Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 53KNZ

Calculation Name: 4R3O-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: I

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-06-20

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2338460.426499
FMO2-HF: Nuclear repulsion 2253733.09285
FMO2-HF: Total energy -84727.333648
FMO2-MP2: Total energy -84968.880297


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(I:1:THR)


Summations of interaction energy for fragment #1(I:1:THR)
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.
-34.861-31.88234.191-14.908-22.263-0.046
Interaction energy analysis for fragmet #1(I:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.002
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].
3I3ILE0-0.037-0.0172.5570.3082.6400.751-1.037-2.0460.002
4I4ALA00.0200.0014.660-0.373-0.364-0.001-0.005-0.0030.000
5I5GLY0-0.015-0.0058.3150.2930.2930.0000.0000.0000.000
6I6VAL00.0390.02111.809-0.085-0.0850.0000.0000.0000.000
7I7VAL0-0.029-0.01315.4900.0740.0740.0000.0000.0000.000
8I8TYR0-0.048-0.03818.971-0.024-0.0240.0000.0000.0000.000
9I9LYS10.8360.91121.7500.1320.1320.0000.0000.0000.000
10I10ASP-1-0.908-0.95424.479-0.064-0.0640.0000.0000.0000.000
11I11GLY0-0.016-0.02821.9810.0310.0310.0000.0000.0000.000
12I12ILE0-0.050-0.00915.562-0.030-0.0300.0000.0000.0000.000
13I13VAL00.0020.00714.0580.0540.0540.0000.0000.0000.000
14I14LEU00.0140.00410.855-0.092-0.0920.0000.0000.0000.000
15I15GLY00.0450.0029.2610.0850.0850.0000.0000.0000.000
16I16ALA00.011-0.0014.643-0.206-0.168-0.001-0.002-0.0350.000
17I17ASP-1-0.665-0.8052.402-1.5790.8943.060-2.742-2.790-0.033
18I18THR0-0.037-0.0244.8540.8870.983-0.001-0.004-0.0910.000
19I19ARG10.8400.9434.586-0.725-0.600-0.001-0.006-0.1180.000
20I20ALA00.015-0.0044.3403.5643.844-0.001-0.029-0.2510.000
21I21THR0-0.045-0.0345.248-0.965-0.9650.0000.0000.0000.000
22I22GLU-1-0.906-0.9347.0051.3081.3080.0000.0000.0000.000
23I23GLY00.006-0.0079.607-0.271-0.2710.0000.0000.0000.000
24I24MET0-0.013-0.0108.4280.1270.1270.0000.0000.0000.000
25I25VAL00.0010.01010.478-0.115-0.1150.0000.0000.0000.000
26I26VAL0-0.011-0.0218.5930.2660.2660.0000.0000.0000.000
27I27ALA00.0080.0209.489-0.218-0.2180.0000.0000.0000.000
28I28ASP-1-0.808-0.9058.9841.9491.9490.0000.0000.0000.000
29I29LYS10.8500.9158.735-0.602-0.6020.0000.0000.0000.000
30I30ASN00.029-0.00110.275-0.228-0.2280.0000.0000.0000.000
31I31CYS00.0600.0636.6700.1020.1020.0000.0000.0000.000
32I32SER00.0150.0017.632-0.037-0.0370.0000.0000.0000.000
33I33LYS10.7780.8631.863-22.998-26.95012.732-3.793-4.9880.043
34I34ILE0-0.0150.0006.371-0.347-0.3470.0000.0000.0000.000
35I35HIS10.8500.9276.752-1.894-1.8940.0000.0000.0000.000
36I36PHE00.0430.02211.471-0.139-0.1390.0000.0000.0000.000
