FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: KGZ53

Calculation Name: 2CVH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CVH

Chain ID: A

ChEMBL ID:

UniProt ID: P95547

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:

Apendix: None


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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2704303.781286
FMO2-HF: Nuclear repulsion 2619084.161075
FMO2-HF: Total energy -85219.62021
FMO2-MP2: Total energy -85471.453057


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.
-24.722-14.84516.095-7.949-18.024-0.071
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 : -0.093 / q_NPA : -0.042
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].
3A3SER0-0.025-0.0293.796-0.3950.867-0.013-0.443-0.8060.002
4A4THR0-0.001-0.0455.4891.0461.0460.0000.0000.0000.000
5A5GLY0-0.001-0.0028.2060.4680.4680.0000.0000.0000.000
6A6THR0-0.053-0.0199.6720.3680.3680.0000.0000.0000.000
7A7LYS10.9680.9829.7061.2331.2330.0000.0000.0000.000
8A8SER0-0.052-0.03510.711-0.276-0.2760.0000.0000.0000.000
9A9LEU00.017-0.0039.207-0.107-0.1070.0000.0000.0000.000
10A10ASP-1-0.688-0.7846.026-4.179-4.1790.0000.0000.0000.000
11A11SER0-0.036-0.0315.819-0.842-0.8420.0000.0000.0000.000
12A12LEU0-0.031-0.0137.590-0.091-0.0910.0000.0000.0000.000
13A13LEU0-0.003-0.0043.4370.2580.5740.006-0.055-0.2680.000
14A14GLY0-0.043-0.0202.605-3.594-2.6951.659-0.907-1.651-0.011
15A15GLY0-0.013-0.0122.525-5.238-2.5981.424-1.727-2.337-0.019
16A16GLY00.0260.0152.6070.1941.1562.044-0.716-2.290-0.010
17A17PHE0-0.003-0.0092.375-3.775-2.8672.467-0.784-2.591-0.024
18A18ALA00.0320.0162.311-1.0020.5036.883-3.971-4.418-0.013
19A19PRO00.0050.0122.379-3.061-3.5070.9981.138-1.6910.002
20A20GLY00.0180.0055.287-0.301-0.209-0.001-0.004-0.0870.000
21A21VAL0-0.107-0.0666.095-0.659-0.6590.0000.0000.0000.000
22A22LEU00.0040.0069.192-0.028-0.0280.0000.0000.0000.000
23A23THR00.0160.0007.0020.0530.0530.0000.0000.0000.000
24A24GLN0-0.004-0.0169.564-0.052-0.0520.0000.0000.0000.000
25A25VAL0-0.013-0.00811.146-0.127-0.1270.0000.0000.0000.000
26A26TYR00.010-0.03113.7350.0450.0450.0000.0000.0000.000
27A27GLY00.0720.02317.240-0.067-0.0670.0000.0000.0000.000
28A28PRO0-0.0160.00219.9040.0320.0320.0000.0000.0000.000
29A29TYR00.1090.06322.109-0.036-0.0360.0000.0000.0000.000
30A30ALA00.010-0.00722.926-0.011-0.0110.0000.0000.0000.000
31A31SER0-0.007-0.02019.471-0.043-0.0430.0000.0000.0000.000
32A32GLY00.0580.01118.053-0.049-0.0490.0000.0000.0000.000
33A33LYS10.8670.94615.6290.0400.0400.0000.0000.0000.000
34A34THR00.0350.02115.366-0.036-0.0360.0000.0000.0000.000
35A35THR0-0.035-0.00416.6330.0030.0030.0000.0000.0000.000
