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: 6Y6KZ

Calculation Name: 1V43-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V43

Chain ID: A

ChEMBL ID:

UniProt ID: O57758

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 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 367
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5757143.322294
FMO2-HF: Nuclear repulsion 5611635.410024
FMO2-HF: Total energy -145507.91227
FMO2-MP2: Total energy -145930.269853


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:7:VAL)


Summations of interaction energy for fragment #1(A:7:VAL)
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.
-13.763-10.68510.494-6.264-7.309-0.065
Interaction energy analysis for fragmet #1(A:7:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.012
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].
3A9LYS10.8440.9262.4480.9393.7811.540-2.007-2.375-0.012
4A10MET0-0.0050.0065.0850.3030.360-0.001-0.005-0.0510.000
5A11VAL0-0.013-0.0068.1970.1260.1260.0000.0000.0000.000
6A12GLU-1-0.822-0.88611.097-0.371-0.3710.0000.0000.0000.000
7A13VAL0-0.030-0.01614.780-0.044-0.0440.0000.0000.0000.000
8A14LYS10.8160.91417.3800.4400.4400.0000.0000.0000.000
9A15LEU0-0.014-0.01320.874-0.009-0.0090.0000.0000.0000.000
10A16GLU-1-0.776-0.88223.989-0.219-0.2190.0000.0000.0000.000
11A17ASN0-0.026-0.04327.2360.0080.0080.0000.0000.0000.000
12A18LEU00.0420.02825.1580.0100.0100.0000.0000.0000.000
13A19THR0-0.053-0.02529.6310.0130.0130.0000.0000.0000.000
14A20LYS10.7860.88331.1770.2000.2000.0000.0000.0000.000
15A21ARG10.8650.90733.5700.1510.1510.0000.0000.0000.000
16A22PHE0-0.0070.00132.4310.0010.0010.0000.0000.0000.000
17A23GLY00.0170.01838.1020.0070.0070.0000.0000.0000.000
18A24ASN0-0.004-0.01741.395-0.001-0.0010.0000.0000.0000.000
19A25PHE00.0270.01736.827-0.001-0.0010.0000.0000.0000.000
20A26THR0-0.009-0.01336.705-0.008-0.0080.0000.0000.0000.000
21A27ALA0-0.0150.00534.3180.0000.0000.0000.0000.0000.000
22A28VAL0-0.016-0.01529.607-0.008-0.0080.0000.0000.0000.000
23A29ASN0-0.026-0.02232.9720.0030.0030.0000.0000.0000.000
24A30LYS10.8680.92832.7950.1500.1500.0000.0000.0000.000
25A31LEU00.0120.02326.4170.0020.0020.0000.0000.0000.000
26A32ASN0-0.021-0.00727.620-0.014-0.0140.0000.0000.0000.000
27A33LEU0-0.001-0.01122.3990.0100.0100.0000.0000.0000.000
28A34THR00.0280.03419.841-0.014-0.0140.0000.0000.0000.000
29A35ILE0-0.038-0.01716.9540.0280.0280.0000.0000.0000.000
30A36LYS10.9910.98016.2610.2390.2390.0000.0000.0000.000
31A37ASP-1-0.868-0.93611.223-0.571-0.5710.0000.0000.0000.000
32A38GLY00.0580.01410.8300.0510.0510.0000.0000.0000.000
33A39GLU-1-0.827-0.85511.519-0.281-0.2810.0000.0000.0000.000
