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: 53MJZ

Calculation Name: 3NFH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NFH

Chain ID: A

ChEMBL ID:

UniProt ID: Q01080

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2453104.891957
FMO2-HF: Nuclear repulsion 2372197.309791
FMO2-HF: Total energy -80907.582166
FMO2-MP2: Total energy -81147.743435


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:185:ASP)


Summations of interaction energy for fragment #1(A:185:ASP)
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.
-77.826-75.611-0.01-1.163-1.040.005
Interaction energy analysis for fragmet #1(A:185:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.858 / q_NPA : -0.939
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].
3A187PRO0-0.043-0.0273.869-5.321-3.572-0.010-1.001-0.7380.005
4A188THR00.0460.0146.516-3.405-3.4050.0000.0000.0000.000
5A189PRO0-0.022-0.0136.7004.1234.1230.0000.0000.0000.000
6A190LEU0-0.012-0.0065.4242.0172.0170.0000.0000.0000.000
7A191ALA00.0420.0227.773-3.426-3.4260.0000.0000.0000.000
8A192ASN0-0.029-0.00910.5571.4281.4280.0000.0000.0000.000
9A193ILE0-0.016-0.03210.880-0.425-0.4250.0000.0000.0000.000
10A194ASP-1-0.897-0.93213.55917.92717.9270.0000.0000.0000.000
11A195ALA0-0.099-0.03416.471-1.190-1.1900.0000.0000.0000.000
12A196THR00.007-0.00518.327-0.029-0.0290.0000.0000.0000.000
13A197ASP-1-0.857-0.92721.24712.58812.5880.0000.0000.0000.000
14A198VAL0-0.016-0.02520.0430.8130.8130.0000.0000.0000.000
15A199GLU-1-0.945-0.96719.26714.09414.0940.0000.0000.0000.000
16A200GLN0-0.070-0.05418.4691.1001.1000.0000.0000.0000.000
17A201ILE00.0170.02314.0340.9870.9870.0000.0000.0000.000
18A202TYR0-0.022-0.03610.2482.3072.3070.0000.0000.0000.000
19A203PRO00.0630.04613.329-1.333-1.3330.0000.0000.0000.000
20A204ILE00.0370.00214.8760.8310.8310.0000.0000.0000.000
21A205GLU-1-0.848-0.92114.48617.60617.6060.0000.0000.0000.000
22A206SER0-0.033-0.02210.7200.2910.2910.0000.0000.0000.000
23A207ILE0-0.074-0.03511.0311.8351.8350.0000.0000.0000.000
24A208ILE0-0.026-0.02113.1360.0090.0090.0000.0000.0000.000
25A209PRO00.0210.02612.646-0.432-0.4320.0000.0000.0000.000
26A210LYS11.0200.99015.271-14.784-14.7840.0000.0000.0000.000
27A211LYS10.8930.93417.581-14.889-14.8890.0000.0000.0000.000
28A212GLU-1-0.748-0.85715.13017.06317.0630.0000.0000.0000.000
29A213LEU00.0410.02719.191-0.601-0.6010.0000.0000.0000.000
30A214GLN0-0.0270.00521.485-0.689-0.6890.0000.0000.0000.000
31A215PHE0-0.057-0.04121.902-0.588-0.5880.0000.0000.0000.000
32A216ILE0-0.0250.01519.511-0.202-0.2020.0000.0000.0000.000
33A217ARG10.9430.97124.084-10.608-10.6080.0000.0000.0000.000
