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: 5214Z

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2987518.682576
FMO2-HF: Nuclear repulsion 2894369.13579
FMO2-HF: Total energy -93149.546786
FMO2-MP2: Total energy -93421.374077


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.
-9.738-4.2154.1-4.252-5.373-0.02
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 : -0.031 / q_NPA : -0.021
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].
3A2ILE0-0.011-0.0103.767-1.4080.169-0.010-0.689-0.8790.004
4A3TYR00.0240.0086.2030.9180.9180.0000.0000.0000.000
5A4ALA0-0.010-0.0029.6470.0410.0410.0000.0000.0000.000
6A5GLN0-0.028-0.04012.8940.0130.0130.0000.0000.0000.000
7A6ILE0-0.0080.00915.8640.0300.0300.0000.0000.0000.000
8A7LEU00.0300.01517.8910.0260.0260.0000.0000.0000.000
9A8ALA0-0.040-0.02621.8300.0150.0150.0000.0000.0000.000
10A9GLY0-0.056-0.02725.625-0.001-0.0010.0000.0000.0000.000
11A10GLY00.0980.06724.2520.0020.0020.0000.0000.0000.000
12A11LYS10.9720.96425.2950.1250.1250.0000.0000.0000.000
13A12GLY00.0620.04828.6950.0010.0010.0000.0000.0000.000
14A13THR0-0.041-0.04632.2320.0030.0030.0000.0000.0000.000
15A14ARG10.9270.95035.5980.0850.0850.0000.0000.0000.000
16A15MET0-0.0210.05033.1900.0030.0030.0000.0000.0000.000
17A16GLY00.0450.00637.554-0.002-0.0020.0000.0000.0000.000
18A17ASN00.025-0.02032.5510.0010.0010.0000.0000.0000.000
19A18VAL00.0560.03435.370-0.004-0.0040.0000.0000.0000.000
20A19SER0-0.070-0.03236.1520.0020.0020.0000.0000.0000.000
21A20MET00.0140.01734.381-0.005-0.0050.0000.0000.0000.000
22A21PRO0-0.0220.00229.669-0.001-0.0010.0000.0000.0000.000
23A22LYS10.9320.94531.7100.1040.1040.0000.0000.0000.000
24A23GLN00.0710.04126.7220.0110.0110.0000.0000.0000.000
25A24PHE00.005-0.00129.033-0.002-0.0020.0000.0000.0000.000
26A25LEU00.0030.00631.9770.0080.0080.0000.0000.0000.000
27A26PRO0-0.026-0.01333.284-0.007-0.0070.0000.0000.0000.000
28A27LEU00.0020.01131.0360.0050.0050.0000.0000.0000.000
29A28ASN0-0.011-0.01433.677-0.001-0.0010.0000.0000.0000.000
30A29GLY00.0280.02135.176-0.001-0.0010.0000.0000.0000.000
31A30LYS10.8230.90428.0320.1450.1450.0000.0000.0000.000
32A31PRO0-0.0050.00430.378-0.001-0.0010.0000.0000.0000.000
33A32ILE0-0.0070.00428.029-0.008-0.0080.0000.0000.0000.000
34A33ILE00.020-0.00523.476-0.009-0.0090.0000.0000.0000.000
35A34VAL0-0.0030.00924.889-0.018-0.0180.0000.0000.0000.000
36A35HIS0-0.025-0.01424.972-0.016-0.0160.0000.0000.0000.000
37A36THR0-0.049-0.03421.557-0.005-0.0050.0000.0000.0000.000
38A37VAL00.0310.01220.344-0.025-0.0250.0000.0000.0000.000
39A38GLU-1-0.780-0.88019.911-0.193-0.1930.0000.0000.0000.000
