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

tag_button

FMODB ID: QV46Y

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 OptH
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2705112.190074
FMO2-HF: Nuclear repulsion 2619893.992519
FMO2-HF: Total energy -85218.197556
FMO2-MP2: Total energy -85470.190615


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.
-21.367-13.57217.211-6.847-18.164-0.058
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 : -0.075 / q_NPA : -0.032
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].
3A3SER0-0.030-0.0193.796-0.2920.993-0.013-0.459-0.8140.002
4A4THR00.020-0.0165.3720.8970.994-0.001-0.006-0.0890.000
5A5GLY0-0.008-0.0138.0900.4370.4370.0000.0000.0000.000
6A6THR0-0.057-0.0169.5530.3360.3360.0000.0000.0000.000
7A7LYS10.9991.0059.6161.0661.0660.0000.0000.0000.000
8A8SER0-0.029-0.02310.667-0.286-0.2860.0000.0000.0000.000
9A9LEU00.0260.0009.205-0.102-0.1020.0000.0000.0000.000
10A10ASP-1-0.693-0.8135.964-3.861-3.8610.0000.0000.0000.000
11A11SER0-0.062-0.0336.023-0.882-0.8820.0000.0000.0000.000
12A12LEU0-0.066-0.0337.653-0.106-0.1060.0000.0000.0000.000
13A13LEU0-0.003-0.0073.6750.2430.4880.001-0.039-0.2070.000
14A14GLY0-0.036-0.0122.507-3.876-2.8121.216-0.834-1.446-0.011
15A15GLY0-0.020-0.0152.468-5.001-2.7131.388-1.574-2.103-0.016
16A16GLY00.0290.0132.6900.2340.8332.200-0.519-2.280-0.010
17A17PHE0-0.029-0.0182.771-2.062-0.8801.168-0.175-2.176-0.016
18A18ALA00.0550.0242.288-0.5870.3518.555-4.686-4.808-0.013
19A19PRO0-0.0180.0032.419-2.735-4.0171.1491.957-1.8250.002
20A20GLY00.0180.0035.307-0.423-0.346-0.001-0.004-0.0720.000
21A21VAL0-0.113-0.0666.027-0.732-0.7320.0000.0000.0000.000
22A22LEU0-0.004-0.0019.0370.0120.0120.0000.0000.0000.000
23A23THR00.0140.0047.459-0.047-0.0470.0000.0000.0000.000
24A24GLN00.007-0.0029.782-0.038-0.0380.0000.0000.0000.000
25A25VAL0-0.019-0.01011.372-0.113-0.1130.0000.0000.0000.000
26A26TYR0-0.015-0.05813.8550.0400.0400.0000.0000.0000.000
27A27GLY00.0840.02817.358-0.066-0.0660.0000.0000.0000.000
28A28PRO0-0.0050.00320.0330.0340.0340.0000.0000.0000.000
29A29TYR00.0660.03822.319-0.034-0.0340.0000.0000.0000.000
30A30ALA00.015-0.00322.933-0.014-0.0140.0000.0000.0000.000
31A31SER0-0.024-0.02119.845-0.042-0.0420.0000.0000.0000.000
32A32GLY00.0580.01517.991-0.046-0.0460.0000.0000.0000.000
33A33LYS10.8810.93215.5750.0270.0270.0000.0000.0000.000
34A34THR00.0520.03515.311-0.022-0.0220.0000.0000.0000.000
35A35THR0-0.0240.00016.5530.0190.0190.0000.0000.0000.000
36A36LEU00.0270.01810.088-0.049-0.0490.0000.0000.0000.000
37A37ALA00.0120.01312.037-0.079-0.0790.0000.0000.0000.000
38A38LEU00.004-0.00513.0340.0080.0080.0000.0000.0000.000
39A39GLN0-0.006-0.01211.8960.1770.1770.0000.0000.0000.000
