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: QVK5Y

Calculation Name: 3CM0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CM0

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SHQ9

Base Structure: X-ray

Registration Date: 2023-09-22

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1877491.026423
FMO2-HF: Nuclear repulsion 1806995.281285
FMO2-HF: Total energy -70495.745138
FMO2-MP2: Total energy -70706.485481


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:3:VAL)


Summations of interaction energy for fragment #1(A:3:VAL)
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.
-6.383-0.7630.503-3.19-2.932-0.008
Interaction energy analysis for fragmet #1(A:3:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.003
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].
3A5GLN0-0.077-0.0373.809-0.8202.119-0.014-1.660-1.2640.005
4A6ALA00.0490.0216.532-0.024-0.0240.0000.0000.0000.000
5A7VAL0-0.0190.0009.9830.1540.1540.0000.0000.0000.000
6A8ILE00.0040.01113.518-0.026-0.0260.0000.0000.0000.000
7A9PHE00.011-0.00116.7700.0390.0390.0000.0000.0000.000
8A10LEU00.0110.00320.3250.0080.0080.0000.0000.0000.000
9A11GLY00.0480.00423.3660.0000.0000.0000.0000.0000.000
10A12PRO00.0110.02026.836-0.008-0.0080.0000.0000.0000.000
11A13PRO00.011-0.00630.241-0.008-0.0080.0000.0000.0000.000
12A14GLY00.0550.02932.4010.0070.0070.0000.0000.0000.000
13A15ALA00.0110.00828.9130.0030.0030.0000.0000.0000.000
14A16GLY00.0140.00629.053-0.001-0.0010.0000.0000.0000.000
15A17LYS10.8340.91423.8380.2120.2120.0000.0000.0000.000
16A18GLY00.0540.02823.589-0.020-0.0200.0000.0000.0000.000
17A19THR0-0.006-0.00923.797-0.019-0.0190.0000.0000.0000.000
18A20GLN00.000-0.00622.716-0.023-0.0230.0000.0000.0000.000
19A21ALA0-0.0100.01019.577-0.022-0.0220.0000.0000.0000.000
20A22SER0-0.010-0.01719.138-0.051-0.0510.0000.0000.0000.000
21A23ARG10.8020.89120.4550.1850.1850.0000.0000.0000.000
22A24LEU00.0190.01015.488-0.006-0.0060.0000.0000.0000.000
23A25ALA0-0.005-0.00315.782-0.045-0.0450.0000.0000.0000.000
24A26GLN0-0.058-0.03916.391-0.028-0.0280.0000.0000.0000.000
25A27GLU-1-0.789-0.86418.353-0.253-0.2530.0000.0000.0000.000
26A28LEU0-0.044-0.02013.0110.0160.0160.0000.0000.0000.000
27A29GLY0-0.0040.00512.369-0.093-0.0930.0000.0000.0000.000
28A30PHE0-0.034-0.0169.984-0.161-0.1610.0000.0000.0000.000
29A31LYS10.8280.89512.6050.9770.9770.0000.0000.0000.000
30A32LYS10.8610.92114.6970.3130.3130.0000.0000.0000.000
31A33LEU00.0080.01913.9780.0490.0490.0000.0000.0000.000
32A34SER0-0.027-0.05618.0570.0440.0440.0000.0000.0000.000
33A35THR00.0660.02619.8850.0100.0100.0000.0000.0000.000
34A36GLY0-0.0120.00522.0150.0150.0150.0000.0000.0000.000
35A37ASP-1-0.804-0.85923.929-0.246-0.2460.0000.0000.0000.000
36A38ILE00.0400.02718.6180.0160.0160.0000.0000.0000.000
37A39LEU00.0050.00822.7470.0130.0130.0000.0000.0000.000
38A40ARG10.8530.89825.3850.2300.2300.0000.0000.0000.000
