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

tag_button

FMODB ID: G5Q71

Calculation Name: 3P0L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P0L

Chain ID: A

ChEMBL ID:

UniProt ID: P49675

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2520365.532245
FMO2-HF: Nuclear repulsion 2435348.37664
FMO2-HF: Total energy -85017.155605
FMO2-MP2: Total energy -85260.183538


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:64:SER)


Summations of interaction energy for fragment #1(A:64: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.
-1.5530.904-0.014-1.262-1.1810.007
Interaction energy analysis for fragmet #1(A:64:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.016
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].
3A66THR0-0.005-0.0073.740-2.644-0.187-0.014-1.262-1.1810.007
4A67LEU0-0.042-0.0246.2250.2520.2520.0000.0000.0000.000
5A68TYR0-0.004-0.0048.767-0.098-0.0980.0000.0000.0000.000
6A69SER0-0.0030.01113.0750.0770.0770.0000.0000.0000.000
7A70ASP-1-0.820-0.93216.410-0.118-0.1180.0000.0000.0000.000
8A71GLN0-0.012-0.00619.284-0.002-0.0020.0000.0000.0000.000
9A72GLU-1-0.891-0.95014.313-0.397-0.3970.0000.0000.0000.000
10A73LEU00.0530.00814.369-0.013-0.0130.0000.0000.0000.000
11A74ALA00.0230.03617.5940.0080.0080.0000.0000.0000.000
12A75TYR0-0.014-0.03019.5140.0020.0020.0000.0000.0000.000
13A76LEU0-0.063-0.04113.740-0.004-0.0040.0000.0000.0000.000
14A77GLN00.0200.02318.2950.0100.0100.0000.0000.0000.000
15A78GLN00.0870.07120.9640.0040.0040.0000.0000.0000.000
16A79GLY0-0.029-0.01420.6640.0100.0100.0000.0000.0000.000
17A80GLU-1-0.988-1.01518.025-0.259-0.2590.0000.0000.0000.000
18A81GLU-1-0.944-0.97722.097-0.100-0.1000.0000.0000.0000.000
19A82ALA0-0.043-0.02525.1890.0130.0130.0000.0000.0000.000
20A83MET0-0.027-0.01621.9870.0030.0030.0000.0000.0000.000
21A84GLN00.005-0.00923.8470.0190.0190.0000.0000.0000.000
22A85LYS10.9290.97226.8850.0810.0810.0000.0000.0000.000
23A86ALA00.0240.01628.9470.0080.0080.0000.0000.0000.000
24A87LEU0-0.009-0.01525.5170.0060.0060.0000.0000.0000.000
25A88GLY00.0140.01630.0980.0070.0070.0000.0000.0000.000
26A89ILE0-0.067-0.02832.4230.0080.0080.0000.0000.0000.000
27A90LEU0-0.039-0.03731.3630.0050.0050.0000.0000.0000.000
28A91SER0-0.033-0.01132.9040.0050.0050.0000.0000.0000.000
29A92ASN0-0.050-0.02134.8040.0060.0060.0000.0000.0000.000
30A93GLN00.0460.01238.155-0.002-0.0020.0000.0000.0000.000
31A94GLU-1-0.946-0.97039.858-0.038-0.0380.0000.0000.0000.000
32A95GLY00.0280.00243.4460.0000.0000.0000.0000.0000.000
33A96TRP0-0.082-0.03937.8270.0020.0020.0000.0000.0000.000
34A97LYN00.0080.01344.3750.0010.0010.0000.0000.0000.000
35A98LYS10.8920.91645.8850.0370.0370.0000.0000.0000.000
