FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4LN7N

Calculation Name: 2C2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C2Y

Chain ID: A

ChEMBL ID:

UniProt ID: P9WG81

Base Structure: X-ray

Registration Date: 2023-09-26

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 280
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3455155.01266
FMO2-HF: Nuclear repulsion 3352827.464532
FMO2-HF: Total energy -102327.548128
FMO2-MP2: Total energy -102628.727146


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:2:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-7.027-2.7292.543-3.525-3.314-0.023
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / 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].
3A4ILE0-0.013-0.0163.8030.7032.130-0.007-0.804-0.6160.005
4A5MET0-0.018-0.0126.6640.3030.3030.0000.0000.0000.000
5A6LEU0-0.051-0.0218.6360.1650.1650.0000.0000.0000.000
6A7ASP-1-0.828-0.93712.164-0.138-0.1380.0000.0000.0000.000
7A8GLY00.0570.02114.2050.0280.0280.0000.0000.0000.000
8A9LYS10.8740.93216.8970.1300.1300.0000.0000.0000.000
9A10ALA00.0610.04617.1960.0210.0210.0000.0000.0000.000
10A11THR00.019-0.00517.5000.0020.0020.0000.0000.0000.000
11A12ARG10.8310.92120.1240.1380.1380.0000.0000.0000.000
12A13ASP-1-0.897-0.95122.375-0.095-0.0950.0000.0000.0000.000
13A14GLU-1-0.812-0.86521.889-0.233-0.2330.0000.0000.0000.000
14A15ILE0-0.0090.00124.0370.0100.0100.0000.0000.0000.000
15A16PHE0-0.031-0.02926.5610.0130.0130.0000.0000.0000.000
16A17GLY0-0.0070.00527.8340.0110.0110.0000.0000.0000.000
17A18ASP-1-0.843-0.92528.908-0.128-0.1280.0000.0000.0000.000
18A19LEU0-0.011-0.02329.8730.0080.0080.0000.0000.0000.000
19A20LYS10.9550.98832.4060.0640.0640.0000.0000.0000.000
20A21GLN0-0.050-0.01831.9060.0060.0060.0000.0000.0000.000
21A22ARG10.7930.86931.9940.1300.1300.0000.0000.0000.000
22A23VAL0-0.0120.00136.3910.0030.0030.0000.0000.0000.000
23A24ALA0-0.0020.00338.2950.0050.0050.0000.0000.0000.000
24A25ALA0-0.008-0.00739.7190.0040.0040.0000.0000.0000.000
25A26LEU0-0.055-0.02639.4930.0020.0020.0000.0000.0000.000
26A27ASP-1-0.898-0.92642.435-0.046-0.0460.0000.0000.0000.000
27A28ALA00.0020.00944.2080.0030.0030.0000.0000.0000.000
28A29ALA0-0.090-0.04445.7580.0020.0020.0000.0000.0000.000
29A30GLY0-0.0080.00047.5910.0010.0010.0000.0000.0000.000
30A31ARG10.8380.91944.3410.0690.0690.0000.0000.0000.000
31A32THR00.024-0.00442.472-0.004-0.0040.0000.0000.0000.000
32A33PRO00.000-0.01039.0820.0000.0000.0000.0000.0000.000
33A34GLY00.0520.00841.6720.0030.0030.0000.0000.0000.000
34A35LEU0-0.019-0.00935.920-0.004-0.0040.0000.0000.0000.000
35A36GLY00.0390.00239.9750.0050.0050.0000.0000.0000.000
36A37THR0-0.041-0.01937.960-0.004-0.0040.0000.0000.0000.000
