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: ZV79N

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1869344.176664
FMO2-HF: Nuclear repulsion 1798849.729345
FMO2-HF: Total energy -70494.447318
FMO2-MP2: Total energy -70705.293253


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.
-8.306-2.6752.646-4.142-4.134-0.014
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 : -0.001 / q_NPA : 0.007
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].
3A5GLN0-0.108-0.0543.750-1.1912.154-0.032-1.799-1.5130.009
4A6ALA00.0450.0246.384-0.048-0.0480.0000.0000.0000.000
5A7VAL0-0.017-0.0069.8980.1680.1680.0000.0000.0000.000
6A8ILE00.0140.02413.287-0.026-0.0260.0000.0000.0000.000
7A9PHE00.007-0.00116.5020.0470.0470.0000.0000.0000.000
8A10LEU00.005-0.00919.9230.0020.0020.0000.0000.0000.000
9A11GLY00.011-0.01223.1380.0070.0070.0000.0000.0000.000
10A12PRO00.0130.02426.596-0.009-0.0090.0000.0000.0000.000
11A13PRO00.019-0.00430.054-0.007-0.0070.0000.0000.0000.000
12A14GLY00.0500.02032.0260.0080.0080.0000.0000.0000.000
13A15ALA00.0140.00528.7850.0050.0050.0000.0000.0000.000
14A16GLY0-0.011-0.00128.706-0.002-0.0020.0000.0000.0000.000
15A17LYS10.9110.95323.3760.2180.2180.0000.0000.0000.000
16A18GLY00.0390.03023.375-0.020-0.0200.0000.0000.0000.000
17A19THR00.004-0.00623.406-0.020-0.0200.0000.0000.0000.000
18A20GLN00.0130.00422.391-0.021-0.0210.0000.0000.0000.000
19A21ALA0-0.0040.01119.321-0.020-0.0200.0000.0000.0000.000
20A22SER0-0.014-0.02718.829-0.048-0.0480.0000.0000.0000.000
21A23ARG10.8240.91220.2470.1740.1740.0000.0000.0000.000
22A24LEU00.0210.01415.046-0.004-0.0040.0000.0000.0000.000
23A25ALA0-0.037-0.01915.406-0.040-0.0400.0000.0000.0000.000
24A26GLN0-0.025-0.02515.745-0.034-0.0340.0000.0000.0000.000
25A27GLU-1-0.842-0.88817.757-0.242-0.2420.0000.0000.0000.000
26A28LEU0-0.036-0.02112.5490.0180.0180.0000.0000.0000.000
27A29GLY0-0.0110.00611.865-0.084-0.0840.0000.0000.0000.000
28A30PHE0-0.023-0.00910.034-0.170-0.1700.0000.0000.0000.000
29A31LYS10.8880.94012.1351.0581.0580.0000.0000.0000.000
30A32LYS10.8680.93614.1620.3110.3110.0000.0000.0000.000
31A33LEU00.0230.01313.7150.0360.0360.0000.0000.0000.000
32A34SER00.0050.00917.9090.0480.0480.0000.0000.0000.000
33A35THR00.0590.01519.8270.0040.0040.0000.0000.0000.000
34A36GLY0-0.029-0.01721.8400.0150.0150.0000.0000.0000.000
35A37ASP-1-0.896-0.97423.364-0.272-0.2720.0000.0000.0000.000
36A38ILE00.0390.03318.3820.0220.0220.0000.0000.0000.000
37A39LEU00.0180.01522.6670.0160.0160.0000.0000.0000.000
38A40ARG10.9250.97225.1810.2380.2380.0000.0000.0000.000
39A41ASP-1-0.920-0.95524.585-0.269-0.2690.0000.0000.0000.000
40A42HIS00.0660.03921.0080.0410.0410.0000.0000.0000.000
41A43VAL0-0.020-0.01526.3400.0160.0160.0000.0000.0000.000
42A44ALA0-0.068-0.02329.7040.0130.0130.0000.0000.0000.000
43A45ARG10.8840.93223.6470.2910.2910.0000.0000.0000.000
