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

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FMODB ID: N9V4Q

Calculation Name: 4R9P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R9P

Chain ID: A

ChEMBL ID:

UniProt ID: A1Z8R1

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2655806.866758
FMO2-HF: Nuclear repulsion 2570005.895284
FMO2-HF: Total energy -85800.971473
FMO2-MP2: Total energy -86048.420798


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:27:GLU)


Summations of interaction energy for fragment #1(A:27:GLU)
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.
-90.911-86.1370.289-2.309-2.7530.01
Interaction energy analysis for fragmet #1(A:27:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.997 / q_NPA : -0.998
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].
3A29ASP-1-0.886-0.9183.31125.31128.610-0.014-1.724-1.5600.005
4A30ILE0-0.018-0.0073.160-4.034-2.8800.304-0.455-1.0020.004
5A31TRP0-0.022-0.0275.740-1.527-1.565-0.001-0.0040.0430.000
6A32PHE00.0590.0135.336-1.379-1.3790.0000.0000.0000.000
7A33GLN00.001-0.00310.302-2.145-2.1450.0000.0000.0000.000
8A34LYS10.8810.92712.827-13.751-13.7510.0000.0000.0000.000
9A35ASP-1-0.777-0.88015.15814.99114.9910.0000.0000.0000.000
10A36LYS10.8070.8809.014-24.872-24.8720.0000.0000.0000.000
11A37LEU00.0130.03511.6540.1350.1350.0000.0000.0000.000
12A38TYR00.0210.00112.767-0.019-0.0190.0000.0000.0000.000
13A39LYS10.9640.98615.275-17.008-17.0080.0000.0000.0000.000
14A40GLU-1-0.748-0.8369.34724.32624.3260.0000.0000.0000.000
15A41HIS00.0190.00511.3150.1170.1170.0000.0000.0000.000
16A42ILE0-0.011-0.00415.247-0.638-0.6380.0000.0000.0000.000
17A43GLN00.017-0.01015.8920.0260.0260.0000.0000.0000.000
18A44GLU-1-0.784-0.86112.24020.97420.9740.0000.0000.0000.000
19A45VAL00.016-0.00516.317-0.360-0.3600.0000.0000.0000.000
20A46LEU0-0.044-0.02519.735-0.618-0.6180.0000.0000.0000.000
21A47ASP-1-0.880-0.91317.51715.12815.1280.0000.0000.0000.000
22A48LYS10.8170.89115.348-17.106-17.1060.0000.0000.0000.000
23A49TRP00.003-0.00121.076-0.168-0.1680.0000.0000.0000.000
24A50THR0-0.010-0.02224.290-0.052-0.0520.0000.0000.0000.000
25A51GLN0-0.029-0.00521.942-0.004-0.0040.0000.0000.0000.000
26A52ILE0-0.092-0.03321.3050.2750.2750.0000.0000.0000.000
27A53ASP-1-0.806-0.88924.9329.9899.9890.0000.0000.0000.000
28A54ASP-1-0.877-0.94427.9899.5489.5480.0000.0000.0000.000
29A55GLU-1-0.867-0.91330.2259.5219.5210.0000.0000.0000.000
30A56ILE0-0.121-0.06024.1080.2100.2100.0000.0000.0000.000
31A57TRP00.011-0.02127.5560.1360.1360.0000.0000.0000.000
32A58ALA0-0.020-0.02624.1820.0690.0690.0000.0000.0000.000
33A59LYS10.8680.95815.666-17.205-17.2050.0000.0000.0000.000