37I37ILE0-0.037-0.01314.5080.0310.0310.0000.0000.0000.000
38I38SER00.022-0.00317.085-0.013-0.0130.0000.0000.0000.000
39I39PRO00.013-0.00419.6670.0050.0050.0000.0000.0000.000
40I40ASN0-0.015-0.00121.6140.0120.0120.0000.0000.0000.000
41I41ILE0-0.008-0.00716.631-0.043-0.0430.0000.0000.0000.000
42I42TYR00.0610.02813.3370.0690.0690.0000.0000.0000.000
43I43CYS0-0.012-0.00911.226-0.114-0.1140.0000.0000.0000.000
44I44CYS0-0.0120.0246.4580.2850.2850.0000.0000.0000.000
45I45GLY00.016-0.0065.815-0.359-0.3590.0000.0000.0000.000
46I46ALA0-0.010-0.0092.5610.3270.8231.179-0.432-1.2420.000
47I47GLY00.0400.0273.511-1.033-0.9900.0120.115-0.1700.000
48I48THR0-0.004-0.0106.0431.2141.2140.0000.0000.0000.000
49I49ALA00.0310.0216.676-0.270-0.2700.0000.0000.0000.000
50I50ALA00.0720.0387.627-0.375-0.3750.0000.0000.0000.000
51I51ASP-1-0.767-0.88110.7840.6990.6990.0000.0000.0000.000
52I52THR0-0.095-0.0446.371-0.126-0.1260.0000.0000.0000.000
53I53ASP-1-0.811-0.9159.6781.6271.6270.0000.0000.0000.000
54I54MET0-0.0170.00111.772-0.173-0.1730.0000.0000.0000.000
55I55THR0-0.033-0.03812.750-0.159-0.1590.0000.0000.0000.000
56I56THR0-0.009-0.00811.596-0.124-0.1240.0000.0000.0000.000
57I57GLN0-0.025-0.02614.040-0.126-0.1260.0000.0000.0000.000
58I58LEU00.0200.02116.805-0.075-0.0750.0000.0000.0000.000
59I59ILE0-0.009-0.01417.175-0.064-0.0640.0000.0000.0000.000
60I60SER0-0.037-0.01817.417-0.041-0.0410.0000.0000.0000.000
61I61SER00.0410.02419.265-0.045-0.0450.0000.0000.0000.000
62I62ASN0-0.028-0.03721.953-0.054-0.0540.0000.0000.0000.000
63I63LEU0-0.023-0.01819.810-0.039-0.0390.0000.0000.0000.000
64I64GLU-1-0.929-0.93823.4180.2620.2620.0000.0000.0000.000
65I65LEU00.0220.00425.179-0.024-0.0240.0000.0000.0000.000
66I66HIS0-0.018-0.00226.365-0.015-0.0150.0000.0000.0000.000
67I67SER0-0.044-0.02726.301-0.015-0.0150.0000.0000.0000.000
68I68LEU00.003-0.00928.370-0.016-0.0160.0000.0000.0000.000
69I69SER0-0.030-0.00431.001-0.011-0.0110.0000.0000.0000.000
70I70THR0-0.074-0.05230.721-0.014-0.0140.0000.0000.0000.000
71I71GLY00.0110.02033.007-0.012-0.0120.0000.0000.0000.000
72I72ARG10.8240.90030.955-0.077-0.0770.0000.0000.0000.000
73I73LEU00.0290.02525.4060.0120.0120.0000.0000.0000.000
74I74PRO00.0110.00423.066-0.014-0.0140.0000.0000.0000.000
75I75ARG10.9570.98524.280-0.042-0.0420.0000.0000.0000.000
76I76VAL00.0420.01018.2430.0180.0180.0000.0000.0000.000
77I77VAL0-0.042-0.01920.268-0.001-0.0010.0000.0000.0000.000
78I78THR0-0.001-0.00322.524-0.008-0.0080.0000.0000.0000.000
79I79ALA00.0670.04118.0220.0130.0130.0000.0000.0000.000
80I80ASN00.0410.01317.1680.0260.0260.0000.0000.0000.000
81I81ARG10.8540.92418.752-0.023-0.0230.0000.0000.0000.000
82I82MET0-0.0010.00120.4170.0080.0080.0000.0000.0000.000
83I83LEU00.0460.02514.1510.0170.0170.0000.0000.0000.000
