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: 89YJY

Calculation Name: 4N30-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N30

Chain ID: A

ChEMBL ID:

UniProt ID: Q7WY37

Base Structure: X-ray

Registration Date: 2023-09-23

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1901284.532305
FMO2-HF: Nuclear repulsion 1831010.409765
FMO2-HF: Total energy -70274.12254
FMO2-MP2: Total energy -70479.429334


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:40:LYS)


Summations of interaction energy for fragment #1(A:40:LYS)
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.
-101.296-95.1620.408-3.268-3.273-0.027
Interaction energy analysis for fragmet #1(A:40:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.936 / q_NPA : 0.949
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].
3A42LEU00.017-0.0033.348-5.797-4.0270.026-0.914-0.882-0.001
4A43PRO0-0.022-0.0035.841-1.020-1.0200.0000.0000.0000.000
5A44ALA00.0210.0176.5443.2323.2320.0000.0000.0000.000
6A45ASN00.003-0.0099.5150.1590.1590.0000.0000.0000.000
7A46HIS0-0.035-0.03812.854-0.003-0.0030.0000.0000.0000.000
8A47SER00.0730.04412.3160.2830.2830.0000.0000.0000.000
9A48LEU0-0.019-0.00810.471-0.659-0.6590.0000.0000.0000.000
10A49TYR0-0.100-0.08713.5151.4841.4840.0000.0000.0000.000
11A50GLY00.0590.01614.387-0.891-0.8910.0000.0000.0000.000
12A51ASP-1-0.835-0.91012.883-23.576-23.5760.0000.0000.0000.000
13A52ALA00.026-0.00210.180-1.971-1.9710.0000.0000.0000.000
14A53LYS10.8390.9118.30724.04724.0470.0000.0000.0000.000
15A54ALA00.0160.0289.136-0.726-0.7260.0000.0000.0000.000
16A55ARG10.9040.9437.48824.14224.1420.0000.0000.0000.000
17A56TRP0-0.047-0.0187.038-5.464-5.4640.0000.0000.0000.000
18A57THR00.014-0.0137.343-0.815-0.8150.0000.0000.0000.000
19A58ILE0-0.013-0.0089.118-0.440-0.4400.0000.0000.0000.000
20A59ASN0-0.065-0.0288.0490.0340.0340.0000.0000.0000.000
21A60GLU-1-0.778-0.89112.054-15.041-15.0410.0000.0000.0000.000
22A61TYR0-0.048-0.02011.820-0.754-0.7540.0000.0000.0000.000
23A62ALA00.064-0.00117.1350.8700.8700.0000.0000.0000.000
24A63ASP-1-0.762-0.86120.432-11.734-11.7340.0000.0000.0000.000
25A64LEU00.0400.00223.1590.1800.1800.0000.0000.0000.000
26A65GLU-1-0.785-0.83225.779-9.569-9.5690.0000.0000.0000.000
27A66CYS0-0.0480.02425.5920.4940.4940.0000.0000.0000.000
28A67PRO00.0390.02727.881-0.227-0.2270.0000.0000.0000.000
29A68PHE00.037-0.02526.4430.0320.0320.0000.0000.0000.000
30A69CYS00.000-0.02023.349-0.426-0.4260.0000.0000.0000.000
31A70LYS10.9591.01324.9049.5459.5450.0000.0000.0000.000
32A71VAL0-0.058-0.03127.5990.0070.0070.0000.0000.0000.000
33A72TYR0-0.035-0.04620.013-0.257-0.2570.0000.0000.0000.000
34A73THR00.016-0.00721.004-0.149-0.1490.0000.0000.0000.000
35A74PRO00.0350.01122.328-0.473-0.4730.0000.0000.0000.000
36A75ARG10.9060.95924.23610.84710.8470.0000.0000.0000.000
37A76LEU00.0170.00917.455-0.191-0.1910.0000.0000.0000.000
