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: MN91Z

Calculation Name: 1BDF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BDF

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7Z4

Base Structure: X-ray

Registration Date: 2023-09-22

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2503514.551731
FMO2-HF: Nuclear repulsion 2414651.683468
FMO2-HF: Total energy -88862.868263
FMO2-MP2: Total energy -89123.086585


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:GLN)


Summations of interaction energy for fragment #1(A:2:GLN)
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.
-5.066-2.0661.291-1.494-2.7970.004
Interaction energy analysis for fragmet #1(A:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.015
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].
3A4SER0-0.014-0.0082.472-1.7370.9891.281-1.395-2.6120.004
4A5VAL00.0310.0084.033-1.136-0.8620.010-0.099-0.1850.000
5A6THR0-0.075-0.0567.5030.1510.1510.0000.0000.0000.000
6A7GLU-1-0.914-0.9348.2152.6692.6690.0000.0000.0000.000
7A8PHE00.0620.0217.601-0.222-0.2220.0000.0000.0000.000
8A9LEU0-0.020-0.01111.111-0.179-0.1790.0000.0000.0000.000
9A10LYS10.8480.9329.523-0.880-0.8800.0000.0000.0000.000
10A11PRO00.0380.03314.841-0.015-0.0150.0000.0000.0000.000
11A12ARG10.9310.93917.958-0.057-0.0570.0000.0000.0000.000
12A13LEU0-0.0040.00120.7320.0230.0230.0000.0000.0000.000
13A14VAL0-0.070-0.03824.046-0.005-0.0050.0000.0000.0000.000
14A15ASP-1-0.919-0.94626.3390.0300.0300.0000.0000.0000.000
15A16ILE0-0.011-0.01828.963-0.009-0.0090.0000.0000.0000.000
16A17GLU-1-0.892-0.94031.5000.0210.0210.0000.0000.0000.000
17A18GLN0-0.019-0.02734.547-0.002-0.0020.0000.0000.0000.000
18A19VAL0-0.0030.00836.4150.0030.0030.0000.0000.0000.000
19A20SER0-0.039-0.03738.5920.0000.0000.0000.0000.0000.000
20A21SER0-0.005-0.00238.897-0.001-0.0010.0000.0000.0000.000
21A22THR0-0.0010.00337.547-0.004-0.0040.0000.0000.0000.000
22A23HIS0-0.0080.01035.567-0.003-0.0030.0000.0000.0000.000
23A24ALA0-0.0050.00132.6020.0040.0040.0000.0000.0000.000
24A25LYS10.9410.98231.079-0.024-0.0240.0000.0000.0000.000
25A26VAL00.0220.02425.7750.0030.0030.0000.0000.0000.000
26A27THR00.0280.01525.8810.0090.0090.0000.0000.0000.000
27A28LEU0-0.004-0.00220.182-0.006-0.0060.0000.0000.0000.000
28A29GLU-1-0.927-0.98122.4440.1710.1710.0000.0000.0000.000
29A30PRO0-0.002-0.00718.6530.0250.0250.0000.0000.0000.000
30A31LEU00.0180.03017.0200.0010.0010.0000.0000.0000.000
31A32GLU-1-0.754-0.83613.2180.8270.8270.0000.0000.0000.000
32A33ARG10.9640.98316.311-0.422-0.4220.0000.0000.0000.000
33A34GLY00.0060.00816.0280.0750.0750.0000.0000.0000.000
34A35PHE0-0.009-0.01810.259-0.083-0.0830.0000.0000.0000.000
35A36GLY00.0200.01916.176-0.075-0.0750.0000.0000.0000.000
