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: ZYQ6N

Calculation Name: 4PVC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PVC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12068

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 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 342
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5418140.870423
FMO2-HF: Nuclear repulsion 5284601.147086
FMO2-HF: Total energy -133539.723337
FMO2-MP2: Total energy -133931.164853


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-17.891-9.62810.913-5.392-13.782-0.008
Interaction energy analysis for fragmet #1(A:1:MET)
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 : -0.016
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].
3A3VAL0-0.0030.0073.302-4.704-2.3850.112-1.039-1.392-0.002
4A4PHE00.0210.0014.9810.4650.526-0.001-0.005-0.0560.000
5A5VAL00.0130.0008.3310.0220.0220.0000.0000.0000.000
6A6SER00.021-0.00811.2360.0560.0560.0000.0000.0000.000
7A7GLY0-0.0030.00114.5280.0310.0310.0000.0000.0000.000
8A8ALA00.0250.00214.3450.0200.0200.0000.0000.0000.000
9A9ASN0-0.012-0.00716.0380.0260.0260.0000.0000.0000.000
10A10GLY0-0.003-0.00119.031-0.006-0.0060.0000.0000.0000.000
11A11PHE0-0.006-0.01219.5830.0270.0270.0000.0000.0000.000
12A12ILE00.0590.01616.8490.0240.0240.0000.0000.0000.000
13A13ALA00.0070.01215.3380.0450.0450.0000.0000.0000.000
14A14GLN00.0150.00814.8480.0780.0780.0000.0000.0000.000
15A15HIS00.006-0.01316.0070.0860.0860.0000.0000.0000.000
16A16ILE0-0.037-0.00610.9900.0620.0620.0000.0000.0000.000
17A17VAL0-0.007-0.00411.2560.1260.1260.0000.0000.0000.000
18A18ASP-1-0.782-0.88711.6780.6750.6750.0000.0000.0000.000
19A19LEU0-0.050-0.02612.1820.0730.0730.0000.0000.0000.000
20A20LEU00.0010.0065.9860.1310.1310.0000.0000.0000.000
21A21LEU0-0.020-0.0117.9010.2920.2920.0000.0000.0000.000
22A22LYS10.8030.8899.848-0.501-0.5010.0000.0000.0000.000
23A23GLU-1-0.925-0.9578.4061.1241.1240.0000.0000.0000.000
24A24ASP-1-0.842-0.9047.2991.7601.7600.0000.0000.0000.000
25A25TYR0-0.0290.0012.374-1.829-0.3872.539-0.951-3.030-0.003
26A26LYS10.8140.8923.598-5.569-4.2100.047-0.621-0.7840.004
27A27VAL0-0.004-0.0025.208-0.641-0.6410.0000.0000.0000.000
28A28ILE00.0240.0197.963-0.039-0.0390.0000.0000.0000.000
29A29GLY00.0510.02010.390-0.114-0.1140.0000.0000.0000.000
30A30SER00.0120.00113.111-0.024-0.0240.0000.0000.0000.000
31A31ALA00.0360.01216.2020.0230.0230.0000.0000.0000.000
32A32ARG10.9000.96319.815-0.023-0.0230.0000.0000.0000.000
33A33SER0-0.059-0.08023.071-0.008-0.0080.0000.0000.0000.000
34A34GLN00.0450.00422.750-0.004-0.0040.0000.0000.0000.000
35A35GLU-1-0.748-0.84124.0530.0840.0840.0000.0000.0000.000
