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: R8LK8

Calculation Name: 3C8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q1GJR2

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2250251.003407
FMO2-HF: Nuclear repulsion 2172085.867993
FMO2-HF: Total energy -78165.135414
FMO2-MP2: Total energy -78394.30757


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:0:GLY)


Summations of interaction energy for fragment #1(A:0: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.
-2.857-5.399.165-3.585-3.047-0.023
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.018
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].
3A2THR00.0370.0133.8622.4583.392-0.013-0.483-0.4380.000
4A3LEU00.0640.0157.199-0.312-0.3120.0000.0000.0000.000
5A4ALA00.0070.01010.386-0.101-0.1010.0000.0000.0000.000
6A5ALA00.0260.0147.822-0.045-0.0450.0000.0000.0000.000
7A6LEU00.0070.0058.816-0.085-0.0850.0000.0000.0000.000
8A7CYS0-0.0030.00110.4200.0260.0260.0000.0000.0000.000
9A8GLN0-0.063-0.03212.8130.0450.0450.0000.0000.0000.000
10A9GLY00.0220.01212.4030.0070.0070.0000.0000.0000.000
11A10VAL00.0260.00513.4070.0240.0240.0000.0000.0000.000
12A11LEU00.005-0.01215.8060.0290.0290.0000.0000.0000.000
13A12GLU-1-0.890-0.92114.903-0.471-0.4710.0000.0000.0000.000
14A13ARG10.7700.87113.9180.5140.5140.0000.0000.0000.000
15A14LEU00.0140.02719.2330.0190.0190.0000.0000.0000.000
16A15ASP-1-0.819-0.90821.696-0.128-0.1280.0000.0000.0000.000
17A16PRO0-0.053-0.03124.5250.0160.0160.0000.0000.0000.000
18A17ARG10.9010.93527.1700.1060.1060.0000.0000.0000.000
19A18GLN00.0060.01426.1910.0150.0150.0000.0000.0000.000
20A19PRO0-0.045-0.02729.9760.0040.0040.0000.0000.0000.000
21A20GLY00.0310.03231.473-0.003-0.0030.0000.0000.0000.000
22A21ARG10.7160.83927.0520.0430.0430.0000.0000.0000.000
23A22GLN0-0.028-0.03223.825-0.018-0.0180.0000.0000.0000.000
24A23LEU0-0.028-0.01823.1060.0100.0100.0000.0000.0000.000
25A24VAL00.005-0.00516.677-0.021-0.0210.0000.0000.0000.000
26A25ALA00.0050.01218.2990.0220.0220.0000.0000.0000.000
27A26LEU0-0.006-0.01312.199-0.038-0.0380.0000.0000.0000.000
28A27SER00.0140.00415.2600.0470.0470.0000.0000.0000.000
29A28GLY00.0100.00614.164-0.034-0.0340.0000.0000.0000.000
30A29ALA00.0360.01315.262-0.012-0.0120.0000.0000.0000.000
31A30PRO0-0.0100.00117.6200.0280.0280.0000.0000.0000.000
32A31GLY00.0540.02818.416-0.001-0.0010.0000.0000.0000.000
33A32SER0-0.060-0.04913.5540.0340.0340.0000.0000.0000.000
34A33GLY00.0530.02213.5520.0550.0550.0000.0000.0000.000
35A34LYS10.8160.92114.2490.0240.0240.0000.0000.0000.000
36A35SER00.017-0.01715.2020.0100.0100.0000.0000.0000.000
37A36THR0-0.093-0.05114.0640.0210.0210.0000.0000.0000.000
38A37LEU0-0.0100.0059.5390.0450.0450.0000.0000.0000.000
39A38SER0-0.005-0.03013.302-0.023-0.0230.0000.0000.0000.000
40A39ASN00.005-0.00616.082-0.028-0.0280.0000.0000.0000.000
41A40PRO00.009-0.00314.358-0.017-0.0170.0000.0000.0000.000
42A41LEU00.0200.02213.102-0.016-0.0160.0000.0000.0000.000
43A42ALA00.0510.02715.546-0.028-0.0280.0000.0000.0000.000
44A43ALA0-0.0170.00418.966-0.010-0.0100.0000.0000.0000.000
45A44ALA0-0.027-0.01916.127-0.008-0.0080.0000.0000.0000.000
46A45LEU00.0500.00117.439-0.016-0.0160.0000.0000.0000.000