84I84LYS10.8820.94317.2600.0710.0710.0000.0000.0000.000
85I85GLN0-0.007-0.00418.383-0.023-0.0230.0000.0000.0000.000
86I86MET0-0.0050.01316.678-0.009-0.0090.0000.0000.0000.000
87I87LEU0-0.004-0.00313.3570.0050.0050.0000.0000.0000.000
88I88PHE00.0320.02117.547-0.008-0.0080.0000.0000.0000.000
89I89ARG10.8660.94320.516-0.202-0.2020.0000.0000.0000.000
90I90TYR0-0.004-0.01118.8320.0060.0060.0000.0000.0000.000
91I91GLN0-0.0160.00119.6930.0020.0020.0000.0000.0000.000
92I92GLY00.0300.01515.967-0.027-0.0270.0000.0000.0000.000
93I93TYR0-0.076-0.04115.3510.0400.0400.0000.0000.0000.000
94I94ILE0-0.0060.01613.6050.0580.0580.0000.0000.0000.000
95I95GLY00.0260.01011.372-0.086-0.0860.0000.0000.0000.000
96I96ALA0-0.042-0.0328.8450.2320.2320.0000.0000.0000.000
97I97ALA0-0.009-0.0086.827-0.270-0.2700.0000.0000.0000.000
98I98LEU0-0.029-0.0256.6910.2460.2460.0000.0000.0000.000
99I99VAL00.0180.0137.598-0.220-0.2200.0000.0000.0000.000
100I100LEU0-0.0210.0009.6560.1540.1540.0000.0000.0000.000
101I101GLY00.0400.00713.060-0.093-0.0930.0000.0000.0000.000
102I102GLY00.0270.00815.4770.0690.0690.0000.0000.0000.000
103I103VAL0-0.0170.00118.872-0.042-0.0420.0000.0000.0000.000
104I104ASP-1-0.796-0.87222.5660.0610.0610.0000.0000.0000.000
105I105VAL0-0.030-0.03425.419-0.009-0.0090.0000.0000.0000.000
106I106THR0-0.020-0.01626.983-0.004-0.0040.0000.0000.0000.000
107I107GLY00.0460.03426.072-0.014-0.0140.0000.0000.0000.000
108I108PRO00.0210.01721.0190.0210.0210.0000.0000.0000.000
109I109HIS0-0.014-0.00420.243-0.037-0.0370.0000.0000.0000.000
110I110LEU00.0260.01313.0620.0420.0420.0000.0000.0000.000
111I111TYR0-0.007-0.03014.791-0.015-0.0150.0000.0000.0000.000
112I112SER00.0350.01711.6280.0180.0180.0000.0000.0000.000
113I113ILE0-0.048-0.03611.3410.0510.0510.0000.0000.0000.000
114I114TYR00.012-0.00511.0410.0000.0000.0000.0000.0000.000
115I115PRO00.0260.01411.0350.0300.0300.0000.0000.0000.000
116I116HIS00.0230.01013.5940.0500.0500.0000.0000.0000.000
117I117GLY00.0050.00616.1810.0000.0000.0000.0000.0000.000
118I118SER0-0.014-0.00716.6400.0070.0070.0000.0000.0000.000
119I119THR0-0.019-0.02715.8150.0330.0330.0000.0000.0000.000
120I120ASP-1-0.789-0.84515.126-0.430-0.4300.0000.0000.0000.000
121I121LYS10.8220.90916.6550.1380.1380.0000.0000.0000.000
122I122LEU00.0200.01515.5420.0020.0020.0000.0000.0000.000
123I123PRO0-0.0070.00217.3490.0190.0190.0000.0000.0000.000
124I124TYR0-0.031-0.04714.5610.0400.0400.0000.0000.0000.000
125I125VAL0-0.0210.00210.8210.0000.0000.0000.0000.0000.000
126I126THR0-0.008-0.0307.7340.0370.0370.0000.0000.0000.000
127I127MET0-0.023-0.0025.4930.2540.2540.0000.0000.0000.000
128I128GLY00.0190.0062.892-1.300-0.7160.129-0.287-0.4250.000
129I129SER0-0.044-0.0351.991-1.402-2.9737.086-2.643-2.873-0.018