39A41ASP-1-0.837-0.89424.573-0.256-0.2560.0000.0000.0000.000
40A42HIS00.0880.05520.9930.0400.0400.0000.0000.0000.000
41A43VAL0-0.015-0.01226.2610.0160.0160.0000.0000.0000.000
42A44ALA0-0.063-0.02029.7330.0130.0130.0000.0000.0000.000
43A45ARG10.7860.86924.0830.2770.2770.0000.0000.0000.000
44A46GLY00.0220.03129.9920.0050.0050.0000.0000.0000.000
45A47THR0-0.031-0.02825.4190.0120.0120.0000.0000.0000.000
46A48PRO0-0.008-0.02326.7240.0060.0060.0000.0000.0000.000
47A49LEU00.0060.01522.3620.0130.0130.0000.0000.0000.000
48A50GLY00.0540.02026.4540.0050.0050.0000.0000.0000.000
49A51GLU-1-0.782-0.87728.787-0.119-0.1190.0000.0000.0000.000
50A52ARG10.8900.95128.2600.1280.1280.0000.0000.0000.000
51A53VAL00.0090.00126.6890.0060.0060.0000.0000.0000.000
52A54ARG10.7910.87229.9420.1260.1260.0000.0000.0000.000
53A55PRO0-0.0080.00032.9080.0050.0050.0000.0000.0000.000
54A56ILE0-0.051-0.01929.4190.0060.0060.0000.0000.0000.000
55A57MET00.021-0.00130.7920.0010.0010.0000.0000.0000.000
56A58GLU-1-0.876-0.93333.961-0.102-0.1020.0000.0000.0000.000
57A59ARG10.7310.84535.1560.0980.0980.0000.0000.0000.000
58A60GLY0-0.0090.00536.8300.0050.0050.0000.0000.0000.000
59A61ASP-1-0.861-0.89433.239-0.093-0.0930.0000.0000.0000.000
60A62LEU0-0.041-0.02830.026-0.008-0.0080.0000.0000.0000.000
61A63VAL00.004-0.00525.6820.0050.0050.0000.0000.0000.000
62A64PRO00.0180.02226.192-0.005-0.0050.0000.0000.0000.000
63A65ASP-1-0.772-0.90522.505-0.188-0.1880.0000.0000.0000.000
64A66ASP-1-0.896-0.94721.079-0.176-0.1760.0000.0000.0000.000
65A67LEU00.0350.01920.432-0.025-0.0250.0000.0000.0000.000
66A68ILE0-0.053-0.02420.177-0.034-0.0340.0000.0000.0000.000
67A69LEU0-0.022-0.02515.466-0.045-0.0450.0000.0000.0000.000
68A70GLU-1-0.807-0.86216.163-0.358-0.3580.0000.0000.0000.000
69A71LEU0-0.018-0.01216.738-0.047-0.0470.0000.0000.0000.000
70A72ILE0-0.055-0.02113.290-0.049-0.0490.0000.0000.0000.000
71A73ARG10.7690.84311.7630.1790.1790.0000.0000.0000.000
72A74GLU-1-0.937-0.97412.310-0.441-0.4410.0000.0000.0000.000
73A75GLU-1-0.849-0.91714.020-0.699-0.6990.0000.0000.0000.000
74A76LEU0-0.046-0.0148.795-0.075-0.0750.0000.0000.0000.000
75A77ALA0-0.003-0.0048.1350.0440.0440.0000.0000.0000.000
76A78GLU-1-0.855-0.9185.422-2.098-2.0980.0000.0000.0000.000
77A79ARG10.8270.9195.8861.1221.1220.0000.0000.0000.000
78A80VAL00.0030.0238.6770.2210.2210.0000.0000.0000.000
79A81ILE0-0.012-0.01111.7740.0760.0760.0000.0000.0000.000
80A82PHE00.0340.01912.3060.0240.0240.0000.0000.0000.000
81A83ASP-1-0.755-0.88517.399-0.240-0.2400.0000.0000.0000.000
82A84GLY0-0.0080.01021.1380.0030.0030.0000.0000.0000.000
83A85PHE0-0.010-0.00316.9530.0190.0190.0000.0000.0000.000
84A86PRO00.0430.02818.184-0.026-0.0260.0000.0000.0000.000
85A87ARG10.8390.89720.8030.2530.2530.0000.0000.0000.000
86A88THR00.0100.01523.7350.0150.0150.0000.0000.0000.000
87A89LEU00.0750.02523.121-0.015-0.0150.0000.0000.0000.000
88A90ALA00.0360.02622.221-0.003-0.0030.0000.0000.0000.000
