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: 6Y67Z

Calculation Name: 1F7C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F7C

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZMW5

Base Structure: X-ray

Registration Date: 2023-09-21

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2184793.860017
FMO2-HF: Nuclear repulsion 2107658.198136
FMO2-HF: Total energy -77135.66188
FMO2-MP2: Total energy -77357.88086


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:191:ALA)


Summations of interaction energy for fragment #1(A:191:ALA)
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.
-10.786-6.30113.886-8.101-10.271-0.022
Interaction energy analysis for fragmet #1(A:191:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.028
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].
3A193LEU00.0000.0103.323-1.3871.5680.039-1.762-1.2320.004
4A194ASP-1-0.823-0.9344.507-0.464-0.263-0.001-0.011-0.1890.000
5A195SER0-0.003-0.0156.9040.0770.0770.0000.0000.0000.000
6A196ILE00.0710.0484.587-0.0270.066-0.001-0.006-0.0850.000
7A197GLY00.0340.0194.1900.1550.236-0.001-0.022-0.0580.000
8A198PHE0-0.028-0.0294.8110.0090.042-0.001-0.003-0.0290.000
9A199SER0-0.0210.0078.1710.0350.0350.0000.0000.0000.000
10A200ILE00.0390.0154.042-0.0710.0520.000-0.019-0.1050.000
11A201ILE0-0.003-0.0117.368-0.003-0.0030.0000.0000.0000.000
12A202LYS10.9600.9799.6140.0580.0580.0000.0000.0000.000
13A203LYS10.8140.92410.955-0.288-0.2880.0000.0000.0000.000
14A204CYS0-0.070-0.03710.2630.0340.0340.0000.0000.0000.000
15A205ILE0-0.022-0.01113.233-0.016-0.0160.0000.0000.0000.000
16A206HIS00.0560.02615.366-0.017-0.0170.0000.0000.0000.000
17A207ALA0-0.0150.01216.526-0.005-0.0050.0000.0000.0000.000
18A208VAL0-0.026-0.01916.642-0.006-0.0060.0000.0000.0000.000
19A209GLU-1-0.838-0.92319.126-0.007-0.0070.0000.0000.0000.000
20A210THR0-0.026-0.02221.019-0.001-0.0010.0000.0000.0000.000
21A211ARG10.8770.94518.880-0.206-0.2060.0000.0000.0000.000
22A212GLY00.004-0.00821.9420.0090.0090.0000.0000.0000.000
23A213ILE00.0130.02122.9430.0000.0000.0000.0000.0000.000
24A214ASN00.021-0.00924.371-0.015-0.0150.0000.0000.0000.000
25A215GLU-1-0.951-0.95023.1590.1340.1340.0000.0000.0000.000
26A216GLN00.003-0.00524.712-0.004-0.0040.0000.0000.0000.000
27A217GLY0-0.035-0.01523.6190.0130.0130.0000.0000.0000.000
28A218LEU00.0370.02919.7400.0190.0190.0000.0000.0000.000
29A219TYR0-0.002-0.03113.958-0.006-0.0060.0000.0000.0000.000
30A220ARG10.9360.98017.264-0.054-0.0540.0000.0000.0000.000
31A221ILE0-0.027-0.01519.8240.0120.0120.0000.0000.0000.000
32A222VAL0-0.029-0.00915.9080.0200.0200.0000.0000.0000.000
33A223GLY00.001-0.00216.566-0.021-0.0210.0000.0000.0000.000
34A224VAL00.0160.00117.5350.0150.0150.0000.0000.0000.000
35A225ASN00.0460.01213.4950.1300.1300.0000.0000.0000.000
36A226SER00.0670.02414.2640.1030.1030.0000.0000.0000.000
37A227ARG10.8970.94915.183-0.305-0.3050.0000.0000.0000.000
38A228VAL00.0080.01010.6050.0260.0260.0000.0000.0000.000
39A229GLN00.0270.0149.5490.3650.3650.0000.0000.0000.000