34A60VAL0-0.022-0.02119.566-0.019-0.0190.0000.0000.0000.000
35A61ILE0-0.038-0.01813.2820.4880.4880.0000.0000.0000.000
36A62VAL00.0030.00915.052-0.766-0.7660.0000.0000.0000.000
37A63PHE00.016-0.00611.0641.7821.7820.0000.0000.0000.000
38A64GLU-1-0.720-0.81912.18019.69619.6960.0000.0000.0000.000
39A65ARG10.7920.88411.755-16.709-16.7090.0000.0000.0000.000
40A66ASN0-0.009-0.0178.827-0.434-0.4340.0000.0000.0000.000
41A67ARG10.9520.9783.725-54.704-54.3450.000-0.126-0.2340.001
42A68ARG10.7690.8638.075-31.350-31.3500.0000.0000.0000.000
43A69VAL0-0.005-0.0078.7741.9671.9670.0000.0000.0000.000
44A70ALA00.0220.02011.258-0.756-0.7560.0000.0000.0000.000
45A71LYS10.7980.88811.601-22.524-22.5240.0000.0000.0000.000
46A72ALA00.0190.02015.799-0.291-0.2910.0000.0000.0000.000
47A73TYR00.0160.00318.4820.3050.3050.0000.0000.0000.000
48A74ALA0-0.005-0.00322.351-0.232-0.2320.0000.0000.0000.000
49A75ARG10.8700.91825.657-10.926-10.9260.0000.0000.0000.000
50A76ALA00.0380.01828.958-0.329-0.3290.0000.0000.0000.000
51A77PRO00.0500.03530.2790.2010.2010.0000.0000.0000.000
52A78VAL0-0.054-0.03631.8240.0640.0640.0000.0000.0000.000
53A79LEU00.0190.02724.0730.0800.0800.0000.0000.0000.000
54A80THR0-0.048-0.01628.356-0.286-0.2860.0000.0000.0000.000
55A81ILE00.0190.01822.7010.3400.3400.0000.0000.0000.000
56A82ASN00.015-0.01024.885-0.008-0.0080.0000.0000.0000.000
57A83GLY00.0440.01824.0110.5520.5520.0000.0000.0000.000
58A84SER0-0.060-0.05725.0980.1940.1940.0000.0000.0000.000
59A85ASP-1-0.870-0.95522.75812.90612.9060.0000.0000.0000.000
60A86ASP-1-0.785-0.84223.02411.84611.8460.0000.0000.0000.000
61A87GLY00.0100.02220.7130.1880.1880.0000.0000.0000.000
62A88PHE0-0.037-0.02721.081-0.398-0.3980.0000.0000.0000.000
63A89ASP-1-0.743-0.85922.74111.16411.1640.0000.0000.0000.000
64A90GLY00.0000.00525.455-0.416-0.4160.0000.0000.0000.000
65A91MET0-0.040-0.03427.018-0.238-0.2380.0000.0000.0000.000
66A92ARG10.7560.86125.649-11.727-11.7270.0000.0000.0000.000
67A93ILE0-0.006-0.00520.5620.2880.2880.0000.0000.0000.000
68A94GLY0-0.014-0.00822.895-0.321-0.3210.0000.0000.0000.000
69A95LEU0-0.025-0.03419.0960.6850.6850.0000.0000.0000.000
70A96CYS0-0.065-0.03418.7861.2161.2160.0000.0000.0000.000
71A97GLY00.0520.04920.1180.0460.0460.0000.0000.0000.000
72A98PHE0-0.080-0.02914.7500.1140.1140.0000.0000.0000.000
73A99ASP-1-0.843-0.90813.08720.42020.4200.0000.0000.0000.000
74A100ASN0-0.053-0.07010.0123.9723.9720.0000.0000.0000.000
75A101PRO00.0110.0218.258-1.486-1.4860.0000.0000.0000.000
76A102MET0-0.033-0.0216.8850.4550.4550.0000.0000.0000.000
77A103ARG10.8010.87710.277-21.486-21.4860.0000.0000.0000.000
78A104ASP-1-0.739-0.83213.48118.84318.8430.0000.0000.0000.000