36A36LEU00.0400.0259.862-0.049-0.0490.0000.0000.0000.000
37A37ALA00.0140.01912.128-0.102-0.1020.0000.0000.0000.000
38A38LEU00.0070.00213.1250.0000.0000.0000.0000.0000.000
39A39GLN0-0.003-0.01612.2830.1640.1640.0000.0000.0000.000
40A40THR0-0.010-0.0187.473-0.177-0.1770.0000.0000.0000.000
41A41GLY00.007-0.00610.2240.0290.0290.0000.0000.0000.000
42A42LEU0-0.0110.00412.2260.0450.0450.0000.0000.0000.000
43A43LEU00.0330.02010.7010.0590.0590.0000.0000.0000.000
44A44SER0-0.047-0.0129.1520.0080.0080.0000.0000.0000.000
45A45GLY00.0070.00310.0590.1190.1190.0000.0000.0000.000
46A46LYS10.9070.9479.029-0.278-0.2780.0000.0000.0000.000
47A47LYS10.8900.96114.050-0.472-0.4720.0000.0000.0000.000
48A48VAL00.0070.01312.6680.1110.1110.0000.0000.0000.000
49A49ALA0-0.0410.00414.720-0.048-0.0480.0000.0000.0000.000
50A50TYR0-0.001-0.03615.8080.0200.0200.0000.0000.0000.000
51A51VAL0-0.039-0.02718.016-0.016-0.0160.0000.0000.0000.000
52A52ASP-1-0.786-0.90320.3210.0040.0040.0000.0000.0000.000
53A53THR0-0.117-0.07122.4340.0090.0090.0000.0000.0000.000
54A54GLU-1-0.823-0.91023.468-0.043-0.0430.0000.0000.0000.000
55A55GLY00.0240.03925.155-0.016-0.0160.0000.0000.0000.000
56A56GLY0-0.030-0.01622.887-0.019-0.0190.0000.0000.0000.000
57A57PHE0-0.067-0.04118.996-0.038-0.0380.0000.0000.0000.000
58A58SER0-0.004-0.00622.3570.0020.0020.0000.0000.0000.000
59A59PRO00.0390.00723.167-0.026-0.0260.0000.0000.0000.000
60A60GLU-1-0.793-0.89724.439-0.120-0.1200.0000.0000.0000.000
61A61ARG10.7990.91020.7670.3220.3220.0000.0000.0000.000
62A62LEU00.0140.00218.067-0.047-0.0470.0000.0000.0000.000
63A63VAL00.0400.02321.156-0.032-0.0320.0000.0000.0000.000
64A64GLN00.0540.04023.776-0.029-0.0290.0000.0000.0000.000
65A65MET0-0.098-0.03216.541-0.020-0.0200.0000.0000.0000.000
66A66ALA0-0.009-0.00919.601-0.046-0.0460.0000.0000.0000.000
67A67GLU-1-0.855-0.92520.634-0.222-0.2220.0000.0000.0000.000
68A68THR0-0.058-0.03522.227-0.011-0.0110.0000.0000.0000.000
69A69ARG10.8180.89614.1010.7690.7690.0000.0000.0000.000
70A70GLY0-0.015-0.00819.765-0.024-0.0240.0000.0000.0000.000
71A71LEU0-0.077-0.05416.4360.0000.0000.0000.0000.0000.000
72A72ASN0-0.0080.00420.8150.0200.0200.0000.0000.0000.000
73A73PRO00.020-0.01022.2220.0000.0000.0000.0000.0000.000
74A74GLU-1-0.860-0.91723.572-0.056-0.0560.0000.0000.0000.000
75A75GLU-1-0.894-0.92121.320-0.061-0.0610.0000.0000.0000.000
76A76ALA0-0.057-0.02818.8780.0230.0230.0000.0000.0000.000
77A77LEU00.016-0.00319.4540.0250.0250.0000.0000.0000.000
78A78SER00.008-0.01021.9130.0340.0340.0000.0000.0000.000
79A79ARG10.7290.87714.3730.1680.1680.0000.0000.0000.000
80A80PHE0-0.043-0.02515.2500.0590.0590.0000.0000.0000.000
