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: 98872

Calculation Name: 4R3O-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: G

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 245
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3088175.744209
FMO2-HF: Nuclear repulsion 2991645.871936
FMO2-HF: Total energy -96529.872273
FMO2-MP2: Total energy -96808.283922


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(G:1:SER)


Summations of interaction energy for fragment #1(G:1: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.
1.7920.45714.492-8.565-4.5930.012
Interaction energy analysis for fragmet #1(G:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.033
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].
3G3ILE0-0.0140.0153.811-0.8671.627-0.030-1.266-1.198-0.002
4G4GLY00.0600.0406.550-0.302-0.3020.0000.0000.0000.000
5G5THR0-0.050-0.0339.8910.0150.0150.0000.0000.0000.000
6G6GLY00.0290.02012.8250.0270.0270.0000.0000.0000.000
7G7TYR0-0.037-0.03510.3320.0150.0150.0000.0000.0000.000
8G8ASP-1-0.842-0.9059.765-0.161-0.1610.0000.0000.0000.000
9G9LEU00.0010.01411.771-0.064-0.0640.0000.0000.0000.000
10G10SER00.003-0.01015.001-0.012-0.0120.0000.0000.0000.000
11G11ALA00.001-0.00514.9490.0290.0290.0000.0000.0000.000
12G12SER0-0.0140.01516.3360.0170.0170.0000.0000.0000.000
13G13THR0-0.061-0.03813.708-0.014-0.0140.0000.0000.0000.000
14G14PHE0-0.0020.01411.9950.0020.0020.0000.0000.0000.000
15G15SER0-0.032-0.0347.208-0.125-0.1250.0000.0000.0000.000
16G16PRO0-0.018-0.0199.340-0.006-0.0060.0000.0000.0000.000
17G17ASP-1-0.842-0.9094.9242.2522.318-0.001-0.002-0.0630.000
18G18GLY0-0.037-0.0088.4280.0010.0010.0000.0000.0000.000
19G19ARG10.7880.8861.574-1.378-5.48114.522-7.248-3.1710.014
20G20VAL00.0880.0418.645-0.123-0.1230.0000.0000.0000.000
21G21PHE00.0640.0123.993-0.1770.0310.001-0.049-0.1610.000
22G22GLN00.0260.0179.242-0.156-0.1560.0000.0000.0000.000
23G23VAL00.0420.01611.839-0.062-0.0620.0000.0000.0000.000
24G24GLU-1-0.808-0.8705.2281.2201.2200.0000.0000.0000.000
25G25TYR0-0.109-0.0816.864-0.236-0.2360.0000.0000.0000.000
26G26ALA00.0110.01010.224-0.017-0.0170.0000.0000.0000.000
27G27MET00.004-0.00510.1090.0240.0240.0000.0000.0000.000
28G28LYS10.9670.9895.6801.7281.7280.0000.0000.0000.000
29G29ALA0-0.016-0.01010.706-0.022-0.0220.0000.0000.0000.000
30G30VAL0-0.059-0.02714.0810.0050.0050.0000.0000.0000.000
31G31GLU-1-0.867-0.93010.5090.1240.1240.0000.0000.0000.000
32G32ASN0-0.048-0.01413.191-0.016-0.0160.0000.0000.0000.000
33G33SER0-0.0140.00015.6440.0020.0020.0000.0000.0000.000
34G34SER0-0.047-0.01418.8040.0030.0030.0000.0000.0000.000
35G35THR00.0270.01320.3480.0090.0090.0000.0000.0000.000
36G36ALA0-0.0100.00321.716-0.005-0.0050.0000.0000.0000.000
