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: K94J3

Calculation Name: 3F1C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F1C

Chain ID: A

ChEMBL ID:

UniProt ID: Q720Y7

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2978134.577274
FMO2-HF: Nuclear repulsion 2884986.978885
FMO2-HF: Total energy -93147.598388
FMO2-MP2: Total energy -93419.35715


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:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-9.023-43.239-3.84-4.422-0.017
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.027
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].
3A2ILE0-0.002-0.0023.818-0.5620.997-0.019-0.650-0.8900.003
4A3TYR00.0100.0126.1550.8000.8000.0000.0000.0000.000
5A4ALA00.0070.0089.5660.0560.0560.0000.0000.0000.000
6A5GLN0-0.031-0.03312.8100.0140.0140.0000.0000.0000.000
7A6ILE0-0.0100.00015.7410.0340.0340.0000.0000.0000.000
8A7LEU0-0.004-0.00218.0140.0270.0270.0000.0000.0000.000
9A8ALA0-0.023-0.00921.7130.0130.0130.0000.0000.0000.000
10A9GLY0-0.040-0.00825.4960.0010.0010.0000.0000.0000.000
11A10GLY00.0830.03524.456-0.001-0.0010.0000.0000.0000.000
12A11LYS10.9800.96025.4690.1200.1200.0000.0000.0000.000
13A12GLY00.0540.03728.8820.0000.0000.0000.0000.0000.000
14A13THR0-0.056-0.05632.2460.0040.0040.0000.0000.0000.000
15A14ARG10.9200.94635.8230.0780.0780.0000.0000.0000.000
16A15MET00.0470.06933.2760.0030.0030.0000.0000.0000.000
17A16GLY00.035-0.00237.882-0.001-0.0010.0000.0000.0000.000
18A17ASN0-0.013-0.02433.661-0.003-0.0030.0000.0000.0000.000
19A18VAL00.0540.04735.552-0.002-0.0020.0000.0000.0000.000
20A19SER0-0.081-0.04635.7880.0010.0010.0000.0000.0000.000
21A20MET00.0160.03134.350-0.004-0.0040.0000.0000.0000.000
22A21PRO00.0020.00629.6120.0000.0000.0000.0000.0000.000
23A22LYS10.9200.93131.4680.1050.1050.0000.0000.0000.000
24A23GLN00.0690.02826.1520.0100.0100.0000.0000.0000.000
25A24PHE00.0080.00228.292-0.004-0.0040.0000.0000.0000.000
26A25LEU0-0.0100.00431.7360.0080.0080.0000.0000.0000.000
27A26PRO0-0.014-0.00832.843-0.007-0.0070.0000.0000.0000.000
28A27LEU00.0030.01130.6440.0050.0050.0000.0000.0000.000
29A28ASN0-0.014-0.01633.4730.0010.0010.0000.0000.0000.000
30A29GLY00.0200.01235.193-0.001-0.0010.0000.0000.0000.000
31A30LYS10.8970.96728.6760.1440.1440.0000.0000.0000.000
32A31PRO00.0320.02029.894-0.001-0.0010.0000.0000.0000.000
33A32ILE0-0.0160.00427.677-0.008-0.0080.0000.0000.0000.000
34A33ILE00.018-0.01223.163-0.008-0.0080.0000.0000.0000.000
35A34VAL00.0010.01524.520-0.019-0.0190.0000.0000.0000.000
36A35HIS0-0.033-0.02524.780-0.016-0.0160.0000.0000.0000.000
37A36THR0-0.044-0.03321.180-0.004-0.0040.0000.0000.0000.000