44A46GLY00.0340.04130.1690.0040.0040.0000.0000.0000.000
45A47THR0-0.046-0.03625.5790.0100.0100.0000.0000.0000.000
46A48PRO00.0310.00026.3920.0070.0070.0000.0000.0000.000
47A49LEU00.0180.01621.8880.0150.0150.0000.0000.0000.000
48A50GLY00.0420.00926.0950.0070.0070.0000.0000.0000.000
49A51GLU-1-0.884-0.96728.468-0.132-0.1320.0000.0000.0000.000
50A52ARG10.8810.95127.4530.1560.1560.0000.0000.0000.000
51A53VAL00.006-0.00426.2740.0080.0080.0000.0000.0000.000
52A54ARG10.9230.97929.6450.1380.1380.0000.0000.0000.000
53A55PRO00.0260.00832.5360.0050.0050.0000.0000.0000.000
54A56ILE0-0.062-0.02529.4160.0070.0070.0000.0000.0000.000
55A57MET00.0100.00730.8090.0000.0000.0000.0000.0000.000
56A58GLU-1-0.907-0.94233.683-0.107-0.1070.0000.0000.0000.000
57A59ARG10.8530.92033.9740.1120.1120.0000.0000.0000.000
58A60GLY0-0.016-0.00236.8430.0050.0050.0000.0000.0000.000
59A61ASP-1-0.941-0.94933.481-0.104-0.1040.0000.0000.0000.000
60A62LEU0-0.065-0.04429.987-0.008-0.0080.0000.0000.0000.000
61A63VAL0-0.028-0.01925.4040.0040.0040.0000.0000.0000.000
62A64PRO00.0070.01725.916-0.004-0.0040.0000.0000.0000.000
63A65ASP-1-0.794-0.93022.512-0.205-0.2050.0000.0000.0000.000
64A66ASP-1-0.910-0.96221.410-0.201-0.2010.0000.0000.0000.000
65A67LEU00.0290.02220.682-0.024-0.0240.0000.0000.0000.000
66A68ILE0-0.047-0.02219.906-0.035-0.0350.0000.0000.0000.000
67A69LEU0-0.032-0.03915.919-0.047-0.0470.0000.0000.0000.000
68A70GLU-1-0.858-0.90416.092-0.418-0.4180.0000.0000.0000.000
69A71LEU0-0.002-0.01116.341-0.053-0.0530.0000.0000.0000.000
70A72ILE0-0.025-0.01013.282-0.057-0.0570.0000.0000.0000.000
71A73ARG10.8670.93211.2950.2570.2570.0000.0000.0000.000
72A74GLU-1-0.972-0.99111.767-0.546-0.5460.0000.0000.0000.000
73A75GLU-1-0.944-0.96713.674-0.654-0.6540.0000.0000.0000.000
74A76LEU0-0.054-0.0138.096-0.057-0.0570.0000.0000.0000.000
75A77ALA0-0.016-0.0178.4780.0780.0780.0000.0000.0000.000
76A78GLU-1-0.914-0.9494.706-2.712-2.504-0.001-0.014-0.1930.000
77A79ARG10.8960.9625.6780.9610.9610.0000.0000.0000.000
78A80VAL00.0220.0358.2480.2600.2600.0000.0000.0000.000
79A81ILE0-0.005-0.01111.4290.0620.0620.0000.0000.0000.000
80A82PHE00.0210.01712.0620.0230.0230.0000.0000.0000.000
81A83ASP-1-0.792-0.92417.025-0.250-0.2500.0000.0000.0000.000
82A84GLY0-0.025-0.00920.7240.0060.0060.0000.0000.0000.000
83A85PHE0-0.032-0.00917.3570.0230.0230.0000.0000.0000.000
84A86PRO00.0380.02417.898-0.031-0.0310.0000.0000.0000.000
85A87ARG10.8990.94220.6580.2520.2520.0000.0000.0000.000
86A88THR00.0270.01323.6360.0150.0150.0000.0000.0000.000
87A89LEU00.0880.03322.840-0.017-0.0170.0000.0000.0000.000
88A90ALA00.0470.03522.161-0.003-0.0030.0000.0000.0000.000
89A91GLN0-0.002-0.01220.597-0.020-0.0200.0000.0000.0000.000
90A92ALA0-0.013-0.00218.457-0.035-0.0350.0000.0000.0000.000
91A93GLU-1-0.929-0.96617.286-0.101-0.1010.0000.0000.0000.000
