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: GY591

Calculation Name: 3CDL-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: 3CDL

Chain ID: A

ChEMBL ID:
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UniProt ID: Q87Z81

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2173062.053185
FMO2-HF: Nuclear repulsion 2094489.694411
FMO2-HF: Total energy -78572.358773
FMO2-MP2: Total energy -78803.00536


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:LEU)


Summations of interaction energy for fragment #1(A:3: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.
-9.076-3.9181.262-2.817-3.603-0.026
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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].
3A5ASP-1-0.885-0.9362.351-9.732-5.0771.260-2.753-3.162-0.026
4A6GLN00.017-0.0024.869-0.0210.148-0.001-0.006-0.1620.000
5A7LYS10.9200.9753.5651.0111.3450.003-0.058-0.2790.000
6A8ARG10.8710.9227.609-0.013-0.0130.0000.0000.0000.000
7A9GLU-1-0.727-0.8359.901-0.128-0.1280.0000.0000.0000.000
8A10SER0-0.033-0.00610.3640.0620.0620.0000.0000.0000.000
9A11ILE0-0.034-0.02411.2780.0570.0570.0000.0000.0000.000
10A12VAL00.0090.01313.8030.0330.0330.0000.0000.0000.000
11A13GLN00.0300.00915.4020.0360.0360.0000.0000.0000.000
12A14ALA0-0.0050.00216.1250.0170.0170.0000.0000.0000.000
13A15ALA0-0.012-0.01517.7350.0170.0170.0000.0000.0000.000
14A16ILE0-0.006-0.00619.7120.0110.0110.0000.0000.0000.000
15A17ALA00.0130.01920.8610.0070.0070.0000.0000.0000.000
16A18GLU-1-0.739-0.84621.511-0.033-0.0330.0000.0000.0000.000
17A19PHE0-0.041-0.03421.9000.0080.0080.0000.0000.0000.000
18A20GLY00.0310.02225.2170.0050.0050.0000.0000.0000.000
19A21ASP-1-0.831-0.89125.605-0.055-0.0550.0000.0000.0000.000
20A22ARG10.7530.85225.2000.0220.0220.0000.0000.0000.000
21A23GLY00.0600.04428.6170.0050.0050.0000.0000.0000.000
22A24PHE0-0.003-0.01024.1170.0000.0000.0000.0000.0000.000
23A25GLU-1-0.731-0.86326.8250.0300.0300.0000.0000.0000.000
24A26ILE0-0.0410.00228.4820.0040.0040.0000.0000.0000.000
25A27THR00.0000.00422.923-0.006-0.0060.0000.0000.0000.000
26A28SER0-0.011-0.01622.9560.0030.0030.0000.0000.0000.000
27A29MET00.0420.00417.676-0.016-0.0160.0000.0000.0000.000
28A30ASP-1-0.785-0.87817.9350.0330.0330.0000.0000.0000.000
29A31ARG10.8240.91918.8500.0200.0200.0000.0000.0000.000
30A32ILE00.0310.01516.450-0.011-0.0110.0000.0000.0000.000
31A33ALA0-0.018-0.02214.625-0.019-0.0190.0000.0000.0000.000
32A34ALA0-0.033-0.01214.809-0.024-0.0240.0000.0000.0000.000
33A35ARG10.7370.85717.0230.0580.0580.0000.0000.0000.000
34A36ALA00.0120.01113.024-0.016-0.0160.0000.0000.0000.000
35A37GLU-1-0.942-0.95412.107-0.240-0.2400.0000.0000.0000.000
36A38VAL0-0.062-0.0298.794-0.029-0.0290.0000.0000.0000.000
37A39SER00.0240.01010.8320.0280.0280.0000.0000.0000.000
38A40LYS10.9230.93012.841-0.054-0.0540.0000.0000.0000.000
39A41ARG10.9470.95913.345-0.152-0.1520.0000.0000.0000.000
40A42THR00.0020.0087.9290.0350.0350.0000.0000.0000.000
41A43VAL00.0500.03710.6460.0050.0050.0000.0000.0000.000
42A44TYR0-0.023-0.02013.3930.0150.0150.0000.0000.0000.000
