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: YYLZ2

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2461617.857269
FMO2-HF: Nuclear repulsion 2380709.870195
FMO2-HF: Total energy -80907.987074
FMO2-MP2: Total energy -81148.093946


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.
-73.351-71.348-0.019-1.012-0.9740.003
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 : -0.818 / q_NPA : -0.900
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].
3A187PRO0-0.023-0.0133.895-4.180-2.577-0.019-0.877-0.7080.003
4A188THR00.029-0.0016.789-2.111-2.1110.0000.0000.0000.000
5A189PRO0-0.006-0.0076.6003.5703.5700.0000.0000.0000.000
6A190LEU0-0.007-0.0055.6513.1443.1440.0000.0000.0000.000
7A191ALA00.0120.0137.601-3.649-3.6490.0000.0000.0000.000
8A192ASN0-0.051-0.02410.0032.0302.0300.0000.0000.0000.000
9A193ILE00.008-0.01110.514-0.290-0.2900.0000.0000.0000.000
10A194ASP-1-0.916-0.94313.16118.37218.3720.0000.0000.0000.000
11A195ALA0-0.075-0.03016.112-1.228-1.2280.0000.0000.0000.000
12A196THR00.009-0.00217.823-0.100-0.1000.0000.0000.0000.000
13A197ASP-1-0.866-0.93520.66412.85712.8570.0000.0000.0000.000
14A198VAL0-0.015-0.01919.7520.9090.9090.0000.0000.0000.000
15A199GLU-1-0.916-0.95418.94714.39114.3910.0000.0000.0000.000
16A200GLN0-0.073-0.05018.3571.2911.2910.0000.0000.0000.000
17A201ILE00.0310.02513.8080.9530.9530.0000.0000.0000.000
18A202TYR0-0.049-0.0449.9852.6952.6950.0000.0000.0000.000
19A203PRO00.0840.04913.496-1.245-1.2450.0000.0000.0000.000
20A204ILE00.0330.00414.7190.8970.8970.0000.0000.0000.000
21A205GLU-1-0.849-0.91814.49617.42417.4240.0000.0000.0000.000
22A206SER0-0.028-0.01910.4510.2740.2740.0000.0000.0000.000
23A207ILE0-0.071-0.02810.9651.8871.8870.0000.0000.0000.000
24A208ILE0-0.022-0.02813.630-0.225-0.2250.0000.0000.0000.000
25A209PRO00.0310.03413.432-0.470-0.4700.0000.0000.0000.000
26A210LYS11.0070.98716.053-14.982-14.9820.0000.0000.0000.000
27A211LYS10.9070.94618.184-14.964-14.9640.0000.0000.0000.000
28A212GLU-1-0.736-0.84615.99816.73816.7380.0000.0000.0000.000
29A213LEU00.0500.03120.121-0.643-0.6430.0000.0000.0000.000
30A214GLN0-0.0130.00922.346-0.642-0.6420.0000.0000.0000.000
31A215PHE0-0.044-0.04022.655-0.609-0.6090.0000.0000.0000.000
32A216ILE0-0.0200.01620.113-0.250-0.2500.0000.0000.0000.000
33A217ARG10.9040.95724.732-10.588-10.5880.0000.0000.0000.000
34A218VAL00.0750.03126.998-0.108-0.1080.0000.0000.0000.000
35A219SER00.011-0.00529.851-0.100-0.1000.0000.0000.0000.000
36A220SER00.0120.00333.257-0.188-0.1880.0000.0000.0000.000
37A221ILE00.0290.03729.320-0.178-0.1780.0000.0000.0000.000
38A222LEU0-0.032-0.01232.489-0.113-0.1130.0000.0000.0000.000
39A223LYS10.8980.93234.645-8.046-8.0460.0000.0000.0000.000
40A224GLU-1-0.850-0.89737.1177.4197.4190.0000.0000.0000.000
41A225ALA00.0170.01138.7520.1510.1510.0000.0000.0000.000
42A226ASP-1-0.820-0.89940.9027.5337.5330.0000.0000.0000.000
43A227LYS10.8230.87735.017-8.579-8.5790.0000.0000.0000.000
44A228GLU-1-0.902-0.95336.2677.7737.7730.0000.0000.0000.000
45A229LYS10.9240.95836.288-7.196-7.1960.0000.0000.0000.000
46A230LYS10.7460.86434.012-8.333-8.3330.0000.0000.0000.000
47A231LEU0-0.009-0.01331.1900.3840.3840.0000.0000.0000.000
48A232GLU-1-0.869-0.92331.5998.3428.3420.0000.0000.0000.000
