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: QYV5Y

Calculation Name: 1OYZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OYZ

Chain ID: A

ChEMBL ID:

UniProt ID: P0ADK6

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptH
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 276
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3617929.570985
FMO2-HF: Nuclear repulsion 3507078.426429
FMO2-HF: Total energy -110851.144556
FMO2-MP2: Total energy -111172.93783


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:5:TYR)


Summations of interaction energy for fragment #1(A:5:TYR)
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.
-5.504-3.836-0.013-0.761-0.8950.002
Interaction energy analysis for fragmet #1(A:5:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.023
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].
3A7LYS10.9510.9823.570-2.708-1.040-0.013-0.761-0.8950.002
4A8ARG10.9770.9796.467-0.894-0.8940.0000.0000.0000.000
5A9LYS10.9550.9799.662-0.737-0.7370.0000.0000.0000.000
6A10ALA00.0340.02112.6780.0090.0090.0000.0000.0000.000
7A11SER00.0270.00616.276-0.007-0.0070.0000.0000.0000.000
8A12LYS11.0080.98716.083-0.373-0.3730.0000.0000.0000.000
9A13GLU-1-0.879-0.93220.4880.2280.2280.0000.0000.0000.000
10A14TYR0-0.041-0.01221.025-0.019-0.0190.0000.0000.0000.000
11A15GLY00.0410.01723.062-0.015-0.0150.0000.0000.0000.000
12A16LEU00.0430.02425.063-0.014-0.0140.0000.0000.0000.000
13A17TYR00.0290.00725.173-0.007-0.0070.0000.0000.0000.000
14A18ASN00.022-0.01524.024-0.009-0.0090.0000.0000.0000.000
15A19GLN0-0.079-0.04528.025-0.006-0.0060.0000.0000.0000.000
16A20CYS00.0230.02230.998-0.009-0.0090.0000.0000.0000.000
17A21LYS10.9300.97426.906-0.175-0.1750.0000.0000.0000.000
18A22LYS10.8740.93930.307-0.125-0.1250.0000.0000.0000.000
19A23LEU0-0.0090.02634.598-0.005-0.0050.0000.0000.0000.000
20A24ASN00.0280.01337.2850.0040.0040.0000.0000.0000.000
21A25ASP-1-0.840-0.94539.4860.1040.1040.0000.0000.0000.000
22A26ASP-1-0.906-0.94740.8380.0810.0810.0000.0000.0000.000
23A27GLU-1-0.871-0.94240.3040.0880.0880.0000.0000.0000.000
24A28LEU0-0.065-0.03135.5030.0040.0040.0000.0000.0000.000
25A29PHE00.036-0.00338.8340.0040.0040.0000.0000.0000.000
26A30ARG11.0011.01841.445-0.084-0.0840.0000.0000.0000.000
27A31LEU0-0.041-0.02836.1000.0010.0010.0000.0000.0000.000
28A32LEU0-0.038-0.01036.9170.0060.0060.0000.0000.0000.000
29A33ASP-1-0.816-0.87038.9150.0970.0970.0000.0000.0000.000
30A34ASP-1-0.900-0.94837.3420.1070.1070.0000.0000.0000.000
31A35HIS00.0500.00738.9440.0060.0060.0000.0000.0000.000
32A36ASN0-0.045-0.02331.9140.0110.0110.0000.0000.0000.000
33A37SER00.041-0.01131.718-0.001-0.0010.0000.0000.0000.000
34A38LEU00.0360.02626.7620.0010.0010.0000.0000.0000.000
35A39LYS10.9380.97030.506-0.109-0.1090.0000.0000.0000.000