79A105GLN00.019-0.02215.712-0.212-0.2120.0000.0000.0000.000
80A106LYS10.8630.91619.223-13.926-13.9260.0000.0000.0000.000
81A107THR0-0.026-0.04315.648-0.952-0.9520.0000.0000.0000.000
82A108ASP-1-0.846-0.89618.58114.97314.9730.0000.0000.0000.000
83A109GLU-1-0.807-0.87820.07612.70312.7030.0000.0000.0000.000
84A110MET0-0.077-0.04521.382-0.830-0.8300.0000.0000.0000.000
85A111LYS10.8560.90016.726-18.447-18.4470.0000.0000.0000.000
86A112ARG10.8680.92222.225-14.374-14.3740.0000.0000.0000.000
87A113VAL0-0.029-0.00825.368-0.588-0.5880.0000.0000.0000.000
88A114ILE0-0.0020.03321.580-0.372-0.3720.0000.0000.0000.000
89A115GLY00.0080.00726.213-0.395-0.3950.0000.0000.0000.000
90A116GLN0-0.005-0.02828.4400.1680.1680.0000.0000.0000.000
91A117GLY00.0050.01327.4700.0110.0110.0000.0000.0000.000
92A118VAL00.013-0.00626.641-0.410-0.4100.0000.0000.0000.000
93A119LYS10.9100.96328.860-9.438-9.4380.0000.0000.0000.000
94A120ILE0-0.001-0.00825.789-0.148-0.1480.0000.0000.0000.000
95A121LYS10.9660.97730.030-8.416-8.4160.0000.0000.0000.000
96A122MET0-0.0110.03829.753-0.032-0.0320.0000.0000.0000.000
97A123ASP-1-0.864-0.92932.8128.2278.2270.0000.0000.0000.000
98A124ASP-1-0.841-0.93436.0237.9427.9420.0000.0000.0000.000
99A125ALA0-0.071-0.03138.354-0.040-0.0400.0000.0000.0000.000
100A126GLY00.0520.02734.0260.0560.0560.0000.0000.0000.000
101A127ASN0-0.094-0.06232.8510.3040.3040.0000.0000.0000.000
102A128ILE00.0180.02127.4270.0570.0570.0000.0000.0000.000
103A129LEU0-0.035-0.03331.565-0.062-0.0620.0000.0000.0000.000
104A130ILE0-0.002-0.00727.7940.3080.3080.0000.0000.0000.000
105A131ARG10.8580.91931.801-8.553-8.5530.0000.0000.0000.000
106A132ARG10.8390.93231.424-9.360-9.3600.0000.0000.0000.000
107A133TYR00.0530.01131.865-0.231-0.2310.0000.0000.0000.000
108A134ALA0-0.0480.00429.588-0.182-0.1820.0000.0000.0000.000
109A135LYS11.0130.99931.690-9.170-9.1700.0000.0000.0000.000
110A136SER0-0.040-0.03028.549-0.206-0.2060.0000.0000.0000.000
111A137ASN00.018-0.00229.301-0.376-0.3760.0000.0000.0000.000
112A138VAL00.0230.00926.0320.3950.3950.0000.0000.0000.000
113A139TYR0-0.027-0.01125.332-0.440-0.4400.0000.0000.0000.000
114A140VAL00.0280.02825.3060.4690.4690.0000.0000.0000.000
115A141LYS10.8940.95422.422-12.573-12.5730.0000.0000.0000.000
116A142SER00.0160.00124.4000.0210.0210.0000.0000.0000.000
117A143THR0-0.010-0.01120.9710.3040.3040.0000.0000.0000.000
118A144ALA0-0.0190.01421.9500.2670.2670.0000.0000.0000.000
119A145SER00.008-0.00720.8390.6950.6950.0000.0000.0000.000
120A146SER0-0.058-0.05722.026-0.033-0.0330.0000.0000.0000.000
121A147PRO00.033-0.00325.018-0.138-0.1380.0000.0000.0000.000
122A148ASN0-0.033-0.01527.6130.0400.0400.0000.0000.0000.000
