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: ZVRLN

Calculation Name: 2CW5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CW5

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLF5

Base Structure: X-ray

Registration Date: 2023-09-20

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2636160.036292
FMO2-HF: Nuclear repulsion 2550896.618705
FMO2-HF: Total energy -85263.417587
FMO2-MP2: Total energy -85519.115928


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.
-11.554-3.6797.925-4.915-10.884-0.041
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 : 0.025 / q_NPA : 0.018
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].
3A3PRO0-0.0090.0063.8990.1051.939-0.008-0.756-1.0700.002
4A4VAL00.0270.0066.168-0.344-0.3440.0000.0000.0000.000
5A5TYR00.006-0.0079.1770.0550.0550.0000.0000.0000.000
6A6PHE00.000-0.00212.801-0.055-0.0550.0000.0000.0000.000
7A7LEU00.011-0.00515.051-0.002-0.0020.0000.0000.0000.000
8A8SER0-0.025-0.00118.848-0.010-0.0100.0000.0000.0000.000
9A9ASP-1-0.761-0.89121.9740.0390.0390.0000.0000.0000.000
10A10PHE0-0.018-0.00721.995-0.004-0.0040.0000.0000.0000.000
11A11GLY00.0790.05725.378-0.005-0.0050.0000.0000.0000.000
12A12LEU0-0.041-0.05421.1210.0040.0040.0000.0000.0000.000
13A13GLU-1-0.960-0.97123.1000.0360.0360.0000.0000.0000.000
14A14ASP-1-0.866-0.91724.2710.0010.0010.0000.0000.0000.000
15A15PRO00.0250.00122.7400.0060.0060.0000.0000.0000.000
16A16TYR0-0.009-0.02819.2250.0020.0020.0000.0000.0000.000
17A17VAL0-0.013-0.01118.6310.0050.0050.0000.0000.0000.000
18A18ALA00.0090.00317.4400.0210.0210.0000.0000.0000.000
19A19VAL00.004-0.00216.555-0.002-0.0020.0000.0000.0000.000
20A20VAL0-0.005-0.00114.035-0.020-0.0200.0000.0000.0000.000
21A21LYS10.8490.90412.637-0.171-0.1710.0000.0000.0000.000
22A22ALA0-0.0060.00311.7620.0160.0160.0000.0000.0000.000
23A23VAL00.0370.01111.818-0.042-0.0420.0000.0000.0000.000
24A24LEU0-0.033-0.0048.548-0.088-0.0880.0000.0000.0000.000
25A25ALA0-0.004-0.0077.249-0.098-0.0980.0000.0000.0000.000
26A26GLU-1-0.913-0.9238.982-0.490-0.4900.0000.0000.0000.000
27A27ARG10.7500.8424.5490.6110.693-0.001-0.003-0.0770.000
28A28ALA00.0030.0235.8690.1240.1240.0000.0000.0000.000
29A29PRO0-0.016-0.0162.510-0.3380.2580.338-0.218-0.7150.000
30A30GLY00.0380.0112.483-3.040-2.1100.770-0.612-1.088-0.005
31A31PRO0-0.0110.0063.0271.4132.6722.117-0.804-2.572-0.001
32A32ALA00.0060.0053.841-0.788-1.9240.0311.370-0.265-0.001
33A33VAL0-0.001-0.0056.820-0.090-0.0900.0000.0000.0000.000
34A34VAL0-0.017-0.0039.846-0.094-0.0940.0000.0000.0000.000
35A35ASP-1-0.771-0.86313.0480.1590.1590.0000.0000.0000.000
36A36LEU0-0.023-0.00515.903-0.002-0.0020.0000.0000.0000.000
37A37ALA00.015-0.00918.273-0.013-0.0130.0000.0000.0000.000