36A36LYS10.8410.93323.145-0.049-0.0490.0000.0000.0000.000
37A37ALA00.0080.00719.9260.0200.0200.0000.0000.0000.000
38A38GLU-1-0.829-0.91020.1910.1680.1680.0000.0000.0000.000
39A39ASN0-0.049-0.04122.4610.0190.0190.0000.0000.0000.000
40A40LEU0-0.019-0.00516.7620.0140.0140.0000.0000.0000.000
41A41THR00.020-0.00316.4940.0290.0290.0000.0000.0000.000
42A42GLU-1-0.959-0.96418.5860.2460.2460.0000.0000.0000.000
43A43ALA0-0.042-0.01320.8780.0150.0150.0000.0000.0000.000
44A44PHE0-0.033-0.02615.8310.0160.0160.0000.0000.0000.000
45A45GLY0-0.026-0.00717.2620.0620.0620.0000.0000.0000.000
46A46ASN0-0.058-0.03818.2900.0080.0080.0000.0000.0000.000
47A47ASN00.0440.02512.6600.0960.0960.0000.0000.0000.000
48A48PRO00.0630.02913.6160.0290.0290.0000.0000.0000.000
49A49LYS10.7490.8686.689-2.558-2.5580.0000.0000.0000.000
50A50PHE0-0.048-0.0249.0090.2290.2290.0000.0000.0000.000
51A51SER0-0.0070.00911.309-0.147-0.1470.0000.0000.0000.000
52A52MET0-0.0330.00113.296-0.027-0.0270.0000.0000.0000.000
53A53GLU-1-0.786-0.86614.611-0.044-0.0440.0000.0000.0000.000
54A54VAL0-0.010-0.01117.1540.0030.0030.0000.0000.0000.000
55A55VAL0-0.002-0.00317.536-0.023-0.0230.0000.0000.0000.000
56A56PRO0-0.023-0.01320.6870.0070.0070.0000.0000.0000.000
57A57ASP-1-0.833-0.89623.697-0.069-0.0690.0000.0000.0000.000
58A58ILE0-0.014-0.01219.933-0.012-0.0120.0000.0000.0000.000
59A59SER0-0.020-0.01222.107-0.021-0.0210.0000.0000.0000.000
60A60LYS10.8710.93624.7730.0710.0710.0000.0000.0000.000
61A61LEU00.028-0.00123.187-0.013-0.0130.0000.0000.0000.000
62A62ASP-1-0.888-0.93221.987-0.180-0.1800.0000.0000.0000.000
63A63ALA0-0.038-0.01220.814-0.005-0.0050.0000.0000.0000.000
64A64PHE0-0.010-0.03015.4610.0210.0210.0000.0000.0000.000
65A65ASP-1-0.754-0.86616.327-0.361-0.3610.0000.0000.0000.000
66A66HIS0-0.028-0.01117.481-0.014-0.0140.0000.0000.0000.000
67A67VAL00.0020.00512.3510.0040.0040.0000.0000.0000.000
68A68PHE00.0560.0119.610-0.038-0.0380.0000.0000.0000.000
69A69GLN0-0.0040.02213.531-0.069-0.0690.0000.0000.0000.000
70A70LYS10.7790.87414.2570.0420.0420.0000.0000.0000.000
71A71HIS0-0.029-0.02310.0360.0390.0390.0000.0000.0000.000
72A72GLY00.0490.0359.520-0.243-0.2430.0000.0000.0000.000
73A73LYS10.9540.9849.2260.1660.1660.0000.0000.0000.000
74A74ASP-1-0.839-0.8944.586-0.511-0.405-0.001-0.015-0.0890.000
75A75ILE0-0.0060.0264.731-1.435-1.425-0.001-0.0370.0280.000
76A76LYS10.8900.9512.1212.7053.5354.477-1.391-3.916-0.002
77A77ILE0-0.0030.0122.468-0.853-0.3273.540-0.706-3.360-0.003
78A78VAL00.0140.0094.8760.2300.244-0.001-0.008-0.0040.000
79A79LEU0-0.003-0.0017.8440.1350.1350.0000.0000.0000.000
80A80HIS00.0100.01210.6450.0250.0250.0000.0000.0000.000
