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: 437JN

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2450940.661958
FMO2-HF: Nuclear repulsion 2370034.055469
FMO2-HF: Total energy -80906.606489
FMO2-MP2: Total energy -81146.671352


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.
-73.605-71.327-0.019-1.179-1.0780.006
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 : -0.931 / q_NPA : -0.965
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].
3A187PRO0-0.020-0.0113.869-4.300-2.390-0.017-1.073-0.8190.006
4A188THR00.0300.0006.825-3.255-3.2550.0000.0000.0000.000
5A189PRO0-0.017-0.0056.3683.4473.4470.0000.0000.0000.000
6A190LEU00.002-0.0015.3441.7971.7970.0000.0000.0000.000
7A191ALA00.0370.0277.932-3.187-3.1870.0000.0000.0000.000
8A192ASN0-0.025-0.00710.7251.3891.3890.0000.0000.0000.000
9A193ILE0-0.029-0.03910.617-0.455-0.4550.0000.0000.0000.000
10A194ASP-1-0.879-0.92013.47617.50817.5080.0000.0000.0000.000
11A195ALA0-0.105-0.04016.428-1.166-1.1660.0000.0000.0000.000
12A196THR00.002-0.01018.310-0.042-0.0420.0000.0000.0000.000
13A197ASP-1-0.856-0.92621.27512.31212.3120.0000.0000.0000.000
14A198VAL0-0.021-0.02820.1940.7900.7900.0000.0000.0000.000
15A199GLU-1-0.975-0.97619.46513.71513.7150.0000.0000.0000.000
16A200GLN0-0.041-0.03918.6121.0421.0420.0000.0000.0000.000
17A201ILE00.0140.02414.2720.9370.9370.0000.0000.0000.000
18A202TYR0-0.022-0.04010.5332.2272.2270.0000.0000.0000.000
19A203PRO00.0860.05913.284-1.283-1.2830.0000.0000.0000.000
20A204ILE00.0410.00114.4900.7980.7980.0000.0000.0000.000
21A205GLU-1-0.880-0.94713.73317.91617.9160.0000.0000.0000.000
22A206SER0-0.035-0.03110.6240.5320.5320.0000.0000.0000.000
23A207ILE0-0.081-0.03710.2551.6621.6620.0000.0000.0000.000
24A208ILE0-0.032-0.01812.6240.0530.0530.0000.0000.0000.000
25A209PRO00.0350.02812.169-0.449-0.4490.0000.0000.0000.000
26A210LYS11.0161.00014.637-14.364-14.3640.0000.0000.0000.000
27A211LYS10.9030.93817.543-14.593-14.5930.0000.0000.0000.000
28A212GLU-1-0.759-0.85915.04017.01417.0140.0000.0000.0000.000
29A213LEU00.0510.02718.628-0.593-0.5930.0000.0000.0000.000
30A214GLN0-0.0320.00520.866-0.703-0.7030.0000.0000.0000.000
31A215PHE0-0.055-0.03721.401-0.567-0.5670.0000.0000.0000.000
32A216ILE0-0.0290.01019.239-0.181-0.1810.0000.0000.0000.000
33A217ARG10.9560.97023.800-10.557-10.5570.0000.0000.0000.000
34A218VAL00.0680.02526.109-0.080-0.0800.0000.0000.0000.000
35A219SER0-0.001-0.00428.955-0.119-0.1190.0000.0000.0000.000
36A220SER00.0180.00632.423-0.192-0.1920.0000.0000.0000.000
37A221ILE00.0400.04228.650-0.176-0.1760.0000.0000.0000.000
38A222LEU0-0.049-0.03531.676-0.158-0.1580.0000.0000.0000.000
39A223LYS10.9030.93833.839-8.108-8.1080.0000.0000.0000.000
40A224GLU-1-0.873-0.91336.0567.4687.4680.0000.0000.0000.000
41A225ALA0-0.001-0.01237.7140.1360.1360.0000.0000.0000.000
42A226ASP-1-0.879-0.93340.2727.4547.4540.0000.0000.0000.000
43A227LYS10.8300.88634.325-8.581-8.5810.0000.0000.0000.000
44A228GLU-1-0.912-0.94835.8637.9327.9320.0000.0000.0000.000
45A229LYS11.0191.00236.136-7.027-7.0270.0000.0000.0000.000
46A230LYS10.8260.92533.329-8.290-8.2900.0000.0000.0000.000
47A231LEU0-0.033-0.02531.1820.3660.3660.0000.0000.0000.000
48A232GLU-1-0.877-0.91631.1538.4538.4530.0000.0000.0000.000