81A81ILE00.0010.00618.5920.0030.0030.0000.0000.0000.000
82A82LEU00.0180.00819.9450.0330.0330.0000.0000.0000.000
83A83PHE0-0.008-0.01119.7650.0220.0220.0000.0000.0000.000
84A84THR00.0750.04123.702-0.005-0.0050.0000.0000.0000.000
85A85PRO0-0.024-0.00624.459-0.006-0.0060.0000.0000.0000.000
86A86SER00.008-0.01527.023-0.009-0.0090.0000.0000.0000.000
87A87ASP-1-0.765-0.82028.5750.0710.0710.0000.0000.0000.000
88A88PHE0-0.002-0.04528.2200.0100.0100.0000.0000.0000.000
89A89LYS10.8310.91229.266-0.081-0.0810.0000.0000.0000.000
90A90GLU-1-0.970-0.98228.2380.1720.1720.0000.0000.0000.000
91A91GLN00.1390.05622.1230.0300.0300.0000.0000.0000.000
92A92ARG10.9370.97822.739-0.329-0.3290.0000.0000.0000.000
93A93ARG10.9410.97725.433-0.138-0.1380.0000.0000.0000.000
94A94VAL00.0530.04922.3520.0230.0230.0000.0000.0000.000
95A95ILE00.0130.00919.6630.0400.0400.0000.0000.0000.000
96A96GLY0-0.085-0.05021.4060.0510.0510.0000.0000.0000.000
97A97SER0-0.032-0.03123.5050.0270.0270.0000.0000.0000.000
98A98LEU00.0220.00317.4850.0240.0240.0000.0000.0000.000
99A99LYS10.8430.93719.408-0.456-0.4560.0000.0000.0000.000
100A100LYS10.8840.93620.338-0.484-0.4840.0000.0000.0000.000
101A101THR00.0350.02420.846-0.006-0.0060.0000.0000.0000.000
102A102VAL0-0.0150.00414.692-0.007-0.0070.0000.0000.0000.000
103A103ASP-1-0.767-0.87617.3120.5470.5470.0000.0000.0000.000
104A104SER00.0490.00314.6520.0500.0500.0000.0000.0000.000
105A105ASN0-0.103-0.04614.4690.0080.0080.0000.0000.0000.000
106A106PHE0-0.023-0.01613.404-0.109-0.1090.0000.0000.0000.000
107A107ALA0-0.0040.0029.1200.2090.2090.0000.0000.0000.000
108A108LEU0-0.029-0.0268.0580.3470.3470.0000.0000.0000.000
109A109VAL0-0.0090.00910.347-0.127-0.1270.0000.0000.0000.000
110A110VAL00.0180.00712.0840.0310.0310.0000.0000.0000.000
111A111VAL0-0.029-0.00714.5280.0050.0050.0000.0000.0000.000
112A112ASP-1-0.790-0.88617.436-0.063-0.0630.0000.0000.0000.000
113A113SER00.0480.00319.9550.0000.0000.0000.0000.0000.000
114A114ILE0-0.100-0.05721.1800.0420.0420.0000.0000.0000.000
115A115THR0-0.007-0.02923.1620.0040.0040.0000.0000.0000.000
116A116ALA00.0540.04525.734-0.014-0.0140.0000.0000.0000.000
117A117HIS10.8090.92028.071-0.102-0.1020.0000.0000.0000.000
118A118TYR00.029-0.01032.308-0.008-0.0080.0000.0000.0000.000
119A119ARG10.9300.98735.916-0.078-0.0780.0000.0000.0000.000
120A120ALA00.0630.01334.5660.0030.0030.0000.0000.0000.000
121A121GLU-1-0.934-0.95533.9690.0640.0640.0000.0000.0000.000
122A122GLU-1-0.913-0.98832.5180.0970.0970.0000.0000.0000.000
123A123ASN0-0.033-0.02629.6070.0080.0080.0000.0000.0000.000
124A124ARG10.9601.01929.776-0.082-0.0820.0000.0000.0000.000
125A125SER00.019-0.01331.4180.0010.0010.0000.0000.0000.000
