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: 4J2LN

Calculation Name: 2CO6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CO6

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZRK3

Base Structure: X-ray

Registration Date: 2023-09-24

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2224995.474005
FMO2-HF: Nuclear repulsion 2143174.266652
FMO2-HF: Total energy -81821.207352
FMO2-MP2: Total energy -82060.81057


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(B:5:LEU)


Summations of interaction energy for fragment #1(B:5:LEU)
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.
-3.778-0.9533.385-2.179-4.031-0.005
Interaction energy analysis for fragmet #1(B:5:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.004
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].
3B7SER0-0.009-0.0092.005-1.6950.2162.716-1.806-2.8210.002
4B8ALA00.0310.0182.836-1.500-0.6880.670-0.372-1.111-0.007
5B9THR00.002-0.0115.3540.2250.327-0.001-0.001-0.0990.000
6B10LYS10.8390.9296.7980.7540.7540.0000.0000.0000.000
7B11LEU00.0000.00710.4180.1050.1050.0000.0000.0000.000
8B12PHE0-0.035-0.03112.834-0.002-0.0020.0000.0000.0000.000
9B13SER0-0.004-0.00416.3000.0360.0360.0000.0000.0000.000
10B14VAL00.0320.00819.787-0.007-0.0070.0000.0000.0000.000
11B15LYS10.9490.99423.5720.1360.1360.0000.0000.0000.000
12B16LEU00.0270.00926.604-0.002-0.0020.0000.0000.0000.000
13B17GLY0-0.063-0.03830.0370.0010.0010.0000.0000.0000.000
14B18ALA0-0.018-0.00332.7900.0070.0070.0000.0000.0000.000
15B19THR00.0350.02331.614-0.004-0.0040.0000.0000.0000.000
16B20ARG10.7820.88633.7340.0670.0670.0000.0000.0000.000
17B21VAL0-0.006-0.00136.800-0.001-0.0010.0000.0000.0000.000
18B22ILE00.0150.01739.4390.0010.0010.0000.0000.0000.000
19B23TYR0-0.036-0.03543.055-0.001-0.0010.0000.0000.0000.000
20B24HIS00.0780.03444.8760.0030.0030.0000.0000.0000.000
21B25ALA00.0090.01948.389-0.001-0.0010.0000.0000.0000.000
22B26GLY00.0180.00950.6070.0000.0000.0000.0000.0000.000
23B27THR0-0.071-0.04848.5620.0000.0000.0000.0000.0000.000
24B28ALA00.0200.01549.786-0.002-0.0020.0000.0000.0000.000
25B29GLY00.0200.03645.893-0.002-0.0020.0000.0000.0000.000
26B30ALA00.0350.02342.2150.0010.0010.0000.0000.0000.000
27B31THR0-0.026-0.02939.695-0.001-0.0010.0000.0000.0000.000
28B32LEU00.0070.00232.9530.0020.0020.0000.0000.0000.000
29B33SER0-0.061-0.02233.826-0.005-0.0050.0000.0000.0000.000
30B34VAL00.0500.02128.760-0.001-0.0010.0000.0000.0000.000
31B35SER0-0.037-0.04927.5910.0080.0080.0000.0000.0000.000
32B36ASN00.0140.00122.893-0.018-0.0180.0000.0000.0000.000
33B37PRO0-0.032-0.00520.9970.0060.0060.0000.0000.0000.000
34B38GLN00.0140.01718.027-0.031-0.0310.0000.0000.0000.000