36A40ARG10.9401.00733.136-0.130-0.1300.0000.0000.0000.000
37A41ILE00.0380.02028.5400.0000.0000.0000.0000.0000.000
38A42SER0-0.033-0.02329.0710.0080.0080.0000.0000.0000.000
39A43SER00.0010.00130.3720.0020.0020.0000.0000.0000.000
40A44ALA00.0720.03633.112-0.002-0.0020.0000.0000.0000.000
41A45ARG10.9280.97223.840-0.234-0.2340.0000.0000.0000.000
42A46VAL0-0.059-0.03030.6040.0030.0030.0000.0000.0000.000
43A47LEU00.0280.01231.913-0.003-0.0030.0000.0000.0000.000
44A48GLN0-0.071-0.03130.4160.0030.0030.0000.0000.0000.000
45A49LEU0-0.081-0.03627.9270.0010.0010.0000.0000.0000.000
46A50ARG10.8070.90431.215-0.119-0.1190.0000.0000.0000.000
47A51GLY00.002-0.00234.291-0.006-0.0060.0000.0000.0000.000
48A52GLY00.0730.03936.8490.0000.0000.0000.0000.0000.000
49A53GLN0-0.020-0.02640.153-0.001-0.0010.0000.0000.0000.000
50A54ASP-1-0.840-0.91443.4990.0820.0820.0000.0000.0000.000
51A55ALA00.006-0.00539.2050.0010.0010.0000.0000.0000.000
52A56VAL0-0.045-0.02439.9200.0020.0020.0000.0000.0000.000
53A57ARG10.9180.95941.795-0.079-0.0790.0000.0000.0000.000
54A58LEU00.0630.05342.234-0.001-0.0010.0000.0000.0000.000
55A59ALA0-0.009-0.00340.2730.0000.0000.0000.0000.0000.000
56A60ILE00.007-0.01342.1100.0010.0010.0000.0000.0000.000
57A61GLU-1-0.913-0.95944.7340.0790.0790.0000.0000.0000.000
58A62PHE0-0.001-0.00941.393-0.001-0.0010.0000.0000.0000.000
59A63CYS0-0.064-0.02142.4650.0030.0030.0000.0000.0000.000
60A64SER0-0.045-0.02844.322-0.001-0.0010.0000.0000.0000.000
61A65ASP-1-0.823-0.89345.7200.0810.0810.0000.0000.0000.000
62A66LYS10.9840.99147.175-0.068-0.0680.0000.0000.0000.000
63A67ASN0-0.012-0.02643.2720.0030.0030.0000.0000.0000.000
64A68TYR00.0440.00739.3260.0040.0040.0000.0000.0000.000
65A69ILE0-0.0070.00638.4100.0050.0050.0000.0000.0000.000
66A70ARG10.7950.86839.426-0.083-0.0830.0000.0000.0000.000
67A71ARG10.7470.84541.110-0.094-0.0940.0000.0000.0000.000
68A72ASP-1-0.877-0.89635.6020.1510.1510.0000.0000.0000.000
69A73ILE00.0360.00834.8080.0070.0070.0000.0000.0000.000
70A74GLY00.0180.01237.1200.0040.0040.0000.0000.0000.000
71A75ALA00.0720.02038.0090.0020.0020.0000.0000.0000.000
72A76PHE00.0050.02929.1610.0060.0060.0000.0000.0000.000
73A77ILE0-0.033-0.00834.0270.0080.0080.0000.0000.0000.000
74A78LEU00.023-0.01235.2280.0040.0040.0000.0000.0000.000
75A79GLY00.0320.03533.943-0.001-0.0010.0000.0000.0000.000
76A80GLN0-0.088-0.07027.5770.0050.0050.0000.0000.0000.000
77A81ILE00.0040.05532.3820.0020.0020.0000.0000.0000.000
78A82LYS10.9390.96232.312-0.142-0.1420.0000.0000.0000.000
79A83ILE00.0390.03636.087-0.005-0.0050.0000.0000.0000.000
80A84CYS0-0.033-0.01139.6650.0020.0020.0000.0000.0000.000
81A85LYS11.0530.99239.302-0.110-0.1100.0000.0000.0000.000
82A86LYS10.9530.96943.156-0.083-0.0830.0000.0000.0000.000
83A87CYS00.0220.02244.027-0.004-0.0040.0000.0000.0000.000
