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: JQ5M9

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1907112.686235
FMO2-HF: Nuclear repulsion 1836836.855748
FMO2-HF: Total energy -70275.830487
FMO2-MP2: Total energy -70480.825066


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.
-149.633-142.84112.122-10.074-8.838-0.128
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 : 0.866 / q_NPA : 0.924
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].
3A42LEU0-0.001-0.0083.378-5.909-3.2090.032-1.509-1.2230.003
4A43PRO0-0.021-0.0015.704-1.304-1.3040.0000.0000.0000.000
5A44ALA00.0280.0206.4953.2733.2730.0000.0000.0000.000
6A45ASN0-0.044-0.0329.3980.5030.5030.0000.0000.0000.000
7A46HIS00.005-0.01912.815-0.152-0.1520.0000.0000.0000.000
8A47SER00.0650.02912.3430.1740.1740.0000.0000.0000.000
9A48LEU0-0.042-0.0179.710-0.695-0.6950.0000.0000.0000.000
10A49TYR0-0.054-0.05112.9771.7961.7960.0000.0000.0000.000
11A50GLY00.0860.03313.484-0.862-0.8620.0000.0000.0000.000
12A51ASP-1-0.834-0.91412.001-25.155-25.1550.0000.0000.0000.000
13A52ALA00.0140.0059.428-2.318-2.3180.0000.0000.0000.000
14A53LYS10.8420.9117.67722.80622.8060.0000.0000.0000.000
15A54ALA00.0050.0268.316-0.996-0.9960.0000.0000.0000.000
16A55ARG10.8470.9226.59323.49923.4990.0000.0000.0000.000
17A56TRP0-0.014-0.0116.717-4.748-4.7480.0000.0000.0000.000
18A57THR0-0.010-0.0196.176-1.925-1.9250.0000.0000.0000.000
19A58ILE0-0.005-0.0077.8860.0280.0280.0000.0000.0000.000
20A59ASN0-0.042-0.0177.5700.1410.1410.0000.0000.0000.000
21A60GLU-1-0.772-0.89111.493-15.582-15.5820.0000.0000.0000.000
22A61TYR0-0.038-0.01011.791-0.228-0.2280.0000.0000.0000.000
23A62ALA00.041-0.00217.1670.9240.9240.0000.0000.0000.000
24A63ASP-1-0.767-0.88720.324-12.009-12.0090.0000.0000.0000.000
25A64LEU00.029-0.00223.2310.2090.2090.0000.0000.0000.000
26A65GLU-1-0.756-0.81625.616-9.682-9.6820.0000.0000.0000.000
27A66CYS0-0.0430.00725.7860.5350.5350.0000.0000.0000.000
28A67PRO00.0320.01927.545-0.268-0.2680.0000.0000.0000.000
29A68PHE00.017-0.02026.345-0.012-0.0120.0000.0000.0000.000
30A69CYS0-0.0160.00723.329-0.495-0.4950.0000.0000.0000.000
31A70LYS10.9420.98824.5559.6649.6640.0000.0000.0000.000
32A71VAL0-0.039-0.01327.2130.1160.1160.0000.0000.0000.000
33A72TYR0-0.039-0.05119.493-0.112-0.1120.0000.0000.0000.000
34A73THR00.031-0.00519.861-0.041-0.0410.0000.0000.0000.000
35A74PRO00.008-0.00221.088-0.520-0.5200.0000.0000.0000.000
36A75ARG10.8730.94223.29711.25111.2510.0000.0000.0000.000
37A76LEU0-0.0010.00716.303-0.209-0.2090.0000.0000.0000.000
38A77LYS10.8200.91018.47613.60313.6030.0000.0000.0000.000
39A78ARG10.9750.99819.42412.42012.4200.0000.0000.0000.000
40A79TRP0-0.059-0.04515.378-0.163-0.1630.0000.0000.0000.000
41A80VAL00.0220.01614.500-0.176-0.1760.0000.0000.0000.000