36A99GLU-1-0.864-0.92145.761-0.042-0.0420.0000.0000.0000.000
37A100SER0-0.010-0.00746.3830.0010.0010.0000.0000.0000.000
38A101GLN0-0.068-0.05847.099-0.002-0.0020.0000.0000.0000.000
39A102GLN00.0280.02445.7080.0030.0030.0000.0000.0000.000
40A103ASP-1-0.839-0.91348.256-0.036-0.0360.0000.0000.0000.000
41A104ASN0-0.046-0.02144.6420.0020.0020.0000.0000.0000.000
42A105GLY0-0.018-0.00545.250-0.001-0.0010.0000.0000.0000.000
43A106ASP-1-0.819-0.91142.848-0.055-0.0550.0000.0000.0000.000
44A107LYS10.8980.95242.5270.0500.0500.0000.0000.0000.000
45A108VAL00.0360.03541.919-0.003-0.0030.0000.0000.0000.000
46A109MET0-0.020-0.00341.4800.0040.0040.0000.0000.0000.000
47A110SER00.0150.00242.070-0.002-0.0020.0000.0000.0000.000
48A111LYS10.9470.98640.3440.0530.0530.0000.0000.0000.000
49A112VAL0-0.022-0.00242.112-0.002-0.0020.0000.0000.0000.000
50A113VAL0-0.053-0.02637.2330.0020.0020.0000.0000.0000.000
51A114PRO0-0.015-0.01440.1410.0000.0000.0000.0000.0000.000
52A115ASP-1-0.848-0.92535.987-0.059-0.0590.0000.0000.0000.000
53A116VAL0-0.0210.00135.331-0.001-0.0010.0000.0000.0000.000
54A117GLY00.1030.03838.2280.0030.0030.0000.0000.0000.000
55A118LYS10.7540.89640.9920.0480.0480.0000.0000.0000.000
56A119VAL0-0.0080.01037.220-0.002-0.0020.0000.0000.0000.000
57A120PHE00.0000.00038.7030.0050.0050.0000.0000.0000.000
58A121ARG10.8720.95836.6470.0580.0580.0000.0000.0000.000
59A122LEU00.0290.03237.1300.0040.0040.0000.0000.0000.000
60A123GLU-1-0.894-0.97537.247-0.070-0.0700.0000.0000.0000.000
61A124VAL00.0580.02137.3000.0040.0040.0000.0000.0000.000
62A125VAL0-0.040-0.00737.031-0.004-0.0040.0000.0000.0000.000
63A126VAL00.0270.01034.7160.0030.0030.0000.0000.0000.000
64A127ASP-1-0.905-0.95837.122-0.051-0.0510.0000.0000.0000.000
65A128GLN00.0160.00334.325-0.001-0.0010.0000.0000.0000.000
66A129PRO00.0410.01531.166-0.003-0.0030.0000.0000.0000.000
67A130MET00.0350.02525.2200.0010.0010.0000.0000.0000.000
68A131GLU-1-0.931-0.98022.478-0.160-0.1600.0000.0000.0000.000
69A132ARG10.9370.97126.2740.0720.0720.0000.0000.0000.000
70A133LEU00.0170.00328.710-0.002-0.0020.0000.0000.0000.000
71A134TYR00.0090.00719.629-0.009-0.0090.0000.0000.0000.000
72A135GLU-1-0.858-0.93924.125-0.119-0.1190.0000.0000.0000.000
73A136GLU-1-0.916-0.98825.089-0.095-0.0950.0000.0000.0000.000
74A137LEU0-0.047-0.01127.4410.0040.0040.0000.0000.0000.000
75A138VAL0-0.081-0.06022.395-0.004-0.0040.0000.0000.0000.000
76A139GLU-1-0.977-0.96821.119-0.177-0.1770.0000.0000.0000.000
77A140ARG10.9170.96922.8070.1050.1050.0000.0000.0000.000
78A141MET0-0.0150.00423.9810.0090.0090.0000.0000.0000.000
79A142GLU-1-0.924-0.96824.967-0.144-0.1440.0000.0000.0000.000
80A143ALA00.0000.01427.8730.0070.0070.0000.0000.0000.000