43A45ASN0-0.044-0.0298.476-0.065-0.0650.0000.0000.0000.000
44A46HIS00.0020.0157.231-0.070-0.0700.0000.0000.0000.000
45A47PHE00.0310.02112.266-0.013-0.0130.0000.0000.0000.000
46A48PRO00.0020.00115.965-0.023-0.0230.0000.0000.0000.000
47A49SER0-0.014-0.01318.110-0.019-0.0190.0000.0000.0000.000
48A50LYS10.8720.92320.503-0.027-0.0270.0000.0000.0000.000
49A51GLU-1-0.769-0.84622.5360.0390.0390.0000.0000.0000.000
50A52GLU-1-0.850-0.90817.2440.1600.1600.0000.0000.0000.000
51A53LEU0-0.001-0.00517.618-0.007-0.0070.0000.0000.0000.000
52A54PHE0-0.001-0.00220.523-0.012-0.0120.0000.0000.0000.000
53A55ALA00.0140.00921.840-0.007-0.0070.0000.0000.0000.000
54A56GLU-1-0.786-0.88716.478-0.021-0.0210.0000.0000.0000.000
55A57MET0-0.043-0.01319.707-0.010-0.0100.0000.0000.0000.000
56A58LEU0-0.0150.00123.166-0.007-0.0070.0000.0000.0000.000
57A59GLN00.0040.02219.7520.0010.0010.0000.0000.0000.000
58A60ARG10.7400.80914.8400.0790.0790.0000.0000.0000.000
59A61LEU00.0060.00822.390-0.006-0.0060.0000.0000.0000.000
60A62TRP0-0.009-0.02225.2990.0000.0000.0000.0000.0000.000
61A63ASN0-0.075-0.04821.057-0.005-0.0050.0000.0000.0000.000
62A64CYS0-0.0240.01024.557-0.009-0.0090.0000.0000.0000.000
63A65ALA0-0.058-0.04127.2060.0000.0000.0000.0000.0000.000
64A66PRO0-0.0130.01627.307-0.001-0.0010.0000.0000.0000.000
65A67PRO00.0080.00624.519-0.004-0.0040.0000.0000.0000.000
66A68GLN0-0.012-0.02926.9790.0080.0080.0000.0000.0000.000
67A69SER0-0.017-0.01029.756-0.006-0.0060.0000.0000.0000.000
68A70GLU-1-0.839-0.90732.554-0.016-0.0160.0000.0000.0000.000
69A71VAL0-0.065-0.04834.8100.0020.0020.0000.0000.0000.000
70A72VAL00.0030.01937.7060.0030.0030.0000.0000.0000.000
71A73TYR0-0.083-0.08039.827-0.001-0.0010.0000.0000.0000.000
72A74ARG10.7880.86640.8620.0180.0180.0000.0000.0000.000
73A75PRO00.0580.03045.7330.0000.0000.0000.0000.0000.000
74A76LEU0-0.033-0.01549.0330.0000.0000.0000.0000.0000.000
75A77VAL00.0070.03546.914-0.001-0.0010.0000.0000.0000.000
76A78SER0-0.043-0.05150.2360.0010.0010.0000.0000.0000.000
77A79LEU00.0190.00548.830-0.001-0.0010.0000.0000.0000.000
78A80ARG10.9190.93747.7920.0100.0100.0000.0000.0000.000
79A81GLU-1-0.787-0.84346.863-0.016-0.0160.0000.0000.0000.000
80A82GLN00.0500.02143.598-0.001-0.0010.0000.0000.0000.000
81A83LEU0-0.0090.00442.9450.0000.0000.0000.0000.0000.000
82A84LEU00.0180.00543.858-0.001-0.0010.0000.0000.0000.000
83A85GLU-1-0.833-0.87939.263-0.023-0.0230.0000.0000.0000.000
84A86LEU00.0110.00139.162-0.002-0.0020.0000.0000.0000.000
85A87LEU0-0.031-0.01839.081-0.001-0.0010.0000.0000.0000.000
86A88TRP00.0580.03140.078-0.002-0.0020.0000.0000.0000.000
87A89GLY0-0.051-0.00236.300-0.003-0.0030.0000.0000.0000.000
88A90LYS10.8440.92732.5450.0210.0210.0000.0000.0000.000
89A91MET00.0380.01636.096-0.001-0.0010.0000.0000.0000.000
90A92ARG10.8970.93934.2550.0330.0330.0000.0000.0000.000
91A93ASN0-0.0090.00630.4720.0010.0010.0000.0000.0000.000
92A94LEU0-0.051-0.03033.019-0.001-0.0010.0000.0000.0000.000
93A95THR0-0.015-0.00835.2670.0020.0020.0000.0000.0000.000
94A96ASP-1-0.808-0.87228.782-0.062-0.0620.0000.0000.0000.000
95A97SER00.0390.01029.6450.0030.0030.0000.0000.0000.000
