Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52YMZ

Calculation Name: 3NWJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NWJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8GY88

Base Structure: X-ray

Registration Date: 2023-06-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2138200.550248
FMO2-HF: Nuclear repulsion 2061787.114165
FMO2-HF: Total energy -76413.436083
FMO2-MP2: Total energy -76635.047375


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:82:GLN)


Summations of interaction energy for fragment #1(A:82:GLN)
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.
-11.644-5.4181.493-3.036-4.6840.002
Interaction energy analysis for fragmet #1(A:82:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.019
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].
3A84ILE00.0390.0143.023-5.331-1.7940.290-1.763-2.0640.009
4A85LEU00.0030.0132.312-2.984-1.1741.135-1.031-1.914-0.006
5A86LYS10.9670.9833.872-0.898-0.4480.004-0.112-0.3420.000
6A87LYS10.9820.9876.343-0.417-0.4170.0000.0000.0000.000
7A88LYS10.9030.9496.7410.2270.2270.0000.0000.0000.000
8A89ALA0-0.025-0.0037.9820.0060.0060.0000.0000.0000.000
9A90GLU-1-0.985-1.0009.8160.2220.2220.0000.0000.0000.000
10A91GLU-1-0.904-0.95811.573-0.039-0.0390.0000.0000.0000.000
11A92VAL00.0290.02611.923-0.006-0.0060.0000.0000.0000.000
12A93LYS10.8660.93914.288-0.077-0.0770.0000.0000.0000.000
13A94PRO0-0.011-0.00816.1540.0040.0040.0000.0000.0000.000
14A95TYR00.0550.05217.1260.0060.0060.0000.0000.0000.000
15A96LEU0-0.015-0.00415.880-0.002-0.0020.0000.0000.0000.000
16A97ASN0-0.024-0.00219.7250.0100.0100.0000.0000.0000.000
17A98GLY00.009-0.00820.6090.0030.0030.0000.0000.0000.000
18A99ARG10.9320.97221.6220.0370.0370.0000.0000.0000.000
19A100SER00.006-0.00120.2800.0020.0020.0000.0000.0000.000
20A101MET0-0.0130.00413.669-0.015-0.0150.0000.0000.0000.000
21A102TYR00.0240.01019.2220.0160.0160.0000.0000.0000.000
22A103LEU0-0.020-0.00714.631-0.016-0.0160.0000.0000.0000.000
23A104VAL00.0180.00719.2590.0190.0190.0000.0000.0000.000
24A105GLY00.0750.01820.975-0.024-0.0240.0000.0000.0000.000
25A106MET00.0320.04822.7510.0210.0210.0000.0000.0000.000
26A107MET00.0060.00823.373-0.008-0.0080.0000.0000.0000.000
27A108GLY00.0840.04822.199-0.006-0.0060.0000.0000.0000.000
28A109SER0-0.012-0.03319.612-0.021-0.0210.0000.0000.0000.000
29A110GLY00.0180.00616.390-0.032-0.0320.0000.0000.0000.000
30A111LYS10.8380.90915.4830.0860.0860.0000.0000.0000.000
31A112THR00.0120.00916.149-0.011-0.0110.0000.0000.0000.000
32A113THR00.003-0.00911.7210.0430.0430.0000.0000.0000.000
33A114VAL00.0220.02011.1000.0030.0030.0000.0000.0000.000
34A115GLY00.0680.03111.399-0.019-0.0190.0000.0000.0000.000
35A116LYS10.9320.97112.585-0.086-0.0860.0000.0000.0000.000
36A117ILE0-0.0200.0066.3060.0770.0770.0000.0000.0000.000
37A118MET00.0060.0078.453-0.003-0.0030.0000.0000.0000.000
38A119ALA00.0010.00710.4160.0280.0280.0000.0000.0000.000
39A120ARG10.9790.9848.127-0.852-0.8520.0000.0000.0000.000
40A121SER0-0.098-0.0596.776-0.001-0.0010.0000.0000.0000.000
41A122LEU00.0120.0178.4330.0330.0330.0000.0000.0000.000
