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: MV1MZ

Calculation Name: 1F6F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F6F

Chain ID: B

ChEMBL ID:

UniProt ID: P16038

Base Structure: X-ray

Registration Date: 2023-09-19

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 OptHSide
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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2147587.605259
FMO2-HF: Nuclear repulsion 2065374.672348
FMO2-HF: Total energy -82212.932911
FMO2-MP2: Total energy -82451.468393


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(B:5:GLY)


Summations of interaction energy for fragment #1(B:5: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.
-7.741-8.15816.208-9.54-6.252-0.043
Interaction energy analysis for fragmet #1(B:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / 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].
3B7PRO00.0090.0133.609-1.0091.138-0.003-1.166-0.9790.002
4B8GLU-1-0.799-0.8845.700-3.069-3.121-0.001-0.0070.0600.000
5B9ILE00.018-0.0028.3480.4870.4870.0000.0000.0000.000
6B10HIS0-0.003-0.0089.2610.1340.1340.0000.0000.0000.000
7B11LYS10.8980.96013.3100.5420.5420.0000.0000.0000.000
8B12CYS00.0050.02116.022-0.018-0.0180.0000.0000.0000.000
9B13ARG10.8120.89019.0720.3800.3800.0000.0000.0000.000
10B14SER0-0.009-0.02422.8780.0110.0110.0000.0000.0000.000
11B15PRO00.0110.01525.9320.0020.0020.0000.0000.0000.000
12B16ASP-1-0.743-0.90329.397-0.164-0.1640.0000.0000.0000.000
13B17LYS10.8470.94328.7880.1470.1470.0000.0000.0000.000
14B18GLU-1-0.889-0.92929.681-0.109-0.1090.0000.0000.0000.000
15B19THR0-0.050-0.01927.1380.0020.0020.0000.0000.0000.000
16B20PHE0-0.0050.00119.292-0.008-0.0080.0000.0000.0000.000
17B21THR00.0160.02820.6510.0190.0190.0000.0000.0000.000
18B23TRP00.0250.00116.2900.0410.0410.0000.0000.0000.000
19B24TRP0-0.0080.00610.906-0.078-0.0780.0000.0000.0000.000
20B25ASN0-0.029-0.02011.3180.2580.2580.0000.0000.0000.000
21B26PRO00.0080.0009.841-0.310-0.3100.0000.0000.0000.000
22B27GLY00.0370.0187.849-0.116-0.1160.0000.0000.0000.000
23B28THR0-0.058-0.0376.8810.1710.1710.0000.0000.0000.000
24B29ASP-1-0.862-0.9318.277-0.296-0.2960.0000.0000.0000.000
25B30GLY0-0.014-0.01010.8680.1120.1120.0000.0000.0000.000
26B31GLY0-0.024-0.00713.4730.0430.0430.0000.0000.0000.000
27B32LEU0-0.038-0.00614.2390.0120.0120.0000.0000.0000.000
28B33PRO0-0.0010.00214.987-0.043-0.0430.0000.0000.0000.000
29B34THR0-0.003-0.01310.1560.0610.0610.0000.0000.0000.000
30B35ASN0-0.033-0.00713.327-0.063-0.0630.0000.0000.0000.000
31B36TYR00.013-0.0188.942-0.024-0.0240.0000.0000.0000.000
32B37SER0-0.0080.01111.2560.0680.0680.0000.0000.0000.000
33B38LEU0-0.047-0.02411.262-0.072-0.0720.0000.0000.0000.000
34B39THR00.0150.01311.9110.0740.0740.0000.0000.0000.000
35B40TYR0-0.040-0.03213.326-0.077-0.0770.0000.0000.0000.000
36B41SER00.0050.01515.5970.0630.0630.0000.0000.0000.000
37B42LYS10.8800.92817.2630.0770.0770.0000.0000.0000.000
38B43GLU-1-0.802-0.89320.269-0.118-0.1180.0000.0000.0000.000
39B44GLY0-0.036-0.02021.8450.0020.0020.0000.0000.0000.000
40B45GLU-1-0.829-0.87223.195-0.075-0.0750.0000.0000.0000.000
