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: 3QZYL

Calculation Name: 2OZV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OZV

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D120

Base Structure: X-ray

Registration Date: 2023-03-13

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2302303.422146
FMO2-HF: Nuclear repulsion 2222508.907529
FMO2-HF: Total energy -79794.514617
FMO2-MP2: Total energy -80023.807699


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:31:MET)


Summations of interaction energy for fragment #1(A:31: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.
-9.657-3.6814.866-2.257-8.587-0.004
Interaction energy analysis for fragmet #1(A:31:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.014
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].
3A33ALA00.0300.0093.539-1.429-0.0660.000-0.475-0.8880.002
4A34MET00.0520.0413.4050.2070.8860.020-0.152-0.5470.000
5A35LEU00.010-0.0072.4570.3611.3241.917-0.530-2.351-0.001
6A36LEU0-0.0280.0085.5110.8420.8420.0000.0000.0000.000
7A37ALA00.0390.0207.8830.3020.3020.0000.0000.0000.000
8A38SER0-0.057-0.0328.3380.3220.3220.0000.0000.0000.000
9A39LEU0-0.003-0.0029.5940.2020.2020.0000.0000.0000.000
10A40VAL00.0100.02512.0790.1170.1170.0000.0000.0000.000
11A41ALA0-0.013-0.00215.099-0.040-0.0400.0000.0000.0000.000
12A42ASP-1-0.851-0.93516.898-0.180-0.1800.0000.0000.0000.000
13A43ASP-1-0.837-0.91919.188-0.412-0.4120.0000.0000.0000.000
14A44ARG10.8810.94921.6810.1980.1980.0000.0000.0000.000
15A45ALA00.0280.02123.250-0.019-0.0190.0000.0000.0000.000
16A46CYS0-0.104-0.03621.1440.0120.0120.0000.0000.0000.000
17A47ARG10.9210.95922.1980.0960.0960.0000.0000.0000.000
18A48ILE0-0.022-0.02615.9220.0100.0100.0000.0000.0000.000
19A49ALA00.0330.03618.8930.0000.0000.0000.0000.0000.000
20A50ASP-1-0.806-0.92412.492-0.224-0.2240.0000.0000.0000.000
21A51LEU0-0.025-0.02515.7060.0320.0320.0000.0000.0000.000
22A52GLY00.0620.06413.1040.0540.0540.0000.0000.0000.000
23A53ALA0-0.028-0.04812.658-0.019-0.0190.0000.0000.0000.000
24A54GLY0-0.039-0.03910.6590.0710.0710.0000.0000.0000.000
25A55ALA00.0310.01811.1260.0030.0030.0000.0000.0000.000
26A56GLY00.0590.03112.927-0.065-0.0650.0000.0000.0000.000
27A57ALA00.003-0.0057.577-0.078-0.0780.0000.0000.0000.000
28A58ALA0-0.0140.0008.524-0.271-0.2710.0000.0000.0000.000
29A59GLY00.0570.0079.364-0.096-0.0960.0000.0000.0000.000
30A60MET0-0.028-0.00311.0530.0070.0070.0000.0000.0000.000
31A61ALA00.0240.0188.198-0.028-0.0280.0000.0000.0000.000
32A62VAL0-0.053-0.02710.3020.0070.0070.0000.0000.0000.000
33A63ALA00.0190.00613.1580.0380.0380.0000.0000.0000.000