81A144MET0-0.023-0.03030.3140.0060.0060.0000.0000.0000.000
82A145GLY0-0.023-0.02232.0630.0040.0040.0000.0000.0000.000
83A146GLU-1-0.952-0.96433.834-0.075-0.0750.0000.0000.0000.000
84A147TRP0-0.051-0.00331.8740.0070.0070.0000.0000.0000.000
85A148ASN00.043-0.00335.3430.0060.0060.0000.0000.0000.000
86A149PRO00.0520.03037.974-0.001-0.0010.0000.0000.0000.000
87A150ASN0-0.069-0.04138.8870.0000.0000.0000.0000.0000.000
88A151VAL0-0.0300.00134.432-0.001-0.0010.0000.0000.0000.000
89A152LYS10.9510.98036.9270.0650.0650.0000.0000.0000.000
90A153GLU-1-0.942-0.98632.239-0.089-0.0890.0000.0000.0000.000
91A154ILE00.0010.01827.966-0.002-0.0020.0000.0000.0000.000
92A155LYS10.9970.99927.5490.1120.1120.0000.0000.0000.000
93A156VAL0-0.022-0.01621.006-0.003-0.0030.0000.0000.0000.000
94A157LEU0-0.036-0.00623.770-0.001-0.0010.0000.0000.0000.000
95A158GLN00.0400.00817.0870.0220.0220.0000.0000.0000.000
96A159LYS10.9440.97915.9150.2830.2830.0000.0000.0000.000
97A160ILE00.0010.00514.051-0.018-0.0180.0000.0000.0000.000
98A161GLY00.0320.03510.650-0.008-0.0080.0000.0000.0000.000
99A162LYS10.8720.9207.3931.1841.1840.0000.0000.0000.000
100A163ASP-1-0.779-0.89612.515-0.378-0.3780.0000.0000.0000.000
101A164THR00.0230.00515.8160.0350.0350.0000.0000.0000.000
102A165PHE0-0.001-0.00916.948-0.021-0.0210.0000.0000.0000.000
103A166ILE00.0000.01519.5510.0210.0210.0000.0000.0000.000
104A167THR0-0.042-0.02222.870-0.002-0.0020.0000.0000.0000.000
105A168HIS0-0.011-0.03925.8440.0020.0020.0000.0000.0000.000
106A169GLU-1-0.940-0.96429.399-0.103-0.1030.0000.0000.0000.000
107A170LEU00.0200.00431.6930.0060.0060.0000.0000.0000.000
108A171ALA00.0180.00935.1380.0000.0000.0000.0000.0000.000
109A172ALA0-0.029-0.00937.6820.0020.0020.0000.0000.0000.000
110A173GLU-1-0.961-0.98541.167-0.051-0.0510.0000.0000.0000.000
111A174ALA00.0590.02143.5480.0010.0010.0000.0000.0000.000
112A175ALA0-0.079-0.03245.2900.0020.0020.0000.0000.0000.000
113A176GLY00.0270.01847.4800.0020.0020.0000.0000.0000.000
114A177ASN00.0260.00749.064-0.002-0.0020.0000.0000.0000.000
115A178LEU0-0.043-0.02150.3560.0010.0010.0000.0000.0000.000
116A179VAL0-0.066-0.02144.8740.0000.0000.0000.0000.0000.000
117A180GLY00.0090.00546.286-0.001-0.0010.0000.0000.0000.000
118A181PRO00.0630.01242.570-0.002-0.0020.0000.0000.0000.000
119A182ARG10.8820.93439.2650.0580.0580.0000.0000.0000.000
120A183ASP-1-0.753-0.85034.980-0.082-0.0820.0000.0000.0000.000
121A184PHE0-0.018-0.02132.2570.0020.0020.0000.0000.0000.000
122A185VAL00.0440.02928.008-0.005-0.0050.0000.0000.0000.000
123A186SER0-0.030-0.02327.6900.0060.0060.0000.0000.0000.000
124A187VAL00.0240.04121.507-0.010-0.0100.0000.0000.0000.000