34A218VAL00.0660.02126.410-0.084-0.0840.0000.0000.0000.000
35A219SER00.0140.00429.268-0.096-0.0960.0000.0000.0000.000
36A220SER00.0130.00432.822-0.175-0.1750.0000.0000.0000.000
37A221ILE00.0480.04128.619-0.178-0.1780.0000.0000.0000.000
38A222LEU0-0.029-0.02132.270-0.170-0.1700.0000.0000.0000.000
39A223LYS10.8960.93534.191-8.076-8.0760.0000.0000.0000.000
40A224GLU-1-0.853-0.90636.1497.4607.4600.0000.0000.0000.000
41A225ALA00.0130.01237.8760.1470.1470.0000.0000.0000.000
42A226ASP-1-0.841-0.91040.3397.4657.4650.0000.0000.0000.000
43A227LYS10.8270.87234.396-8.593-8.5930.0000.0000.0000.000
44A228GLU-1-0.923-0.95735.7137.8907.8900.0000.0000.0000.000
45A229LYS10.9600.97535.852-7.099-7.0990.0000.0000.0000.000
46A230LYS10.7690.87733.312-8.327-8.3270.0000.0000.0000.000
47A231LEU0-0.028-0.02430.7730.3620.3620.0000.0000.0000.000
48A232GLU-1-0.854-0.90630.8398.4398.4390.0000.0000.0000.000
49A233LEU0-0.053-0.02331.0900.1240.1240.0000.0000.0000.000
50A234PHE0-0.050-0.02525.5850.4370.4370.0000.0000.0000.000
51A235PRO00.0000.01322.860-0.202-0.2020.0000.0000.0000.000
52A236TYR0-0.054-0.03123.1040.0140.0140.0000.0000.0000.000
53A237GLN00.013-0.01725.241-0.171-0.1710.0000.0000.0000.000
54A238ASN0-0.038-0.00526.224-0.597-0.5970.0000.0000.0000.000
55A239ASN0-0.025-0.02428.2460.0550.0550.0000.0000.0000.000
56A240SER00.0030.00924.895-0.012-0.0120.0000.0000.0000.000
57A241LYS10.8880.92327.572-10.656-10.6560.0000.0000.0000.000
58A242TYR0-0.037-0.03523.894-0.075-0.0750.0000.0000.0000.000
59A243VAL00.0170.00625.162-0.094-0.0940.0000.0000.0000.000
60A244ALA00.0630.03127.429-0.187-0.1870.0000.0000.0000.000
61A245LYS10.8120.90928.690-10.925-10.9250.0000.0000.0000.000
62A246LYS10.8430.90026.297-11.437-11.4370.0000.0000.0000.000
63A247LEU00.015-0.00829.392-0.045-0.0450.0000.0000.0000.000
64A248ASP-1-0.837-0.88731.2398.6198.6190.0000.0000.0000.000
65A249SER0-0.052-0.01431.219-0.140-0.1400.0000.0000.0000.000
66A250LEU0-0.102-0.04227.1770.0940.0940.0000.0000.0000.000
67A251THR00.0490.02531.753-0.139-0.1390.0000.0000.0000.000
68A252GLN00.0030.00134.223-0.316-0.3160.0000.0000.0000.000
69A253PRO00.0310.00033.1870.3200.3200.0000.0000.0000.000
70A254SER00.0080.00832.1360.2540.2540.0000.0000.0000.000
71A255GLN00.0120.00029.5520.1810.1810.0000.0000.0000.000
72A256MET00.0330.02628.5360.2510.2510.0000.0000.0000.000
73A257THR00.0540.02323.0570.0940.0940.0000.0000.0000.000
74A258LYS10.9220.95823.900-11.889-11.8890.0000.0000.0000.000
75A259LEU00.0570.02624.5690.3160.3160.0000.0000.0000.000
76A260GLN0-0.041-0.02922.8500.2360.2360.0000.0000.0000.000
77A261LEU00.0190.01018.8610.3720.3720.0000.0000.0000.000