34A40PHE00.003-0.00915.073-0.073-0.0730.0000.0000.0000.000
35A41LEU00.0060.00217.1620.0570.0570.0000.0000.0000.000
36A42VAL00.000-0.00520.078-0.019-0.0190.0000.0000.0000.000
37A43LEU0-0.025-0.00922.9870.0210.0210.0000.0000.0000.000
38A44LEU00.0370.02025.4070.0020.0020.0000.0000.0000.000
39A45GLY00.0330.00428.6220.0050.0050.0000.0000.0000.000
40A46PRO00.0610.03932.177-0.005-0.0050.0000.0000.0000.000
41A47SER00.029-0.00633.700-0.015-0.0150.0000.0000.0000.000
42A48GLY00.0030.00234.4790.0060.0060.0000.0000.0000.000
43A49CYS0-0.099-0.00732.118-0.003-0.0030.0000.0000.0000.000
44A50GLY00.1330.06531.7490.0020.0020.0000.0000.0000.000
45A51LYS10.8290.91727.5440.1830.1830.0000.0000.0000.000
46A52THR00.011-0.01526.736-0.014-0.0140.0000.0000.0000.000
47A53THR0-0.029-0.02026.798-0.017-0.0170.0000.0000.0000.000
48A54THR00.0380.01324.513-0.006-0.0060.0000.0000.0000.000
49A55LEU00.0170.01320.357-0.021-0.0210.0000.0000.0000.000
50A56ARG10.8320.90522.4960.2210.2210.0000.0000.0000.000
51A57MET0-0.0200.00423.990-0.005-0.0050.0000.0000.0000.000
52A58ILE00.0050.00419.116-0.012-0.0120.0000.0000.0000.000
53A59ALA0-0.023-0.01719.221-0.041-0.0410.0000.0000.0000.000
54A60GLY00.0590.02320.106-0.022-0.0220.0000.0000.0000.000
55A61LEU0-0.088-0.04121.9080.0190.0190.0000.0000.0000.000
56A62GLU-1-0.845-0.92124.620-0.186-0.1860.0000.0000.0000.000
57A63GLU-1-0.762-0.87025.315-0.319-0.3190.0000.0000.0000.000
58A64PRO00.020-0.00526.7530.0190.0190.0000.0000.0000.000
59A65THR0-0.036-0.01829.8810.0070.0070.0000.0000.0000.000
60A66GLU-1-0.764-0.86232.259-0.139-0.1390.0000.0000.0000.000
61A67GLY00.0060.01229.714-0.008-0.0080.0000.0000.0000.000
62A68ARG10.8350.91024.5710.2440.2440.0000.0000.0000.000
63A69ILE0-0.012-0.00620.342-0.002-0.0020.0000.0000.0000.000
64A70TYR0-0.015-0.00919.428-0.001-0.0010.0000.0000.0000.000
65A71PHE0-0.043-0.02214.169-0.016-0.0160.0000.0000.0000.000
66A72GLY00.0410.01014.661-0.027-0.0270.0000.0000.0000.000
67A73ASP-1-0.860-0.92415.348-0.328-0.3280.0000.0000.0000.000
68A74ARG10.8440.93013.9660.7490.7490.0000.0000.0000.000
69A75ASP-1-0.772-0.85818.122-0.341-0.3410.0000.0000.0000.000
70A76VAL0-0.040-0.04216.675-0.012-0.0120.0000.0000.0000.000
71A77THR0-0.046-0.04620.0220.0000.0000.0000.0000.0000.000
72A78TYR00.0060.01323.4540.0130.0130.0000.0000.0000.000
73A79LEU0-0.0270.01117.7980.0120.0120.0000.0000.0000.000
74A80PRO00.0410.01720.531-0.007-0.0070.0000.0000.0000.000
75A81PRO00.0610.03319.028-0.046-0.0460.0000.0000.0000.000
76A82LYS10.7460.85016.3570.3040.3040.0000.0000.0000.000
77A83ASP-1-0.775-0.86614.888-0.497-0.4970.0000.0000.0000.000
78A84ARG10.8140.91014.9000.3800.3800.0000.0000.0000.000
79A85ASN0-0.078-0.0339.4660.0950.0950.0000.0000.0000.000
