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: MN16Z

Calculation Name: 1V8E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V8E

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W25

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2514977.270082
FMO2-HF: Nuclear repulsion 2434322.529742
FMO2-HF: Total energy -80654.74034
FMO2-MP2: Total energy -80896.46563


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:8:PRO)


Summations of interaction energy for fragment #1(A:8:PRO)
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.
-7.306-1.9489.108-4.594-9.871-0.036
Interaction energy analysis for fragmet #1(A:8:PRO)
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 : -0.019
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].
3A10ARG10.7750.8623.8821.4082.813-0.005-0.544-0.8560.002
4A11LEU0-0.040-0.0225.8240.6840.6840.0000.0000.0000.000
5A12GLY00.0790.0248.6460.0610.0610.0000.0000.0000.000
6A13HIS0-0.064-0.06212.1310.0860.0860.0000.0000.0000.000
7A14ARG10.8490.92813.9390.3140.3140.0000.0000.0000.000
8A15GLY00.0040.01915.7490.0510.0510.0000.0000.0000.000
9A16ALA00.006-0.01215.042-0.082-0.0820.0000.0000.0000.000
10A17PRO00.0380.02516.6090.0400.0400.0000.0000.0000.000
11A18LEU0-0.046-0.01318.1950.0300.0300.0000.0000.0000.000
12A19LYS10.8430.92318.2830.3140.3140.0000.0000.0000.000
13A20ALA00.0430.03221.8570.0200.0200.0000.0000.0000.000
14A21LYS10.8750.93422.7230.1310.1310.0000.0000.0000.000
15A22GLU-1-0.766-0.87721.045-0.236-0.2360.0000.0000.0000.000
16A23ASN0-0.050-0.05620.2690.0100.0100.0000.0000.0000.000
17A24THR00.0240.01521.7600.0190.0190.0000.0000.0000.000
18A25LEU00.024-0.00622.160-0.021-0.0210.0000.0000.0000.000
19A26GLU-1-0.944-0.96122.672-0.175-0.1750.0000.0000.0000.000
20A27SER00.020-0.00219.531-0.026-0.0260.0000.0000.0000.000
21A28PHE0-0.007-0.01917.413-0.037-0.0370.0000.0000.0000.000
22A29ARG10.8350.90517.7730.1260.1260.0000.0000.0000.000
23A30LEU00.0070.00318.452-0.020-0.0200.0000.0000.0000.000
24A31ALA0-0.0220.00014.177-0.028-0.0280.0000.0000.0000.000
25A32LEU0-0.0020.00513.299-0.060-0.0600.0000.0000.0000.000
26A33GLU-1-0.830-0.90914.771-0.179-0.1790.0000.0000.0000.000
27A34ALA0-0.065-0.02114.8480.0260.0260.0000.0000.0000.000
28A35GLY0-0.0050.00012.442-0.017-0.0170.0000.0000.0000.000
29A36LEU0-0.065-0.0299.239-0.109-0.1090.0000.0000.0000.000
30A37ASP-1-0.772-0.8495.438-2.110-2.1100.0000.0000.0000.000
31A38GLY00.033-0.0068.7480.2560.2560.0000.0000.0000.000
32A39VAL0-0.053-0.01111.137-0.111-0.1110.0000.0000.0000.000
33A40GLH0-0.051-0.04012.5900.0240.0240.0000.0000.0000.000
34A41LEU0-0.010-0.01314.1130.0130.0130.0000.0000.0000.000
35A42ASP-1-0.732-0.82817.949-0.259-0.2590.0000.0000.0000.000