40A40THR00.002-0.0137.313-0.168-0.1680.0000.0000.0000.000
41A41GLY00.004-0.00610.1100.0200.0200.0000.0000.0000.000
42A42LEU0-0.026-0.00512.2140.0320.0320.0000.0000.0000.000
43A43LEU00.014-0.00210.5690.0410.0410.0000.0000.0000.000
44A44SER0-0.040-0.0109.186-0.001-0.0010.0000.0000.0000.000
45A45GLY0-0.006-0.00110.0590.1020.1020.0000.0000.0000.000
46A46LYS10.9090.9499.204-0.349-0.3490.0000.0000.0000.000
47A47LYS10.9740.99314.008-0.398-0.3980.0000.0000.0000.000
48A48VAL00.0180.02412.6840.1200.1200.0000.0000.0000.000
49A49ALA0-0.0360.00514.717-0.057-0.0570.0000.0000.0000.000
50A50TYR00.012-0.01715.8060.0340.0340.0000.0000.0000.000
51A51VAL0-0.033-0.02418.010-0.023-0.0230.0000.0000.0000.000
52A52ASP-1-0.781-0.90420.3110.0630.0630.0000.0000.0000.000
53A53THR0-0.145-0.08322.4220.0060.0060.0000.0000.0000.000
54A54GLU-1-0.908-0.97423.592-0.015-0.0150.0000.0000.0000.000
55A55GLY00.0300.04825.107-0.017-0.0170.0000.0000.0000.000
56A56GLY00.0140.01022.834-0.021-0.0210.0000.0000.0000.000
57A57PHE0-0.086-0.05419.154-0.034-0.0340.0000.0000.0000.000
58A58SER00.0020.00022.265-0.001-0.0010.0000.0000.0000.000
59A59PRO00.0440.00623.063-0.023-0.0230.0000.0000.0000.000
60A60GLU-1-0.817-0.91024.323-0.083-0.0830.0000.0000.0000.000
61A61ARG10.8250.92721.2040.2620.2620.0000.0000.0000.000
62A62LEU00.0300.00717.879-0.045-0.0450.0000.0000.0000.000
63A63VAL00.0280.02621.028-0.031-0.0310.0000.0000.0000.000
64A64GLN00.0480.02823.641-0.023-0.0230.0000.0000.0000.000
65A65MET0-0.109-0.03816.293-0.019-0.0190.0000.0000.0000.000
66A66ALA0-0.013-0.01019.512-0.047-0.0470.0000.0000.0000.000
67A67GLU-1-0.855-0.92920.514-0.199-0.1990.0000.0000.0000.000
68A68THR0-0.059-0.03421.889-0.012-0.0120.0000.0000.0000.000
69A69ARG10.7820.86814.2430.6680.6680.0000.0000.0000.000
70A70GLY0-0.012-0.00419.710-0.024-0.0240.0000.0000.0000.000
71A71LEU0-0.055-0.04716.1670.0010.0010.0000.0000.0000.000
72A72ASN0-0.0070.02720.7580.0250.0250.0000.0000.0000.000
73A73PRO00.040-0.00922.2220.0030.0030.0000.0000.0000.000
74A74GLU-1-0.857-0.91623.572-0.025-0.0250.0000.0000.0000.000
75A75GLU-1-0.924-0.94721.444-0.040-0.0400.0000.0000.0000.000
76A76ALA0-0.053-0.03118.8820.0260.0260.0000.0000.0000.000
77A77LEU00.016-0.00319.4540.0310.0310.0000.0000.0000.000
78A78SER00.001-0.01521.9080.0360.0360.0000.0000.0000.000
79A79ARG10.7630.90814.8000.1140.1140.0000.0000.0000.000
80A80PHE0-0.041-0.02015.4970.0670.0670.0000.0000.0000.000
81A81ILE0-0.0090.00118.591-0.004-0.0040.0000.0000.0000.000
82A82LEU00.0160.00219.9450.0390.0390.0000.0000.0000.000
83A83PHE0-0.007-0.00219.9490.0160.0160.0000.0000.0000.000
84A84THR00.0670.03323.695-0.001-0.0010.0000.0000.0000.000
85A85PRO0-0.035-0.02724.473-0.009-0.0090.0000.0000.0000.000
