FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3J6RL

Calculation Name: 3CYG-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3CYG

Chain ID: A

ChEMBL ID:
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UniProt ID: A7HM60

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 -2627750.01111
FMO2-HF: Nuclear repulsion 2540181.500548
FMO2-HF: Total energy -87568.510562
FMO2-MP2: Total energy -87828.255144


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:36:LEU)


Summations of interaction energy for fragment #1(A:36: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.
-1.7820.4650.018-1.004-1.2610.004
Interaction energy analysis for fragmet #1(A:36:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.078 / q_NPA : 0.032
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].
3A38MET00.0240.0303.595-2.0920.1550.018-1.004-1.2610.004
4A39LYS10.7850.8925.4921.0191.0190.0000.0000.0000.000
5A40VAL00.0390.0097.1710.0390.0390.0000.0000.0000.000
6A41PHE00.0070.00010.1730.0980.0980.0000.0000.0000.000
7A42GLU-1-0.833-0.89010.131-0.574-0.5740.0000.0000.0000.000
8A43ILE00.0350.01312.2130.0410.0410.0000.0000.0000.000
9A44VAL0-0.0040.00514.7330.0000.0000.0000.0000.0000.000
10A45LYS10.8350.91215.2190.1410.1410.0000.0000.0000.000
11A46SER0-0.049-0.01718.969-0.004-0.0040.0000.0000.0000.000
12A47SER00.0160.00622.5760.0040.0040.0000.0000.0000.000
13A48THR0-0.051-0.02225.994-0.001-0.0010.0000.0000.0000.000
14A49GLU-1-0.791-0.88429.752-0.039-0.0390.0000.0000.0000.000
15A50ASN0-0.018-0.00932.5830.0020.0020.0000.0000.0000.000
16A51GLU-1-0.927-0.96336.415-0.028-0.0280.0000.0000.0000.000
17A52ILE00.0550.05038.8220.0020.0020.0000.0000.0000.000
18A53VAL0-0.043-0.02533.9500.0000.0000.0000.0000.0000.000
19A54ARG10.7920.87329.0860.0340.0340.0000.0000.0000.000
20A55ILE0-0.045-0.01828.454-0.001-0.0010.0000.0000.0000.000
21A56HIS0-0.021-0.02324.665-0.008-0.0080.0000.0000.0000.000
22A57VAL00.0130.00123.1350.0010.0010.0000.0000.0000.000
23A58GLU-1-0.793-0.88318.267-0.117-0.1170.0000.0000.0000.000
24A59LEU00.0370.02820.0260.0030.0030.0000.0000.0000.000
25A60PRO0-0.028-0.00416.557-0.026-0.0260.0000.0000.0000.000
26A61ARG10.8970.93315.7440.3230.3230.0000.0000.0000.000
27A62LEU0-0.019-0.00814.576-0.044-0.0440.0000.0000.0000.000
28A63LYS10.8210.90410.1580.7190.7190.0000.0000.0000.000
29A64TYR0-0.004-0.01411.331-0.097-0.0970.0000.0000.0000.000
30A65LEU0-0.001-0.00114.329-0.025-0.0250.0000.0000.0000.000
31A66LYS10.7840.88416.2210.2480.2480.0000.0000.0000.000
32A67ASP-1-0.826-0.91218.312-0.171-0.1710.0000.0000.0000.000
33A68SER0-0.009-0.01020.572-0.007-0.0070.0000.0000.0000.000
