FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6NJJZ

Calculation Name: 1P4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P4X

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0R2

Base Structure: X-ray

Registration Date: 2023-09-20

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 250
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3460171.534762
FMO2-HF: Nuclear repulsion 3355865.595644
FMO2-HF: Total energy -104305.939118
FMO2-MP2: Total energy -104611.520407


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-14.552-6.07210.709-5.205-13.985-0.029
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.014
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].
3A3TYR0-0.036-0.0323.837-1.7380.055-0.014-0.831-0.9480.002
4A4ASN0-0.054-0.0414.2591.0151.089-0.001-0.008-0.0660.000
5A5ASN00.0220.0277.702-0.067-0.0670.0000.0000.0000.000
6A6HIS0-0.011-0.02611.2670.0360.0360.0000.0000.0000.000
7A7ASP-1-0.717-0.82913.7180.3510.3510.0000.0000.0000.000
8A8LYS10.8800.92815.706-0.164-0.1640.0000.0000.0000.000
9A9ILE0-0.0050.00811.452-0.010-0.0100.0000.0000.0000.000
10A10ARG10.9170.96510.495-0.478-0.4780.0000.0000.0000.000
11A11ASP-1-0.811-0.89912.8010.2680.2680.0000.0000.0000.000
12A12PHE0-0.037-0.01213.882-0.026-0.0260.0000.0000.0000.000
13A13ILE00.003-0.0028.842-0.015-0.0150.0000.0000.0000.000
14A14ILE00.0060.00511.408-0.021-0.0210.0000.0000.0000.000
15A15ILE00.0240.02013.729-0.056-0.0560.0000.0000.0000.000
16A16GLU-1-0.804-0.89114.6840.2090.2090.0000.0000.0000.000
17A17ALA0-0.004-0.00612.143-0.037-0.0370.0000.0000.0000.000
18A18TYR0-0.031-0.03614.137-0.058-0.0580.0000.0000.0000.000
19A19MET0-0.022-0.00616.805-0.035-0.0350.0000.0000.0000.000
20A20PHE0-0.082-0.03715.113-0.016-0.0160.0000.0000.0000.000
21A21ARG10.8180.86913.371-0.038-0.0380.0000.0000.0000.000
22A22PHE00.0720.03417.512-0.016-0.0160.0000.0000.0000.000
23A23LYS10.9200.95421.021-0.116-0.1160.0000.0000.0000.000
24A24LYS10.8960.94416.7210.0690.0690.0000.0000.0000.000
25A25LYS10.8990.95921.0110.0480.0480.0000.0000.0000.000
26A26VAL00.0410.03022.817-0.004-0.0040.0000.0000.0000.000
27A27LYS10.9060.95525.412-0.038-0.0380.0000.0000.0000.000
28A28PRO0-0.077-0.04625.3960.0020.0020.0000.0000.0000.000
29A29GLU-1-0.886-0.92727.631-0.024-0.0240.0000.0000.0000.000
30A30VAL0-0.017-0.00930.1950.0010.0010.0000.0000.0000.000
31A31ASP-1-0.923-0.94432.2700.0120.0120.0000.0000.0000.000
32A32MET0-0.093-0.01633.5200.0020.0020.0000.0000.0000.000
33A33THR0-0.058-0.06530.8510.0040.0040.0000.0000.0000.000
34A34ILE00.0600.00925.2040.0010.0010.0000.0000.0000.000
35A35LYS10.7980.90129.393-0.062-0.0620.0000.0000.0000.000