36A43VAL0-0.029-0.03220.5670.0160.0160.0000.0000.0000.000
37A44TRP00.0100.00723.6810.0080.0080.0000.0000.0000.000
38A45PRO0-0.072-0.02827.1320.0030.0030.0000.0000.0000.000
39A46THR0-0.006-0.04530.083-0.001-0.0010.0000.0000.0000.000
40A47ARG10.7430.85733.1350.0560.0560.0000.0000.0000.000
41A48ASP-1-0.833-0.87935.593-0.057-0.0570.0000.0000.0000.000
42A49GLY0-0.081-0.04433.1430.0040.0040.0000.0000.0000.000
43A50VAL0-0.050-0.01630.0910.0010.0010.0000.0000.0000.000
44A51PHE00.0240.00125.529-0.001-0.0010.0000.0000.0000.000
45A52ALA00.0220.01426.717-0.005-0.0050.0000.0000.0000.000
46A53VAL0-0.053-0.02621.952-0.005-0.0050.0000.0000.0000.000
47A54ARG10.7900.83624.1920.1210.1210.0000.0000.0000.000
48A55HIS00.0400.01621.970-0.007-0.0070.0000.0000.0000.000
49A56ASP-1-0.878-0.93523.498-0.125-0.1250.0000.0000.0000.000
50A57PRO00.0080.02327.0700.0030.0030.0000.0000.0000.000
51A58ASP-1-0.881-0.95029.549-0.083-0.0830.0000.0000.0000.000
52A59THR0-0.019-0.02532.091-0.006-0.0060.0000.0000.0000.000
53A60PRO0-0.029-0.02634.5430.0040.0040.0000.0000.0000.000
54A61LEU0-0.026-0.00337.4820.0050.0050.0000.0000.0000.000
55A62GLY00.0020.01637.7180.0050.0050.0000.0000.0000.000
56A63PRO00.0400.03534.113-0.005-0.0050.0000.0000.0000.000
57A64VAL00.012-0.01229.9800.0050.0050.0000.0000.0000.000
58A65PHE0-0.027-0.01033.0140.0050.0050.0000.0000.0000.000
59A66GLN0-0.046-0.02334.4190.0050.0050.0000.0000.0000.000
60A67VAL00.0010.00836.3430.0040.0040.0000.0000.0000.000
61A68ASP-1-0.794-0.86836.116-0.052-0.0520.0000.0000.0000.000
62A69TYR00.017-0.03430.2210.0000.0000.0000.0000.0000.000
63A70ALA0-0.031-0.01434.773-0.003-0.0030.0000.0000.0000.000
64A71ASP-1-0.822-0.91237.807-0.056-0.0560.0000.0000.0000.000
65A72LEU00.009-0.01132.615-0.003-0.0030.0000.0000.0000.000
66A73LYS10.8010.90730.5330.0950.0950.0000.0000.0000.000
67A74ALA0-0.017-0.01334.885-0.001-0.0010.0000.0000.0000.000
68A75GLN0-0.059-0.02436.3050.0030.0030.0000.0000.0000.000
69A76GLU-1-0.830-0.88329.974-0.125-0.1250.0000.0000.0000.000
70A77PRO00.0290.01132.371-0.005-0.0050.0000.0000.0000.000
71A78ASP-1-0.848-0.91628.781-0.132-0.1320.0000.0000.0000.000
72A79LEU00.0030.01927.511-0.011-0.0110.0000.0000.0000.000
73A80PRO00.0060.01824.3360.0120.0120.0000.0000.0000.000
74A81ARG10.8160.88827.2480.0690.0690.0000.0000.0000.000
75A82LEU00.020-0.00120.947-0.004-0.0040.0000.0000.0000.000
76A83GLU-1-0.831-0.90123.294-0.077-0.0770.0000.0000.0000.000
77A84GLU-1-0.852-0.92124.993-0.098-0.0980.0000.0000.0000.000
78A85VAL0-0.001-0.00719.564-0.005-0.0050.0000.0000.0000.000
79A86LEU0-0.032-0.02118.860-0.008-0.0080.0000.0000.0000.000
80A87ALA00.0330.02621.0330.0090.0090.0000.0000.0000.000
81A88LEU0-0.012-0.00119.8720.0050.0050.0000.0000.0000.000