123A149GLU-1-0.784-0.83924.91911.70811.7080.0000.0000.0000.000
124A150GLU-1-0.796-0.88529.2428.5878.5870.0000.0000.0000.000
125A151THR00.0170.02028.4920.2530.2530.0000.0000.0000.000
126A152SER00.024-0.02328.331-0.347-0.3470.0000.0000.0000.000
127A153ILE00.0560.06227.073-0.142-0.1420.0000.0000.0000.000
128A154GLY00.0650.04731.167-0.294-0.2940.0000.0000.0000.000
129A155ALA0-0.003-0.02334.5340.0870.0870.0000.0000.0000.000
130A156GLU-1-0.917-0.97137.0228.0348.0340.0000.0000.0000.000
131A157ILE00.0110.01030.6320.0160.0160.0000.0000.0000.000
132A158LEU0-0.030-0.01531.6350.0550.0550.0000.0000.0000.000
133A159LYS10.9080.95634.291-7.673-7.6730.0000.0000.0000.000
134A160LEU0-0.0170.01534.017-0.158-0.1580.0000.0000.0000.000
135A161PRO00.043-0.00334.1580.2250.2250.0000.0000.0000.000
136A162ASN0-0.037-0.00528.1390.3150.3150.0000.0000.0000.000
137A163GLN0-0.031-0.02028.2050.1620.1620.0000.0000.0000.000
138A164ALA00.0010.00529.7630.3400.3400.0000.0000.0000.000
139A165LEU00.0180.01129.619-0.348-0.3480.0000.0000.0000.000
140A166GLU-1-0.778-0.87932.6487.9587.9580.0000.0000.0000.000
141A167SER0-0.010-0.02235.6270.1800.1800.0000.0000.0000.000
142A168GLU-1-0.871-0.92435.9628.1798.1790.0000.0000.0000.000
143A169LYS10.8290.91737.102-7.976-7.9760.0000.0000.0000.000
144A170ILE0-0.050-0.02736.1780.2590.2590.0000.0000.0000.000
145A171VAL00.0370.02833.347-0.151-0.1510.0000.0000.0000.000
146A172LYS10.8830.93734.071-8.071-8.0710.0000.0000.0000.000
147A173LEU00.0060.00026.1350.0150.0150.0000.0000.0000.000
148A174PHE00.0130.00028.3790.1550.1550.0000.0000.0000.000
149A175ASP-1-0.872-0.94830.7998.1278.1270.0000.0000.0000.000
150A176MET00.0680.03732.0730.0880.0880.0000.0000.0000.000
151A177LYS10.9670.99034.916-7.550-7.5500.0000.0000.0000.000
152A178LYS10.8090.90234.018-9.112-9.1120.0000.0000.0000.000
153A179PHE00.0410.02428.623-0.072-0.0720.0000.0000.0000.000
154A180GLN00.0450.02033.5020.0530.0530.0000.0000.0000.000
155A181SER0-0.079-0.04436.192-0.204-0.2040.0000.0000.0000.000
156A182ASN0-0.010-0.01132.238-0.396-0.3960.0000.0000.0000.000
157A183VAL00.0330.02432.1280.0090.0090.0000.0000.0000.000
158A184ASN0-0.064-0.03834.524-0.220-0.2200.0000.0000.0000.000
159A185ARG10.8940.91736.824-8.236-8.2360.0000.0000.0000.000
160A186GLU-1-0.751-0.86331.7349.2079.2070.0000.0000.0000.000
161A187LEU0-0.051-0.01735.109-0.044-0.0440.0000.0000.0000.000
162A188ARG10.8590.92636.612-7.574-7.5740.0000.0000.0000.000
163A189ARG10.7550.85733.967-8.805-8.8050.0000.0000.0000.000
164A190ALA00.0230.00737.9280.0120.0120.0000.0000.0000.000
165A191TYR0-0.027-0.01833.398-0.013-0.0130.0000.0000.0000.000
166A192PRO0-0.0190.01433.0800.2440.2440.0000.0000.0000.000