125A188ARG10.9000.94422.4190.1670.1670.0000.0000.0000.000
126A189CYS00.0240.02719.136-0.037-0.0370.0000.0000.0000.000
127A190ALA00.0090.02319.2420.0270.0270.0000.0000.0000.000
128A191LYS10.9740.98316.7710.2890.2890.0000.0000.0000.000
129A192ARG10.9390.93515.5800.3770.3770.0000.0000.0000.000
130A193ARG10.8540.95319.3070.1300.1300.0000.0000.0000.000
131A194GLY00.0260.01320.6400.0160.0160.0000.0000.0000.000
132A195SER00.0270.01821.4710.0000.0000.0000.0000.0000.000
133A196THR00.0150.00224.4150.0090.0090.0000.0000.0000.000
134A197CYS00.0040.00222.923-0.021-0.0210.0000.0000.0000.000
135A198VAL0-0.035-0.02123.1590.0170.0170.0000.0000.0000.000
136A199LEU00.0090.02523.201-0.019-0.0190.0000.0000.0000.000
137A200ALA0-0.031-0.01923.6990.0170.0170.0000.0000.0000.000
138A201GLY00.0590.00025.219-0.009-0.0090.0000.0000.0000.000
139A202MET0-0.041-0.00426.4330.0120.0120.0000.0000.0000.000
140A203ALA0-0.011-0.01027.743-0.009-0.0090.0000.0000.0000.000
141A204THR0-0.037-0.01225.302-0.003-0.0030.0000.0000.0000.000
142A205ASP-1-0.859-0.92427.716-0.091-0.0910.0000.0000.0000.000
143A206PHE0-0.015-0.00722.750-0.006-0.0060.0000.0000.0000.000
144A207GLY00.0380.00727.4120.0050.0050.0000.0000.0000.000
145A208ASN0-0.087-0.03925.0490.0140.0140.0000.0000.0000.000
146A209MET0-0.0280.00428.3530.0000.0000.0000.0000.0000.000
147A210PRO00.0360.02030.5850.0000.0000.0000.0000.0000.000
148A211GLU-1-0.916-0.94933.742-0.066-0.0660.0000.0000.0000.000
149A212GLN00.005-0.01533.8900.0040.0040.0000.0000.0000.000
150A213LYS10.9340.95638.8220.0500.0500.0000.0000.0000.000
151A214GLY0-0.013-0.01142.5030.0000.0000.0000.0000.0000.000
152A215VAL0-0.031-0.00138.8010.0020.0020.0000.0000.0000.000
153A216ILE0-0.0320.00040.5550.0000.0000.0000.0000.0000.000
154A217ARG10.8920.93732.8300.0850.0850.0000.0000.0000.000
155A218ALA0-0.0430.00337.3520.0020.0020.0000.0000.0000.000
156A219GLU-1-0.834-0.93234.402-0.080-0.0800.0000.0000.0000.000
157A220HIS10.8610.93131.5710.0990.0990.0000.0000.0000.000
158A221GLY00.0840.04232.226-0.003-0.0030.0000.0000.0000.000
159A222PRO0-0.004-0.02930.086-0.006-0.0060.0000.0000.0000.000
160A223THR0-0.041-0.00629.8620.0090.0090.0000.0000.0000.000
161A224CYS0-0.053-0.01528.247-0.008-0.0080.0000.0000.0000.000
162A225MET00.0180.00228.1360.0120.0120.0000.0000.0000.000
163A226VAL0-0.019-0.00827.829-0.012-0.0120.0000.0000.0000.000
164A227LEU00.0120.01226.8450.0090.0090.0000.0000.0000.000
165A228HIS00.017-0.00628.271-0.012-0.0120.0000.0000.0000.000
166A229PRO00.0460.03329.0870.0070.0070.0000.0000.0000.000
167A230LEU0-0.0270.00132.0660.0030.0030.0000.0000.0000.000
168A231ALA0-0.007-0.01735.4070.0010.0010.0000.0000.0000.000
169A232GLY00.0150.01037.0110.0010.0010.0000.0000.0000.000