34A64ALA0-0.0330.00412.4200.0500.0500.0000.0000.0000.000
35A65ARG10.8300.91111.9110.8330.8330.0000.0000.0000.000
36A66LEU0-0.038-0.01014.7570.0620.0620.0000.0000.0000.000
37A67GLU-1-0.844-0.92517.881-0.274-0.2740.0000.0000.0000.000
38A68LYS10.7680.87520.8350.3380.3380.0000.0000.0000.000
39A69ALA00.0000.00818.4830.0260.0260.0000.0000.0000.000
40A70GLU-1-0.916-0.95320.460-0.151-0.1510.0000.0000.0000.000
41A71VAL0-0.028-0.02015.862-0.003-0.0030.0000.0000.0000.000
42A72THR00.0160.01819.2580.0110.0110.0000.0000.0000.000
43A73LEU0-0.0210.00214.5540.0020.0020.0000.0000.0000.000
44A74TYR0-0.025-0.04217.7660.0100.0100.0000.0000.0000.000
45A75GLU-1-0.842-0.92715.3260.1150.1150.0000.0000.0000.000
46A76ARG10.8460.90819.348-0.186-0.1860.0000.0000.0000.000
47A77SER0-0.059-0.04521.324-0.011-0.0110.0000.0000.0000.000
48A78GLN00.018-0.00122.198-0.002-0.0020.0000.0000.0000.000
49A79GLU-1-0.888-0.92621.1020.1520.1520.0000.0000.0000.000
50A80MET0-0.0200.00515.2250.0100.0100.0000.0000.0000.000
51A81ALA00.0440.01518.380-0.021-0.0210.0000.0000.0000.000
52A82GLU-1-0.808-0.89120.399-0.047-0.0470.0000.0000.0000.000
53A83PHE0-0.041-0.01113.869-0.016-0.0160.0000.0000.0000.000
54A84ALA00.015-0.00316.028-0.025-0.0250.0000.0000.0000.000
55A85ARG10.7310.82217.012-0.017-0.0170.0000.0000.0000.000
56A86ARG10.7810.84419.4880.0270.0270.0000.0000.0000.000
57A87SER0-0.0130.00313.465-0.030-0.0300.0000.0000.0000.000
58A88LEU0-0.004-0.00716.056-0.047-0.0470.0000.0000.0000.000
59A89GLU-1-0.848-0.89018.094-0.099-0.0990.0000.0000.0000.000
60A90LEU0-0.038-0.00515.8570.0060.0060.0000.0000.0000.000
61A91PRO0-0.015-0.03319.210-0.026-0.0260.0000.0000.0000.000
62A92ASP-1-0.958-0.97014.303-0.480-0.4800.0000.0000.0000.000
63A93ASN00.020-0.00113.973-0.118-0.1180.0000.0000.0000.000
64A94ALA00.0070.01216.7760.0030.0030.0000.0000.0000.000
65A95ALA0-0.053-0.02018.1950.0170.0170.0000.0000.0000.000
66A96PHE0-0.009-0.02013.427-0.007-0.0070.0000.0000.0000.000
67A97SER00.0100.00818.3740.0130.0130.0000.0000.0000.000
68A98ALA0-0.014-0.00419.2790.0220.0220.0000.0000.0000.000
69A99ARG10.7910.88818.4850.3790.3790.0000.0000.0000.000
70A100ILE0-0.036-0.01615.458-0.018-0.0180.0000.0000.0000.000
71A101GLU-1-0.897-0.93619.628-0.072-0.0720.0000.0000.0000.000
72A102VAL0-0.019-0.01118.339-0.008-0.0080.0000.0000.0000.000
73A103LEU0-0.0030.01320.9190.0130.0130.0000.0000.0000.000
74A104GLU-1-0.782-0.88022.1280.0280.0280.0000.0000.0000.000
75A105ALA00.0160.01023.248-0.002-0.0020.0000.0000.0000.000
76A106ASP-1-0.811-0.87022.9670.1600.1600.0000.0000.0000.000
77A107VAL00.0700.02619.565-0.010-0.0100.0000.0000.0000.000
78A108THR0-0.077-0.05422.749-0.002-0.0020.0000.0000.0000.000