35B39ASN00.0220.01419.6410.0500.0500.0000.0000.0000.000
36B40TYR00.038-0.00315.739-0.007-0.0070.0000.0000.0000.000
37B41PRO0-0.027-0.00921.3810.0070.0070.0000.0000.0000.000
38B42ILE0-0.0110.00321.189-0.028-0.0280.0000.0000.0000.000
39B43LEU00.0050.00423.7020.0250.0250.0000.0000.0000.000
40B44VAL0-0.006-0.01025.294-0.008-0.0080.0000.0000.0000.000
41B45GLN00.0360.01627.9790.0070.0070.0000.0000.0000.000
42B46SER0-0.0140.00730.100-0.003-0.0030.0000.0000.0000.000
43B47SER0-0.053-0.02832.3320.0070.0070.0000.0000.0000.000
44B48VAL00.025-0.00434.5420.0000.0000.0000.0000.0000.000
45B49LYS10.8870.97232.9950.1080.1080.0000.0000.0000.000
46B50ALA00.1030.04237.5420.0020.0020.0000.0000.0000.000
47B51ALA00.0310.00338.475-0.003-0.0030.0000.0000.0000.000
48B52ASP-1-0.751-0.85038.312-0.072-0.0720.0000.0000.0000.000
49B53LYS10.8740.95232.1790.0770.0770.0000.0000.0000.000
50B54SER0-0.055-0.02934.184-0.008-0.0080.0000.0000.0000.000
51B55SER0-0.010-0.03336.353-0.003-0.0030.0000.0000.0000.000
52B56PRO0-0.042-0.02038.771-0.002-0.0020.0000.0000.0000.000
53B57ALA00.0070.01039.6940.0050.0050.0000.0000.0000.000
54B58PRO00.0030.00941.643-0.002-0.0020.0000.0000.0000.000
55B59PHE00.001-0.02041.5000.0020.0020.0000.0000.0000.000
56B60LEU00.0010.00739.938-0.004-0.0040.0000.0000.0000.000
57B61VAL0-0.023-0.01235.5650.0020.0020.0000.0000.0000.000
58B62MET0-0.0050.02438.426-0.003-0.0030.0000.0000.0000.000
59B63PRO00.0390.00434.5450.0030.0030.0000.0000.0000.000
60B64PRO00.0310.00835.144-0.004-0.0040.0000.0000.0000.000
61B65LEU0-0.020-0.02229.956-0.006-0.0060.0000.0000.0000.000
62B66PHE0-0.017-0.01431.1380.0060.0060.0000.0000.0000.000
63B67ARG10.8910.93525.2650.2230.2230.0000.0000.0000.000
64B68LEU0-0.0260.01127.0140.0130.0130.0000.0000.0000.000
65B69GLU-1-0.741-0.88726.390-0.232-0.2320.0000.0000.0000.000
66B70ALA0-0.0160.00924.146-0.001-0.0010.0000.0000.0000.000
67B71ASN0-0.032-0.02924.0380.0100.0100.0000.0000.0000.000
68B72GLN00.0100.03826.0070.0110.0110.0000.0000.0000.000
69B73GLN00.0320.00728.613-0.002-0.0020.0000.0000.0000.000
70B74SER0-0.020-0.00631.3750.0060.0060.0000.0000.0000.000
71B75GLN00.0330.00934.0730.0030.0030.0000.0000.0000.000
72B76LEU00.0160.02432.4150.0010.0010.0000.0000.0000.000
73B77ARG10.8570.92736.7840.0810.0810.0000.0000.0000.000
74B78ILE00.016-0.00237.092-0.004-0.0040.0000.0000.0000.000
75B79VAL0-0.009-0.01041.0080.0040.0040.0000.0000.0000.000
76B80ARG10.8950.95443.9850.0510.0510.0000.0000.0000.000
77B81THR0-0.015-0.02044.6420.0020.0020.0000.0000.0000.000
78B82GLY00.0260.01247.2530.0020.0020.0000.0000.0000.000
79B83GLY0-0.0020.00349.085-0.001-0.0010.0000.0000.0000.000
80B84ASP-1-0.916-0.95750.214-0.041-0.0410.0000.0000.0000.000
81B85MET0-0.050-0.02446.801-0.002-0.0020.0000.0000.0000.000
