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: M3GLZ

Calculation Name: 3WRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WRV

Chain ID: A

ChEMBL ID:

UniProt ID: A7M6E7

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1974800.707515
FMO2-HF: Nuclear repulsion 1902633.053824
FMO2-HF: Total energy -72167.65369
FMO2-MP2: Total energy -72376.500353


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:ASN)


Summations of interaction energy for fragment #1(A:7:ASN)
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.
-29.214-28.95611.619-5.849-6.028-0.054
Interaction energy analysis for fragmet #1(A:7:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.045
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].
3A9PRO0-0.0120.0053.004-5.198-3.1580.162-1.068-1.135-0.002
4A10ARG10.8390.9114.4033.7523.947-0.001-0.005-0.1890.000
5A11VAL0-0.0110.0006.2710.1590.1590.0000.0000.0000.000
6A12PHE00.0280.0086.0690.1850.1850.0000.0000.0000.000
7A13CYS0-0.037-0.01411.6550.1730.1730.0000.0000.0000.000
8A14ILE00.0310.01313.5870.0520.0520.0000.0000.0000.000
9A15GLY00.026-0.00716.7020.0890.0890.0000.0000.0000.000
10A16THR0-0.034-0.00520.021-0.026-0.0260.0000.0000.0000.000
11A17ALA00.0520.02620.2890.0510.0510.0000.0000.0000.000
12A18ASP-1-0.772-0.85522.386-0.381-0.3810.0000.0000.0000.000
13A19THR0-0.072-0.05525.5230.0410.0410.0000.0000.0000.000
14A20LYS10.8350.91124.5190.4340.4340.0000.0000.0000.000
15A21PHE0-0.0040.01721.498-0.037-0.0370.0000.0000.0000.000
16A22ASP-1-0.854-0.93322.912-0.302-0.3020.0000.0000.0000.000
17A23GLU-1-0.771-0.90224.623-0.376-0.3760.0000.0000.0000.000
18A24LEU00.0150.01218.249-0.024-0.0240.0000.0000.0000.000
19A25ARG10.8970.95019.6980.1750.1750.0000.0000.0000.000
20A26PHE0-0.023-0.01820.551-0.003-0.0030.0000.0000.0000.000
21A27LEU00.0030.00419.4820.0150.0150.0000.0000.0000.000
22A28SER00.038-0.00916.189-0.078-0.0780.0000.0000.0000.000
23A29GLU-1-0.792-0.87617.103-0.293-0.2930.0000.0000.0000.000
24A30HIS00.0040.00619.4770.0480.0480.0000.0000.0000.000
25A31VAL0-0.0080.02114.5100.0140.0140.0000.0000.0000.000
26A32ARG10.7750.86314.6330.2170.2170.0000.0000.0000.000
27A33SER0-0.007-0.00515.9140.0460.0460.0000.0000.0000.000
28A34SER00.014-0.00918.5760.0590.0590.0000.0000.0000.000
29A35LEU00.0120.00011.9050.0270.0270.0000.0000.0000.000
30A36ASN0-0.113-0.06814.8420.1520.1520.0000.0000.0000.000
31A37SER0-0.049-0.01516.6960.0710.0710.0000.0000.0000.000
32A38PHE0-0.006-0.01518.3960.0340.0340.0000.0000.0000.000
33A39SER0-0.047-0.01314.8680.0260.0260.0000.0000.0000.000
34A40ASN0-0.051-0.04616.8880.1230.1230.0000.0000.0000.000
35A41LYS10.9480.96913.378-0.285-0.2850.0000.0000.0000.000
36A42SER0-0.013-0.01314.3630.0980.0980.0000.0000.0000.000
37A43SER0-0.010-0.00911.7790.0790.0790.0000.0000.0000.000
38A44PHE00.0270.0016.8900.2320.2320.0000.0000.0000.000
39A45LYS10.8180.9257.824-0.332-0.3320.0000.0000.0000.000
40A46VAL00.0760.0577.946-0.068-0.0680.0000.0000.0000.000
41A47GLY00.0140.0226.9670.5090.5090.0000.0000.0000.000
42A48VAL0-0.026-0.0318.085-0.410-0.4100.0000.0000.0000.000