38A38HIS10.7920.88317.319-0.121-0.1210.0000.0000.0000.000
39A39ALA00.0170.01822.606-0.010-0.0100.0000.0000.0000.000
40A40LEU00.0100.01323.524-0.001-0.0010.0000.0000.0000.000
41A41PRO00.016-0.00227.155-0.004-0.0040.0000.0000.0000.000
42A42PRO00.0230.00929.6530.0000.0000.0000.0000.0000.000
43A43GLN0-0.066-0.05328.960-0.006-0.0060.0000.0000.0000.000
44A44ASP-1-0.829-0.89930.1990.0400.0400.0000.0000.0000.000
45A45LEU0-0.005-0.01926.1480.0060.0060.0000.0000.0000.000
46A46ARG10.7600.88127.527-0.033-0.0330.0000.0000.0000.000
47A47ARG10.7620.85826.607-0.071-0.0710.0000.0000.0000.000
48A48ALA0-0.009-0.00124.0910.0080.0080.0000.0000.0000.000
49A49ALA00.0330.02023.7760.0080.0080.0000.0000.0000.000
50A50TYR0-0.035-0.03424.5650.0080.0080.0000.0000.0000.000
51A51ALA00.0170.00823.0920.0070.0070.0000.0000.0000.000
52A52LEU0-0.058-0.02818.4700.0150.0150.0000.0000.0000.000
53A53PHE0-0.022-0.01520.5350.0120.0120.0000.0000.0000.000
54A54GLU-1-0.822-0.90422.8910.0980.0980.0000.0000.0000.000
55A55ALA0-0.0030.00117.9510.0090.0090.0000.0000.0000.000
56A56LEU0-0.0010.00215.9400.0160.0160.0000.0000.0000.000
57A57PRO0-0.024-0.01517.2500.0190.0190.0000.0000.0000.000
58A58TYR0-0.052-0.01317.4090.0070.0070.0000.0000.0000.000
59A59LEU0-0.0260.00312.8960.0240.0240.0000.0000.0000.000
60A60PRO0-0.007-0.0059.085-0.002-0.0020.0000.0000.0000.000
61A61GLU-1-0.758-0.85410.9470.2860.2860.0000.0000.0000.000
62A62GLY00.000-0.0048.0170.1220.1220.0000.0000.0000.000
63A63ALA0-0.070-0.0277.443-0.153-0.1530.0000.0000.0000.000
64A64VAL00.0130.0056.951-0.042-0.0420.0000.0000.0000.000
65A65VAL00.0100.0019.6660.0820.0820.0000.0000.0000.000
66A66LEU00.0030.01612.544-0.040-0.0400.0000.0000.0000.000
67A67ALA0-0.002-0.00814.2620.0220.0220.0000.0000.0000.000
68A68VAL0-0.026-0.02917.924-0.019-0.0190.0000.0000.0000.000
69A69VAL00.0230.02920.6120.0010.0010.0000.0000.0000.000
70A70ASP-1-0.768-0.87123.787-0.016-0.0160.0000.0000.0000.000
71A71PRO00.0520.01825.724-0.004-0.0040.0000.0000.0000.000
72A72GLY0-0.0080.01928.375-0.001-0.0010.0000.0000.0000.000
73A73VAL0-0.025-0.01629.206-0.006-0.0060.0000.0000.0000.000
74A74GLY00.0050.01029.6970.0000.0000.0000.0000.0000.000
75A75THR0-0.062-0.03630.6450.0010.0010.0000.0000.0000.000
76A76ALA00.009-0.00430.165-0.004-0.0040.0000.0000.0000.000
77A77ARG10.8110.88125.1890.0310.0310.0000.0000.0000.000
78A78ARG10.8100.86723.4330.0170.0170.0000.0000.0000.000
79A79ALA00.0210.02320.2840.0100.0100.0000.0000.0000.000
80A80VAL0-0.007-0.01618.935-0.009-0.0090.0000.0000.0000.000
81A81ALA00.0300.01613.4270.0030.0030.0000.0000.0000.000
82A82ALA0-0.008-0.00414.5440.0030.0030.0000.0000.0000.000
83A83LEU00.0120.00610.114-0.006-0.0060.0000.0000.0000.000