34A69ASN0-0.006-0.00721.7500.0130.0130.0000.0000.0000.000
35A70PHE0-0.006-0.00919.3350.0090.0090.0000.0000.0000.000
36A71GLU-1-0.861-0.94017.247-0.369-0.3690.0000.0000.0000.000
37A72GLU-1-0.893-0.93820.579-0.200-0.2000.0000.0000.0000.000
38A73LYS10.8110.90623.4500.1410.1410.0000.0000.0000.000
39A74PHE0-0.0040.00419.8040.0100.0100.0000.0000.0000.000
40A75ASN0-0.004-0.01418.6630.0060.0060.0000.0000.0000.000
41A76SER00.007-0.00922.2450.0130.0130.0000.0000.0000.000
42A77GLU-1-0.809-0.88825.821-0.113-0.1130.0000.0000.0000.000
43A78VAL0-0.015-0.00721.2240.0100.0100.0000.0000.0000.000
44A79GLU-1-0.883-0.96024.141-0.145-0.1450.0000.0000.0000.000
45A80GLU-1-0.897-0.94525.387-0.088-0.0880.0000.0000.0000.000
46A81LYS10.8250.90726.6720.1070.1070.0000.0000.0000.000
47A82ILE0-0.0120.00123.6130.0070.0070.0000.0000.0000.000
48A83LYS10.8410.91127.0840.1170.1170.0000.0000.0000.000
49A84LYS10.8410.91929.6660.0700.0700.0000.0000.0000.000
50A85PHE00.0630.02729.0180.0050.0050.0000.0000.0000.000
51A86VAL00.0200.00728.1640.0050.0050.0000.0000.0000.000
52A87ASN0-0.018-0.01731.3770.0060.0060.0000.0000.0000.000
53A88GLU-1-0.861-0.90834.652-0.055-0.0550.0000.0000.0000.000
54A89VAL00.0060.00433.0970.0040.0040.0000.0000.0000.000
55A90LYS10.8740.93333.0600.0700.0700.0000.0000.0000.000
56A91GLY0-0.0030.00736.6220.0020.0020.0000.0000.0000.000
57A92ILE00.0070.00138.2020.0020.0020.0000.0000.0000.000
58A93ALA00.0020.00038.0650.0020.0020.0000.0000.0000.000
59A94GLN0-0.071-0.04140.1240.0010.0010.0000.0000.0000.000
60A95GLU-1-0.841-0.89742.364-0.030-0.0300.0000.0000.0000.000
61A96ASP-1-0.802-0.89243.238-0.027-0.0270.0000.0000.0000.000
62A97HIS0-0.042-0.02143.6720.0030.0030.0000.0000.0000.000
63A98ASP-1-0.866-0.92245.489-0.032-0.0320.0000.0000.0000.000
64A99LYS10.6720.81946.3210.0300.0300.0000.0000.0000.000
65A100ASP-1-0.972-0.97449.082-0.018-0.0180.0000.0000.0000.000
66A101VAL0-0.025-0.01647.7440.0010.0010.0000.0000.0000.000
67A102GLN0-0.014-0.01539.8780.0010.0010.0000.0000.0000.000
68A103HIS0-0.080-0.04744.7060.0020.0020.0000.0000.0000.000
69A104THR0-0.056-0.02839.5980.0020.0020.0000.0000.0000.000
70A105PRO00.0140.01236.972-0.001-0.0010.0000.0000.0000.000
71A106TYR0-0.075-0.04436.8570.0010.0010.0000.0000.0000.000
72A107GLU-1-0.811-0.90631.321-0.035-0.0350.0000.0000.0000.000
73A108ALA0-0.002-0.00230.0540.0010.0010.0000.0000.0000.000
74A109TYR0-0.043-0.04120.8870.0010.0010.0000.0000.0000.000
75A110VAL0-0.0070.01222.7940.0020.0020.0000.0000.0000.000
76A111SER00.003-0.00820.456-0.007-0.0070.0000.0000.0000.000
77A112VAL0-0.012-0.00215.744-0.002-0.0020.0000.0000.0000.000
78A113ASP-1-0.811-0.85816.439-0.058-0.0580.0000.0000.0000.000