38A37VAL00.0170.00420.054-0.025-0.0250.0000.0000.0000.000
39A38GLU-1-0.871-0.94519.788-0.203-0.2030.0000.0000.0000.000
40A39LYS10.8560.94119.5730.1910.1910.0000.0000.0000.000
41A40PHE0-0.009-0.00914.687-0.002-0.0020.0000.0000.0000.000
42A41ILE00.0170.01715.336-0.059-0.0590.0000.0000.0000.000
43A42LEU0-0.052-0.02816.959-0.001-0.0010.0000.0000.0000.000
44A43ASN0-0.054-0.02711.498-0.087-0.0870.0000.0000.0000.000
45A44THR00.010-0.02811.752-0.010-0.0100.0000.0000.0000.000
46A45ARG10.8870.9635.6790.5410.5410.0000.0000.0000.000
47A46PHE0-0.0190.0047.527-0.408-0.4080.0000.0000.0000.000
48A47ASP-1-0.776-0.8856.588-2.291-2.2910.0000.0000.0000.000
49A48LYS10.8470.9199.9260.6570.6570.0000.0000.0000.000
50A49ILE0-0.035-0.01912.587-0.100-0.1000.0000.0000.0000.000
51A50LEU00.0000.00113.7490.0920.0920.0000.0000.0000.000
52A51ILE0-0.025-0.00916.8930.0010.0010.0000.0000.0000.000
53A52SER00.0180.01620.4080.0070.0070.0000.0000.0000.000
54A53SER0-0.046-0.03222.1040.0100.0100.0000.0000.0000.000
55A54PRO00.0460.02925.852-0.001-0.0010.0000.0000.0000.000
56A55LYS11.0291.00928.6410.0930.0930.0000.0000.0000.000
57A56GLU-1-0.927-0.96229.761-0.105-0.1050.0000.0000.0000.000
58A57TRP0-0.029-0.03430.3750.0040.0040.0000.0000.0000.000
59A58MET00.0120.02124.665-0.003-0.0030.0000.0000.0000.000
60A59ASN00.0530.02228.210-0.010-0.0100.0000.0000.0000.000
61A60HIS0-0.0070.00530.6970.0040.0040.0000.0000.0000.000
62A61ALA0-0.017-0.01926.492-0.002-0.0020.0000.0000.0000.000
63A62GLU-1-0.864-0.94024.209-0.194-0.1940.0000.0000.0000.000
64A63ASP-1-0.906-0.95827.101-0.110-0.1100.0000.0000.0000.000
65A64ASN0-0.086-0.05628.8170.0090.0090.0000.0000.0000.000
66A65ILE00.0090.00123.3880.0030.0030.0000.0000.0000.000
67A66LYS10.9991.00324.7990.1450.1450.0000.0000.0000.000
68A67LYS10.8880.96527.2790.1090.1090.0000.0000.0000.000
69A68TYR0-0.076-0.04327.9450.0100.0100.0000.0000.0000.000
70A69ILE0-0.014-0.00221.999-0.002-0.0020.0000.0000.0000.000
71A70SER0-0.035-0.01924.5380.0010.0010.0000.0000.0000.000
72A71ASP-1-0.827-0.91717.706-0.343-0.3430.0000.0000.0000.000
73A72ASP-1-0.897-0.93916.977-0.280-0.2800.0000.0000.0000.000
74A73ARG10.7860.88612.6500.5770.5770.0000.0000.0000.000
75A74ILE0-0.0170.00416.178-0.055-0.0550.0000.0000.0000.000
76A75VAL0-0.0030.00116.5460.0340.0340.0000.0000.0000.000
77A76VAL0-0.0210.00019.432-0.029-0.0290.0000.0000.0000.000
78A77ILE0-0.027-0.01117.5740.0160.0160.0000.0000.0000.000
79A78GLU-1-0.913-0.98321.596-0.127-0.1270.0000.0000.0000.000
80A79GLY0-0.063-0.04022.590-0.018-0.0180.0000.0000.0000.000
81A80GLY0-0.009-0.01424.1920.0110.0110.0000.0000.0000.000
82A81GLU-1-0.933-0.96725.503-0.114-0.1140.0000.0000.0000.000
83A82ASP-1-0.880-0.92225.297-0.151-0.1510.0000.0000.0000.000