40A39LYS10.7970.89519.5580.1940.1940.0000.0000.0000.000
41A40PHE00.0210.01014.702-0.006-0.0060.0000.0000.0000.000
42A41ILE00.0050.01315.430-0.044-0.0440.0000.0000.0000.000
43A42LEU0-0.072-0.03717.026-0.001-0.0010.0000.0000.0000.000
44A43ASN0-0.019-0.01412.033-0.044-0.0440.0000.0000.0000.000
45A44THR00.006-0.01311.950-0.022-0.0220.0000.0000.0000.000
46A45ARG10.7480.8397.0530.4780.4780.0000.0000.0000.000
47A46PHE0-0.0150.0047.667-0.379-0.3790.0000.0000.0000.000
48A47ASP-1-0.775-0.8826.667-1.921-1.9210.0000.0000.0000.000
49A48LYS10.8320.8819.9300.6070.6070.0000.0000.0000.000
50A49ILE0-0.028-0.01612.518-0.130-0.1300.0000.0000.0000.000
51A50LEU00.0140.01613.4200.0940.0940.0000.0000.0000.000
52A51ILE0-0.030-0.02617.0000.0000.0000.0000.0000.0000.000
53A52SER00.0110.01920.1130.0090.0090.0000.0000.0000.000
54A53SER0-0.045-0.03921.9750.0100.0100.0000.0000.0000.000
55A54PRO00.0260.01825.7470.0000.0000.0000.0000.0000.000
56A55LYS10.8900.92628.5010.1120.1120.0000.0000.0000.000
57A56GLU-1-0.860-0.94429.464-0.115-0.1150.0000.0000.0000.000
58A57TRP0-0.021-0.02630.3510.0050.0050.0000.0000.0000.000
59A58MET0-0.0170.01624.379-0.004-0.0040.0000.0000.0000.000
60A59ASN0-0.002-0.00628.003-0.005-0.0050.0000.0000.0000.000
61A60HIS0-0.0060.00530.2940.0020.0020.0000.0000.0000.000
62A61ALA0-0.011-0.02026.285-0.001-0.0010.0000.0000.0000.000
63A62GLU-1-0.756-0.87923.758-0.196-0.1960.0000.0000.0000.000
64A63ASP-1-0.846-0.92227.044-0.103-0.1030.0000.0000.0000.000
65A64ASN0-0.068-0.04329.2380.0150.0150.0000.0000.0000.000
66A65ILE00.001-0.00623.4040.0030.0030.0000.0000.0000.000
67A66LYS10.8610.91822.2610.1870.1870.0000.0000.0000.000
68A67LYS10.8430.94427.0180.1170.1170.0000.0000.0000.000
69A68TYR0-0.070-0.04128.1200.0090.0090.0000.0000.0000.000
70A69ILE0-0.014-0.01022.204-0.001-0.0010.0000.0000.0000.000
71A70SER0-0.004-0.00624.500-0.005-0.0050.0000.0000.0000.000
72A71ASP-1-0.794-0.87617.807-0.320-0.3200.0000.0000.0000.000
73A72ASP-1-0.838-0.92817.328-0.245-0.2450.0000.0000.0000.000
74A73ARG10.7020.85112.9150.5170.5170.0000.0000.0000.000
75A74ILE0-0.0040.01816.543-0.053-0.0530.0000.0000.0000.000
76A75VAL00.0060.00616.9690.0410.0410.0000.0000.0000.000
77A76VAL0-0.033-0.00219.534-0.031-0.0310.0000.0000.0000.000
78A77ILE0-0.027-0.01117.3950.0140.0140.0000.0000.0000.000
79A78GLU-1-0.766-0.88221.525-0.127-0.1270.0000.0000.0000.000
80A79GLY0-0.020-0.01222.405-0.020-0.0200.0000.0000.0000.000
81A80GLY00.0220.00323.9920.0110.0110.0000.0000.0000.000
82A81GLU-1-0.940-0.97425.865-0.135-0.1350.0000.0000.0000.000
83A82ASP-1-0.772-0.87624.577-0.186-0.1860.0000.0000.0000.000
84A83ARG10.7840.88520.5050.2430.2430.0000.0000.0000.000
