FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 4JKZN

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:


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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2700532.566552
FMO2-HF: Nuclear repulsion 2615311.840403
FMO2-HF: Total energy -85220.726148
FMO2-MP2: Total energy -85472.317274


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.
-28.172-16.5815.012-8.553-18.055-0.056
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 : -0.069 / q_NPA : -0.034
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].
3A3SER0-0.025-0.0263.882-0.3500.848-0.012-0.467-0.7180.002
4A4THR0-0.022-0.0575.6781.0411.0410.0000.0000.0000.000
5A5GLY00.0160.0108.5470.4090.4090.0000.0000.0000.000
6A6THR0-0.038-0.0199.8300.3650.3650.0000.0000.0000.000
7A7LYS10.9540.98310.0331.3481.3480.0000.0000.0000.000
8A8SER0-0.053-0.03710.277-0.301-0.3010.0000.0000.0000.000
9A9LEU00.0320.0049.272-0.119-0.1190.0000.0000.0000.000
10A10ASP-1-0.691-0.7905.754-3.788-3.7880.0000.0000.0000.000
11A11SER0-0.050-0.0405.636-0.906-0.9060.0000.0000.0000.000
12A12LEU0-0.0410.0007.9030.0290.0290.0000.0000.0000.000
13A13LEU00.0160.0043.4940.0200.3620.013-0.056-0.2990.000
14A14GLY0-0.019-0.0092.842-2.656-1.3701.266-0.955-1.598-0.011
15A15GLY0-0.011-0.0182.594-6.465-4.1382.071-1.646-2.753-0.021
16A16GLY00.0350.0112.518-0.5480.7871.314-0.799-1.850-0.008
17A17PHE00.001-0.0082.430-2.972-1.9722.266-1.039-2.228-0.018
18A18ALA00.0360.0172.430-0.6031.3605.479-3.662-3.781-0.008
19A19PRO00.0120.0092.365-3.889-4.2402.0490.854-2.5530.004
20A20GLY00.0170.0155.322-0.610-0.500-0.001-0.005-0.1040.000
21A21VAL0-0.097-0.0616.705-0.896-0.8960.0000.0000.0000.000
22A22LEU00.0010.0099.3300.0420.0420.0000.0000.0000.000
23A23THR0-0.007-0.0106.7950.1660.1660.0000.0000.0000.000
24A24GLN0-0.007-0.0169.220-0.084-0.0840.0000.0000.0000.000
25A25VAL0-0.005-0.00310.726-0.141-0.1410.0000.0000.0000.000
26A26TYR0-0.005-0.02913.1690.0440.0440.0000.0000.0000.000
27A27GLY00.0980.03916.705-0.067-0.0670.0000.0000.0000.000
28A28PRO0-0.0260.00219.5420.0350.0350.0000.0000.0000.000
29A29TYR00.1110.05822.154-0.029-0.0290.0000.0000.0000.000
30A30ALA00.004-0.00723.122-0.015-0.0150.0000.0000.0000.000
31A31SER0-0.003-0.01319.239-0.035-0.0350.0000.0000.0000.000
32A32GLY00.0710.01917.796-0.053-0.0530.0000.0000.0000.000
33A33LYS10.7740.88915.766-0.054-0.0540.0000.0000.0000.000
34A34THR00.0360.00615.768-0.022-0.0220.0000.0000.0000.000
35A35THR0-0.021-0.00417.0620.0100.0100.0000.0000.0000.000
36A36LEU00.0260.01510.527-0.036-0.0360.0000.0000.0000.000
37A37ALA00.0230.02012.242-0.076-0.0760.0000.0000.0000.000