37G37ILE00.000-0.00422.6840.0130.0130.0000.0000.0000.000
38G38GLY00.020-0.00524.977-0.006-0.0060.0000.0000.0000.000
39G39ILE0-0.016-0.00926.6330.0090.0090.0000.0000.0000.000
40G40ARG10.9180.97329.221-0.069-0.0690.0000.0000.0000.000
41G41CYS0-0.036-0.00931.6160.0010.0010.0000.0000.0000.000
42G42LYS10.9140.96034.812-0.025-0.0250.0000.0000.0000.000
43G43ASP-1-0.765-0.87937.9970.0270.0270.0000.0000.0000.000
44G44GLY00.000-0.02836.997-0.002-0.0020.0000.0000.0000.000
45G45VAL0-0.064-0.03130.8620.0040.0040.0000.0000.0000.000
46G46VAL0-0.0050.00632.339-0.004-0.0040.0000.0000.0000.000
47G47PHE0-0.028-0.01427.4080.0050.0050.0000.0000.0000.000
48G48GLY00.0550.01328.627-0.005-0.0050.0000.0000.0000.000
49G49VAL0-0.040-0.02126.1560.0040.0040.0000.0000.0000.000
50G50GLU-1-0.768-0.87024.054-0.050-0.0500.0000.0000.0000.000
51G51LYS10.8090.92425.9270.0120.0120.0000.0000.0000.000
52G52LEU00.001-0.00523.398-0.001-0.0010.0000.0000.0000.000
53G53VAL00.0070.01927.7150.0010.0010.0000.0000.0000.000
54G54LEU0-0.018-0.01426.189-0.005-0.0050.0000.0000.0000.000
55G55SER00.004-0.01230.254-0.002-0.0020.0000.0000.0000.000
56G56LYS10.9580.97134.0060.0550.0550.0000.0000.0000.000
57G57LEU00.0040.00737.0980.0030.0030.0000.0000.0000.000
58G58TYR0-0.078-0.02731.4980.0000.0000.0000.0000.0000.000
59G59GLU-1-0.859-0.93636.774-0.019-0.0190.0000.0000.0000.000
60G60GLU-1-0.921-0.94236.899-0.015-0.0150.0000.0000.0000.000
61G61GLY0-0.032-0.01735.7470.0030.0030.0000.0000.0000.000
62G62SER0-0.026-0.01833.6060.0040.0040.0000.0000.0000.000
63G63ASN0-0.073-0.05829.438-0.001-0.0010.0000.0000.0000.000
64G64LYS10.9470.97730.0750.0030.0030.0000.0000.0000.000
65G65ARG10.8810.95222.0070.0190.0190.0000.0000.0000.000
66G66LEU00.0280.02028.0980.0070.0070.0000.0000.0000.000
67G67PHE0-0.036-0.02628.063-0.004-0.0040.0000.0000.0000.000
68G68ASN00.0340.02732.4210.0050.0050.0000.0000.0000.000
69G69VAL00.0080.00830.818-0.002-0.0020.0000.0000.0000.000
70G70ASP-1-0.731-0.86334.1730.0350.0350.0000.0000.0000.000
71G71ARG10.8790.94437.340-0.028-0.0280.0000.0000.0000.000
72G72HIS0-0.054-0.03737.513-0.005-0.0050.0000.0000.0000.000
73G73VAL0-0.010-0.00232.5470.0030.0030.0000.0000.0000.000
74G74GLY00.0560.03432.987-0.003-0.0030.0000.0000.0000.000
75G75MET0-0.034-0.02425.8950.0050.0050.0000.0000.0000.000
76G76ALA00.0380.03026.449-0.008-0.0080.0000.0000.0000.000
77G77VAL0-0.032-0.01123.6590.0100.0100.0000.0000.0000.000
78G78ALA00.019-0.01019.865-0.010-0.0100.0000.0000.0000.000
79G79GLY00.0310.01718.7340.0130.0130.0000.0000.0000.000
80G80LEU0-0.033-0.01919.305-0.008-0.0080.0000.0000.0000.000
81G81LEU00.0120.00021.1160.0130.0130.0000.0000.0000.000
82G82ALA0-0.011-0.01324.7280.0080.0080.0000.0000.0000.000
