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

tag_button

FMODB ID: 53ZMZ

Calculation Name: 3NFH-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2466187.132665
FMO2-HF: Nuclear repulsion 2384958.346605
FMO2-HF: Total energy -81228.78606
FMO2-MP2: Total energy -81469.81397


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:184:ACE )


Summations of interaction energy for fragment #1(A:184:ACE )
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.
-1.0920.2320.032-0.56-0.7950
Interaction energy analysis for fragmet #1(A:184:ACE )
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 : -0.037
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].
3A186ARG 10.9651.0003.8131.7872.748-0.006-0.451-0.503-0.001
4A187PRO 0-0.031-0.0165.3100.4540.4540.0000.0000.0000.000
5A188THR 00.0350.0037.5830.1560.1560.0000.0000.0000.000
6A189PRO 0-0.020-0.0077.0120.0400.0400.0000.0000.0000.000
7A190LEU 0-0.003-0.0036.225-0.160-0.1600.0000.0000.0000.000
8A191ALA 00.0430.0298.4170.0500.0500.0000.0000.0000.000
9A192ASN 0-0.030-0.00912.022-0.039-0.0390.0000.0000.0000.000
10A193ILE 0-0.031-0.04013.848-0.007-0.0070.0000.0000.0000.000
11A194ASP -1-0.883-0.92216.411-0.053-0.0530.0000.0000.0000.000
12A195ALA 0-0.113-0.04518.3430.0110.0110.0000.0000.0000.000
13A196THR 00.0180.00020.141-0.007-0.0070.0000.0000.0000.000
14A197ASP -1-0.854-0.92422.6770.0400.0400.0000.0000.0000.000
15A198VAL 0-0.005-0.01721.4480.0030.0030.0000.0000.0000.000
16A199GLU -1-0.990-0.98520.0680.0900.0900.0000.0000.0000.000
17A200GLN 0-0.047-0.04318.8230.0260.0260.0000.0000.0000.000
18A201ILE 00.0290.03315.4940.0030.0030.0000.0000.0000.000
19A202TYR 0-0.028-0.04411.5820.0000.0000.0000.0000.0000.000
20A203PRO 00.0870.05913.2390.0180.0180.0000.0000.0000.000
21A204ILE 00.039-0.00213.9980.0460.0460.0000.0000.0000.000
22A205GLU -1-0.883-0.94712.6850.3830.3830.0000.0000.0000.000
23A206SER 0-0.032-0.02910.0810.0830.0830.0000.0000.0000.000
24A207ILE 0-0.082-0.0379.3670.1500.1500.0000.0000.0000.000
25A208ILE 0-0.034-0.02011.3600.0890.0890.0000.0000.0000.000
26A209PRO 00.0340.02710.345-0.058-0.0580.0000.0000.0000.000
27A210LYS 11.0171.00012.952-0.216-0.2160.0000.0000.0000.000
28A211LYS 10.9030.93915.536-0.275-0.2750.0000.0000.0000.000
29A212GLU -1-0.760-0.86012.9050.6290.6290.0000.0000.0000.000
30A213LEU 00.0530.02816.779-0.029-0.0290.0000.0000.0000.000
31A214GLN 0-0.0320.00519.146-0.033-0.0330.0000.0000.0000.000
32A215PHE 0-0.057-0.03819.364-0.021-0.0210.0000.0000.0000.000
33A216ILE 0-0.0310.01017.588-0.005-0.0050.0000.0000.0000.000
34A217ARG 10.9580.97122.083-0.178-0.1780.0000.0000.0000.000
35A218VAL 00.0670.02424.639-0.002-0.0020.0000.0000.0000.000