38A38LEU00.0110.01113.1260.0390.0390.0000.0000.0000.000
39A39GLN00.004-0.01012.6500.1470.1470.0000.0000.0000.000
40A40THR0-0.014-0.0277.755-0.133-0.1330.0000.0000.0000.000
41A41GLY00.013-0.00710.2790.0720.0720.0000.0000.0000.000
42A42LEU0-0.0030.02012.3540.0470.0470.0000.0000.0000.000
43A43LEU00.0470.01811.0310.0350.0350.0000.0000.0000.000
44A44SER0-0.070-0.0299.6050.0060.0060.0000.0000.0000.000
45A45GLY00.0140.01310.5530.1440.1440.0000.0000.0000.000
46A46LYS10.8800.9439.213-0.521-0.5210.0000.0000.0000.000
47A47LYS10.8930.94714.194-0.551-0.5510.0000.0000.0000.000
48A48VAL0-0.0120.00312.9050.1510.1510.0000.0000.0000.000
49A49ALA0-0.0270.00314.769-0.066-0.0660.0000.0000.0000.000
50A50TYR0-0.016-0.04115.7400.0440.0440.0000.0000.0000.000
51A51VAL0-0.017-0.01318.108-0.038-0.0380.0000.0000.0000.000
52A52ASP-1-0.762-0.86920.4210.1150.1150.0000.0000.0000.000
53A53THR0-0.100-0.07822.4910.0110.0110.0000.0000.0000.000
54A54GLU-1-0.840-0.88523.3910.0610.0610.0000.0000.0000.000
55A55GLY00.0070.01625.344-0.019-0.0190.0000.0000.0000.000
56A56GLY0-0.032-0.01322.657-0.022-0.0220.0000.0000.0000.000
57A57PHE0-0.050-0.04219.302-0.028-0.0280.0000.0000.0000.000
58A58SER0-0.006-0.01422.682-0.003-0.0030.0000.0000.0000.000
59A59PRO00.033-0.00323.499-0.017-0.0170.0000.0000.0000.000
60A60GLU-1-0.805-0.87724.717-0.047-0.0470.0000.0000.0000.000
61A61ARG10.7680.88320.8680.2330.2330.0000.0000.0000.000
62A62LEU00.0100.00018.270-0.039-0.0390.0000.0000.0000.000
63A63VAL00.0360.01821.504-0.029-0.0290.0000.0000.0000.000
64A64GLN00.0560.04524.058-0.027-0.0270.0000.0000.0000.000
65A65MET0-0.077-0.01717.068-0.023-0.0230.0000.0000.0000.000
66A66ALA00.0020.00719.996-0.051-0.0510.0000.0000.0000.000
67A67GLU-1-0.874-0.93620.985-0.170-0.1700.0000.0000.0000.000
68A68THR0-0.060-0.04122.949-0.014-0.0140.0000.0000.0000.000
69A69ARG10.8020.88514.5790.6460.6460.0000.0000.0000.000
70A70GLY00.0030.02120.222-0.034-0.0340.0000.0000.0000.000
71A71LEU0-0.091-0.05416.7070.0030.0030.0000.0000.0000.000
72A72ASN00.001-0.02620.7230.0250.0250.0000.0000.0000.000
73A73PRO00.0450.02722.7050.0130.0130.0000.0000.0000.000
74A74GLU-1-0.864-0.92323.8150.0020.0020.0000.0000.0000.000
75A75GLU-1-0.884-0.91821.175-0.014-0.0140.0000.0000.0000.000
76A76ALA0-0.059-0.02519.1100.0250.0250.0000.0000.0000.000
77A77LEU00.014-0.00219.5530.0360.0360.0000.0000.0000.000
78A78SER0-0.012-0.02721.7610.0390.0390.0000.0000.0000.000
79A79ARG10.7610.88514.6950.0110.0110.0000.0000.0000.000
80A80PHE0-0.031-0.02315.3100.0890.0890.0000.0000.0000.000
81A81ILE00.0040.00518.770-0.014-0.0140.0000.0000.0000.000
82A82LEU00.0150.00720.0110.0480.0480.0000.0000.0000.000