82A89LYS10.8020.89515.1470.0030.0030.0000.0000.0000.000
83A90GLU-1-0.967-0.98519.381-0.019-0.0190.0000.0000.0000.000
84A91ALA0-0.057-0.01921.2340.0130.0130.0000.0000.0000.000
85A92PHE0-0.038-0.01915.932-0.009-0.0090.0000.0000.0000.000
86A93PRO00.0540.03016.447-0.009-0.0090.0000.0000.0000.000
87A94GLN0-0.023-0.02112.280-0.013-0.0130.0000.0000.0000.000
88A95ALA00.0020.03312.1360.0130.0130.0000.0000.0000.000
89A96VAL0-0.038-0.0208.9320.0850.0850.0000.0000.0000.000
90A97PHE00.002-0.00312.254-0.111-0.1110.0000.0000.0000.000
91A98ASN00.0310.02912.1270.1140.1140.0000.0000.0000.000
92A99VAL00.004-0.01314.120-0.022-0.0220.0000.0000.0000.000
93A100GLU-1-0.760-0.88717.516-0.216-0.2160.0000.0000.0000.000
94A101LEU0-0.014-0.01318.8430.0130.0130.0000.0000.0000.000
95A102LYS10.7810.91819.8370.2230.2230.0000.0000.0000.000
96A103SER0-0.057-0.05924.1390.0100.0100.0000.0000.0000.000
97A104PHE00.0470.03527.117-0.004-0.0040.0000.0000.0000.000
98A105PRO00.015-0.01728.9860.0070.0070.0000.0000.0000.000
99A106GLY00.0140.02131.0260.0030.0030.0000.0000.0000.000
100A107LEU0-0.015-0.00532.5020.0050.0050.0000.0000.0000.000
101A108GLY00.0310.02328.7540.0000.0000.0000.0000.0000.000
102A109GLU-1-0.851-0.94328.366-0.048-0.0480.0000.0000.0000.000
103A110GLU-1-0.925-0.95630.252-0.033-0.0330.0000.0000.0000.000
104A111ALA00.0220.01128.1900.0020.0020.0000.0000.0000.000
105A112ALA00.0360.02025.927-0.001-0.0010.0000.0000.0000.000
106A113ARG10.9080.95926.8760.0340.0340.0000.0000.0000.000
107A114ARG10.8430.91029.4030.0490.0490.0000.0000.0000.000
108A115LEU00.0390.03021.8950.0030.0030.0000.0000.0000.000
109A116ALA00.014-0.00324.5980.0030.0030.0000.0000.0000.000
110A117ALA0-0.055-0.02725.6450.0080.0080.0000.0000.0000.000
111A118LEU0-0.0130.00326.0480.0060.0060.0000.0000.0000.000
112A119LEU00.0420.01320.3170.0000.0000.0000.0000.0000.000
113A120ARG10.9170.97023.018-0.003-0.0030.0000.0000.0000.000
114A121GLY0-0.010-0.00823.2880.0000.0000.0000.0000.0000.000
115A122ARG10.8480.93520.8900.0450.0450.0000.0000.0000.000
116A123GLU-1-0.890-0.94417.4810.1370.1370.0000.0000.0000.000
117A124GLY0-0.032-0.02313.904-0.021-0.0210.0000.0000.0000.000
118A125VAL0-0.012-0.00414.347-0.061-0.0610.0000.0000.0000.000
119A126TRP0-0.036-0.0189.2280.0540.0540.0000.0000.0000.000
120A127VAL0-0.0070.00415.403-0.035-0.0350.0000.0000.0000.000
121A128SER00.021-0.00315.3880.0010.0010.0000.0000.0000.000
122A129SER0-0.006-0.02817.4400.0020.0020.0000.0000.0000.000
123A130PHE00.0390.03018.1400.0040.0040.0000.0000.0000.000
124A131ASP-1-0.768-0.86821.426-0.063-0.0630.0000.0000.0000.000
125A132PRO00.019-0.01023.9090.0060.0060.0000.0000.0000.000
126A133LEU0-0.0080.00424.8820.0110.0110.0000.0000.0000.000