40A230LYS10.9570.98910.261-0.337-0.3370.0000.0000.0000.000
41A231LEU00.0210.02310.826-0.012-0.0120.0000.0000.0000.000
42A232LEU00.0200.0005.468-0.070-0.0700.0000.0000.0000.000
43A233SER0-0.032-0.0217.266-0.025-0.0250.0000.0000.0000.000
44A234ILE0-0.077-0.0608.912-0.106-0.1060.0000.0000.0000.000
45A235LEU00.0060.0207.360-0.094-0.0940.0000.0000.0000.000
46A236MET0-0.083-0.0322.348-0.685-0.1790.605-0.253-0.8590.000
47A237ASP-1-0.846-0.9376.4980.2080.2080.0000.0000.0000.000
48A238PRO0-0.0390.0149.4460.0530.0530.0000.0000.0000.000
49A239LYS10.8780.93911.618-0.834-0.8340.0000.0000.0000.000
50A240THR0-0.023-0.03114.878-0.063-0.0630.0000.0000.0000.000
51A241ALA0-0.0220.00714.0310.0130.0130.0000.0000.0000.000
52A242THR0-0.019-0.04215.789-0.016-0.0160.0000.0000.0000.000
53A243GLU-1-0.844-0.91911.2180.4520.4520.0000.0000.0000.000
54A244THR0-0.017-0.02013.3180.0020.0020.0000.0000.0000.000
55A245GLU-1-0.897-0.94315.1600.1770.1770.0000.0000.0000.000
56A246THR00.0650.05414.8460.0030.0030.0000.0000.0000.000
57A247GLU-1-0.922-0.96716.5370.1240.1240.0000.0000.0000.000
58A248ILE0-0.059-0.02412.8440.0210.0210.0000.0000.0000.000
59A249CYS00.0120.01916.420-0.040-0.0400.0000.0000.0000.000
60A250ALA00.0530.00319.2380.0170.0170.0000.0000.0000.000
61A251GLU-1-0.905-0.96020.5600.2580.2580.0000.0000.0000.000
62A252TRP0-0.107-0.04515.5840.0430.0430.0000.0000.0000.000
63A253GLU-1-0.854-0.94218.7110.2530.2530.0000.0000.0000.000
64A254ILE00.1340.06617.8310.0450.0450.0000.0000.0000.000
65A255LYS10.9580.98417.420-0.207-0.2070.0000.0000.0000.000
66A256THR0-0.038-0.03414.5030.0260.0260.0000.0000.0000.000
67A257ILE00.0440.02213.4360.0990.0990.0000.0000.0000.000
68A258THR0-0.0090.01112.8320.0280.0280.0000.0000.0000.000
69A259SER00.008-0.00912.770-0.031-0.0310.0000.0000.0000.000
70A260ALA00.0010.0079.2840.0860.0860.0000.0000.0000.000
71A261LEU00.0400.0298.1150.2270.2270.0000.0000.0000.000
72A262LYS10.8860.9358.151-0.286-0.2860.0000.0000.0000.000
73A263THR0-0.085-0.0497.753-0.031-0.0310.0000.0000.0000.000
74A264TYR00.0980.0351.8850.051-1.8566.582-2.052-2.624-0.012
75A265LEU00.0180.0083.331-2.460-1.8770.023-0.334-0.271-0.003
76A266ARG10.8740.9316.010-0.633-0.6330.0000.0000.0000.000
77A267MET0-0.020-0.0042.290-2.781-3.4115.024-1.775-2.6190.008
78A268LEU0-0.0280.0182.404-6.785-4.5351.617-1.838-2.029-0.019
79A269PRO00.0210.0273.9441.4931.6900.000-0.026-0.1710.000
80A270GLY00.0090.0046.2660.6690.6690.0000.0000.0000.000
81A271PRO0-0.055-0.0148.041-0.315-0.3150.0000.0000.0000.000
82A272LEU00.0680.0388.906-0.009-0.0090.0000.0000.0000.000
83A273MET0-0.0040.00910.5010.0650.0650.0000.0000.0000.000
84A274MET0-0.015-0.00612.8690.0960.0960.0000.0000.0000.000
85A275TYR00.0690.01411.9890.0360.0360.0000.0000.0000.000
86A276GLN0-0.030-0.01015.8050.0240.0240.0000.0000.0000.000
87A277PHE00.0290.00817.7880.0490.0490.0000.0000.0000.000
88A278GLN00.0150.01515.258-0.013-0.0130.0000.0000.0000.000
89A279ARG10.9380.96619.3040.2720.2720.0000.0000.0000.000
90A280SER0-0.0100.00022.6280.0340.0340.0000.0000.0000.000
91A281PHE00.0600.01218.4530.0220.0220.0000.0000.0000.000
