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: R8Q48

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1870341.331384
FMO2-HF: Nuclear repulsion 1799845.98278
FMO2-HF: Total energy -70495.348604
FMO2-MP2: Total energy -70706.147985


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.
-8.029-2.7572.656-4.07-3.857-0.015
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 : -0.009 / q_NPA : -0.001
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].
3A5GLN0-0.098-0.0473.750-0.9912.198-0.033-1.694-1.4620.009
4A6ALA00.0440.0196.482-0.053-0.0530.0000.0000.0000.000
5A7VAL0-0.019-0.0069.9830.1700.1700.0000.0000.0000.000
6A8ILE00.0060.01913.373-0.027-0.0270.0000.0000.0000.000
7A9PHE00.0150.00416.5770.0480.0480.0000.0000.0000.000
8A10LEU00.005-0.01120.0050.0010.0010.0000.0000.0000.000
9A11GLY00.0310.00023.2110.0070.0070.0000.0000.0000.000
10A12PRO00.0200.02926.673-0.008-0.0080.0000.0000.0000.000
11A13PRO00.016-0.00330.141-0.007-0.0070.0000.0000.0000.000
12A14GLY00.0490.02032.1140.0080.0080.0000.0000.0000.000
13A15ALA00.0130.00728.8380.0050.0050.0000.0000.0000.000
14A16GLY0-0.0060.00228.850-0.002-0.0020.0000.0000.0000.000
15A17LYS10.8760.93323.4780.2160.2160.0000.0000.0000.000
16A18GLY00.0330.02323.534-0.019-0.0190.0000.0000.0000.000
17A19THR00.005-0.00623.831-0.019-0.0190.0000.0000.0000.000
18A20GLN00.011-0.00122.710-0.021-0.0210.0000.0000.0000.000
19A21ALA0-0.0110.00719.685-0.019-0.0190.0000.0000.0000.000
20A22SER0-0.011-0.02919.249-0.048-0.0480.0000.0000.0000.000
21A23ARG10.8170.90720.6590.1670.1670.0000.0000.0000.000
22A24LEU00.0190.01115.459-0.004-0.0040.0000.0000.0000.000
23A25ALA0-0.039-0.01615.809-0.037-0.0370.0000.0000.0000.000
24A26GLN0-0.016-0.02116.141-0.033-0.0330.0000.0000.0000.000
25A27GLU-1-0.806-0.86918.109-0.228-0.2280.0000.0000.0000.000
26A28LEU0-0.043-0.02312.9630.0160.0160.0000.0000.0000.000
27A29GLY0-0.0120.00812.212-0.076-0.0760.0000.0000.0000.000
28A30PHE0-0.029-0.01610.150-0.170-0.1700.0000.0000.0000.000
29A31LYS10.8340.90312.5590.9900.9900.0000.0000.0000.000
30A32LYS10.8400.90814.5830.3030.3030.0000.0000.0000.000
31A33LEU00.0200.01813.7970.0420.0420.0000.0000.0000.000
32A34SER0-0.035-0.04617.8800.0480.0480.0000.0000.0000.000
33A35THR00.0550.01319.7720.0050.0050.0000.0000.0000.000
34A36GLY0-0.024-0.00821.8150.0140.0140.0000.0000.0000.000
35A37ASP-1-0.795-0.87123.541-0.257-0.2570.0000.0000.0000.000
36A38ILE00.0380.03518.3830.0200.0200.0000.0000.0000.000
37A39LEU00.0190.01422.6300.0150.0150.0000.0000.0000.000
38A40ARG10.8700.91325.1510.2380.2380.0000.0000.0000.000
39A41ASP-1-0.836-0.89524.592-0.263-0.2630.0000.0000.0000.000
40A42HIS00.0820.04720.9240.0400.0400.0000.0000.0000.000
41A43VAL0-0.015-0.01726.3050.0150.0150.0000.0000.0000.000
42A44ALA0-0.068-0.01929.6680.0130.0130.0000.0000.0000.000
43A45ARG10.7810.86724.0960.2870.2870.0000.0000.0000.000