126A126GLY00.0680.02532.0920.0010.0010.0000.0000.0000.000
127A127LEU00.0250.01529.2400.0200.0200.0000.0000.0000.000
128A128ILE00.0850.06225.7110.0220.0220.0000.0000.0000.000
129A129ALA00.0260.00225.9120.0290.0290.0000.0000.0000.000
130A130GLU-1-0.831-0.92826.5460.2950.2950.0000.0000.0000.000
131A131LEU00.0260.03521.8640.0320.0320.0000.0000.0000.000
132A132SER00.004-0.01122.0500.0480.0480.0000.0000.0000.000
133A133ARG10.8550.92522.273-0.219-0.2190.0000.0000.0000.000
134A134GLN0-0.025-0.02421.6370.0480.0480.0000.0000.0000.000
135A135LEU00.0780.05617.2030.0660.0660.0000.0000.0000.000
136A136GLN00.0330.02417.7790.0910.0910.0000.0000.0000.000
137A137VAL0-0.067-0.03118.8270.0750.0750.0000.0000.0000.000
138A138LEU00.0550.03515.3490.0700.0700.0000.0000.0000.000
139A139LEU00.0180.01312.8360.1570.1570.0000.0000.0000.000
140A140TRP00.006-0.00614.4160.1350.1350.0000.0000.0000.000
141A141ILE00.016-0.00514.1440.0870.0870.0000.0000.0000.000
142A142ALA00.0450.02710.3960.0730.0730.0000.0000.0000.000
143A143ARG10.8770.93010.947-1.352-1.3520.0000.0000.0000.000
144A144LYS10.8200.91113.005-1.071-1.0710.0000.0000.0000.000
145A145HIS00.0310.02212.514-0.021-0.0210.0000.0000.0000.000
146A146ASN0-0.0290.0036.9080.2090.2090.0000.0000.0000.000
147A147ILE00.0300.0276.9750.6980.6980.0000.0000.0000.000
148A148PRO0-0.0100.0014.462-0.134-0.042-0.001-0.007-0.0830.000
149A149VAL0-0.012-0.0087.322-0.423-0.4230.0000.0000.0000.000
150A150ILE0-0.0100.0098.9540.0230.0230.0000.0000.0000.000
151A151VAL0-0.015-0.01411.730-0.006-0.0060.0000.0000.0000.000
152A152ILE00.0160.01515.073-0.076-0.0760.0000.0000.0000.000
153A153ASN00.0360.00917.1650.0630.0630.0000.0000.0000.000
154A154GLN00.0370.01119.670-0.059-0.0590.0000.0000.0000.000
155A155VAL0-0.051-0.02021.3350.0160.0160.0000.0000.0000.000
156A156HIS0-0.021-0.01422.2040.0230.0230.0000.0000.0000.000
157A157PHE00.0290.02024.3090.0050.0050.0000.0000.0000.000
158A158ASP-1-0.764-0.88722.6590.1010.1010.0000.0000.0000.000
159A159SER0-0.012-0.00521.6180.0060.0060.0000.0000.0000.000
160A160ARG10.9060.94824.050-0.097-0.0970.0000.0000.0000.000
161A161THR0-0.043-0.00725.1630.0090.0090.0000.0000.0000.000
162A162GLU-1-0.857-0.93327.974-0.003-0.0030.0000.0000.0000.000
163A163MET0-0.0080.01826.221-0.008-0.0080.0000.0000.0000.000
164A164THR0-0.012-0.00825.0840.0080.0080.0000.0000.0000.000
165A165LYS10.8150.91919.1530.1480.1480.0000.0000.0000.000
166A166PRO0-0.058-0.03519.0650.0070.0070.0000.0000.0000.000
167A167VAL0-0.005-0.01819.1000.0120.0120.0000.0000.0000.000
168A168ALA0-0.032-0.02417.6880.0040.0040.0000.0000.0000.000
169A169GLU-1-0.826-0.91519.1540.1900.1900.0000.0000.0000.000
170A170GLN00.0240.01321.6060.0320.0320.0000.0000.0000.000