78A262LEU00.0060.01320.6850.4520.4520.0000.0000.0000.000
79A263TYR00.0290.00822.3690.2420.2420.0000.0000.0000.000
80A264TYR00.021-0.01414.2660.3370.3370.0000.0000.0000.000
81A265LEU0-0.0090.00318.4450.4070.4070.0000.0000.0000.000
82A266SER00.0020.00119.5020.0840.0840.0000.0000.0000.000
83A267LEU00.0200.01218.276-0.092-0.0920.0000.0000.0000.000
84A268LEU00.0010.00013.3910.1340.1340.0000.0000.0000.000
85A269LEU0-0.0050.00016.8510.3080.3080.0000.0000.0000.000
86A270GLY00.0640.02019.387-0.204-0.2040.0000.0000.0000.000
87A271VAL0-0.018-0.01114.801-0.227-0.2270.0000.0000.0000.000
88A272TYR0-0.059-0.05715.005-0.267-0.2670.0000.0000.0000.000
89A273GLU-1-0.856-0.91517.19911.87311.8730.0000.0000.0000.000
90A274ASN0-0.080-0.02920.007-0.973-0.9730.0000.0000.0000.000
91A275ARG10.8790.94015.955-15.389-15.3890.0000.0000.0000.000
92A276ARG10.9320.96117.517-11.907-11.9070.0000.0000.0000.000
93A277VAL0-0.050-0.00120.243-0.401-0.4010.0000.0000.0000.000
94A278ASN00.0350.02518.7440.3880.3880.0000.0000.0000.000
95A279ASN00.0090.00219.634-0.009-0.0090.0000.0000.0000.000
96A280LYS10.8810.90019.976-12.561-12.5610.0000.0000.0000.000
97A281THR00.0240.01521.2150.0370.0370.0000.0000.0000.000
98A282LYS10.8490.89424.052-9.885-9.8850.0000.0000.0000.000
99A283LEU0-0.022-0.01018.272-0.135-0.1350.0000.0000.0000.000
100A284LEU00.019-0.01022.476-0.022-0.0220.0000.0000.0000.000
101A285GLU-1-0.814-0.86924.5729.4939.4930.0000.0000.0000.000
102A286ARG10.8270.91424.071-11.018-11.0180.0000.0000.0000.000
103A287LEU0-0.061-0.02120.6410.1490.1490.0000.0000.0000.000
104A288ASN0-0.031-0.02625.280-0.479-0.4790.0000.0000.0000.000
105A289SER0-0.0110.00127.290-0.038-0.0380.0000.0000.0000.000
106A290PRO00.0110.01722.534-0.039-0.0390.0000.0000.0000.000
107A291PRO0-0.037-0.03623.422-0.082-0.0820.0000.0000.0000.000
108A292GLU-1-0.808-0.89322.14711.75911.7590.0000.0000.0000.000
109A293ILE00.0100.00419.2790.4730.4730.0000.0000.0000.000
110A294LEU0-0.0050.00317.9830.7540.7540.0000.0000.0000.000
111A295VAL00.0080.01316.7120.8460.8460.0000.0000.0000.000
112A296ASP-1-0.812-0.89116.27114.18014.1800.0000.0000.0000.000
113A297GLY00.0100.01114.1040.8400.8400.0000.0000.0000.000
114A298ILE0-0.023-0.02112.1971.4601.4600.0000.0000.0000.000
115A299LEU0-0.012-0.01311.5821.1911.1910.0000.0000.0000.000
116A300SER0-0.042-0.01111.5260.9610.9610.0000.0000.0000.000
117A301ARG10.8170.8957.752-19.522-19.5220.0000.0000.0000.000
118A302PHE0-0.037-0.0096.7523.3003.3000.0000.0000.0000.000
119A303THR0-0.087-0.0498.833-1.127-1.1270.0000.0000.0000.000
120A304VAL00.0480.0318.6530.6390.6390.0000.0000.0000.000
121A305ILE00.020-0.00611.050-1.334-1.3340.0000.0000.0000.000