42A81ASP-1-0.850-0.89916.934-15.166-15.1660.0000.0000.0000.000
43A82SER0-0.103-0.06019.7790.5780.5780.0000.0000.0000.000
44A83HIS10.8160.90316.57716.28716.2870.0000.0000.0000.000
45A84PRO00.0850.03515.150-1.137-1.1370.0000.0000.0000.000
46A85ASP-1-0.920-0.94512.393-21.996-21.9960.0000.0000.0000.000
47A86VAL0-0.063-0.03410.669-3.014-3.0140.0000.0000.0000.000
48A87ASN0-0.0100.0127.5111.1361.1360.0000.0000.0000.000
49A88LEU0-0.0090.00111.011-0.584-0.5840.0000.0000.0000.000
50A89VAL0-0.040-0.0248.773-0.363-0.3630.0000.0000.0000.000
51A90TRP00.0300.00912.0170.2330.2330.0000.0000.0000.000
52A91ARG10.7810.8568.23525.16925.1690.0000.0000.0000.000
53A92HIS0-0.018-0.01714.9731.5511.5510.0000.0000.0000.000
54A93LEU0-0.006-0.01917.349-0.261-0.2610.0000.0000.0000.000
55A94PRO0-0.0070.00319.8310.4750.4750.0000.0000.0000.000
56A95LEU00.0080.00523.2960.1340.1340.0000.0000.0000.000
57A96GLN00.0520.01425.4880.1290.1290.0000.0000.0000.000
58A97MET0-0.073-0.03127.8650.3430.3430.0000.0000.0000.000
59A98HIS0-0.027-0.03027.4620.5540.5540.0000.0000.0000.000
60A99GLY00.0170.00330.2410.0720.0720.0000.0000.0000.000
61A100GLU-1-0.797-0.89128.231-10.791-10.7910.0000.0000.0000.000
62A101ALA00.0220.03428.998-0.240-0.2400.0000.0000.0000.000
63A102ALA00.0500.01725.825-0.226-0.2260.0000.0000.0000.000
64A103ARG10.8230.89924.29910.17510.1750.0000.0000.0000.000
65A104HIS0-0.001-0.00924.702-0.555-0.5550.0000.0000.0000.000
66A105GLN00.021-0.01626.2780.1140.1140.0000.0000.0000.000
67A106ALA00.0080.00421.079-0.301-0.3010.0000.0000.0000.000
68A107ARG10.8080.88121.53410.93310.9330.0000.0000.0000.000
69A108LEU00.0120.00823.184-0.190-0.1900.0000.0000.0000.000
70A109VAL00.0000.00820.167-0.036-0.0360.0000.0000.0000.000
71A110GLU-1-0.764-0.85616.645-17.749-17.7490.0000.0000.0000.000
72A111CYS0-0.087-0.03219.923-0.414-0.4140.0000.0000.0000.000
73A112ALA00.0270.01422.9050.2150.2150.0000.0000.0000.000
74A113GLY0-0.035-0.02119.137-0.029-0.0290.0000.0000.0000.000
75A114ILE0-0.046-0.02619.582-0.095-0.0950.0000.0000.0000.000
76A115GLN0-0.057-0.03521.1530.4860.4860.0000.0000.0000.000
77A116GLY00.0230.00422.7450.3950.3950.0000.0000.0000.000
78A117GLY0-0.0040.01018.798-0.158-0.1580.0000.0000.0000.000
79A118ALA00.0340.01616.7390.4210.4210.0000.0000.0000.000
80A119LYS10.9480.98218.51712.42612.4260.0000.0000.0000.000
81A120ALA00.0290.03622.1530.4270.4270.0000.0000.0000.000
82A121PHE00.0270.01217.2490.2750.2750.0000.0000.0000.000
83A122TRP00.020-0.01915.6520.8740.8740.0000.0000.0000.000
84A123SER0-0.040-0.03121.5210.5050.5050.0000.0000.0000.000
85A124ALA00.0230.01723.9800.4850.4850.0000.0000.0000.000
86A125ILE0-0.0050.00619.5570.3580.3580.0000.0000.0000.000
87A126ASP-1-0.835-0.90824.011-12.748-12.7480.0000.0000.0000.000
88A127ALA00.0000.00626.4230.4490.4490.0000.0000.0000.000