83A83PHE0-0.018-0.02019.6830.0180.0180.0000.0000.0000.000
84A84THR00.0590.03123.4420.0040.0040.0000.0000.0000.000
85A85PRO0-0.021-0.00524.389-0.015-0.0150.0000.0000.0000.000
86A86SER0-0.013-0.02027.095-0.011-0.0110.0000.0000.0000.000
87A87ASP-1-0.730-0.81428.6710.1270.1270.0000.0000.0000.000
88A88PHE00.0480.01328.1150.0060.0060.0000.0000.0000.000
89A89LYS10.7690.86628.959-0.118-0.1180.0000.0000.0000.000
90A90GLU-1-0.914-0.96628.2910.2240.2240.0000.0000.0000.000
91A91GLN00.0960.04621.5880.0420.0420.0000.0000.0000.000
92A92ARG10.8980.95422.912-0.406-0.4060.0000.0000.0000.000
93A93ARG10.8990.96025.780-0.192-0.1920.0000.0000.0000.000
94A94VAL00.0630.04422.1570.0260.0260.0000.0000.0000.000
95A95ILE00.0280.01319.6880.0440.0440.0000.0000.0000.000
96A96GLY0-0.077-0.04421.4760.0570.0570.0000.0000.0000.000
97A97SER0-0.025-0.02223.6380.0260.0260.0000.0000.0000.000
98A98LEU00.0380.02917.5490.0220.0220.0000.0000.0000.000
99A99LYS10.8570.94819.540-0.542-0.5420.0000.0000.0000.000
100A100LYS10.8050.89320.578-0.596-0.5960.0000.0000.0000.000
101A101THR00.0600.02521.342-0.010-0.0100.0000.0000.0000.000
102A102VAL0-0.0170.01215.069-0.006-0.0060.0000.0000.0000.000
103A103ASP-1-0.784-0.88417.2560.5750.5750.0000.0000.0000.000
104A104SER00.0580.01414.2980.0730.0730.0000.0000.0000.000
105A105ASN0-0.062-0.02814.383-0.015-0.0150.0000.0000.0000.000
106A106PHE0-0.020-0.01213.359-0.104-0.1040.0000.0000.0000.000
107A107ALA00.0030.0028.9330.1590.1590.0000.0000.0000.000
108A108LEU0-0.024-0.0157.9460.4840.4840.0000.0000.0000.000
109A109VAL0-0.0140.00110.378-0.202-0.2020.0000.0000.0000.000
110A110VAL00.0100.01012.0260.0790.0790.0000.0000.0000.000
111A111VAL0-0.029-0.00814.545-0.015-0.0150.0000.0000.0000.000
112A112ASP-1-0.729-0.83117.5890.0760.0760.0000.0000.0000.000
113A113SER00.031-0.00719.842-0.015-0.0150.0000.0000.0000.000
114A114ILE0-0.038-0.03321.3920.0460.0460.0000.0000.0000.000
115A115THR0-0.027-0.01122.539-0.005-0.0050.0000.0000.0000.000
116A116ALA00.0470.03125.021-0.020-0.0200.0000.0000.0000.000
117A117HIS10.7910.90927.705-0.167-0.1670.0000.0000.0000.000
118A118TYR00.017-0.01431.733-0.011-0.0110.0000.0000.0000.000
119A119ARG10.8170.92035.046-0.114-0.1140.0000.0000.0000.000
120A120ALA00.0790.02233.8460.0050.0050.0000.0000.0000.000
121A121GLU-1-0.807-0.88133.7950.1010.1010.0000.0000.0000.000
122A122GLU-1-0.884-0.97431.9130.1500.1500.0000.0000.0000.000
123A123ASN0-0.018-0.00729.5370.0160.0160.0000.0000.0000.000
124A124ARG10.9701.00229.586-0.126-0.1260.0000.0000.0000.000
125A125SER00.0260.00631.129-0.001-0.0010.0000.0000.0000.000
126A126GLY00.0780.02731.4630.0050.0050.0000.0000.0000.000