96A98SER0-0.020-0.02425.7910.0000.0000.0000.0000.0000.000
97A99PHE0-0.016-0.02327.5590.0060.0060.0000.0000.0000.000
98A100LEU0-0.035-0.01629.1490.0060.0060.0000.0000.0000.000
99A101ASP-1-0.815-0.89128.054-0.041-0.0410.0000.0000.0000.000
100A102LEU0-0.026-0.01124.0140.0050.0050.0000.0000.0000.000
101A103ALA00.010-0.00927.4410.0070.0070.0000.0000.0000.000
102A104ARG10.8090.88730.3170.0360.0360.0000.0000.0000.000
103A105VAL0-0.029-0.00525.5450.0050.0050.0000.0000.0000.000
104A106VAL0-0.0130.00127.5220.0060.0060.0000.0000.0000.000
105A107VAL00.0040.00229.7810.0050.0050.0000.0000.0000.000
106A108GLY00.0420.02832.5730.0030.0030.0000.0000.0000.000
107A109ALA0-0.042-0.02828.8860.0030.0030.0000.0000.0000.000
108A110THR0-0.026-0.01530.9230.0050.0050.0000.0000.0000.000
109A111ILE0-0.015-0.01433.7980.0020.0020.0000.0000.0000.000
110A112HIS0-0.068-0.03133.132-0.001-0.0010.0000.0000.0000.000
111A113SER00.0060.00932.1210.0020.0020.0000.0000.0000.000
112A114PRO00.0450.01934.5190.0000.0000.0000.0000.0000.000
113A115GLU-1-0.918-0.95032.1380.0440.0440.0000.0000.0000.000
114A116ARG10.7170.79428.118-0.032-0.0320.0000.0000.0000.000
115A117ALA0-0.012-0.01532.2590.0000.0000.0000.0000.0000.000
116A118GLN0-0.052-0.01834.8070.0000.0000.0000.0000.0000.000
117A119VAL0-0.0120.00731.1480.0000.0000.0000.0000.0000.000
118A120TRP0-0.010-0.00125.574-0.002-0.0020.0000.0000.0000.000
119A121LEU0-0.002-0.02032.122-0.005-0.0050.0000.0000.0000.000
120A122ALA00.0470.04634.2570.0010.0010.0000.0000.0000.000
121A123ARG10.7870.89231.604-0.016-0.0160.0000.0000.0000.000
122A124ILE00.002-0.00335.948-0.004-0.0040.0000.0000.0000.000
123A125ASN00.015-0.02735.664-0.001-0.0010.0000.0000.0000.000
124A126GLU-1-0.706-0.84430.7150.0090.0090.0000.0000.0000.000
125A127ARG10.7370.85431.506-0.002-0.0020.0000.0000.0000.000
126A128GLU-1-0.823-0.86933.627-0.005-0.0050.0000.0000.0000.000
127A129GLU-1-0.743-0.83835.8380.0050.0050.0000.0000.0000.000
128A130THR00.0130.01934.7670.0000.0000.0000.0000.0000.000
129A131PHE00.0330.00637.392-0.001-0.0010.0000.0000.0000.000
130A132SER0-0.039-0.03440.6080.0010.0010.0000.0000.0000.000
131A133ALA00.000-0.01739.4640.0010.0010.0000.0000.0000.000
132A134TRP00.0180.00241.4300.0010.0010.0000.0000.0000.000
133A135ILE00.0140.00643.0890.0000.0000.0000.0000.0000.000
134A136ARG10.8610.91441.187-0.005-0.0050.0000.0000.0000.000
135A137ALA00.0330.01944.5730.0010.0010.0000.0000.0000.000
136A138ALA00.0740.03046.6030.0000.0000.0000.0000.0000.000
137A139GLN0-0.077-0.04449.0350.0010.0010.0000.0000.0000.000
138A140LYS10.7760.89248.779-0.002-0.0020.0000.0000.0000.000
139A141ASP-1-0.802-0.86050.237-0.005-0.0050.0000.0000.0000.000
140A142GLY0-0.0020.00652.224-0.001-0.0010.0000.0000.0000.000
141A143ARG10.8070.87651.5890.0070.0070.0000.0000.0000.000
142A144LEU0-0.023-0.00848.785-0.001-0.0010.0000.0000.0000.000
143A145LYS10.8520.91053.1190.0040.0040.0000.0000.0000.000
144A146PRO0-0.027-0.01153.4410.0000.0000.0000.0000.0000.000
145A147VAL0-0.002-0.00150.3580.0000.0000.0000.0000.0000.000
146A148ASP-1-0.785-0.89046.9960.0060.0060.0000.0000.0000.000
