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: 6YRVZ

Calculation Name: 2BDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BDV

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646010.560796
FMO2-HF: Nuclear repulsion 2561800.571649
FMO2-HF: Total energy -84209.989147
FMO2-MP2: Total energy -84459.29126


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-34.235-28.97331.162-15.841-20.582-0.105
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.019
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].
3A4ARG10.7650.8603.597-4.518-1.1630.039-1.856-1.5380.005
4A5ILE00.0180.0113.455-0.6340.3070.346-0.299-0.989-0.002
5A6ALA0-0.0040.0045.861-0.327-0.323-0.001-0.0040.0010.000
6A7GLN0-0.030-0.0209.171-0.031-0.0310.0000.0000.0000.000
7A8LYS10.8290.90212.077-0.055-0.0550.0000.0000.0000.000
8A9SER00.006-0.00814.760-0.049-0.0490.0000.0000.0000.000
9A10ALA0-0.0090.01216.8000.0360.0360.0000.0000.0000.000
10A11PRO0-0.026-0.02117.7980.0160.0160.0000.0000.0000.000
11A12GLU-1-0.854-0.94818.8820.1550.1550.0000.0000.0000.000
12A13ASP-1-0.838-0.91418.1840.0970.0970.0000.0000.0000.000
13A14TYR0-0.064-0.06813.3620.0190.0190.0000.0000.0000.000
14A15VAL00.0290.01116.892-0.003-0.0030.0000.0000.0000.000
15A16GLU-1-0.780-0.84119.9010.0540.0540.0000.0000.0000.000
16A17ILE0-0.004-0.00216.433-0.019-0.0190.0000.0000.0000.000
17A18LEU0-0.014-0.01216.320-0.015-0.0150.0000.0000.0000.000
18A19TRP0-0.019-0.02318.818-0.006-0.0060.0000.0000.0000.000
19A20PRO00.0360.02522.1750.0010.0010.0000.0000.0000.000
20A21ASN0-0.083-0.04524.707-0.002-0.0020.0000.0000.0000.000
21A22ALA0-0.0030.00925.431-0.003-0.0030.0000.0000.0000.000
22A23ARG10.8050.86725.097-0.068-0.0680.0000.0000.0000.000
23A24LEU0-0.007-0.00321.7880.0000.0000.0000.0000.0000.000
24A25ILE0-0.024-0.00625.878-0.006-0.0060.0000.0000.0000.000
25A26PHE00.002-0.00222.9470.0020.0020.0000.0000.0000.000
26A27ASP-1-0.910-0.95521.3460.1830.1830.0000.0000.0000.000
27A28ASP-1-0.798-0.89119.1410.3400.3400.0000.0000.0000.000
28A29VAL00.0320.01721.364-0.017-0.0170.0000.0000.0000.000
29A30ALA0-0.0040.01119.040-0.011-0.0110.0000.0000.0000.000
30A31GLY00.0030.01420.344-0.002-0.0020.0000.0000.0000.000
31A32PRO00.0220.02116.7610.0420.0420.0000.0000.0000.000
32A33ARG10.8430.90013.533-0.307-0.3070.0000.0000.0000.000
33A34TYR00.0670.03211.3260.0870.0870.0000.0000.0000.000
34A35ASN00.0500.03210.2750.0520.0520.0000.0000.0000.000
35A36ILE00.0030.0238.708-0.072-0.0720.0000.0000.0000.000
36A37PRO00.0280.0137.8670.4250.4250.0000.0000.0000.000
37A38PRO00.0160.0047.296-0.074-0.0740.0000.0000.0000.000
38A39GLY0-0.020-0.0019.854-0.138-0.1380.0000.0000.0000.000
39A40THR0-0.038-0.02511.246-0.097-0.0970.0000.0000.0000.000