81A81THR00.011-0.01513.9420.0360.0360.0000.0000.0000.000
82A82ALA0-0.053-0.01116.4340.0210.0210.0000.0000.0000.000
83A83SER00.002-0.01518.867-0.026-0.0260.0000.0000.0000.000
84A84PRO00.0180.01022.3400.0090.0090.0000.0000.0000.000
85A85PHE0-0.035-0.01925.2170.0150.0150.0000.0000.0000.000
86A86CYS0-0.053-0.01827.225-0.005-0.0050.0000.0000.0000.000
87A87PHE00.024-0.00630.307-0.005-0.0050.0000.0000.0000.000
88A88ASP-1-0.781-0.90332.841-0.020-0.0200.0000.0000.0000.000
89A89ILE0-0.050-0.03236.254-0.004-0.0040.0000.0000.0000.000
90A90THR0-0.048-0.00638.6120.0000.0000.0000.0000.0000.000
91A91ASP-1-0.845-0.91738.754-0.054-0.0540.0000.0000.0000.000
92A92SER00.0470.01536.214-0.002-0.0020.0000.0000.0000.000
93A93GLU-1-0.827-0.89834.616-0.080-0.0800.0000.0000.0000.000
94A94ARG10.7670.84533.8470.0380.0380.0000.0000.0000.000
95A95ASP-1-0.811-0.87833.454-0.049-0.0490.0000.0000.0000.000
96A96LEU0-0.041-0.02830.1900.0040.0040.0000.0000.0000.000
97A97LEU0-0.043-0.02329.900-0.006-0.0060.0000.0000.0000.000
98A98ILE00.0160.00929.318-0.012-0.0120.0000.0000.0000.000
99A99PRO00.0070.00527.848-0.015-0.0150.0000.0000.0000.000
100A100ALA0-0.0110.00025.456-0.011-0.0110.0000.0000.0000.000
101A101VAL0-0.0110.00024.197-0.016-0.0160.0000.0000.0000.000
102A102ASN00.010-0.00523.772-0.033-0.0330.0000.0000.0000.000
103A103GLY0-0.006-0.00222.139-0.018-0.0180.0000.0000.0000.000
104A104VAL0-0.0320.00018.688-0.014-0.0140.0000.0000.0000.000
105A105LYS10.9610.96618.9680.1980.1980.0000.0000.0000.000
106A106GLY00.0290.02420.128-0.029-0.0290.0000.0000.0000.000
107A107ILE0-0.008-0.00413.096-0.031-0.0310.0000.0000.0000.000
108A108LEU00.0020.01214.392-0.077-0.0770.0000.0000.0000.000
109A109HIS00.0330.01316.308-0.073-0.0730.0000.0000.0000.000
110A110SER0-0.025-0.03016.108-0.007-0.0070.0000.0000.0000.000
111A111ILE0-0.050-0.01611.355-0.042-0.0420.0000.0000.0000.000
112A112LYS10.8860.93513.8970.3330.3330.0000.0000.0000.000
113A113LYS10.8230.91316.1240.2870.2870.0000.0000.0000.000
114A114TYR0-0.062-0.05315.2940.0420.0420.0000.0000.0000.000
115A115ALA0-0.022-0.01010.412-0.023-0.0230.0000.0000.0000.000
116A116ALA00.0310.03710.928-0.185-0.1850.0000.0000.0000.000
117A117ASP-1-0.912-0.95711.701-1.038-1.0380.0000.0000.0000.000
118A118SER0-0.055-0.0497.735-0.116-0.1160.0000.0000.0000.000
119A119VAL0-0.012-0.0136.098-0.845-0.8450.0000.0000.0000.000
120A120GLU-1-0.881-0.9403.337-6.510-5.4120.105-0.477-0.726-0.003
121A121ARG10.8060.9045.4651.3541.3540.0000.0000.0000.000
122A122VAL00.0170.0146.979-0.038-0.0380.0000.0000.0000.000
123A123VAL0-0.001-0.0079.3940.0930.0930.0000.0000.0000.000
124A124LEU0-0.010-0.00411.8580.0120.0120.0000.0000.0000.000