92A94ALA0-0.053-0.03616.9510.0010.0010.0000.0000.0000.000
93A95LEU00.0060.00013.159-0.027-0.0270.0000.0000.0000.000
94A96ASP-1-0.804-0.88912.802-0.282-0.2820.0000.0000.0000.000
95A97ARG10.9070.95712.0620.1410.1410.0000.0000.0000.000
96A98LEU00.0480.04111.0400.0250.0250.0000.0000.0000.000
97A99LEU0-0.026-0.0188.457-0.153-0.1530.0000.0000.0000.000
98A100SER0-0.050-0.0177.113-0.067-0.0670.0000.0000.0000.000
99A101GLU-1-0.956-0.9877.863-0.026-0.0260.0000.0000.0000.000
100A102THR0-0.068-0.0326.1800.0100.0100.0000.0000.0000.000
101A103GLY0-0.0120.0143.470-1.297-0.9930.009-0.092-0.2210.000
102A104THR0-0.033-0.0262.354-4.053-2.3972.671-2.232-2.096-0.023
103A105ARG10.9320.9634.8340.5250.643-0.001-0.005-0.1110.000
104A106LEU00.0210.0116.596-0.236-0.2360.0000.0000.0000.000
105A107LEU0-0.057-0.0428.2320.1710.1710.0000.0000.0000.000
106A108GLY00.006-0.00510.9450.0920.0920.0000.0000.0000.000
107A109VAL0-0.0170.00914.539-0.065-0.0650.0000.0000.0000.000
108A110VAL00.016-0.00117.4200.0370.0370.0000.0000.0000.000
109A111LEU00.0000.00719.809-0.013-0.0130.0000.0000.0000.000
110A112VAL0-0.047-0.02723.4330.0120.0120.0000.0000.0000.000
111A113GLU-1-0.868-0.93225.867-0.082-0.0820.0000.0000.0000.000
112A114VAL0-0.032-0.02329.1930.0000.0000.0000.0000.0000.000
113A115PRO00.0630.03732.5550.0000.0000.0000.0000.0000.000
114A116GLU-1-0.828-0.92436.098-0.074-0.0740.0000.0000.0000.000
115A117GLU-1-0.879-0.94837.679-0.062-0.0620.0000.0000.0000.000
116A118GLU-1-0.861-0.93836.824-0.071-0.0710.0000.0000.0000.000
117A119LEU0-0.073-0.03132.548-0.005-0.0050.0000.0000.0000.000
118A120VAL00.0350.01036.684-0.003-0.0030.0000.0000.0000.000
119A121ARG10.8940.94940.0890.0650.0650.0000.0000.0000.000
120A122ARG10.8610.93832.1710.1040.1040.0000.0000.0000.000
121A123ILE0-0.042-0.02435.752-0.003-0.0030.0000.0000.0000.000
122A124LEU00.0300.01338.998-0.001-0.0010.0000.0000.0000.000
123A125ARG11.0051.02640.5560.0840.0840.0000.0000.0000.000
124A126ARG10.8540.92036.4800.1150.1150.0000.0000.0000.000
125A127ALA00.0000.00640.601-0.001-0.0010.0000.0000.0000.000
126A128GLU-1-0.923-0.96442.643-0.066-0.0660.0000.0000.0000.000
127A129LEU0-0.092-0.05041.8430.0010.0010.0000.0000.0000.000
128A130GLU-1-0.942-0.98238.354-0.115-0.1150.0000.0000.0000.000
129A131GLY00.0050.02143.302-0.001-0.0010.0000.0000.0000.000
130A132ARG10.7840.89039.2920.1050.1050.0000.0000.0000.000
131A133SER00.008-0.01044.8520.0040.0040.0000.0000.0000.000
132A134ASP-1-0.859-0.92041.444-0.093-0.0930.0000.0000.0000.000
133A135ASP-1-0.915-0.95540.846-0.096-0.0960.0000.0000.0000.000
134A136ASN00.0480.03243.7760.0030.0030.0000.0000.0000.000
135A137GLU-1-0.788-0.89244.569-0.058-0.0580.0000.0000.0000.000
136A138GLU-1-0.907-0.94144.089-0.059-0.0590.0000.0000.0000.000
137A139THR0-0.056-0.04443.056-0.002-0.0020.0000.0000.0000.000