79A109LEU0-0.0200.00224.681-0.002-0.0020.0000.0000.0000.000
80A110ARG10.8560.90027.643-0.122-0.1220.0000.0000.0000.000
81A111ALA0-0.011-0.01730.422-0.004-0.0040.0000.0000.0000.000
82A112LYS10.9650.98632.559-0.025-0.0250.0000.0000.0000.000
83A113ALA00.0920.05132.696-0.004-0.0040.0000.0000.0000.000
84A114ARG10.8140.89926.922-0.030-0.0300.0000.0000.0000.000
85A115VAL00.0180.01129.235-0.005-0.0050.0000.0000.0000.000
86A116GLU-1-0.935-0.98231.3080.0200.0200.0000.0000.0000.000
87A117ALA0-0.039-0.01028.196-0.002-0.0020.0000.0000.0000.000
88A118GLY00.0470.02927.582-0.001-0.0010.0000.0000.0000.000
89A119LEU0-0.050-0.00522.788-0.010-0.0100.0000.0000.0000.000
90A120PRO0-0.010-0.00526.3400.0090.0090.0000.0000.0000.000
91A121ASP-1-0.797-0.90127.8490.0100.0100.0000.0000.0000.000
92A122GLU-1-0.941-0.97628.200-0.025-0.0250.0000.0000.0000.000
93A123HIS00.0410.04125.623-0.002-0.0020.0000.0000.0000.000
94A124PHE00.0300.01022.163-0.011-0.0110.0000.0000.0000.000
95A125HIS00.0240.01922.6460.0080.0080.0000.0000.0000.000
96A126HIS0-0.018-0.03617.5770.0000.0000.0000.0000.0000.000
97A127VAL0-0.001-0.00617.6370.0090.0090.0000.0000.0000.000
98A128ILE0-0.020-0.01011.9360.0010.0010.0000.0000.0000.000
99A129MET0-0.0150.00112.4940.0640.0640.0000.0000.0000.000
100A130ASN00.027-0.0107.163-0.032-0.0320.0000.0000.0000.000
101A131PRO00.0180.03410.5800.0730.0730.0000.0000.0000.000
102A132PRO0-0.0210.00012.7440.1250.1250.0000.0000.0000.000
103A133TYR0-0.038-0.0298.2820.0780.0780.0000.0000.0000.000
104A155GLY00.0240.01319.5470.0100.0100.0000.0000.0000.000
105A156LEU0-0.051-0.03817.780-0.028-0.0280.0000.0000.0000.000
106A157PHE00.0350.00112.663-0.035-0.0350.0000.0000.0000.000
107A158GLU-1-0.779-0.85618.8140.1070.1070.0000.0000.0000.000
108A159ASP-1-0.785-0.87322.6350.1370.1370.0000.0000.0000.000
109A160TRP00.0570.02515.243-0.010-0.0100.0000.0000.0000.000
110A161ILE00.0160.00417.082-0.031-0.0310.0000.0000.0000.000
111A162ARG10.7310.86020.593-0.142-0.1420.0000.0000.0000.000
112A163THR0-0.016-0.02622.631-0.019-0.0190.0000.0000.0000.000
113A164ALA00.0170.00519.729-0.019-0.0190.0000.0000.0000.000
114A165SER0-0.038-0.02321.792-0.023-0.0230.0000.0000.0000.000
115A166ALA0-0.047-0.01224.628-0.009-0.0090.0000.0000.0000.000
116A167ILE00.0440.02421.521-0.008-0.0080.0000.0000.0000.000
117A168MET0-0.0680.03419.505-0.023-0.0230.0000.0000.0000.000
118A169VAL00.0070.01424.5830.0130.0130.0000.0000.0000.000
119A170SER00.019-0.00826.2070.0040.0040.0000.0000.0000.000
120A171GLY0-0.018-0.00526.283-0.009-0.0090.0000.0000.0000.000
121A172GLY00.0330.01723.440-0.013-0.0130.0000.0000.0000.000