40A41ARG10.8890.92913.254-0.359-0.3590.0000.0000.0000.000
41A42PRO0-0.0150.0049.281-0.081-0.0810.0000.0000.0000.000
42A43LEU00.0070.01112.071-0.066-0.0660.0000.0000.0000.000
43A44THR0-0.060-0.04311.5490.1280.1280.0000.0000.0000.000
44A45MET0-0.0060.00313.629-0.075-0.0750.0000.0000.0000.000
45A46HIS0-0.008-0.02015.5190.0030.0030.0000.0000.0000.000
46A47ARG10.9440.96918.088-0.137-0.1370.0000.0000.0000.000
47A48LEU0-0.063-0.02417.319-0.014-0.0140.0000.0000.0000.000
48A49VAL0-0.038-0.02521.579-0.005-0.0050.0000.0000.0000.000
49A50ASP-1-0.838-0.91325.0030.1300.1300.0000.0000.0000.000
50A51GLN0-0.016-0.01025.515-0.014-0.0140.0000.0000.0000.000
51A52ALA00.0410.04125.970-0.006-0.0060.0000.0000.0000.000
52A53GLU-1-0.904-0.95622.5930.1390.1390.0000.0000.0000.000
53A54ALA0-0.0060.00221.231-0.005-0.0050.0000.0000.0000.000
54A55LEU00.0150.00016.8050.0310.0310.0000.0000.0000.000
55A56ALA00.0060.00217.432-0.025-0.0250.0000.0000.0000.000
56A57ARG10.8170.88814.642-0.388-0.3880.0000.0000.0000.000
57A58LEU00.0110.01814.609-0.034-0.0340.0000.0000.0000.000
58A59PRO0-0.006-0.00613.8700.0760.0760.0000.0000.0000.000
59A60TRP0-0.054-0.0144.031-0.4340.1130.047-0.138-0.4560.000
60A61GLY00.002-0.01910.1400.0150.0150.0000.0000.0000.000
61A62TYR0-0.034-0.00110.980-0.128-0.1280.0000.0000.0000.000
62A63LYS10.8610.91413.144-0.303-0.3030.0000.0000.0000.000
63A64PRO0-0.031-0.01615.295-0.040-0.0400.0000.0000.0000.000
64A65HIS00.0320.00018.2170.0010.0010.0000.0000.0000.000
65A66GLY00.0240.02921.609-0.015-0.0150.0000.0000.0000.000
66A67SER0-0.069-0.04719.229-0.014-0.0140.0000.0000.0000.000
67A68SER00.0250.03119.4540.0100.0100.0000.0000.0000.000
68A69PHE0-0.026-0.01614.6230.0190.0190.0000.0000.0000.000
69A70PHE00.0310.00311.520-0.005-0.0050.0000.0000.0000.000
70A71MET0-0.030-0.01010.1740.1230.1230.0000.0000.0000.000
71A72ILE00.0740.0355.661-0.073-0.0730.0000.0000.0000.000
72A73ASN0-0.030-0.0092.6501.6302.7270.280-0.490-0.886-0.002
73A74ALA00.0120.0115.762-0.106-0.1060.0000.0000.0000.000
74A75LYS10.8820.9368.032-0.177-0.1770.0000.0000.0000.000
75A76LEU00.0790.0349.2480.0660.0660.0000.0000.0000.000
76A77GLU-1-0.781-0.88011.120-0.094-0.0940.0000.0000.0000.000
77A78THR0-0.030-0.01913.0750.0320.0320.0000.0000.0000.000
78A79ILE00.0200.01910.4190.0310.0310.0000.0000.0000.000
79A80GLU-1-0.796-0.86914.776-0.086-0.0860.0000.0000.0000.000
80A81ARG10.8100.87817.1910.1160.1160.0000.0000.0000.000
81A82HIS00.0190.02218.3780.0090.0090.0000.0000.0000.000
82A83GLY00.0240.01817.8090.0060.0060.0000.0000.0000.000
83A84TRP0-0.022-0.00617.5970.0170.0170.0000.0000.0000.000
84A85PRO00.0330.00614.331-0.003-0.0030.0000.0000.0000.000