42A123GLY0-0.027-0.00711.6820.0320.0320.0000.0000.0000.000
43A124TYR0-0.061-0.03713.5420.0000.0000.0000.0000.0000.000
44A125THR00.0120.01515.2820.0310.0310.0000.0000.0000.000
45A126PHE00.003-0.01015.259-0.020-0.0200.0000.0000.0000.000
46A127PHE00.004-0.01317.3340.0230.0230.0000.0000.0000.000
47A128ASP-1-0.811-0.89920.375-0.024-0.0240.0000.0000.0000.000
48A129CYS00.0100.00321.8200.0090.0090.0000.0000.0000.000
49A130ASP-1-0.836-0.93725.193-0.018-0.0180.0000.0000.0000.000
50A131THR0-0.025-0.02523.6720.0100.0100.0000.0000.0000.000
51A132LEU0-0.045-0.02224.8100.0080.0080.0000.0000.0000.000
52A133ILE0-0.025-0.00327.4800.0030.0030.0000.0000.0000.000
53A134GLU-1-0.928-0.96828.6240.0270.0270.0000.0000.0000.000
54A135GLN0-0.032-0.01025.8130.0060.0060.0000.0000.0000.000
55A136ALA0-0.039-0.02130.9430.0040.0040.0000.0000.0000.000
56A137MET0-0.059-0.01733.283-0.003-0.0030.0000.0000.0000.000
57A138LYS10.8870.93333.339-0.058-0.0580.0000.0000.0000.000
58A139GLY0-0.0020.00337.869-0.002-0.0020.0000.0000.0000.000
59A140THR00.0160.02438.556-0.002-0.0020.0000.0000.0000.000
60A141SER0-0.055-0.05235.5670.0020.0020.0000.0000.0000.000
61A142VAL00.032-0.00532.040-0.003-0.0030.0000.0000.0000.000
62A143ALA00.0190.00535.261-0.004-0.0040.0000.0000.0000.000
63A144GLU-1-0.748-0.83237.0150.0170.0170.0000.0000.0000.000
64A145ILE0-0.028-0.01437.689-0.002-0.0020.0000.0000.0000.000
65A146PHE0-0.048-0.03934.428-0.004-0.0040.0000.0000.0000.000
66A147GLU-1-0.952-0.96039.514-0.001-0.0010.0000.0000.0000.000
67A148HIS0-0.061-0.03442.537-0.001-0.0010.0000.0000.0000.000
68A149PHE0-0.035-0.03242.0270.0000.0000.0000.0000.0000.000
69A150GLY00.0290.04041.388-0.002-0.0020.0000.0000.0000.000
70A151GLU-1-0.854-0.93435.346-0.037-0.0370.0000.0000.0000.000
71A152SER0-0.013-0.01237.704-0.001-0.0010.0000.0000.0000.000
72A153VAL00.0640.03239.4560.0000.0000.0000.0000.0000.000
73A154PHE00.0310.01830.2430.0020.0020.0000.0000.0000.000
74A155ARG10.7160.82831.2220.0350.0350.0000.0000.0000.000
75A156GLU-1-0.934-0.96834.940-0.006-0.0060.0000.0000.0000.000
76A157LYS10.8690.92834.268-0.006-0.0060.0000.0000.0000.000
77A158GLU-1-0.777-0.88929.534-0.030-0.0300.0000.0000.0000.000
78A159THR0-0.053-0.04131.0600.0000.0000.0000.0000.0000.000
79A160GLU-1-0.877-0.91732.8780.0110.0110.0000.0000.0000.000
80A161ALA00.0210.00229.0820.0040.0040.0000.0000.0000.000
81A162LEU00.002-0.01126.5470.0030.0030.0000.0000.0000.000
82A163LYS10.9200.96729.190-0.006-0.0060.0000.0000.0000.000
83A164LYS10.8750.93529.587-0.047-0.0470.0000.0000.0000.000
84A165LEU00.000-0.01424.3960.0040.0040.0000.0000.0000.000
85A166SER0-0.040-0.00726.6650.0020.0020.0000.0000.0000.000
86A167LEU0-0.042-0.02528.1100.0000.0000.0000.0000.0000.000
87A168MET0-0.0100.01329.5480.0020.0020.0000.0000.0000.000
88A169TYR0-0.035-0.01324.2170.0060.0060.0000.0000.0000.000
89A170HIS00.0610.03424.048-0.012-0.0120.0000.0000.0000.000
90A171GLN0-0.023-0.01419.1270.0140.0140.0000.0000.0000.000
91A172VAL00.0010.00918.9720.0160.0160.0000.0000.0000.000
92A173VAL0-0.037-0.01414.320-0.020-0.0200.0000.0000.0000.000