37A38ILE00.0180.01340.7900.0040.0040.0000.0000.0000.000
38A39LEU0-0.010-0.00339.017-0.004-0.0040.0000.0000.0000.000
39A40VAL00.0010.00642.0940.0030.0030.0000.0000.0000.000
40A41GLY0-0.007-0.01343.075-0.001-0.0010.0000.0000.0000.000
41A42ASP-1-0.944-0.96442.370-0.024-0.0240.0000.0000.0000.000
42A43ASP-1-0.803-0.89236.447-0.039-0.0390.0000.0000.0000.000
43A44PRO00.022-0.00736.404-0.003-0.0030.0000.0000.0000.000
44A45GLY00.0080.00633.4750.0000.0000.0000.0000.0000.000
45A46SER0-0.011-0.01933.839-0.007-0.0070.0000.0000.0000.000
46A47GLN00.0050.00136.047-0.002-0.0020.0000.0000.0000.000
47A48ALA0-0.062-0.02932.5350.0000.0000.0000.0000.0000.000
48A49TYR0-0.030-0.01628.070-0.003-0.0030.0000.0000.0000.000
49A50VAL00.0320.01832.836-0.005-0.0050.0000.0000.0000.000
50A51ARG10.9590.97234.3810.0270.0270.0000.0000.0000.000
51A52GLY0-0.029-0.00831.4760.0010.0010.0000.0000.0000.000
52A53LYS10.9160.96231.6520.0860.0860.0000.0000.0000.000
53A54HIS00.0650.04633.355-0.003-0.0030.0000.0000.0000.000
54A55ALA0-0.0200.00132.9340.0020.0020.0000.0000.0000.000
55A56ASP-1-0.852-0.93629.375-0.083-0.0830.0000.0000.0000.000
56A57CYS0-0.0100.00032.205-0.004-0.0040.0000.0000.0000.000
57A58ALA00.0280.01635.3590.0010.0010.0000.0000.0000.000
58A59LYS10.8560.93729.3900.0590.0590.0000.0000.0000.000
59A60VAL0-0.047-0.02631.7750.0000.0000.0000.0000.0000.000
60A61GLY00.0130.01434.704-0.001-0.0010.0000.0000.0000.000
61A62ILE0-0.037-0.01235.3960.0000.0000.0000.0000.0000.000
62A63THR00.0410.01538.9720.0040.0040.0000.0000.0000.000
63A64SER0-0.033-0.04939.324-0.003-0.0030.0000.0000.0000.000
64A65ILE0-0.0110.00641.6960.0040.0040.0000.0000.0000.000
65A66ARG10.8600.92339.1150.0370.0370.0000.0000.0000.000
66A67ARG10.7940.87444.1180.0450.0450.0000.0000.0000.000
67A68ASP-1-0.834-0.91043.329-0.040-0.0400.0000.0000.0000.000
68A69LEU0-0.002-0.00745.8910.0020.0020.0000.0000.0000.000
69A70PRO00.0700.04146.8390.0000.0000.0000.0000.0000.000
70A71ALA00.042-0.01646.560-0.002-0.0020.0000.0000.0000.000
71A72ASP-1-0.968-0.97247.855-0.026-0.0260.0000.0000.0000.000
72A73ILE00.0050.02648.1940.0000.0000.0000.0000.0000.000
73A74SER00.0510.02551.685-0.001-0.0010.0000.0000.0000.000
74A75THR00.0550.00251.305-0.002-0.0020.0000.0000.0000.000
75A76ALA0-0.017-0.01352.190-0.002-0.0020.0000.0000.0000.000
76A77THR00.0660.04151.9390.0000.0000.0000.0000.0000.000
77A78LEU00.0250.01545.874-0.001-0.0010.0000.0000.0000.000
78A79ASN0-0.011-0.03049.421-0.004-0.0040.0000.0000.0000.000
79A80GLU-1-0.909-0.94051.357-0.036-0.0360.0000.0000.0000.000
80A81THR0-0.026-0.00847.5610.0000.0000.0000.0000.0000.000
81A82ILE0-0.029-0.01145.956-0.001-0.0010.0000.0000.0000.000
82A83ASP-1-0.810-0.88748.315-0.050-0.0500.0000.0000.0000.000
