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: KGRR3

Calculation Name: 3CCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CCY

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W6R8

Base Structure: X-ray

Registration Date: 2023-09-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2113803.227243
FMO2-HF: Nuclear repulsion 2035284.765777
FMO2-HF: Total energy -78518.461466
FMO2-MP2: Total energy -78744.206134


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:9:TYR)


Summations of interaction energy for fragment #1(A:9:TYR)
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.
-9.946-0.3865.538-5.146-9.954-0.011
Interaction energy analysis for fragmet #1(A:9:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.002
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].
3A11ASN0-0.053-0.0172.310-7.303-1.1282.546-3.592-5.129-0.013
4A12ILE00.0240.0052.413-0.3780.9581.480-0.586-2.2300.002
5A13ARG10.8640.9103.6972.8273.3070.001-0.120-0.3620.000
6A14ASP-1-0.842-0.9285.641-1.818-1.8180.0000.0000.0000.000
7A15THR00.0000.0127.5600.3530.3530.0000.0000.0000.000
8A16ILE00.0080.0047.0360.3400.3400.0000.0000.0000.000
9A17ILE0-0.040-0.0099.8950.2150.2150.0000.0000.0000.000
10A18GLU-1-0.961-0.98011.848-0.892-0.8920.0000.0000.0000.000
11A19ARG10.8810.91112.8240.8130.8130.0000.0000.0000.000
12A20ALA0-0.052-0.03214.3000.1030.1030.0000.0000.0000.000
13A21ALA0-0.0060.00315.9640.0770.0770.0000.0000.0000.000
14A22ALA00.0340.02117.9190.0630.0630.0000.0000.0000.000
15A23MET0-0.059-0.02817.6470.0640.0640.0000.0000.0000.000
16A24PHE0-0.031-0.03717.1680.0370.0370.0000.0000.0000.000
17A25ALA00.0010.00921.9270.0290.0290.0000.0000.0000.000
18A26ARG10.7170.85122.3010.3810.3810.0000.0000.0000.000
19A27GLN00.0620.02922.9510.0030.0030.0000.0000.0000.000
20A28GLY00.0840.05524.9420.0190.0190.0000.0000.0000.000
21A29TYR00.0470.00519.068-0.003-0.0030.0000.0000.0000.000
22A30SER0-0.018-0.00923.0360.0000.0000.0000.0000.0000.000
23A31GLU-1-0.913-0.94325.554-0.117-0.1170.0000.0000.0000.000
24A32THR0-0.0330.00119.6090.0010.0010.0000.0000.0000.000
25A33SER0-0.051-0.06221.0650.0090.0090.0000.0000.0000.000
26A34ILE00.0640.00215.352-0.028-0.0280.0000.0000.0000.000
27A35GLY0-0.030-0.02016.4730.0030.0030.0000.0000.0000.000
28A36ASP-1-0.782-0.85318.205-0.135-0.1350.0000.0000.0000.000
29A37ILE00.0350.01913.234-0.016-0.0160.0000.0000.0000.000
30A38ALA0-0.044-0.02413.512-0.040-0.0400.0000.0000.0000.000
31A39ARG10.8980.94114.1670.1030.1030.0000.0000.0000.000
32A40ALA00.0380.03715.960-0.003-0.0030.0000.0000.0000.000
33A41CYS0-0.091-0.01710.958-0.109-0.1090.0000.0000.0000.000
34A42GLU-1-0.867-0.92612.457-0.343-0.3430.0000.0000.0000.000
35A43CYS0-0.0040.00410.8500.1720.1720.0000.0000.0000.000
36A44SER00.0060.00012.999-0.018-0.0180.0000.0000.0000.000
37A45LYS10.9750.95212.918-0.065-0.0650.0000.0000.0000.000
38A46SER00.0200.00213.187-0.051-0.0510.0000.0000.0000.000
39A47ARG10.9550.9675.337-1.445-1.4450.0000.0000.0000.000
40A48LEU00.0280.0248.0270.0270.0270.0000.0000.0000.000
