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: K2953

Calculation Name: 5KDO-B-Xray372

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

ligand 3-letter code: GDP

PDB ID: 5KDO

Chain ID: B

ChEMBL ID:

UniProt ID: P62871

Base Structure: X-ray

Registration Date: 2023-09-26

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 339
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5201583.256814
FMO2-HF: Nuclear repulsion 5067173.730814
FMO2-HF: Total energy -134409.526
FMO2-MP2: Total energy -134790.139138


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(B:2:SER)


Summations of interaction energy for fragment #1(B:2:SER)
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.
-24.828-19.60814.26-9.001-10.482-0.038
Interaction energy analysis for fragmet #1(B:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.006
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].
3B4LEU00.013-0.0012.249-9.004-5.7503.389-2.834-3.8100.023
4B5ASP-1-0.856-0.9292.022-19.933-18.46010.861-6.024-6.311-0.061
5B6GLN0-0.036-0.0183.7660.7941.2870.010-0.143-0.3610.000
6B7LEU00.0550.0345.9690.5560.5560.0000.0000.0000.000
7B8ARG10.8870.9435.6933.0473.0470.0000.0000.0000.000
8B9GLN0-0.011-0.0108.273-0.015-0.0150.0000.0000.0000.000
9B10GLU-1-0.915-0.95110.016-0.292-0.2920.0000.0000.0000.000
10B11ALA00.0250.00911.6530.1550.1550.0000.0000.0000.000
11B12GLU-1-0.852-0.91612.589-0.568-0.5680.0000.0000.0000.000
12B13GLN0-0.035-0.01214.2550.0600.0600.0000.0000.0000.000
13B14LEU00.0070.00015.9740.0880.0880.0000.0000.0000.000
14B15LYS10.8330.89415.2550.6060.6060.0000.0000.0000.000
15B16ASN0-0.018-0.01017.5920.0780.0780.0000.0000.0000.000
16B17GLN00.0300.02518.8860.0060.0060.0000.0000.0000.000
17B18ILE00.0000.00521.2720.0330.0330.0000.0000.0000.000
18B19ARG10.9300.96922.8980.3300.3300.0000.0000.0000.000
19B20ASP-1-0.893-0.95123.907-0.259-0.2590.0000.0000.0000.000
20B21ALA0-0.037-0.02126.1960.0210.0210.0000.0000.0000.000
21B22ARG10.8070.87725.8080.2060.2060.0000.0000.0000.000
22B23LYS10.9190.96329.1360.1670.1670.0000.0000.0000.000
23B24ALA0-0.051-0.02730.4670.0120.0120.0000.0000.0000.000
24B25CYS0-0.046-0.01932.3170.0130.0130.0000.0000.0000.000
25B26ALA0-0.0340.00634.1290.0070.0070.0000.0000.0000.000
26B27ASP-1-0.951-0.98535.760-0.102-0.1020.0000.0000.0000.000
27B28ALA0-0.025-0.00838.9940.0050.0050.0000.0000.0000.000
28B29THR00.0150.00538.646-0.003-0.0030.0000.0000.0000.000
29B30LEU00.0560.01440.5380.0060.0060.0000.0000.0000.000
30B31SER00.0250.00342.4190.0040.0040.0000.0000.0000.000
31B32GLN00.0230.00842.7580.0010.0010.0000.0000.0000.000
32B33ILE0-0.0130.00844.3190.0050.0050.0000.0000.0000.000
33B34THR0-0.020-0.02346.4970.0050.0050.0000.0000.0000.000
34B35ASN0-0.0110.01148.8230.0010.0010.0000.0000.0000.000
