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: 4L9ZN

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 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 339
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5201014.882781
FMO2-HF: Nuclear repulsion 5066605.090806
FMO2-HF: Total energy -134409.791975
FMO2-MP2: Total energy -134790.323046


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.
-22.269-16.79111.308-7.993-8.794-0.042
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 : 0.020 / q_NPA : 0.001
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].
3B4LEU00.0180.0092.453-8.455-4.3541.353-2.407-3.0480.017
4B5ASP-1-0.821-0.9041.967-18.706-17.8269.954-5.424-5.410-0.059
5B6GLN0-0.027-0.0103.9591.1801.6770.001-0.162-0.3360.000
6B7LEU00.0600.0325.9200.5380.5380.0000.0000.0000.000
7B8ARG10.8420.9165.3733.3733.3730.0000.0000.0000.000
8B9GLN0-0.026-0.0198.0010.1070.1070.0000.0000.0000.000
9B10GLU-1-0.921-0.9649.808-0.280-0.2800.0000.0000.0000.000
10B11ALA00.0290.01311.6360.1710.1710.0000.0000.0000.000
11B12GLU-1-0.832-0.90512.632-0.617-0.6170.0000.0000.0000.000
12B13GLN0-0.043-0.01413.9880.0680.0680.0000.0000.0000.000
13B14LEU00.002-0.00415.6820.0930.0930.0000.0000.0000.000
14B15LYS10.8350.89815.2070.6750.6750.0000.0000.0000.000
15B16ASN0-0.040-0.02917.5020.0880.0880.0000.0000.0000.000
16B17GLN00.0560.03818.6280.0100.0100.0000.0000.0000.000
17B18ILE00.0050.01021.0790.0340.0340.0000.0000.0000.000
18B19ARG10.9120.96321.9520.3550.3550.0000.0000.0000.000
19B20ASP-1-0.898-0.95023.394-0.264-0.2640.0000.0000.0000.000
20B21ALA0-0.030-0.01525.8380.0220.0220.0000.0000.0000.000
21B22ARG10.8070.88325.8270.2250.2250.0000.0000.0000.000
22B23LYS10.8940.94228.8790.1670.1670.0000.0000.0000.000
23B24ALA0-0.050-0.02730.1130.0130.0130.0000.0000.0000.000
24B25CYS0-0.067-0.02731.8180.0140.0140.0000.0000.0000.000
25B26ALA0-0.0190.01233.7930.0070.0070.0000.0000.0000.000
26B27ASP-1-0.910-0.95735.470-0.105-0.1050.0000.0000.0000.000
27B28ALA0-0.036-0.01338.4860.0030.0030.0000.0000.0000.000
28B29THR00.016-0.00538.167-0.005-0.0050.0000.0000.0000.000
29B30LEU00.0400.00840.4490.0060.0060.0000.0000.0000.000
30B31SER00.003-0.00442.5560.0050.0050.0000.0000.0000.000
31B32GLN00.0370.02642.2700.0000.0000.0000.0000.0000.000
32B33ILE0-0.019-0.00244.2370.0050.0050.0000.0000.0000.000
33B34THR0-0.023-0.03146.4670.0040.0040.0000.0000.0000.000
34B35ASN0-0.0010.01248.7220.0010.0010.0000.0000.0000.000
35B36ASN0-0.029-0.02750.2220.0000.0000.0000.0000.0000.000
36B37ILE0-0.0340.00451.3610.0030.0030.0000.0000.0000.000
37B38ASP-1-0.845-0.91453.595-0.056-0.0560.0000.0000.0000.000
38B39PRO0-0.0030.00453.153-0.001-0.0010.0000.0000.0000.000
39B40VAL0-0.037-0.03052.4880.0020.0020.0000.0000.0000.000
