEU0-0.041-0.02828.902-0.006-0.0060.0000.0000.0000.000
19A19ASP-1-0.923-0.95931.942-0.021-0.0210.0000.0000.0000.000
20A20PHE0-0.023-0.00830.084-0.005-0.0050.0000.0000.0000.000
21A21ILE0-0.047-0.01932.809-0.005-0.0050.0000.0000.0000.000
22A22SER0-0.008-0.00636.6490.0020.0020.0000.0000.0000.000
23A23HIS00.0040.01040.0250.0050.0050.0000.0000.0000.000
24A24PRO0-0.021-0.02241.0650.0010.0010.0000.0000.0000.000
25A25GLU-1-0.911-0.97038.767-0.049-0.0490.0000.0000.0000.000
26A26GLY0-0.071-0.03737.7390.0020.0020.0000.0000.0000.000
27A27SER00.0010.00134.741-0.001-0.0010.0000.0000.0000.000
28A28VAL00.0270.01728.9040.0050.0050.0000.0000.0000.000
29A29LEU0-0.0300.01026.623-0.010-0.0100.0000.0000.0000.000
30A30ILE0-0.023-0.00522.6200.0100.0100.0000.0000.0000.000
31A31THR0-0.034-0.02520.113-0.021-0.0210.0000.0000.0000.000
32A32ALA00.0530.03017.6370.0290.0290.0000.0000.0000.000
33A33GLY00.0360.02715.588-0.044-0.0440.0000.0000.0000.000
34A34ASN0-0.074-0.04614.9560.0660.0660.0000.0000.0000.000
35A35THR00.0040.00118.352-0.003-0.0030.0000.0000.0000.000
36A36LYS10.8860.93120.5080.1490.1490.0000.0000.0000.000
37A37VAL0-0.016-0.01523.871-0.011-0.0110.0000.0000.0000.000
38A38ILE00.0310.02826.7920.0120.0120.0000.0000.0000.000
39A39CYS0-0.048-0.00328.928-0.005-0.0050.0000.0000.0000.000
40A40ASN00.0390.01731.8020.0110.0110.0000.0000.0000.000
41A41ALA00.0160.02235.466-0.002-0.0020.0000.0000.0000.000
42A42SER0-0.021-0.00837.6090.0040.0040.0000.0000.0000.000
43A43VAL0-0.006-0.00441.3480.0000.0000.0000.0000.0000.000
44A44GLU-1-0.759-0.84144.062-0.038-0.0380.0000.0000.0000.000
45A45ASP-1-0.828-0.90447.146-0.021-0.0210.0000.0000.0000.000
46A46ARG10.7770.86148.8520.0370.0370.0000.0000.0000.000
47A47VAL00.0740.04146.886-0.001-0.0010.0000.0000.0000.000
48A48PRO00.0450.02745.3000.0000.0000.0000.0000.0000.000
49A49PRO00.0520.00548.5270.0020.0020.0000.0000.0000.000
50A50PHE0-0.048-0.02044.7850.0020.0020.0000.0000.0000.000
51A51LEU00.001-0.00545.8620.0010.0010.0000.0000.0000.000
52A52ARG10.8420.93850.5890.0320.0320.0000.0000.0000.000
53A53GLY0-0.032-0.01753.4600.0000.0000.0000.0000.0000.000
54A54GLY0-0.040-0.02452.0210.0020.0020.0000.0000.0000.000
55A55GLY0-0.023-0.01852.1060.0020.0020.0000.0000.0000.000
56A56LYS10.8060.89046.9200.0140.0140.0000.0000.0000.000
57A57GLY00.0400.02545.267-0.002-0.0020.0000.0000.0000.000
58A58TRP0-0.062-0.04841.3760.0000.0000.0000.0000.0000.000
59A59ILE00.0600.04836.7130.0010.0010.0000.0000.0000.000
60A60THR0-0.041-0.02338.204-0.002-0.0020.0000.0000.0000.000
61A61ALA00.0130.00534.3470.0020.0020.0000.0000.0000.000
62A62GLU-1-0.879-0.92436.236-0.077-0.0770.0000.0000.0000.000
63A63TYR00.000-0.02126.277-0.004-0.0040.0000.0000.0000.000
64A64SER0-0.025-0.03032.4040.0000.0000.0000.0000.0000.000
65A65MET00.0000.01425.289-0.017-0.0170.0000.0000.0000.000
66A85GLY00.0410.01333.990-0.002-0.0020.0000.0000.0000.000
67A86ARG10.9840.97323.7760.2170.2170.0000.0000.0000.000
68A87THR00.0450.03030.324-0.004-0.0040.0000.0000.0000.000