41B46LYS10.9190.97521.142-0.032-0.0320.0000.0000.0000.000
42B47THR00.003-0.01720.9920.0280.0280.0000.0000.0000.000
43B48THR0-0.0100.00615.122-0.011-0.0110.0000.0000.0000.000
44B49TYR0-0.069-0.05118.0660.0310.0310.0000.0000.0000.000
45B50GLU-1-0.775-0.87116.091-0.158-0.1580.0000.0000.0000.000
46B51CYS0-0.050-0.00716.7330.0290.0290.0000.0000.0000.000
47B52PRO0-0.017-0.00818.4390.0220.0220.0000.0000.0000.000
48B53ASP-1-0.787-0.88621.254-0.158-0.1580.0000.0000.0000.000
49B54TYR0-0.026-0.04015.800-0.042-0.0420.0000.0000.0000.000
50B55LYS10.8880.94620.8070.1110.1110.0000.0000.0000.000
51B56THR0-0.026-0.03724.041-0.004-0.0040.0000.0000.0000.000
52B57SER0-0.034-0.02422.3310.0150.0150.0000.0000.0000.000
53B58GLY00.0030.02122.845-0.021-0.0210.0000.0000.0000.000
54B59PRO0-0.003-0.00519.690-0.014-0.0140.0000.0000.0000.000
55B60ASN0-0.027-0.01114.955-0.010-0.0100.0000.0000.0000.000
56B61SER00.004-0.01316.287-0.059-0.0590.0000.0000.0000.000
57B63PHE0-0.024-0.01018.989-0.011-0.0110.0000.0000.0000.000
58B64PHE00.0490.01617.8550.0200.0200.0000.0000.0000.000
59B65SER00.0400.00323.8040.0050.0050.0000.0000.0000.000
60B66LYS10.8880.91327.3890.1160.1160.0000.0000.0000.000
61B67GLN0-0.0430.00229.0000.0000.0000.0000.0000.0000.000
62B68TYR0-0.027-0.02124.1570.0070.0070.0000.0000.0000.000
63B69THR0-0.0120.01424.616-0.023-0.0230.0000.0000.0000.000
64B70SER0-0.028-0.00725.4160.0200.0200.0000.0000.0000.000
65B71ILE0-0.015-0.01825.486-0.016-0.0160.0000.0000.0000.000
66B72TRP0-0.026-0.02026.6200.0180.0180.0000.0000.0000.000
67B73LYS10.8670.92823.3980.1260.1260.0000.0000.0000.000
68B74ILE00.0040.00717.665-0.027-0.0270.0000.0000.0000.000
69B75TYR0-0.034-0.02317.6290.0370.0370.0000.0000.0000.000
70B76ILE0-0.030-0.02112.134-0.044-0.0440.0000.0000.0000.000
71B77ILE00.010-0.01112.5690.0700.0700.0000.0000.0000.000
72B78THR00.0010.0127.830-0.128-0.1280.0000.0000.0000.000
73B79VAL00.0280.0037.9830.2240.2240.0000.0000.0000.000
74B80ASN0-0.031-0.0216.463-0.262-0.2620.0000.0000.0000.000
75B81ALA00.0250.0186.628-0.057-0.0570.0000.0000.0000.000
76B82THR00.0290.0067.7740.2770.2770.0000.0000.0000.000
77B83ASN00.0680.03310.5070.0010.0010.0000.0000.0000.000
78B84GLN0-0.031-0.02112.8440.0620.0620.0000.0000.0000.000
79B85MET0-0.027-0.00612.7300.0170.0170.0000.0000.0000.000
80B86GLY0-0.014-0.0029.6830.1250.1250.0000.0000.0000.000
81B87SER0-0.009-0.0137.596-0.238-0.2380.0000.0000.0000.000
82B88SER0-0.018-0.0052.695-0.5270.0511.884-1.250-1.212-0.010
83B89SER00.007-0.0032.488-1.792-1.0920.428-0.535-0.593-0.002
84B90SER00.0020.0422.0901.319-2.80913.901-6.526-3.247-0.033
85B91ASP-1-0.907-0.9414.223-4.081-3.7660.000-0.055-0.2600.000
86B92PRO0-0.042-0.0385.0280.4510.474-0.001-0.001-0.0210.000
87B93LEU0-0.0040.0198.5300.0000.0000.0000.0000.0000.000
88B94TYR0-0.013-0.01511.2680.1380.1380.0000.0000.0000.000
89B95VAL00.001-0.01314.686-0.010-0.0100.0000.0000.0000.000
90B96ASP-1-0.706-0.81817.781-0.177-0.1770.0000.0000.0000.000
91B97VAL0-0.020-0.02721.473-0.006-0.0060.0000.0000.0000.000
92B98THR0-0.069-0.07023.5110.0130.0130.0000.0000.0000.000
93B99TYR0-0.058-0.03123.0690.0180.0180.0000.0000.0000.000