83A84GLU-1-0.763-0.85950.300-0.045-0.0450.0000.0000.0000.000
84A85LEU0-0.026-0.02644.603-0.001-0.0010.0000.0000.0000.000
85A86ASN00.0210.01146.888-0.005-0.0050.0000.0000.0000.000
86A87ALA0-0.028-0.00748.658-0.001-0.0010.0000.0000.0000.000
87A88ASN0-0.053-0.02248.4830.0010.0010.0000.0000.0000.000
88A89PRO0-0.022-0.02048.535-0.003-0.0030.0000.0000.0000.000
89A90ASP-1-0.845-0.90947.153-0.048-0.0480.0000.0000.0000.000
90A91CYS0-0.145-0.05444.332-0.004-0.0040.0000.0000.0000.000
91A92THR0-0.0520.01741.185-0.002-0.0020.0000.0000.0000.000
92A93GLY00.0610.01939.956-0.004-0.0040.0000.0000.0000.000
93A94TYR0-0.025-0.03739.9200.0040.0040.0000.0000.0000.000
94A95ILE0-0.0400.00735.239-0.004-0.0040.0000.0000.0000.000
95A96VAL00.0440.00838.5880.0060.0060.0000.0000.0000.000
96A97GLN0-0.044-0.02633.658-0.006-0.0060.0000.0000.0000.000
97A98LEU0-0.0050.02635.9160.0030.0030.0000.0000.0000.000
98A99PRO0-0.056-0.04235.866-0.001-0.0010.0000.0000.0000.000
99A100LEU00.0280.00238.4730.0030.0030.0000.0000.0000.000
100A101PRO0-0.028-0.01642.2000.0000.0000.0000.0000.0000.000
101A102LYS10.9750.96840.2690.0470.0470.0000.0000.0000.000
102A103HIS0-0.080-0.02345.744-0.001-0.0010.0000.0000.0000.000
103A104LEU0-0.041-0.01946.2830.0000.0000.0000.0000.0000.000
104A105ASP-1-0.871-0.94445.849-0.059-0.0590.0000.0000.0000.000
105A106GLU-1-0.818-0.93439.451-0.068-0.0680.0000.0000.0000.000
106A107ASN0-0.037-0.01741.659-0.006-0.0060.0000.0000.0000.000
107A108ALA00.0220.02443.167-0.002-0.0020.0000.0000.0000.000
108A109ALA0-0.011-0.00544.2040.0000.0000.0000.0000.0000.000
109A110LEU0-0.019-0.02338.858-0.001-0.0010.0000.0000.0000.000
110A111GLU-1-0.937-0.97642.542-0.077-0.0770.0000.0000.0000.000
111A112ARG10.7820.89444.7660.0500.0500.0000.0000.0000.000
112A113VAL0-0.028-0.00241.8150.0020.0020.0000.0000.0000.000
113A114ASP-1-0.831-0.92245.012-0.072-0.0720.0000.0000.0000.000
114A115PRO0-0.024-0.01142.156-0.003-0.0030.0000.0000.0000.000
115A116ALA0-0.038-0.02141.573-0.006-0.0060.0000.0000.0000.000
116A117LYS10.8330.93142.1030.0610.0610.0000.0000.0000.000
117A118ASP-1-0.763-0.87437.778-0.106-0.1060.0000.0000.0000.000
118A119ALA0-0.008-0.00236.080-0.007-0.0070.0000.0000.0000.000
119A120ASP-1-0.846-0.94533.412-0.115-0.1150.0000.0000.0000.000
120A121GLY0-0.051-0.01932.907-0.011-0.0110.0000.0000.0000.000
121A122LEU0-0.068-0.05331.744-0.009-0.0090.0000.0000.0000.000
122A123HIS00.0560.05535.631-0.002-0.0020.0000.0000.0000.000
123A124PRO00.0530.01738.781-0.007-0.0070.0000.0000.0000.000
124A125THR0-0.009-0.01540.270-0.002-0.0020.0000.0000.0000.000
125A126ASN0-0.059-0.05437.6200.0000.0000.0000.0000.0000.000
126A127LEU00.0020.00833.484-0.009-0.0090.0000.0000.0000.000
127A128GLY00.0140.00836.846-0.006-0.0060.0000.0000.0000.000