85A86TRP00.0890.00710.851-0.017-0.0170.0000.0000.0000.000
86A87LYS10.9610.99215.370-0.111-0.1110.0000.0000.0000.000
87A88LEU0-0.042-0.01818.689-0.015-0.0150.0000.0000.0000.000
88A89MET0-0.068-0.01914.7870.0210.0210.0000.0000.0000.000
89A90ILE00.0100.00915.3450.0020.0020.0000.0000.0000.000
90A91GLY0-0.0030.00117.374-0.017-0.0170.0000.0000.0000.000
91A92THR00.0250.01120.1550.0020.0020.0000.0000.0000.000
92A93GLY00.0310.00617.3710.0050.0050.0000.0000.0000.000
93A94ARG10.7840.89114.935-0.065-0.0650.0000.0000.0000.000
94A95ILE0-0.013-0.00511.377-0.010-0.0100.0000.0000.0000.000
95A96LEU00.0200.02311.731-0.014-0.0140.0000.0000.0000.000
96A97VAL0-0.021-0.0167.7740.0330.0330.0000.0000.0000.000
97A98PRO00.0100.0278.8420.1070.1070.0000.0000.0000.000
98A99ALA00.0080.0057.3770.1960.1960.0000.0000.0000.000
99A100ASP-1-0.712-0.8099.2770.0710.0710.0000.0000.0000.000
100A101GLY00.0070.0117.151-0.173-0.1730.0000.0000.0000.000
101A102TRP0-0.062-0.0492.194-2.361-1.2243.575-1.725-2.987-0.017
102A103TYR0-0.042-0.0343.999-0.301-0.1170.000-0.041-0.1430.000
103A104GLU-1-0.754-0.8443.730-4.638-4.0960.006-0.153-0.395-0.001
104A105TRP0-0.001-0.0095.5830.3430.3430.0000.0000.0000.000
105A106LYS10.8960.9628.7350.7330.7330.0000.0000.0000.000
106A107ALA00.001-0.01011.0350.1070.1070.0000.0000.0000.000
107A108LEU0-0.021-0.01113.369-0.028-0.0280.0000.0000.0000.000
108A109ASP-1-0.810-0.90517.047-0.140-0.1400.0000.0000.0000.000
109A110SER0-0.074-0.04417.314-0.031-0.0310.0000.0000.0000.000
110A111GLY00.0560.03418.5090.0150.0150.0000.0000.0000.000
111A112PRO0-0.029-0.01418.290-0.003-0.0030.0000.0000.0000.000
112A113LYS10.9100.94216.717-0.037-0.0370.0000.0000.0000.000
113A114PRO00.0200.04314.8180.0060.0060.0000.0000.0000.000
114A115ALA00.0220.00715.7470.0010.0010.0000.0000.0000.000
115A116LYS10.8630.9188.6980.5080.5080.0000.0000.0000.000
116A117GLN0-0.0190.00113.6650.0730.0730.0000.0000.0000.000
117A118PRO00.0010.01210.233-0.136-0.1360.0000.0000.0000.000
118A119TYR00.023-0.0039.3980.0830.0830.0000.0000.0000.000
119A120TYR0-0.045-0.0368.234-0.065-0.0650.0000.0000.0000.000
120A121ILE0-0.015-0.0125.6710.1280.1280.0000.0000.0000.000
121A122HIS10.8680.9297.4710.3880.3880.0000.0000.0000.000
122A123GLY00.1060.0499.887-0.090-0.0900.0000.0000.0000.000
123A124ASP-1-0.941-0.96112.314-0.208-0.2080.0000.0000.0000.000
124A125ALA00.0100.00414.4960.0330.0330.0000.0000.0000.000
125A126PRO0-0.026-0.00712.564-0.029-0.0290.0000.0000.0000.000
126A127LEU0-0.024-0.0017.566-0.074-0.0740.0000.0000.0000.000
127A128LEU00.0500.00710.8330.1390.1390.0000.0000.0000.000
128A129PHE0-0.020-0.0074.8480.2210.2210.0000.0000.0000.000
129A130ALA00.0720.0408.3240.0420.0420.0000.0000.0000.000