35B36ASN0-0.024-0.02550.3520.0000.0000.0000.0000.0000.000
36B37ILE0-0.050-0.01351.2940.0030.0030.0000.0000.0000.000
37B38ASP-1-0.842-0.91353.874-0.053-0.0530.0000.0000.0000.000
38B39PRO0-0.020-0.01553.561-0.001-0.0010.0000.0000.0000.000
39B40VAL0-0.019-0.01152.6640.0020.0020.0000.0000.0000.000
40B41GLY0-0.0120.00855.3610.0020.0020.0000.0000.0000.000
41B42ARG10.9450.95955.5940.0530.0530.0000.0000.0000.000
42B43ILE00.0290.01853.3640.0020.0020.0000.0000.0000.000
43B44GLN0-0.030-0.02855.5670.0000.0000.0000.0000.0000.000
44B45MET0-0.0150.01353.7150.0020.0020.0000.0000.0000.000
45B46ARG10.9600.97057.7630.0400.0400.0000.0000.0000.000
46B47THR00.0120.00757.1600.0000.0000.0000.0000.0000.000
47B48ARG10.8560.92059.0100.0410.0410.0000.0000.0000.000
48B49ARG10.8550.92659.0870.0340.0340.0000.0000.0000.000
49B50THR00.0040.00757.477-0.002-0.0020.0000.0000.0000.000
50B51LEU0-0.0110.00854.6940.0020.0020.0000.0000.0000.000
51B52ARG11.0311.01155.8140.0340.0340.0000.0000.0000.000
52B53GLY0-0.020-0.03556.4370.0020.0020.0000.0000.0000.000
53B54HIS00.0090.03450.6940.0010.0010.0000.0000.0000.000
54B55LEU0-0.036-0.02252.6130.0000.0000.0000.0000.0000.000
55B56ALA0-0.006-0.00448.1860.0000.0000.0000.0000.0000.000
56B57LYS10.9280.98643.1700.0610.0610.0000.0000.0000.000
57B58ILE0-0.006-0.00146.5590.0020.0020.0000.0000.0000.000
58B59TYR0-0.042-0.02039.898-0.004-0.0040.0000.0000.0000.000
59B60ALA00.0410.03042.018-0.003-0.0030.0000.0000.0000.000
60B61MET0-0.040-0.02843.9910.0030.0030.0000.0000.0000.000
61B62HIS00.0510.03545.574-0.002-0.0020.0000.0000.0000.000
62B63TRP0-0.018-0.02347.4780.0030.0030.0000.0000.0000.000
63B64GLY00.0430.02049.8190.0000.0000.0000.0000.0000.000
64B65THR00.015-0.00150.726-0.001-0.0010.0000.0000.0000.000
65B66ASP-1-0.844-0.91152.995-0.031-0.0310.0000.0000.0000.000
66B67SER0-0.057-0.02154.9560.0000.0000.0000.0000.0000.000
67B68ARG10.8090.88156.0210.0270.0270.0000.0000.0000.000
68B69LEU00.0090.00855.6940.0000.0000.0000.0000.0000.000
69B70LEU0-0.0100.00451.546-0.002-0.0020.0000.0000.0000.000
70B71VAL0-0.004-0.00247.9760.0020.0020.0000.0000.0000.000
71B72SER00.011-0.01448.384-0.002-0.0020.0000.0000.0000.000
72B73ALA00.0260.01344.8890.0030.0030.0000.0000.0000.000
73B74SER00.0320.00746.138-0.004-0.0040.0000.0000.0000.000
74B75GLN00.0080.01140.0220.0020.0020.0000.0000.0000.000
75B76ASP-1-0.802-0.88845.712-0.037-0.0370.0000.0000.0000.000
76B77GLY00.013-0.00747.3270.0020.0020.0000.0000.0000.000
77B78LYS10.8520.94848.3400.0310.0310.0000.0000.0000.000
78B79LEU00.0580.03446.346-0.003-0.0030.0000.0000.0000.000
79B80ILE0-0.063-0.02050.0390.0030.0030.0000.0000.0000.000
80B81ILE00.0160.02152.366-0.002-0.0020.0000.0000.0000.000
81B82TRP0-0.012-0.03352.9070.0030.0030.0000.0000.0000.000
82B83ASP-1-0.708-0.79856.911-0.029-0.0290.0000.0000.0000.000