36A219SER 00.000-0.00427.467-0.007-0.0070.0000.0000.0000.000
37A220SER 00.0160.00630.914-0.006-0.0060.0000.0000.0000.000
38A221ILE 00.0390.04127.235-0.005-0.0050.0000.0000.0000.000
39A222LEU 0-0.045-0.03230.544-0.006-0.0060.0000.0000.0000.000
40A223LYS 10.9000.93732.576-0.079-0.0790.0000.0000.0000.000
41A224GLU -1-0.871-0.91334.7230.0660.0660.0000.0000.0000.000
42A225ALA 0-0.003-0.01336.4870.0010.0010.0000.0000.0000.000
43A226ASP -1-0.882-0.93539.0850.0590.0590.0000.0000.0000.000
44A227LYS 10.8300.88633.658-0.065-0.0650.0000.0000.0000.000
45A228GLU -1-0.913-0.94934.7570.0680.0680.0000.0000.0000.000
46A229LYS 11.0191.00234.775-0.057-0.0570.0000.0000.0000.000
47A230LYS 10.8280.92632.167-0.073-0.0730.0000.0000.0000.000
48A231LEU 0-0.031-0.02430.1270.0100.0100.0000.0000.0000.000
49A232GLU -1-0.879-0.91629.7280.0880.0880.0000.0000.0000.000
50A233LEU 0-0.058-0.02729.6460.0060.0060.0000.0000.0000.000
51A234PHE 0-0.062-0.02924.5760.0150.0150.0000.0000.0000.000
52A235PRO 00.0120.00521.587-0.005-0.0050.0000.0000.0000.000
53A236TYR 0-0.063-0.03721.9770.0050.0050.0000.0000.0000.000
54A237GLN 00.023-0.00624.098-0.012-0.0120.0000.0000.0000.000
55A238ASN 0-0.040-0.00325.977-0.017-0.0170.0000.0000.0000.000
56A239ASN 0-0.017-0.01527.532-0.002-0.0020.0000.0000.0000.000
57A240SER 0-0.0030.00724.427-0.007-0.0070.0000.0000.0000.000
58A241LYS 10.8930.92627.018-0.072-0.0720.0000.0000.0000.000
59A242TYR 0-0.008-0.00123.3610.0030.0030.0000.0000.0000.000
60A243VAL 00.0310.01124.406-0.002-0.0020.0000.0000.0000.000
61A244ALA 00.0600.03126.834-0.004-0.0040.0000.0000.0000.000
62A245LYS 10.8500.93129.382-0.066-0.0660.0000.0000.0000.000
63A246LYS 10.8510.90625.550-0.086-0.0860.0000.0000.0000.000
64A247LEU 00.021-0.00828.7150.0000.0000.0000.0000.0000.000
65A248ASP -1-0.852-0.91230.3050.0640.0640.0000.0000.0000.000
66A249SER 0-0.066-0.02430.307-0.004-0.0040.0000.0000.0000.000
67A250LEU 0-0.094-0.04026.1760.0010.0010.0000.0000.0000.000
68A251THR 00.0470.02030.5000.0010.0010.0000.0000.0000.000
69A252GLN 00.0030.01032.745-0.004-0.0040.0000.0000.0000.000
70A253PRO 00.0370.00231.5320.0060.0060.0000.0000.0000.000
71A254SER 00.0070.00930.3200.0070.0070.0000.0000.0000.000
72A255GLN 00.009-0.00428.0190.0030.0030.0000.0000.0000.000
73A256MET 00.0340.02726.8020.0070.0070.0000.0000.0000.000
74A257THR 00.0570.02521.2740.0060.0060.0000.0000.0000.000
75A258LYS 10.9760.98922.217-0.081-0.0810.0000.0000.0000.000
76A259LEU 00.0480.02323.2010.0100.0100.0000.0000.0000.000
77A260GLN 0-0.037-0.02620.9820.0060.0060.0000.0000.0000.000
78A261LEU 00.0190.01217.3420.0230.0230.0000.0000.0000.000
79A262LEU 00.0110.01619.4770.0160.0160.0000.0000.0000.000