170A233SER0-0.052-0.04036.5950.0020.0020.0000.0000.0000.000
171A234PRO00.0690.02832.314-0.003-0.0030.0000.0000.0000.000
172A235SER0-0.025-0.00933.083-0.003-0.0030.0000.0000.0000.000
173A236LYS10.9140.98435.5840.0480.0480.0000.0000.0000.000
174A237THR00.0180.00930.997-0.005-0.0050.0000.0000.0000.000
175A238LYS10.8070.90433.7880.0670.0670.0000.0000.0000.000
176A239LEU00.0100.00832.147-0.005-0.0050.0000.0000.0000.000
177A240THR0-0.034-0.01632.6320.0070.0070.0000.0000.0000.000
178A241TRP00.0320.01032.281-0.006-0.0060.0000.0000.0000.000
179A242LEU0-0.017-0.00132.7470.0070.0070.0000.0000.0000.000
180A243LEU00.0110.00233.214-0.006-0.0060.0000.0000.0000.000
181A244SER00.005-0.00534.4000.0050.0050.0000.0000.0000.000
182A245ILE0-0.017-0.01634.996-0.006-0.0060.0000.0000.0000.000
183A246ASP-1-0.831-0.90837.373-0.055-0.0550.0000.0000.0000.000
184A247LEU0-0.007-0.02939.437-0.001-0.0010.0000.0000.0000.000
185A248LYS10.9120.99138.0090.0660.0660.0000.0000.0000.000
186A249GLY00.004-0.01842.7480.0010.0010.0000.0000.0000.000
187A250TRP00.0020.00045.9830.0000.0000.0000.0000.0000.000
188A251LEU0-0.065-0.01346.0560.0020.0020.0000.0000.0000.000
189A252PRO00.0550.02649.5060.0000.0000.0000.0000.0000.000
190A253LYS11.0321.00649.1290.0360.0360.0000.0000.0000.000
191A254SER0-0.034-0.01949.136-0.002-0.0020.0000.0000.0000.000
192A255ILE00.0690.02348.330-0.001-0.0010.0000.0000.0000.000
193A256ILE00.0410.01644.340-0.002-0.0020.0000.0000.0000.000
194A257ASN00.003-0.01345.249-0.003-0.0030.0000.0000.0000.000
195A258GLN00.0500.03345.810-0.002-0.0020.0000.0000.0000.000
196A259VAL00.0230.03243.905-0.001-0.0010.0000.0000.0000.000
197A260LEU00.0320.03240.255-0.002-0.0020.0000.0000.0000.000
198A261SER0-0.030-0.02741.502-0.003-0.0030.0000.0000.0000.000
199A262GLN0-0.009-0.02443.132-0.002-0.0020.0000.0000.0000.000
200A263THR00.0290.01538.888-0.001-0.0010.0000.0000.0000.000
201A264GLN0-0.052-0.03336.9170.0000.0000.0000.0000.0000.000
202A265VAL0-0.042-0.02239.817-0.002-0.0020.0000.0000.0000.000
203A266ASP-1-0.864-0.93541.908-0.052-0.0520.0000.0000.0000.000
204A267PHE0-0.012-0.00832.3930.0000.0000.0000.0000.0000.000
205A268ALA00.000-0.00337.686-0.002-0.0020.0000.0000.0000.000
206A269ASN0-0.020-0.01139.0600.0000.0000.0000.0000.0000.000
207A270HIS0-0.012-0.01838.7440.0010.0010.0000.0000.0000.000
208A271LEU00.0240.02732.987-0.001-0.0010.0000.0000.0000.000
209A272ARG10.8180.88936.5900.0560.0560.0000.0000.0000.000
210A273LYS10.9460.98738.8340.0540.0540.0000.0000.0000.000
211A274ARG10.8770.94533.7610.0800.0800.0000.0000.0000.000
212A275LEU0-0.095-0.03833.301-0.001-0.0010.0000.0000.0000.000
213A276GLU-1-0.937-0.96136.188-0.055-0.0550.0000.0000.0000.000