86A86SER00.0320.00027.019-0.011-0.0110.0000.0000.0000.000
87A87ASP-1-0.782-0.85728.5640.0920.0920.0000.0000.0000.000
88A88PHE00.000-0.04328.1980.0100.0100.0000.0000.0000.000
89A89LYS10.8520.93729.257-0.107-0.1070.0000.0000.0000.000
90A90GLU-1-0.955-1.00128.2140.2050.2050.0000.0000.0000.000
91A91GLN00.1340.06422.3940.0380.0380.0000.0000.0000.000
92A92ARG10.9600.97322.804-0.355-0.3550.0000.0000.0000.000
93A93ARG10.9140.98625.437-0.161-0.1610.0000.0000.0000.000
94A94VAL00.0680.05622.2610.0220.0220.0000.0000.0000.000
95A95ILE00.0160.02319.7680.0440.0440.0000.0000.0000.000
96A96GLY0-0.088-0.04921.4140.0520.0520.0000.0000.0000.000
97A97SER0-0.030-0.04223.5170.0280.0280.0000.0000.0000.000
98A98LEU00.0260.00217.7050.0250.0250.0000.0000.0000.000
99A99LYS10.8500.94019.423-0.460-0.4600.0000.0000.0000.000
100A100LYS10.9000.94020.357-0.506-0.5060.0000.0000.0000.000
101A101THR0-0.0050.01420.576-0.023-0.0230.0000.0000.0000.000
102A102VAL0-0.0140.00514.726-0.007-0.0070.0000.0000.0000.000
103A103ASP-1-0.832-0.91917.3620.5920.5920.0000.0000.0000.000
104A104SER00.011-0.02014.6490.0570.0570.0000.0000.0000.000
105A105ASN0-0.0220.00214.4620.0250.0250.0000.0000.0000.000
106A106PHE0-0.058-0.03713.501-0.112-0.1120.0000.0000.0000.000
107A107ALA0-0.016-0.0039.1420.2070.2070.0000.0000.0000.000
108A108LEU0-0.024-0.0168.2040.3900.3900.0000.0000.0000.000
109A109VAL00.0020.01610.350-0.154-0.1540.0000.0000.0000.000
110A110VAL00.0090.00312.0780.0580.0580.0000.0000.0000.000
111A111VAL0-0.031-0.01214.519-0.009-0.0090.0000.0000.0000.000
112A112ASP-1-0.868-0.92017.4210.0310.0310.0000.0000.0000.000
113A113SER00.1090.04119.939-0.011-0.0110.0000.0000.0000.000
114A114ILE0-0.129-0.07321.1670.0420.0420.0000.0000.0000.000
115A115THR00.003-0.02323.3380.0040.0040.0000.0000.0000.000
116A116ALA00.0510.04325.991-0.016-0.0160.0000.0000.0000.000
117A117HIS10.8150.92328.104-0.130-0.1300.0000.0000.0000.000
118A118TYR00.0270.00432.523-0.008-0.0080.0000.0000.0000.000
119A119ARG10.9390.98136.169-0.094-0.0940.0000.0000.0000.000
120A120ALA00.0670.02634.8150.0020.0020.0000.0000.0000.000
121A121GLU-1-0.932-0.95334.2000.0800.0800.0000.0000.0000.000
122A122GLU-1-0.924-0.99732.7760.1140.1140.0000.0000.0000.000
123A123ASN0-0.044-0.03229.9260.0060.0060.0000.0000.0000.000
124A124ARG10.9581.01729.919-0.096-0.0960.0000.0000.0000.000
125A125SER00.019-0.01031.4860.0000.0000.0000.0000.0000.000
126A126GLY00.0640.02132.1730.0020.0020.0000.0000.0000.000
127A127LEU00.0320.02629.3020.0210.0210.0000.0000.0000.000
128A128ILE00.0910.06525.8840.0240.0240.0000.0000.0000.000
129A129ALA00.0210.00125.9330.0310.0310.0000.0000.0000.000
130A130GLU-1-0.910-0.98026.5100.3080.3080.0000.0000.0000.000