79A114VAL0-0.017-0.01811.741-0.008-0.0080.0000.0000.0000.000
80A115ARG10.7670.83214.0030.0550.0550.0000.0000.0000.000
81A116TYR0-0.059-0.05612.0230.0260.0260.0000.0000.0000.000
82A117GLU-1-0.747-0.8436.253-0.447-0.4470.0000.0000.0000.000
83A118GLY00.0300.0068.8020.0700.0700.0000.0000.0000.000
84A119LYS10.7820.8749.2340.0730.0730.0000.0000.0000.000
85A120ASP-1-0.768-0.88110.036-0.198-0.1980.0000.0000.0000.000
86A121PHE00.0290.01212.7630.0080.0080.0000.0000.0000.000
87A122LEU0-0.052-0.01311.794-0.019-0.0190.0000.0000.0000.000
88A123SER00.012-0.00514.2600.0160.0160.0000.0000.0000.000
89A124PHE0-0.025-0.02215.666-0.005-0.0050.0000.0000.0000.000
90A125VAL00.0550.03717.5830.0040.0040.0000.0000.0000.000
91A126VAL0-0.024-0.01319.527-0.014-0.0140.0000.0000.0000.000
92A127TYR0-0.035-0.04020.9450.0100.0100.0000.0000.0000.000
93A128TYR0-0.018-0.04724.576-0.009-0.0090.0000.0000.0000.000
94A129TYR0-0.053-0.02327.4010.0060.0060.0000.0000.0000.000
95A130GLN00.011-0.00329.177-0.001-0.0010.0000.0000.0000.000
96A131PHE0-0.043-0.01432.5030.0040.0040.0000.0000.0000.000
97A132THR00.0470.00635.180-0.002-0.0020.0000.0000.0000.000
98A133GLY00.0530.04638.6090.0010.0010.0000.0000.0000.000
99A134GLY0-0.017-0.00839.7100.0000.0000.0000.0000.0000.000
100A135ALA0-0.013-0.01940.5480.0000.0000.0000.0000.0000.000
101A136HIS10.8380.91535.5860.0200.0200.0000.0000.0000.000
102A137GLY00.0870.06033.973-0.001-0.0010.0000.0000.0000.000
103A138ILE0-0.048-0.01534.1270.0030.0030.0000.0000.0000.000
104A139THR00.0450.00027.800-0.002-0.0020.0000.0000.0000.000
105A140PHE0-0.0170.01729.6570.0040.0040.0000.0000.0000.000
106A141PHE0-0.006-0.02525.283-0.003-0.0030.0000.0000.0000.000
107A142GLU-1-0.753-0.79725.016-0.092-0.0920.0000.0000.0000.000
108A143THR0-0.038-0.03922.561-0.003-0.0030.0000.0000.0000.000
109A144TYR0-0.030-0.04420.031-0.002-0.0020.0000.0000.0000.000
110A145ASN00.0090.01819.101-0.010-0.0100.0000.0000.0000.000
111A146ILE00.004-0.00717.1740.0020.0020.0000.0000.0000.000
112A147ASP-1-0.714-0.81016.860-0.131-0.1310.0000.0000.0000.000
113A148LEU00.001-0.00712.115-0.012-0.0120.0000.0000.0000.000
114A149LYS10.8180.91616.0340.0710.0710.0000.0000.0000.000
115A150ASN0-0.040-0.04017.575-0.007-0.0070.0000.0000.0000.000
116A151SER0-0.0170.01219.475-0.001-0.0010.0000.0000.0000.000
117A152LYS10.8660.93020.7120.0970.0970.0000.0000.0000.000
118A153VAL00.0000.00421.382-0.003-0.0030.0000.0000.0000.000
119A154LEU0-0.051-0.02821.2940.0080.0080.0000.0000.0000.000
120A155LYS10.8810.92224.4560.0740.0740.0000.0000.0000.000
121A156LEU00.0540.03527.0290.0010.0010.0000.0000.0000.000