49A233LEU0-0.019-0.00331.8440.1030.1030.0000.0000.0000.000
50A234PHE0-0.037-0.02026.1760.4380.4380.0000.0000.0000.000
51A235PRO0-0.0120.00923.548-0.240-0.2400.0000.0000.0000.000
52A236TYR0-0.045-0.03923.8140.0260.0260.0000.0000.0000.000
53A237GLN00.005-0.02425.933-0.170-0.1700.0000.0000.0000.000
54A238ASN0-0.0440.00126.826-0.609-0.6090.0000.0000.0000.000
55A239ASN0-0.030-0.02828.8690.0720.0720.0000.0000.0000.000
56A240SER00.0200.01125.1840.0470.0470.0000.0000.0000.000
57A241LYS10.8800.92827.870-10.570-10.5700.0000.0000.0000.000
58A242TYR0-0.018-0.03124.537-0.107-0.1070.0000.0000.0000.000
59A243VAL00.0040.00325.678-0.057-0.0570.0000.0000.0000.000
60A244ALA00.0400.01828.034-0.218-0.2180.0000.0000.0000.000
61A245LYS10.7990.89928.966-11.035-11.0350.0000.0000.0000.000
62A246LYS10.8340.89726.614-11.504-11.5040.0000.0000.0000.000
63A247LEU00.0280.00330.076-0.025-0.0250.0000.0000.0000.000
64A248ASP-1-0.809-0.87331.8098.6528.6520.0000.0000.0000.000
65A249SER0-0.076-0.03130.988-0.103-0.1030.0000.0000.0000.000
66A250LEU0-0.086-0.04327.7060.1560.1560.0000.0000.0000.000
67A251THR00.0410.02132.081-0.128-0.1280.0000.0000.0000.000
68A252GLN00.0110.01034.306-0.331-0.3310.0000.0000.0000.000
69A253PRO00.033-0.00433.3630.3250.3250.0000.0000.0000.000
70A254SER0-0.006-0.00332.2220.2630.2630.0000.0000.0000.000
71A255GLN00.0420.01929.5240.1410.1410.0000.0000.0000.000
72A256MET00.0170.02428.5510.3330.3330.0000.0000.0000.000
73A257THR00.0480.01622.8420.0600.0600.0000.0000.0000.000
74A258LYS10.8950.94823.969-11.878-11.8780.0000.0000.0000.000
75A259LEU00.0480.02725.3090.2310.2310.0000.0000.0000.000
76A260GLN0-0.057-0.04023.5830.2480.2480.0000.0000.0000.000
77A261LEU00.0160.00518.9950.3460.3460.0000.0000.0000.000
78A262LEU00.0200.01721.3930.4400.4400.0000.0000.0000.000
79A263TYR00.0180.00623.2230.1880.1880.0000.0000.0000.000
80A264TYR00.001-0.03314.9190.3040.3040.0000.0000.0000.000
81A265LEU0-0.0010.01119.1220.4340.4340.0000.0000.0000.000
82A266SER00.0090.00820.1800.0360.0360.0000.0000.0000.000
83A267LEU00.0190.01318.919-0.114-0.1140.0000.0000.0000.000
84A268LEU0-0.002-0.00214.0200.1480.1480.0000.0000.0000.000
85A269LEU0-0.003-0.00317.5290.3060.3060.0000.0000.0000.000
86A270GLY00.0540.01920.010-0.211-0.2110.0000.0000.0000.000
87A271VAL0-0.016-0.01515.334-0.231-0.2310.0000.0000.0000.000
88A272TYR0-0.026-0.03215.666-0.170-0.1700.0000.0000.0000.000
89A273GLU-1-0.845-0.88917.74911.80211.8020.0000.0000.0000.000
90A274ASN0-0.039-0.01720.712-0.852-0.8520.0000.0000.0000.000
91A275ARG10.8180.90515.849-15.588-15.5880.0000.0000.0000.000
92A276ARG10.9540.97017.707-11.889-11.8890.0000.0000.0000.000
93A277VAL0-0.046-0.00720.446-0.412-0.4120.0000.0000.0000.000
94A278ASN00.0300.02319.1290.4560.4560.0000.0000.0000.000
95A279ASN00.0220.00419.9300.0160.0160.0000.0000.0000.000
96A280LYS10.8640.90920.437-12.415-12.4150.0000.0000.0000.000
97A281THR00.0360.01821.5570.0440.0440.0000.0000.0000.000
98A282LYS10.8190.88624.297-9.774-9.7740.0000.0000.0000.000
99A283LEU0-0.015-0.00618.679-0.090-0.0900.0000.0000.0000.000
100A284LEU00.0290.00622.8810.0010.0010.0000.0000.0000.000
101A285GLU-1-0.809-0.88125.1529.3409.3400.0000.0000.0000.000