36A36GLU-1-0.762-0.84131.3320.0410.0410.0000.0000.0000.000
37A37PHE00.0840.03731.2980.0000.0000.0000.0000.0000.000
38A38ILE0-0.0130.01427.4840.0010.0010.0000.0000.0000.000
39A39LEU0-0.023-0.01932.1070.0010.0010.0000.0000.0000.000
40A40LEU0-0.006-0.00535.505-0.001-0.0010.0000.0000.0000.000
41A41THR00.025-0.00932.254-0.002-0.0020.0000.0000.0000.000
42A42TYR0-0.079-0.07334.733-0.002-0.0020.0000.0000.0000.000
43A43LEU0-0.055-0.02636.294-0.001-0.0010.0000.0000.0000.000
44A44PHE00.0160.02337.892-0.002-0.0020.0000.0000.0000.000
45A45HIS0-0.0170.00034.501-0.002-0.0020.0000.0000.0000.000
46A46GLN00.002-0.02338.8810.0030.0030.0000.0000.0000.000
47A47GLN00.0200.00141.897-0.001-0.0010.0000.0000.0000.000
48A48GLU-1-0.869-0.91545.5790.0390.0390.0000.0000.0000.000
49A49ASN0-0.0070.00946.2210.0020.0020.0000.0000.0000.000
50A50THR0-0.078-0.06547.818-0.001-0.0010.0000.0000.0000.000
51A51LEU00.0680.04242.1750.0010.0010.0000.0000.0000.000
52A52PRO00.0210.01444.778-0.001-0.0010.0000.0000.0000.000
53A53PHE00.007-0.02739.8530.0020.0020.0000.0000.0000.000
54A54LYN00.0260.00941.0960.0020.0020.0000.0000.0000.000
55A55LYS10.8570.92139.898-0.052-0.0520.0000.0000.0000.000
56A56ILE00.0080.01337.1410.0030.0030.0000.0000.0000.000
57A57VAL0-0.072-0.05336.3320.0040.0040.0000.0000.0000.000
58A58SER0-0.031-0.01435.3460.0040.0040.0000.0000.0000.000
59A59ASP-1-0.767-0.82735.3980.0650.0650.0000.0000.0000.000
60A60LEU0-0.027-0.01431.7540.0040.0040.0000.0000.0000.000
61A61CYS0-0.064-0.04826.591-0.001-0.0010.0000.0000.0000.000
62A62TYR0-0.005-0.00428.8050.0050.0050.0000.0000.0000.000
63A63LYS10.9020.94030.701-0.084-0.0840.0000.0000.0000.000
64A64GLN00.0780.03233.894-0.002-0.0020.0000.0000.0000.000
65A65SER0-0.008-0.03834.672-0.002-0.0020.0000.0000.0000.000
66A66ASP-1-0.859-0.88531.9410.0750.0750.0000.0000.0000.000
67A67LEU00.0670.03534.2510.0000.0000.0000.0000.0000.000
68A68VAL00.0040.00936.855-0.003-0.0030.0000.0000.0000.000
69A69GLN00.0390.00237.788-0.004-0.0040.0000.0000.0000.000
70A70HIS00.0290.01333.5800.0010.0010.0000.0000.0000.000
71A71ILE00.0390.02638.094-0.002-0.0020.0000.0000.0000.000
72A72LYS10.9030.95941.094-0.035-0.0350.0000.0000.0000.000
73A73VAL00.0100.01238.412-0.003-0.0030.0000.0000.0000.000
74A74LEU00.0180.00838.081-0.002-0.0020.0000.0000.0000.000
75A75VAL00.0030.00341.817-0.002-0.0020.0000.0000.0000.000
76A76LYS10.8530.93144.080-0.021-0.0210.0000.0000.0000.000
77A77HIS0-0.010-0.00341.884-0.004-0.0040.0000.0000.0000.000
78A78SER00.0330.01144.880-0.001-0.0010.0000.0000.0000.000
79A79TYR00.0180.01140.401-0.001-0.0010.0000.0000.0000.000
80A80ILE00.0190.01642.5570.0010.0010.0000.0000.0000.000
81A81SER00.0330.02445.970-0.001-0.0010.0000.0000.0000.000