147A149PRO0-0.018-0.01444.838-0.001-0.0010.0000.0000.0000.000
148A150GLY00.0470.03743.346-0.001-0.0010.0000.0000.0000.000
149A151PHE0-0.015-0.00644.305-0.001-0.0010.0000.0000.0000.000
150A152ALA00.0240.01347.078-0.001-0.0010.0000.0000.0000.000
151A153ALA00.007-0.00242.133-0.001-0.0010.0000.0000.0000.000
152A154THR00.003-0.00842.885-0.001-0.0010.0000.0000.0000.000
153A155GLN00.0080.01443.910-0.001-0.0010.0000.0000.0000.000
154A156MET0-0.0190.01544.337-0.001-0.0010.0000.0000.0000.000
155A157HIS10.8110.88839.0130.0060.0060.0000.0000.0000.000
156A158ALA0-0.0060.00742.501-0.001-0.0010.0000.0000.0000.000
157A159LEU0-0.0090.00244.728-0.001-0.0010.0000.0000.0000.000
158A160LEU00.0380.03241.777-0.001-0.0010.0000.0000.0000.000
159A161LYS10.8910.94737.7200.0060.0060.0000.0000.0000.000
160A162SER0-0.061-0.03941.726-0.001-0.0010.0000.0000.0000.000
161A163PHE0-0.0090.00244.2440.0000.0000.0000.0000.0000.000
162A164ALA00.0210.01240.035-0.001-0.0010.0000.0000.0000.000
163A165PHE00.0180.01034.126-0.001-0.0010.0000.0000.0000.000
164A166TRP00.0700.01338.3040.0000.0000.0000.0000.0000.000
165A167PRO00.0480.03740.5370.0010.0010.0000.0000.0000.000
166A168GLN0-0.040-0.02537.0990.0010.0010.0000.0000.0000.000
167A169VAL0-0.005-0.01334.492-0.001-0.0010.0000.0000.0000.000
168A170THR0-0.098-0.06936.4260.0010.0010.0000.0000.0000.000
169A171PHE0-0.004-0.00339.1750.0010.0010.0000.0000.0000.000
170A172ASN0-0.042-0.01235.422-0.001-0.0010.0000.0000.0000.000
171A173ALA0-0.0040.01238.530-0.002-0.0020.0000.0000.0000.000
172A174ALA00.0220.01139.527-0.002-0.0020.0000.0000.0000.000
173A175LEU00.0160.01335.3070.0020.0020.0000.0000.0000.000
174A176LEU0-0.0190.00339.8500.0000.0000.0000.0000.0000.000
175A177THR00.008-0.02541.878-0.002-0.0020.0000.0000.0000.000
176A178PRO00.022-0.00142.0360.0010.0010.0000.0000.0000.000
177A179GLN00.0690.03344.0300.0000.0000.0000.0000.0000.000
178A180GLU-1-0.811-0.86245.946-0.021-0.0210.0000.0000.0000.000
179A181GLN0-0.036-0.03540.1850.0010.0010.0000.0000.0000.000
180A182SER00.000-0.01444.3500.0010.0010.0000.0000.0000.000
181A183ASN0-0.029-0.01346.8440.0010.0010.0000.0000.0000.000
182A184VAL00.001-0.00544.7760.0010.0010.0000.0000.0000.000
183A185VAL0-0.0010.00643.2920.0010.0010.0000.0000.0000.000
184A186GLU-1-0.834-0.93646.368-0.017-0.0170.0000.0000.0000.000
185A187SER0-0.0100.00149.8430.0010.0010.0000.0000.0000.000
186A188ALA0-0.003-0.01047.0470.0010.0010.0000.0000.0000.000
187A189LEU0-0.005-0.00646.4450.0010.0010.0000.0000.0000.000
188A190ASN0-0.048-0.04349.6910.0010.0010.0000.0000.0000.000
189A191MET0-0.0290.00051.9330.0010.0010.0000.0000.0000.000
190A192PHE00.0140.00048.3480.0010.0010.0000.0000.0000.000
191A193LEU0-0.042-0.01850.1070.0010.0010.0000.0000.0000.000
192A194GLY00.0120.01653.0930.0010.0010.0000.0000.0000.000
193A195TRP0-0.0300.00554.1140.0010.0010.0000.0000.0000.000
194A196TYR00.005-0.02751.0520.0010.0010.0000.0000.0000.000
195A197GLU-1-0.831-0.91253.583-0.008-0.0080.0000.0000.0000.000
196A198ILE0-0.056-0.02455.0740.0000.0000.0000.0000.0000.000
197A199PRO0-0.0020.01057.2030.0000.0000.0000.0000.0000.000