83B84SER0-0.041-0.04256.9190.0000.0000.0000.0000.0000.000
84B85TYR0-0.001-0.00358.9990.0000.0000.0000.0000.0000.000
85B86THR0-0.013-0.03462.4740.0000.0000.0000.0000.0000.000
86B87THR0-0.076-0.03260.5290.0000.0000.0000.0000.0000.000
87B88ASN0-0.015-0.00361.2230.0000.0000.0000.0000.0000.000
88B89LYS10.8770.93857.7500.0300.0300.0000.0000.0000.000
89B90VAL0-0.034-0.01558.1620.0010.0010.0000.0000.0000.000
90B91HIS00.0460.01455.6570.0010.0010.0000.0000.0000.000
91B92ALA00.000-0.00554.759-0.002-0.0020.0000.0000.0000.000
92B93ILE0-0.004-0.00350.7560.0020.0020.0000.0000.0000.000
93B94PRO0-0.070-0.03251.422-0.002-0.0020.0000.0000.0000.000
94B95LEU00.0240.00945.2090.0020.0020.0000.0000.0000.000
95B96ARG10.8600.90945.6100.0160.0160.0000.0000.0000.000
96B97SER00.0260.02240.8150.0000.0000.0000.0000.0000.000
97B98SER00.007-0.00644.043-0.001-0.0010.0000.0000.0000.000
98B99TRP00.0040.01339.617-0.003-0.0030.0000.0000.0000.000
99B100VAL0-0.010-0.00339.784-0.003-0.0030.0000.0000.0000.000
100B101MET0-0.040-0.03234.527-0.001-0.0010.0000.0000.0000.000
101B102THR00.0160.01538.161-0.003-0.0030.0000.0000.0000.000
102B103CYS0-0.040-0.02340.7260.0030.0030.0000.0000.0000.000
103B104ALA0-0.0060.00442.805-0.003-0.0030.0000.0000.0000.000
104B105TYR00.007-0.01344.8520.0030.0030.0000.0000.0000.000
105B106ALA00.0000.01047.332-0.002-0.0020.0000.0000.0000.000
106B107PRO00.0450.00846.9140.0010.0010.0000.0000.0000.000
107B108SER0-0.043-0.05449.9730.0000.0000.0000.0000.0000.000
108B109GLY00.0030.00451.9090.0010.0010.0000.0000.0000.000
109B110ASN0-0.079-0.07452.6360.0010.0010.0000.0000.0000.000
110B111TYR00.0080.00748.6500.0020.0020.0000.0000.0000.000
111B112VAL0-0.0030.00547.986-0.002-0.0020.0000.0000.0000.000
112B113ALA00.0120.00842.9200.0020.0020.0000.0000.0000.000
113B114CYS0-0.020-0.01642.499-0.002-0.0020.0000.0000.0000.000
114B115GLY00.0550.03639.4420.0040.0040.0000.0000.0000.000
115B116GLY00.0250.01637.417-0.004-0.0040.0000.0000.0000.000
116B117LEU00.0270.01134.5020.0000.0000.0000.0000.0000.000
117B118ASP-1-0.888-0.94935.600-0.037-0.0370.0000.0000.0000.000
118B119ASN0-0.0100.00131.912-0.001-0.0010.0000.0000.0000.000
119B120ILE0-0.047-0.00334.8550.0040.0040.0000.0000.0000.000
120B121CYS0-0.0330.00437.793-0.004-0.0040.0000.0000.0000.000
121B122SER00.0370.00939.5460.0040.0040.0000.0000.0000.000
122B123ILE00.0130.00542.480-0.002-0.0020.0000.0000.0000.000
123B124TYR0-0.004-0.02345.7970.0030.0030.0000.0000.0000.000
124B125ASN00.0580.02649.477-0.002-0.0020.0000.0000.0000.000
125B126LEU0-0.032-0.02152.4020.0000.0000.0000.0000.0000.000
126B127LYS10.8500.94355.0080.0220.0220.0000.0000.0000.000
127B128THR00.0170.00955.9400.0010.0010.0000.0000.0000.000
128B129ARG10.8010.85958.4850.0120.0120.0000.0000.0000.000