84A83ARG10.9000.96619.2420.2470.2470.0000.0000.0000.000
85A84ASN00.0310.01320.826-0.046-0.0460.0000.0000.0000.000
86A85GLU-1-0.879-0.94120.445-0.162-0.1620.0000.0000.0000.000
87A86THR0-0.008-0.00420.752-0.005-0.0050.0000.0000.0000.000
88A87ILE00.0030.01315.682-0.022-0.0220.0000.0000.0000.000
89A88MET0-0.058-0.01716.576-0.041-0.0410.0000.0000.0000.000
90A89ASN0-0.010-0.00817.5580.0060.0060.0000.0000.0000.000
91A90GLY00.0180.01815.9870.0100.0100.0000.0000.0000.000
92A91ILE00.005-0.00211.823-0.032-0.0320.0000.0000.0000.000
93A92ARG10.9020.94213.4730.2030.2030.0000.0000.0000.000
94A93PHE0-0.0130.00215.3210.0380.0380.0000.0000.0000.000
95A94VAL00.0320.0189.2890.0550.0550.0000.0000.0000.000
96A95GLU-1-0.886-0.94411.873-0.046-0.0460.0000.0000.0000.000
97A96LYS10.8870.95212.8010.1550.1550.0000.0000.0000.000
98A97THR0-0.089-0.05514.7710.0490.0490.0000.0000.0000.000
99A98TYR0-0.043-0.03910.4690.0090.0090.0000.0000.0000.000
100A99GLY0-0.0020.03410.5440.1400.1400.0000.0000.0000.000
101A100LEU0-0.002-0.0107.673-0.080-0.0800.0000.0000.0000.000
102A101THR0-0.052-0.0203.942-0.0410.2060.000-0.060-0.1870.000
103A102ASP-1-0.925-0.9856.347-0.400-0.4000.0000.0000.0000.000
104A103ASP-1-0.866-0.9272.081-1.874-1.9412.672-1.417-1.188-0.006
105A104ASP-1-0.839-0.9002.856-6.447-3.8040.530-1.539-1.634-0.014
106A105ILE0-0.006-0.0014.3070.9831.117-0.001-0.019-0.1140.000
107A106ILE0-0.024-0.0236.279-0.126-0.1260.0000.0000.0000.000
108A107VAL00.0110.0049.7100.1530.1530.0000.0000.0000.000
109A108THR0-0.056-0.04812.1630.0590.0590.0000.0000.0000.000
110A109HIS00.0830.01915.5670.0220.0220.0000.0000.0000.000
111A110ASP-1-0.843-0.92818.688-0.207-0.2070.0000.0000.0000.000
112A111ALA00.0690.01622.4830.0020.0020.0000.0000.0000.000
113A112VAL0-0.082-0.03723.9240.0090.0090.0000.0000.0000.000
114A113ARG10.8900.95423.1290.1990.1990.0000.0000.0000.000
115A114PRO00.0540.04523.618-0.018-0.0180.0000.0000.0000.000
116A115PHE0-0.089-0.05624.900-0.004-0.0040.0000.0000.0000.000
117A116LEU00.0520.04418.5990.0130.0130.0000.0000.0000.000
118A117THR00.020-0.00521.543-0.006-0.0060.0000.0000.0000.000
119A118HIS00.0520.00717.907-0.007-0.0070.0000.0000.0000.000
120A119ARG10.8100.92616.7050.1170.1170.0000.0000.0000.000
121A120ILE0-0.0220.00716.906-0.009-0.0090.0000.0000.0000.000
122A121ILE00.0240.00813.420-0.012-0.0120.0000.0000.0000.000
123A122GLU-1-0.848-0.92412.113-0.483-0.4830.0000.0000.0000.000
124A123GLU-1-0.835-0.92912.119-0.139-0.1390.0000.0000.0000.000
125A124ASN0-0.066-0.03812.9090.0060.0060.0000.0000.0000.000
126A125ILE0-0.0080.0007.337-0.051-0.0510.0000.0000.0000.000
127A126ASP-1-0.864-0.9348.089-0.111-0.1110.0000.0000.0000.000