82A82LYS10.8920.94446.421-0.032-0.0320.0000.0000.0000.000
83A83VAL00.0060.01049.004-0.002-0.0020.0000.0000.0000.000
84A84ARG10.8060.87150.638-0.025-0.0250.0000.0000.0000.000
85A85SER0-0.022-0.02851.063-0.001-0.0010.0000.0000.0000.000
86A86LYS10.9770.98152.895-0.025-0.0250.0000.0000.0000.000
87A87ILE00.0580.03654.185-0.001-0.0010.0000.0000.0000.000
88A88ASP-1-0.770-0.84350.7300.0350.0350.0000.0000.0000.000
89A89GLU-1-0.781-0.86952.2210.0270.0270.0000.0000.0000.000
90A90ARG10.8110.89349.307-0.037-0.0370.0000.0000.0000.000
91A91ASN0-0.042-0.02347.9140.0020.0020.0000.0000.0000.000
92A92THR0-0.036-0.03146.163-0.002-0.0020.0000.0000.0000.000
93A93TYR00.0360.03146.9180.0020.0020.0000.0000.0000.000
94A94ILE0-0.006-0.00743.470-0.001-0.0010.0000.0000.0000.000
95A95SER0-0.034-0.00846.6950.0000.0000.0000.0000.0000.000
96A96ILE00.0280.01444.2030.0000.0000.0000.0000.0000.000
97A97SER00.0400.01948.3930.0000.0000.0000.0000.0000.000
98A98GLU-1-0.831-0.93049.3090.0260.0260.0000.0000.0000.000
99A99GLU-1-0.941-0.96249.0140.0180.0180.0000.0000.0000.000
100A100GLN0-0.047-0.03046.9690.0010.0010.0000.0000.0000.000
101A101ARG10.8560.91343.629-0.034-0.0340.0000.0000.0000.000
102A102GLU-1-0.870-0.93044.0870.0240.0240.0000.0000.0000.000
103A103LYS10.8680.94143.579-0.021-0.0210.0000.0000.0000.000
104A104ILE0-0.080-0.04839.7170.0010.0010.0000.0000.0000.000
105A105ALA00.0430.03139.7430.0010.0010.0000.0000.0000.000
106A106GLU-1-0.906-0.93939.5190.0180.0180.0000.0000.0000.000
107A107ARG10.8810.92236.027-0.022-0.0220.0000.0000.0000.000
108A108VAL0-0.028-0.01534.7560.0010.0010.0000.0000.0000.000
109A109THR00.0420.01434.5000.0010.0010.0000.0000.0000.000
110A110LEU0-0.022-0.01133.844-0.001-0.0010.0000.0000.0000.000
111A111PHE0-0.020-0.01128.228-0.001-0.0010.0000.0000.0000.000
112A112ASP-1-0.766-0.87230.0800.0440.0440.0000.0000.0000.000
113A113GLN0-0.061-0.03029.7980.0010.0010.0000.0000.0000.000
114A114ILE0-0.017-0.01427.288-0.004-0.0040.0000.0000.0000.000
115A115ILE0-0.038-0.00524.901-0.005-0.0050.0000.0000.0000.000
116A116LYS10.9860.99625.005-0.018-0.0180.0000.0000.0000.000
117A117GLN0-0.006-0.01125.679-0.005-0.0050.0000.0000.0000.000
118A118PHE0-0.037-0.00818.518-0.012-0.0120.0000.0000.0000.000
119A119ASN00.024-0.00220.914-0.010-0.0100.0000.0000.0000.000
120A120LEU0-0.026-0.00120.813-0.005-0.0050.0000.0000.0000.000
121A121ALA0-0.0210.00121.745-0.012-0.0120.0000.0000.0000.000
122A122ASP-1-0.793-0.87216.548-0.055-0.0550.0000.0000.0000.000
123A123GLN0-0.0170.00211.624-0.047-0.0470.0000.0000.0000.000
124A124SER0-0.041-0.02513.9350.0120.0120.0000.0000.0000.000
125A125GLU-1-0.886-0.92010.1000.3070.3070.0000.0000.0000.000