129B130GLU-1-0.765-0.85262.315-0.012-0.0120.0000.0000.0000.000
130B131GLY0-0.037-0.00759.7660.0000.0000.0000.0000.0000.000
131B132ASN0-0.0040.00257.0810.0000.0000.0000.0000.0000.000
132B133VAL00.0550.04453.1810.0010.0010.0000.0000.0000.000
133B134ARG10.8580.91753.2900.0120.0120.0000.0000.0000.000
134B135VAL00.0020.00246.860-0.001-0.0010.0000.0000.0000.000
135B136SER0-0.052-0.02148.5170.0020.0020.0000.0000.0000.000
136B137ARG10.8590.91542.9580.0100.0100.0000.0000.0000.000
137B138GLU-1-0.838-0.90441.814-0.018-0.0180.0000.0000.0000.000
138B139LEU0-0.034-0.00138.3140.0030.0030.0000.0000.0000.000
139B140ALA00.0380.00836.440-0.004-0.0040.0000.0000.0000.000
140B141GLY00.024-0.00532.7990.0040.0040.0000.0000.0000.000
141B142HIS00.0020.02829.6210.0020.0020.0000.0000.0000.000
142B143THR0-0.065-0.03926.7080.0020.0020.0000.0000.0000.000
143B144GLY0-0.003-0.00128.425-0.005-0.0050.0000.0000.0000.000
144B145TYR0-0.042-0.04629.3570.0090.0090.0000.0000.0000.000
145B146LEU0-0.0060.01032.200-0.003-0.0030.0000.0000.0000.000
146B147SER0-0.016-0.04232.1590.0030.0030.0000.0000.0000.000
147B148CYS0-0.033-0.01835.0080.0010.0010.0000.0000.0000.000
148B149CYS0-0.0160.01636.4460.0030.0030.0000.0000.0000.000
149B150ARG10.8850.93538.8620.0540.0540.0000.0000.0000.000
150B151PHE0-0.0120.00240.6950.0010.0010.0000.0000.0000.000
151B152LEU00.0140.01239.440-0.002-0.0020.0000.0000.0000.000
152B153ASP-1-0.838-0.93343.534-0.022-0.0220.0000.0000.0000.000
153B154ASP-1-0.788-0.85646.050-0.023-0.0230.0000.0000.0000.000
154B155ASN0-0.053-0.02846.0170.0020.0020.0000.0000.0000.000
155B156GLN00.0000.01841.0070.0020.0020.0000.0000.0000.000
156B157ILE0-0.035-0.02039.559-0.003-0.0030.0000.0000.0000.000
157B158VAL00.0350.02434.7020.0020.0020.0000.0000.0000.000
158B159THR0-0.029-0.03733.6810.0000.0000.0000.0000.0000.000
159B160SER00.032-0.00631.5950.0000.0000.0000.0000.0000.000
160B161SER00.0120.00029.6130.0020.0020.0000.0000.0000.000
161B162GLY00.0710.02728.518-0.009-0.0090.0000.0000.0000.000
162B163ASP-1-0.781-0.84925.736-0.066-0.0660.0000.0000.0000.000
163B164THR0-0.082-0.03822.200-0.002-0.0020.0000.0000.0000.000
164B165THR0-0.070-0.05124.5950.0000.0000.0000.0000.0000.000
165B166CYS0-0.013-0.01226.847-0.004-0.0040.0000.0000.0000.000
166B167ALA00.0000.00929.7280.0050.0050.0000.0000.0000.000
167B168LEU00.0070.01032.378-0.004-0.0040.0000.0000.0000.000
168B169TRP0-0.045-0.03934.2410.0070.0070.0000.0000.0000.000
169B170ASP-1-0.772-0.85538.001-0.009-0.0090.0000.0000.0000.000
170B171ILE0-0.017-0.02541.0170.0010.0010.0000.0000.0000.000
171B172GLU-1-0.949-0.96443.348-0.003-0.0030.0000.0000.0000.000
172B173THR0-0.029-0.05441.5020.0020.0020.0000.0000.0000.000
173B174GLY0-0.078-0.04441.0030.0020.0020.0000.0000.0000.000
174B175GLN0-0.019-0.00136.2690.0010.0010.0000.0000.0000.000