127A134ALA00.0210.01324.8960.0090.0090.0000.0000.0000.000
128A135LEU00.0050.00919.5320.0070.0070.0000.0000.0000.000
129A136LEU0-0.017-0.00423.1000.0140.0140.0000.0000.0000.000
130A137ALA0-0.053-0.02625.8210.0100.0100.0000.0000.0000.000
131A138LEU00.0070.00121.3050.0070.0070.0000.0000.0000.000
132A139ARG10.7760.87418.086-0.038-0.0380.0000.0000.0000.000
133A140LYS10.9070.94924.0320.0040.0040.0000.0000.0000.000
134A141ALA0-0.049-0.02327.2910.0040.0040.0000.0000.0000.000
135A142ALA0-0.007-0.01123.9660.0030.0030.0000.0000.0000.000
136A143PRO0-0.025-0.01723.3210.0030.0030.0000.0000.0000.000
137A144GLY00.0120.00921.2980.0090.0090.0000.0000.0000.000
138A145LEU0-0.0150.01319.0230.0120.0120.0000.0000.0000.000
139A146PRO00.0360.01614.642-0.006-0.0060.0000.0000.0000.000
140A147LEU0-0.031-0.02216.133-0.035-0.0350.0000.0000.0000.000
141A148GLY00.0150.00514.3200.0220.0220.0000.0000.0000.000
142A149PHE0-0.026-0.02115.274-0.009-0.0090.0000.0000.0000.000
143A150LEU0-0.0140.00814.556-0.021-0.0210.0000.0000.0000.000
144A151MET0-0.052-0.01415.8410.0380.0380.0000.0000.0000.000
145A152ALA00.0450.00917.033-0.031-0.0310.0000.0000.0000.000
146A153GLU-1-0.890-0.92419.562-0.115-0.1150.0000.0000.0000.000
147A154ASP-1-0.789-0.87218.826-0.116-0.1160.0000.0000.0000.000
148A155HIS0-0.057-0.03220.3640.0260.0260.0000.0000.0000.000
149A156SER00.035-0.04218.1960.0120.0120.0000.0000.0000.000
150A157ALA0-0.058-0.02920.1080.0160.0160.0000.0000.0000.000
151A158LEU00.0070.00222.4630.0110.0110.0000.0000.0000.000
152A159LEU00.0320.02616.6600.0100.0100.0000.0000.0000.000
153A160PRO0-0.098-0.06420.5040.0170.0170.0000.0000.0000.000
154A161CYS0-0.058-0.01823.1820.0100.0100.0000.0000.0000.000
155A162LEU00.0150.02220.821-0.003-0.0030.0000.0000.0000.000
156A163GLY0-0.029-0.00821.1310.0110.0110.0000.0000.0000.000
157A164VAL0-0.024-0.02116.653-0.007-0.0070.0000.0000.0000.000
158A165GLU-1-0.760-0.84313.4180.0800.0800.0000.0000.0000.000
159A166ALA00.0050.00311.1880.0370.0370.0000.0000.0000.000
160A167VAL0-0.008-0.00511.789-0.001-0.0010.0000.0000.0000.000
161A168HIS0-0.009-0.00911.031-0.058-0.0580.0000.0000.0000.000
162A169PRO00.0150.01910.8610.0250.0250.0000.0000.0000.000
163A170HIS00.0840.04312.337-0.071-0.0710.0000.0000.0000.000
164A171HIS0-0.035-0.04911.9960.0330.0330.0000.0000.0000.000
165A172ALA0-0.007-0.00412.9890.0120.0120.0000.0000.0000.000
166A173LEU0-0.048-0.01715.5400.0310.0310.0000.0000.0000.000
167A174VAL0-0.042-0.0079.9610.0250.0250.0000.0000.0000.000
168A175THR0-0.019-0.03313.353-0.019-0.0190.0000.0000.0000.000
169A176GLU-1-0.906-0.95714.134-0.052-0.0520.0000.0000.0000.000
170A177GLU-1-0.864-0.91815.190-0.064-0.0640.0000.0000.0000.000