92A282ILE0-0.0060.01221.2740.0210.0210.0000.0000.0000.000
93A283LYS10.8940.95724.0990.1850.1850.0000.0000.0000.000
94A284ALA0-0.015-0.00825.7640.0150.0150.0000.0000.0000.000
95A285ALA00.0390.00825.0240.0140.0140.0000.0000.0000.000
96A286LYS10.8450.92027.0940.1450.1450.0000.0000.0000.000
97A287LEU0-0.063-0.01230.0780.0090.0090.0000.0000.0000.000
98A288GLU-1-0.866-0.93932.581-0.077-0.0770.0000.0000.0000.000
99A289ASN0-0.0090.00735.2980.0080.0080.0000.0000.0000.000
100A290GLN00.0450.01830.873-0.010-0.0100.0000.0000.0000.000
101A291GLU-1-0.898-0.94932.310-0.084-0.0840.0000.0000.0000.000
102A292SER0-0.032-0.00932.740-0.004-0.0040.0000.0000.0000.000
103A293ARG10.8890.94528.8880.0910.0910.0000.0000.0000.000
104A294VAL00.0320.02227.780-0.015-0.0150.0000.0000.0000.000
105A295SER00.0200.00227.792-0.011-0.0110.0000.0000.0000.000
106A296GLU-1-0.917-0.97127.825-0.180-0.1800.0000.0000.0000.000
107A297ILE00.0000.00422.596-0.021-0.0210.0000.0000.0000.000
108A298HIS0-0.018-0.00323.696-0.020-0.0200.0000.0000.0000.000
109A299SER00.025-0.00424.759-0.021-0.0210.0000.0000.0000.000
110A300LEU0-0.093-0.05122.202-0.016-0.0160.0000.0000.0000.000
111A301VAL00.0130.01019.270-0.038-0.0380.0000.0000.0000.000
112A302HIS0-0.025-0.02420.139-0.038-0.0380.0000.0000.0000.000
113A303ARG10.8980.96922.2690.2350.2350.0000.0000.0000.000
114A304LEU0-0.0480.00316.003-0.031-0.0310.0000.0000.0000.000
115A305PRO00.0310.02014.6920.0420.0420.0000.0000.0000.000
116A306GLU-1-0.765-0.86615.517-0.353-0.3530.0000.0000.0000.000
117A307LYS10.9090.9579.7350.9540.9540.0000.0000.0000.000
118A308ASN00.005-0.01511.667-0.034-0.0340.0000.0000.0000.000
119A309ARG10.9010.93612.6610.3660.3660.0000.0000.0000.000
120A310GLN0-0.029-0.04413.7520.0300.0300.0000.0000.0000.000
121A311MET0-0.0300.0016.602-0.019-0.0190.0000.0000.0000.000
122A312LEU0-0.012-0.01311.8740.0580.0580.0000.0000.0000.000
123A313HIS00.0220.01714.3240.0500.0500.0000.0000.0000.000
124A314LEU0-0.014-0.00612.2490.0410.0410.0000.0000.0000.000
125A315LEU0-0.001-0.01210.8240.0430.0430.0000.0000.0000.000
126A316MET0-0.023-0.00315.0280.0450.0450.0000.0000.0000.000
127A317ASN0-0.0040.01418.4920.0390.0390.0000.0000.0000.000
128A318HIS00.0230.00916.6160.0370.0370.0000.0000.0000.000
129A319LEU0-0.016-0.02316.2880.0240.0240.0000.0000.0000.000
130A320ALA00.0260.01919.8240.0140.0140.0000.0000.0000.000
131A321LYS10.9210.97422.0020.0290.0290.0000.0000.0000.000
132A322VAL0-0.054-0.01819.7180.0130.0130.0000.0000.0000.000
133A323ALA00.017-0.00523.0590.0090.0090.0000.0000.0000.000
134A324ASP-1-0.939-0.95625.156-0.012-0.0120.0000.0000.0000.000
135A325ASN0-0.030-0.00926.7860.0010.0010.0000.0000.0000.000
136A326HIS0-0.017-0.01527.6920.0100.0100.0000.0000.0000.000
137A327LYS10.8860.94928.5740.0050.0050.0000.0000.0000.000
138A328GLN00.0160.01229.5970.0090.0090.0000.0000.0000.000
139A329ASN00.0630.03025.0100.0000.0000.0000.0000.0000.000
140A330LEU0-0.039-0.03426.0810.0060.0060.0000.0000.0000.000
141A331MET0-0.083-0.03120.892-0.002-0.0020.0000.0000.0000.000