47A46SER00.003-0.00419.645-0.006-0.0060.0000.0000.0000.000
48A47ALA0-0.075-0.03520.631-0.001-0.0010.0000.0000.0000.000
49A48GLN0-0.063-0.02518.772-0.012-0.0120.0000.0000.0000.000
50A49GLY0-0.0070.00722.151-0.013-0.0130.0000.0000.0000.000
51A50LEU0-0.060-0.03621.572-0.003-0.0030.0000.0000.0000.000
52A51PRO0-0.006-0.00523.1750.0010.0010.0000.0000.0000.000
53A52ALA00.0150.01321.560-0.010-0.0100.0000.0000.0000.000
54A53GLU-1-0.828-0.91723.4900.0060.0060.0000.0000.0000.000
55A54VAL0-0.039-0.02119.800-0.013-0.0130.0000.0000.0000.000
56A55VAL0-0.0020.00422.3660.0060.0060.0000.0000.0000.000
57A56PRO0-0.008-0.01322.646-0.011-0.0110.0000.0000.0000.000
58A57MET00.0470.05623.060-0.003-0.0030.0000.0000.0000.000
59A58ASP-1-0.796-0.88723.3700.0170.0170.0000.0000.0000.000
60A59GLY0-0.0110.00826.3160.0030.0030.0000.0000.0000.000
61A60PHE00.012-0.00228.799-0.001-0.0010.0000.0000.0000.000
62A61HIS0-0.074-0.02426.532-0.004-0.0040.0000.0000.0000.000
63A62LEU0-0.021-0.01631.2620.0020.0020.0000.0000.0000.000
64A63ASP-1-0.759-0.85634.7710.0090.0090.0000.0000.0000.000
65A64ASN00.0940.02536.315-0.004-0.0040.0000.0000.0000.000
66A65ARG10.8250.88338.571-0.006-0.0060.0000.0000.0000.000
67A66LEU0-0.046-0.02338.959-0.002-0.0020.0000.0000.0000.000
68A67LEU0-0.012-0.00734.103-0.002-0.0020.0000.0000.0000.000
69A68GLU-1-0.945-0.97338.3010.0010.0010.0000.0000.0000.000
70A69PRO00.0270.02440.998-0.001-0.0010.0000.0000.0000.000
71A70ARG10.8990.95437.8210.0140.0140.0000.0000.0000.000
72A71GLY00.0250.01639.991-0.002-0.0020.0000.0000.0000.000
73A72LEU0-0.018-0.01834.8790.0000.0000.0000.0000.0000.000
74A73LEU00.0020.01634.6290.0010.0010.0000.0000.0000.000
75A74PRO0-0.033-0.02334.4010.0030.0030.0000.0000.0000.000
76A75ARG10.7950.87128.8500.0220.0220.0000.0000.0000.000
77A76LYS10.7870.88830.290-0.017-0.0170.0000.0000.0000.000
78A77GLY00.0500.03627.1250.0070.0070.0000.0000.0000.000
79A78ALA0-0.0210.02525.975-0.006-0.0060.0000.0000.0000.000
80A79PRO00.0480.03025.7770.0030.0030.0000.0000.0000.000
81A80GLU-1-0.806-0.88728.120-0.029-0.0290.0000.0000.0000.000
82A81THR0-0.073-0.05229.8940.0060.0060.0000.0000.0000.000
83A82PHE00.0150.00526.0560.0040.0040.0000.0000.0000.000
84A83ASP-1-0.845-0.91931.303-0.032-0.0320.0000.0000.0000.000
85A84PHE00.0070.01528.557-0.001-0.0010.0000.0000.0000.000
86A85GLU-1-0.848-0.90831.239-0.041-0.0410.0000.0000.0000.000
87A86GLY0-0.038-0.02433.757-0.002-0.0020.0000.0000.0000.000
88A87PHE00.0160.01024.0460.0000.0000.0000.0000.0000.000
89A88GLN00.0480.03229.459-0.005-0.0050.0000.0000.0000.000
90A89ARG10.8160.89430.6110.0320.0320.0000.0000.0000.000
91A90LEU0-0.0150.00328.7250.0000.0000.0000.0000.0000.000
92A91CYS0-0.031-0.01626.818-0.002-0.0020.0000.0000.0000.000
93A92HIS00.006-0.01328.764-0.005-0.0050.0000.0000.0000.000
94A93ALA0-0.027-0.01031.6310.0000.0000.0000.0000.0000.000
95A94LEU00.004-0.01327.1360.0010.0010.0000.0000.0000.000
96A95LYS10.8300.92926.5650.1080.1080.0000.0000.0000.000
97A96HIS00.005-0.00830.2880.0020.0020.0000.0000.0000.000
98A97GLN0-0.056-0.01133.8790.0030.0030.0000.0000.0000.000
99A98GLU-1-0.865-0.93334.003-0.035-0.0350.0000.0000.0000.000
100A99ARG10.7920.88634.4100.0110.0110.0000.0000.0000.000
101A100VAL0-0.038-0.01432.3340.0000.0000.0000.0000.0000.000