122A306LYS10.9020.95914.486-14.295-14.2950.0000.0000.0000.000
123A307PRO00.0190.01016.064-0.822-0.8220.0000.0000.0000.000
124A316ARG10.9210.96218.677-13.826-13.8260.0000.0000.0000.000
125A317SER0-0.016-0.00519.1280.3440.3440.0000.0000.0000.000
126A318TYR00.0430.00214.5040.2420.2420.0000.0000.0000.000
127A319PHE0-0.033-0.03613.286-0.945-0.9450.0000.0000.0000.000
128A320ILE00.0460.04311.7291.0121.0120.0000.0000.0000.000
129A321ASP-1-0.818-0.8818.88125.26425.2640.0000.0000.0000.000
130A322PRO00.030-0.02011.2430.3080.3080.0000.0000.0000.000
131A323GLN00.0000.0143.843-2.897-2.5390.001-0.144-0.2140.000
132A324ASN0-0.020-0.0476.5811.9461.9460.0000.0000.0000.000
133A325GLU-1-0.817-0.8818.35716.12316.1230.0000.0000.0000.000
134A326ASP-1-0.788-0.90810.65720.42820.4280.0000.0000.0000.000
135A327LYS10.8890.9643.831-37.182-37.074-0.001-0.018-0.0880.000
136A328ILE0-0.031-0.0068.698-0.643-0.6430.0000.0000.0000.000
137A329LEU0-0.017-0.00711.737-0.849-0.8490.0000.0000.0000.000
138A330CYS0-0.041-0.02110.230-0.601-0.6010.0000.0000.0000.000
139A331TYR00.0200.0147.6730.4690.4690.0000.0000.0000.000
140A332ILE0-0.0040.00512.656-1.145-1.1450.0000.0000.0000.000
141A333LEU0-0.015-0.01815.574-0.908-0.9080.0000.0000.0000.000
142A334ALA00.0120.01213.861-0.703-0.7030.0000.0000.0000.000
143A335ILE0-0.027-0.01016.012-0.873-0.8730.0000.0000.0000.000
144A336ILE0-0.008-0.00618.381-0.734-0.7340.0000.0000.0000.000
145A337MET0-0.0550.00318.491-0.898-0.8980.0000.0000.0000.000
146A338HIS00.0120.01917.579-1.510-1.5100.0000.0000.0000.000
147A339LEU0-0.085-0.04421.558-0.881-0.8810.0000.0000.0000.000
148A340ASP-1-0.820-0.88424.03911.45311.4530.0000.0000.0000.000
149A341ASN0-0.049-0.02725.190-0.027-0.0270.0000.0000.0000.000
150A342PHE00.0630.01418.952-0.189-0.1890.0000.0000.0000.000
151A343ILE0-0.033-0.01523.4150.1500.1500.0000.0000.0000.000
152A344VAL00.0250.01622.418-0.238-0.2380.0000.0000.0000.000
153A345GLU-1-0.845-0.88825.54910.34910.3490.0000.0000.0000.000
154A346ILE0-0.018-0.02222.9010.1600.1600.0000.0000.0000.000
155A347THR0-0.008-0.00726.1910.2610.2610.0000.0000.0000.000
156A348PRO00.0420.02428.7740.0330.0330.0000.0000.0000.000
157A349LEU00.0600.04321.5460.0110.0110.0000.0000.0000.000
158A350ALA0-0.022-0.01724.2500.1930.1930.0000.0000.0000.000
159A351HIS00.0320.01625.3020.1460.1460.0000.0000.0000.000
160A352GLU-1-0.824-0.91526.59810.75410.7540.0000.0000.0000.000
161A353LEU00.0000.00020.2500.0420.0420.0000.0000.0000.000
162A354ASN0-0.0160.02623.104-0.173-0.1730.0000.0000.0000.000
163A355LEU0-0.0030.00519.2780.4070.4070.0000.0000.0000.000
164A356LYS10.9800.98023.027-12.906-12.9060.0000.0000.0000.000