126A126SER0-0.009-0.03212.6340.0590.0590.0000.0000.0000.000
127A127GLN00.037-0.00915.060-0.001-0.0010.0000.0000.0000.000
128A128MET0-0.031-0.00616.613-0.020-0.0200.0000.0000.0000.000
129A129ILE0-0.0460.00017.075-0.005-0.0050.0000.0000.0000.000
130A130PRO0-0.029-0.00119.580-0.002-0.0020.0000.0000.0000.000
131A131LYS10.8230.90322.272-0.116-0.1160.0000.0000.0000.000
132A132ASP-1-0.836-0.90825.4480.0580.0580.0000.0000.0000.000
133A133SER00.022-0.03127.8870.0090.0090.0000.0000.0000.000
134A134LYS10.8560.91230.039-0.059-0.0590.0000.0000.0000.000
135A135GLU-1-0.770-0.87725.0840.1070.1070.0000.0000.0000.000
136A136PHE0-0.006-0.02023.8770.0120.0120.0000.0000.0000.000
137A137LEU0-0.044-0.01426.1200.0090.0090.0000.0000.0000.000
138A138ASN00.0440.00727.4230.0070.0070.0000.0000.0000.000
139A139LEU00.0460.02421.5180.0120.0120.0000.0000.0000.000
140A140MET0-0.034-0.01022.5900.0200.0200.0000.0000.0000.000
141A141MET00.0080.01923.9880.0090.0090.0000.0000.0000.000
142A142TYR00.0530.01918.256-0.002-0.0020.0000.0000.0000.000
143A143THR0-0.059-0.03819.1120.0120.0120.0000.0000.0000.000
144A144MET0-0.060-0.03420.7940.0090.0090.0000.0000.0000.000
145A145TYR00.0450.01823.428-0.005-0.0050.0000.0000.0000.000
146A146PHE00.0460.02614.886-0.002-0.0020.0000.0000.0000.000
147A147LYS10.7690.86318.321-0.223-0.2230.0000.0000.0000.000
148A148ASN0-0.053-0.04220.921-0.005-0.0050.0000.0000.0000.000
149A149ILE00.0210.02920.898-0.010-0.0100.0000.0000.0000.000
150A150ILE0-0.0070.00216.776-0.007-0.0070.0000.0000.0000.000
151A151LYS10.8850.94620.273-0.148-0.1480.0000.0000.0000.000
152A152LYS10.9010.96222.890-0.121-0.1210.0000.0000.0000.000
153A153HIS00.001-0.00422.590-0.013-0.0130.0000.0000.0000.000
154A154LEU0-0.0070.01417.3430.0030.0030.0000.0000.0000.000
155A155THR00.0040.00321.008-0.003-0.0030.0000.0000.0000.000
156A156LEU0-0.0280.00714.7440.0030.0030.0000.0000.0000.000
157A157SER0-0.026-0.05516.8760.0060.0060.0000.0000.0000.000
158A158PHE00.0650.00615.5470.0200.0200.0000.0000.0000.000
159A159VAL0-0.0420.00713.2020.0530.0530.0000.0000.0000.000
160A160GLU-1-0.765-0.85111.8280.3820.3820.0000.0000.0000.000
161A161PHE00.0700.03011.4720.0590.0590.0000.0000.0000.000
162A162THR0-0.017-0.0259.0290.0030.0030.0000.0000.0000.000
163A163ILE0-0.018-0.0117.1770.1350.1350.0000.0000.0000.000
164A164LEU00.0310.0226.5810.0710.0710.0000.0000.0000.000
165A165ALA00.0270.0397.961-0.091-0.0910.0000.0000.0000.000
166A166ILE0-0.023-0.0172.463-0.829-0.2620.819-0.206-1.180-0.001
167A167ILE00.006-0.0013.552-1.090-0.5600.010-0.175-0.364-0.001
168A168THR00.0570.0114.774-0.246-0.214-0.0010.000-0.0310.000
169A169SER0-0.033-0.0045.1450.0570.0570.0000.0000.0000.000