93A174VAL00.0030.00517.6710.0220.0220.0000.0000.0000.000
94A175SER0-0.0130.02218.551-0.021-0.0210.0000.0000.0000.000
95A176THR00.000-0.01020.3230.0190.0190.0000.0000.0000.000
96A177GLY00.1540.08323.408-0.013-0.0130.0000.0000.0000.000
97A178GLY0-0.061-0.04325.956-0.005-0.0050.0000.0000.0000.000
98A179GLY00.007-0.00326.789-0.004-0.0040.0000.0000.0000.000
99A180ALA00.0500.04626.9730.0040.0040.0000.0000.0000.000
100A181VAL0-0.032-0.01226.4130.0050.0050.0000.0000.0000.000
101A182ILE00.0000.01929.357-0.001-0.0010.0000.0000.0000.000
102A183ARG10.9420.98832.9830.0220.0220.0000.0000.0000.000
103A184PRO00.0820.02533.2360.0000.0000.0000.0000.0000.000
104A185ILE0-0.032-0.01334.1700.0010.0010.0000.0000.0000.000
105A186ASN00.024-0.00830.0280.0080.0080.0000.0000.0000.000
106A187TRP00.0290.01325.4840.0010.0010.0000.0000.0000.000
107A188LYS10.9440.99430.2280.0130.0130.0000.0000.0000.000
108A189TYR0-0.027-0.03229.8000.0040.0040.0000.0000.0000.000
109A190MET0-0.008-0.00425.5960.0000.0000.0000.0000.0000.000
110A191HIS00.0270.02525.627-0.001-0.0010.0000.0000.0000.000
111A192LYS10.8470.94127.7600.0120.0120.0000.0000.0000.000
112A193GLY0-0.033-0.01423.8530.0070.0070.0000.0000.0000.000
113A194ILE0-0.0050.01318.981-0.005-0.0050.0000.0000.0000.000
114A195SER00.0310.01520.488-0.004-0.0040.0000.0000.0000.000
115A196ILE00.009-0.01014.954-0.010-0.0100.0000.0000.0000.000
116A197TRP00.0220.00018.8560.0060.0060.0000.0000.0000.000
117A198LEU0-0.037-0.01214.968-0.020-0.0200.0000.0000.0000.000
118A199ASP-1-0.825-0.89418.479-0.179-0.1790.0000.0000.0000.000
119A200VAL0-0.031-0.02618.674-0.032-0.0320.0000.0000.0000.000
120A201PRO00.0780.03921.0700.0190.0190.0000.0000.0000.000
121A202LEU00.0720.02924.046-0.004-0.0040.0000.0000.0000.000
122A203GLU-1-0.841-0.92526.157-0.166-0.1660.0000.0000.0000.000
123A204ALA00.007-0.00321.117-0.002-0.0020.0000.0000.0000.000
124A205LEU0-0.058-0.02621.8660.0010.0010.0000.0000.0000.000
125A206ALA00.0130.00624.0250.0110.0110.0000.0000.0000.000
126A207HIS0-0.020-0.00821.7480.0260.0260.0000.0000.0000.000
127A208ARG10.8660.93616.3090.3010.3010.0000.0000.0000.000
128A209ILE0-0.067-0.03722.8380.0160.0160.0000.0000.0000.000
129A210ALA0-0.042-0.01625.9250.0120.0120.0000.0000.0000.000
130A211ALA0-0.0250.00623.1740.0110.0110.0000.0000.0000.000
131A228THR00.0260.00132.0610.0010.0010.0000.0000.0000.000
132A229TYR00.0780.03527.6180.0000.0000.0000.0000.0000.000
133A230THR00.0480.01231.435-0.001-0.0010.0000.0000.0000.000
134A231ALA0-0.0020.01234.2560.0030.0030.0000.0000.0000.000
135A232ALA00.010-0.00329.6910.0040.0040.0000.0000.0000.000
136A233LEU00.0390.01029.4820.0020.0020.0000.0000.0000.000
137A234ASN00.0230.01831.652-0.003-0.0030.0000.0000.0000.000
138A235ARG10.9530.98333.2230.0590.0590.0000.0000.0000.000
139A236LEU0-0.009-0.00627.5080.0030.0030.0000.0000.0000.000
140A237SER00.0380.02531.177-0.003-0.0030.0000.0000.0000.000
141A238THR0-0.019-0.00933.2180.0040.0040.0000.0000.0000.000
142A239ILE0-0.063-0.03230.6360.0030.0030.0000.0000.0000.000
143A240TRP00.019-0.00826.627-0.002-0.0020.0000.0000.0000.000