122A157TYR00.0610.03428.5120.0020.0020.0000.0000.0000.000
123A158ASP-1-0.840-0.92926.910-0.073-0.0730.0000.0000.0000.000
124A159ILE0-0.048-0.02723.4340.0010.0010.0000.0000.0000.000
125A160ILE00.000-0.00327.1810.0050.0050.0000.0000.0000.000
126A161LYS10.8240.91330.2160.0180.0180.0000.0000.0000.000
127A162GLU-1-0.730-0.86333.979-0.033-0.0330.0000.0000.0000.000
128A163GLU-1-0.893-0.96136.241-0.019-0.0190.0000.0000.0000.000
129A164ALA0-0.033-0.01032.6450.0030.0030.0000.0000.0000.000
130A165GLU-1-0.793-0.89834.707-0.020-0.0200.0000.0000.0000.000
131A166ASP-1-0.883-0.93936.213-0.010-0.0100.0000.0000.0000.000
132A167THR0-0.069-0.03533.6440.0030.0030.0000.0000.0000.000
133A168ILE00.008-0.00330.6180.0030.0030.0000.0000.0000.000
134A169LYS10.8200.90933.6250.0200.0200.0000.0000.0000.000
135A170SER0-0.031-0.01336.6680.0020.0020.0000.0000.0000.000
136A171ASN0-0.0260.00730.7230.0030.0030.0000.0000.0000.000
137A172ILE00.0720.02131.5430.0020.0020.0000.0000.0000.000
138A173LEU0-0.017-0.00634.2630.0010.0010.0000.0000.0000.000
139A174LYS10.8620.93635.725-0.003-0.0030.0000.0000.0000.000
140A175GLN0-0.055-0.04929.4950.0010.0010.0000.0000.0000.000
141A176ILE0-0.0180.01034.3050.0000.0000.0000.0000.0000.000
142A177GLU-1-0.932-0.96836.8030.0100.0100.0000.0000.0000.000
143A178GLN0-0.071-0.05735.7900.0030.0030.0000.0000.0000.000
144A179ASN0-0.055-0.03433.6210.0030.0030.0000.0000.0000.000
145A180ASN00.0040.00437.5410.0000.0000.0000.0000.0000.000
146A181THR0-0.089-0.06638.508-0.001-0.0010.0000.0000.0000.000
147A182ASP-1-0.839-0.87035.1530.0080.0080.0000.0000.0000.000
148A183PHE00.003-0.00433.444-0.003-0.0030.0000.0000.0000.000
149A184PHE0-0.024-0.01038.7130.0010.0010.0000.0000.0000.000
150A185PRO00.013-0.00341.8800.0000.0000.0000.0000.0000.000
151A186ASP-1-0.883-0.93544.099-0.010-0.0100.0000.0000.0000.000
152A187ALA00.0260.02538.842-0.001-0.0010.0000.0000.0000.000
153A188PRO00.0300.00240.176-0.001-0.0010.0000.0000.0000.000
154A189MET00.001-0.00141.532-0.001-0.0010.0000.0000.0000.000
155A190ASN0-0.007-0.01640.286-0.001-0.0010.0000.0000.0000.000
156A191ILE00.0430.02435.388-0.002-0.0020.0000.0000.0000.000
157A192LEU0-0.050-0.02538.903-0.001-0.0010.0000.0000.0000.000
158A193LYS10.8410.91041.7600.0130.0130.0000.0000.0000.000
159A194ASP-1-0.796-0.85535.314-0.027-0.0270.0000.0000.0000.000
160A195ASP-1-0.799-0.85436.253-0.033-0.0330.0000.0000.0000.000
161A196ILE0-0.005-0.02231.929-0.002-0.0020.0000.0000.0000.000
162A197PHE0-0.060-0.03231.844-0.003-0.0030.0000.0000.0000.000
163A198SER0-0.107-0.07632.077-0.005-0.0050.0000.0000.0000.000
164A199ARG10.7810.89030.9400.0280.0280.0000.0000.0000.000
165A200GLU-1-0.752-0.83826.966-0.072-0.0720.0000.0000.0000.000