80A263TYR 00.0310.00820.6630.0120.0120.0000.0000.0000.000
81A264TYR 00.025-0.00812.7350.0280.0280.0000.0000.0000.000
82A265LEU 0-0.0050.00817.5570.0230.0230.0000.0000.0000.000
83A266SER 0-0.007-0.00418.6720.0020.0020.0000.0000.0000.000
84A267LEU 00.0180.01116.860-0.005-0.0050.0000.0000.0000.000
85A268LEU 00.0120.00312.4530.0060.0060.0000.0000.0000.000
86A269LEU 00.0000.00115.882-0.006-0.0060.0000.0000.0000.000
87A270GLY 00.0560.02418.697-0.018-0.0180.0000.0000.0000.000
88A271VAL 0-0.020-0.01313.504-0.015-0.0150.0000.0000.0000.000
89A272TYR 00.0220.00014.913-0.028-0.0280.0000.0000.0000.000
90A273GLU -1-0.887-0.93516.6160.0920.0920.0000.0000.0000.000
91A274ASN 0-0.073-0.02819.232-0.037-0.0370.0000.0000.0000.000
92A275ARG 10.9440.97815.593-0.113-0.1130.0000.0000.0000.000
93A276ARG 10.9350.96116.820-0.082-0.0820.0000.0000.0000.000
94A277VAL 0-0.075-0.01519.341-0.017-0.0170.0000.0000.0000.000
95A278ASN 00.0320.02117.5990.0190.0190.0000.0000.0000.000
96A279ASN 00.0190.00618.2930.0080.0080.0000.0000.0000.000
97A280LYS 10.8520.89717.865-0.255-0.2550.0000.0000.0000.000
98A281THR 00.0360.02319.4930.0050.0050.0000.0000.0000.000
99A282LYS 10.9880.99222.863-0.099-0.0990.0000.0000.0000.000
100A283LEU 0-0.036-0.01816.715-0.005-0.0050.0000.0000.0000.000
101A284LEU 00.020-0.01020.8920.0010.0010.0000.0000.0000.000
102A285GLU -1-0.933-0.94922.9390.1010.1010.0000.0000.0000.000
103A286ARG 10.8260.91322.810-0.125-0.1250.0000.0000.0000.000
104A287LEU 0-0.066-0.02619.1710.0030.0030.0000.0000.0000.000
105A288ASN 0-0.026-0.01623.872-0.012-0.0120.0000.0000.0000.000
106A289SER 0-0.0090.00125.5540.0010.0010.0000.0000.0000.000
107A290PRO 00.0070.01720.8360.0000.0000.0000.0000.0000.000
108A291PRO 0-0.042-0.03621.351-0.003-0.0030.0000.0000.0000.000
109A292GLU -1-0.814-0.90620.2500.2270.2270.0000.0000.0000.000
110A293ILE 00.0190.01117.0250.0270.0270.0000.0000.0000.000
111A294LEU 00.0000.00316.0420.0560.0560.0000.0000.0000.000
112A295VAL 00.0060.01114.8640.0630.0630.0000.0000.0000.000
113A296ASP -1-0.818-0.89514.3660.3710.3710.0000.0000.0000.000
114A297GLY 00.0130.00812.0000.0800.0800.0000.0000.0000.000
115A298ILE 0-0.045-0.02610.1860.2060.2060.0000.0000.0000.000
116A299LEU 0-0.008-0.0189.8220.1230.1230.0000.0000.0000.000
117A300SER 0-0.0400.0059.3600.0800.0800.0000.0000.0000.000
118A301ARG 10.8130.8845.639-0.863-0.8630.0000.0000.0000.000
119A302PHE 0-0.030-0.0045.0580.6370.7610.000-0.007-0.1170.000
120A303THR 0-0.084-0.0527.446-0.331-0.3310.0000.0000.0000.000
121A304VAL 00.0590.0367.7460.1180.1180.0000.0000.0000.000
122A305ILE 00.020-0.0089.814-0.051-0.0510.0000.0000.0000.000
123A306LYS 10.9130.95813.032-0.124-0.1240.0000.0000.0000.000