142A332THR00.0380.02224.962-0.007-0.0070.0000.0000.0000.000
143A333VAL00.1060.04424.1370.0020.0020.0000.0000.0000.000
144A334ALA00.0520.03023.500-0.007-0.0070.0000.0000.0000.000
145A335ASN0-0.085-0.05423.862-0.007-0.0070.0000.0000.0000.000
146A336LEU0-0.015-0.00119.2740.0070.0070.0000.0000.0000.000
147A337GLY00.0750.03219.066-0.015-0.0150.0000.0000.0000.000
148A338VAL0-0.034-0.01519.664-0.019-0.0190.0000.0000.0000.000
149A339VAL0-0.063-0.02415.6560.0010.0010.0000.0000.0000.000
150A340PHE00.004-0.02412.5550.0000.0000.0000.0000.0000.000
151A341GLY00.0610.04314.987-0.058-0.0580.0000.0000.0000.000
152A342PRO0-0.058-0.03415.782-0.050-0.0500.0000.0000.0000.000
153A343THR0-0.106-0.05610.2770.0010.0010.0000.0000.0000.000
154A344LEU0-0.021-0.00810.639-0.146-0.1460.0000.0000.0000.000
155A345LEU0-0.0080.00212.570-0.086-0.0860.0000.0000.0000.000
156A346ARG10.8550.9186.6661.4301.4300.0000.0000.0000.000
157A347PRO0-0.017-0.02114.054-0.009-0.0090.0000.0000.0000.000
158A348GLN0-0.065-0.04216.575-0.020-0.0200.0000.0000.0000.000
159A349GLU-1-0.841-0.90117.908-0.260-0.2600.0000.0000.0000.000
160A350GLU-1-0.898-0.95319.215-0.176-0.1760.0000.0000.0000.000
161A351THR0-0.033-0.02421.2200.0150.0150.0000.0000.0000.000
162A352VAL00.0140.00723.6010.0110.0110.0000.0000.0000.000
163A353ALA00.0610.03427.3180.0100.0100.0000.0000.0000.000
164A354ALA00.0220.01024.1830.0050.0050.0000.0000.0000.000
165A355ILE00.0200.01024.393-0.008-0.0080.0000.0000.0000.000
166A356MET0-0.062-0.04325.8990.0070.0070.0000.0000.0000.000
167A357ASP-1-0.826-0.92324.969-0.135-0.1350.0000.0000.0000.000
168A358ILE0-0.003-0.00420.673-0.013-0.0130.0000.0000.0000.000
169A359LYS10.9370.96522.4820.0770.0770.0000.0000.0000.000
170A360PHE00.0380.01224.4800.0030.0030.0000.0000.0000.000
171A361GLN00.0050.00717.991-0.027-0.0270.0000.0000.0000.000
172A362ASN00.015-0.01020.185-0.030-0.0300.0000.0000.0000.000
173A363ILE00.0420.03821.7650.0010.0010.0000.0000.0000.000
174A364VAL00.0020.00919.7210.0010.0010.0000.0000.0000.000
175A365ILE0-0.035-0.01116.582-0.006-0.0060.0000.0000.0000.000
176A366GLU-1-0.887-0.95220.152-0.077-0.0770.0000.0000.0000.000
177A367ILE0-0.0120.00223.5640.0060.0060.0000.0000.0000.000
178A368LEU0-0.024-0.01818.5180.0000.0000.0000.0000.0000.000
179A369ILE0-0.012-0.00719.9870.0030.0030.0000.0000.0000.000
180A370GLU-1-0.930-0.97822.596-0.065-0.0650.0000.0000.0000.000
181A371ASN0-0.061-0.01725.3370.0130.0130.0000.0000.0000.000
182A372HIS00.001-0.00121.906-0.008-0.0080.0000.0000.0000.000
183A373GLU-1-0.913-0.95423.773-0.088-0.0880.0000.0000.0000.000
184A374LYS10.9110.94226.1060.1060.1060.0000.0000.0000.000
185A375ILE0-0.007-0.00122.377-0.006-0.0060.0000.0000.0000.000
186A376PHE0-0.025-0.02918.080-0.022-0.0220.0000.0000.0000.000
187A377ASN0-0.031-0.00522.750-0.014-0.0140.0000.0000.0000.000
188A378THR0-0.056-0.01625.3940.0110.0110.0000.0000.0000.000
189A379VAL00.0170.00426.653-0.014-0.0140.0000.0000.0000.000
190A380PRO0-0.060-0.01326.6900.0090.0090.0000.0000.0000.000
191A381GLU-1-0.855-0.92129.574-0.118-0.1180.0000.0000.0000.000