69A88MET00.0330.01131.8830.0060.0060.0000.0000.0000.000
70A89GLU-1-0.857-0.91027.561-0.149-0.1490.0000.0000.0000.000
71A90ILE00.0270.01626.5680.0060.0060.0000.0000.0000.000
72A91GLN0-0.0040.00629.9380.0020.0020.0000.0000.0000.000
73A92ARG10.8820.92833.2720.0980.0980.0000.0000.0000.000
74A93LEU0-0.030-0.00226.4170.0070.0070.0000.0000.0000.000
75A94ILE00.0550.02829.1150.0080.0080.0000.0000.0000.000
76A95GLY0-0.003-0.00131.4170.0080.0080.0000.0000.0000.000
77A96ARG10.7490.85730.4450.0840.0840.0000.0000.0000.000
78A97ALA00.0420.01329.5850.0070.0070.0000.0000.0000.000
79A98LEU00.0350.01131.4570.0080.0080.0000.0000.0000.000
80A99ARG10.8190.90433.6540.0520.0520.0000.0000.0000.000
81A100ALA0-0.0260.00732.9700.0040.0040.0000.0000.0000.000
82A101VAL0-0.0180.00331.7350.0050.0050.0000.0000.0000.000
83A102VAL00.000-0.00634.9950.0030.0030.0000.0000.0000.000
84A103ASP-1-0.814-0.90038.333-0.007-0.0070.0000.0000.0000.000
85A104LEU00.003-0.02740.4430.0000.0000.0000.0000.0000.000
86A105GLU-1-0.880-0.91843.487-0.009-0.0090.0000.0000.0000.000
87A106LYS10.8290.91543.9960.0000.0000.0000.0000.0000.000
88A107LEU0-0.0210.01341.9660.0010.0010.0000.0000.0000.000
89A108GLY00.0200.02045.326-0.001-0.0010.0000.0000.0000.000
90A109GLU-1-0.827-0.91347.546-0.023-0.0230.0000.0000.0000.000
91A110ARG10.8050.89345.6350.0180.0180.0000.0000.0000.000
92A111THR0-0.006-0.02143.0610.0000.0000.0000.0000.0000.000
93A112ILE0-0.041-0.02438.8150.0000.0000.0000.0000.0000.000
94A113TRP0-0.076-0.05439.823-0.003-0.0030.0000.0000.0000.000
95A114ILE00.013-0.00933.1380.0020.0020.0000.0000.0000.000
96A115ASP-1-0.918-0.95235.386-0.082-0.0820.0000.0000.0000.000
97A116CYS0-0.036-0.03329.8950.0030.0030.0000.0000.0000.000
98A117ASP-1-0.783-0.87031.086-0.118-0.1180.0000.0000.0000.000
99A118VAL0-0.053-0.03825.188-0.002-0.0020.0000.0000.0000.000
100A119ILE0-0.0050.00026.503-0.004-0.0040.0000.0000.0000.000
101A120GLN0-0.087-0.05520.9680.0020.0020.0000.0000.0000.000
102A121ALA0-0.026-0.01822.1120.0080.0080.0000.0000.0000.000
103A122ASP-1-0.779-0.89915.688-0.540-0.5400.0000.0000.0000.000
104A123GLY00.1230.08316.317-0.036-0.0360.0000.0000.0000.000
105A124GLY00.0850.05117.4040.0410.0410.0000.0000.0000.000
106A125THR00.0130.00718.7840.0390.0390.0000.0000.0000.000
107A126ARG10.8620.93422.3260.2020.2020.0000.0000.0000.000
108A127THR00.0350.01819.3450.0160.0160.0000.0000.0000.000
109A128ALA00.0540.02920.9990.0250.0250.0000.0000.0000.000
110A129SER00.011-0.02922.7100.0170.0170.0000.0000.0000.000
111A130ILE0-0.027-0.00425.2800.0130.0130.0000.0000.0000.000
112A131THR00.0280.01623.0740.0160.0160.0000.0000.0000.000
113A132GLY00.0450.01225.7960.0110.0110.0000.0000.0000.000
114A133ALA00.000-0.01727.7510.0070.0070.0000.0000.0000.000
115A134PHE0-0.023-0.01029.0540.0060.0060.0000.0000.0000.000
116A135LEU00.0300.02827.4220.0060.0060.0000.0000.0000.000
117A136ALA00.0600.03831.3230.0040.0040.0000.0000.0000.000
118A137MET0-0.017-0.00433.7880.0020.0020.0000.0000.0000.000
119A138ALA0-0.014-0.00633.8500.0030.0030.0000.0000.0000.000