84A84GLY00.0430.00312.9190.0000.0000.0000.0000.0000.000
85A85ARG10.7430.85112.820-0.216-0.2160.0000.0000.0000.000
86A86TRP0-0.033-0.02311.1510.0450.0450.0000.0000.0000.000
87A87THR0-0.0050.0029.046-0.050-0.0500.0000.0000.0000.000
88A88TYR0-0.037-0.03711.1880.0310.0310.0000.0000.0000.000
89A89VAL00.0140.00311.975-0.035-0.0350.0000.0000.0000.000
90A90GLY00.0510.02014.9780.0270.0270.0000.0000.0000.000
91A91PRO0-0.035-0.00718.680-0.014-0.0140.0000.0000.0000.000
92A92ASP-1-0.780-0.85722.354-0.001-0.0010.0000.0000.0000.000
93A93ASN0-0.008-0.02323.8470.0030.0030.0000.0000.0000.000
94A94GLY00.0490.03525.0530.0030.0030.0000.0000.0000.000
95A95LEU0-0.0210.01621.2050.0070.0070.0000.0000.0000.000
96A96PHE00.0400.00817.1420.0080.0080.0000.0000.0000.000
97A97THR0-0.019-0.02321.6100.0050.0050.0000.0000.0000.000
98A98LEU00.0230.00324.4730.0020.0020.0000.0000.0000.000
99A99ALA00.0310.02019.1700.0060.0060.0000.0000.0000.000
100A100TRP0-0.014-0.02317.5140.0030.0030.0000.0000.0000.000
101A101LEU0-0.027-0.00821.467-0.003-0.0030.0000.0000.0000.000
102A102LEU0-0.050-0.01020.8770.0020.0020.0000.0000.0000.000
103A103ASP-1-0.787-0.87215.8150.1490.1490.0000.0000.0000.000
104A104PRO00.0200.01818.919-0.008-0.0080.0000.0000.0000.000
105A105PRO0-0.032-0.01017.5500.0080.0080.0000.0000.0000.000
106A106ARG10.8490.92115.985-0.149-0.1490.0000.0000.0000.000
107A107ARG10.7350.83614.3230.0460.0460.0000.0000.0000.000
108A108ALA0-0.010-0.00616.4170.0040.0040.0000.0000.0000.000
109A109PHE00.0360.02014.437-0.005-0.0050.0000.0000.0000.000
110A110LEU0-0.034-0.01217.8220.0090.0090.0000.0000.0000.000
111A111LEU0-0.026-0.01815.144-0.013-0.0130.0000.0000.0000.000
112A112GLU-1-0.880-0.95318.920-0.099-0.0990.0000.0000.0000.000
113A113PRO0-0.044-0.01720.413-0.013-0.0130.0000.0000.0000.000
114A114PRO0-0.0070.00020.2910.0010.0010.0000.0000.0000.000
115A134GLY00.0330.01724.4580.0050.0050.0000.0000.0000.000
116A135ARG10.8800.92621.3310.0040.0040.0000.0000.0000.000
117A136ASP-1-0.891-0.93819.827-0.079-0.0790.0000.0000.0000.000
118A137VAL00.0540.02818.220-0.015-0.0150.0000.0000.0000.000
119A138PHE0-0.025-0.00116.072-0.020-0.0200.0000.0000.0000.000
120A139ALA00.0230.01913.6610.0010.0010.0000.0000.0000.000
121A140PRO00.0440.01612.033-0.013-0.0130.0000.0000.0000.000
122A141ALA00.0400.02511.657-0.076-0.0760.0000.0000.0000.000
123A142ALA00.001-0.00410.178-0.063-0.0630.0000.0000.0000.000
124A143ALA00.0090.0037.7880.0370.0370.0000.0000.0000.000
125A144HIS0-0.029-0.0286.794-0.266-0.2660.0000.0000.0000.000
126A145LEU00.0180.0006.718-0.307-0.3070.0000.0000.0000.000
127A146ALA0-0.032-0.0074.684-0.756-0.572-0.001-0.054-0.1290.000
128A147LEU0-0.019-0.0242.354-3.214-0.9104.345-2.878-3.771-0.028