171A171THR00.0070.00319.5810.0200.0200.0000.0000.0000.000
172A172LEU0-0.017-0.00618.7740.0740.0740.0000.0000.0000.000
173A173GLY00.0730.04317.4700.0310.0310.0000.0000.0000.000
174A174TYR0-0.027-0.02615.1100.0400.0400.0000.0000.0000.000
175A175ARG10.8460.92014.918-0.341-0.3410.0000.0000.0000.000
176A176CYS0-0.068-0.00712.1910.1580.1580.0000.0000.0000.000
177A177LYS10.8490.9028.744-0.917-0.9170.0000.0000.0000.000
178A178ASP-1-0.796-0.8825.2141.1951.1950.0000.0000.0000.000
179A179ILE0-0.037-0.0208.4500.0800.0800.0000.0000.0000.000
180A180LEU00.0060.0058.334-0.134-0.1340.0000.0000.0000.000
181A181ARG10.7940.87911.9540.4100.4100.0000.0000.0000.000
182A182LEU0-0.036-0.00713.284-0.103-0.1030.0000.0000.0000.000
183A183ASP-1-0.811-0.88516.897-0.261-0.2610.0000.0000.0000.000
184A184LYS10.8650.92020.1320.1800.1800.0000.0000.0000.000
185A185LEU00.005-0.00221.7050.0200.0200.0000.0000.0000.000
186A186PRO0-0.017-0.01024.3890.0040.0040.0000.0000.0000.000
187A187LYS10.9730.98326.5770.3280.3280.0000.0000.0000.000
188A188PRO00.0460.01526.474-0.017-0.0170.0000.0000.0000.000
189A189GLY00.0340.02923.849-0.014-0.0140.0000.0000.0000.000
190A190LEU00.0100.01521.177-0.047-0.0470.0000.0000.0000.000
191A191ARG10.8010.92418.4560.4340.4340.0000.0000.0000.000
192A192VAL00.0380.01916.934-0.050-0.0500.0000.0000.0000.000
193A193ALA0-0.0020.00912.5060.0650.0650.0000.0000.0000.000
194A194VAL0-0.005-0.01014.098-0.057-0.0570.0000.0000.0000.000
195A195LEU00.0000.0077.2320.0500.0500.0000.0000.0000.000
196A196GLU-1-0.779-0.86711.298-0.144-0.1440.0000.0000.0000.000
197A197ARG10.8930.96911.168-0.144-0.1440.0000.0000.0000.000
198A198HIS00.0310.0233.0740.0940.4990.034-0.090-0.3480.000
199A199ARG10.8700.9323.278-4.171-3.6520.015-0.161-0.3730.001
200A200PHE0-0.019-0.0162.384-0.726-0.0030.580-0.222-1.0810.001
201A201ARG10.8230.9304.8511.9101.9100.0000.0000.0000.000
202A202PRO00.009-0.0087.6110.1590.1590.0000.0000.0000.000
203A203GLU-1-0.779-0.89410.864-0.193-0.1930.0000.0000.0000.000
204A204GLY0-0.039-0.02312.4800.0230.0230.0000.0000.0000.000
205A205LEU0-0.020-0.00711.414-0.018-0.0180.0000.0000.0000.000
206A206MET0-0.005-0.02513.4270.0120.0120.0000.0000.0000.000
207A207ALA0-0.0120.01211.740-0.088-0.0880.0000.0000.0000.000
208A208TYR00.0140.00313.8050.0880.0880.0000.0000.0000.000
209A209PHE0-0.006-0.00715.113-0.086-0.0860.0000.0000.0000.000
210A210ARG10.8120.87017.2490.6710.6710.0000.0000.0000.000
211A211ILE0-0.038-0.01618.926-0.041-0.0410.0000.0000.0000.000
212A212THR0-0.007-0.02420.4370.0330.0330.0000.0000.0000.000
213A213GLU-1-0.807-0.91121.959-0.333-0.3330.0000.0000.0000.000
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