165A357PRO00.1000.03223.0740.5860.5860.0000.0000.0000.000
166A358SER0-0.029-0.01423.5700.4330.4330.0000.0000.0000.000
167A359LYS10.8690.94015.355-17.588-17.5880.0000.0000.0000.000
168A360VAL00.0550.03118.6640.9630.9630.0000.0000.0000.000
169A361VAL0-0.019-0.01319.6110.5630.5630.0000.0000.0000.000
170A362SER0-0.038-0.02117.4330.8190.8190.0000.0000.0000.000
171A363LEU00.0450.01413.1920.9730.9730.0000.0000.0000.000
172A364PHE00.0600.01614.7481.0261.0260.0000.0000.0000.000
173A365ARG10.8600.92616.061-14.988-14.9880.0000.0000.0000.000
174A366VAL0-0.0200.00110.1410.6760.6760.0000.0000.0000.000
175A367LEU0-0.027-0.00611.0952.0792.0790.0000.0000.0000.000
176A368GLY00.0330.04312.9470.3260.3260.0000.0000.0000.000
177A369ALA00.011-0.00214.488-1.217-1.2170.0000.0000.0000.000
178A370ILE0-0.050-0.02418.023-0.053-0.0530.0000.0000.0000.000
179A371VAL0-0.028-0.01820.263-0.469-0.4690.0000.0000.0000.000
180A372LYS10.8980.94622.946-11.317-11.3170.0000.0000.0000.000
181A373GLY00.0110.01826.591-0.004-0.0040.0000.0000.0000.000
182A374ALA00.0190.01830.1930.1580.1580.0000.0000.0000.000
183A375THR0-0.040-0.03131.686-0.279-0.2790.0000.0000.0000.000
184A376VAL00.0650.00734.040-0.009-0.0090.0000.0000.0000.000
185A377ALA00.0400.02935.350-0.128-0.1280.0000.0000.0000.000
186A378GLN00.0560.02428.786-0.151-0.1510.0000.0000.0000.000
187A379ALA0-0.021-0.00734.3290.0070.0070.0000.0000.0000.000
188A380GLU-1-0.838-0.90136.8657.6577.6570.0000.0000.0000.000
189A381ALA0-0.032-0.01035.199-0.104-0.1040.0000.0000.0000.000
190A382PHE0-0.024-0.03229.9430.1040.1040.0000.0000.0000.000
191A383GLY00.0250.04235.831-0.038-0.0380.0000.0000.0000.000
192A384ILE0-0.045-0.01534.292-0.039-0.0390.0000.0000.0000.000
193A385PRO00.028-0.00638.441-0.099-0.0990.0000.0000.0000.000
194A386LYS10.8920.92439.212-7.368-7.3680.0000.0000.0000.000
195A387SER0-0.019-0.00639.6450.2070.2070.0000.0000.0000.000
196A388THR00.0440.02638.2340.0350.0350.0000.0000.0000.000
197A389ALA00.0570.04435.5120.2790.2790.0000.0000.0000.000
198A390ALA00.0300.01933.2530.3330.3330.0000.0000.0000.000
199A391SER0-0.072-0.05932.0570.4090.4090.0000.0000.0000.000
200A392TYR0-0.034-0.04231.7020.2550.2550.0000.0000.0000.000
201A393LYS10.8540.92226.436-10.914-10.9140.0000.0000.0000.000
202A394ILE00.0380.01726.410-0.042-0.0420.0000.0000.0000.000
203A395ALA0-0.013-0.00121.1530.2740.2740.0000.0000.0000.000
204A396THR0-0.031-0.01622.295-0.522-0.5220.0000.0000.0000.000
205A397MET00.0310.04215.3600.4740.4740.0000.0000.0000.000
206A398LYS10.9240.94719.586-13.704-13.7040.0000.0000.0000.000
207A399VAL00.0530.04819.3810.5810.5810.0000.0000.0000.000