130A131GLY0-0.001-0.0028.1630.1690.1690.0000.0000.0000.000
131A132LEU0-0.043-0.0139.904-0.129-0.1290.0000.0000.0000.000
132A133SER00.0390.00711.7540.0960.0960.0000.0000.0000.000
133A134ALA00.0170.01914.428-0.060-0.0600.0000.0000.0000.000
134A135TRP0-0.027-0.01117.187-0.030-0.0300.0000.0000.0000.000
135A136ARG10.8560.90718.292-0.258-0.2580.0000.0000.0000.000
136A137ARG10.8980.93822.446-0.140-0.1400.0000.0000.0000.000
137A138GLY00.0110.00525.445-0.017-0.0170.0000.0000.0000.000
138A139ALA0-0.046-0.00422.678-0.005-0.0050.0000.0000.0000.000
139A140GLU-1-0.881-0.92523.3690.2370.2370.0000.0000.0000.000
140A141LEU0-0.013-0.01618.8180.0230.0230.0000.0000.0000.000
141A142ASP-1-0.718-0.84619.2380.3390.3390.0000.0000.0000.000
142A143GLU-1-0.730-0.87915.6900.3820.3820.0000.0000.0000.000
143A144ALA0-0.052-0.00516.2040.0320.0320.0000.0000.0000.000
144A145HIS10.7810.86218.209-0.309-0.3090.0000.0000.0000.000
145A146GLY00.0450.02714.1120.0050.0050.0000.0000.0000.000
146A147PHE0-0.040-0.0327.934-0.064-0.0640.0000.0000.0000.000
147A148ALA0-0.0030.0007.7820.1170.1170.0000.0000.0000.000
148A149ILE00.0070.0093.369-1.216-0.3730.284-0.219-0.9080.000
149A150VAL00.006-0.0045.352-0.225-0.2250.0000.0000.0000.000
150A151THR0-0.016-0.0172.750-0.7140.0570.503-0.346-0.9280.000
151A152ASN00.015-0.0025.6300.6700.6700.0000.0000.0000.000
152A153ASP-1-0.771-0.8926.591-0.335-0.3350.0000.0000.0000.000
153A154ALA0-0.0280.0007.6120.0110.0110.0000.0000.0000.000
154A155LEU0-0.009-0.0019.3890.1110.1110.0000.0000.0000.000
155A156GLY00.0390.0327.282-0.034-0.0340.0000.0000.0000.000
156A157GLY0-0.019-0.0105.169-0.800-0.8000.0000.0000.0000.000
157A158MET0-0.031-0.0086.0730.6480.6480.0000.0000.0000.000
158A159VAL0-0.034-0.0168.1020.4060.4060.0000.0000.0000.000
159A160ASP-1-0.832-0.9266.958-0.556-0.5560.0000.0000.0000.000
160A161VAL00.0440.0237.195-0.431-0.4310.0000.0000.0000.000
161A162HIS0-0.067-0.0318.0150.1220.1220.0000.0000.0000.000
162A163ASP-1-0.848-0.9261.801-7.752-13.81712.109-3.581-2.462-0.041
163A164ARG10.8270.9142.384-2.479-0.8431.259-1.085-1.8090.006
164A165ARG10.8650.9211.886-10.553-12.22610.451-4.768-4.012-0.054
165A166PRO0-0.018-0.0052.335-0.8650.1192.201-0.751-2.4330.000
166A167VAL00.008-0.0074.0140.0440.1790.005-0.038-0.1020.000
167A168ALA0-0.0080.0057.8400.3580.3580.0000.0000.0000.000
168A169LEU00.0110.0089.515-0.127-0.1270.0000.0000.0000.000
169A170PRO00.0360.01613.1570.0330.0330.0000.0000.0000.000
170A171PRO00.0410.02116.3130.0270.0270.0000.0000.0000.000
171A172GLU-1-0.826-0.90117.8310.0040.0040.0000.0000.0000.000
172A173LEU00.0150.00217.3900.0080.0080.0000.0000.0000.000
173A174ALA0-0.011-0.00315.2110.0190.0190.0000.0000.0000.000