41A49TYR0-0.009-0.0119.196-0.161-0.1610.0000.0000.0000.000
42A50HIS0-0.079-0.0184.601-0.0290.111-0.001-0.013-0.1260.000
43A51TYR0-0.037-0.0232.461-2.005-0.5761.512-0.835-2.1070.000
44A52PHE00.0150.0076.037-0.237-0.2370.0000.0000.0000.000
45A53ASP-1-0.834-0.9199.6130.0730.0730.0000.0000.0000.000
46A54SER0-0.070-0.06012.8310.0370.0370.0000.0000.0000.000
47A55LYS10.8260.90714.1610.1090.1090.0000.0000.0000.000
48A56GLU-1-0.822-0.90216.482-0.179-0.1790.0000.0000.0000.000
49A57ALA0-0.033-0.00912.538-0.033-0.0330.0000.0000.0000.000
50A58VAL00.0020.00911.518-0.085-0.0850.0000.0000.0000.000
51A59LEU00.0130.00813.257-0.075-0.0750.0000.0000.0000.000
52A60ARG10.9350.95613.6250.2670.2670.0000.0000.0000.000
53A61ASP-1-0.843-0.87910.366-1.252-1.2520.0000.0000.0000.000
54A62MET00.0060.00713.458-0.009-0.0090.0000.0000.0000.000
55A63LEU0-0.023-0.00514.9190.0220.0220.0000.0000.0000.000
56A64THR0-0.029-0.03715.4420.0520.0520.0000.0000.0000.000
57A65THR00.003-0.00312.1320.0310.0310.0000.0000.0000.000
58A66HIS0-0.0090.00815.570-0.015-0.0150.0000.0000.0000.000
59A67VAL0-0.002-0.01718.5980.0370.0370.0000.0000.0000.000
60A68ASP-1-0.809-0.88917.608-0.362-0.3620.0000.0000.0000.000
61A69SER0-0.024-0.00418.0010.0410.0410.0000.0000.0000.000
62A70LEU0-0.0040.00019.7900.0350.0350.0000.0000.0000.000
63A71LEU0-0.035-0.01422.9220.0310.0310.0000.0000.0000.000
64A72GLU-1-0.864-0.91521.348-0.269-0.2690.0000.0000.0000.000
65A73ARG10.8460.88221.7570.4420.4420.0000.0000.0000.000
66A74CYS0-0.050-0.02924.9560.0260.0260.0000.0000.0000.000
67A75ARG10.8350.90822.9350.2880.2880.0000.0000.0000.000
68A76GLN0-0.008-0.00124.1260.0020.0020.0000.0000.0000.000
69A77VAL0-0.0060.00428.4160.0140.0140.0000.0000.0000.000
70A78LEU0-0.073-0.03431.1030.0180.0180.0000.0000.0000.000
71A79TYR0-0.060-0.05228.6810.0110.0110.0000.0000.0000.000
72A80GLY00.0390.04033.0020.0040.0040.0000.0000.0000.000
73A81SER0-0.018-0.00934.1360.0140.0140.0000.0000.0000.000
74A82ASN00.0280.01237.5180.0040.0040.0000.0000.0000.000
75A83GLU-1-0.854-0.91540.689-0.123-0.1230.0000.0000.0000.000
76A84PRO00.0310.00540.526-0.008-0.0080.0000.0000.0000.000
77A85LYS10.8510.91940.5600.1140.1140.0000.0000.0000.000
78A86THR0-0.030-0.02538.270-0.006-0.0060.0000.0000.0000.000
79A87ARG10.8790.93535.9310.1340.1340.0000.0000.0000.000
80A88PHE00.0140.01235.647-0.012-0.0120.0000.0000.0000.000
81A89LEU00.0180.00836.400-0.009-0.0090.0000.0000.0000.000
82A90GLN00.012-0.01433.443-0.006-0.0060.0000.0000.0000.000
83A91ILE00.0140.01431.576-0.017-0.0170.0000.0000.0000.000
84A92VAL0-0.030-0.00931.736-0.014-0.0140.0000.0000.0000.000
85A93LYS10.7910.86132.6930.1900.1900.0000.0000.0000.000
86A94LEU00.0050.01925.797-0.017-0.0170.0000.0000.0000.000
87A95PHE0-0.012-0.01927.901-0.024-0.0240.0000.0000.0000.000
88A96LEU00.001-0.00528.381-0.016-0.0160.0000.0000.0000.000
89A97GLU-1-0.812-0.85824.921-0.407-0.4070.0000.0000.0000.000
90A98ILE00.0240.00522.927-0.031-0.0310.0000.0000.0000.000
91A99TYR0-0.059-0.01823.927-0.035-0.0350.0000.0000.0000.000
92A100ALA0-0.005-0.01925.447-0.010-0.0100.0000.0000.0000.000