80A86ILE00.0330.03011.548-0.158-0.1580.0000.0000.0000.000
81A87SER0-0.055-0.05412.0490.0130.0130.0000.0000.0000.000
82A88MET00.0080.01214.1790.0020.0020.0000.0000.0000.000
83A89VAL0-0.011-0.00616.5930.0350.0350.0000.0000.0000.000
84A90PHE00.007-0.01219.1220.0180.0180.0000.0000.0000.000
85A91GLN00.011-0.00722.9090.0210.0210.0000.0000.0000.000
86A92SER0-0.0130.00026.2210.0080.0080.0000.0000.0000.000
87A93TYR00.0010.02228.7230.0020.0020.0000.0000.0000.000
88A94ALA00.0020.00127.138-0.004-0.0040.0000.0000.0000.000
89A95VAL00.0160.02727.8240.0100.0100.0000.0000.0000.000
90A96TRP0-0.006-0.01524.960-0.018-0.0180.0000.0000.0000.000
91A97PRO00.0240.01223.8560.0130.0130.0000.0000.0000.000
92A98HIS00.024-0.01026.1590.0010.0010.0000.0000.0000.000
93A99MET0-0.0370.00121.5790.0030.0030.0000.0000.0000.000
94A100THR00.0330.01021.765-0.008-0.0080.0000.0000.0000.000
95A101VAL00.000-0.00818.836-0.025-0.0250.0000.0000.0000.000
96A102TYR00.009-0.02616.346-0.057-0.0570.0000.0000.0000.000
97A103GLU-1-0.781-0.89316.998-0.099-0.0990.0000.0000.0000.000
98A104ASN0-0.053-0.02818.425-0.060-0.0600.0000.0000.0000.000
99A105ILE00.0170.00412.796-0.051-0.0510.0000.0000.0000.000
100A106ALA00.0440.02113.528-0.069-0.0690.0000.0000.0000.000
101A107PHE0-0.043-0.01615.020-0.017-0.0170.0000.0000.0000.000
102A108PRO0-0.033-0.01312.7610.0090.0090.0000.0000.0000.000
103A109LEU0-0.0100.0049.297-0.065-0.0650.0000.0000.0000.000
104A110LYS10.8350.89813.1610.1100.1100.0000.0000.0000.000
105A111ILE00.0620.03915.9260.0240.0240.0000.0000.0000.000
106A112LYS10.9220.98010.2400.9660.9660.0000.0000.0000.000
107A113LYS10.8730.92815.1830.2390.2390.0000.0000.0000.000
108A114PHE00.0260.0027.721-0.016-0.0160.0000.0000.0000.000
109A115PRO00.0490.02711.545-0.001-0.0010.0000.0000.0000.000
110A116LYS10.9780.98013.154-0.099-0.0990.0000.0000.0000.000
111A117ASP-1-0.842-0.91513.8300.2910.2910.0000.0000.0000.000
112A118GLU-1-0.773-0.8726.2631.2761.2760.0000.0000.0000.000
113A119ILE0-0.034-0.0249.454-0.061-0.0610.0000.0000.0000.000
114A120ASP-1-0.789-0.84011.5150.2470.2470.0000.0000.0000.000
115A121LYS10.8810.9295.190-2.655-2.6550.0000.0000.0000.000
116A122ARG10.7580.8563.4882.3202.517-0.001-0.058-0.1390.000
117A123VAL0-0.002-0.0048.498-0.157-0.1570.0000.0000.0000.000
118A124ARG10.8500.89612.037-0.346-0.3460.0000.0000.0000.000
119A125TRP00.0060.0104.309-0.440-0.217-0.001-0.017-0.2050.000
120A126ALA00.012-0.0069.496-0.080-0.0800.0000.0000.0000.000
121A127ALA0-0.024-0.02110.597-0.022-0.0220.0000.0000.0000.000
122A128GLU-1-0.749-0.86311.4370.1400.1400.0000.0000.0000.000
123A129LEU0-0.029-0.0067.342-0.055-0.0550.0000.0000.0000.000
124A130LEU0-0.052-0.01612.002-0.050-0.0500.0000.0000.0000.000