36A37HIS00.0930.02219.743-0.028-0.0280.0000.0000.0000.000
37A38THR0-0.0320.02013.465-0.054-0.0540.0000.0000.0000.000
38A39LEU00.0270.01014.087-0.074-0.0740.0000.0000.0000.000
39A40GLY00.0350.01417.373-0.044-0.0440.0000.0000.0000.000
40A41ASN0-0.073-0.07019.914-0.035-0.0350.0000.0000.0000.000
41A42ALA0-0.0070.01416.887-0.024-0.0240.0000.0000.0000.000
42A43LEU00.0440.00518.916-0.028-0.0280.0000.0000.0000.000
43A44ARG10.9420.99121.1140.0230.0230.0000.0000.0000.000
44A45ALA0-0.013-0.00121.9690.0020.0020.0000.0000.0000.000
45A46ILE0-0.0010.01819.726-0.010-0.0100.0000.0000.0000.000
46A47LEU00.019-0.02423.3860.0000.0000.0000.0000.0000.000
47A48LEU0-0.033-0.01426.2450.0050.0050.0000.0000.0000.000
48A49SER0-0.059-0.02726.124-0.003-0.0030.0000.0000.0000.000
49A50SER0-0.043-0.01024.550-0.017-0.0170.0000.0000.0000.000
50A51MET0-0.0420.01626.319-0.030-0.0300.0000.0000.0000.000
51A52PRO0-0.053-0.05027.6780.0040.0040.0000.0000.0000.000
52A53GLY00.0940.04130.7660.0080.0080.0000.0000.0000.000
53A54CYS0-0.059-0.03534.088-0.008-0.0080.0000.0000.0000.000
54A55ALA00.0310.01237.4930.0070.0070.0000.0000.0000.000
55A56VAL00.0120.02240.277-0.005-0.0050.0000.0000.0000.000
56A57THR0-0.059-0.03741.3690.0030.0030.0000.0000.0000.000
57A58GLU-1-0.849-0.93544.352-0.108-0.1080.0000.0000.0000.000
58A59VAL0-0.012-0.01047.9420.0000.0000.0000.0000.0000.000
59A60GLU-1-0.910-0.96551.062-0.082-0.0820.0000.0000.0000.000
60A61ILE00.000-0.01554.3070.0010.0010.0000.0000.0000.000
61A62ASP-1-0.833-0.91257.186-0.066-0.0660.0000.0000.0000.000
62A63GLY0-0.055-0.02860.5750.0020.0020.0000.0000.0000.000
63A64VAL0-0.0080.00358.5110.0020.0020.0000.0000.0000.000
64A65LEU0-0.013-0.00459.513-0.002-0.0020.0000.0000.0000.000
65A66HIS00.022-0.00157.178-0.001-0.0010.0000.0000.0000.000
66A67GLU-1-0.880-0.95353.878-0.067-0.0670.0000.0000.0000.000
67A68TYR0-0.073-0.03357.1750.0030.0030.0000.0000.0000.000
68A69SER0-0.042-0.01060.2530.0020.0020.0000.0000.0000.000
69A70THR00.0400.01860.798-0.001-0.0010.0000.0000.0000.000
70A71LYS10.9380.95561.7150.0510.0510.0000.0000.0000.000
71A72GLU-1-0.922-0.94863.967-0.040-0.0400.0000.0000.0000.000
72A73GLY00.005-0.00866.330-0.001-0.0010.0000.0000.0000.000
73A74VAL0-0.073-0.03759.9540.0000.0000.0000.0000.0000.000
74A75GLN0-0.086-0.03959.9450.0030.0030.0000.0000.0000.000
75A76GLU-1-0.789-0.88856.939-0.045-0.0450.0000.0000.0000.000
76A77ASP-1-0.853-0.94058.274-0.050-0.0500.0000.0000.0000.000
77A78ILE00.031-0.01256.013-0.002-0.0020.0000.0000.0000.000
78A79LEU0-0.0060.01054.058-0.003-0.0030.0000.0000.0000.000
79A80GLU-1-0.886-0.94453.384-0.048-0.0480.0000.0000.0000.000
80A81ILE0-0.016-0.00253.406-0.002-0.0020.0000.0000.0000.000
81A82LEU0-0.002-0.00550.574-0.003-0.0030.0000.0000.0000.000