102A286ARG10.8130.91124.269-10.834-10.8340.0000.0000.0000.000
103A287LEU0-0.029-0.01621.2360.2590.2590.0000.0000.0000.000
104A288ASN0-0.043-0.02325.853-0.459-0.4590.0000.0000.0000.000
105A289SER0-0.015-0.00628.075-0.060-0.0600.0000.0000.0000.000
106A290PRO00.0110.01323.386-0.039-0.0390.0000.0000.0000.000
107A291PRO0-0.015-0.02824.478-0.010-0.0100.0000.0000.0000.000
108A292GLU-1-0.805-0.88622.73411.73011.7300.0000.0000.0000.000
109A293ILE00.0120.00719.8230.4790.4790.0000.0000.0000.000
110A294LEU0-0.011-0.00418.7320.7930.7930.0000.0000.0000.000
111A295VAL00.0070.01217.5320.7780.7780.0000.0000.0000.000
112A296ASP-1-0.799-0.88416.86414.04014.0400.0000.0000.0000.000
113A297GLY0-0.0050.01414.8650.8770.8770.0000.0000.0000.000
114A298ILE0-0.008-0.00612.9531.4081.4080.0000.0000.0000.000
115A299LEU0-0.005-0.01512.1711.1901.1900.0000.0000.0000.000
116A300SER0-0.066-0.03712.0741.0611.0610.0000.0000.0000.000
117A301ARG10.8150.8978.358-19.186-19.1860.0000.0000.0000.000
118A302PHE0-0.0250.0037.5243.2403.2400.0000.0000.0000.000
119A303THR0-0.078-0.0499.504-1.420-1.4200.0000.0000.0000.000
120A304VAL00.0300.0198.6360.9380.9380.0000.0000.0000.000
121A305ILE00.017-0.00711.147-1.290-1.2900.0000.0000.0000.000
122A306LYS10.9010.95714.512-13.923-13.9230.0000.0000.0000.000
123A307PRO00.0380.02915.921-0.765-0.7650.0000.0000.0000.000
124A316ARG10.8980.93918.776-13.601-13.6010.0000.0000.0000.000
125A317SER0-0.030-0.02719.5570.2880.2880.0000.0000.0000.000
126A318TYR00.0470.01414.5440.2210.2210.0000.0000.0000.000
127A319PHE0-0.055-0.03813.158-1.008-1.0080.0000.0000.0000.000
128A320ILE00.0520.03911.9630.8390.8390.0000.0000.0000.000
129A321ASP-1-0.794-0.8698.72924.27724.2770.0000.0000.0000.000
130A322PRO00.037-0.01211.2880.3560.3560.0000.0000.0000.000
131A323GLN0-0.0020.0173.838-2.641-2.3000.001-0.130-0.2130.000
132A324ASN0-0.017-0.0476.7822.2592.2590.0000.0000.0000.000
133A325GLU-1-0.819-0.8848.78915.72815.7280.0000.0000.0000.000
134A326ASP-1-0.756-0.89010.88320.11320.1130.0000.0000.0000.000
135A327LYS10.8980.9654.470-36.628-36.569-0.001-0.005-0.0530.000
136A328ILE0-0.0300.0009.196-0.528-0.5280.0000.0000.0000.000
137A329LEU0-0.033-0.01212.435-0.787-0.7870.0000.0000.0000.000
138A330CYS0-0.034-0.00910.622-0.527-0.5270.0000.0000.0000.000
139A331TYR00.002-0.0028.3900.1950.1950.0000.0000.0000.000
140A332ILE0-0.0030.00413.311-1.092-1.0920.0000.0000.0000.000
141A333LEU0-0.011-0.01215.935-0.881-0.8810.0000.0000.0000.000
142A334ALA00.0170.01213.688-0.663-0.6630.0000.0000.0000.000
143A335ILE0-0.026-0.00715.833-0.808-0.8080.0000.0000.0000.000
144A336ILE0-0.002-0.00518.564-0.714-0.7140.0000.0000.0000.000
145A337MET0-0.070-0.00618.115-0.871-0.8710.0000.0000.0000.000
146A338HIS00.0410.02817.260-1.458-1.4580.0000.0000.0000.000
147A339LEU0-0.076-0.02921.145-0.862-0.8620.0000.0000.0000.000
148A340ASP-1-0.844-0.89123.87411.32811.3280.0000.0000.0000.000
149A341ASN0-0.029-0.02024.5290.0090.0090.0000.0000.0000.000
150A342PHE00.0640.02018.485-0.177-0.1770.0000.0000.0000.000
151A343ILE0-0.021-0.01322.9390.1570.1570.0000.0000.0000.000
152A344VAL00.0250.01622.273-0.385-0.3850.0000.0000.0000.000
153A345GLU-1-0.846-0.90025.27210.47510.4750.0000.0000.0000.000
154A346ILE0-0.037-0.02623.0930.2380.2380.0000.0000.0000.000