40B41GLY0-0.0030.01855.0370.0020.0020.0000.0000.0000.000
41B42ARG10.9360.95455.2670.0550.0550.0000.0000.0000.000
42B43ILE00.0300.01853.1090.0030.0030.0000.0000.0000.000
43B44GLN0-0.025-0.01855.233-0.002-0.0020.0000.0000.0000.000
44B45MET0-0.0030.01353.2750.0020.0020.0000.0000.0000.000
45B46ARG10.9470.96057.7540.0450.0450.0000.0000.0000.000
46B47THR00.0190.01857.1260.0000.0000.0000.0000.0000.000
47B48ARG10.8510.91958.9540.0460.0460.0000.0000.0000.000
48B49ARG10.8420.91458.9880.0400.0400.0000.0000.0000.000
49B50THR00.0110.00757.233-0.003-0.0030.0000.0000.0000.000
50B51LEU0-0.0110.00554.7660.0020.0020.0000.0000.0000.000
51B52ARG11.0251.01055.9690.0400.0400.0000.0000.0000.000
52B53GLY0-0.033-0.04156.6370.0020.0020.0000.0000.0000.000
53B54HIS00.0100.03550.6060.0010.0010.0000.0000.0000.000
54B55LEU0-0.039-0.03152.6970.0010.0010.0000.0000.0000.000
55B56ALA0-0.012-0.00348.5270.0000.0000.0000.0000.0000.000
56B57LYS10.9370.98443.6080.0720.0720.0000.0000.0000.000
57B58ILE00.0220.02046.1780.0000.0000.0000.0000.0000.000
58B59TYR0-0.050-0.01840.107-0.004-0.0040.0000.0000.0000.000
59B60ALA00.0460.03242.207-0.003-0.0030.0000.0000.0000.000
60B61MET0-0.026-0.02144.1400.0040.0040.0000.0000.0000.000
61B62HIS00.0480.02645.586-0.004-0.0040.0000.0000.0000.000
62B63TRP0-0.014-0.03047.7250.0040.0040.0000.0000.0000.000
63B64GLY00.0240.01950.100-0.001-0.0010.0000.0000.0000.000
64B65THR00.016-0.00851.1550.0000.0000.0000.0000.0000.000
65B66ASP-1-0.842-0.91353.353-0.039-0.0390.0000.0000.0000.000
66B67SER0-0.038-0.00455.1730.0000.0000.0000.0000.0000.000
67B68ARG10.7950.87556.1570.0340.0340.0000.0000.0000.000
68B69LEU00.0040.00355.6640.0000.0000.0000.0000.0000.000
69B70LEU0-0.0190.00451.770-0.002-0.0020.0000.0000.0000.000
70B71VAL0-0.012-0.00648.2810.0020.0020.0000.0000.0000.000
71B72SER00.019-0.00848.551-0.002-0.0020.0000.0000.0000.000
72B73ALA00.0270.01245.1840.0030.0030.0000.0000.0000.000
73B74SER00.015-0.01746.345-0.004-0.0040.0000.0000.0000.000
74B75GLN00.0390.02740.4230.0020.0020.0000.0000.0000.000
75B76ASP-1-0.785-0.86546.037-0.048-0.0480.0000.0000.0000.000
76B77GLY00.0310.01947.5330.0030.0030.0000.0000.0000.000
77B78LYS10.7960.89648.5660.0440.0440.0000.0000.0000.000
78B79LEU00.0670.04446.555-0.003-0.0030.0000.0000.0000.000
79B80ILE0-0.071-0.03450.1160.0030.0030.0000.0000.0000.000
80B81ILE00.0050.00952.539-0.002-0.0020.0000.0000.0000.000
81B82TRP0-0.017-0.03053.1500.0030.0030.0000.0000.0000.000
82B83ASP-1-0.705-0.79257.174-0.036-0.0360.0000.0000.0000.000
83B84SER0-0.023-0.03156.8690.0000.0000.0000.0000.0000.000
84B85TYR00.003-0.00258.9300.0010.0010.0000.0000.0000.000
85B86THR0-0.043-0.04162.3800.0010.0010.0000.0000.0000.000
86B87THR0-0.066-0.03060.4920.0000.0000.0000.0000.0000.000