49A233LEU0-0.058-0.02831.1690.1250.1250.0000.0000.0000.000
50A234PHE0-0.061-0.02825.7720.4430.4430.0000.0000.0000.000
51A235PRO00.0090.00423.162-0.175-0.1750.0000.0000.0000.000
52A236TYR0-0.058-0.03523.7340.0160.0160.0000.0000.0000.000
53A237GLN00.020-0.00725.842-0.231-0.2310.0000.0000.0000.000
54A238ASN0-0.041-0.00327.512-0.493-0.4930.0000.0000.0000.000
55A239ASN0-0.015-0.01328.9180.0950.0950.0000.0000.0000.000
56A240SER0-0.0020.00725.303-0.055-0.0550.0000.0000.0000.000
57A241LYS10.8920.92728.061-10.665-10.6650.0000.0000.0000.000
58A242TYR0-0.0040.00023.831-0.062-0.0620.0000.0000.0000.000
59A243VAL00.0270.00925.270-0.105-0.1050.0000.0000.0000.000
60A244ALA00.0650.03327.557-0.198-0.1980.0000.0000.0000.000
61A245LYS10.8440.92829.553-10.699-10.6990.0000.0000.0000.000
62A246LYS10.8510.90526.042-11.437-11.4370.0000.0000.0000.000
63A247LEU00.024-0.00629.237-0.052-0.0520.0000.0000.0000.000
64A248ASP-1-0.854-0.91331.0818.5578.5570.0000.0000.0000.000
65A249SER0-0.066-0.02430.814-0.123-0.1230.0000.0000.0000.000
66A250LEU0-0.095-0.04126.8920.0890.0890.0000.0000.0000.000
67A251THR00.0480.02031.288-0.138-0.1380.0000.0000.0000.000
68A252GLN00.0040.01133.611-0.329-0.3290.0000.0000.0000.000
69A253PRO00.0390.00332.5140.3200.3200.0000.0000.0000.000
70A254SER00.0060.00831.4020.2600.2600.0000.0000.0000.000
71A255GLN00.005-0.00528.8300.1620.1620.0000.0000.0000.000
72A256MET00.0390.02927.9700.2370.2370.0000.0000.0000.000
73A257THR00.0550.02422.3180.1110.1110.0000.0000.0000.000
74A258LYS10.9730.98823.241-11.449-11.4490.0000.0000.0000.000
75A259LEU00.0490.02424.0880.3120.3120.0000.0000.0000.000
76A260GLN0-0.034-0.02522.3470.2340.2340.0000.0000.0000.000
77A261LEU00.0140.01118.2250.3800.3800.0000.0000.0000.000
78A262LEU00.0100.01520.4540.4560.4560.0000.0000.0000.000
79A263TYR00.0340.01022.1610.2490.2490.0000.0000.0000.000
80A264TYR00.023-0.00914.1430.3670.3670.0000.0000.0000.000
81A265LEU0-0.0070.00718.5520.4250.4250.0000.0000.0000.000
82A266SER0-0.004-0.00319.5910.1120.1120.0000.0000.0000.000
83A267LEU00.0210.01218.740-0.063-0.0630.0000.0000.0000.000
84A268LEU00.0060.00213.8750.1490.1490.0000.0000.0000.000
85A269LEU00.0000.00117.3660.3410.3410.0000.0000.0000.000
86A270GLY00.0590.02520.022-0.188-0.1880.0000.0000.0000.000
87A271VAL0-0.016-0.01115.527-0.219-0.2190.0000.0000.0000.000
88A272TYR00.020-0.00115.9130.0940.0940.0000.0000.0000.000
89A273GLU-1-0.890-0.93717.99812.03512.0350.0000.0000.0000.000
90A274ASN0-0.075-0.02820.865-0.969-0.9690.0000.0000.0000.000
91A275ARG10.9440.97817.030-15.145-15.1450.0000.0000.0000.000
92A276ARG10.9370.96218.493-12.005-12.0050.0000.0000.0000.000
93A277VAL0-0.073-0.01521.185-0.456-0.4560.0000.0000.0000.000
94A278ASN00.0290.01919.5310.3260.3260.0000.0000.0000.000
95A279ASN00.0210.00820.2760.0140.0140.0000.0000.0000.000
96A280LYS10.8600.90220.225-12.618-12.6180.0000.0000.0000.000
97A281THR00.0390.02421.7950.0460.0460.0000.0000.0000.000
98A282LYS10.9860.99125.015-10.381-10.3810.0000.0000.0000.000
99A283LEU0-0.039-0.01918.983-0.130-0.1300.0000.0000.0000.000
100A284LEU00.019-0.01023.294-0.005-0.0050.0000.0000.0000.000
101A285GLU-1-0.927-0.94825.3009.5119.5110.0000.0000.0000.000