82B86PRO00.0070.02750.5460.0010.0010.0000.0000.0000.000
83B87THR00.030-0.01353.029-0.001-0.0010.0000.0000.0000.000
84B88ASP-1-0.817-0.87755.201-0.034-0.0340.0000.0000.0000.000
85B89ARG10.8370.87750.8960.0350.0350.0000.0000.0000.000
86B90GLU-1-0.742-0.85746.282-0.049-0.0490.0000.0000.0000.000
87B91THR0-0.083-0.05545.4550.0010.0010.0000.0000.0000.000
88B92LEU0-0.0080.01538.583-0.002-0.0020.0000.0000.0000.000
89B93GLN0-0.039-0.03639.6780.0020.0020.0000.0000.0000.000
90B94TRP0-0.049-0.03233.3620.0000.0000.0000.0000.0000.000
91B95VAL00.000-0.00134.304-0.002-0.0020.0000.0000.0000.000
92B96CYS0-0.128-0.04927.4840.0010.0010.0000.0000.0000.000
93B97ILE00.0650.01628.290-0.001-0.0010.0000.0000.0000.000
94B98LYS10.8920.95725.2110.1660.1660.0000.0000.0000.000
95B99ALA00.0050.00423.0770.0040.0040.0000.0000.0000.000
96B100VAL00.015-0.00521.269-0.007-0.0070.0000.0000.0000.000
97B101PRO0-0.0150.02217.1030.0200.0200.0000.0000.0000.000
98B102PRO00.000-0.00918.5290.0190.0190.0000.0000.0000.000
99B103GLU-1-0.859-0.92016.570-0.464-0.4640.0000.0000.0000.000
100B104ASN0-0.083-0.05611.3850.0730.0730.0000.0000.0000.000
101B105GLU-1-0.931-0.96514.374-0.488-0.4880.0000.0000.0000.000
102B106PRO0-0.013-0.00112.122-0.110-0.1100.0000.0000.0000.000
103B107SER0-0.030-0.03011.874-0.096-0.0960.0000.0000.0000.000
104B108ASP-1-0.729-0.8538.092-1.644-1.6440.0000.0000.0000.000
105B109THR0-0.010-0.0128.0720.1490.1490.0000.0000.0000.000
106B110GLN0-0.050-0.0286.5470.4090.4090.0000.0000.0000.000
107B111ALA0-0.0180.0016.2920.2570.2570.0000.0000.0000.000
108B112LYS10.8180.9067.9250.6030.6030.0000.0000.0000.000
109B113GLY00.0560.03110.0370.1260.1260.0000.0000.0000.000
110B114ALA0-0.031-0.0089.871-0.117-0.1170.0000.0000.0000.000
111B115THR0-0.072-0.0426.2040.0680.0680.0000.0000.0000.000
112B116LEU0-0.0100.0016.0940.1590.1590.0000.0000.0000.000
113B117ASP-1-0.770-0.8466.802-1.256-1.2560.0000.0000.0000.000
114B118LEU0-0.032-0.0146.0520.1480.1480.0000.0000.0000.000
115B119ASN00.041-0.00210.116-0.052-0.0520.0000.0000.0000.000
116B120LEU0-0.029-0.00913.1340.0430.0430.0000.0000.0000.000
117B121SER0-0.032-0.02616.0820.0160.0160.0000.0000.0000.000
118B122ILE0-0.0110.00919.2020.0100.0100.0000.0000.0000.000
119B123ASN00.002-0.02621.8890.0120.0120.0000.0000.0000.000
120B124ALA00.0400.03525.6140.0070.0070.0000.0000.0000.000
121B126ASP-1-0.728-0.87630.759-0.092-0.0920.0000.0000.0000.000
122B127LYS10.8140.92033.2950.0630.0630.0000.0000.0000.000
123B128LEU00.0000.01236.7400.0010.0010.0000.0000.0000.000
124B129ILE0-0.011-0.01239.3800.0010.0010.0000.0000.0000.000
125B130PHE00.0000.00442.6610.0000.0000.0000.0000.0000.000
126B131ARG10.7810.84345.6400.0480.0480.0000.0000.0000.000