122A173GLN0-0.048-0.04115.5530.0460.0460.0000.0000.0000.000
123A174LEU00.0010.00616.468-0.021-0.0210.0000.0000.0000.000
124A175SER00.004-0.01312.671-0.008-0.0080.0000.0000.0000.000
125A176LEU0-0.007-0.00111.275-0.003-0.0030.0000.0000.0000.000
126A177ILE0-0.019-0.0054.126-0.177-0.0210.000-0.026-0.1300.000
127A178SER0-0.002-0.0148.450-0.032-0.0320.0000.0000.0000.000
128A179ARG10.9870.9988.437-0.619-0.6190.0000.0000.0000.000
129A180PRO00.0340.0249.385-0.238-0.2380.0000.0000.0000.000
130A181GLN00.0420.01012.364-0.058-0.0580.0000.0000.0000.000
131A182SER0-0.016-0.00414.047-0.047-0.0470.0000.0000.0000.000
132A183VAL0-0.0040.00315.539-0.076-0.0760.0000.0000.0000.000
133A184ALA00.0240.00616.664-0.056-0.0560.0000.0000.0000.000
134A185GLU-1-0.799-0.90117.7540.3950.3950.0000.0000.0000.000
135A186ILE00.0150.01013.628-0.042-0.0420.0000.0000.0000.000
136A187ILE00.004-0.00218.117-0.047-0.0470.0000.0000.0000.000
137A188ALA0-0.020-0.00720.778-0.030-0.0300.0000.0000.0000.000
138A189ALA0-0.0080.01320.337-0.024-0.0240.0000.0000.0000.000
139A190CYS0-0.023-0.00119.663-0.028-0.0280.0000.0000.0000.000
140A191GLY00.0430.02222.456-0.021-0.0210.0000.0000.0000.000
141A192SER0-0.079-0.05226.117-0.004-0.0040.0000.0000.0000.000
142A193ARG10.7730.87424.041-0.127-0.1270.0000.0000.0000.000
143A194PHE00.0240.00721.405-0.013-0.0130.0000.0000.0000.000
144A195GLY00.0350.02723.5350.0190.0190.0000.0000.0000.000
145A196GLY0-0.019-0.02522.456-0.017-0.0170.0000.0000.0000.000
146A197LEU00.0080.01318.763-0.014-0.0140.0000.0000.0000.000
147A198GLU-1-0.804-0.89016.450-0.055-0.0550.0000.0000.0000.000
148A199ILE00.0330.01913.740-0.005-0.0050.0000.0000.0000.000
149A200THR0-0.016-0.01610.224-0.103-0.1030.0000.0000.0000.000
150A201LEU00.0170.0259.9920.1340.1340.0000.0000.0000.000
151A202ILE00.0190.0183.825-0.815-0.3110.114-0.142-0.4760.001
152A203HIS00.013-0.0127.2470.3470.3470.0000.0000.0000.000
153A204PRO0-0.0080.0085.159-0.204-0.2040.0000.0000.0000.000
154A205ARG10.8860.9176.235-0.481-0.4810.0000.0000.0000.000
155A206PRO0-0.014-0.0159.4370.1140.1140.0000.0000.0000.000
156A207GLY00.0040.00812.969-0.025-0.0250.0000.0000.0000.000
157A208GLU-1-0.838-0.88710.0320.4270.4270.0000.0000.0000.000
158A209ASP-1-0.878-0.93511.6290.6270.6270.0000.0000.0000.000
159A210ALA0-0.050-0.0249.4010.1420.1420.0000.0000.0000.000
160A211VAL00.007-0.0094.866-0.149-0.0400.000-0.016-0.0920.000
161A212ARG10.7780.8603.821-3.583-3.0200.033-0.093-0.5030.000
162A213MET0-0.027-0.0046.721-0.387-0.3870.0000.0000.0000.000
163A214LEU00.0410.0346.114-0.034-0.0340.0000.0000.0000.000
164A215VAL0-0.028-0.0289.2310.0410.0410.0000.0000.0000.000
165A216THR00.0650.04912.891-0.069-0.0690.0000.0000.0000.000