102A286ARG10.8220.91224.899-11.181-11.1810.0000.0000.0000.000
103A287LEU0-0.065-0.02621.3700.1540.1540.0000.0000.0000.000
104A288ASN0-0.027-0.01626.007-0.452-0.4520.0000.0000.0000.000
105A289SER0-0.0080.00327.858-0.044-0.0440.0000.0000.0000.000
106A290PRO00.0070.01722.879-0.051-0.0510.0000.0000.0000.000
107A291PRO0-0.044-0.03723.366-0.137-0.1370.0000.0000.0000.000
108A292GLU-1-0.812-0.90422.42711.79811.7980.0000.0000.0000.000
109A293ILE00.0170.01019.3230.4730.4730.0000.0000.0000.000
110A294LEU0-0.0030.00118.0550.7560.7560.0000.0000.0000.000
111A295VAL00.0060.01117.0250.8690.8690.0000.0000.0000.000
112A296ASP-1-0.815-0.89416.77514.28114.2810.0000.0000.0000.000
113A297GLY00.0120.00714.2780.8770.8770.0000.0000.0000.000
114A298ILE0-0.046-0.02712.5411.5011.5010.0000.0000.0000.000
115A299LEU0-0.007-0.01712.2121.2851.2850.0000.0000.0000.000
116A300SER0-0.0390.00411.7121.1071.1070.0000.0000.0000.000
117A301ARG10.8120.8837.999-19.551-19.5510.0000.0000.0000.000
118A302PHE0-0.029-0.0037.4133.6723.6720.0000.0000.0000.000
119A303THR0-0.086-0.0529.644-1.125-1.1250.0000.0000.0000.000
120A304VAL00.0600.0379.0970.7150.7150.0000.0000.0000.000
121A305ILE00.021-0.00811.477-1.459-1.4590.0000.0000.0000.000
122A306LYS10.9150.96114.727-14.332-14.3320.0000.0000.0000.000
123A307PRO00.0050.00816.159-0.898-0.8980.0000.0000.0000.000
124A316ARG10.9520.96918.589-14.062-14.0620.0000.0000.0000.000
125A317SER0-0.015-0.00419.5020.3980.3980.0000.0000.0000.000
126A318TYR00.0350.00315.0230.3810.3810.0000.0000.0000.000
127A319PHE0-0.033-0.03413.965-0.965-0.9650.0000.0000.0000.000
128A320ILE00.0240.02712.4581.0951.0950.0000.0000.0000.000
129A321ASP-1-0.869-0.9169.42126.73026.7300.0000.0000.0000.000
130A322PRO00.040-0.01412.1560.3350.3350.0000.0000.0000.000
131A323GLN00.0260.0304.048-3.104-2.824-0.001-0.088-0.1910.000
132A324ASN00.013-0.0167.2282.8102.8100.0000.0000.0000.000
133A325GLU-1-0.960-0.9789.28116.72416.7240.0000.0000.0000.000
134A326ASP-1-0.876-0.94910.83921.54021.5400.0000.0000.0000.000
135A327LYS10.8680.9544.531-38.050-37.962-0.001-0.018-0.0680.000
136A328ILE0-0.042-0.0129.285-0.958-0.9580.0000.0000.0000.000
137A329LEU0-0.015-0.01112.368-1.042-1.0420.0000.0000.0000.000
138A330CYS0-0.024-0.01210.463-0.769-0.7690.0000.0000.0000.000
139A331TYR00.0230.0177.2520.4440.4440.0000.0000.0000.000
140A332ILE0-0.0060.00412.562-1.179-1.1790.0000.0000.0000.000
141A333LEU0-0.013-0.02115.665-0.932-0.9320.0000.0000.0000.000
142A334ALA00.0150.01613.424-0.701-0.7010.0000.0000.0000.000
143A335ILE0-0.030-0.01215.527-0.866-0.8660.0000.0000.0000.000
144A336ILE00.008-0.00217.952-0.736-0.7360.0000.0000.0000.000
145A337MET0-0.0580.00418.325-0.919-0.9190.0000.0000.0000.000
146A338HIS0-0.018-0.00316.906-1.460-1.4600.0000.0000.0000.000
147A339LEU0-0.093-0.05221.177-0.812-0.8120.0000.0000.0000.000
148A340ASP-1-0.866-0.92823.59511.44111.4410.0000.0000.0000.000
149A341ASN0-0.058-0.02824.867-0.051-0.0510.0000.0000.0000.000
150A342PHE00.0530.00819.109-0.164-0.1640.0000.0000.0000.000
151A343ILE0-0.037-0.02023.4850.1420.1420.0000.0000.0000.000
152A344VAL00.0350.02522.166-0.207-0.2070.0000.0000.0000.000
153A345GLU-1-0.831-0.85525.44710.26710.2670.0000.0000.0000.000
154A346ILE0-0.025-0.02623.2350.1690.1690.0000.0000.0000.000