83G83ASP-1-0.716-0.84721.1000.0030.0030.0000.0000.0000.000
84G84ALA00.0480.03923.8950.0110.0110.0000.0000.0000.000
85G85ARG10.9100.95724.9950.0150.0150.0000.0000.0000.000
86G86SER0-0.011-0.01426.1270.0040.0040.0000.0000.0000.000
87G87LEU00.0430.00322.4600.0040.0040.0000.0000.0000.000
88G88ALA0-0.023-0.00927.0940.0050.0050.0000.0000.0000.000
89G89ASP-1-0.921-0.96629.8560.0210.0210.0000.0000.0000.000
90G90ILE00.0090.01527.7260.0020.0020.0000.0000.0000.000
91G91ALA0-0.014-0.01029.5350.0020.0020.0000.0000.0000.000
92G92ARG10.8390.91531.329-0.022-0.0220.0000.0000.0000.000
93G93GLU-1-0.931-0.94934.4500.0370.0370.0000.0000.0000.000
94G94GLU-1-0.859-0.92532.2580.0640.0640.0000.0000.0000.000
95G95ALA0-0.008-0.01734.7760.0000.0000.0000.0000.0000.000
96G96SER0-0.054-0.01936.658-0.002-0.0020.0000.0000.0000.000
97G97ASN00.0470.00737.191-0.004-0.0040.0000.0000.0000.000
98G98PHE0-0.0010.00337.5210.0000.0000.0000.0000.0000.000
99G99ARG10.8900.92339.584-0.035-0.0350.0000.0000.0000.000
100G100SER0-0.056-0.03142.498-0.002-0.0020.0000.0000.0000.000
101G101ASN0-0.022-0.00440.817-0.003-0.0030.0000.0000.0000.000
102G102PHE0-0.039-0.01439.9970.0010.0010.0000.0000.0000.000
103G103GLY0-0.0020.01444.372-0.001-0.0010.0000.0000.0000.000
104G104TYR0-0.045-0.02540.538-0.002-0.0020.0000.0000.0000.000
105G105ASN0-0.018-0.02940.4670.0000.0000.0000.0000.0000.000
106G106ILE00.0360.04134.6300.0010.0010.0000.0000.0000.000
107G107PRO00.0400.03135.5690.0000.0000.0000.0000.0000.000
108G108LEU0-0.003-0.00430.3770.0030.0030.0000.0000.0000.000
109G109LYS10.9090.95530.027-0.067-0.0670.0000.0000.0000.000
110G110HIS00.0380.02629.9410.0080.0080.0000.0000.0000.000
111G111LEU00.0060.00330.7430.0030.0030.0000.0000.0000.000
112G112ALA0-0.020-0.01526.6800.0010.0010.0000.0000.0000.000
113G113ASP-1-0.874-0.93826.6670.1240.1240.0000.0000.0000.000
114G114ARG10.8020.90727.158-0.068-0.0680.0000.0000.0000.000
115G115VAL00.0180.00125.6470.0020.0020.0000.0000.0000.000
116G116ALA0-0.0060.00322.9000.0000.0000.0000.0000.0000.000
117G117MET00.0160.00823.0450.0160.0160.0000.0000.0000.000
118G118TYR0-0.014-0.00524.8440.0010.0010.0000.0000.0000.000
119G119VAL0-0.017-0.01619.774-0.005-0.0050.0000.0000.0000.000
120G120HIS00.0550.02819.332-0.009-0.0090.0000.0000.0000.000
121G121ALA0-0.0110.00520.9630.0090.0090.0000.0000.0000.000
122G122TYR0-0.067-0.03920.914-0.009-0.0090.0000.0000.0000.000
123G123THR0-0.132-0.06816.5010.0040.0040.0000.0000.0000.000
124G124LEU00.0200.01517.4600.0240.0240.0000.0000.0000.000
125G125TYR0-0.008-0.00419.9130.0020.0020.0000.0000.0000.000
126G126SER0-0.017-0.00320.344-0.002-0.0020.0000.0000.0000.000
127G127ALA0-0.022-0.01221.333-0.014-0.0140.0000.0000.0000.000
128G128VAL0-0.0150.00622.158-0.011-0.0110.0000.0000.0000.000