102A101ILE00.0210.01633.0000.0020.0020.0000.0000.0000.000
103A102TYR0-0.024-0.01627.015-0.003-0.0030.0000.0000.0000.000
104A103PRO0-0.0260.00131.3340.0040.0040.0000.0000.0000.000
105A104LEU00.0300.01527.8280.0000.0000.0000.0000.0000.000
106A105PHE0-0.037-0.02428.343-0.001-0.0010.0000.0000.0000.000
107A106ASP-1-0.779-0.86129.4550.0450.0450.0000.0000.0000.000
108A107ARG10.8540.88824.665-0.042-0.0420.0000.0000.0000.000
109A108ALA0-0.0030.01130.1980.0010.0010.0000.0000.0000.000
110A109ARG10.8290.88333.194-0.031-0.0310.0000.0000.0000.000
111A110ASP-1-0.807-0.87432.8910.0170.0170.0000.0000.0000.000
112A111ILE0-0.010-0.00634.030-0.005-0.0050.0000.0000.0000.000
113A112ALA00.0280.02232.9610.0030.0030.0000.0000.0000.000
114A113ILE0-0.047-0.02133.727-0.001-0.0010.0000.0000.0000.000
115A114ALA00.034-0.00534.612-0.001-0.0010.0000.0000.0000.000
116A115GLY00.001-0.01036.0790.0020.0020.0000.0000.0000.000
117A116ALA0-0.039-0.01033.0960.0010.0010.0000.0000.0000.000
118A117ALA00.0040.01230.2520.0050.0050.0000.0000.0000.000
119A118GLU-1-0.848-0.91931.522-0.010-0.0100.0000.0000.0000.000
120A119VAL00.0100.02427.8930.0020.0020.0000.0000.0000.000
121A120GLY00.0430.02030.617-0.002-0.0020.0000.0000.0000.000
122A121PRO00.0060.00131.509-0.003-0.0030.0000.0000.0000.000
123A122GLU-1-0.912-0.95331.408-0.015-0.0150.0000.0000.0000.000
124A123CYS0-0.098-0.02726.620-0.004-0.0040.0000.0000.0000.000
125A124ARG10.9480.97526.2660.0690.0690.0000.0000.0000.000
126A125VAL0-0.006-0.00920.760-0.011-0.0110.0000.0000.0000.000
127A126ALA00.0560.02923.3540.0130.0130.0000.0000.0000.000
128A127ILE0-0.018-0.01017.008-0.016-0.0160.0000.0000.0000.000
129A128ILE00.0170.02320.3000.0220.0220.0000.0000.0000.000
130A129GLU-1-0.694-0.80918.1730.0250.0250.0000.0000.0000.000
131A130GLY0-0.019-0.05818.5760.0120.0120.0000.0000.0000.000
132A131ASN0-0.031-0.01918.398-0.001-0.0010.0000.0000.0000.000
133A132TYR0-0.007-0.04820.073-0.011-0.0110.0000.0000.0000.000
134A133LEU00.0220.01718.8100.0010.0010.0000.0000.0000.000
135A134LEU00.0070.01315.550-0.011-0.0110.0000.0000.0000.000
136A135PHE0-0.027-0.00819.184-0.010-0.0100.0000.0000.0000.000
137A136ASP-1-0.777-0.86821.897-0.119-0.1190.0000.0000.0000.000
138A137ALA0-0.017-0.00524.4500.0100.0100.0000.0000.0000.000
139A138PRO0-0.025-0.03027.700-0.004-0.0040.0000.0000.0000.000
140A139GLY00.0410.02930.4000.0050.0050.0000.0000.0000.000
141A140TRP0-0.010-0.03725.181-0.003-0.0030.0000.0000.0000.000
142A141ARG10.8790.90424.6770.0980.0980.0000.0000.0000.000
143A142ASP-1-0.883-0.93325.427-0.104-0.1040.0000.0000.0000.000
144A143LEU0-0.021-0.01524.5660.0010.0010.0000.0000.0000.000
145A144THR0-0.058-0.03921.406-0.006-0.0060.0000.0000.0000.000
146A145ALA0-0.0220.00123.524-0.012-0.0120.0000.0000.0000.000
147A146ILE0-0.058-0.02725.6870.0050.0050.0000.0000.0000.000
148A147TRP0-0.051-0.03720.4350.0120.0120.0000.0000.0000.000
149A148ASP-1-0.726-0.82822.363-0.132-0.1320.0000.0000.0000.000
150A149VAL0-0.0060.00015.743-0.026-0.0260.0000.0000.0000.000
151A150SER0-0.039-0.04516.4080.0240.0240.0000.0000.0000.000
152A151ILE0-0.008-0.01110.575-0.074-0.0740.0000.0000.0000.000
153A152ARG10.8540.93811.0950.4190.4190.0000.0000.0000.000