38A77LYS10.9470.98119.51013.44113.4410.0000.0000.0000.000
39A78ARG10.9911.00920.58211.78211.7820.0000.0000.0000.000
40A79TRP00.010-0.00716.124-0.232-0.2320.0000.0000.0000.000
41A80VAL00.0000.00815.729-0.213-0.2130.0000.0000.0000.000
42A81ASP-1-0.834-0.87618.059-14.855-14.8550.0000.0000.0000.000
43A82SER0-0.119-0.05320.5710.2510.2510.0000.0000.0000.000
44A83HIS10.7990.89217.25615.90115.9010.0000.0000.0000.000
45A84PRO00.0760.01316.125-1.053-1.0530.0000.0000.0000.000
46A85ASP-1-0.881-0.91713.205-21.873-21.8730.0000.0000.0000.000
47A86VAL0-0.088-0.04411.607-2.545-2.5450.0000.0000.0000.000
48A87ASN0-0.0100.0208.3900.8770.8770.0000.0000.0000.000
49A88LEU00.0190.01312.250-0.398-0.3980.0000.0000.0000.000
50A89VAL0-0.021-0.0179.489-0.106-0.1060.0000.0000.0000.000
51A90TRP00.0130.00912.8770.3060.3060.0000.0000.0000.000
52A91ARG10.7770.8868.83324.32024.3200.0000.0000.0000.000
53A92HIS0-0.025-0.04214.8251.4911.4910.0000.0000.0000.000
54A93LEU0-0.028-0.03517.084-0.312-0.3120.0000.0000.0000.000
55A94PRO0-0.0050.01619.6060.4580.4580.0000.0000.0000.000
56A95LEU00.0120.00623.0280.0470.0470.0000.0000.0000.000
57A96GLN00.0260.00425.2650.0630.0630.0000.0000.0000.000
58A97MET0-0.078-0.04327.5700.3360.3360.0000.0000.0000.000
59A98HIS0-0.030-0.04227.3930.5530.5530.0000.0000.0000.000
60A99GLY0-0.002-0.00329.6260.0960.0960.0000.0000.0000.000
61A100GLU-1-0.820-0.92128.465-10.307-10.3070.0000.0000.0000.000
62A101ALA00.0390.04128.866-0.257-0.2570.0000.0000.0000.000
63A102ALA00.0400.01625.612-0.258-0.2580.0000.0000.0000.000
64A103ARG10.8380.90924.1029.8839.8830.0000.0000.0000.000
65A104HIS0-0.017-0.00224.494-0.538-0.5380.0000.0000.0000.000
66A105GLN00.044-0.02226.2400.1510.1510.0000.0000.0000.000
67A106ALA0-0.006-0.00520.711-0.294-0.2940.0000.0000.0000.000
68A107ARG10.9190.97521.51710.76410.7640.0000.0000.0000.000
69A108LEU00.0240.01423.105-0.212-0.2120.0000.0000.0000.000
70A109VAL00.0080.00920.361-0.063-0.0630.0000.0000.0000.000
71A110GLU-1-0.764-0.85216.820-17.426-17.4260.0000.0000.0000.000
72A111CYS0-0.105-0.03919.995-0.388-0.3880.0000.0000.0000.000
73A112ALA00.0270.00822.9230.2010.2010.0000.0000.0000.000
74A113GLY0-0.023-0.01519.1840.0820.0820.0000.0000.0000.000
75A114ILE0-0.041-0.01519.681-0.124-0.1240.0000.0000.0000.000
76A115GLN0-0.056-0.01521.0140.2720.2720.0000.0000.0000.000
77A116GLY00.013-0.01022.8210.3210.3210.0000.0000.0000.000
78A117GLY0-0.0370.00018.944-0.117-0.1170.0000.0000.0000.000
79A118ALA00.0600.02517.0340.3500.3500.0000.0000.0000.000
80A119LYS10.9490.96818.90712.31812.3180.0000.0000.0000.000
81A120ALA00.0170.01222.3480.3970.3970.0000.0000.0000.000
82A121PHE00.0370.02117.7180.3090.3090.0000.0000.0000.000
83A122TRP0-0.027-0.03616.1240.8830.8830.0000.0000.0000.000
84A123SER0-0.0110.00622.0440.4790.4790.0000.0000.0000.000
85A124ALA00.0350.01824.1420.4730.4730.0000.0000.0000.000
86A125ILE0-0.011-0.00120.1030.3600.3600.0000.0000.0000.000
87A126ASP-1-0.955-0.96524.594-11.908-11.9080.0000.0000.0000.000