87B88ASN0-0.020-0.01261.0220.0000.0000.0000.0000.0000.000
88B89LYS10.8760.94857.8840.0370.0370.0000.0000.0000.000
89B90VAL0-0.017-0.00658.3370.0010.0010.0000.0000.0000.000
90B91HIS00.0450.01455.6570.0010.0010.0000.0000.0000.000
91B92ALA00.005-0.00755.000-0.002-0.0020.0000.0000.0000.000
92B93ILE0-0.0030.01650.9550.0020.0020.0000.0000.0000.000
93B94PRO0-0.031-0.01451.667-0.002-0.0020.0000.0000.0000.000
94B95LEU00.004-0.00245.5450.0010.0010.0000.0000.0000.000
95B96ARG10.8380.89245.9660.0310.0310.0000.0000.0000.000
96B97SER0-0.028-0.02241.3230.0000.0000.0000.0000.0000.000
97B98SER00.021-0.00344.3510.0000.0000.0000.0000.0000.000
98B99TRP00.0030.00639.752-0.002-0.0020.0000.0000.0000.000
99B100VAL0-0.0060.00339.928-0.004-0.0040.0000.0000.0000.000
100B101MET0-0.045-0.02734.809-0.001-0.0010.0000.0000.0000.000
101B102THR00.0150.02237.986-0.002-0.0020.0000.0000.0000.000
102B103CYS0-0.039-0.02040.8400.0040.0040.0000.0000.0000.000
103B104ALA00.0080.01543.128-0.003-0.0030.0000.0000.0000.000
104B105TYR00.020-0.00745.1860.0030.0030.0000.0000.0000.000
105B106ALA00.0060.01347.338-0.002-0.0020.0000.0000.0000.000
106B107PRO00.0240.00047.1270.0010.0010.0000.0000.0000.000
107B108SER0-0.022-0.03150.1570.0000.0000.0000.0000.0000.000
108B109GLY0-0.0070.00052.3340.0010.0010.0000.0000.0000.000
109B110ASN0-0.088-0.08652.8130.0010.0010.0000.0000.0000.000
110B111TYR0-0.0030.00248.9400.0020.0020.0000.0000.0000.000
111B112VAL00.0000.00648.223-0.002-0.0020.0000.0000.0000.000
112B113ALA00.0160.00943.1530.0020.0020.0000.0000.0000.000
113B114CYS0-0.034-0.01742.8020.0000.0000.0000.0000.0000.000
114B115GLY00.0820.05239.2960.0030.0030.0000.0000.0000.000
115B116GLY00.0480.01537.617-0.002-0.0020.0000.0000.0000.000
116B117LEU0-0.004-0.00834.682-0.001-0.0010.0000.0000.0000.000
117B118ASP-1-0.816-0.88536.053-0.058-0.0580.0000.0000.0000.000
118B119ASN0-0.0200.00031.4980.0000.0000.0000.0000.0000.000
119B120ILE0-0.054-0.01434.8460.0030.0030.0000.0000.0000.000
120B121CYS0-0.030-0.00237.917-0.003-0.0030.0000.0000.0000.000
121B122SER00.0210.00739.6520.0040.0040.0000.0000.0000.000
122B123ILE00.0120.00742.409-0.002-0.0020.0000.0000.0000.000
123B124TYR0-0.014-0.03845.8140.0040.0040.0000.0000.0000.000
124B125ASN00.0530.02149.612-0.001-0.0010.0000.0000.0000.000
125B126LEU0-0.014-0.01252.6500.0000.0000.0000.0000.0000.000
126B127LYS10.8690.95055.4060.0310.0310.0000.0000.0000.000
127B128THR0-0.015-0.02055.8740.0010.0010.0000.0000.0000.000
128B129ARG10.8180.87358.4810.0190.0190.0000.0000.0000.000
129B130GLU-1-0.783-0.86562.344-0.019-0.0190.0000.0000.0000.000
130B131GLY0-0.0340.00359.7270.0000.0000.0000.0000.0000.000
131B132ASN0-0.025-0.00557.1500.0000.0000.0000.0000.0000.000