127A127LEU00.0200.02128.9200.0220.0220.0000.0000.0000.000
128A128ILE00.0710.04525.8030.0240.0240.0000.0000.0000.000
129A129ALA00.0240.00225.9650.0360.0360.0000.0000.0000.000
130A130GLU-1-0.809-0.88826.8810.3620.3620.0000.0000.0000.000
131A131LEU00.0460.03221.6580.0390.0390.0000.0000.0000.000
132A132SER0-0.003-0.00522.2310.0590.0590.0000.0000.0000.000
133A133ARG10.8480.91022.112-0.268-0.2680.0000.0000.0000.000
134A134GLN0-0.037-0.03921.9490.0500.0500.0000.0000.0000.000
135A135LEU00.0750.04416.8890.0720.0720.0000.0000.0000.000
136A136GLN00.0120.00917.8660.0980.0980.0000.0000.0000.000
137A137VAL0-0.057-0.02518.9980.0780.0780.0000.0000.0000.000
138A138LEU00.0520.03515.5340.0670.0670.0000.0000.0000.000
139A139LEU00.0200.01712.9600.1720.1720.0000.0000.0000.000
140A140TRP00.007-0.00914.7520.1220.1220.0000.0000.0000.000
141A141ILE00.0170.00014.4230.0580.0580.0000.0000.0000.000
142A142ALA00.0470.03310.6490.0650.0650.0000.0000.0000.000
143A143ARG10.8920.92911.480-1.621-1.6210.0000.0000.0000.000
144A144LYS10.8090.90313.357-1.313-1.3130.0000.0000.0000.000
145A145HIS00.0370.02412.783-0.074-0.0740.0000.0000.0000.000
146A146ASN0-0.036-0.0056.375-0.005-0.0050.0000.0000.0000.000
147A147ILE00.0240.0307.4100.9090.9090.0000.0000.0000.000
148A148PRO0-0.0090.0004.440-0.225-0.118-0.001-0.010-0.0960.000
149A149VAL0-0.031-0.0217.246-0.590-0.5900.0000.0000.0000.000
150A150ILE00.0290.0199.295-0.012-0.0120.0000.0000.0000.000
151A151VAL0-0.021-0.01211.665-0.070-0.0700.0000.0000.0000.000
152A152ILE00.0070.00714.472-0.078-0.0780.0000.0000.0000.000
153A153ASN0-0.008-0.01616.6150.0560.0560.0000.0000.0000.000
154A154GLN00.0500.01819.268-0.054-0.0540.0000.0000.0000.000
155A155VAL0-0.056-0.03320.6230.0180.0180.0000.0000.0000.000
156A156HIS00.0020.00022.0210.0230.0230.0000.0000.0000.000
157A157PHE00.0430.03223.8880.0040.0040.0000.0000.0000.000
158A158ASP-1-0.786-0.88422.6190.1660.1660.0000.0000.0000.000
159A159SER0-0.035-0.02721.8450.0120.0120.0000.0000.0000.000
160A160ARG10.8490.90624.025-0.153-0.1530.0000.0000.0000.000
161A161THR0-0.031-0.02025.1680.0080.0080.0000.0000.0000.000
162A162GLU-1-0.882-0.93128.1030.0260.0260.0000.0000.0000.000
163A163MET0-0.006-0.00225.759-0.005-0.0050.0000.0000.0000.000
164A164THR0-0.026-0.00825.1730.0090.0090.0000.0000.0000.000
165A165LYS10.8160.91218.9330.0650.0650.0000.0000.0000.000
166A166PRO0-0.023-0.00818.9760.0020.0020.0000.0000.0000.000
167A167VAL0-0.042-0.02818.8430.0130.0130.0000.0000.0000.000
168A168ALA00.005-0.00617.8940.0100.0100.0000.0000.0000.000
169A169GLU-1-0.850-0.92718.9590.2890.2890.0000.0000.0000.000