84A88GLU-1-0.907-0.96238.3730.1260.1260.0000.0000.0000.000
85A89ASP-1-0.780-0.86942.2630.1030.1030.0000.0000.0000.000
86A90ASN0-0.021-0.01444.4710.0020.0020.0000.0000.0000.000
87A91VAL00.0270.01640.0220.0000.0000.0000.0000.0000.000
88A92PHE00.0270.02138.3940.0030.0030.0000.0000.0000.000
89A93ASN00.000-0.01841.6840.0040.0040.0000.0000.0000.000
90A94ILE0-0.031-0.00543.330-0.001-0.0010.0000.0000.0000.000
91A95LEU0-0.013-0.01638.1760.0000.0000.0000.0000.0000.000
92A96ASN0-0.023-0.01641.203-0.003-0.0030.0000.0000.0000.000
93A97ASN00.0120.00742.353-0.001-0.0010.0000.0000.0000.000
94A98MET0-0.0070.00341.617-0.001-0.0010.0000.0000.0000.000
95A99ALA0-0.017-0.01339.3040.0000.0000.0000.0000.0000.000
96A100LEU0-0.048-0.02040.8030.0010.0010.0000.0000.0000.000
97A101ASN0-0.040-0.02443.827-0.004-0.0040.0000.0000.0000.000
98A102ASP-1-0.758-0.83142.6980.0990.0990.0000.0000.0000.000
99A103LYS10.9820.97644.216-0.075-0.0750.0000.0000.0000.000
100A104SER0-0.0420.00240.6630.0010.0010.0000.0000.0000.000
101A105ALA00.0580.01038.8320.0030.0030.0000.0000.0000.000
102A106CYS0-0.065-0.03036.3370.0060.0060.0000.0000.0000.000
103A107VAL00.0360.02636.5020.0060.0060.0000.0000.0000.000
104A108ARG10.7880.88838.165-0.107-0.1070.0000.0000.0000.000
105A109ALA00.008-0.00133.5900.0030.0030.0000.0000.0000.000
106A110THR00.014-0.02533.4270.0100.0100.0000.0000.0000.000
107A111ALA0-0.0120.00034.5140.0050.0050.0000.0000.0000.000
108A112ILE00.0130.01434.2010.0010.0010.0000.0000.0000.000
109A113GLU-1-0.880-0.94329.9680.2060.2060.0000.0000.0000.000
110A114SER0-0.051-0.06332.2160.0100.0100.0000.0000.0000.000
111A115THR0-0.086-0.03634.280-0.001-0.0010.0000.0000.0000.000
112A116ALA00.0560.02631.488-0.002-0.0020.0000.0000.0000.000
113A117GLN0-0.028-0.00627.9570.0080.0080.0000.0000.0000.000
114A118ARG10.7810.86631.605-0.141-0.1410.0000.0000.0000.000
115A119CYS00.0280.03834.082-0.006-0.0060.0000.0000.0000.000
116A120LYS10.9780.99824.469-0.280-0.2800.0000.0000.0000.000
117A121LYS10.8080.90330.700-0.173-0.1730.0000.0000.0000.000
118A122ASN0-0.013-0.00432.565-0.005-0.0050.0000.0000.0000.000
119A123PRO00.0760.03033.833-0.005-0.0050.0000.0000.0000.000
120A124ILE00.0140.03236.363-0.003-0.0030.0000.0000.0000.000
121A125TYR0-0.094-0.06737.956-0.004-0.0040.0000.0000.0000.000
122A126SER00.032-0.00636.7970.0030.0030.0000.0000.0000.000
123A127PRO00.0250.01638.4320.0010.0010.0000.0000.0000.000
124A128LYS10.9810.97641.698-0.101-0.1010.0000.0000.0000.000
125A129ILE00.0220.02635.497-0.002-0.0020.0000.0000.0000.000
126A130VAL00.0090.01137.9970.0020.0020.0000.0000.0000.000
127A131GLU-1-0.967-0.98639.6730.0940.0940.0000.0000.0000.000
128A132GLN00.0110.01237.751-0.008-0.0080.0000.0000.0000.000
129A133SER0-0.017-0.04737.1390.0030.0030.0000.0000.0000.000