127B132PRO00.0100.01148.853-0.001-0.0010.0000.0000.0000.000
128B133ASP-1-0.846-0.91852.391-0.037-0.0370.0000.0000.0000.000
129B134ALA00.010-0.00154.7390.0010.0010.0000.0000.0000.000
130B135VAL0-0.054-0.00651.1160.0020.0020.0000.0000.0000.000
131B136LYS10.8150.89752.6620.0340.0340.0000.0000.0000.000
132B137GLY00.0290.02752.6360.0010.0010.0000.0000.0000.000
133B138THR0-0.050-0.05747.342-0.003-0.0030.0000.0000.0000.000
134B139PRO00.025-0.00444.7020.0020.0020.0000.0000.0000.000
135B140GLU-1-0.866-0.95245.934-0.033-0.0330.0000.0000.0000.000
136B141ASP-1-0.851-0.89247.830-0.030-0.0300.0000.0000.0000.000
137B142VAL0-0.036-0.02350.7520.0020.0020.0000.0000.0000.000
138B143ALA00.0640.01647.1810.0010.0010.0000.0000.0000.000
139B144GLY00.0050.00449.1720.0010.0010.0000.0000.0000.000
140B145ASN0-0.080-0.04351.6060.0030.0030.0000.0000.0000.000
141B146LEU0-0.056-0.01246.1140.0000.0000.0000.0000.0000.000
142B147ARG10.8950.94550.6120.0220.0220.0000.0000.0000.000
143B148TRP00.0240.00244.454-0.002-0.0020.0000.0000.0000.000
144B149VAL00.0070.00650.5950.0020.0020.0000.0000.0000.000
145B150GLU-1-0.778-0.87349.031-0.007-0.0070.0000.0000.0000.000
146B151THR0-0.039-0.03449.8770.0000.0000.0000.0000.0000.000
147B152GLY00.0440.03549.596-0.001-0.0010.0000.0000.0000.000
148B153ASN0-0.007-0.00144.295-0.002-0.0020.0000.0000.0000.000
149B154LYS10.8620.91342.2790.0140.0140.0000.0000.0000.000
150B155LEU00.0230.01045.4450.0020.0020.0000.0000.0000.000
151B156LYS10.7900.90446.0220.0200.0200.0000.0000.0000.000
152B157VAL00.0000.00144.7970.0010.0010.0000.0000.0000.000
153B158GLU-1-0.775-0.86848.119-0.021-0.0210.0000.0000.0000.000
154B159ASN0-0.008-0.00948.0060.0020.0020.0000.0000.0000.000
155B160PRO0-0.036-0.00350.489-0.001-0.0010.0000.0000.0000.000
156B161THR0-0.014-0.02850.4870.0000.0000.0000.0000.0000.000
157B162PRO00.0550.02651.576-0.001-0.0010.0000.0000.0000.000
158B163PHE00.0390.01347.409-0.002-0.0020.0000.0000.0000.000
159B164TYR0-0.006-0.01642.9630.0000.0000.0000.0000.0000.000
160B165MET00.0080.03744.154-0.001-0.0010.0000.0000.0000.000
161B166ASN0-0.032-0.03039.349-0.003-0.0030.0000.0000.0000.000
162B167LEU00.0120.01239.8740.0000.0000.0000.0000.0000.000
163B168ALA0-0.037-0.00437.054-0.004-0.0040.0000.0000.0000.000
164B169SER0-0.009-0.01236.5520.0000.0000.0000.0000.0000.000
165B170VAL00.0370.00838.8580.0000.0000.0000.0000.0000.000
166B171THR0-0.058-0.01140.0710.0010.0010.0000.0000.0000.000
167B172VAL00.0300.00342.3550.0000.0000.0000.0000.0000.000
168B173GLY00.0160.00444.4320.0020.0020.0000.0000.0000.000
169B174GLY00.0030.00643.1950.0020.0020.0000.0000.0000.000
170B175LYS10.8380.91739.634-0.004-0.0040.0000.0000.0000.000