43A49THR0-0.023-0.0268.347-0.043-0.0430.0000.0000.0000.000
44A50VAL0-0.046-0.01910.664-0.037-0.0370.0000.0000.0000.000
45A51VAL00.0170.00212.326-0.024-0.0240.0000.0000.0000.000
46A52ASP-1-0.784-0.85514.294-0.558-0.5580.0000.0000.0000.000
47A53VAL00.015-0.00617.195-0.063-0.0630.0000.0000.0000.000
48A54SER0-0.116-0.07719.5540.0710.0710.0000.0000.0000.000
49A55THR00.0390.01722.578-0.001-0.0010.0000.0000.0000.000
50A56SER0-0.081-0.06825.3420.0480.0480.0000.0000.0000.000
51A57TRP00.0420.00626.841-0.018-0.0180.0000.0000.0000.000
52A58LYS10.8300.94026.6620.3090.3090.0000.0000.0000.000
53A59GLU-1-0.858-0.93523.360-0.283-0.2830.0000.0000.0000.000
54A60THR0-0.038-0.03620.5470.0360.0360.0000.0000.0000.000
55A61ASN0-0.009-0.01818.781-0.074-0.0740.0000.0000.0000.000
56A62SER0-0.0090.00617.2330.0360.0360.0000.0000.0000.000
57A63CYS00.0020.00217.1740.0000.0000.0000.0000.0000.000
58A64ALA0-0.002-0.00718.348-0.006-0.0060.0000.0000.0000.000
59A65ASP-1-0.834-0.88617.808-0.077-0.0770.0000.0000.0000.000
60A66PHE0-0.047-0.02113.7090.0400.0400.0000.0000.0000.000
61A67ASP-1-0.834-0.8738.532-1.127-1.1270.0000.0000.0000.000
62A68PHE00.001-0.00911.790-0.195-0.1950.0000.0000.0000.000
63A69VAL00.0240.0209.7520.0110.0110.0000.0000.0000.000
64A70PRO00.0260.01312.7890.0040.0040.0000.0000.0000.000
65A71SER00.0550.00815.581-0.082-0.0820.0000.0000.0000.000
66A72LYS10.8140.88115.3160.5110.5110.0000.0000.0000.000
67A73ASP-1-0.800-0.88512.275-0.701-0.7010.0000.0000.0000.000
68A74VAL00.0270.02713.556-0.127-0.1270.0000.0000.0000.000
69A75LEU00.011-0.01014.658-0.012-0.0120.0000.0000.0000.000
70A76SER0-0.101-0.04913.8260.0270.0270.0000.0000.0000.000
71A77CYS0-0.069-0.01712.096-0.025-0.0250.0000.0000.0000.000
72A78HIS00.0400.02614.040-0.135-0.1350.0000.0000.0000.000
73A79THR0-0.043-0.02117.4240.0850.0850.0000.0000.0000.000
74A80LEU0-0.039-0.01720.856-0.009-0.0090.0000.0000.0000.000
75A81GLY00.022-0.00124.1380.0130.0130.0000.0000.0000.000
76A82GLU-1-0.943-0.97426.340-0.418-0.4180.0000.0000.0000.000
77A83GLU-1-0.775-0.87023.599-0.550-0.5500.0000.0000.0000.000
78A84THR0-0.025-0.04326.7980.0240.0240.0000.0000.0000.000
79A85MET0-0.071-0.03229.0810.0370.0370.0000.0000.0000.000
80A86GLY00.0090.01231.2500.0130.0130.0000.0000.0000.000
81A87THR0-0.039-0.03532.6310.0080.0080.0000.0000.0000.000
82A88PHE0-0.044-0.00329.5140.0120.0120.0000.0000.0000.000
83A89ALA00.0250.01634.6150.0130.0130.0000.0000.0000.000
84A90ASP-1-0.845-0.91633.703-0.299-0.2990.0000.0000.0000.000
85A91THR00.036-0.00431.371-0.014-0.0140.0000.0000.0000.000
86A92ARG10.8630.93628.9000.3150.3150.0000.0000.0000.000
87A93GLY00.0280.00629.007-0.033-0.0330.0000.0000.0000.000
88A94LEU00.0170.01529.077-0.028-0.0280.0000.0000.0000.000
89A95ALA0-0.004-0.00326.263-0.032-0.0320.0000.0000.0000.000
90A96ILE0-0.021-0.01824.724-0.051-0.0510.0000.0000.0000.000
91A97ALA00.0070.01124.291-0.054-0.0540.0000.0000.0000.000
92A98ILE00.0170.01222.648-0.048-0.0480.0000.0000.0000.000
93A99MET0-0.0530.00419.452-0.101-0.1010.0000.0000.0000.000
94A100SER0-0.073-0.05119.566-0.095-0.0950.0000.0000.0000.000