89A91GLN0-0.024-0.02920.532-0.022-0.0220.0000.0000.0000.000
90A92ALA00.0100.00518.497-0.034-0.0340.0000.0000.0000.000
91A93GLU-1-0.826-0.89117.363-0.079-0.0790.0000.0000.0000.000
92A94ALA0-0.052-0.02717.2470.0100.0100.0000.0000.0000.000
93A95LEU00.0100.01313.259-0.028-0.0280.0000.0000.0000.000
94A96ASP-1-0.769-0.86612.864-0.245-0.2450.0000.0000.0000.000
95A97ARG10.8280.89112.1450.0930.0930.0000.0000.0000.000
96A98LEU00.0540.04011.1220.0260.0260.0000.0000.0000.000
97A99LEU0-0.024-0.0168.521-0.146-0.1460.0000.0000.0000.000
98A100SER0-0.025-0.0117.183-0.082-0.0820.0000.0000.0000.000
99A101GLU-1-0.960-0.9797.968-0.019-0.0190.0000.0000.0000.000
100A102THR0-0.044-0.0236.0800.0400.0400.0000.0000.0000.000
101A103GLY0-0.0110.0123.146-1.367-0.8800.044-0.198-0.332-0.001
102A104THR0-0.022-0.0192.871-3.305-1.2330.474-1.327-1.220-0.012
103A105ARG10.9400.9674.5340.6020.724-0.001-0.005-0.1160.000
104A106LEU00.0140.0056.382-0.162-0.1620.0000.0000.0000.000
105A107LEU0-0.062-0.0347.9830.1590.1590.0000.0000.0000.000
106A108GLY0-0.002-0.01811.1350.0940.0940.0000.0000.0000.000
107A109VAL0-0.024-0.00614.666-0.065-0.0650.0000.0000.0000.000
108A110VAL00.0310.01717.6020.0370.0370.0000.0000.0000.000
109A111LEU00.0010.00520.116-0.007-0.0070.0000.0000.0000.000
110A112VAL0-0.015-0.00523.7330.0110.0110.0000.0000.0000.000
111A113GLU-1-0.846-0.91326.184-0.092-0.0920.0000.0000.0000.000
112A114VAL0-0.022-0.02529.3920.0000.0000.0000.0000.0000.000
113A115PRO00.0400.02632.9030.0000.0000.0000.0000.0000.000
114A116GLU-1-0.792-0.88136.518-0.073-0.0730.0000.0000.0000.000
115A117GLU-1-0.863-0.94438.050-0.066-0.0660.0000.0000.0000.000
116A118GLU-1-0.830-0.90137.233-0.076-0.0760.0000.0000.0000.000
117A119LEU0-0.063-0.02432.807-0.005-0.0050.0000.0000.0000.000
118A120VAL00.0410.01236.890-0.003-0.0030.0000.0000.0000.000
119A121ARG10.8510.90640.3980.0700.0700.0000.0000.0000.000
120A122ARG10.8040.89732.1070.1120.1120.0000.0000.0000.000
121A123ILE0-0.041-0.02135.821-0.003-0.0030.0000.0000.0000.000
122A124LEU00.0300.01739.024-0.001-0.0010.0000.0000.0000.000
123A125ARG10.9991.01341.5460.0830.0830.0000.0000.0000.000
124A126ARG10.7420.85936.8620.1090.1090.0000.0000.0000.000
125A127ALA00.003-0.00640.951-0.001-0.0010.0000.0000.0000.000
126A128GLU-1-0.919-0.95943.069-0.068-0.0680.0000.0000.0000.000
127A129LEU0-0.071-0.03742.4110.0010.0010.0000.0000.0000.000
128A130GLU-1-0.838-0.91138.890-0.113-0.1130.0000.0000.0000.000
129A131GLY0-0.0140.01443.6600.0000.0000.0000.0000.0000.000
130A132ARG10.7670.87539.4690.1040.1040.0000.0000.0000.000
131A133SER0-0.003-0.02145.7750.0040.0040.0000.0000.0000.000
132A134ASP-1-0.801-0.85741.509-0.092-0.0920.0000.0000.0000.000
133A135ASP-1-0.832-0.89840.510-0.097-0.0970.0000.0000.0000.000
134A136ASN00.0290.00843.5200.0040.0040.0000.0000.0000.000
135A137GLU-1-0.795-0.88544.482-0.061-0.0610.0000.0000.0000.000
136A138GLU-1-0.778-0.87144.213-0.065-0.0650.0000.0000.0000.000