82A83LEU0-0.033-0.03248.346-0.005-0.0050.0000.0000.0000.000
83A84ASN0-0.017-0.00748.6800.0000.0000.0000.0000.0000.000
84A85LEU0-0.038-0.02848.369-0.002-0.0020.0000.0000.0000.000
85A86LYS10.8700.95544.7060.0720.0720.0000.0000.0000.000
86A87GLY0-0.053-0.00843.616-0.004-0.0040.0000.0000.0000.000
87A88LEU0-0.046-0.01544.9450.0030.0030.0000.0000.0000.000
88A89ALA00.0120.01240.984-0.006-0.0060.0000.0000.0000.000
89A90VAL0-0.017-0.02340.7690.0040.0040.0000.0000.0000.000
90A91ARG10.8440.94834.0600.1030.1030.0000.0000.0000.000
91A92VAL00.0380.00137.6380.0030.0030.0000.0000.0000.000
92A93GLN00.0600.01436.365-0.013-0.0130.0000.0000.0000.000
93A94GLY0-0.026-0.00234.764-0.011-0.0110.0000.0000.0000.000
94A95LYN00.0130.01835.651-0.001-0.0010.0000.0000.0000.000
95A96ASP-1-0.871-0.95234.528-0.215-0.2150.0000.0000.0000.000
96A97GLU-1-0.938-1.00637.345-0.134-0.1340.0000.0000.0000.000
97A98VAL0-0.0020.02841.066-0.001-0.0010.0000.0000.0000.000
98A99ILE0-0.005-0.00243.7520.0030.0030.0000.0000.0000.000
99A100LEU00.0320.02045.3700.0020.0020.0000.0000.0000.000
100A101THR00.0090.05348.9370.0030.0030.0000.0000.0000.000
101A102LEU00.0240.01452.7270.0010.0010.0000.0000.0000.000
102A103ASN0-0.0020.00554.6770.0010.0010.0000.0000.0000.000
103A104LYS10.9400.96958.0590.0480.0480.0000.0000.0000.000
104A105SER00.0370.01560.2880.0000.0000.0000.0000.0000.000
105A106GLY0-0.020-0.00463.9860.0000.0000.0000.0000.0000.000
106A107ILE00.0110.02965.2040.0000.0000.0000.0000.0000.000
107A108GLY0-0.024-0.01462.6750.0000.0000.0000.0000.0000.000
108A109PRO0-0.044-0.03157.147-0.001-0.0010.0000.0000.0000.000
109A110VAL0-0.0220.00255.5320.0000.0000.0000.0000.0000.000
110A111THR0-0.019-0.02752.718-0.001-0.0010.0000.0000.0000.000
111A112ALA00.0270.00348.358-0.002-0.0020.0000.0000.0000.000
112A113ALA0-0.040-0.02650.240-0.003-0.0030.0000.0000.0000.000
113A114ASP-1-0.873-0.93451.864-0.053-0.0530.0000.0000.0000.000
114A115ILE0-0.062-0.02248.633-0.001-0.0010.0000.0000.0000.000
115A116THR0-0.090-0.09951.768-0.001-0.0010.0000.0000.0000.000
116A117HIS0-0.016-0.01549.503-0.001-0.0010.0000.0000.0000.000
117A118ASP-1-0.862-0.93146.057-0.107-0.1070.0000.0000.0000.000
118A119GLY0-0.054-0.02145.7620.0010.0010.0000.0000.0000.000
119A120ASP-1-0.968-0.98440.884-0.130-0.1300.0000.0000.0000.000
120A121VAL0-0.061-0.03741.427-0.002-0.0020.0000.0000.0000.000
121A122GLU-1-0.832-0.89339.438-0.093-0.0930.0000.0000.0000.000
122A123ILE0-0.040-0.03942.127-0.003-0.0030.0000.0000.0000.000
123A124VAL00.0390.02639.4870.0050.0050.0000.0000.0000.000
124A125LYS10.9220.96842.7480.0560.0560.0000.0000.0000.000
125A126PRO00.0600.03045.7840.0000.0000.0000.0000.0000.000
126A127GLN00.013-0.00948.234-0.002-0.0020.0000.0000.0000.000