155A347THR0-0.027-0.01926.2470.2200.2200.0000.0000.0000.000
156A348PRO00.0300.02529.158-0.029-0.0290.0000.0000.0000.000
157A349LEU00.0570.03322.1280.0050.0050.0000.0000.0000.000
158A350ALA0-0.022-0.01624.6780.2350.2350.0000.0000.0000.000
159A351HIS00.0460.02725.7360.1650.1650.0000.0000.0000.000
160A352GLU-1-0.821-0.91626.96710.86210.8620.0000.0000.0000.000
161A353LEU00.005-0.00120.7420.0330.0330.0000.0000.0000.000
162A354ASN0-0.0330.00423.176-0.053-0.0530.0000.0000.0000.000
163A355LEU00.0110.01219.7250.3320.3320.0000.0000.0000.000
164A356LYS10.9850.98023.183-12.771-12.7710.0000.0000.0000.000
165A357PRO00.0860.02823.0240.6460.6460.0000.0000.0000.000
166A358SER0-0.024-0.00823.1410.4150.4150.0000.0000.0000.000
167A359LYS10.8310.91315.413-17.450-17.4500.0000.0000.0000.000
168A360VAL00.0410.03018.5330.9480.9480.0000.0000.0000.000
169A361VAL00.000-0.01019.6030.5680.5680.0000.0000.0000.000
170A362SER0-0.037-0.01217.2070.8500.8500.0000.0000.0000.000
171A363LEU00.0400.00813.0361.0061.0060.0000.0000.0000.000
172A364PHE00.0440.01014.7880.9940.9940.0000.0000.0000.000
173A365ARG10.8670.92616.123-15.147-15.1470.0000.0000.0000.000
174A366VAL0-0.031-0.00410.3260.7190.7190.0000.0000.0000.000
175A367LEU0-0.025-0.00511.0732.3712.3710.0000.0000.0000.000
176A368GLY00.0410.03912.8870.2300.2300.0000.0000.0000.000
177A369ALA0-0.001-0.00714.382-1.260-1.2600.0000.0000.0000.000
178A370ILE0-0.027-0.01418.030-0.180-0.1800.0000.0000.0000.000
179A371VAL0-0.032-0.00320.047-0.608-0.6080.0000.0000.0000.000
180A372LYS10.8540.92522.778-11.341-11.3410.0000.0000.0000.000
181A373GLY00.0220.02126.421-0.028-0.0280.0000.0000.0000.000
182A374ALA00.0330.02830.0220.1880.1880.0000.0000.0000.000
183A375THR0-0.015-0.01231.755-0.191-0.1910.0000.0000.0000.000
184A376VAL00.0640.00734.094-0.015-0.0150.0000.0000.0000.000
185A377ALA00.0640.04035.695-0.140-0.1400.0000.0000.0000.000
186A378GLN00.0470.01628.563-0.022-0.0220.0000.0000.0000.000
187A379ALA0-0.018-0.01534.1200.0190.0190.0000.0000.0000.000
188A380GLU-1-0.852-0.90336.7527.7497.7490.0000.0000.0000.000
189A381ALA0-0.026-0.00934.733-0.092-0.0920.0000.0000.0000.000
190A382PHE0-0.019-0.02129.6060.1240.1240.0000.0000.0000.000
191A383GLY00.0220.03435.580-0.056-0.0560.0000.0000.0000.000
192A384ILE0-0.043-0.01234.551-0.093-0.0930.0000.0000.0000.000
193A385PRO00.031-0.00638.816-0.087-0.0870.0000.0000.0000.000
194A386LYS10.8990.92839.392-7.472-7.4720.0000.0000.0000.000
195A387SER0-0.016-0.00239.5810.1970.1970.0000.0000.0000.000
196A388THR00.0330.01738.3020.0210.0210.0000.0000.0000.000
197A389ALA00.0440.05035.4900.2790.2790.0000.0000.0000.000
198A390ALA00.0340.02033.0350.3270.3270.0000.0000.0000.000
199A391SER0-0.073-0.05432.1650.3930.3930.0000.0000.0000.000
200A392TYR0-0.003-0.03231.6840.3090.3090.0000.0000.0000.000
201A393LYS10.8480.91526.740-10.850-10.8500.0000.0000.0000.000
202A394ILE00.0240.01426.388-0.061-0.0610.0000.0000.0000.000
203A395ALA0-0.008-0.00421.1680.2810.2810.0000.0000.0000.000
204A396THR0-0.037-0.02922.154-0.563-0.5630.0000.0000.0000.000
205A397MET00.0290.03315.1440.3850.3850.0000.0000.0000.000
206A398LYS10.9020.93819.148-14.187-14.1870.0000.0000.0000.000
207A399VAL00.0470.04718.7470.5630.5630.0000.0000.0000.000