174A175ARG10.8000.87616.620-0.011-0.0110.0000.0000.0000.000
175A176GLU-1-0.795-0.85820.0890.0030.0030.0000.0000.0000.000
176A177TRP0-0.048-0.03212.829-0.032-0.0320.0000.0000.0000.000
177A178VAL0-0.032-0.01017.2360.0220.0220.0000.0000.0000.000
178A179ASP-1-0.812-0.88318.6910.0920.0920.0000.0000.0000.000
179A180PRO0-0.033-0.01422.018-0.002-0.0020.0000.0000.0000.000
180A181ALA0-0.014-0.00323.444-0.004-0.0040.0000.0000.0000.000
181A182THR0-0.037-0.01621.629-0.009-0.0090.0000.0000.0000.000
182A183PRO00.0200.01323.0510.0110.0110.0000.0000.0000.000
183A184VAL00.019-0.00920.363-0.005-0.0050.0000.0000.0000.000
184A185ALA0-0.020-0.01120.650-0.008-0.0080.0000.0000.0000.000
185A186ARG10.8350.86921.7210.0220.0220.0000.0000.0000.000
186A187ALA00.0300.01517.712-0.012-0.0120.0000.0000.0000.000
187A188LYS10.8220.89117.026-0.026-0.0260.0000.0000.0000.000
188A189GLU-1-0.918-0.93817.425-0.089-0.0890.0000.0000.0000.000
189A190ILE00.0000.00215.837-0.034-0.0340.0000.0000.0000.000
190A191LEU0-0.041-0.01111.434-0.028-0.0280.0000.0000.0000.000
191A192ARG10.8000.87012.5830.0860.0860.0000.0000.0000.000
192A193ALA0-0.039-0.00714.681-0.051-0.0510.0000.0000.0000.000
193A194GLY00.001-0.00311.6170.0430.0430.0000.0000.0000.000
194A195LEU0-0.017-0.01111.579-0.013-0.0130.0000.0000.0000.000
195A196PRO00.0090.01511.600-0.144-0.1440.0000.0000.0000.000
196A197GLU-1-0.810-0.92011.821-0.901-0.9010.0000.0000.0000.000
197A198THR0-0.020-0.01812.8540.0040.0040.0000.0000.0000.000
198A199ALA0-0.0360.00113.7450.0690.0690.0000.0000.0000.000
199A200PHE0-0.039-0.0268.946-0.031-0.0310.0000.0000.0000.000
200A201SER00.0270.01812.1860.0350.0350.0000.0000.0000.000
201A202TRP00.003-0.01610.426-0.090-0.0900.0000.0000.0000.000
202A203TYR0-0.017-0.00512.2630.0610.0610.0000.0000.0000.000
203A204PRO0-0.0050.00912.730-0.051-0.0510.0000.0000.0000.000
204A205VAL0-0.021-0.01912.3660.0510.0510.0000.0000.0000.000
205A206ARG10.9320.95314.7140.1620.1620.0000.0000.0000.000
206A207GLN00.0370.02215.9710.0080.0080.0000.0000.0000.000
207A208GLU-1-0.863-0.93115.967-0.028-0.0280.0000.0000.0000.000
208A209VAL0-0.003-0.00411.3640.0380.0380.0000.0000.0000.000
209A210GLY00.0450.03112.1260.0730.0730.0000.0000.0000.000
210A211SER00.0050.00112.946-0.046-0.0460.0000.0000.0000.000
211A212SER00.009-0.01410.073-0.094-0.0940.0000.0000.0000.000
212A213LYS10.8390.9312.8940.0550.8790.058-0.347-0.5350.001
213A214TYR00.001-0.0017.3280.2070.2070.0000.0000.0000.000
214A215GLN0-0.032-0.0029.689-0.048-0.0480.0000.0000.0000.000
215A216LEU00.0280.01411.8340.0000.0000.0000.0000.0000.000
216A217PRO0-0.048-0.01613.454-0.038-0.0380.0000.0000.0000.000
217A218ASP-1-0.930-0.95516.0980.1120.1120.0000.0000.0000.000