166A217ALA0-0.043-0.02815.3860.0400.0400.0000.0000.0000.000
167A218ILE00.0150.01619.125-0.021-0.0210.0000.0000.0000.000
168A219LYS10.8140.89222.3310.0310.0310.0000.0000.0000.000
169A220GLY00.0120.00124.709-0.009-0.0090.0000.0000.0000.000
170A221SER0-0.061-0.01524.9930.0020.0020.0000.0000.0000.000
171A222ARG10.9890.97327.107-0.003-0.0030.0000.0000.0000.000
172A223ALA0-0.0260.00825.5650.0060.0060.0000.0000.0000.000
173A224ARG10.9580.97524.568-0.067-0.0670.0000.0000.0000.000
174A225LEU00.0240.02120.480-0.012-0.0120.0000.0000.0000.000
175A226THR0-0.076-0.05220.069-0.016-0.0160.0000.0000.0000.000
176A227PHE00.0400.01515.7860.0160.0160.0000.0000.0000.000
177A228ARG10.8140.91314.6670.0770.0770.0000.0000.0000.000
178A229ALA00.0090.00115.6280.0520.0520.0000.0000.0000.000
179A230PRO0-0.0100.00411.458-0.009-0.0090.0000.0000.0000.000
180A231LEU00.0440.0147.381-0.093-0.0930.0000.0000.0000.000
181A232ILE0-0.016-0.0077.5420.3780.3780.0000.0000.0000.000
182A233MET0-0.0130.0043.020-0.651-0.3682.112-0.389-2.006-0.003
183A234HIS10.8210.9234.7860.5520.625-0.0010.000-0.0720.000
184A235GLU-1-0.811-0.9158.214-0.126-0.1260.0000.0000.0000.000
185A236THR0-0.019-0.03211.7660.0080.0080.0000.0000.0000.000
186A237GLY00.0090.01513.260-0.009-0.0090.0000.0000.0000.000
187A238SER0-0.032-0.00411.911-0.022-0.0220.0000.0000.0000.000
188A239HIS00.0540.00910.528-0.051-0.0510.0000.0000.0000.000
189A240ALA0-0.0100.0069.623-0.152-0.1520.0000.0000.0000.000
190A241PHE00.025-0.0062.558-0.745-0.2080.658-0.199-0.997-0.001
191A242THR0-0.0030.0037.6870.0550.0550.0000.0000.0000.000
192A243PRO00.022-0.0019.019-0.175-0.1750.0000.0000.0000.000
193A244PHE00.0500.02810.932-0.124-0.1240.0000.0000.0000.000
194A245VAL00.0080.0004.519-0.208-0.123-0.001-0.005-0.0800.000
195A246ASP-1-0.817-0.8956.627-2.170-2.1700.0000.0000.0000.000
196A247ASP-1-0.810-0.8918.247-1.046-1.0460.0000.0000.0000.000
197A248LEU0-0.059-0.0246.845-0.015-0.0150.0000.0000.0000.000
198A249ASN0-0.074-0.0343.503-2.172-1.5460.015-0.230-0.411-0.002
199A250ASN0-0.085-0.0595.367-0.097-0.062-0.0010.000-0.0340.000
200A251GLY00.0010.0108.2530.2530.2530.0000.0000.0000.000
201A252ARG10.7640.85210.0671.3071.3070.0000.0000.0000.000
202A253ALA0-0.021-0.00411.6240.1600.1600.0000.0000.0000.000
203A254ALA00.008-0.00211.699-0.143-0.1430.0000.0000.0000.000
204A255TYR0-0.050-0.03910.4130.0820.0820.0000.0000.0000.000
205A256ALA00.0270.01412.4500.0590.0590.0000.0000.0000.000
206A257ARG10.8320.91815.9980.0950.0950.0000.0000.0000.000
207A258ASN0-0.037-0.02917.910-0.022-0.0220.0000.0000.0000.000
208A259VAL0-0.0240.00220.719-0.001-0.0010.0000.0000.0000.000