85A84ASN0-0.032-0.03920.361-0.043-0.0430.0000.0000.0000.000
86A85GLU-1-0.926-0.95620.083-0.184-0.1840.0000.0000.0000.000
87A86THR0-0.012-0.01220.624-0.007-0.0070.0000.0000.0000.000
88A87ILE00.0080.01515.272-0.023-0.0230.0000.0000.0000.000
89A88MET0-0.054-0.01016.251-0.037-0.0370.0000.0000.0000.000
90A89ASN0-0.063-0.02617.2730.0050.0050.0000.0000.0000.000
91A90GLY00.0190.01615.6200.0100.0100.0000.0000.0000.000
92A91ILE00.0200.00711.772-0.019-0.0190.0000.0000.0000.000
93A92ARG10.8980.92913.2220.2350.2350.0000.0000.0000.000
94A93PHE0-0.018-0.00415.0190.0470.0470.0000.0000.0000.000
95A94VAL00.0290.0239.0310.0530.0530.0000.0000.0000.000
96A95GLU-1-0.843-0.92811.650-0.078-0.0780.0000.0000.0000.000
97A96LYS10.8820.93712.7140.1740.1740.0000.0000.0000.000
98A97THR0-0.089-0.05114.4270.0510.0510.0000.0000.0000.000
99A98TYR0-0.059-0.04010.2630.0030.0030.0000.0000.0000.000
100A99GLY0-0.0070.02610.3130.1680.1680.0000.0000.0000.000
101A100LEU0-0.050-0.0237.284-0.115-0.1150.0000.0000.0000.000
102A101THR0-0.019-0.0452.827-0.7420.0180.071-0.297-0.533-0.001
103A102ASP-1-0.873-0.9485.680-0.578-0.5780.0000.0000.0000.000
104A103ASP-1-0.875-0.9172.251-2.389-2.4262.629-1.265-1.327-0.005
105A104ASP-1-0.819-0.8622.588-5.931-3.3711.334-1.849-2.046-0.018
106A105ILE0-0.022-0.0083.8951.2021.3810.004-0.021-0.1620.000
107A106ILE0-0.025-0.0206.089-0.072-0.0720.0000.0000.0000.000
108A107VAL00.0090.0079.6200.1500.1500.0000.0000.0000.000
109A108THR0-0.044-0.02812.2350.0680.0680.0000.0000.0000.000
110A109HIS00.0920.03115.6050.0270.0270.0000.0000.0000.000
111A110ASP-1-0.788-0.88618.859-0.210-0.2100.0000.0000.0000.000
112A111ALA00.026-0.01222.6740.0050.0050.0000.0000.0000.000
113A112VAL0-0.063-0.02924.0400.0110.0110.0000.0000.0000.000
114A113ARG10.8570.95223.0940.2160.2160.0000.0000.0000.000
115A114PRO00.0390.02523.894-0.018-0.0180.0000.0000.0000.000
116A115PHE0-0.051-0.03125.5990.0020.0020.0000.0000.0000.000
117A116LEU00.0690.05218.8340.0130.0130.0000.0000.0000.000
118A117THR00.009-0.01621.2980.0050.0050.0000.0000.0000.000
119A118HIS00.0710.02017.790-0.012-0.0120.0000.0000.0000.000
120A119ARG10.7310.83916.6850.1340.1340.0000.0000.0000.000
121A120ILE0-0.0260.01317.054-0.010-0.0100.0000.0000.0000.000
122A121ILE0-0.0040.00413.288-0.020-0.0200.0000.0000.0000.000
123A122GLU-1-0.782-0.87012.273-0.535-0.5350.0000.0000.0000.000
124A123GLU-1-0.804-0.89912.238-0.177-0.1770.0000.0000.0000.000
125A124ASN0-0.046-0.02812.888-0.008-0.0080.0000.0000.0000.000
126A125ILE00.0020.0057.387-0.060-0.0600.0000.0000.0000.000
127A126ASP-1-0.780-0.8658.088-0.140-0.1400.0000.0000.0000.000