120A139ILE00.0090.00233.5330.0040.0040.0000.0000.0000.000
121A140ALA0-0.040-0.01937.1080.0020.0020.0000.0000.0000.000
122A141ILE00.021-0.00838.1670.0020.0020.0000.0000.0000.000
123A142GLY00.0220.01739.6210.0030.0030.0000.0000.0000.000
124A143LYS10.8920.94440.4690.0260.0260.0000.0000.0000.000
125A144LEU00.0200.02143.4410.0010.0010.0000.0000.0000.000
126A145ILE0-0.021-0.01541.9040.0010.0010.0000.0000.0000.000
127A146LYS10.9160.95641.7820.0020.0020.0000.0000.0000.000
128A147ALA0-0.0260.00646.8450.0010.0010.0000.0000.0000.000
129A148GLY0-0.021-0.00248.9820.0000.0000.0000.0000.0000.000
130A149THR0-0.049-0.02148.4260.0000.0000.0000.0000.0000.000
131A150ILE0-0.020-0.00744.0940.0000.0000.0000.0000.0000.000
132A151LYS10.9530.97048.3970.0030.0030.0000.0000.0000.000
133A152THR0-0.009-0.00445.6220.0020.0020.0000.0000.0000.000
134A153ASN00.0400.00938.625-0.005-0.0050.0000.0000.0000.000
135A154PRO0-0.0190.00040.6840.0020.0020.0000.0000.0000.000
136A155ILE00.0020.01734.941-0.001-0.0010.0000.0000.0000.000
137A156THR00.001-0.01735.6210.0030.0030.0000.0000.0000.000
138A157ASP-1-0.810-0.87931.6200.0260.0260.0000.0000.0000.000
139A158PHE0-0.010-0.00828.754-0.004-0.0040.0000.0000.0000.000
140A159LEU00.0010.00527.5210.0010.0010.0000.0000.0000.000
141A160ALA00.0060.01923.212-0.002-0.0020.0000.0000.0000.000
142A161ALA0-0.019-0.01022.6050.0010.0010.0000.0000.0000.000
143A162ILE00.0090.00715.639-0.003-0.0030.0000.0000.0000.000
144A163SER00.0130.00816.2600.0130.0130.0000.0000.0000.000
145A164VAL0-0.022-0.01713.6340.0150.0150.0000.0000.0000.000
146A165GLY00.0590.02012.3720.0010.0010.0000.0000.0000.000
147A166ILE0-0.040-0.02010.4890.0280.0280.0000.0000.0000.000
148A167ASP-1-0.725-0.8685.937-2.471-2.4710.0000.0000.0000.000
149A168LYS10.8240.9078.7340.5990.5990.0000.0000.0000.000
150A169GLU-1-0.989-0.9994.833-1.294-1.2940.0000.0000.0000.000
151A170GLN0-0.063-0.0412.119-1.953-1.0402.528-0.921-2.520-0.004
152A171GLY0-0.0130.0124.3360.1820.352-0.001-0.008-0.1610.000
153A172ILE0-0.041-0.0147.223-0.222-0.2220.0000.0000.0000.000
154A173LEU00.0190.0114.9360.0800.0800.0000.0000.0000.000
155A174LEU0-0.014-0.0168.9580.0750.0750.0000.0000.0000.000
156A175ASP-1-0.829-0.90010.619-0.190-0.1900.0000.0000.0000.000
157A176LEU00.0260.03310.530-0.023-0.0230.0000.0000.0000.000
158A177ASN0-0.026-0.01410.2960.1060.1060.0000.0000.0000.000
159A178TYR0-0.040-0.02313.623-0.023-0.0230.0000.0000.0000.000
160A179GLU-1-0.862-0.9259.706-1.914-1.9140.0000.0000.0000.000
161A180GLU-1-0.747-0.8557.644-1.404-1.4040.0000.0000.0000.000
162A181ASP-1-1.006-1.00710.917-0.404-0.4040.0000.0000.0000.000
163A182SER0-0.066-0.03614.1330.0440.0440.0000.0000.0000.000
164A183SER0-0.052-0.02210.6410.0260.0260.0000.0000.0000.000
165A184ALA00.0020.02611.695-0.063-0.0630.0000.0000.0000.000
166A185GLU-1-0.869-0.93112.352-0.291-0.2910.0000.0000.0000.000
167A186VAL0-0.065-0.03813.9380.0960.0960.0000.0000.0000.000
168A187ASP-1-0.816-0.88814.430-0.390-0.3900.0000.0000.0000.000
169A188MET0-0.011-0.01216.8100.0660.0660.0000.0000.0000.000