94B100ILE0-0.0390.00320.600-0.016-0.0160.0000.0000.0000.000
95B101VAL00.0170.00124.010-0.006-0.0060.0000.0000.0000.000
96B102GLU-1-0.862-0.92525.811-0.311-0.3110.0000.0000.0000.000
97B103PRO0-0.0020.00428.5280.0000.0000.0000.0000.0000.000
98B104GLU-1-0.906-0.95131.958-0.183-0.1830.0000.0000.0000.000
99B105PRO0-0.032-0.03234.1830.0050.0050.0000.0000.0000.000
100B106PRO0-0.0190.00437.3180.0040.0040.0000.0000.0000.000
101B107ARG10.8790.94040.5520.0990.0990.0000.0000.0000.000
102B108ASN0-0.050-0.04243.2890.0000.0000.0000.0000.0000.000
103B109LEU00.0260.03045.4560.0020.0020.0000.0000.0000.000
104B110THR0-0.002-0.00447.9590.0030.0030.0000.0000.0000.000
105B111LEU0-0.018-0.01050.7750.0000.0000.0000.0000.0000.000
106B112GLU-1-0.816-0.88954.037-0.057-0.0570.0000.0000.0000.000
107B113VAL00.017-0.00757.515-0.001-0.0010.0000.0000.0000.000
108B114LYS10.8560.94260.0700.0510.0510.0000.0000.0000.000
109B115GLN0-0.065-0.04260.3420.0010.0010.0000.0000.0000.000
110B116LEU0-0.007-0.01663.4580.0010.0010.0000.0000.0000.000
111B117LYS10.8790.92666.2670.0430.0430.0000.0000.0000.000
112B118ASP-1-0.791-0.86767.894-0.043-0.0430.0000.0000.0000.000
113B119LYS11.0060.98367.9490.0420.0420.0000.0000.0000.000
114B120LYS10.9660.99860.9940.0530.0530.0000.0000.0000.000
115B121THR00.004-0.00861.9510.0000.0000.0000.0000.0000.000
116B122TYR0-0.035-0.01557.4210.0000.0000.0000.0000.0000.000
117B123LEU00.0510.03453.2030.0010.0010.0000.0000.0000.000
118B124TRP0-0.047-0.03153.660-0.001-0.0010.0000.0000.0000.000
119B125VAL00.0440.02748.4900.0000.0000.0000.0000.0000.000
120B126LYS10.8940.93849.8210.0650.0650.0000.0000.0000.000
121B127TRP0-0.0130.00343.2090.0010.0010.0000.0000.0000.000
122B128SER0-0.028-0.01444.8650.0030.0030.0000.0000.0000.000
123B129PRO00.0500.03639.963-0.003-0.0030.0000.0000.0000.000
124B130PRO00.0880.03936.3780.0060.0060.0000.0000.0000.000
125B131THR0-0.046-0.03139.1530.0000.0000.0000.0000.0000.000
126B132ILE00.0140.00534.2170.0040.0040.0000.0000.0000.000
127B133THR00.0040.02634.379-0.003-0.0030.0000.0000.0000.000
128B134ASP-1-0.765-0.86936.789-0.086-0.0860.0000.0000.0000.000
129B135VAL00.017-0.00738.9200.0010.0010.0000.0000.0000.000
130B136LYS10.8090.90440.7680.0900.0900.0000.0000.0000.000
131B137THR0-0.034-0.04140.6660.0030.0030.0000.0000.0000.000
132B138GLY00.0170.01941.1620.0030.0030.0000.0000.0000.000
133B139TRP0-0.0150.00831.9410.0000.0000.0000.0000.0000.000
134B140PHE0-0.019-0.02032.367-0.007-0.0070.0000.0000.0000.000
135B141THR00.0230.00635.9650.0080.0080.0000.0000.0000.000
136B142MET0-0.020-0.00635.587-0.011-0.0110.0000.0000.0000.000
137B143GLU-1-0.824-0.89236.360-0.130-0.1300.0000.0000.0000.000
138B144TYR0-0.002-0.01438.268-0.008-0.0080.0000.0000.0000.000
139B145GLU-1-0.813-0.87938.514-0.136-0.1360.0000.0000.0000.000
140B146ILE0-0.034-0.01541.464-0.001-0.0010.0000.0000.0000.000
141B147ARG10.8700.93840.3070.1250.1250.0000.0000.0000.000
142B148LEU0-0.027-0.02344.8760.0010.0010.0000.0000.0000.000
143B149LYS10.8740.92446.9320.0890.0890.0000.0000.0000.000
144B150PRO00.0540.03750.155-0.001-0.0010.0000.0000.0000.000
145B151GLU-1-0.865-0.95251.492-0.077-0.0770.0000.0000.0000.000