129A148GLY0-0.039-0.0072.944-4.504-2.7870.325-0.944-1.099-0.008
130A149LEU0-0.044-0.0123.6400.7600.8650.009-0.016-0.0980.000
131A150PRO00.0270.0047.3480.1420.1420.0000.0000.0000.000
132A151PRO00.0220.0349.870-0.027-0.0270.0000.0000.0000.000
133A152GLU-1-0.763-0.89411.779-0.131-0.1310.0000.0000.0000.000
134A153GLY0-0.071-0.02613.4650.0160.0160.0000.0000.0000.000
135A154LEU0-0.053-0.02211.601-0.008-0.0080.0000.0000.0000.000
136A155GLY00.0660.04315.4710.0220.0220.0000.0000.0000.000
137A156PRO0-0.043-0.00718.283-0.003-0.0030.0000.0000.0000.000
138A157GLU-1-0.798-0.88018.362-0.034-0.0340.0000.0000.0000.000
139A158VAL0-0.063-0.03719.8810.0060.0060.0000.0000.0000.000
140A159PRO00.0280.00921.4540.0050.0050.0000.0000.0000.000
141A160VAL00.0670.04219.671-0.002-0.0020.0000.0000.0000.000
142A161GLU-1-0.838-0.90822.4000.0320.0320.0000.0000.0000.000
143A162THR0-0.067-0.03124.645-0.003-0.0030.0000.0000.0000.000
144A163LEU0-0.058-0.00519.796-0.003-0.0030.0000.0000.0000.000
145A164ALA00.0250.01324.2690.0060.0060.0000.0000.0000.000
146A165ARG10.7880.86624.561-0.022-0.0220.0000.0000.0000.000
147A166LEU0-0.010-0.00927.828-0.003-0.0030.0000.0000.0000.000
148A167PRO0-0.033-0.01029.9670.0020.0020.0000.0000.0000.000
149A168LEU0-0.009-0.01129.6150.0010.0010.0000.0000.0000.000
150A169ALA00.0120.00331.4260.0010.0010.0000.0000.0000.000
151A170LEU0-0.0210.00328.002-0.001-0.0010.0000.0000.0000.000
152A171THR00.0040.00232.185-0.001-0.0010.0000.0000.0000.000
153A172GLU-1-0.787-0.86434.8390.0620.0620.0000.0000.0000.000
154A173GLY00.0010.02237.4090.0000.0000.0000.0000.0000.000
155A174PRO0-0.063-0.03640.448-0.001-0.0010.0000.0000.0000.000
156A175GLU-1-0.761-0.87242.0440.0310.0310.0000.0000.0000.000
157A176GLY00.0310.01138.7890.0020.0020.0000.0000.0000.000
158A177GLU-1-0.838-0.89736.1720.0340.0340.0000.0000.0000.000
159A178VAL00.0090.00137.1570.0040.0040.0000.0000.0000.000
160A179LEU00.0290.00829.748-0.003-0.0030.0000.0000.0000.000
161A180THR00.0260.00730.323-0.001-0.0010.0000.0000.0000.000
162A181PHE00.001-0.00133.2050.0000.0000.0000.0000.0000.000
163A182ASP-1-0.747-0.86831.2830.0700.0700.0000.0000.0000.000
164A183ARG10.8760.93029.840-0.081-0.0810.0000.0000.0000.000
165A184PHE0-0.039-0.01932.962-0.002-0.0020.0000.0000.0000.000
166A185GLY00.0410.02235.745-0.003-0.0030.0000.0000.0000.000
167A186ASN0-0.051-0.03234.775-0.005-0.0050.0000.0000.0000.000
168A187ALA00.0150.00935.4250.0020.0020.0000.0000.0000.000
169A188ILE0-0.0060.00731.0000.0010.0010.0000.0000.0000.000
170A189THR0-0.056-0.04634.292-0.005-0.0050.0000.0000.0000.000
171A190THR00.0480.01732.8910.0040.0040.0000.0000.0000.000
172A191LEU0-0.0020.01834.0600.0010.0010.0000.0000.0000.000
173A192LEU00.0320.01530.4920.0030.0030.0000.0000.0000.000