129G129ARG10.8640.92618.5600.0130.0130.0000.0000.0000.000
130G130PRO00.0460.01415.242-0.002-0.0020.0000.0000.0000.000
131G131PHE00.0340.02118.083-0.026-0.0260.0000.0000.0000.000
132G132GLY00.0200.01416.7200.0120.0120.0000.0000.0000.000
133G133CYS0-0.087-0.05217.771-0.022-0.0220.0000.0000.0000.000
134G134SER00.0680.03816.9150.0360.0360.0000.0000.0000.000
135G135PHE0-0.028-0.01819.298-0.021-0.0210.0000.0000.0000.000
136G136MET0-0.0180.01522.8160.0130.0130.0000.0000.0000.000
137G137LEU00.0120.01025.119-0.011-0.0110.0000.0000.0000.000
138G138GLY00.0370.01228.5180.0050.0050.0000.0000.0000.000
139G139SER0-0.059-0.03731.330-0.004-0.0040.0000.0000.0000.000
140G140TYR00.0450.02134.7540.0020.0020.0000.0000.0000.000
141G141SER0-0.015-0.00337.798-0.003-0.0030.0000.0000.0000.000
142G142VAL00.0560.02340.6710.0010.0010.0000.0000.0000.000
143G143ASN0-0.022-0.01142.794-0.001-0.0010.0000.0000.0000.000
144G144ASP-1-0.896-0.93437.2280.0590.0590.0000.0000.0000.000
145G145GLY00.0090.02037.5840.0030.0030.0000.0000.0000.000
146G146ALA0-0.013-0.00335.207-0.001-0.0010.0000.0000.0000.000
147G147GLN0-0.048-0.04031.6230.0090.0090.0000.0000.0000.000
148G148LEU00.0400.01026.646-0.005-0.0050.0000.0000.0000.000
149G149TYR0-0.024-0.00325.7350.0070.0070.0000.0000.0000.000
150G150MET0-0.043-0.02017.604-0.016-0.0160.0000.0000.0000.000
151G151ILE00.0480.02720.6820.0140.0140.0000.0000.0000.000
152G152ASP-1-0.741-0.81515.3270.2860.2860.0000.0000.0000.000
153G153PRO0-0.043-0.03914.5370.0020.0020.0000.0000.0000.000
154G154SER0-0.103-0.10814.038-0.001-0.0010.0000.0000.0000.000
155G155GLY00.0100.00016.000-0.006-0.0060.0000.0000.0000.000
156G156VAL0-0.0310.00316.065-0.015-0.0150.0000.0000.0000.000
157G157SER00.0390.00519.090-0.018-0.0180.0000.0000.0000.000
158G158TYR00.0060.00718.225-0.007-0.0070.0000.0000.0000.000
159G159GLY00.0090.00422.898-0.013-0.0130.0000.0000.0000.000
160G160TYR0-0.053-0.03418.8130.0080.0080.0000.0000.0000.000
161G161TRP00.006-0.01325.701-0.011-0.0110.0000.0000.0000.000
162G162GLY00.0460.01625.821-0.011-0.0110.0000.0000.0000.000
163G163CYS0-0.0460.00021.4190.0200.0200.0000.0000.0000.000
164G164ALA00.018-0.00120.570-0.017-0.0170.0000.0000.0000.000
165G165ILE0-0.013-0.00817.6360.0270.0270.0000.0000.0000.000
166G166GLY00.0300.02416.839-0.017-0.0170.0000.0000.0000.000
167G167LYS10.9260.95616.0970.1460.1460.0000.0000.0000.000
168G168ALA00.0030.02216.0890.0080.0080.0000.0000.0000.000
169G169ARG10.9000.94610.986-0.285-0.2850.0000.0000.0000.000
170G170GLN00.025-0.01215.4640.0030.0030.0000.0000.0000.000
171G171ALA00.0640.04517.481-0.002-0.0020.0000.0000.0000.000
172G172ALA00.0940.07920.4720.0000.0000.0000.0000.0000.000
173G173LYS10.9290.95516.929-0.180-0.1800.0000.0000.0000.000