137A139THR0-0.030-0.03943.112-0.002-0.0020.0000.0000.0000.000
138A140VAL0-0.032-0.01339.246-0.005-0.0050.0000.0000.0000.000
139A141ARG10.8300.87639.3430.0590.0590.0000.0000.0000.000
140A142ARG10.8660.92539.6640.0680.0680.0000.0000.0000.000
141A143ARG10.7670.85937.0830.0920.0920.0000.0000.0000.000
142A144LEU0-0.031-0.01334.675-0.007-0.0070.0000.0000.0000.000
143A145GLU-1-0.748-0.84034.954-0.073-0.0730.0000.0000.0000.000
144A146VAL00.0040.00335.308-0.003-0.0030.0000.0000.0000.000
145A147TYR0-0.047-0.03427.205-0.005-0.0050.0000.0000.0000.000
146A148ARG10.8000.87031.2140.0630.0630.0000.0000.0000.000
147A149GLU-1-0.908-0.95531.653-0.073-0.0730.0000.0000.0000.000
148A150LYS10.8990.94530.1620.1130.1130.0000.0000.0000.000
149A151THR0-0.052-0.03325.976-0.013-0.0130.0000.0000.0000.000
150A152GLU-1-0.870-0.91626.945-0.069-0.0690.0000.0000.0000.000
151A153PRO00.003-0.00727.3300.0020.0020.0000.0000.0000.000
152A154LEU0-0.011-0.00322.6010.0020.0020.0000.0000.0000.000
153A155VAL00.005-0.00122.713-0.007-0.0070.0000.0000.0000.000
154A156GLY00.0510.02823.6960.0040.0040.0000.0000.0000.000
155A157TYR0-0.076-0.05917.8840.0220.0220.0000.0000.0000.000
156A158TYR00.005-0.02016.1460.0020.0020.0000.0000.0000.000
157A159GLU-1-0.850-0.89919.660-0.062-0.0620.0000.0000.0000.000
158A160ALA0-0.025-0.01122.0150.0140.0140.0000.0000.0000.000
159A161ARG10.8070.90316.8400.0900.0900.0000.0000.0000.000
160A162GLY0-0.0140.00617.2620.0120.0120.0000.0000.0000.000
161A163VAL0-0.029-0.01513.865-0.005-0.0050.0000.0000.0000.000
162A164LEU0-0.0180.00116.808-0.040-0.0400.0000.0000.0000.000
163A165LYS10.8270.91815.5950.1600.1600.0000.0000.0000.000
164A166ARG10.8080.86920.5010.0640.0640.0000.0000.0000.000
165A167VAL0-0.028-0.01722.4750.0050.0050.0000.0000.0000.000
166A168ASP-1-0.787-0.87625.489-0.097-0.0970.0000.0000.0000.000
167A169GLY00.0400.00428.571-0.008-0.0080.0000.0000.0000.000
168A170LEU0-0.069-0.02929.851-0.002-0.0020.0000.0000.0000.000
169A171GLY00.0450.02132.1520.0050.0050.0000.0000.0000.000
170A172THR0-0.062-0.04831.942-0.007-0.0070.0000.0000.0000.000
171A173PRO00.016-0.00728.916-0.004-0.0040.0000.0000.0000.000
172A174ASP-1-0.779-0.87626.863-0.170-0.1700.0000.0000.0000.000
173A175GLU-1-0.787-0.84826.641-0.100-0.1000.0000.0000.0000.000
174A176VAL0-0.028-0.00726.090-0.004-0.0040.0000.0000.0000.000
175A177TYR0-0.046-0.05419.558-0.017-0.0170.0000.0000.0000.000
176A178ALA00.0200.00922.250-0.014-0.0140.0000.0000.0000.000
177A179ARG10.7760.86722.7050.1050.1050.0000.0000.0000.000
178A180ILE00.0100.00819.3970.0000.0000.0000.0000.0000.000
179A181ARG10.8720.91616.9900.2550.2550.0000.0000.0000.000
180A182ALA0-0.019-0.00217.994-0.003-0.0030.0000.0000.0000.000
181A183ALA00.0010.00719.2870.0120.0120.0000.0000.0000.000
182A184LEU0-0.038-0.02714.5610.0090.0090.0000.0000.0000.000
183A185GLY00.0010.02414.310-0.002-0.0020.0000.0000.0000.000
184A186ILE0-0.0290.00211.5950.0110.0110.0000.0000.0000.000