44A46GLY00.0270.03430.1270.0050.0050.0000.0000.0000.000
45A47THR0-0.051-0.03525.4480.0110.0110.0000.0000.0000.000
46A48PRO00.032-0.00126.3080.0070.0070.0000.0000.0000.000
47A49LEU00.0120.01321.9810.0140.0140.0000.0000.0000.000
48A50GLY00.0480.01426.0740.0060.0060.0000.0000.0000.000
49A51GLU-1-0.794-0.89628.442-0.128-0.1280.0000.0000.0000.000
50A52ARG10.8860.95527.7460.1500.1500.0000.0000.0000.000
51A53VAL0-0.001-0.00926.2660.0070.0070.0000.0000.0000.000
52A54ARG10.8200.90629.6300.1360.1360.0000.0000.0000.000
53A55PRO00.014-0.00432.7250.0050.0050.0000.0000.0000.000
54A56ILE0-0.068-0.03029.2740.0060.0060.0000.0000.0000.000
55A57MET00.001-0.00230.665-0.001-0.0010.0000.0000.0000.000
56A58GLU-1-0.877-0.93433.667-0.109-0.1090.0000.0000.0000.000
57A59ARG10.7450.86234.4200.1100.1100.0000.0000.0000.000
58A60GLY0-0.0080.00136.8230.0050.0050.0000.0000.0000.000
59A61ASP-1-0.853-0.88933.368-0.103-0.1030.0000.0000.0000.000
60A62LEU0-0.051-0.03229.987-0.008-0.0080.0000.0000.0000.000
61A63VAL0-0.018-0.01525.4180.0040.0040.0000.0000.0000.000
62A64PRO00.0230.02026.213-0.004-0.0040.0000.0000.0000.000
63A65ASP-1-0.779-0.90822.513-0.208-0.2080.0000.0000.0000.000
64A66ASP-1-0.917-0.96221.426-0.200-0.2000.0000.0000.0000.000
65A67LEU00.0320.02220.687-0.025-0.0250.0000.0000.0000.000
66A68ILE0-0.047-0.02419.973-0.036-0.0360.0000.0000.0000.000
67A69LEU0-0.019-0.02715.774-0.047-0.0470.0000.0000.0000.000
68A70GLU-1-0.803-0.85316.091-0.416-0.4160.0000.0000.0000.000
69A71LEU0-0.019-0.01316.330-0.052-0.0520.0000.0000.0000.000
70A72ILE0-0.024-0.01413.309-0.057-0.0570.0000.0000.0000.000
71A73ARG10.8210.88211.3860.2460.2460.0000.0000.0000.000
72A74GLU-1-0.975-0.99311.748-0.531-0.5310.0000.0000.0000.000
73A75GLU-1-0.875-0.92813.639-0.701-0.7010.0000.0000.0000.000
74A76LEU0-0.060-0.0128.374-0.057-0.0570.0000.0000.0000.000
75A77ALA0-0.001-0.0088.4110.0720.0720.0000.0000.0000.000
76A78GLU-1-0.916-0.9495.045-2.383-2.3830.0000.0000.0000.000
77A79ARG10.8900.9566.1080.9650.9650.0000.0000.0000.000
78A80VAL00.0200.0338.6790.2540.2540.0000.0000.0000.000
79A81ILE00.002-0.00711.6660.0650.0650.0000.0000.0000.000
80A82PHE00.0330.01911.9890.0230.0230.0000.0000.0000.000
81A83ASP-1-0.756-0.87617.011-0.238-0.2380.0000.0000.0000.000
82A84GLY0-0.012-0.00120.7130.0060.0060.0000.0000.0000.000
83A85PHE0-0.021-0.00417.0390.0240.0240.0000.0000.0000.000
84A86PRO00.0430.02717.913-0.030-0.0300.0000.0000.0000.000
85A87ARG10.8670.92420.6410.2590.2590.0000.0000.0000.000
86A88THR00.0250.01523.6140.0160.0160.0000.0000.0000.000
87A89LEU00.0890.03222.825-0.016-0.0160.0000.0000.0000.000
88A90ALA00.0340.02922.148-0.003-0.0030.0000.0000.0000.000
89A91GLN0-0.013-0.03020.544-0.019-0.0190.0000.0000.0000.000
90A92ALA0-0.013-0.00518.442-0.035-0.0350.0000.0000.0000.000
91A93GLU-1-0.857-0.91717.275-0.097-0.0970.0000.0000.0000.000