128A129ARG10.8990.94239.3580.0940.0940.0000.0000.0000.000
129A130LEU0-0.0190.01131.547-0.003-0.0030.0000.0000.0000.000
130A131VAL0-0.053-0.02835.696-0.006-0.0060.0000.0000.0000.000
131A132LEU0-0.045-0.02537.093-0.001-0.0010.0000.0000.0000.000
132A133GLY0-0.0140.01237.2290.0010.0010.0000.0000.0000.000
133A134THR0-0.072-0.04038.2820.0040.0040.0000.0000.0000.000
134A135PRO0-0.015-0.02237.729-0.003-0.0030.0000.0000.0000.000
135A136ALA00.0060.00137.2280.0080.0080.0000.0000.0000.000
136A137PRO0-0.036-0.00435.732-0.009-0.0090.0000.0000.0000.000
137A138LEU00.0410.02330.789-0.001-0.0010.0000.0000.0000.000
138A139PRO00.0170.02629.8060.0020.0020.0000.0000.0000.000
139A140CYS0-0.0010.00628.443-0.013-0.0130.0000.0000.0000.000
140A141THR0-0.013-0.01623.335-0.008-0.0080.0000.0000.0000.000
141A142PRO0-0.008-0.01023.806-0.026-0.0260.0000.0000.0000.000
142A143ARG10.8420.91324.2470.1510.1510.0000.0000.0000.000
143A144GLY00.0230.00523.385-0.012-0.0120.0000.0000.0000.000
144A145ILE0-0.025-0.01519.075-0.029-0.0290.0000.0000.0000.000
145A146VAL00.0080.00319.610-0.047-0.0470.0000.0000.0000.000
146A147HIS0-0.0010.00721.151-0.023-0.0230.0000.0000.0000.000
147A148LEU00.003-0.00115.604-0.006-0.0060.0000.0000.0000.000
148A149LEU0-0.003-0.00415.355-0.055-0.0550.0000.0000.0000.000
149A150ARG10.8960.93417.1020.2800.2800.0000.0000.0000.000
150A151ARG10.7600.87117.8820.3290.3290.0000.0000.0000.000
151A152TYR0-0.007-0.01912.1580.0350.0350.0000.0000.0000.000
152A153ASP-1-0.917-0.93814.781-0.554-0.5540.0000.0000.0000.000
153A154ILE0-0.056-0.01312.748-0.023-0.0230.0000.0000.0000.000
154A155SER0-0.018-0.01216.3090.0660.0660.0000.0000.0000.000
155A156ILE0-0.023-0.01919.211-0.019-0.0190.0000.0000.0000.000
156A157ALA00.007-0.00521.8330.0130.0130.0000.0000.0000.000
157A158GLY0-0.039-0.02223.276-0.018-0.0180.0000.0000.0000.000
158A159ALA0-0.0160.01419.707-0.007-0.0070.0000.0000.0000.000
159A160HIS0-0.002-0.01220.5310.0630.0630.0000.0000.0000.000
160A161VAL0-0.015-0.02019.522-0.050-0.0500.0000.0000.0000.000
161A162VAL00.0150.01519.2320.0500.0500.0000.0000.0000.000
162A163VAL0-0.016-0.00819.662-0.030-0.0300.0000.0000.0000.000
163A164ILE00.0020.00918.2420.0320.0320.0000.0000.0000.000
164A165GLY00.0430.01822.1520.0030.0030.0000.0000.0000.000
165A166ARG10.9040.94425.0590.1270.1270.0000.0000.0000.000
166A167GLY00.0340.01627.4250.0130.0130.0000.0000.0000.000
167A168VAL00.031-0.01629.101-0.011-0.0110.0000.0000.0000.000
168A169THR00.0500.03729.148-0.004-0.0040.0000.0000.0000.000
169A170VAL00.0210.00223.256-0.009-0.0090.0000.0000.0000.000
170A171GLY00.0430.02125.289-0.008-0.0080.0000.0000.0000.000
171A172ARG10.9180.95426.2480.1330.1330.0000.0000.0000.000
172A173PRO00.0240.02228.839-0.002-0.0020.0000.0000.0000.000