125A131GLN0-0.039-0.00515.2850.0280.0280.0000.0000.0000.000
126A132ILE0-0.038-0.01216.086-0.012-0.0120.0000.0000.0000.000
127A133GLU-1-0.812-0.92315.8710.0750.0750.0000.0000.0000.000
128A134GLU-1-0.872-0.92618.2750.0830.0830.0000.0000.0000.000
129A135LEU0-0.070-0.04820.973-0.010-0.0100.0000.0000.0000.000
130A136LEU0-0.0020.00716.220-0.017-0.0170.0000.0000.0000.000
131A137ASN00.0060.00320.375-0.015-0.0150.0000.0000.0000.000
132A138ARG10.8890.96323.621-0.006-0.0060.0000.0000.0000.000
133A139TYR00.0450.02324.411-0.014-0.0140.0000.0000.0000.000
134A140PRO0-0.014-0.00924.0900.0020.0020.0000.0000.0000.000
135A141ALA00.0080.00026.4460.0000.0000.0000.0000.0000.000
136A142GLN00.0280.02228.7630.0020.0020.0000.0000.0000.000
137A143LEU0-0.038-0.00323.2580.0070.0070.0000.0000.0000.000
138A144SER00.004-0.01127.367-0.005-0.0050.0000.0000.0000.000
139A145GLY0-0.032-0.00227.9230.0020.0020.0000.0000.0000.000
140A146GLY00.0330.00524.3090.0080.0080.0000.0000.0000.000
141A147GLN00.0420.03122.679-0.012-0.0120.0000.0000.0000.000
142A148ARG10.8870.92920.7110.1780.1780.0000.0000.0000.000
143A149GLN00.0290.01321.229-0.007-0.0070.0000.0000.0000.000
144A150ARG10.8810.91518.3340.0680.0680.0000.0000.0000.000
145A151VAL00.0210.01117.126-0.035-0.0350.0000.0000.0000.000
146A152ALA0-0.069-0.03717.307-0.032-0.0320.0000.0000.0000.000
147A153VAL00.0430.02014.340-0.051-0.0510.0000.0000.0000.000
148A154ALA00.0430.02312.927-0.106-0.1060.0000.0000.0000.000
149A155ARG10.8870.93912.2030.2230.2230.0000.0000.0000.000
150A156ALA00.0060.01813.323-0.045-0.0450.0000.0000.0000.000
151A157ILE00.0400.0348.671-0.171-0.1710.0000.0000.0000.000
152A158VAL00.0150.0227.734-0.504-0.5040.0000.0000.0000.000
153A159VAL0-0.072-0.0467.433-0.091-0.0910.0000.0000.0000.000
154A160GLU-1-0.858-0.9072.206-12.946-13.1878.957-4.177-4.539-0.053
155A161PRO0-0.072-0.0125.815-0.229-0.2290.0000.0000.0000.000
156A162ASP-1-0.785-0.8928.218-2.656-2.6560.0000.0000.0000.000
157A163VAL0-0.011-0.0089.7750.1750.1750.0000.0000.0000.000
158A164LEU0-0.030-0.00111.9070.0210.0210.0000.0000.0000.000
159A165LEU00.0040.00213.8520.1080.1080.0000.0000.0000.000
160A166MET0-0.005-0.01015.8740.0290.0290.0000.0000.0000.000
161A167ASP-1-0.843-0.91720.103-0.248-0.2480.0000.0000.0000.000
162A168GLU-1-0.710-0.82723.940-0.197-0.1970.0000.0000.0000.000
163A169PRO0-0.016-0.00121.2900.0160.0160.0000.0000.0000.000
164A170LEU0-0.010-0.00822.1610.0090.0090.0000.0000.0000.000
165A171SER0-0.064-0.03425.9930.0230.0230.0000.0000.0000.000
166A172ASN0-0.034-0.02428.8930.0080.0080.0000.0000.0000.000
167A173LEU0-0.0050.01725.1650.0050.0050.0000.0000.0000.000
168A174ASP-1-0.800-0.89929.901-0.095-0.0950.0000.0000.0000.000