130A134GLN0-0.015-0.01139.096-0.003-0.0030.0000.0000.0000.000
131A135ILE00.0350.02841.939-0.004-0.0040.0000.0000.0000.000
132A136THR00.0120.00737.566-0.002-0.0020.0000.0000.0000.000
133A137ALA0-0.0280.00037.3350.0040.0040.0000.0000.0000.000
134A138PHE0-0.039-0.03038.3150.0010.0010.0000.0000.0000.000
135A139ASP-1-0.760-0.84639.1730.1110.1110.0000.0000.0000.000
136A140LYS10.9900.98539.923-0.098-0.0980.0000.0000.0000.000
137A141SER0-0.055-0.04337.3090.0040.0040.0000.0000.0000.000
138A142THR00.0400.00633.3670.0020.0020.0000.0000.0000.000
139A143ASN0-0.031-0.00932.4610.0030.0030.0000.0000.0000.000
140A144VAL00.0290.03033.1010.0090.0090.0000.0000.0000.000
141A145ARG10.8010.89234.916-0.131-0.1310.0000.0000.0000.000
142A146ARG10.9650.98127.479-0.205-0.2050.0000.0000.0000.000
143A147ALA00.0210.01430.5030.0100.0100.0000.0000.0000.000
144A148THR0-0.045-0.04231.8400.0000.0000.0000.0000.0000.000
145A149ALA00.0160.00929.5380.0000.0000.0000.0000.0000.000
146A150PHE0-0.0180.00526.0090.0060.0060.0000.0000.0000.000
147A151ALA00.0190.02829.1020.0050.0050.0000.0000.0000.000
148A152ILE00.0100.00932.122-0.001-0.0010.0000.0000.0000.000
149A153SER0-0.034-0.04227.0480.0050.0050.0000.0000.0000.000
150A154VAL0-0.114-0.04928.5080.0090.0090.0000.0000.0000.000
151A155ILE0-0.061-0.01730.020-0.007-0.0070.0000.0000.0000.000
152A156ASN00.0410.04932.454-0.002-0.0020.0000.0000.0000.000
153A157ASP-1-0.877-0.98234.5740.1240.1240.0000.0000.0000.000
154A158LYS10.9210.95537.719-0.105-0.1050.0000.0000.0000.000
155A159ALA0-0.0130.01937.307-0.005-0.0050.0000.0000.0000.000
156A160THR00.005-0.02334.892-0.001-0.0010.0000.0000.0000.000
157A161ILE00.0260.02334.8700.0010.0010.0000.0000.0000.000
158A162PRO00.0350.00936.3700.0030.0030.0000.0000.0000.000
159A163LEU0-0.014-0.00336.791-0.001-0.0010.0000.0000.0000.000
160A164LEU00.0240.00531.5390.0010.0010.0000.0000.0000.000
161A165ILE00.0400.01634.0490.0030.0030.0000.0000.0000.000
162A166ASN0-0.032-0.02336.001-0.005-0.0050.0000.0000.0000.000
163A167LEU0-0.031-0.01332.932-0.001-0.0010.0000.0000.0000.000
164A168LEU00.0230.01830.4040.0060.0060.0000.0000.0000.000
165A169LYS10.9200.96133.134-0.110-0.1100.0000.0000.0000.000
166A170ASP-1-0.756-0.82533.1850.1400.1400.0000.0000.0000.000
167A171PRO00.0210.00234.0460.0040.0040.0000.0000.0000.000
168A172ASN0-0.052-0.04530.0620.0140.0140.0000.0000.0000.000
169A173GLY00.0430.00228.5790.0020.0020.0000.0000.0000.000
170A174ASP-1-0.891-0.94325.6020.2680.2680.0000.0000.0000.000
171A175VAL0-0.042-0.02227.0810.0110.0110.0000.0000.0000.000
172A176ARG10.7280.83829.292-0.159-0.1590.0000.0000.0000.000
173A177ASN00.0850.04021.754-0.006-0.0060.0000.0000.0000.000
174A178TRP00.0140.00624.1530.0140.0140.0000.0000.0000.000
175A179ALA0-0.032-0.00326.4600.0030.0030.0000.0000.0000.000