155A347THR0-0.016-0.01226.2800.2520.2520.0000.0000.0000.000
156A348PRO00.0460.02729.1100.0260.0260.0000.0000.0000.000
157A349LEU00.0620.04821.6330.0320.0320.0000.0000.0000.000
158A350ALA0-0.022-0.01824.6930.2100.2100.0000.0000.0000.000
159A351HIS00.0190.01425.7330.1270.1270.0000.0000.0000.000
160A352GLU-1-0.837-0.92926.86710.82810.8280.0000.0000.0000.000
161A353LEU0-0.014-0.00720.6130.0450.0450.0000.0000.0000.000
162A354ASN00.0010.03723.714-0.123-0.1230.0000.0000.0000.000
163A355LEU0-0.013-0.00519.7330.4540.4540.0000.0000.0000.000
164A356LYS10.9860.98323.625-13.109-13.1090.0000.0000.0000.000
165A357PRO00.1080.03923.4430.6080.6080.0000.0000.0000.000
166A358SER0-0.036-0.02123.6890.4120.4120.0000.0000.0000.000
167A359LYS10.9730.99617.519-16.398-16.3980.0000.0000.0000.000
168A360VAL00.0600.03518.8230.9480.9480.0000.0000.0000.000
169A361VAL0-0.023-0.01419.6730.5080.5080.0000.0000.0000.000
170A362SER0-0.050-0.02717.5100.7760.7760.0000.0000.0000.000
171A363LEU00.0510.01813.4970.9100.9100.0000.0000.0000.000
172A364PHE00.0650.02115.0670.9710.9710.0000.0000.0000.000
173A365ARG10.8680.93416.507-14.989-14.9890.0000.0000.0000.000
174A366VAL0-0.0170.00210.6860.6350.6350.0000.0000.0000.000
175A367LEU0-0.022-0.00611.5461.9361.9360.0000.0000.0000.000
176A368GLY00.0300.04813.3680.2700.2700.0000.0000.0000.000
177A369ALA00.0010.00314.855-1.173-1.1730.0000.0000.0000.000
178A370ILE0-0.039-0.02218.407-0.076-0.0760.0000.0000.0000.000
179A371VAL0-0.029-0.02020.790-0.452-0.4520.0000.0000.0000.000
180A372LYS10.9100.94923.391-11.492-11.4920.0000.0000.0000.000
181A373GLY00.0230.02527.0340.0290.0290.0000.0000.0000.000
182A374ALA00.0140.01330.6400.1300.1300.0000.0000.0000.000
183A375THR0-0.045-0.03032.153-0.265-0.2650.0000.0000.0000.000
184A376VAL00.0550.00334.428-0.012-0.0120.0000.0000.0000.000
185A377ALA00.0470.03235.644-0.120-0.1200.0000.0000.0000.000
186A378GLN00.0420.01529.107-0.130-0.1300.0000.0000.0000.000
187A379ALA0-0.023-0.00634.7030.0050.0050.0000.0000.0000.000
188A380GLU-1-0.938-0.96337.2717.6417.6410.0000.0000.0000.000
189A381ALA0-0.030-0.00935.531-0.101-0.1010.0000.0000.0000.000
190A382PHE0-0.023-0.03430.3620.1090.1090.0000.0000.0000.000
191A383GLY00.0250.04235.871-0.034-0.0340.0000.0000.0000.000
192A384ILE0-0.050-0.01835.290-0.035-0.0350.0000.0000.0000.000
193A385PRO00.031-0.00338.710-0.106-0.1060.0000.0000.0000.000
194A386LYS10.9810.97939.662-7.245-7.2450.0000.0000.0000.000
195A387SER0-0.036-0.01640.0830.2070.2070.0000.0000.0000.000
196A388THR00.0580.03638.6900.0320.0320.0000.0000.0000.000
197A389ALA00.0580.04135.8570.2690.2690.0000.0000.0000.000
198A390ALA00.0090.00533.6960.3160.3160.0000.0000.0000.000
199A391SER0-0.082-0.05432.5260.3480.3480.0000.0000.0000.000
200A392TYR0-0.065-0.08332.1580.2860.2860.0000.0000.0000.000
201A393LYS10.9080.94326.616-11.659-11.6590.0000.0000.0000.000
202A394ILE00.0380.02426.791-0.016-0.0160.0000.0000.0000.000
203A395ALA0-0.007-0.00321.5610.2810.2810.0000.0000.0000.000
204A396THR0-0.050-0.02322.683-0.507-0.5070.0000.0000.0000.000
205A397MET00.0470.04115.6730.5070.5070.0000.0000.0000.000
206A398LYS10.9280.94519.847-13.578-13.5780.0000.0000.0000.000
207A399VAL00.0450.04519.4320.5520.5520.0000.0000.0000.000