132B133VAL00.0570.05453.3540.0000.0000.0000.0000.0000.000
133B134ARG10.8610.91953.4330.0220.0220.0000.0000.0000.000
134B135VAL00.0030.00646.968-0.001-0.0010.0000.0000.0000.000
135B136SER0-0.036-0.01348.3690.0030.0030.0000.0000.0000.000
136B137ARG10.8360.90042.8280.0260.0260.0000.0000.0000.000
137B138GLU-1-0.804-0.89341.937-0.034-0.0340.0000.0000.0000.000
138B139LEU0-0.0280.01538.3500.0030.0030.0000.0000.0000.000
139B140ALA00.0430.01036.232-0.004-0.0040.0000.0000.0000.000
140B141GLY00.017-0.00332.5870.0050.0050.0000.0000.0000.000
141B142HIS00.0180.02729.6200.0020.0020.0000.0000.0000.000
142B143THR0-0.061-0.04426.7590.0020.0020.0000.0000.0000.000
143B144GLY0-0.0190.00128.766-0.005-0.0050.0000.0000.0000.000
144B145TYR0-0.043-0.05129.5120.0110.0110.0000.0000.0000.000
145B146LEU0-0.025-0.00732.480-0.005-0.0050.0000.0000.0000.000
146B147SER0-0.029-0.04132.2580.0040.0040.0000.0000.0000.000
147B148CYS0-0.039-0.01335.0310.0040.0040.0000.0000.0000.000
148B149CYS0-0.023-0.00336.5650.0030.0030.0000.0000.0000.000
149B150ARG10.8750.92239.0220.0690.0690.0000.0000.0000.000
150B151PHE0-0.0010.00840.7880.0000.0000.0000.0000.0000.000
151B152LEU0-0.0010.00939.657-0.002-0.0020.0000.0000.0000.000
152B153ASP-1-0.813-0.91043.808-0.033-0.0330.0000.0000.0000.000
153B154ASP-1-0.773-0.85746.152-0.034-0.0340.0000.0000.0000.000
154B155ASN0-0.060-0.02946.2240.0020.0020.0000.0000.0000.000
155B156GLN0-0.018-0.00741.3860.0000.0000.0000.0000.0000.000
156B157ILE0-0.035-0.01939.730-0.002-0.0020.0000.0000.0000.000
157B158VAL00.0400.03134.9850.0010.0010.0000.0000.0000.000
158B159THR0-0.023-0.03233.8420.0020.0020.0000.0000.0000.000
159B160SER00.024-0.00731.651-0.001-0.0010.0000.0000.0000.000
160B161SER00.003-0.01429.6560.0050.0050.0000.0000.0000.000
161B162GLY00.0840.04128.493-0.011-0.0110.0000.0000.0000.000
162B163ASP-1-0.774-0.83925.513-0.110-0.1100.0000.0000.0000.000
163B164THR0-0.067-0.02521.848-0.008-0.0080.0000.0000.0000.000
164B165THR0-0.065-0.05324.6290.0000.0000.0000.0000.0000.000
165B166CYS00.002-0.00126.856-0.001-0.0010.0000.0000.0000.000
166B167ALA0-0.012-0.00229.7890.0030.0030.0000.0000.0000.000
167B168LEU00.0070.00332.447-0.003-0.0030.0000.0000.0000.000
168B169TRP0-0.050-0.03934.3160.0060.0060.0000.0000.0000.000
169B170ASP-1-0.773-0.84938.130-0.025-0.0250.0000.0000.0000.000
170B171ILE0-0.035-0.03941.1560.0010.0010.0000.0000.0000.000
171B172GLU-1-0.960-0.96443.668-0.016-0.0160.0000.0000.0000.000
172B173THR0-0.038-0.05741.4730.0020.0020.0000.0000.0000.000
173B174GLY0-0.060-0.03541.3930.0010.0010.0000.0000.0000.000
174B175GLN0-0.022-0.00536.402-0.001-0.0010.0000.0000.0000.000
175B176GLN00.0160.00130.329-0.007-0.0070.0000.0000.0000.000
176B177THR00.0080.00834.1910.0040.0040.0000.0000.0000.000