125A125THR0-0.009-0.02115.4290.0310.0310.0000.0000.0000.000
126A126SER0-0.072-0.05417.751-0.007-0.0070.0000.0000.0000.000
127A127SER0-0.013-0.03120.9330.0230.0230.0000.0000.0000.000
128A128TYR00.004-0.00324.060-0.015-0.0150.0000.0000.0000.000
129A129ALA00.0300.01626.626-0.005-0.0050.0000.0000.0000.000
130A130ALA00.0200.00825.046-0.003-0.0030.0000.0000.0000.000
131A131VAL0-0.088-0.03025.633-0.008-0.0080.0000.0000.0000.000
132A132PHE0-0.0140.00428.218-0.001-0.0010.0000.0000.0000.000
133A133ASP-1-0.756-0.88231.714-0.044-0.0440.0000.0000.0000.000
134A134MET00.0100.00435.2130.0040.0040.0000.0000.0000.000
135A135ALA00.001-0.00236.5860.0050.0050.0000.0000.0000.000
136A136LYS10.8600.91238.2150.0390.0390.0000.0000.0000.000
137A137GLU-1-0.733-0.82834.084-0.004-0.0040.0000.0000.0000.000
138A138ASN00.000-0.00637.7320.0060.0060.0000.0000.0000.000
139A139ASP-1-0.849-0.90140.659-0.015-0.0150.0000.0000.0000.000
140A140LYS10.9090.94240.195-0.006-0.0060.0000.0000.0000.000
141A141SER0-0.113-0.05640.402-0.001-0.0010.0000.0000.0000.000
142A142LEU0-0.0050.00637.997-0.004-0.0040.0000.0000.0000.000
143A143THR0-0.023-0.02632.7940.0060.0060.0000.0000.0000.000
144A144PHE0-0.0010.01230.932-0.006-0.0060.0000.0000.0000.000
145A145ASN00.007-0.01628.1260.0070.0070.0000.0000.0000.000
146A146GLU-1-0.755-0.86822.441-0.046-0.0460.0000.0000.0000.000
147A147GLU-1-0.932-0.95024.734-0.115-0.1150.0000.0000.0000.000
148A148SER0-0.0250.00226.9790.0000.0000.0000.0000.0000.000
149A149TRP0-0.0010.00023.2410.0000.0000.0000.0000.0000.000
150A150ASN00.0170.01429.3570.0030.0030.0000.0000.0000.000
151A151PRO00.0180.00731.591-0.009-0.0090.0000.0000.0000.000
152A152ALA0-0.0100.01834.131-0.002-0.0020.0000.0000.0000.000
153A153THR0-0.014-0.02233.694-0.006-0.0060.0000.0000.0000.000
154A154TRP0-0.012-0.02630.1270.0010.0010.0000.0000.0000.000
155A155GLU-1-0.791-0.88635.087-0.070-0.0700.0000.0000.0000.000
156A156SER0-0.026-0.02938.3810.0050.0050.0000.0000.0000.000
157A157CYS0-0.082-0.02234.9580.0040.0040.0000.0000.0000.000
158A158GLN0-0.033-0.03636.9690.0080.0080.0000.0000.0000.000
159A159SER0-0.042-0.00638.8700.0020.0020.0000.0000.0000.000
160A160ASP-1-0.798-0.88039.601-0.020-0.0200.0000.0000.0000.000
161A161PRO00.0580.01737.691-0.003-0.0030.0000.0000.0000.000
162A162VAL0-0.0080.00535.610-0.002-0.0020.0000.0000.0000.000
163A163ASN0-0.022-0.04034.732-0.005-0.0050.0000.0000.0000.000
164A164ALA00.0410.04834.580-0.006-0.0060.0000.0000.0000.000
165A165TYR00.0050.00427.437-0.009-0.0090.0000.0000.0000.000
166A166CYS0-0.048-0.02830.164-0.004-0.0040.0000.0000.0000.000
167A167GLY00.0370.01429.872-0.007-0.0070.0000.0000.0000.000
168A168SER0-0.058-0.04729.064-0.011-0.0110.0000.0000.0000.000