128A127ALA00.010-0.0039.6000.1070.1070.0000.0000.0000.000
129A128ALA0-0.039-0.0218.4180.0340.0340.0000.0000.0000.000
130A129LEU0-0.035-0.0233.340-0.666-0.1590.057-0.155-0.4090.000
131A130GLU-1-0.992-0.9706.5230.1470.1470.0000.0000.0000.000
132A131THR0-0.027-0.0389.921-0.010-0.0100.0000.0000.0000.000
133A132GLY0-0.027-0.0119.468-0.022-0.0220.0000.0000.0000.000
134A133ALA00.009-0.01310.408-0.045-0.0450.0000.0000.0000.000
135A134VAL0-0.0220.00912.2480.0450.0450.0000.0000.0000.000
136A135ASP-1-0.816-0.93515.036-0.231-0.2310.0000.0000.0000.000
137A136THR0-0.032-0.01217.9950.0120.0120.0000.0000.0000.000
138A137VAL00.0290.01519.9540.0070.0070.0000.0000.0000.000
139A138ILE0-0.075-0.02823.5210.0000.0000.0000.0000.0000.000
140A139GLU-1-0.875-0.93526.700-0.067-0.0670.0000.0000.0000.000
141A140ALA0-0.043-0.02329.676-0.002-0.0020.0000.0000.0000.000
142A141LEU0-0.020-0.01232.1840.0050.0050.0000.0000.0000.000
143A142ASP-1-0.942-0.97434.632-0.069-0.0690.0000.0000.0000.000
144A143THR0-0.077-0.04636.360-0.001-0.0010.0000.0000.0000.000
145A144ILE00.0300.02633.741-0.001-0.0010.0000.0000.0000.000
146A145VAL0-0.017-0.01137.2020.0030.0030.0000.0000.0000.000
147A146GLU-1-0.922-0.96036.087-0.061-0.0610.0000.0000.0000.000
148A147SER0-0.008-0.06639.4940.0040.0040.0000.0000.0000.000
149A148SER0-0.021-0.01740.593-0.002-0.0020.0000.0000.0000.000
150A149ASN0-0.008-0.01541.920-0.001-0.0010.0000.0000.0000.000
151A150HIS0-0.069-0.01440.153-0.001-0.0010.0000.0000.0000.000
152A151GLU-1-0.882-0.93144.724-0.043-0.0430.0000.0000.0000.000
153A152VAL0-0.044-0.02047.4530.0010.0010.0000.0000.0000.000
154A153ILE0-0.0180.02543.558-0.002-0.0020.0000.0000.0000.000
155A154THR0-0.065-0.03941.5820.0020.0020.0000.0000.0000.000
156A155ASP-1-0.852-0.92839.597-0.041-0.0410.0000.0000.0000.000
157A156ILE0-0.083-0.04140.259-0.002-0.0020.0000.0000.0000.000
158A157PRO00.0410.04135.7850.0030.0030.0000.0000.0000.000
159A158VAL00.002-0.00135.5190.0000.0000.0000.0000.0000.000
160A159ARG10.9600.96535.1150.0520.0520.0000.0000.0000.000
161A160ASP-1-0.881-0.93632.921-0.049-0.0490.0000.0000.0000.000
162A161HIS0-0.051-0.02530.790-0.001-0.0010.0000.0000.0000.000
163A162MET0-0.054-0.00929.956-0.007-0.0070.0000.0000.0000.000
164A163TYR00.0270.01226.532-0.002-0.0020.0000.0000.0000.000
165A164GLN0-0.036-0.02028.135-0.004-0.0040.0000.0000.0000.000
166A165GLY00.0480.02424.536-0.006-0.0060.0000.0000.0000.000
167A166GLN0-0.083-0.07322.902-0.005-0.0050.0000.0000.0000.000
168A167THR0-0.013-0.00619.6020.0000.0000.0000.0000.0000.000
169A168PRO0-0.023-0.03715.6550.0240.0240.0000.0000.0000.000
170A169GLN0-0.0350.01416.3440.0260.0260.0000.0000.0000.000