92A94ALA0-0.063-0.03516.9330.0000.0000.0000.0000.0000.000
93A95LEU00.0120.00513.145-0.029-0.0290.0000.0000.0000.000
94A96ASP-1-0.789-0.88212.779-0.268-0.2680.0000.0000.0000.000
95A97ARG10.8510.91412.0500.1230.1230.0000.0000.0000.000
96A98LEU00.0570.04311.0780.0210.0210.0000.0000.0000.000
97A99LEU0-0.027-0.0158.430-0.152-0.1520.0000.0000.0000.000
98A100SER0-0.015-0.0037.092-0.099-0.0990.0000.0000.0000.000
99A101GLU-1-0.999-1.0017.843-0.047-0.0470.0000.0000.0000.000
100A102THR0-0.054-0.0346.1730.0350.0350.0000.0000.0000.000
101A103GLY0-0.0170.0113.440-1.286-0.9950.010-0.095-0.2060.000
102A104THR0-0.038-0.0272.354-4.214-2.5452.680-2.276-2.073-0.024
103A105ARG10.9430.9684.8270.5030.626-0.001-0.005-0.1160.000
104A106LEU00.0180.0096.610-0.226-0.2260.0000.0000.0000.000
105A107LEU0-0.061-0.0427.8320.1680.1680.0000.0000.0000.000
106A108GLY00.009-0.00511.0010.0900.0900.0000.0000.0000.000
107A109VAL0-0.0220.00214.592-0.065-0.0650.0000.0000.0000.000
108A110VAL00.0100.00017.4770.0350.0350.0000.0000.0000.000
109A111LEU00.0010.00719.881-0.013-0.0130.0000.0000.0000.000
110A112VAL0-0.041-0.02423.5000.0120.0120.0000.0000.0000.000
111A113GLU-1-0.855-0.91725.947-0.080-0.0800.0000.0000.0000.000
112A114VAL0-0.032-0.02629.2660.0000.0000.0000.0000.0000.000
113A115PRO00.0600.03932.6340.0000.0000.0000.0000.0000.000
114A116GLU-1-0.807-0.90036.172-0.070-0.0700.0000.0000.0000.000
115A117GLU-1-0.860-0.94037.754-0.059-0.0590.0000.0000.0000.000
116A118GLU-1-0.839-0.91037.011-0.068-0.0680.0000.0000.0000.000
117A119LEU0-0.068-0.02632.635-0.005-0.0050.0000.0000.0000.000
118A120VAL00.0420.01136.772-0.003-0.0030.0000.0000.0000.000
119A121ARG10.8600.91640.1760.0630.0630.0000.0000.0000.000
120A122ARG10.8350.92431.9830.1020.1020.0000.0000.0000.000
121A123ILE0-0.034-0.02035.797-0.003-0.0030.0000.0000.0000.000
122A124LEU00.0250.00939.095-0.001-0.0010.0000.0000.0000.000
123A125ARG11.0041.02240.8860.0800.0800.0000.0000.0000.000
124A126ARG10.7890.88136.7880.1100.1100.0000.0000.0000.000
125A127ALA0-0.007-0.00540.931-0.001-0.0010.0000.0000.0000.000
126A128GLU-1-0.910-0.95442.889-0.064-0.0640.0000.0000.0000.000
127A129LEU0-0.088-0.04842.4730.0010.0010.0000.0000.0000.000
128A130GLU-1-0.863-0.93438.804-0.111-0.1110.0000.0000.0000.000
129A131GLY00.0050.02043.731-0.001-0.0010.0000.0000.0000.000
130A132ARG10.7790.89439.4790.1010.1010.0000.0000.0000.000
131A133SER00.012-0.01045.0800.0040.0040.0000.0000.0000.000
132A134ASP-1-0.842-0.89841.408-0.091-0.0910.0000.0000.0000.000
133A135ASP-1-0.881-0.93140.712-0.094-0.0940.0000.0000.0000.000
134A136ASN00.0400.02543.8230.0030.0030.0000.0000.0000.000
135A137GLU-1-0.786-0.89144.652-0.057-0.0570.0000.0000.0000.000
136A138GLU-1-0.899-0.94244.167-0.059-0.0590.0000.0000.0000.000
137A139THR0-0.022-0.02942.978-0.002-0.0020.0000.0000.0000.000