130I130GLY00.0410.0203.5662.1652.5140.000-0.101-0.2470.000
131I131SER0-0.060-0.0315.4521.5871.5870.0000.0000.0000.000
132I132LEU00.0520.0257.3760.6670.6670.0000.0000.0000.000
133I133ALA00.0230.0238.7830.3700.3700.0000.0000.0000.000
134I134ALA0-0.002-0.0068.6190.3730.3730.0000.0000.0000.000
135I135MET0-0.004-0.00410.5330.3560.3560.0000.0000.0000.000
136I136ALA0-0.0030.00312.6610.2030.2030.0000.0000.0000.000
137I137VAL00.0050.00213.8900.1440.1440.0000.0000.0000.000
138I138PHE0-0.043-0.03411.6380.1010.1010.0000.0000.0000.000
139I139GLU-1-0.863-0.92316.163-0.565-0.5650.0000.0000.0000.000
140I140ASP-1-0.971-0.97018.492-0.528-0.5280.0000.0000.0000.000
141I141LYS10.8120.90018.8290.6600.6600.0000.0000.0000.000
142I142PHE0-0.012-0.00818.1910.0530.0530.0000.0000.0000.000
143I143ARG10.8120.88920.1810.2640.2640.0000.0000.0000.000
144I144PRO00.0130.00622.637-0.003-0.0030.0000.0000.0000.000
145I145ASP-1-0.905-0.96524.569-0.174-0.1740.0000.0000.0000.000
146I146MET0-0.064-0.00219.0800.0030.0030.0000.0000.0000.000
147I147GLU-1-0.760-0.87824.191-0.101-0.1010.0000.0000.0000.000
148I148GLU-1-0.759-0.85621.362-0.058-0.0580.0000.0000.0000.000
149I149GLU-1-0.815-0.90420.664-0.108-0.1080.0000.0000.0000.000
150I150GLU-1-0.814-0.87720.864-0.270-0.2700.0000.0000.0000.000
151I151ALA00.0570.02318.364-0.050-0.0500.0000.0000.0000.000
152I152LYS10.7810.86316.4460.0110.0110.0000.0000.0000.000
153I153ASN0-0.0430.00416.062-0.018-0.0180.0000.0000.0000.000
154I154LEU00.0260.02216.042-0.073-0.0730.0000.0000.0000.000
155I155VAL00.0140.00511.235-0.138-0.1380.0000.0000.0000.000
156I156SER0-0.049-0.04611.700-0.162-0.1620.0000.0000.0000.000
157I157GLU-1-0.807-0.90012.386-0.715-0.7150.0000.0000.0000.000
158I158ALA00.0140.02611.239-0.172-0.1720.0000.0000.0000.000
159I159ILE0-0.050-0.0356.382-0.470-0.4700.0000.0000.0000.000
160I160ALA0-0.024-0.0118.045-0.392-0.3920.0000.0000.0000.000
161I161ALA00.0140.00810.275-0.082-0.0820.0000.0000.0000.000
162I162GLY00.0390.0246.608-0.108-0.1080.0000.0000.0000.000
163I163ILE0-0.082-0.0556.208-0.421-0.4210.0000.0000.0000.000
164I164PHE0-0.065-0.0297.1220.3280.3280.0000.0000.0000.000
165I165ASN0-0.066-0.0328.0620.4830.4830.0000.0000.0000.000
166I166ASP-1-0.743-0.8182.300-17.489-16.2542.313-1.721-1.828-0.022
167I167LEU0-0.006-0.0035.0110.0560.095-0.001-0.002-0.0360.000
168I168GLY00.0050.0092.7170.8490.8880.743-0.110-0.6720.002
169I169SER0-0.033-0.0192.1530.8391.7506.066-2.746-4.231-0.020
170I170GLY0-0.019-0.0392.9841.5430.9960.1260.637-0.2170.000
171I171SER0-0.086-0.0376.5260.4170.4170.0000.0000.0000.000
172I172ASN00.0270.0129.287-0.422-0.4220.0000.0000.0000.000
173I173ILE00.0320.0228.442-0.003-0.0030.0000.0000.0000.000
174I174ASP-1-0.776-0.8668.5251.1291.1290.0000.0000.0000.000