127A128HIS0-0.079-0.04447.7560.0060.0060.0000.0000.0000.000
128A129VAL00.0140.00349.909-0.002-0.0020.0000.0000.0000.000
129A130ILE00.0100.01050.431-0.001-0.0010.0000.0000.0000.000
130A131CYS0-0.031-0.02053.2440.0000.0000.0000.0000.0000.000
131A132HIS0-0.0180.00157.0450.0020.0020.0000.0000.0000.000
132A133LEU0-0.0430.01860.4720.0000.0000.0000.0000.0000.000
133A134THR00.014-0.01263.4040.0010.0010.0000.0000.0000.000
134A135ASP-1-0.861-0.94066.638-0.037-0.0370.0000.0000.0000.000
135A136GLU-1-0.924-0.98868.003-0.035-0.0350.0000.0000.0000.000
136A137ASN0-0.119-0.04269.714-0.001-0.0010.0000.0000.0000.000
137A138ALA0-0.0030.03465.800-0.001-0.0010.0000.0000.0000.000
138A139SER0-0.009-0.03463.434-0.001-0.0010.0000.0000.0000.000
139A140ILE0-0.025-0.02257.6050.0000.0000.0000.0000.0000.000
140A141SER0-0.009-0.00458.453-0.001-0.0010.0000.0000.0000.000
141A142MET0-0.0140.00253.878-0.001-0.0010.0000.0000.0000.000
142A143ARG10.8420.90551.9070.0740.0740.0000.0000.0000.000
143A144ILE00.006-0.00247.165-0.001-0.0010.0000.0000.0000.000
144A145LYS10.9010.97544.3800.1170.1170.0000.0000.0000.000
145A146VAL00.0100.01140.8350.0010.0010.0000.0000.0000.000
146A147GLN00.0490.02439.1820.0010.0010.0000.0000.0000.000
147A148ARG10.8010.91732.6710.1840.1840.0000.0000.0000.000
148A149GLY00.0040.00233.805-0.005-0.0050.0000.0000.0000.000
149A150ARG10.8920.93026.7970.2630.2630.0000.0000.0000.000
150A151GLY00.0300.02632.2160.0040.0040.0000.0000.0000.000
151A152TYR0-0.027-0.00233.4760.0020.0020.0000.0000.0000.000
152A153VAL00.0050.01736.353-0.001-0.0010.0000.0000.0000.000
153A154PRO00.0450.00438.8310.0030.0030.0000.0000.0000.000
154A155ALA00.0820.05842.504-0.006-0.0060.0000.0000.0000.000
155A156SER00.0160.00445.279-0.003-0.0030.0000.0000.0000.000
156A157THR0-0.164-0.09340.167-0.003-0.0030.0000.0000.0000.000
157A158ARG10.8780.94241.7720.1110.1110.0000.0000.0000.000
158A159ILE0-0.0130.02945.4760.0010.0010.0000.0000.0000.000
159A160HIS0-0.019-0.00547.3450.0040.0040.0000.0000.0000.000
160A161SER0-0.048-0.05349.6320.0040.0040.0000.0000.0000.000
161A162GLU-1-0.794-0.86952.210-0.075-0.0750.0000.0000.0000.000
162A163GLU-1-0.978-0.99552.476-0.103-0.1030.0000.0000.0000.000
163A164ASP-1-0.907-0.96155.694-0.080-0.0800.0000.0000.0000.000
164A165GLU-1-1.002-1.00558.962-0.063-0.0630.0000.0000.0000.000
165A166ARG10.7370.85959.4210.0670.0670.0000.0000.0000.000
166A167PRO0-0.0020.00257.314-0.003-0.0030.0000.0000.0000.000
167A168ILE00.0810.03953.1420.0020.0020.0000.0000.0000.000
168A169GLY00.0040.01754.9910.0030.0030.0000.0000.0000.000
169A170ARG10.7750.89254.3210.0770.0770.0000.0000.0000.000
170A171LEU00.0320.00452.702-0.003-0.0030.0000.0000.0000.000
171A172LEU00.0750.07247.509-0.004-0.0040.0000.0000.0000.000