173A174LEU00.0310.01121.954-0.002-0.0020.0000.0000.0000.000
174A175GLY00.0250.01726.662-0.012-0.0120.0000.0000.0000.000
175A176LEU0-0.0210.00327.7910.0000.0000.0000.0000.0000.000
176A177LEU0-0.032-0.01026.2130.0030.0030.0000.0000.0000.000
177A178LEU00.016-0.01222.442-0.003-0.0030.0000.0000.0000.000
178A179THR0-0.0080.00726.522-0.003-0.0030.0000.0000.0000.000
179A180ARG10.8770.95229.4850.2160.2160.0000.0000.0000.000
180A181ARG10.9900.97030.2400.1450.1450.0000.0000.0000.000
181A182SER0-0.034-0.01830.227-0.001-0.0010.0000.0000.0000.000
182A183GLU-1-0.852-0.90125.855-0.251-0.2510.0000.0000.0000.000
183A184ASN0-0.026-0.01826.400-0.012-0.0120.0000.0000.0000.000
184A185ALA00.0330.03623.398-0.008-0.0080.0000.0000.0000.000
185A186THR0-0.012-0.00524.6230.0380.0380.0000.0000.0000.000
186A187VAL0-0.002-0.00524.032-0.027-0.0270.0000.0000.0000.000
187A188THR0-0.016-0.00323.8900.0270.0270.0000.0000.0000.000
188A189LEU0-0.008-0.01024.302-0.014-0.0140.0000.0000.0000.000
189A190CYS00.0020.01623.6230.0170.0170.0000.0000.0000.000
190A191HIS00.001-0.02225.7550.0070.0070.0000.0000.0000.000
191A192THR00.0620.01226.986-0.002-0.0020.0000.0000.0000.000
192A193GLY0-0.0260.00228.6370.0090.0090.0000.0000.0000.000
193A194THR0-0.045-0.01825.569-0.001-0.0010.0000.0000.0000.000
194A195ARG10.9890.99327.8200.1400.1400.0000.0000.0000.000
195A196ASP-1-0.915-0.97124.577-0.192-0.1920.0000.0000.0000.000
196A197LEU00.0550.02320.722-0.010-0.0100.0000.0000.0000.000
197A198PRO00.0610.02619.285-0.025-0.0250.0000.0000.0000.000
198A199ALA00.0000.01619.618-0.037-0.0370.0000.0000.0000.000
199A200LEU0-0.027-0.01022.021-0.010-0.0100.0000.0000.0000.000
200A201THR00.004-0.02116.767-0.002-0.0020.0000.0000.0000.000
201A202ARG10.8740.93616.3450.2400.2400.0000.0000.0000.000
202A203GLN0-0.100-0.06417.193-0.031-0.0310.0000.0000.0000.000
203A204ALA0-0.0330.00016.8410.0030.0030.0000.0000.0000.000
204A205ASP-1-0.813-0.89315.763-0.658-0.6580.0000.0000.0000.000
205A206ILE0-0.015-0.00114.673-0.116-0.1160.0000.0000.0000.000
206A207VAL00.0230.01114.5090.0980.0980.0000.0000.0000.000
207A208VAL0-0.019-0.00715.493-0.041-0.0410.0000.0000.0000.000
208A209ALA00.0070.01016.5420.0460.0460.0000.0000.0000.000
209A210ALA0-0.005-0.01318.2710.0090.0090.0000.0000.0000.000
210A211VAL0-0.069-0.04921.1690.0220.0220.0000.0000.0000.000
211A212GLY0-0.058-0.01622.0100.0200.0200.0000.0000.0000.000
212A213VAL0-0.062-0.03921.4480.0200.0200.0000.0000.0000.000
213A214ALA00.0230.01019.667-0.022-0.0220.0000.0000.0000.000
214A215HIS0-0.039-0.03315.3080.0200.0200.0000.0000.0000.000
215A216LEU0-0.0110.01016.745-0.002-0.0020.0000.0000.0000.000
216A217LEU0-0.043-0.02613.0110.0010.0010.0000.0000.0000.000
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