175I175LEU0-0.016-0.0239.854-0.187-0.1870.0000.0000.0000.000
176I176CYS0-0.093-0.03412.2540.1020.1020.0000.0000.0000.000
177I177VAL00.0080.02414.237-0.069-0.0690.0000.0000.0000.000
178I178ILE00.0100.00316.2600.0500.0500.0000.0000.0000.000
179I179SER00.0490.01719.697-0.032-0.0320.0000.0000.0000.000
180I180LYS10.8710.91423.2370.0680.0680.0000.0000.0000.000
181I181ASN0-0.088-0.03726.2550.0040.0040.0000.0000.0000.000
182I182LYS10.8000.88922.624-0.004-0.0040.0000.0000.0000.000
183I183LEU0-0.0030.00318.356-0.002-0.0020.0000.0000.0000.000
184I184ASP-1-0.813-0.89219.1020.0680.0680.0000.0000.0000.000
185I185PHE00.0300.00112.985-0.023-0.0230.0000.0000.0000.000
186I186LEU0-0.022-0.01015.5940.0380.0380.0000.0000.0000.000
187I187ARG10.7860.8949.525-1.264-1.2640.0000.0000.0000.000
188I188PRO0-0.044-0.03212.5800.0290.0290.0000.0000.0000.000
189I189TYR00.0430.01513.193-0.035-0.0350.0000.0000.0000.000
190I190THR0-0.013-0.02413.892-0.053-0.0530.0000.0000.0000.000
191I191VAL0-0.0060.00613.2820.0090.0090.0000.0000.0000.000
192I192PRO00.0210.02511.7770.0200.0200.0000.0000.0000.000
193I193ASN0-0.031-0.00910.458-0.045-0.0450.0000.0000.0000.000
194I194LYS10.9150.93313.9090.0560.0560.0000.0000.0000.000
195I195LYS10.8770.95216.669-0.216-0.2160.0000.0000.0000.000
196I196GLY00.0800.04218.271-0.011-0.0110.0000.0000.0000.000
197I197THR00.0460.01321.6500.0370.0370.0000.0000.0000.000
198I198ARG10.8940.94324.730-0.201-0.2010.0000.0000.0000.000
199I199LEU00.0720.03526.292-0.001-0.0010.0000.0000.0000.000
200I200GLY00.0380.03529.077-0.009-0.0090.0000.0000.0000.000
201I201ARG10.9240.94330.047-0.084-0.0840.0000.0000.0000.000
202I202TYR00.0320.01627.9840.0010.0010.0000.0000.0000.000
203I203ARG10.8330.91531.287-0.133-0.1330.0000.0000.0000.000
204I204CYS00.0250.01632.504-0.012-0.0120.0000.0000.0000.000
205I205GLU-1-0.792-0.89734.6320.1420.1420.0000.0000.0000.000
206I206LYS10.9490.96537.844-0.139-0.1390.0000.0000.0000.000
207I207GLY00.0560.02639.326-0.008-0.0080.0000.0000.0000.000
208I208THR0-0.057-0.01436.445-0.006-0.0060.0000.0000.0000.000
209I209THR0-0.046-0.02835.2670.0060.0060.0000.0000.0000.000
210I210ALA00.0180.02038.150-0.001-0.0010.0000.0000.0000.000
211I211VAL00.012-0.00138.8490.0090.0090.0000.0000.0000.000
212I212LEU00.0210.01340.712-0.007-0.0070.0000.0000.0000.000
213I213THR0-0.052-0.03741.594-0.005-0.0050.0000.0000.0000.000
214I214GLU-1-0.876-0.92840.8170.1760.1760.0000.0000.0000.000
215I215LYS10.8380.90241.608-0.165-0.1650.0000.0000.0000.000
216I216ILE00.0520.03041.2980.0070.0070.0000.0000.0000.000
217I217THR0-0.021-0.01340.598-0.010-0.0100.0000.0000.0000.000
218I218PRO0-0.0050.00641.4030.0080.0080.0000.0000.0000.000
219I219LEU0-0.021-0.00737.7670.0060.0060.0000.0000.0000.000
220I220GLU-1-0.934-0.95240.9710.1430.1430.0000.0000.0000.000