177B178THR0-0.042-0.02330.8530.0020.0020.0000.0000.0000.000
178B179THR0-0.0030.00127.1990.0010.0010.0000.0000.0000.000
179B180PHE0-0.019-0.00327.5680.0040.0040.0000.0000.0000.000
180B181THR00.0430.01822.142-0.005-0.0050.0000.0000.0000.000
181B182GLY00.039-0.00421.4060.0060.0060.0000.0000.0000.000
182B183HIS0-0.066-0.02821.874-0.004-0.0040.0000.0000.0000.000
183B184THR0-0.070-0.05017.761-0.009-0.0090.0000.0000.0000.000
184B185GLY00.0370.01420.326-0.024-0.0240.0000.0000.0000.000
185B186ASP-1-0.836-0.88823.205-0.157-0.1570.0000.0000.0000.000
186B187VAL0-0.0050.00726.840-0.005-0.0050.0000.0000.0000.000
187B188MET00.0030.03928.8990.0130.0130.0000.0000.0000.000
188B189SER00.003-0.00832.1060.0120.0120.0000.0000.0000.000
189B190LEU00.009-0.00833.128-0.007-0.0070.0000.0000.0000.000
190B191SER0-0.024-0.00135.3500.0060.0060.0000.0000.0000.000
191B192LEU00.0110.00337.265-0.003-0.0030.0000.0000.0000.000
192B193ALA00.0400.02038.882-0.002-0.0020.0000.0000.0000.000
193B194PRO0-0.035-0.02940.4900.0040.0040.0000.0000.0000.000
194B195ASP-1-0.812-0.88541.839-0.056-0.0560.0000.0000.0000.000
195B196THR0-0.089-0.05141.4040.0040.0040.0000.0000.0000.000
196B197ARG10.8830.93439.7470.0490.0490.0000.0000.0000.000
197B198LEU00.0100.01234.711-0.001-0.0010.0000.0000.0000.000
198B199PHE0-0.011-0.00731.7940.0030.0030.0000.0000.0000.000
199B200VAL00.0000.00832.718-0.004-0.0040.0000.0000.0000.000
200B201SER00.012-0.00629.0150.0090.0090.0000.0000.0000.000
201B202GLY00.0220.01029.478-0.007-0.0070.0000.0000.0000.000
202B203ALA00.0010.00826.1100.0110.0110.0000.0000.0000.000
203B204CYS00.001-0.01225.920-0.001-0.0010.0000.0000.0000.000
204B205ASP-1-0.756-0.82621.566-0.255-0.2550.0000.0000.0000.000
205B206ALA0-0.0080.00223.145-0.019-0.0190.0000.0000.0000.000
206B207SER0-0.084-0.05623.8000.0090.0090.0000.0000.0000.000
207B208ALA00.0390.00325.9050.0150.0150.0000.0000.0000.000
208B209LYS10.8180.91622.2920.2130.2130.0000.0000.0000.000
209B210LEU00.0080.01328.5870.0110.0110.0000.0000.0000.000
210B211TRP0-0.018-0.01925.277-0.005-0.0050.0000.0000.0000.000
211B212ASP-1-0.775-0.88731.310-0.059-0.0590.0000.0000.0000.000
212B213VAL0-0.006-0.00233.1390.0020.0020.0000.0000.0000.000
213B214ARG10.8100.90035.7730.0430.0430.0000.0000.0000.000
214B215GLU-1-0.823-0.90131.874-0.049-0.0490.0000.0000.0000.000
215B216GLY00.0170.01930.3210.0020.0020.0000.0000.0000.000
216B217MET0-0.046-0.01827.244-0.010-0.0100.0000.0000.0000.000
217B218CYS0-0.020-0.00325.087-0.005-0.0050.0000.0000.0000.000
218B219ARG10.7890.86526.6660.0750.0750.0000.0000.0000.000
219B220GLN0-0.037-0.04527.2950.0040.0040.0000.0000.0000.000
220B221THR00.0250.01022.934-0.002-0.0020.0000.0000.0000.000
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