128A127ALA00.0110.0049.5680.0930.0930.0000.0000.0000.000
129A128ALA0-0.035-0.0258.2840.0330.0330.0000.0000.0000.000
130A129LEU0-0.007-0.0113.135-0.639-0.1550.072-0.131-0.4260.000
131A130GLU-1-0.877-0.8966.5290.0950.0950.0000.0000.0000.000
132A131THR0-0.044-0.02510.0380.0080.0080.0000.0000.0000.000
133A132GLY00.0280.0198.995-0.030-0.0300.0000.0000.0000.000
134A133ALA0-0.006-0.0179.899-0.051-0.0510.0000.0000.0000.000
135A134VAL0-0.0210.01012.3140.0540.0540.0000.0000.0000.000
136A135ASP-1-0.762-0.87614.938-0.274-0.2740.0000.0000.0000.000
137A136THR0-0.029-0.01217.9940.0180.0180.0000.0000.0000.000
138A137VAL00.020-0.00119.8700.0090.0090.0000.0000.0000.000
139A138ILE0-0.060-0.02323.4260.0010.0010.0000.0000.0000.000
140A139GLU-1-0.855-0.93226.655-0.080-0.0800.0000.0000.0000.000
141A140ALA0-0.038-0.01129.670-0.002-0.0020.0000.0000.0000.000
142A141LEU00.0180.00532.2460.0070.0070.0000.0000.0000.000
143A142ASP-1-0.918-0.95234.629-0.078-0.0780.0000.0000.0000.000
144A143THR0-0.030-0.03136.282-0.002-0.0020.0000.0000.0000.000
145A144ILE00.0360.02333.5030.0010.0010.0000.0000.0000.000
146A145VAL0-0.010-0.00336.9960.0040.0040.0000.0000.0000.000
147A146GLU-1-0.920-0.95035.667-0.074-0.0740.0000.0000.0000.000
148A147SER0-0.005-0.03839.4350.0040.0040.0000.0000.0000.000
149A148SER0-0.014-0.01940.791-0.003-0.0030.0000.0000.0000.000
150A149ASN0-0.021-0.01541.793-0.001-0.0010.0000.0000.0000.000
151A150HIS0-0.090-0.04839.741-0.001-0.0010.0000.0000.0000.000
152A151GLU-1-0.921-0.93544.321-0.046-0.0460.0000.0000.0000.000
153A152VAL0-0.031-0.02647.0250.0020.0020.0000.0000.0000.000
154A153ILE0-0.0150.01243.285-0.002-0.0020.0000.0000.0000.000
155A154THR0-0.051-0.03241.4800.0020.0020.0000.0000.0000.000
156A155ASP-1-0.826-0.90639.278-0.051-0.0510.0000.0000.0000.000
157A156ILE0-0.089-0.05240.258-0.002-0.0020.0000.0000.0000.000
158A157PRO00.0430.03235.7310.0020.0020.0000.0000.0000.000
159A158VAL0-0.011-0.00235.1120.0000.0000.0000.0000.0000.000
160A159ARG10.8620.91134.9980.0650.0650.0000.0000.0000.000
161A160ASP-1-0.839-0.90833.058-0.060-0.0600.0000.0000.0000.000
162A161HIS0-0.048-0.02830.592-0.004-0.0040.0000.0000.0000.000
163A162MET0-0.066-0.00830.284-0.007-0.0070.0000.0000.0000.000
164A163TYR0-0.004-0.00426.752-0.002-0.0020.0000.0000.0000.000
165A164GLN0-0.072-0.04228.159-0.002-0.0020.0000.0000.0000.000
166A165GLY00.0520.03124.604-0.005-0.0050.0000.0000.0000.000
167A166GLN0-0.078-0.06222.931-0.002-0.0020.0000.0000.0000.000
168A167THR0-0.0340.00019.715-0.002-0.0020.0000.0000.0000.000
169A168PRO0-0.003-0.02315.8030.0310.0310.0000.0000.0000.000
170A169GLN0-0.0270.00716.4260.0330.0330.0000.0000.0000.000