131A131LEU00.0350.04221.5930.0350.0350.0000.0000.0000.000
132A132SER0-0.007-0.02722.0150.0510.0510.0000.0000.0000.000
133A133ARG10.9230.96822.199-0.241-0.2410.0000.0000.0000.000
134A134GLN0-0.046-0.01921.5750.0530.0530.0000.0000.0000.000
135A135LEU00.0810.06217.0030.0650.0650.0000.0000.0000.000
136A136GLN00.0240.00817.7060.1040.1040.0000.0000.0000.000
137A137VAL0-0.065-0.03018.8370.0730.0730.0000.0000.0000.000
138A138LEU00.0670.03715.3270.0720.0720.0000.0000.0000.000
139A139LEU00.0210.01712.7130.1640.1640.0000.0000.0000.000
140A140TRP0-0.011-0.02214.4320.1520.1520.0000.0000.0000.000
141A141ILE00.0180.00014.0630.0840.0840.0000.0000.0000.000
142A142ALA00.0490.02510.3610.0740.0740.0000.0000.0000.000
143A143ARG10.8970.94010.970-1.232-1.2320.0000.0000.0000.000
144A144LYS10.8000.91313.029-1.118-1.1180.0000.0000.0000.000
145A145HIS00.0360.02312.519-0.036-0.0360.0000.0000.0000.000
146A146ASN0-0.0140.0117.5400.4800.4800.0000.0000.0000.000
147A147ILE00.0270.0247.0010.7420.7420.0000.0000.0000.000
148A148PRO0-0.016-0.0044.538-0.217-0.118-0.001-0.009-0.0890.000
149A149VAL0-0.019-0.0027.325-0.464-0.4640.0000.0000.0000.000
150A150ILE0-0.0050.0049.1030.0260.0260.0000.0000.0000.000
151A151VAL0-0.030-0.01811.716-0.030-0.0300.0000.0000.0000.000
152A152ILE00.0400.02115.186-0.071-0.0710.0000.0000.0000.000
153A153ASN00.0650.01217.2980.0460.0460.0000.0000.0000.000
154A154GLN00.0590.04519.801-0.047-0.0470.0000.0000.0000.000
155A155VAL0-0.057-0.01521.3890.0170.0170.0000.0000.0000.000
156A156HIS0-0.017-0.01922.3940.0200.0200.0000.0000.0000.000
157A157PHE00.0310.01724.6160.0020.0020.0000.0000.0000.000
158A158ASP-1-0.815-0.91422.6650.1200.1200.0000.0000.0000.000
159A159SER0-0.021-0.01721.8480.0070.0070.0000.0000.0000.000
160A160ARG10.9790.98924.265-0.103-0.1030.0000.0000.0000.000
161A161THR0-0.036-0.00625.1780.0090.0090.0000.0000.0000.000
162A162GLU-1-0.848-0.92528.1370.0100.0100.0000.0000.0000.000
163A163MET00.0050.02126.146-0.008-0.0080.0000.0000.0000.000
164A164THR0-0.030-0.01524.9460.0090.0090.0000.0000.0000.000
165A165LYS10.8510.94320.1720.1400.1400.0000.0000.0000.000
166A166PRO0-0.073-0.04019.3460.0030.0030.0000.0000.0000.000
167A167VAL00.014-0.01419.0350.0110.0110.0000.0000.0000.000
168A168ALA0-0.019-0.01417.9550.0080.0080.0000.0000.0000.000
169A169GLU-1-0.857-0.92619.3460.1990.1990.0000.0000.0000.000
170A170GLN00.0290.01521.6690.0340.0340.0000.0000.0000.000
171A171THR00.0020.00119.6010.0200.0200.0000.0000.0000.000
172A172LEU0-0.014-0.01518.7400.0720.0720.0000.0000.0000.000
173A173GLY00.1030.05017.5830.0380.0380.0000.0000.0000.000
174A174TYR0-0.053-0.04015.2040.0430.0430.0000.0000.0000.000
175A175ARG10.8390.93314.831-0.370-0.3700.0000.0000.0000.000