172A173VAL0-0.018-0.00545.6780.0050.0050.0000.0000.0000.000
173A174ASP-1-0.871-0.95043.722-0.093-0.0930.0000.0000.0000.000
174A175ALA00.0340.02739.9610.0030.0030.0000.0000.0000.000
175A176CYS0-0.022-0.03538.483-0.002-0.0020.0000.0000.0000.000
176A177TYR0-0.009-0.01634.8590.0030.0030.0000.0000.0000.000
177A178SER0-0.033-0.00732.744-0.008-0.0080.0000.0000.0000.000
178A179PRO00.0190.03231.3510.0090.0090.0000.0000.0000.000
179A180VAL0-0.031-0.01729.7210.0090.0090.0000.0000.0000.000
180A181GLU-1-0.830-0.90132.764-0.083-0.0830.0000.0000.0000.000
181A182ARG10.8860.93532.8710.0370.0370.0000.0000.0000.000
182A183ILE0-0.0120.00326.661-0.002-0.0020.0000.0000.0000.000
183A184ALA0-0.021-0.00629.4020.0050.0050.0000.0000.0000.000
184A185TYR0-0.048-0.03123.4880.0070.0070.0000.0000.0000.000
185A186ASN0-0.0040.00426.9250.0130.0130.0000.0000.0000.000
186A187VAL0-0.042-0.03622.267-0.003-0.0030.0000.0000.0000.000
187A188GLU-1-0.854-0.94124.6300.1170.1170.0000.0000.0000.000
188A189ALA00.0330.03425.0790.0110.0110.0000.0000.0000.000
189A190ALA0-0.0110.00523.679-0.026-0.0260.0000.0000.0000.000
190A191ARG10.8960.92725.663-0.203-0.2030.0000.0000.0000.000
191A192VAL00.0570.02722.772-0.006-0.0060.0000.0000.0000.000
192A193GLU-1-0.938-0.95725.6390.1760.1760.0000.0000.0000.000
193A194GLN0-0.018-0.00318.779-0.015-0.0150.0000.0000.0000.000
194A195ARG10.7730.84015.624-0.664-0.6640.0000.0000.0000.000
195A196THR00.008-0.01822.536-0.039-0.0390.0000.0000.0000.000
196A197ASP-1-0.947-0.95119.8250.4740.4740.0000.0000.0000.000
197A198LEU0-0.053-0.03517.8710.0650.0650.0000.0000.0000.000
198A199ASP-1-0.892-0.94820.5760.2720.2720.0000.0000.0000.000
199A200LYS10.9150.97321.882-0.117-0.1170.0000.0000.0000.000
200A201LEU0-0.0430.00220.265-0.007-0.0070.0000.0000.0000.000
201A202VAL00.0110.00023.384-0.018-0.0180.0000.0000.0000.000
202A203ILE0-0.037-0.03322.552-0.003-0.0030.0000.0000.0000.000
203A204GLU-1-0.925-0.96027.0070.0020.0020.0000.0000.0000.000
204A205MET0-0.051-0.03028.104-0.013-0.0130.0000.0000.0000.000
205A206GLU-1-0.884-0.93631.668-0.036-0.0360.0000.0000.0000.000
206A207THR0-0.080-0.03833.372-0.007-0.0070.0000.0000.0000.000
207A208ASN00.1740.15235.0700.0060.0060.0000.0000.0000.000
208A209GLY0-0.014-0.03036.8220.0020.0020.0000.0000.0000.000
209A210THR0-0.119-0.11736.326-0.004-0.0040.0000.0000.0000.000
210A211ILE0-0.028-0.00829.224-0.012-0.0120.0000.0000.0000.000
211A212ASP-1-0.901-0.95231.423-0.089-0.0890.0000.0000.0000.000
212A213PRO00.055-0.01430.092-0.011-0.0110.0000.0000.0000.000
213A214GLU-1-0.885-0.95925.892-0.105-0.1050.0000.0000.0000.000
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215A216ALA00.0430.02326.477-0.024-0.0240.0000.0000.0000.000
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