171A170SER0-0.012-0.00311.093-0.056-0.0560.0000.0000.0000.000
172A171PHE00.016-0.00410.7440.0920.0920.0000.0000.0000.000
173A172ASN00.0360.0195.8470.0050.0050.0000.0000.0000.000
174A173MET0-0.062-0.0227.2160.3720.3720.0000.0000.0000.000
175A174LYS10.8430.9048.4620.4530.4530.0000.0000.0000.000
176A175LYS10.8500.90510.5090.4320.4320.0000.0000.0000.000
177A176VAL00.0310.01612.2530.0850.0850.0000.0000.0000.000
178A177PHE0-0.008-0.00813.6910.0740.0740.0000.0000.0000.000
179A178ASN0-0.005-0.00614.0880.0740.0740.0000.0000.0000.000
180A179HIS0-0.039-0.03615.5060.0460.0460.0000.0000.0000.000
181A180TYR00.025-0.00118.0440.0320.0320.0000.0000.0000.000
182A181GLN00.003-0.02419.2480.0470.0470.0000.0000.0000.000
183A182ASN00.0120.01920.1110.0300.0300.0000.0000.0000.000
184A183LEU0-0.0560.00122.5780.0180.0180.0000.0000.0000.000
185A184THR0-0.005-0.01725.4040.0010.0010.0000.0000.0000.000
186A185PRO00.0390.00828.558-0.006-0.0060.0000.0000.0000.000
187A186GLU-1-0.800-0.90629.783-0.096-0.0960.0000.0000.0000.000
188A187LYS10.9130.96127.6860.0930.0930.0000.0000.0000.000
189A188LYS10.8510.93323.3710.1420.1420.0000.0000.0000.000
190A189GLN0-0.065-0.02526.887-0.011-0.0110.0000.0000.0000.000
191A190ILE0-0.040-0.01529.8580.0010.0010.0000.0000.0000.000
192A191LEU0-0.083-0.03424.9000.0020.0020.0000.0000.0000.000
193A192THR00.013-0.00124.699-0.015-0.0150.0000.0000.0000.000
194A193ASP-1-0.804-0.88721.627-0.233-0.2330.0000.0000.0000.000
195A194ALA00.0700.03517.4960.0080.0080.0000.0000.0000.000
196A195CYS0-0.036-0.02018.025-0.022-0.0220.0000.0000.0000.000
197A196LYS10.9650.98019.2020.1390.1390.0000.0000.0000.000
198A197ILE0-0.032-0.01719.3770.0140.0140.0000.0000.0000.000
199A198CYS0-0.034-0.00916.183-0.006-0.0060.0000.0000.0000.000
200A199LEU00.0240.01918.3970.0150.0150.0000.0000.0000.000
201A200LEU0-0.083-0.05021.0260.0180.0180.0000.0000.0000.000
202A201ALA0-0.057-0.01819.2300.0140.0140.0000.0000.0000.000
203A202GLY0-0.032-0.01020.7550.0070.0070.0000.0000.0000.000
204A203ASP-1-0.808-0.88114.777-0.257-0.2570.0000.0000.0000.000
205A204ASP-1-0.902-0.94516.646-0.097-0.0970.0000.0000.0000.000
206A205VAL0-0.087-0.03815.976-0.024-0.0240.0000.0000.0000.000
207A206LYS10.8310.90914.5850.1080.1080.0000.0000.0000.000
208A207LEU00.009-0.00117.023-0.024-0.0240.0000.0000.0000.000
209A208VAL00.0040.00415.4570.0150.0150.0000.0000.0000.000
210A209LYS10.8860.95518.8140.1210.1210.0000.0000.0000.000
211A210GLY00.0880.02921.385-0.017-0.0170.0000.0000.0000.000
212A211GLU-1-0.851-0.91323.102-0.116-0.1160.0000.0000.0000.000
213A212ILE00.0560.03526.303-0.006-0.0060.0000.0000.0000.000
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