170A170GLN0-0.048-0.0392.608-1.547-0.8773.357-1.048-2.980-0.015
171A171ASN0-0.031-0.0085.6250.0310.0310.0000.0000.0000.000
172A172LYS10.8440.9169.269-0.056-0.0560.0000.0000.0000.000
173A173ASN0-0.069-0.0196.290-0.035-0.0350.0000.0000.0000.000
174A174ILE0-0.018-0.0106.690-0.013-0.0130.0000.0000.0000.000
175A175VAL0-0.013-0.0052.439-1.372-1.3393.336-0.551-2.8180.000
176A176LEU0-0.0040.0014.6200.3720.481-0.001-0.013-0.0950.000
177A177LEU0-0.003-0.0115.3700.3280.3280.0000.0000.0000.000
178A178LYS10.9150.9537.2551.2451.2450.0000.0000.0000.000
179A179ASP-1-0.807-0.9052.963-2.113-1.6570.084-0.126-0.4140.000
180A180LEU00.0030.0203.181-2.934-1.0100.850-0.901-1.873-0.001
181A181ILE0-0.067-0.0594.189-0.160-0.2450.0000.239-0.1540.000
182A182GLU-1-0.939-0.9625.454-0.787-0.7870.0000.0000.0000.000
183A183THR0-0.047-0.0222.641-4.631-2.3142.271-1.569-3.019-0.013
184A184ILE0-0.072-0.0314.8770.2120.272-0.001-0.016-0.0430.000
185A185HIS00.0200.0138.323-0.166-0.1660.0000.0000.0000.000
186A186HIS0-0.038-0.01510.581-0.152-0.1520.0000.0000.0000.000
187A187LYS11.0191.00611.470-0.005-0.0050.0000.0000.0000.000
188A188TYR00.1050.04812.6300.0610.0610.0000.0000.0000.000
189A189PRO0-0.012-0.01013.7570.0300.0300.0000.0000.0000.000
190A190GLN0-0.028-0.01614.861-0.010-0.0100.0000.0000.0000.000
191A191THR00.0720.0239.1010.0100.0100.0000.0000.0000.000
192A192VAL00.0020.00412.2980.0410.0410.0000.0000.0000.000
193A193ARG10.9270.96513.996-0.183-0.1830.0000.0000.0000.000
194A194ALA00.0390.02612.818-0.022-0.0220.0000.0000.0000.000
195A195LEU00.0690.0228.399-0.053-0.0530.0000.0000.0000.000
196A196ASN0-0.047-0.00812.571-0.047-0.0470.0000.0000.0000.000
197A197ASN0-0.041-0.02716.263-0.046-0.0460.0000.0000.0000.000
198A198LEU00.0060.00310.896-0.023-0.0230.0000.0000.0000.000
199A199LYS10.9150.96814.560-0.102-0.1020.0000.0000.0000.000
200A200LYS10.8820.93715.696-0.133-0.1330.0000.0000.0000.000
201A201GLN0-0.062-0.04817.954-0.025-0.0250.0000.0000.0000.000
202A202GLY00.0410.04017.773-0.007-0.0070.0000.0000.0000.000
203A203TYR0-0.011-0.00913.381-0.005-0.0050.0000.0000.0000.000
204A204LEU0-0.0030.0029.1780.0180.0180.0000.0000.0000.000
205A205ILE00.0160.01811.864-0.002-0.0020.0000.0000.0000.000
206A206LYS10.8840.92411.150-0.206-0.2060.0000.0000.0000.000
207A207GLU-1-0.889-0.94112.748-0.062-0.0620.0000.0000.0000.000
208A208ARG10.8750.92113.8800.0670.0670.0000.0000.0000.000
209A209SER0-0.032-0.01814.4800.0000.0000.0000.0000.0000.000
210A210THR00.027-0.03116.2160.0050.0050.0000.0000.0000.000
211A211GLU-1-0.855-0.88619.236-0.121-0.1210.0000.0000.0000.000
212A212ASP-1-0.846-0.92415.881-0.294-0.2940.0000.0000.0000.000
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