88A127ALA0-0.020-0.00327.3720.4390.4390.0000.0000.0000.000
89A128ILE00.022-0.00125.9130.3950.3950.0000.0000.0000.000
90A129PHE0-0.016-0.00524.1870.3260.3260.0000.0000.0000.000
91A130ALA0-0.108-0.04929.6590.3350.3350.0000.0000.0000.000
92A131GLN0-0.018-0.02232.4490.3760.3760.0000.0000.0000.000
93A132SER0-0.038-0.03931.5410.3940.3940.0000.0000.0000.000
94A133ALA0-0.025-0.00533.5730.0500.0500.0000.0000.0000.000
95A134GLY0-0.039-0.01632.0800.0190.0190.0000.0000.0000.000
96A135ASN0-0.048-0.03431.8280.0790.0790.0000.0000.0000.000
97A136GLY00.004-0.01232.0750.1690.1690.0000.0000.0000.000
98A137GLY0-0.101-0.03832.9900.1510.1510.0000.0000.0000.000
99A138GLY00.001-0.01132.3040.1350.1350.0000.0000.0000.000
100A139LEU0-0.0120.01530.3340.1480.1480.0000.0000.0000.000
101A140PRO00.0480.02034.3270.1450.1450.0000.0000.0000.000
102A141GLY00.0190.01137.329-0.038-0.0380.0000.0000.0000.000
103A142GLY0-0.018-0.00833.700-0.040-0.0400.0000.0000.0000.000
104A143THR0-0.048-0.01732.899-0.253-0.2530.0000.0000.0000.000
105A144LEU0-0.020-0.01628.689-0.039-0.0390.0000.0000.0000.000
106A145ASP-1-0.933-0.96432.783-8.423-8.4230.0000.0000.0000.000
107A146PHE0-0.047-0.04526.670-0.370-0.3700.0000.0000.0000.000
108A147PRO00.0080.01232.220-0.158-0.1580.0000.0000.0000.000
109A148GLU-1-0.925-0.96830.926-9.438-9.4380.0000.0000.0000.000
110A149LEU0-0.094-0.03626.253-0.321-0.3210.0000.0000.0000.000
111A150ASP-1-0.873-0.93830.044-8.951-8.9510.0000.0000.0000.000
112A151GLN00.0850.01930.879-0.072-0.0720.0000.0000.0000.000
113A152ALA00.0880.04732.303-0.089-0.0890.0000.0000.0000.000
114A153ARG10.8810.95125.64310.75510.7550.0000.0000.0000.000
115A154LEU0-0.045-0.02826.021-0.259-0.2590.0000.0000.0000.000
116A155GLU-1-0.894-0.93928.171-9.072-9.0720.0000.0000.0000.000
117A156LYS10.9150.96030.0848.9568.9560.0000.0000.0000.000
118A158ALA00.0490.02025.462-0.262-0.2620.0000.0000.0000.000
119A159LYS10.7790.87826.4778.9608.9600.0000.0000.0000.000
120A160ASP-1-0.829-0.90527.562-9.427-9.4270.0000.0000.0000.000
121A161ASN0-0.042-0.00921.345-0.418-0.4180.0000.0000.0000.000
122A162GLU-1-0.847-0.94622.055-11.346-11.3460.0000.0000.0000.000
123A163LEU0-0.038-0.01917.307-0.400-0.4000.0000.0000.0000.000
124A164ILE00.0700.03017.158-0.569-0.5690.0000.0000.0000.000
125A165ASP-1-0.831-0.89318.187-12.567-12.5670.0000.0000.0000.000
126A166SER0-0.024-0.03316.071-0.115-0.1150.0000.0000.0000.000
127A167ASP-1-0.902-0.93513.827-18.407-18.4070.0000.0000.0000.000
128A168ILE0-0.049-0.03214.323-0.667-0.6670.0000.0000.0000.000
129A169LYS10.8180.89116.65012.05012.0500.0000.0000.0000.000
130A170LEU00.0600.0439.488-0.121-0.1210.0000.0000.0000.000
131A171ASP-1-0.793-0.89411.983-21.487-21.4870.0000.0000.0000.000
132A172ILE00.0050.00313.599-0.040-0.0400.0000.0000.0000.000
133A173ASP-1-0.899-0.94314.579-14.502-14.5020.0000.0000.0000.000
134A174ILE0-0.046-0.0378.892-0.305-0.3050.0000.0000.0000.000