176A180ALA00.0470.00626.529-0.001-0.0010.0000.0000.0000.000
177A181PHE00.0250.03018.7870.0030.0030.0000.0000.0000.000
178A182ALA0-0.015-0.02524.4600.0100.0100.0000.0000.0000.000
179A183ILE0-0.061-0.02826.687-0.008-0.0080.0000.0000.0000.000
180A184ASN00.010-0.01823.606-0.033-0.0330.0000.0000.0000.000
181A185ILE0-0.053-0.01420.9430.0020.0020.0000.0000.0000.000
182A186ASN0-0.050-0.02324.4380.0110.0110.0000.0000.0000.000
183A187LYS10.8950.94824.580-0.258-0.2580.0000.0000.0000.000
184A188TYR0-0.0210.00228.371-0.014-0.0140.0000.0000.0000.000
185A189ASP-1-0.757-0.89031.1850.1390.1390.0000.0000.0000.000
186A190ASN00.0160.01533.512-0.007-0.0070.0000.0000.0000.000
187A191SER00.0730.02436.0690.0020.0020.0000.0000.0000.000
188A192ASP-1-0.895-0.93037.6560.1010.1010.0000.0000.0000.000
189A193ILE0-0.070-0.02731.8880.0040.0040.0000.0000.0000.000
190A194ARG10.8240.89232.644-0.114-0.1140.0000.0000.0000.000
191A195ASP-1-0.829-0.92233.7690.0980.0980.0000.0000.0000.000
192A196CYS0-0.079-0.04634.033-0.001-0.0010.0000.0000.0000.000
193A197PHE00.006-0.00327.8290.0060.0060.0000.0000.0000.000
194A198VAL00.005-0.01130.9680.0020.0020.0000.0000.0000.000
195A199GLU-1-0.912-0.95132.9390.0960.0960.0000.0000.0000.000
196A200MET0-0.104-0.03229.2850.0040.0040.0000.0000.0000.000
197A201LEU0-0.018-0.00328.0670.0110.0110.0000.0000.0000.000
198A202GLN0-0.012-0.01229.6670.0000.0000.0000.0000.0000.000
199A203ASP-1-0.784-0.83028.5790.1660.1660.0000.0000.0000.000
200A204LYS10.9350.95228.874-0.129-0.1290.0000.0000.0000.000
201A205ASN0-0.051-0.03524.4460.0140.0140.0000.0000.0000.000
202A206GLU-1-0.878-0.94919.1750.3290.3290.0000.0000.0000.000
203A207GLU-1-0.889-0.95319.7840.3580.3580.0000.0000.0000.000
204A208VAL0-0.034-0.00822.0340.0050.0050.0000.0000.0000.000
205A209ARG10.8110.91724.153-0.163-0.1630.0000.0000.0000.000
206A210ILE00.0240.01818.443-0.014-0.0140.0000.0000.0000.000
207A211GLU-1-0.827-0.91620.5970.3550.3550.0000.0000.0000.000
208A212ALA0-0.0080.00623.284-0.011-0.0110.0000.0000.0000.000
209A213ILE00.0150.00522.787-0.015-0.0150.0000.0000.0000.000
210A214ILE00.0090.02919.695-0.020-0.0200.0000.0000.0000.000
211A215GLY00.0220.00422.793-0.009-0.0090.0000.0000.0000.000
212A216LEU0-0.066-0.05325.875-0.014-0.0140.0000.0000.0000.000
213A217SER0-0.013-0.02824.026-0.018-0.0180.0000.0000.0000.000
214A218TYR00.0100.01519.108-0.011-0.0110.0000.0000.0000.000
215A219ARG10.8140.93225.763-0.193-0.1930.0000.0000.0000.000
216A220LYS10.7900.88526.430-0.162-0.1620.0000.0000.0000.000
217A221ASP-1-0.826-0.91130.1240.0910.0910.0000.0000.0000.000
218A222LYS10.9490.95031.067-0.061-0.0610.0000.0000.0000.000
219A223ARG10.8590.94232.795-0.102-0.1020.0000.0000.0000.000
220A224VAL00.0110.01326.880-0.002-0.0020.0000.0000.0000.000
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