167A193ASP-1-0.786-0.86926.86011.23611.2360.0000.0000.0000.000
168A194ARG10.8830.91025.194-10.934-10.9340.0000.0000.0000.000
169A195ARG10.8900.91222.454-11.576-11.5760.0000.0000.0000.000
170A196ARG10.8900.94824.416-10.329-10.3290.0000.0000.0000.000
171A197LEU0-0.0220.00126.680-0.045-0.0450.0000.0000.0000.000
172A198GLU-1-0.796-0.89822.92412.26212.2620.0000.0000.0000.000
173A199THR0-0.011-0.00821.2570.1770.1770.0000.0000.0000.000
174A200GLN0-0.0040.00723.339-0.158-0.1580.0000.0000.0000.000
175A201CYS0-0.0500.00024.174-0.402-0.4020.0000.0000.0000.000
176A202LEU0-0.0260.00519.0900.2900.2900.0000.0000.0000.000
177A203SER0-0.024-0.01822.795-0.625-0.6250.0000.0000.0000.000
178A204ALA00.0430.03020.5140.5890.5890.0000.0000.0000.000
179A205VAL0-0.025-0.01021.524-0.691-0.6910.0000.0000.0000.000
180A206ALA00.0290.01521.3420.7030.7030.0000.0000.0000.000
181A207PHE00.018-0.00521.659-0.915-0.9150.0000.0000.0000.000
182A208VAL0-0.0090.02123.0690.3820.3820.0000.0000.0000.000
183A209LYS10.7940.85522.837-13.535-13.5350.0000.0000.0000.000
184A210SER00.0060.01022.8130.3690.3690.0000.0000.0000.000
185A211GLU-1-0.818-0.89320.09713.58613.5860.0000.0000.0000.000
186A212ASN0-0.038-0.03522.744-0.245-0.2450.0000.0000.0000.000
187A213ASP-1-0.818-0.89817.47016.71916.7190.0000.0000.0000.000
188A214ILE00.013-0.00816.6460.1610.1610.0000.0000.0000.000
189A215LEU0-0.033-0.01812.3650.6530.6530.0000.0000.0000.000
190A216GLU-1-0.887-0.94414.14817.54417.5440.0000.0000.0000.000
191A217CYS0-0.104-0.02816.765-0.921-0.9210.0000.0000.0000.000
192A218PRO00.0240.00816.4861.0051.0050.0000.0000.0000.000
193A219ILE00.0040.00116.6020.8490.8490.0000.0000.0000.000
194A220TRP0-0.047-0.02814.125-1.859-1.8590.0000.0000.0000.000
195A221VAL00.0020.01117.2050.8060.8060.0000.0000.0000.000
196A222LEU0-0.0050.00116.195-0.631-0.6310.0000.0000.0000.000
197A223ILE0-0.019-0.01818.7840.1140.1140.0000.0000.0000.000
198A224VAL00.0030.00319.076-0.225-0.2250.0000.0000.0000.000
199A225ASN00.0330.01422.129-0.233-0.2330.0000.0000.0000.000
200A226VAL00.0620.01523.957-0.023-0.0230.0000.0000.0000.000
201A227VAL00.0910.04126.288-0.212-0.2120.0000.0000.0000.000
202A228ALA0-0.039-0.01427.871-0.241-0.2410.0000.0000.0000.000
203A229MET0-0.036-0.03221.825-0.030-0.0300.0000.0000.0000.000
204A230ASP-1-0.856-0.92727.2779.5659.5650.0000.0000.0000.000
205A231MET0-0.032-0.02229.934-0.296-0.2960.0000.0000.0000.000
206A232LEU0-0.0240.00327.078-0.226-0.2260.0000.0000.0000.000
207A233LYS10.8650.94926.399-10.915-10.9150.0000.0000.0000.000
208A234SER00.0150.01830.411-0.231-0.2310.0000.0000.0000.000
209A235LYS10.8290.91333.207-8.587-8.5870.0000.0000.0000.000
210A236LEU0-0.0020.01332.034-0.030-0.0300.0000.0000.0000.000