171A178ALA0-0.0010.01515.1860.0200.0200.0000.0000.0000.000
172A179VAL00.0320.01410.0540.0190.0190.0000.0000.0000.000
173A180ALA0-0.0050.00512.8090.0490.0490.0000.0000.0000.000
174A181GLY0-0.027-0.01415.3260.0320.0320.0000.0000.0000.000
175A182TRP00.000-0.03011.4550.0100.0100.0000.0000.0000.000
176A183ARG10.7800.8496.250-0.222-0.2220.0000.0000.0000.000
177A184LYS10.9170.96813.450-0.018-0.0180.0000.0000.0000.000
178A185ARG10.8540.93016.390-0.035-0.0350.0000.0000.0000.000
179A186GLY0-0.016-0.00214.2550.0010.0010.0000.0000.0000.000
180A187LEU0-0.059-0.00912.8790.0420.0420.0000.0000.0000.000
181A188PHE00.0320.0115.274-0.004-0.0040.0000.0000.0000.000
182A189VAL0-0.024-0.0227.447-0.076-0.0760.0000.0000.0000.000
183A190VAL0-0.025-0.0096.212-0.172-0.1720.0000.0000.0000.000
184A191ALA00.0340.0247.0910.1300.1300.0000.0000.0000.000
185A192TRP0-0.037-0.0158.821-0.130-0.1300.0000.0000.0000.000
186A193THR0-0.011-0.00311.5560.0620.0620.0000.0000.0000.000
187A194VAL0-0.018-0.0198.5470.0620.0620.0000.0000.0000.000
188A195ASN00.002-0.02010.966-0.127-0.1270.0000.0000.0000.000
189A196GLU-1-0.915-0.96212.703-0.290-0.2900.0000.0000.0000.000
190A197GLU-1-0.858-0.91711.091-0.452-0.4520.0000.0000.0000.000
191A198GLY00.0220.00710.955-0.036-0.0360.0000.0000.0000.000
192A199GLU-1-0.716-0.81111.639-0.400-0.4000.0000.0000.0000.000
193A200ALA00.005-0.0067.673-0.038-0.0380.0000.0000.0000.000
194A201ARG10.8720.9096.9910.3260.3260.0000.0000.0000.000
195A202ARG10.7690.8558.2900.3850.3850.0000.0000.0000.000
196A203LEU0-0.011-0.0127.5190.0360.0360.0000.0000.0000.000
197A204LEU00.010-0.0042.275-0.685-0.5332.668-0.567-2.253-0.001
198A205ALA0-0.044-0.0084.9500.0810.137-0.001-0.001-0.0540.000
199A206LEU0-0.044-0.0167.9860.1090.1090.0000.0000.0000.000
200A207GLY0-0.0090.0055.6170.0800.0800.0000.0000.0000.000
201A208LEU0-0.024-0.0164.8720.1110.256-0.001-0.035-0.1090.000
202A209ASP-1-0.749-0.8332.569-3.254-0.9511.129-1.403-2.029-0.018
203A210GLY0-0.003-0.0042.478-2.585-0.9963.512-2.407-2.694-0.021
204A211LEU0-0.051-0.0213.3860.7860.7670.0020.358-0.3410.000
205A212ILE00.0310.0245.719-0.119-0.1190.0000.0000.0000.000
206A213GLY00.0450.0129.2200.1010.1010.0000.0000.0000.000
207A214ASP-1-0.810-0.88211.476-0.433-0.4330.0000.0000.0000.000
208A215ARG10.8520.92513.1830.4330.4330.0000.0000.0000.000
209A216PRO00.0600.01811.903-0.092-0.0920.0000.0000.0000.000
210A217GLU-1-0.835-0.91511.417-0.572-0.5720.0000.0000.0000.000
211A218VAL0-0.045-0.01810.2880.0170.0170.0000.0000.0000.000
212A219LEU0-0.0040.0016.913-0.096-0.0960.0000.0000.0000.000
213A220LEU0-0.014-0.0036.636-0.391-0.3910.0000.0000.0000.000
214A221PRO0-0.040-0.0137.941-0.074-0.0740.0000.0000.0000.000
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