95A101LYS10.8640.90219.6160.6660.6660.0000.0000.0000.000
96A102ALA0-0.0010.01717.564-0.082-0.0820.0000.0000.0000.000
97A103LEU0-0.022-0.01514.516-0.165-0.1650.0000.0000.0000.000
98A104GLU-1-0.793-0.89314.704-1.047-1.0470.0000.0000.0000.000
99A105THR0-0.017-0.00914.328-0.130-0.1300.0000.0000.0000.000
100A106PHE00.002-0.0089.301-0.281-0.2810.0000.0000.0000.000
101A107LEU0-0.040-0.02910.138-0.505-0.5050.0000.0000.0000.000
102A108SER0-0.033-0.01411.066-0.218-0.2180.0000.0000.0000.000
103A109ILE00.0340.0237.645-0.187-0.1870.0000.0000.0000.000
104A110ALA00.0220.0166.260-0.616-0.6160.0000.0000.0000.000
105A111ASN0-0.053-0.0467.050-0.752-0.7520.0000.0000.0000.000
106A112ASP-1-0.874-0.9319.788-1.830-1.8300.0000.0000.0000.000
107A113GLU-1-0.995-0.9985.022-5.508-5.5080.0000.0000.0000.000
108A114GLN0-0.079-0.0425.124-1.481-1.402-0.001-0.001-0.0770.000
109A115ASN00.0060.0181.842-15.979-18.08311.460-4.772-4.583-0.052
110A116LEU0-0.0240.0034.8150.9751.023-0.001-0.003-0.0440.000
111A117ALA00.0400.0278.2740.7630.7630.0000.0000.0000.000
112A118GLY00.013-0.0039.8830.4950.4950.0000.0000.0000.000
113A119VAL0-0.034-0.01311.954-0.256-0.2560.0000.0000.0000.000
114A120ILE00.0190.00814.4600.2020.2020.0000.0000.0000.000
115A121GLY00.0850.02916.941-0.077-0.0770.0000.0000.0000.000
116A122LEU0-0.046-0.00919.6140.0800.0800.0000.0000.0000.000
117A123GLY00.005-0.00223.041-0.015-0.0150.0000.0000.0000.000
118A124GLY00.0470.03125.9240.0230.0230.0000.0000.0000.000
119A125SER00.0190.01628.332-0.041-0.0410.0000.0000.0000.000
120A126GLY00.0420.03228.851-0.022-0.0220.0000.0000.0000.000
121A127GLY00.0500.02124.857-0.027-0.0270.0000.0000.0000.000
122A128THR00.0190.01224.003-0.054-0.0540.0000.0000.0000.000
123A129SER0-0.024-0.01524.885-0.032-0.0320.0000.0000.0000.000
124A130LEU0-0.0240.00720.590-0.024-0.0240.0000.0000.0000.000
125A131LEU00.0100.01819.009-0.059-0.0590.0000.0000.0000.000
126A132SER0-0.014-0.03120.408-0.063-0.0630.0000.0000.0000.000
127A133SER0-0.069-0.03022.2760.0060.0060.0000.0000.0000.000
128A134ALA00.0650.04116.990-0.021-0.0210.0000.0000.0000.000
129A135PHE0-0.005-0.00717.211-0.101-0.1010.0000.0000.0000.000
130A136ARG10.8380.90218.5690.5960.5960.0000.0000.0000.000
131A137SER0-0.046-0.02117.5490.0140.0140.0000.0000.0000.000
132A138LEU00.0010.00613.753-0.040-0.0400.0000.0000.0000.000
133A139PRO00.0410.01515.6860.1330.1330.0000.0000.0000.000
134A140ILE0-0.008-0.00318.214-0.064-0.0640.0000.0000.0000.000
135A141GLY0-0.018-0.00619.0300.0110.0110.0000.0000.0000.000
136A142ILE0-0.0120.00213.443-0.039-0.0390.0000.0000.0000.000
137A143PRO0-0.013-0.00714.5610.0950.0950.0000.0000.0000.000
138A144LYS10.8050.89015.9990.9370.9370.0000.0000.0000.000
139A145VAL0-0.007-0.00218.5220.1250.1250.0000.0000.0000.000
140A146ILE00.0200.00720.231-0.043-0.0430.0000.0000.0000.000
141A147ILE0-0.023-0.00622.7900.0670.0670.0000.0000.0000.000
142A148SER00.039-0.01125.2510.0090.0090.0000.0000.0000.000
143A149THR0-0.012-0.02027.9370.0190.0190.0000.0000.0000.000
144A150VAL0-0.046-0.02730.5840.0280.0280.0000.0000.0000.000
145A151ALA00.0130.01929.5600.0030.0030.0000.0000.0000.000