166A201PHE0-0.011-0.01523.7990.0050.0050.0000.0000.0000.000
167A202THR00.0060.00720.000-0.008-0.0080.0000.0000.0000.000
168A203ILE0-0.003-0.00818.3040.0090.0090.0000.0000.0000.000
169A204SER00.0360.01016.017-0.006-0.0060.0000.0000.0000.000
170A205LYS10.8160.88014.419-0.069-0.0690.0000.0000.0000.000
171A206ASP-1-0.813-0.89216.6120.0570.0570.0000.0000.0000.000
172A207GLY00.016-0.00619.6030.0030.0030.0000.0000.0000.000
173A208LEU00.0040.02121.067-0.007-0.0070.0000.0000.0000.000
174A209ILE0-0.028-0.01020.3150.0080.0080.0000.0000.0000.000
175A210ILE00.0210.02124.464-0.008-0.0080.0000.0000.0000.000
176A211MET0-0.0340.00123.3610.0010.0010.0000.0000.0000.000
177A212TYR0-0.037-0.05128.070-0.002-0.0020.0000.0000.0000.000
178A213PRO00.0050.01230.1360.0000.0000.0000.0000.0000.000
179A214HIS00.0680.01430.9030.0050.0050.0000.0000.0000.000
180A215TYR0-0.026-0.02334.150-0.002-0.0020.0000.0000.0000.000
181A216ASP-1-0.814-0.89235.194-0.025-0.0250.0000.0000.0000.000
182A217LEU0-0.026-0.01334.2450.0010.0010.0000.0000.0000.000
183A218ALA00.0520.02835.3680.0030.0030.0000.0000.0000.000
184A219PRO0-0.0090.00937.375-0.003-0.0030.0000.0000.0000.000
185A220TYR0-0.005-0.02533.4860.0010.0010.0000.0000.0000.000
186A221ALA0-0.058-0.02634.2710.0000.0000.0000.0000.0000.000
187A222SER0-0.013-0.01533.8930.0020.0020.0000.0000.0000.000
188A223GLY0-0.0310.00230.4840.0010.0010.0000.0000.0000.000
189A224MET0-0.049-0.02527.088-0.001-0.0010.0000.0000.0000.000
190A225PRO00.0170.01428.5290.0010.0010.0000.0000.0000.000
191A226GLU-1-0.771-0.85923.811-0.033-0.0330.0000.0000.0000.000
192A227PHE00.0080.00327.7630.0050.0050.0000.0000.0000.000
193A228VAL00.0070.01023.530-0.004-0.0040.0000.0000.0000.000
194A229ILE0-0.019-0.00725.6360.0030.0030.0000.0000.0000.000
195A230PRO00.0080.00524.314-0.002-0.0020.0000.0000.0000.000
196A231TRP00.0630.02419.955-0.003-0.0030.0000.0000.0000.000
197A232ASN0-0.006-0.00924.905-0.003-0.0030.0000.0000.0000.000
198A233VAL0-0.058-0.02627.4620.0000.0000.0000.0000.0000.000
199A234ILE00.003-0.00326.100-0.002-0.0020.0000.0000.0000.000
200A235GLU-1-0.908-0.94526.276-0.006-0.0060.0000.0000.0000.000
201A236LYS10.9510.97428.8060.0000.0000.0000.0000.0000.000
202A237PHE00.012-0.00231.502-0.001-0.0010.0000.0000.0000.000
203A238LEU0-0.0110.02225.376-0.004-0.0040.0000.0000.0000.000
204A239LYS10.7270.85428.8420.0410.0410.0000.0000.0000.000
205A240TYR0-0.072-0.03821.264-0.005-0.0050.0000.0000.0000.000
206A241ASP-1-0.800-0.89820.829-0.042-0.0420.0000.0000.0000.000
207A242ILE00.0590.02120.657-0.003-0.0030.0000.0000.0000.000
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