138A140VAL0-0.021-0.00839.071-0.005-0.0050.0000.0000.0000.000
139A141ARG10.8580.88539.4320.0550.0550.0000.0000.0000.000
140A142ARG10.9781.00540.0630.0730.0730.0000.0000.0000.000
141A143ARG10.7510.85736.8670.0900.0900.0000.0000.0000.000
142A144LEU0-0.013-0.01134.588-0.007-0.0070.0000.0000.0000.000
143A145GLU-1-0.735-0.82935.228-0.068-0.0680.0000.0000.0000.000
144A146VAL0-0.0070.00034.590-0.002-0.0020.0000.0000.0000.000
145A147TYR0-0.029-0.02027.162-0.003-0.0030.0000.0000.0000.000
146A148ARG10.8190.88431.0590.0590.0590.0000.0000.0000.000
147A149GLU-1-0.922-0.95431.761-0.070-0.0700.0000.0000.0000.000
148A150LYS10.8880.93329.9630.1170.1170.0000.0000.0000.000
149A151THR0-0.053-0.03725.896-0.013-0.0130.0000.0000.0000.000
150A152GLU-1-0.877-0.92526.837-0.066-0.0660.0000.0000.0000.000
151A153PRO0-0.005-0.00927.0990.0030.0030.0000.0000.0000.000
152A154LEU0-0.008-0.00222.4080.0010.0010.0000.0000.0000.000
153A155VAL0-0.003-0.00222.817-0.004-0.0040.0000.0000.0000.000
154A156GLY00.0360.02724.0100.0070.0070.0000.0000.0000.000
155A157TYR0-0.087-0.07217.4060.0250.0250.0000.0000.0000.000
156A158TYR00.020-0.01216.2450.0060.0060.0000.0000.0000.000
157A159GLU-1-0.854-0.90819.892-0.040-0.0400.0000.0000.0000.000
158A160ALA0-0.025-0.00522.2470.0160.0160.0000.0000.0000.000
159A161ARG10.8370.92116.8750.0820.0820.0000.0000.0000.000
160A162GLY0-0.0010.01117.4510.0150.0150.0000.0000.0000.000
161A163VAL0-0.031-0.01214.1280.0010.0010.0000.0000.0000.000
162A164LEU0-0.026-0.00216.899-0.039-0.0390.0000.0000.0000.000
163A165LYS10.8550.92915.6070.1000.1000.0000.0000.0000.000
164A166ARG10.8310.89520.4390.0480.0480.0000.0000.0000.000
165A167VAL0-0.032-0.02521.9890.0070.0070.0000.0000.0000.000
166A168ASP-1-0.820-0.90225.070-0.080-0.0800.0000.0000.0000.000
167A169GLY00.021-0.01428.285-0.007-0.0070.0000.0000.0000.000
168A170LEU0-0.044-0.01929.206-0.004-0.0040.0000.0000.0000.000
169A171GLY00.0280.01631.6720.0020.0020.0000.0000.0000.000
170A172THR0-0.077-0.05832.057-0.008-0.0080.0000.0000.0000.000
171A173PRO00.042-0.00128.631-0.003-0.0030.0000.0000.0000.000
172A174ASP-1-0.802-0.89127.104-0.146-0.1460.0000.0000.0000.000
173A175GLU-1-0.817-0.87726.863-0.082-0.0820.0000.0000.0000.000
174A176VAL0-0.018-0.00625.441-0.001-0.0010.0000.0000.0000.000
175A177TYR0-0.067-0.07119.446-0.015-0.0150.0000.0000.0000.000
176A178ALA00.0060.00122.184-0.010-0.0100.0000.0000.0000.000
177A179ARG10.8520.92522.6100.0920.0920.0000.0000.0000.000
178A180ILE00.0100.01318.8220.0010.0010.0000.0000.0000.000
179A181ARG10.8920.95116.9610.2060.2060.0000.0000.0000.000
180A182ALA0-0.0070.00417.7170.0080.0080.0000.0000.0000.000
181A183ALA0-0.0050.00318.9520.0170.0170.0000.0000.0000.000
182A184LEU0-0.052-0.03514.0730.0130.0130.0000.0000.0000.000
183A185GLY0-0.0010.01713.9310.0130.0130.0000.0000.0000.000
184A186ILE0-0.030-0.00511.2540.0260.0260.0000.0000.0000.000