176A176CYS0-0.072-0.01312.3110.1630.1630.0000.0000.0000.000
177A177LYS10.8800.9378.606-0.949-0.9490.0000.0000.0000.000
178A178ASP-1-0.758-0.8705.0570.9651.051-0.001-0.001-0.0840.000
179A179ILE0-0.050-0.0258.6200.0900.0900.0000.0000.0000.000
180A180LEU00.0140.0018.926-0.138-0.1380.0000.0000.0000.000
181A181ARG10.7900.89412.0680.3590.3590.0000.0000.0000.000
182A182LEU0-0.036-0.01013.510-0.098-0.0980.0000.0000.0000.000
183A183ASP-1-0.822-0.89717.037-0.214-0.2140.0000.0000.0000.000
184A184LYS10.8780.92020.3050.1430.1430.0000.0000.0000.000
185A185LEU0-0.004-0.00221.6290.0170.0170.0000.0000.0000.000
186A186PRO0-0.018-0.01224.5660.0040.0040.0000.0000.0000.000
187A187LYS10.9700.98326.2560.3090.3090.0000.0000.0000.000
188A188PRO00.0470.01626.632-0.015-0.0150.0000.0000.0000.000
189A189GLY00.0460.03523.776-0.014-0.0140.0000.0000.0000.000
190A190LEU00.0290.02521.897-0.044-0.0440.0000.0000.0000.000
191A191ARG10.7910.90718.7400.3800.3800.0000.0000.0000.000
192A192VAL00.0360.02116.903-0.050-0.0500.0000.0000.0000.000
193A193ALA0-0.0020.00712.5830.0670.0670.0000.0000.0000.000
194A194VAL0-0.012-0.01014.111-0.062-0.0620.0000.0000.0000.000
195A195LEU00.0050.0087.6420.0590.0590.0000.0000.0000.000
196A196GLU-1-0.789-0.86511.404-0.119-0.1190.0000.0000.0000.000
197A197ARG10.9000.97511.526-0.177-0.1770.0000.0000.0000.000
198A198HIS00.0260.0073.362-0.0830.2780.019-0.077-0.3030.000
199A199ARG10.8670.9303.013-3.384-2.9000.023-0.142-0.3650.001
200A200PHE0-0.025-0.0092.217-0.337-0.0651.509-0.279-1.5030.003
201A201ARG10.8620.9505.0951.8621.8620.0000.0000.0000.000
202A202PRO00.001-0.0117.8110.1730.1730.0000.0000.0000.000
203A203GLU-1-0.787-0.89511.037-0.192-0.1920.0000.0000.0000.000
204A204GLY0-0.038-0.02012.7160.0170.0170.0000.0000.0000.000
205A205LEU0-0.014-0.00811.672-0.015-0.0150.0000.0000.0000.000
206A206MET0-0.004-0.02013.3570.0200.0200.0000.0000.0000.000
207A207ALA0-0.0090.01111.875-0.087-0.0870.0000.0000.0000.000
208A208TYR00.0130.00613.9420.0950.0950.0000.0000.0000.000
209A209PHE0-0.015-0.01215.092-0.089-0.0890.0000.0000.0000.000
210A210ARG10.9060.94517.2530.6070.6070.0000.0000.0000.000
211A211ILE0-0.034-0.01618.834-0.035-0.0350.0000.0000.0000.000
212A212THR0-0.040-0.05820.3400.0340.0340.0000.0000.0000.000
213A213GLU-1-0.806-0.91121.848-0.285-0.2850.0000.0000.0000.000
214A214ARG10.8780.95118.6460.5610.5610.0000.0000.0000.000
215A215GLY00.0260.02917.499-0.040-0.0400.0000.0000.0000.000
216A216ILE0-0.073-0.04214.0680.0530.0530.0000.0000.0000.000
217A217GLU-1-0.826-0.87315.494-0.624-0.6240.0000.0000.0000.000
218A218ASP-1-0.721-0.86714.402-1.228-1.2280.0000.0000.0000.000
219A219VAL0-0.067-0.03816.8000.0830.0830.0000.0000.0000.000
220A220GLU-1-0.919-0.95220.216-0.517-0.5170.0000.0000.0000.000