175B176GLN00.000-0.00230.145-0.007-0.0070.0000.0000.0000.000
176B177THR0-0.016-0.00534.3710.0050.0050.0000.0000.0000.000
177B178THR0-0.011-0.00531.0340.0040.0040.0000.0000.0000.000
178B179THR0-0.0090.00227.039-0.001-0.0010.0000.0000.0000.000
179B180PHE0-0.026-0.01327.7350.0030.0030.0000.0000.0000.000
180B181THR00.0480.01522.381-0.002-0.0020.0000.0000.0000.000
181B182GLY00.018-0.01721.1500.0030.0030.0000.0000.0000.000
182B183HIS0-0.065-0.03821.018-0.009-0.0090.0000.0000.0000.000
183B184THR0-0.042-0.02517.535-0.003-0.0030.0000.0000.0000.000
184B185GLY00.0300.01720.373-0.018-0.0180.0000.0000.0000.000
185B186ASP-1-0.826-0.88023.231-0.120-0.1200.0000.0000.0000.000
186B187VAL0-0.0030.00226.607-0.006-0.0060.0000.0000.0000.000
187B188MET00.0030.04028.8880.0110.0110.0000.0000.0000.000
188B189SER0-0.006-0.00432.2040.0090.0090.0000.0000.0000.000
189B190LEU00.005-0.00933.265-0.005-0.0050.0000.0000.0000.000
190B191SER0-0.0060.00435.4170.0040.0040.0000.0000.0000.000
191B192LEU0-0.007-0.00537.462-0.003-0.0030.0000.0000.0000.000
192B193ALA00.0180.01138.965-0.001-0.0010.0000.0000.0000.000
193B194PRO00.0110.00440.6700.0040.0040.0000.0000.0000.000
194B195ASP-1-0.827-0.89741.761-0.045-0.0450.0000.0000.0000.000
195B196THR0-0.092-0.05141.2970.0040.0040.0000.0000.0000.000
196B197ARG10.8800.92839.5190.0400.0400.0000.0000.0000.000
197B198LEU00.0010.00634.771-0.001-0.0010.0000.0000.0000.000
198B199PHE0-0.010-0.00631.7820.0020.0020.0000.0000.0000.000
199B200VAL0-0.0010.00932.758-0.003-0.0030.0000.0000.0000.000
200B201SER00.0210.00229.0400.0090.0090.0000.0000.0000.000
201B202GLY00.0020.00130.002-0.008-0.0080.0000.0000.0000.000
202B203ALA00.0070.00626.2090.0100.0100.0000.0000.0000.000
203B204CYS0-0.002-0.02626.004-0.003-0.0030.0000.0000.0000.000
204B205ASP-1-0.777-0.83721.686-0.210-0.2100.0000.0000.0000.000
205B206ALA0-0.0090.00323.284-0.018-0.0180.0000.0000.0000.000
206B207SER0-0.085-0.06224.0190.0030.0030.0000.0000.0000.000
207B208ALA00.021-0.00526.1070.0130.0130.0000.0000.0000.000
208B209LYS10.8510.93622.1060.1690.1690.0000.0000.0000.000
209B210LEU00.0130.01728.4830.0100.0100.0000.0000.0000.000
210B211TRP0-0.024-0.02925.223-0.002-0.0020.0000.0000.0000.000
211B212ASP-1-0.793-0.90231.365-0.044-0.0440.0000.0000.0000.000
212B213VAL00.000-0.00132.8920.0030.0030.0000.0000.0000.000
213B214ARG10.8090.89834.9680.0280.0280.0000.0000.0000.000
214B215GLU-1-0.865-0.93831.939-0.028-0.0280.0000.0000.0000.000
215B216GLY00.0050.02030.6530.0030.0030.0000.0000.0000.000
216B217MET0-0.0260.00027.364-0.003-0.0030.0000.0000.0000.000
217B218CYS0-0.041-0.01725.262-0.008-0.0080.0000.0000.0000.000
218B219ARG10.8440.90626.9130.0630.0630.0000.0000.0000.000
219B220GLN0-0.053-0.05227.3390.0020.0020.0000.0000.0000.000
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