138A140VAL00.001-0.00338.918-0.005-0.0050.0000.0000.0000.000
139A141ARG10.9060.91839.3570.0570.0570.0000.0000.0000.000
140A142ARG10.9831.01339.6680.0770.0770.0000.0000.0000.000
141A143ARG10.8180.90436.8610.0920.0920.0000.0000.0000.000
142A144LEU0-0.005-0.00434.662-0.008-0.0080.0000.0000.0000.000
143A145GLU-1-0.739-0.83435.198-0.070-0.0700.0000.0000.0000.000
144A146VAL0-0.0010.00434.486-0.002-0.0020.0000.0000.0000.000
145A147TYR0-0.036-0.02027.140-0.002-0.0020.0000.0000.0000.000
146A148ARG10.8540.90531.0580.0610.0610.0000.0000.0000.000
147A149GLU-1-0.919-0.95631.754-0.072-0.0720.0000.0000.0000.000
148A150LYS10.8880.93529.9380.1220.1220.0000.0000.0000.000
149A151THR0-0.047-0.03025.924-0.013-0.0130.0000.0000.0000.000
150A152GLU-1-0.916-0.95126.830-0.068-0.0680.0000.0000.0000.000
151A153PRO0-0.004-0.00527.1950.0030.0030.0000.0000.0000.000
152A154LEU0-0.005-0.00122.1750.0010.0010.0000.0000.0000.000
153A155VAL0-0.008-0.00422.804-0.004-0.0040.0000.0000.0000.000
154A156GLY00.0380.02523.9890.0070.0070.0000.0000.0000.000
155A157TYR0-0.080-0.06117.2340.0250.0250.0000.0000.0000.000
156A158TYR00.042-0.00616.5070.0060.0060.0000.0000.0000.000
157A159GLU-1-0.876-0.91619.884-0.036-0.0360.0000.0000.0000.000
158A160ALA0-0.020-0.00522.2490.0170.0170.0000.0000.0000.000
159A161ARG10.8640.93117.0340.0690.0690.0000.0000.0000.000
160A162GLY00.0030.01517.4660.0150.0150.0000.0000.0000.000
161A163VAL0-0.033-0.01114.2010.0020.0020.0000.0000.0000.000
162A164LEU0-0.028-0.00516.881-0.039-0.0390.0000.0000.0000.000
163A165LYS10.8960.95315.9310.0960.0960.0000.0000.0000.000
164A166ARG10.8550.91220.3870.0500.0500.0000.0000.0000.000
165A167VAL0-0.021-0.01621.9460.0070.0070.0000.0000.0000.000
166A168ASP-1-0.836-0.91224.997-0.083-0.0830.0000.0000.0000.000
167A169GLY00.017-0.01728.199-0.007-0.0070.0000.0000.0000.000
168A170LEU0-0.048-0.01829.117-0.004-0.0040.0000.0000.0000.000
169A171GLY00.0390.03031.5810.0020.0020.0000.0000.0000.000
170A172THR0-0.058-0.04131.457-0.009-0.0090.0000.0000.0000.000
171A173PRO00.026-0.00828.231-0.004-0.0040.0000.0000.0000.000
172A174ASP-1-0.777-0.88226.776-0.150-0.1500.0000.0000.0000.000
173A175GLU-1-0.868-0.91226.541-0.086-0.0860.0000.0000.0000.000
174A176VAL0-0.009-0.00325.239-0.001-0.0010.0000.0000.0000.000
175A177TYR0-0.070-0.06819.107-0.016-0.0160.0000.0000.0000.000
176A178ALA00.0040.00221.943-0.011-0.0110.0000.0000.0000.000
177A179ARG10.8760.92422.5180.0940.0940.0000.0000.0000.000
178A180ILE00.0060.01318.6980.0010.0010.0000.0000.0000.000
179A181ARG10.8970.95616.8580.2070.2070.0000.0000.0000.000
180A182ALA0-0.0050.00217.6310.0070.0070.0000.0000.0000.000
181A183ALA0-0.030-0.01018.8850.0170.0170.0000.0000.0000.000
182A184LEU0-0.065-0.04414.0060.0090.0090.0000.0000.0000.000
183A185GLY0-0.0040.01613.8630.0110.0110.0000.0000.0000.000
184A186ILE0-0.031-0.01311.2680.0220.0220.0000.0000.0000.000