144A241ASP-1-0.875-0.93631.573-0.088-0.0880.0000.0000.0000.000
145A242ALA0-0.058-0.01434.4250.0050.0050.0000.0000.0000.000
146A243ARG10.8920.93230.3000.0670.0670.0000.0000.0000.000
147A244GLY00.0400.02829.409-0.002-0.0020.0000.0000.0000.000
148A245GLU-1-0.851-0.92329.181-0.077-0.0770.0000.0000.0000.000
149A246ALA0-0.027-0.00530.334-0.001-0.0010.0000.0000.0000.000
150A247TYR0-0.039-0.04224.8780.0010.0010.0000.0000.0000.000
151A248THR0-0.052-0.04525.474-0.005-0.0050.0000.0000.0000.000
152A249LYS10.8470.93127.1280.0710.0710.0000.0000.0000.000
153A250ALA0-0.034-0.02022.3810.0060.0060.0000.0000.0000.000
154A251SER00.0010.01321.3520.0000.0000.0000.0000.0000.000
155A252ALA00.0170.01818.157-0.004-0.0040.0000.0000.0000.000
156A253ARG10.8600.91519.7660.2120.2120.0000.0000.0000.000
157A254VAL00.0080.00613.793-0.014-0.0140.0000.0000.0000.000
158A255SER0-0.001-0.01516.8480.0070.0070.0000.0000.0000.000
159A256LEU00.009-0.02115.068-0.036-0.0360.0000.0000.0000.000
160A257GLU-1-0.884-0.93616.952-0.289-0.2890.0000.0000.0000.000
161A258ASN00.0070.00418.171-0.006-0.0060.0000.0000.0000.000
162A259ILE0-0.0110.00511.838-0.014-0.0140.0000.0000.0000.000
163A260THR00.0280.01014.574-0.049-0.0490.0000.0000.0000.000
164A261LEU0-0.0350.00016.224-0.017-0.0170.0000.0000.0000.000
165A262LYS10.8400.91412.6810.4520.4520.0000.0000.0000.000
166A263LEU0-0.037-0.02310.326-0.008-0.0080.0000.0000.0000.000
167A264GLY00.0000.01914.246-0.062-0.0620.0000.0000.0000.000
168A265TYR0-0.124-0.0919.6790.0290.0290.0000.0000.0000.000
169A266ARG10.8750.92116.7410.4580.4580.0000.0000.0000.000
170A267SER0-0.022-0.01218.6780.0620.0620.0000.0000.0000.000
171A268VAL00.035-0.00716.933-0.045-0.0450.0000.0000.0000.000
172A269SER0-0.077-0.03916.113-0.009-0.0090.0000.0000.0000.000
173A270ASP-1-0.791-0.88015.104-0.485-0.4850.0000.0000.0000.000
174A271LEU0-0.0250.01411.693-0.123-0.1230.0000.0000.0000.000
175A272THR0-0.021-0.0217.1530.1120.1120.0000.0000.0000.000
176A273PRO0-0.009-0.0309.493-0.005-0.0050.0000.0000.0000.000
177A274ALA00.013-0.0043.975-0.0690.032-0.001-0.022-0.0780.000
178A275GLU-1-0.756-0.8346.059-1.638-1.6380.0000.0000.0000.000
179A276ILE00.0210.0147.4570.2000.2000.0000.0000.0000.000
180A277ALA00.0070.0057.0520.1150.1150.0000.0000.0000.000
181A278ILE0-0.018-0.0102.883-0.2360.0920.065-0.108-0.286-0.001
182A279GLU-1-0.762-0.8497.174-0.287-0.2870.0000.0000.0000.000
183A280ALA0-0.031-0.03210.8000.0920.0920.0000.0000.0000.000
184A281PHE0-0.038-0.0387.5620.0640.0640.0000.0000.0000.000
185A282GLU-1-0.827-0.91210.388-0.291-0.2910.0000.0000.0000.000
186A283GLN0-0.062-0.04212.6200.0730.0730.0000.0000.0000.000
187A284VAL0-0.032-0.01614.3730.0330.0330.0000.0000.0000.000
188A285GLN0-0.007-0.01713.5330.0320.0320.0000.0000.0000.000
189A286SER00.0290.02816.0970.0210.0210.0000.0000.0000.000
190A287TYR0-0.026-0.02918.6040.0140.0140.0000.0000.0000.000
191A288LEU0-0.050-0.03117.5210.0140.0140.0000.0000.0000.000
192A289GLU-1-0.921-0.95518.347-0.103-0.1030.0000.0000.0000.000
193A290LYS10.8350.92421.4430.1360.1360.0000.0000.0000.000
194A291GLU-1-0.998-0.98424.379-0.038-0.0380.0000.0000.0000.000