171A170SER0-0.0050.01410.910-0.062-0.0620.0000.0000.0000.000
172A171PHE00.0170.00210.9980.0890.0890.0000.0000.0000.000
173A172ASN00.0370.0246.773-0.132-0.1320.0000.0000.0000.000
174A173MET0-0.046-0.0237.4620.3230.3230.0000.0000.0000.000
175A174LYS10.9030.9529.1270.3440.3440.0000.0000.0000.000
176A175LYS10.9420.97811.0260.3050.3050.0000.0000.0000.000
177A176VAL00.0510.03512.7610.0680.0680.0000.0000.0000.000
178A177PHE0-0.033-0.01814.0880.0600.0600.0000.0000.0000.000
179A178ASN0-0.008-0.02314.6400.0500.0500.0000.0000.0000.000
180A179HIS0-0.009-0.00416.3810.0350.0350.0000.0000.0000.000
181A180TYR00.018-0.00418.6560.0260.0260.0000.0000.0000.000
182A181GLN0-0.062-0.04519.5980.0370.0370.0000.0000.0000.000
183A182ASN00.0190.02020.9160.0190.0190.0000.0000.0000.000
184A183LEU0-0.068-0.01123.2180.0150.0150.0000.0000.0000.000
185A184THR0-0.011-0.00625.6870.0030.0030.0000.0000.0000.000
186A185PRO00.042-0.00628.774-0.006-0.0060.0000.0000.0000.000
187A186GLU-1-0.853-0.94030.260-0.083-0.0830.0000.0000.0000.000
188A187LYS10.9070.95627.8710.0750.0750.0000.0000.0000.000
189A188LYS10.8900.96124.0570.1230.1230.0000.0000.0000.000
190A189GLN00.0300.04127.191-0.014-0.0140.0000.0000.0000.000
191A190ILE0-0.073-0.03130.0920.0000.0000.0000.0000.0000.000
192A191LEU0-0.058-0.03724.6010.0010.0010.0000.0000.0000.000
193A192THR00.0300.01225.224-0.012-0.0120.0000.0000.0000.000
194A193ASP-1-0.881-0.93721.933-0.203-0.2030.0000.0000.0000.000
195A194ALA00.0640.01418.1040.0080.0080.0000.0000.0000.000
196A195CYS00.0020.01018.465-0.020-0.0200.0000.0000.0000.000
197A196LYS10.9400.98519.5110.1210.1210.0000.0000.0000.000
198A197ILE0-0.021-0.01420.1520.0150.0150.0000.0000.0000.000
199A198CYS0-0.0090.00416.466-0.002-0.0020.0000.0000.0000.000
200A199LEU00.0250.02918.8140.0140.0140.0000.0000.0000.000
201A200LEU0-0.098-0.06221.5230.0150.0150.0000.0000.0000.000
202A201ALA0-0.048-0.01419.7610.0130.0130.0000.0000.0000.000
203A202GLY0-0.031-0.01120.8410.0050.0050.0000.0000.0000.000
204A203ASP-1-0.875-0.93615.497-0.195-0.1950.0000.0000.0000.000
205A204ASP-1-0.879-0.93316.731-0.062-0.0620.0000.0000.0000.000
206A205VAL0-0.062-0.01915.985-0.025-0.0250.0000.0000.0000.000
207A206LYS10.9620.98714.9640.0910.0910.0000.0000.0000.000
208A207LEU00.012-0.00217.243-0.023-0.0230.0000.0000.0000.000
209A208VAL0-0.0020.01315.5170.0170.0170.0000.0000.0000.000
210A209LYS10.9450.97818.7790.1060.1060.0000.0000.0000.000
211A210GLY00.0560.00921.620-0.013-0.0130.0000.0000.0000.000
212A211GLU-1-0.927-0.97723.192-0.109-0.1090.0000.0000.0000.000
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214A213PHE00.0330.00826.1080.0000.0000.0000.0000.0000.000
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