171B176PRO00.0350.00936.235-0.002-0.0020.0000.0000.0000.000
172B177ILE0-0.036-0.00938.0200.0020.0020.0000.0000.0000.000
173B178THR0-0.015-0.01132.971-0.003-0.0030.0000.0000.0000.000
174B179GLY0-0.005-0.00933.7190.0010.0010.0000.0000.0000.000
175B180LEU0-0.0110.00534.8760.0000.0000.0000.0000.0000.000
176B181GLU-1-0.827-0.90636.012-0.049-0.0490.0000.0000.0000.000
177B182TYR00.0220.00437.1940.0000.0000.0000.0000.0000.000
178B183VAL00.0320.01240.7920.0000.0000.0000.0000.0000.000
179B184PRO0-0.024-0.01844.145-0.001-0.0010.0000.0000.0000.000
180B185PRO0-0.0120.00946.0290.0020.0020.0000.0000.0000.000
181B186PHE0-0.060-0.02349.3980.0000.0000.0000.0000.0000.000
182B187ALA0-0.0020.01848.4490.0000.0000.0000.0000.0000.000
183B188ASP-1-0.788-0.90148.811-0.024-0.0240.0000.0000.0000.000
184B189LYS10.7690.86940.5970.0380.0380.0000.0000.0000.000
185B190THR0-0.002-0.00444.1350.0020.0020.0000.0000.0000.000
186B191LEU00.0240.02840.676-0.002-0.0020.0000.0000.0000.000
187B192ASN00.0200.00038.3150.0040.0040.0000.0000.0000.000
188B193MET00.0350.03041.6090.0000.0000.0000.0000.0000.000
189B194PRO00.0260.03239.8070.0010.0010.0000.0000.0000.000
190B195GLY0-0.001-0.01140.6540.0030.0030.0000.0000.0000.000
191B196SER0-0.020-0.00242.3080.0020.0020.0000.0000.0000.000
192B197ALA00.020-0.01244.7980.0000.0000.0000.0000.0000.000
193B198HIS10.7710.85347.4530.0040.0040.0000.0000.0000.000
194B199GLY00.0440.04048.8040.0000.0000.0000.0000.0000.000
195B200ASP-1-0.827-0.90549.425-0.006-0.0060.0000.0000.0000.000
196B201ILE0-0.054-0.04146.3070.0000.0000.0000.0000.0000.000
197B202GLU-1-0.794-0.86643.381-0.016-0.0160.0000.0000.0000.000
198B203TRP0-0.043-0.03343.3400.0000.0000.0000.0000.0000.000
199B204ARG10.8980.93840.4320.0210.0210.0000.0000.0000.000
200B205VAL00.006-0.00341.347-0.001-0.0010.0000.0000.0000.000
201B206ILE00.0030.00635.1920.0000.0000.0000.0000.0000.000
202B207THR00.0570.03339.414-0.003-0.0030.0000.0000.0000.000
203B208ASP-1-0.739-0.85640.560-0.050-0.0500.0000.0000.0000.000
204B209PHE0-0.030-0.02440.529-0.004-0.0040.0000.0000.0000.000
205B210GLY0-0.033-0.01236.810-0.003-0.0030.0000.0000.0000.000
206B211GLY00.0100.01436.193-0.002-0.0020.0000.0000.0000.000
207B212GLU-1-0.950-0.99336.954-0.034-0.0340.0000.0000.0000.000
208B213SER00.004-0.00539.7710.0000.0000.0000.0000.0000.000
209B214HIS0-0.0190.00743.1050.0010.0010.0000.0000.0000.000
210B215PRO0-0.061-0.01344.753-0.001-0.0010.0000.0000.0000.000
211B216PHE0-0.019-0.00445.9720.0010.0010.0000.0000.0000.000
212B217HIS00.0210.00047.5410.0010.0010.0000.0000.0000.000
213B218TYR0-0.015-0.01750.426-0.001-0.0010.0000.0000.0000.000
214B219VAL00.0110.00751.5300.0010.0010.0000.0000.0000.000
215B220LEU0-0.062-0.01350.3530.0000.0000.0000.0000.0000.000