124A307PRO 0-0.008-0.00415.0880.0100.0100.0000.0000.0000.000
125A308NME 00.0200.01317.633-0.005-0.0050.0000.0000.0000.000
126A315ACE 00.0400.01319.7770.0020.0020.0000.0000.0000.000
127A316ARG 10.9130.95416.797-0.143-0.1430.0000.0000.0000.000
128A317SER 0-0.0160.00417.4160.0210.0210.0000.0000.0000.000
129A318TYR 00.0320.00313.0250.0060.0060.0000.0000.0000.000
130A319PHE 0-0.033-0.03412.849-0.036-0.0360.0000.0000.0000.000
131A320ILE 00.0260.02710.9210.0560.0560.0000.0000.0000.000
132A321ASP -1-0.869-0.9179.125-0.084-0.0840.0000.0000.0000.000
133A322PRO 00.041-0.01411.3680.0350.0350.0000.0000.0000.000
134A323GLN 00.0270.0306.6990.0270.0270.0000.0000.0000.000
135A324ASN 00.011-0.0185.7010.3080.3080.0000.0000.0000.000
136A325GLU -1-0.956-0.9768.2950.1760.1760.0000.0000.0000.000
137A326ASP -1-0.877-0.94911.2210.0320.0320.0000.0000.0000.000
138A327LYS 10.8650.9513.048-4.366-4.1270.038-0.102-0.1750.001
139A328ILE 0-0.045-0.0138.9310.0450.0450.0000.0000.0000.000
140A329LEU 0-0.022-0.01311.384-0.027-0.0270.0000.0000.0000.000
141A330CYS 0-0.014-0.00910.793-0.048-0.0480.0000.0000.0000.000
142A331TYR 00.0200.0166.4720.1050.1050.0000.0000.0000.000
143A332ILE 0-0.0130.00012.259-0.039-0.0390.0000.0000.0000.000
144A333LEU 0-0.012-0.02015.693-0.026-0.0260.0000.0000.0000.000
145A334ALA 00.0210.01913.601-0.024-0.0240.0000.0000.0000.000
146A335ILE 0-0.031-0.01315.178-0.017-0.0170.0000.0000.0000.000
147A336ILE 00.001-0.00617.605-0.021-0.0210.0000.0000.0000.000
148A337MET 0-0.0550.00618.585-0.017-0.0170.0000.0000.0000.000
149A338HIS 0-0.0160.00016.778-0.020-0.0200.0000.0000.0000.000
150A339LEU 0-0.098-0.05521.054-0.012-0.0120.0000.0000.0000.000
151A340ASP -1-0.869-0.93123.5640.0720.0720.0000.0000.0000.000
152A341ASN 0-0.058-0.02824.870-0.005-0.0050.0000.0000.0000.000
153A342PHE 00.0600.01219.399-0.010-0.0100.0000.0000.0000.000
154A343ILE 0-0.032-0.01623.924-0.012-0.0120.0000.0000.0000.000
155A344VAL 00.0340.02322.5620.0050.0050.0000.0000.0000.000
156A345GLU -1-0.838-0.85825.9460.0280.0280.0000.0000.0000.000
157A346ILE 0-0.025-0.02624.1630.0050.0050.0000.0000.0000.000
158A347THR 0-0.015-0.01126.8850.0040.0040.0000.0000.0000.000
159A348PRO 00.0460.02629.2830.0020.0020.0000.0000.0000.000
160A349LEU 00.0640.04921.8600.0040.0040.0000.0000.0000.000
161A350ALA 0-0.025-0.01924.7020.0070.0070.0000.0000.0000.000
162A351HIS 00.0190.01525.7630.0030.0030.0000.0000.0000.000
163A352GLU -1-0.838-0.92926.6280.0730.0730.0000.0000.0000.000
164A353LEU 0-0.014-0.00720.3290.0090.0090.0000.0000.0000.000
165A354ASN 00.0010.03823.103-0.003-0.0030.0000.0000.0000.000
166A355LEU 0-0.014-0.00619.528-0.002-0.0020.0000.0000.0000.000