93A101THR0-0.058-0.01721.266-0.025-0.0250.0000.0000.0000.000
94A102SER0-0.027-0.02020.115-0.069-0.0690.0000.0000.0000.000
95A103ARG10.9260.96721.3020.3120.3120.0000.0000.0000.000
96A104ASP-1-0.781-0.86919.984-0.415-0.4150.0000.0000.0000.000
97A105ARG11.0130.99713.2001.0041.0040.0000.0000.0000.000
98A106HIS00.0450.02520.1640.0060.0060.0000.0000.0000.000
99A107VAL0-0.015-0.01123.6620.0280.0280.0000.0000.0000.000
100A108VAL00.015-0.00419.6870.0270.0270.0000.0000.0000.000
101A109MET0-0.029-0.01022.1500.0160.0160.0000.0000.0000.000
102A110LEU0-0.085-0.04123.5350.0270.0270.0000.0000.0000.000
103A111THR0-0.040-0.02725.8190.0280.0280.0000.0000.0000.000
104A112CYS0-0.0150.00722.7540.0130.0130.0000.0000.0000.000
105A113LEU0-0.0120.00223.4030.0030.0030.0000.0000.0000.000
106A114ASP-1-0.900-0.95624.740-0.172-0.1720.0000.0000.0000.000
107A115ALA0-0.0020.01023.1140.0170.0170.0000.0000.0000.000
108A116LEU0-0.056-0.01719.0710.0050.0050.0000.0000.0000.000
109A117PRO00.0210.00021.5900.0140.0140.0000.0000.0000.000
110A118GLU-1-0.802-0.88824.545-0.113-0.1130.0000.0000.0000.000
111A119ASP-1-0.846-0.91522.339-0.129-0.1290.0000.0000.0000.000
112A120GLN00.033-0.00819.167-0.040-0.0400.0000.0000.0000.000
113A121ARG10.8700.94122.1920.1160.1160.0000.0000.0000.000
114A122LYS10.9100.93224.5870.0910.0910.0000.0000.0000.000
115A123ALA00.0000.01622.3640.0020.0020.0000.0000.0000.000
116A124LEU00.0080.00219.527-0.008-0.0080.0000.0000.0000.000
117A125ILE0-0.005-0.01123.5640.0000.0000.0000.0000.0000.000
118A126ALA0-0.072-0.03826.3770.0060.0060.0000.0000.0000.000
119A127LYS10.8850.92620.0030.3180.3180.0000.0000.0000.000
120A128GLN00.0370.01525.5780.0120.0120.0000.0000.0000.000
121A129ARG10.9270.96227.6280.1470.1470.0000.0000.0000.000
122A130GLU-1-0.821-0.89925.760-0.220-0.2200.0000.0000.0000.000
123A131LEU00.0050.01326.6650.0060.0060.0000.0000.0000.000
124A132ILE0-0.011-0.02129.3360.0070.0070.0000.0000.0000.000
125A133ALA0-0.024-0.00932.5220.0090.0090.0000.0000.0000.000
126A134TYR00.0060.00127.5290.0080.0080.0000.0000.0000.000
127A135VAL00.0080.01632.7340.0050.0050.0000.0000.0000.000
128A136ARG10.8140.89235.2400.1280.1280.0000.0000.0000.000
129A137ASP-1-0.854-0.92036.695-0.119-0.1190.0000.0000.0000.000
130A138ALA00.0150.01136.5650.0060.0060.0000.0000.0000.000
131A139LEU00.0150.00338.5800.0050.0050.0000.0000.0000.000
132A140LEU0-0.029-0.01841.2660.0070.0070.0000.0000.0000.000
133A141GLN0-0.026-0.00238.8650.0020.0020.0000.0000.0000.000
134A142LEU0-0.048-0.00641.9880.0030.0030.0000.0000.0000.000
135A143ARG10.8230.87845.0820.0950.0950.0000.0000.0000.000
136A144PRO00.0490.03346.8440.0010.0010.0000.0000.0000.000
137A145ASP-1-0.841-0.88447.788-0.083-0.0830.0000.0000.0000.000
138A146MET00.013-0.00346.9530.0040.0040.0000.0000.0000.000
139A147ALA0-0.021-0.00645.5950.0000.0000.0000.0000.0000.000
140A148ALA0-0.035-0.01846.6860.0000.0000.0000.0000.0000.000
141A149ASN00.0050.01148.8340.0010.0010.0000.0000.0000.000
142A150ARG11.0110.98341.2750.0870.0870.0000.0000.0000.000