169A169LYS10.9190.95622.3600.0450.0450.0000.0000.0000.000
170A170LYS10.8100.90525.0680.0760.0760.0000.0000.0000.000
171A171PHE00.004-0.01825.878-0.016-0.0160.0000.0000.0000.000
172A172ALA00.0100.01822.948-0.016-0.0160.0000.0000.0000.000
173A173GLU-1-0.696-0.80220.413-0.156-0.1560.0000.0000.0000.000
174A174LYS10.7840.88121.4430.1330.1330.0000.0000.0000.000
175A175ALA00.0160.01122.859-0.018-0.0180.0000.0000.0000.000
176A176ALA00.000-0.00317.543-0.026-0.0260.0000.0000.0000.000
177A177TRP0-0.058-0.04516.612-0.055-0.0550.0000.0000.0000.000
178A178GLU-1-0.746-0.85720.058-0.200-0.2000.0000.0000.0000.000
179A179PHE00.0000.00816.574-0.011-0.0110.0000.0000.0000.000
180A180LEU00.0220.00314.554-0.012-0.0120.0000.0000.0000.000
181A181GLU-1-1.007-1.01518.009-0.275-0.2750.0000.0000.0000.000
182A182GLU-1-0.953-0.96921.185-0.255-0.2550.0000.0000.0000.000
183A183ASN0-0.063-0.03118.7320.0100.0100.0000.0000.0000.000
184A184ARG10.9510.98217.0000.3610.3610.0000.0000.0000.000
185A185ASP-1-0.878-0.93017.081-0.445-0.4450.0000.0000.0000.000
186A186SER0-0.152-0.07318.172-0.001-0.0010.0000.0000.0000.000
187A187VAL0-0.042-0.02813.370-0.029-0.0290.0000.0000.0000.000
188A188LYS10.8570.9496.9042.4742.4740.0000.0000.0000.000
189A189PHE0-0.066-0.0269.046-0.023-0.0230.0000.0000.0000.000
190A190GLU-1-0.869-0.9389.309-0.504-0.5040.0000.0000.0000.000
191A191LEU0-0.050-0.02310.327-0.068-0.0680.0000.0000.0000.000
192A192THR0-0.042-0.03112.4740.0150.0150.0000.0000.0000.000
193A193ALA00.0070.02714.0550.0000.0000.0000.0000.0000.000
194A194VAL00.0090.00215.0620.0250.0250.0000.0000.0000.000
195A195ASN0-0.054-0.06017.903-0.012-0.0120.0000.0000.0000.000
196A196PRO0-0.0080.00020.5910.0080.0080.0000.0000.0000.000
197A197VAL0-0.0340.00523.202-0.015-0.0150.0000.0000.0000.000
198A198TYR0-0.0090.00326.4380.0030.0030.0000.0000.0000.000
199A199VAL0-0.020-0.00922.7230.0070.0070.0000.0000.0000.000
200A200PHE00.0380.01326.009-0.003-0.0030.0000.0000.0000.000
201A201GLY00.0800.03125.4950.0130.0130.0000.0000.0000.000
202A202PRO0-0.0130.00724.230-0.008-0.0080.0000.0000.0000.000
203A203GLN00.006-0.02023.8520.0070.0070.0000.0000.0000.000
204A204MET0-0.0240.01818.1160.0020.0020.0000.0000.0000.000
205A205PHE00.0080.00019.0190.0010.0010.0000.0000.0000.000
206A206ASP-1-0.816-0.91224.3540.1700.1700.0000.0000.0000.000
207A207LYS10.8120.90024.239-0.223-0.2230.0000.0000.0000.000
208A208ASP-1-0.807-0.90424.4780.1750.1750.0000.0000.0000.000
209A209VAL00.0180.01828.156-0.014-0.0140.0000.0000.0000.000
210A210LYS10.8680.95730.632-0.100-0.1000.0000.0000.0000.000
211A211LYS10.9450.95030.632-0.094-0.0940.0000.0000.0000.000
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