174A193ARG10.7720.85032.897-0.063-0.0630.0000.0000.0000.000
175A194ALA00.0770.03137.251-0.003-0.0030.0000.0000.0000.000
176A195PRO0-0.0200.00139.2120.0010.0010.0000.0000.0000.000
177A196VAL00.021-0.00140.522-0.002-0.0020.0000.0000.0000.000
178A197GLY0-0.057-0.01743.212-0.001-0.0010.0000.0000.0000.000
179A198GLY0-0.0060.00245.905-0.002-0.0020.0000.0000.0000.000
180A199PHE0-0.016-0.03446.8950.0000.0000.0000.0000.0000.000
181A200VAL00.0390.03142.1480.0010.0010.0000.0000.0000.000
182A201GLU-1-0.946-0.97445.4290.0270.0270.0000.0000.0000.000
183A202VAL00.0490.01742.9900.0010.0010.0000.0000.0000.000
184A203GLY00.0430.02145.921-0.001-0.0010.0000.0000.0000.000
185A204GLY0-0.037-0.00548.177-0.001-0.0010.0000.0000.0000.000
186A205ARG10.9270.96449.102-0.026-0.0260.0000.0000.0000.000
187A206ARG10.9140.96848.581-0.028-0.0280.0000.0000.0000.000
188A207VAL00.0120.01344.179-0.001-0.0010.0000.0000.0000.000
189A208PRO0-0.027-0.00246.5770.0010.0010.0000.0000.0000.000
190A209VAL00.0360.02441.3180.0010.0010.0000.0000.0000.000
191A210ARG10.8370.91641.927-0.042-0.0420.0000.0000.0000.000
192A211ARG10.9580.96839.237-0.054-0.0540.0000.0000.0000.000
193A212THR00.0130.00337.7030.0030.0030.0000.0000.0000.000
194A213PHE00.0370.01735.491-0.003-0.0030.0000.0000.0000.000
195A214GLY00.0340.01740.575-0.002-0.0020.0000.0000.0000.000
196A215GLU-1-0.883-0.94442.4600.0480.0480.0000.0000.0000.000
197A216VAL0-0.042-0.02144.763-0.002-0.0020.0000.0000.0000.000
198A217PRO00.0280.00846.7450.0010.0010.0000.0000.0000.000
199A218GLU-1-0.813-0.89946.8210.0350.0350.0000.0000.0000.000
200A219GLY00.0090.00746.528-0.002-0.0020.0000.0000.0000.000
201A220ALA0-0.025-0.00847.813-0.001-0.0010.0000.0000.0000.000
202A221PRO00.002-0.01345.1850.0020.0020.0000.0000.0000.000
203A222VAL0-0.043-0.01341.5250.0000.0000.0000.0000.0000.000
204A223ALA00.0270.01840.4280.0010.0010.0000.0000.0000.000
205A224TYR0-0.056-0.04934.083-0.002-0.0020.0000.0000.0000.000
206A225LEU0-0.002-0.00532.982-0.001-0.0010.0000.0000.0000.000
207A226GLY00.0360.02331.8750.0010.0010.0000.0000.0000.000
208A227SER0-0.019-0.01526.9620.0000.0000.0000.0000.0000.000
209A228ALA00.0030.00626.2090.0080.0080.0000.0000.0000.000
210A229GLY0-0.011-0.00527.2310.0000.0000.0000.0000.0000.000
211A230LEU0-0.0160.00429.549-0.003-0.0030.0000.0000.0000.000
212A231LEU0-0.040-0.01532.4700.0000.0000.0000.0000.0000.000
213A232GLU-1-0.809-0.87831.4360.0720.0720.0000.0000.0000.000
214A233VAL0-0.025-0.02636.222-0.002-0.0020.0000.0000.0000.000
215A234ALA00.0190.00638.4330.0000.0000.0000.0000.0000.000
216A235VAL00.0110.00240.321-0.002-0.0020.0000.0000.0000.000
217A236ASN0-0.053-0.01742.0820.0030.0030.0000.0000.0000.000
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