146A152SER0-0.039-0.01131.3290.0120.0120.0000.0000.0000.000
147A153GLY00.022-0.00334.8930.0190.0190.0000.0000.0000.000
148A154GLN0-0.032-0.01635.544-0.013-0.0130.0000.0000.0000.000
149A155THR00.0140.00130.754-0.013-0.0130.0000.0000.0000.000
150A156GLU-1-0.856-0.90330.581-0.374-0.3740.0000.0000.0000.000
151A157SER0-0.015-0.01230.888-0.029-0.0290.0000.0000.0000.000
152A158TYR0-0.0010.00426.880-0.016-0.0160.0000.0000.0000.000
153A159ILE00.0430.02826.235-0.046-0.0460.0000.0000.0000.000
154A160GLY00.0000.01026.854-0.036-0.0360.0000.0000.0000.000
155A161THR0-0.036-0.02027.2620.0440.0440.0000.0000.0000.000
156A162SER0-0.041-0.01923.146-0.029-0.0290.0000.0000.0000.000
157A163ASP-1-0.754-0.87220.804-0.860-0.8600.0000.0000.0000.000
158A164LEU0-0.030-0.01021.258-0.027-0.0270.0000.0000.0000.000
159A165VAL00.0110.01222.9910.0710.0710.0000.0000.0000.000
160A166LEU00.000-0.00424.086-0.031-0.0310.0000.0000.0000.000
161A167PHE00.0410.01324.2760.0420.0420.0000.0000.0000.000
162A168PRO00.0180.01027.486-0.005-0.0050.0000.0000.0000.000
163A169SER0-0.004-0.02628.6130.0070.0070.0000.0000.0000.000
164A170VAL0-0.037-0.00630.5350.0130.0130.0000.0000.0000.000
165A171VAL0-0.045-0.02333.0630.0130.0130.0000.0000.0000.000
166A172ASP-1-0.780-0.88134.621-0.184-0.1840.0000.0000.0000.000
167A173ILE0-0.033-0.01534.8270.0140.0140.0000.0000.0000.000
168A174CYS0-0.025-0.00630.342-0.028-0.0280.0000.0000.0000.000
169A175GLY00.0130.01929.4970.0200.0200.0000.0000.0000.000
170A176ILE0-0.016-0.00726.663-0.009-0.0090.0000.0000.0000.000
171A177ASN00.009-0.01230.5410.0080.0080.0000.0000.0000.000
172A178ASN0-0.030-0.02132.860-0.007-0.0070.0000.0000.0000.000
173A179VAL00.0400.00333.672-0.008-0.0080.0000.0000.0000.000
174A180SER00.0230.01630.630-0.013-0.0130.0000.0000.0000.000
175A181LYS10.9100.96628.8790.1900.1900.0000.0000.0000.000
176A182VAL00.0310.03628.271-0.022-0.0220.0000.0000.0000.000
177A183VAL00.0080.01328.624-0.016-0.0160.0000.0000.0000.000
178A184LEU0-0.021-0.00624.607-0.039-0.0390.0000.0000.0000.000
179A185SER0-0.027-0.03623.826-0.035-0.0350.0000.0000.0000.000
180A186ASN0-0.008-0.01224.027-0.018-0.0180.0000.0000.0000.000
181A187ALA0-0.0100.00823.148-0.022-0.0220.0000.0000.0000.000
182A188GLY00.0310.00319.865-0.062-0.0620.0000.0000.0000.000
183A189ALA00.0150.00919.478-0.053-0.0530.0000.0000.0000.000
184A190ALA00.006-0.00420.996-0.018-0.0180.0000.0000.0000.000
185A191PHE0-0.038-0.01414.171-0.007-0.0070.0000.0000.0000.000
186A192ALA00.0290.01016.140-0.085-0.0850.0000.0000.0000.000
187A193GLY00.0190.00916.919-0.018-0.0180.0000.0000.0000.000
188A194MET0-0.051-0.02318.7090.0090.0090.0000.0000.0000.000
189A195VAL0-0.014-0.00212.195-0.050-0.0500.0000.0000.0000.000
190A196ILE0-0.009-0.00913.568-0.075-0.0750.0000.0000.0000.000
191A197GLY00.0070.01015.7010.0420.0420.0000.0000.0000.000
192A198ARG10.8250.91711.4961.9031.9030.0000.0000.0000.000
193A199LEU0-0.033-0.01810.353-0.087-0.0870.0000.0000.0000.000
194A200GLU-1-0.835-0.87514.074-0.212-0.2120.0000.0000.0000.000
195A201SER0-0.063-0.03216.9410.0970.0970.0000.0000.0000.000