167A356LYS 10.9840.98223.535-0.007-0.0070.0000.0000.0000.000
168A357PRO 00.1090.03923.8680.0000.0000.0000.0000.0000.000
169A358SER 0-0.038-0.02124.5560.0010.0010.0000.0000.0000.000
170A359LYS 10.9720.99617.559-0.060-0.0600.0000.0000.0000.000
171A360VAL 00.0560.03319.673-0.001-0.0010.0000.0000.0000.000
172A361VAL 0-0.017-0.01220.587-0.003-0.0030.0000.0000.0000.000
173A362SER 0-0.053-0.02819.234-0.009-0.0090.0000.0000.0000.000
174A363LEU 00.0520.01714.242-0.016-0.0160.0000.0000.0000.000
175A364PHE 00.0620.02016.300-0.002-0.0020.0000.0000.0000.000
176A365ARG 10.8720.93618.2680.0300.0300.0000.0000.0000.000
177A366VAL 0-0.0190.00012.765-0.016-0.0160.0000.0000.0000.000
178A367LEU 0-0.028-0.01012.718-0.020-0.0200.0000.0000.0000.000
179A368GLY 00.0370.05115.0180.0030.0030.0000.0000.0000.000
180A369ALA 00.0060.00617.6750.0050.0050.0000.0000.0000.000
181A370ILE 0-0.036-0.01820.533-0.011-0.0110.0000.0000.0000.000
182A371VAL 0-0.031-0.02222.8310.0090.0090.0000.0000.0000.000
183A372LYS 10.9110.94925.600-0.001-0.0010.0000.0000.0000.000
184A373GLY 00.0220.02429.4320.0050.0050.0000.0000.0000.000
185A374ALA 00.0090.01132.687-0.001-0.0010.0000.0000.0000.000
186A375THR 0-0.040-0.02733.980-0.002-0.0020.0000.0000.0000.000
187A376VAL 00.0520.00136.4270.0020.0020.0000.0000.0000.000
188A377ALA 00.0470.03237.3520.0010.0010.0000.0000.0000.000
189A378GLN 00.0490.01830.694-0.001-0.0010.0000.0000.0000.000
190A379ALA 0-0.026-0.00735.8350.0020.0020.0000.0000.0000.000
191A380GLU -1-0.938-0.96338.2590.0120.0120.0000.0000.0000.000
192A381ALA 0-0.029-0.00836.0990.0020.0020.0000.0000.0000.000
193A382PHE 0-0.020-0.03330.9260.0020.0020.0000.0000.0000.000
194A383GLY 00.0220.04136.3460.0020.0020.0000.0000.0000.000
195A384ILE 0-0.051-0.01936.0600.0000.0000.0000.0000.0000.000
196A385PRO 00.030-0.00539.347-0.002-0.0020.0000.0000.0000.000
197A386LYS 10.9810.97940.818-0.009-0.0090.0000.0000.0000.000
198A387SER 0-0.037-0.01541.795-0.001-0.0010.0000.0000.0000.000
199A388THR 00.0560.03440.168-0.001-0.0010.0000.0000.0000.000
200A389ALA 00.0620.04337.3950.0000.0000.0000.0000.0000.000
201A390ALA 00.0080.00735.7500.0000.0000.0000.0000.0000.000
202A391SER 0-0.083-0.05534.619-0.001-0.0010.0000.0000.0000.000
203A392TYR 0-0.067-0.08532.7820.0000.0000.0000.0000.0000.000
204A393LYS 10.9070.94228.4600.0080.0080.0000.0000.0000.000
205A394ILE 00.0390.02327.9950.0060.0060.0000.0000.0000.000
206A395ALA 0-0.013-0.00622.625-0.008-0.0080.0000.0000.0000.000
207A396THR 0-0.047-0.02324.3890.0050.0050.0000.0000.0000.000
208A397MET 00.0370.03217.369-0.008-0.0080.0000.0000.0000.000
209A398LYS 10.8930.92622.1770.0130.0130.0000.0000.0000.000
210A399VAL -1-0.879-0.91421.758-0.024-0.0240.0000.0000.0000.000