143A151THR00.0060.00644.037-0.005-0.0050.0000.0000.0000.000
144A152LEU00.0420.01044.859-0.004-0.0040.0000.0000.0000.000
145A153ALA00.0600.05142.998-0.004-0.0040.0000.0000.0000.000
146A154HIS0-0.035-0.00637.485-0.003-0.0030.0000.0000.0000.000
147A155VAL00.0190.00240.726-0.006-0.0060.0000.0000.0000.000
148A156ASP-1-0.869-0.93542.400-0.109-0.1090.0000.0000.0000.000
149A157THR0-0.039-0.04436.854-0.007-0.0070.0000.0000.0000.000
150A158MET0-0.036-0.01734.966-0.012-0.0120.0000.0000.0000.000
151A159LEU0-0.027-0.00738.425-0.006-0.0060.0000.0000.0000.000
152A160PHE00.0220.01135.118-0.005-0.0050.0000.0000.0000.000
153A161PHE00.018-0.00831.253-0.007-0.0070.0000.0000.0000.000
154A162GLY00.0010.01934.971-0.011-0.0110.0000.0000.0000.000
155A163MET0-0.040-0.01936.818-0.003-0.0030.0000.0000.0000.000
156A164ILE00.0180.01232.434-0.006-0.0060.0000.0000.0000.000
157A165ASN0-0.0060.00231.216-0.024-0.0240.0000.0000.0000.000
158A166TRP00.0280.01232.125-0.010-0.0100.0000.0000.0000.000
159A167THR0-0.002-0.00932.350-0.003-0.0030.0000.0000.0000.000
160A168TYR00.0110.01529.2030.0020.0020.0000.0000.0000.000
161A169THR0-0.049-0.02631.1070.0000.0000.0000.0000.0000.000
162A170TRP0-0.016-0.01333.9270.0060.0060.0000.0000.0000.000
163A171TYR0-0.057-0.03931.766-0.001-0.0010.0000.0000.0000.000
164A172LYS10.9010.95731.3070.1900.1900.0000.0000.0000.000
165A173ALA00.0200.00128.5320.0080.0080.0000.0000.0000.000
166A174ASP-1-0.920-0.94929.184-0.267-0.2670.0000.0000.0000.000
167A175GLY00.0080.01131.1470.0110.0110.0000.0000.0000.000
168A176SER0-0.025-0.02834.855-0.001-0.0010.0000.0000.0000.000
169A177VAL0-0.0230.00037.2690.0020.0020.0000.0000.0000.000
170A178SER00.0830.06333.743-0.008-0.0080.0000.0000.0000.000
171A179PRO00.0730.02329.7540.0100.0100.0000.0000.0000.000
172A180ASP-1-0.807-0.89732.712-0.220-0.2200.0000.0000.0000.000
173A181ALA00.0190.01334.8280.0110.0110.0000.0000.0000.000
174A182LEU0-0.010-0.00234.2870.0110.0110.0000.0000.0000.000
175A183ALA00.0180.02134.6830.0090.0090.0000.0000.0000.000
176A184GLU-1-0.843-0.91936.748-0.163-0.1630.0000.0000.0000.000
177A185ARG10.9130.97440.0030.1400.1400.0000.0000.0000.000
178A186THR0-0.020-0.03137.8900.0080.0080.0000.0000.0000.000
179A187VAL00.003-0.00538.8060.0070.0070.0000.0000.0000.000
180A188GLN00.0140.00941.4950.0090.0090.0000.0000.0000.000
181A189LEU0-0.028-0.01043.2310.0070.0070.0000.0000.0000.000
182A190PHE0-0.041-0.02642.2260.0050.0050.0000.0000.0000.000
183A191LEU0-0.046-0.02142.6050.0040.0040.0000.0000.0000.000
184A192ASP-1-0.818-0.90145.930-0.110-0.1100.0000.0000.0000.000
185A193GLY00.0280.03348.1090.0060.0060.0000.0000.0000.000
186A194TYR0-0.005-0.03248.390-0.001-0.0010.0000.0000.0000.000
187A195LEU0-0.047-0.03550.3670.0010.0010.0000.0000.0000.000
188A196ASN0-0.040-0.00952.5340.0060.0060.0000.0000.0000.000
189A197LEU0-0.0470.00046.716-0.002-0.0020.0000.0000.0000.000
190A198LEU00.0220.00550.6960.0030.0030.0000.0000.0000.000
191A199SER0-0.054-0.02550.547-0.006-0.0060.0000.0000.0000.000
192A200ALA00.0160.01449.6560.0040.0040.0000.0000.0000.000