154A153LEU0-0.057-0.0269.004-0.115-0.1150.0000.0000.0000.000
155A154GLU-1-0.784-0.8727.486-0.389-0.3890.0000.0000.0000.000
156A155VAL0-0.021-0.0288.4390.1040.1040.0000.0000.0000.000
157A156PRO00.0360.0219.936-0.027-0.0270.0000.0000.0000.000
158A157MET00.0230.00913.1030.0390.0390.0000.0000.0000.000
159A158ALA00.0560.02816.2920.0130.0130.0000.0000.0000.000
160A159ASP-1-0.839-0.90512.8340.3720.3720.0000.0000.0000.000
161A160LEU0-0.035-0.02014.7510.0220.0220.0000.0000.0000.000
162A161GLU-1-0.864-0.92916.8530.0610.0610.0000.0000.0000.000
163A162ALA00.0050.00517.5360.0000.0000.0000.0000.0000.000
164A163ARG10.8290.90810.981-0.363-0.3630.0000.0000.0000.000
165A164LEU0-0.048-0.02119.060-0.008-0.0080.0000.0000.0000.000
166A165VAL00.002-0.00121.975-0.008-0.0080.0000.0000.0000.000
167A166GLN0-0.045-0.02521.728-0.002-0.0020.0000.0000.0000.000
168A167ARG10.8500.91222.516-0.079-0.0790.0000.0000.0000.000
169A168TRP0-0.084-0.05524.381-0.010-0.0100.0000.0000.0000.000
170A169LEU0-0.0010.00026.052-0.008-0.0080.0000.0000.0000.000
171A170ASP-1-0.855-0.91624.6200.1380.1380.0000.0000.0000.000
172A171HIS0-0.101-0.04528.221-0.003-0.0030.0000.0000.0000.000
173A172GLY00.0000.00330.704-0.007-0.0070.0000.0000.0000.000
174A173LEU0-0.085-0.03131.027-0.007-0.0070.0000.0000.0000.000
175A174ASN00.002-0.02732.2920.0040.0040.0000.0000.0000.000
176A175HIS00.0620.02526.7320.0030.0030.0000.0000.0000.000
177A176ASP-1-0.825-0.90230.0760.0580.0580.0000.0000.0000.000
178A177ALA0-0.014-0.00931.923-0.004-0.0040.0000.0000.0000.000
179A178ALA0-0.010-0.00327.989-0.004-0.0040.0000.0000.0000.000
180A179VAL00.0140.00226.7200.0000.0000.0000.0000.0000.000
181A180ALA00.0010.00428.039-0.005-0.0050.0000.0000.0000.000
182A181ARG10.8890.95129.254-0.045-0.0450.0000.0000.0000.000
183A182ALA00.0030.00824.190-0.004-0.0040.0000.0000.0000.000
184A183GLN0-0.039-0.04625.509-0.012-0.0120.0000.0000.0000.000
185A184GLY00.0000.01326.748-0.009-0.0090.0000.0000.0000.000
186A185ASN00.004-0.01427.269-0.010-0.0100.0000.0000.0000.000
187A186ASP-1-0.783-0.86923.0760.0370.0370.0000.0000.0000.000
188A187LEU00.0500.01120.473-0.009-0.0090.0000.0000.0000.000
189A188ALA0-0.033-0.01523.077-0.012-0.0120.0000.0000.0000.000
190A189ASN00.0160.00424.292-0.015-0.0150.0000.0000.0000.000
191A190ALA00.001-0.00418.961-0.012-0.0120.0000.0000.0000.000
192A191ARG10.9360.97419.780-0.005-0.0050.0000.0000.0000.000
193A192ALA0-0.010-0.00221.799-0.012-0.0120.0000.0000.0000.000
194A193ILE0-0.033-0.01717.821-0.008-0.0080.0000.0000.0000.000
195A194GLU-1-0.859-0.91415.765-0.221-0.2210.0000.0000.0000.000
196A195ALA0-0.057-0.02918.743-0.017-0.0170.0000.0000.0000.000
197A196ALA0-0.0180.00121.0700.0010.0010.0000.0000.0000.000
198A197ARG10.7440.83112.1380.3270.3270.0000.0000.0000.000
199A198LEU00.0030.02718.749-0.009-0.0090.0000.0000.0000.000
200A199PRO00.012-0.00316.314-0.030-0.0300.0000.0000.0000.000
201A200ALA00.0080.00013.1290.0350.0350.0000.0000.0000.000
202A201ASP-1-0.852-0.88014.340-0.385-0.3850.0000.0000.0000.000
203A202LEU0-0.027-0.01010.270-0.113-0.1130.0000.0000.0000.000
204A203THR0-0.046-0.0397.4930.1940.1940.0000.0000.0000.000
205A204TRP00.0060.0085.181-0.458-0.4580.0000.0000.0000.000
206A205PRO00.0310.0341.902-4.160-7.6279.178-3.102-2.609-0.023