174G174THR0-0.056-0.04920.519-0.005-0.0050.0000.0000.0000.000
175G175GLU-1-0.867-0.96423.000-0.004-0.0040.0000.0000.0000.000
176G176ILE0-0.036-0.01523.6890.0000.0000.0000.0000.0000.000
177G177GLU-1-1.014-1.00122.3680.0880.0880.0000.0000.0000.000
178G178LYS10.8850.95826.662-0.007-0.0070.0000.0000.0000.000
179G179LEU0-0.039-0.01029.637-0.004-0.0040.0000.0000.0000.000
180G180GLN00.0110.00531.1550.0070.0070.0000.0000.0000.000
181G181MET00.0510.00328.425-0.002-0.0020.0000.0000.0000.000
182G182LYS10.8950.94630.864-0.066-0.0660.0000.0000.0000.000
183G183GLU-1-0.898-0.94435.0880.0350.0350.0000.0000.0000.000
184G184MET0-0.052-0.00535.717-0.002-0.0020.0000.0000.0000.000
185G185THR00.0230.00238.1430.0020.0020.0000.0000.0000.000
186G186CYS0-0.005-0.00836.919-0.001-0.0010.0000.0000.0000.000
187G187ARG10.9190.96037.896-0.011-0.0110.0000.0000.0000.000
188G188ASP-1-0.878-0.94238.7150.0140.0140.0000.0000.0000.000
189G189ILE0-0.031-0.01133.073-0.001-0.0010.0000.0000.0000.000
190G190VAL00.0250.01134.330-0.001-0.0010.0000.0000.0000.000
191G191LYS10.8830.94134.728-0.007-0.0070.0000.0000.0000.000
192G192GLU-1-0.799-0.90832.5020.0060.0060.0000.0000.0000.000
193G193VAL0-0.021-0.00229.629-0.001-0.0010.0000.0000.0000.000
194G194ALA00.018-0.00230.185-0.003-0.0030.0000.0000.0000.000
195G195LYS10.9490.98231.584-0.006-0.0060.0000.0000.0000.000
196G196ILE00.0120.00726.078-0.004-0.0040.0000.0000.0000.000
197G197ILE0-0.042-0.01626.309-0.004-0.0040.0000.0000.0000.000
198G198TYR0-0.029-0.03927.447-0.009-0.0090.0000.0000.0000.000
199G199ILE0-0.069-0.01126.249-0.006-0.0060.0000.0000.0000.000
200G200VAL0-0.031-0.01922.450-0.006-0.0060.0000.0000.0000.000
201G201HIS10.7730.89123.6030.0470.0470.0000.0000.0000.000
202G202ASP-1-0.812-0.91423.125-0.113-0.1130.0000.0000.0000.000
203G203GLU-1-0.859-0.92925.176-0.064-0.0640.0000.0000.0000.000
204G204VAL00.0040.00226.057-0.001-0.0010.0000.0000.0000.000
205G205LYS10.8360.92719.9240.1280.1280.0000.0000.0000.000
206G206ASP-1-0.884-0.95123.033-0.108-0.1080.0000.0000.0000.000
207G207LYS10.7580.88425.8000.0950.0950.0000.0000.0000.000
208G208ALA00.0590.02629.5660.0030.0030.0000.0000.0000.000
209G209PHE0-0.043-0.03428.981-0.003-0.0030.0000.0000.0000.000
210G210GLU-1-0.810-0.90430.809-0.018-0.0180.0000.0000.0000.000
211G211LEU00.0020.00130.7630.0010.0010.0000.0000.0000.000
212G212GLU-1-0.862-0.93430.643-0.002-0.0020.0000.0000.0000.000
213G213LEU00.011-0.01431.6360.0030.0030.0000.0000.0000.000
214G214SER0-0.016-0.00932.790-0.002-0.0020.0000.0000.0000.000
215G215TRP0-0.0050.00734.4750.0030.0030.0000.0000.0000.000
216G216VAL00.0250.00334.3830.0010.0010.0000.0000.0000.000
217G217GLY00.0360.00736.9890.0040.0040.0000.0000.0000.000
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