169A175ALA00.0570.01230.857-0.007-0.0070.0000.0000.0000.000
170A176LYS10.9640.99130.8840.0560.0560.0000.0000.0000.000
171A177LEU0-0.011-0.00926.128-0.004-0.0040.0000.0000.0000.000
172A178ARG10.8150.87026.4400.1700.1700.0000.0000.0000.000
173A179VAL00.0370.01026.004-0.015-0.0150.0000.0000.0000.000
174A180ALA0-0.020-0.01125.264-0.006-0.0060.0000.0000.0000.000
175A181MET0-0.028-0.01719.807-0.003-0.0030.0000.0000.0000.000
176A182ARG10.8260.88921.1710.1390.1390.0000.0000.0000.000
177A183ALA00.0400.02220.769-0.020-0.0200.0000.0000.0000.000
178A184GLU-1-0.873-0.92217.809-0.142-0.1420.0000.0000.0000.000
179A185ILE0-0.002-0.00916.659-0.026-0.0260.0000.0000.0000.000
180A186LYS10.7990.90015.7690.2410.2410.0000.0000.0000.000
181A187LYS10.9050.94415.4770.1010.1010.0000.0000.0000.000
182A188LEU0-0.0140.00010.894-0.001-0.0010.0000.0000.0000.000
183A189GLN0-0.016-0.02611.1220.0190.0190.0000.0000.0000.000
184A190GLN00.002-0.00611.167-0.055-0.0550.0000.0000.0000.000
185A191LYS10.7870.8849.191-0.046-0.0460.0000.0000.0000.000
186A192LEU0-0.032-0.0215.9230.0520.0520.0000.0000.0000.000
187A193LYS10.8330.9206.6360.2590.2590.0000.0000.0000.000
188A194VAL00.0510.0418.274-0.108-0.1080.0000.0000.0000.000
189A195THR00.002-0.0179.1080.2130.2130.0000.0000.0000.000
190A196THR0-0.045-0.01412.212-0.073-0.0730.0000.0000.0000.000
191A197ILE0-0.0050.00815.0420.0780.0780.0000.0000.0000.000
192A198TYR0-0.014-0.05118.610-0.013-0.0130.0000.0000.0000.000
193A199VAL0-0.001-0.00521.2150.0310.0310.0000.0000.0000.000
194A200THR0-0.018-0.04124.8600.0060.0060.0000.0000.0000.000
195A201HIS0-0.039-0.03427.6200.0020.0020.0000.0000.0000.000
196A202ASP-1-0.823-0.89129.384-0.139-0.1390.0000.0000.0000.000
197A203GLN00.0970.03529.291-0.013-0.0130.0000.0000.0000.000
198A204VAL00.0280.02030.111-0.002-0.0020.0000.0000.0000.000
199A205GLU-1-0.748-0.80025.161-0.215-0.2150.0000.0000.0000.000
200A206ALA00.002-0.01425.430-0.014-0.0140.0000.0000.0000.000
201A207MET0-0.028-0.00125.299-0.014-0.0140.0000.0000.0000.000
202A208THR0-0.080-0.04224.1810.0090.0090.0000.0000.0000.000
203A209MET0-0.047-0.00719.9260.0030.0030.0000.0000.0000.000
204A210GLY00.0190.02320.348-0.031-0.0310.0000.0000.0000.000
205A211ASP-1-0.837-0.90316.800-0.317-0.3170.0000.0000.0000.000
206A212ARG10.7140.81120.2770.3230.3230.0000.0000.0000.000
207A213ILE00.0030.01122.659-0.020-0.0200.0000.0000.0000.000
208A214ALA00.014-0.00125.3000.0100.0100.0000.0000.0000.000
209A215VAL00.0160.01526.896-0.006-0.0060.0000.0000.0000.000
210A216MET0-0.006-0.00828.807-0.001-0.0010.0000.0000.0000.000
211A217ASN00.010-0.00231.8240.0070.0070.0000.0000.0000.000
212A218ARG10.9320.95735.5160.1150.1150.0000.0000.0000.000
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