170A170GLN00.0220.01621.6120.0330.0330.0000.0000.0000.000
171A171THR00.012-0.01019.8260.0280.0280.0000.0000.0000.000
172A172LEU0-0.056-0.01619.3710.0800.0800.0000.0000.0000.000
173A173GLY00.0780.04317.3410.0620.0620.0000.0000.0000.000
174A174TYR00.002-0.00415.2750.0540.0540.0000.0000.0000.000
175A175ARG10.8150.90515.328-0.437-0.4370.0000.0000.0000.000
176A176CYS0-0.0420.00712.1690.2040.2040.0000.0000.0000.000
177A177LYS10.8800.9169.060-1.125-1.1250.0000.0000.0000.000
178A178ASP-1-0.791-0.8715.7301.8241.8240.0000.0000.0000.000
179A179ILE0-0.038-0.0208.3320.1010.1010.0000.0000.0000.000
180A180LEU0-0.0010.0018.322-0.160-0.1600.0000.0000.0000.000
181A181ARG10.8090.88611.4460.3260.3260.0000.0000.0000.000
182A182LEU0-0.035-0.01513.218-0.113-0.1130.0000.0000.0000.000
183A183ASP-1-0.788-0.87916.732-0.193-0.1930.0000.0000.0000.000
184A184LYS10.8600.91920.1850.1150.1150.0000.0000.0000.000
185A185LEU00.0290.02621.8460.0170.0170.0000.0000.0000.000
186A186PRO0-0.0080.00124.5120.0070.0070.0000.0000.0000.000
187A187LYS10.9600.96026.3630.2730.2730.0000.0000.0000.000
188A188PRO00.0520.02426.557-0.007-0.0070.0000.0000.0000.000
189A189GLY00.0500.03924.091-0.018-0.0180.0000.0000.0000.000
190A190LEU0-0.018-0.00120.971-0.031-0.0310.0000.0000.0000.000
191A191ARG10.7730.90118.5190.3490.3490.0000.0000.0000.000
192A192VAL00.0190.01117.036-0.051-0.0510.0000.0000.0000.000
193A193ALA0-0.0020.00712.3830.0590.0590.0000.0000.0000.000
194A194VAL00.003-0.01213.801-0.069-0.0690.0000.0000.0000.000
195A195LEU00.0040.0077.2620.0590.0590.0000.0000.0000.000
196A196GLU-1-0.772-0.87111.121-0.061-0.0610.0000.0000.0000.000
197A197ARG10.8820.95810.721-0.306-0.3060.0000.0000.0000.000
198A198HIS0-0.023-0.0062.8700.4760.9330.047-0.127-0.3770.000
199A199ARG10.8750.9253.292-6.331-5.3930.127-0.375-0.6900.004
200A200PHE0-0.021-0.0132.466-0.937-0.0570.394-0.266-1.0080.000
201A201ARG10.8140.9124.8391.8741.8740.0000.0000.0000.000
202A202PRO00.012-0.0067.5820.1850.1850.0000.0000.0000.000
203A203GLU-1-0.775-0.89211.035-0.081-0.0810.0000.0000.0000.000
204A204GLY0-0.042-0.02212.379-0.002-0.0020.0000.0000.0000.000
205A205LEU0-0.018-0.00511.279-0.021-0.0210.0000.0000.0000.000
206A206MET0-0.013-0.01913.1710.0260.0260.0000.0000.0000.000
207A207ALA0-0.0160.00511.830-0.122-0.1220.0000.0000.0000.000
208A208TYR00.0100.00313.8910.1120.1120.0000.0000.0000.000
209A209PHE00.0120.00015.076-0.067-0.0670.0000.0000.0000.000
210A210ARG10.8100.86817.2000.6010.6010.0000.0000.0000.000
211A211ILE0-0.047-0.02719.476-0.031-0.0310.0000.0000.0000.000
212A212THR0-0.011-0.01520.9180.0250.0250.0000.0000.0000.000
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