135A175ALA0-0.0060.00012.898-0.166-0.1660.0000.0000.0000.000
136A176ARG10.9310.96615.56413.59913.5990.0000.0000.0000.000
137A177SER0-0.068-0.02013.5310.1660.1660.0000.0000.0000.000
138A178LYS10.9010.9569.66324.11424.1140.0000.0000.0000.000
139A179GLY0-0.003-0.01315.8590.1240.1240.0000.0000.0000.000
140A180ILE0-0.086-0.03315.1830.3140.3140.0000.0000.0000.000
141A181THR0-0.014-0.01519.4340.3200.3200.0000.0000.0000.000
142A182ALA00.0350.03022.3010.4570.4570.0000.0000.0000.000
143A183THR00.0080.04920.978-0.542-0.5420.0000.0000.0000.000
144A184PRO00.017-0.00920.3960.6370.6370.0000.0000.0000.000
145A185THR0-0.004-0.02716.8520.4350.4350.0000.0000.0000.000
146A186LEU0-0.029-0.01115.265-0.812-0.8120.0000.0000.0000.000
147A187VAL0-0.038-0.0259.8030.2450.2450.0000.0000.0000.000
148A188ILE00.0310.02310.976-1.674-1.6740.0000.0000.0000.000
149A189ARG10.9130.9493.50543.88844.1530.006-0.042-0.2290.000
150A190ASP-1-0.720-0.8526.732-36.204-36.2040.0000.0000.0000.000
151A191ASN0-0.101-0.0692.896-19.170-18.3720.055-0.291-0.562-0.002
152A192GLN0-0.0140.0042.704-22.125-19.0340.324-2.001-1.414-0.024
153A193THR0-0.025-0.0155.322-0.920-0.877-0.001-0.001-0.0410.000
154A194GLY0-0.0100.0014.1560.2870.393-0.001-0.018-0.0870.000
155A195ARG10.8910.9664.95525.89925.960-0.001-0.001-0.0580.000
156A196SER0-0.043-0.0387.925-2.509-2.5090.0000.0000.0000.000
157A197VAL00.0290.0159.7601.5841.5840.0000.0000.0000.000
158A198LYS10.8830.95413.29515.97715.9770.0000.0000.0000.000
159A199LEU0-0.010-0.00815.3700.8390.8390.0000.0000.0000.000
160A200GLU-1-0.935-0.95718.459-13.283-13.2830.0000.0000.0000.000
161A201GLY00.0470.02221.1210.5170.5170.0000.0000.0000.000
162A202MET0-0.062-0.02321.658-0.539-0.5390.0000.0000.0000.000
163A203ALA0-0.0250.00520.2580.4300.4300.0000.0000.0000.000
164A204ASP-1-0.792-0.88122.356-12.545-12.5450.0000.0000.0000.000
165A205GLU-1-0.911-0.98322.273-12.782-12.7820.0000.0000.0000.000
166A206THR00.0390.01621.993-0.588-0.5880.0000.0000.0000.000
167A207THR0-0.0110.00620.470-0.333-0.3330.0000.0000.0000.000
168A208LEU0-0.030-0.00717.253-0.852-0.8520.0000.0000.0000.000
169A209LEU0-0.011-0.00717.425-1.074-1.0740.0000.0000.0000.000
170A210SER0-0.027-0.02318.592-0.489-0.4890.0000.0000.0000.000
171A211ALA0-0.0020.01015.954-0.350-0.3500.0000.0000.0000.000
172A212ILE00.0360.00313.070-1.073-1.0730.0000.0000.0000.000
173A213ASP-1-0.861-0.92814.506-16.168-16.1680.0000.0000.0000.000
174A214TRP0-0.043-0.03713.645-0.543-0.5430.0000.0000.0000.000
175A215LEU0-0.123-0.06210.241-0.481-0.4810.0000.0000.0000.000
176A216ALA0-0.008-0.00611.492-0.982-0.9820.0000.0000.0000.000
177A217LYS10.9440.99613.50016.20116.2010.0000.0000.0000.000
178A218ASP-1-0.932-0.96216.685-15.322-15.3220.0000.0000.0000.000
179A219LEU0-0.141-0.07811.119-0.441-0.4410.0000.0000.0000.000
180A220LEU00.015-0.00213.503-1.639-1.6390.0000.0000.0000.000
181A221GLU-1-0.970-0.95815.916-18.308-18.3080.0000.0000.0000.000