170A189ASN0-0.059-0.01318.020-0.002-0.0020.0000.0000.0000.000
171A190VAL00.004-0.00419.5040.0180.0180.0000.0000.0000.000
172A191ILE00.0160.00122.0230.0000.0000.0000.0000.0000.000
173A192MET00.0170.00922.9840.0010.0010.0000.0000.0000.000
174A193THR0-0.009-0.01325.844-0.003-0.0030.0000.0000.0000.000
175A194GLY00.0460.01927.0000.0060.0060.0000.0000.0000.000
176A195SER0-0.162-0.10328.0430.0080.0080.0000.0000.0000.000
177A196GLY00.0520.02526.1600.0050.0050.0000.0000.0000.000
178A197ARG10.8830.95527.130-0.016-0.0160.0000.0000.0000.000
179A198PHE00.0330.00623.042-0.004-0.0040.0000.0000.0000.000
180A199VAL0-0.071-0.02227.6950.0010.0010.0000.0000.0000.000
181A200GLU-1-0.841-0.93827.216-0.084-0.0840.0000.0000.0000.000
182A201LEU0-0.0190.00421.9320.0020.0020.0000.0000.0000.000
183A202GLN0-0.020-0.00723.248-0.004-0.0040.0000.0000.0000.000
184A203GLY00.0360.01820.504-0.016-0.0160.0000.0000.0000.000
185A204THR0-0.069-0.03720.0230.0320.0320.0000.0000.0000.000
186A205GLY0-0.0040.00218.840-0.030-0.0300.0000.0000.0000.000
187A206GLU-1-0.912-0.96717.744-0.296-0.2960.0000.0000.0000.000
188A207GLU-1-1.004-0.97919.084-0.217-0.2170.0000.0000.0000.000
189A208ALA0-0.021-0.01117.0300.0110.0110.0000.0000.0000.000
190A209THR0-0.049-0.03318.8850.0160.0160.0000.0000.0000.000
191A210PHE0-0.015-0.00417.1990.0020.0020.0000.0000.0000.000
192A211SER0-0.048-0.04617.6150.0190.0190.0000.0000.0000.000
193A212ARG10.9550.95819.570-0.042-0.0420.0000.0000.0000.000
194A213GLU-1-0.907-0.96517.5420.0790.0790.0000.0000.0000.000
195A214ASP-1-0.766-0.84414.5020.0230.0230.0000.0000.0000.000
196A215LEU0-0.015-0.00316.090-0.011-0.0110.0000.0000.0000.000
197A216ASN0-0.047-0.03818.652-0.015-0.0150.0000.0000.0000.000
198A217GLY00.0200.01614.5350.0150.0150.0000.0000.0000.000
199A218LEU00.004-0.00113.1930.0090.0090.0000.0000.0000.000
200A219LEU0-0.026-0.02615.441-0.006-0.0060.0000.0000.0000.000
201A220GLY00.0130.02117.1540.0050.0050.0000.0000.0000.000
202A221LEU00.0190.00610.0060.0240.0240.0000.0000.0000.000
203A222ALA00.0200.00114.5950.0050.0050.0000.0000.0000.000
204A223GLU-1-0.913-0.95817.0670.0740.0740.0000.0000.0000.000
205A224LYS10.7840.88612.794-0.322-0.3220.0000.0000.0000.000
206A225GLY00.0420.01616.2630.0070.0070.0000.0000.0000.000
207A226ILE0-0.010-0.02016.803-0.010-0.0100.0000.0000.0000.000
208A227GLN0-0.044-0.02620.3170.0080.0080.0000.0000.0000.000
209A228GLU-1-0.838-0.89815.8640.2130.2130.0000.0000.0000.000
210A229LEU0-0.033-0.01419.389-0.009-0.0090.0000.0000.0000.000
211A230ILE0-0.021-0.01721.729-0.006-0.0060.0000.0000.0000.000
212A231ASP-1-0.858-0.91423.0800.0830.0830.0000.0000.0000.000
213A232LYS10.9110.94121.263-0.074-0.0740.0000.0000.0000.000
214A233GLN0-0.037-0.03124.853-0.001-0.0010.0000.0000.0000.000
215A234LYS10.8240.90726.883-0.063-0.0630.0000.0000.0000.000
216A235GLU-1-0.915-0.93725.2080.0620.0620.0000.0000.0000.000
217A236VAL0-0.042-0.00427.517-0.003-0.0030.0000.0000.0000.000
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