146B152GLU-1-0.946-0.96651.777-0.066-0.0660.0000.0000.0000.000
147B153ALA0-0.015-0.02150.8210.0020.0020.0000.0000.0000.000
148B154GLU-1-0.926-0.95746.739-0.092-0.0920.0000.0000.0000.000
149B155GLU-1-0.882-0.90145.814-0.095-0.0950.0000.0000.0000.000
150B156TRP0-0.082-0.04043.6570.0030.0030.0000.0000.0000.000
151B157GLH0-0.018-0.02845.756-0.001-0.0010.0000.0000.0000.000
152B158ILE0-0.043-0.03541.080-0.001-0.0010.0000.0000.0000.000
153B159HIS00.0460.02744.4980.0030.0030.0000.0000.0000.000
154B160PHE00.0050.00038.831-0.002-0.0020.0000.0000.0000.000
155B161THR0-0.005-0.00843.3820.0030.0030.0000.0000.0000.000
156B162GLY00.0200.01642.1500.0040.0040.0000.0000.0000.000
157B163HIS0-0.016-0.04139.099-0.001-0.0010.0000.0000.0000.000
158B164GLN0-0.0270.00843.2640.0030.0030.0000.0000.0000.000
159B165THR00.0100.00744.295-0.003-0.0030.0000.0000.0000.000
160B166GLN00.0150.00446.6000.0040.0040.0000.0000.0000.000
161B167PHE00.0100.00548.627-0.001-0.0010.0000.0000.0000.000
162B168LYS10.8900.95650.7310.0650.0650.0000.0000.0000.000
163B169VAL00.0400.01951.2960.0000.0000.0000.0000.0000.000
164B170PHE0-0.051-0.06054.0350.0030.0030.0000.0000.0000.000
165B171ASP-1-0.927-0.94753.965-0.069-0.0690.0000.0000.0000.000
166B172LEU0-0.0220.00153.282-0.001-0.0010.0000.0000.0000.000
167B173TYR00.0260.01157.0580.0030.0030.0000.0000.0000.000
168B174PRO0-0.033-0.03859.432-0.001-0.0010.0000.0000.0000.000
169B175GLY00.0120.01862.2910.0000.0000.0000.0000.0000.000
170B176GLN00.0020.01457.164-0.001-0.0010.0000.0000.0000.000
171B177LYS10.8490.92054.8650.0690.0690.0000.0000.0000.000
172B178TYR0-0.024-0.02452.212-0.001-0.0010.0000.0000.0000.000
173B179LEU00.0310.02848.3510.0010.0010.0000.0000.0000.000
174B180VAL0-0.021-0.03047.420-0.001-0.0010.0000.0000.0000.000
175B181GLN00.0340.03340.885-0.002-0.0020.0000.0000.0000.000
176B182THR0-0.005-0.01242.2200.0020.0020.0000.0000.0000.000
177B183ARG10.8500.90934.1530.1530.1530.0000.0000.0000.000
178B184CYS0-0.007-0.01035.6920.0080.0080.0000.0000.0000.000
179B185LYS10.8490.92132.1870.1470.1470.0000.0000.0000.000
180B186PRO00.0260.02830.4500.0110.0110.0000.0000.0000.000
181B187ASP-1-0.808-0.89633.059-0.147-0.1470.0000.0000.0000.000
182B188HIS10.8050.87928.9540.1580.1580.0000.0000.0000.000
183B189GLY0-0.0010.02427.651-0.014-0.0140.0000.0000.0000.000
184B190TYR0-0.006-0.00922.601-0.012-0.0120.0000.0000.0000.000
185B191TRP0-0.021-0.01728.8320.0110.0110.0000.0000.0000.000
186B192SER00.0360.03131.022-0.009-0.0090.0000.0000.0000.000
187B193ARG10.9520.96429.6170.2100.2100.0000.0000.0000.000
188B194TRP00.0280.00334.4060.0060.0060.0000.0000.0000.000
189B195SER00.0290.01838.144-0.001-0.0010.0000.0000.0000.000
190B196GLN0-0.039-0.02040.499-0.001-0.0010.0000.0000.0000.000
191B197GLU-1-0.890-0.96843.002-0.104-0.1040.0000.0000.0000.000
192B198SER0-0.0210.00745.9430.0030.0030.0000.0000.0000.000
193B199SER00.021-0.00149.396-0.001-0.0010.0000.0000.0000.000
194B200VAL0-0.031-0.01452.6090.0020.0020.0000.0000.0000.000
195B201GLU-1-0.834-0.88555.750-0.062-0.0620.0000.0000.0000.000
196B202MET0-0.038-0.00457.7810.0010.0010.0000.0000.0000.000
197B203PRO00.000-0.00260.2580.0010.0010.0000.0000.0000.000