89A128ILE00.0120.00225.8170.4270.4270.0000.0000.0000.000
90A129PHE0-0.013-0.00323.2730.2990.2990.0000.0000.0000.000
91A130ALA0-0.077-0.03528.8520.3520.3520.0000.0000.0000.000
92A131GLN0-0.026-0.02532.0100.3640.3640.0000.0000.0000.000
93A132SER0-0.048-0.04031.3330.4070.4070.0000.0000.0000.000
94A133ALA0-0.035-0.02233.2240.0110.0110.0000.0000.0000.000
95A134GLY0-0.026-0.00431.8040.0090.0090.0000.0000.0000.000
96A135ASN0-0.070-0.06131.7090.1770.1770.0000.0000.0000.000
97A136GLY00.020-0.00432.0020.1260.1260.0000.0000.0000.000
98A137GLY0-0.105-0.03032.9250.1560.1560.0000.0000.0000.000
99A138GLY0-0.012-0.01032.2820.1460.1460.0000.0000.0000.000
100A139LEU0-0.0050.00430.0350.1490.1490.0000.0000.0000.000
101A140PRO00.0310.00933.9920.1580.1580.0000.0000.0000.000
102A141GLY00.0080.01037.131-0.022-0.0220.0000.0000.0000.000
103A142GLY0-0.016-0.00833.565-0.010-0.0100.0000.0000.0000.000
104A143THR0-0.032-0.01132.723-0.251-0.2510.0000.0000.0000.000
105A144LEU0-0.015-0.00528.267-0.036-0.0360.0000.0000.0000.000
106A145ASP-1-0.909-0.95032.395-8.647-8.6470.0000.0000.0000.000
107A146PHE0-0.032-0.03126.205-0.390-0.3900.0000.0000.0000.000
108A147PRO00.0520.03531.733-0.165-0.1650.0000.0000.0000.000
109A148GLU-1-0.956-0.97730.621-9.561-9.5610.0000.0000.0000.000
110A149LEU0-0.070-0.02626.271-0.386-0.3860.0000.0000.0000.000
111A150ASP-1-0.871-0.93530.289-9.012-9.0120.0000.0000.0000.000
112A151GLN00.031-0.00230.826-0.346-0.3460.0000.0000.0000.000
113A152ALA00.0680.04632.019-0.134-0.1340.0000.0000.0000.000
114A153ARG10.8370.91825.43411.09311.0930.0000.0000.0000.000
115A154LEU0-0.017-0.00425.997-0.349-0.3490.0000.0000.0000.000
116A155GLU-1-0.858-0.93028.050-9.350-9.3500.0000.0000.0000.000
117A156LYS10.9200.96330.3659.0659.0650.0000.0000.0000.000
118A158ALA00.028-0.00325.808-0.273-0.2730.0000.0000.0000.000
119A159LYS10.7500.86526.8629.1499.1490.0000.0000.0000.000
120A160ASP-1-0.804-0.88828.189-9.388-9.3880.0000.0000.0000.000
121A161ASN0-0.020-0.01821.284-0.181-0.1810.0000.0000.0000.000
122A162GLU-1-0.885-0.95722.685-11.565-11.5650.0000.0000.0000.000
123A163LEU0-0.0480.00618.291-0.417-0.4170.0000.0000.0000.000
124A164ILE00.0930.03717.780-0.474-0.4740.0000.0000.0000.000
125A165ASP-1-0.793-0.87318.748-12.508-12.5080.0000.0000.0000.000
126A166SER0-0.043-0.03817.3450.0470.0470.0000.0000.0000.000
127A167ASP-1-0.909-0.94813.718-18.655-18.6550.0000.0000.0000.000
128A168ILE0-0.036-0.02214.793-0.671-0.6710.0000.0000.0000.000
129A169LYS10.8390.91317.25212.27312.2730.0000.0000.0000.000
130A170LEU00.0340.02310.226-0.173-0.1730.0000.0000.0000.000
131A171ASP-1-0.750-0.86112.311-22.419-22.4190.0000.0000.0000.000
132A172ILE00.0200.01713.767-0.109-0.1090.0000.0000.0000.000
133A173ASP-1-0.833-0.89815.459-14.151-14.1510.0000.0000.0000.000
134A174ILE0-0.050-0.0198.984-0.386-0.3860.0000.0000.0000.000
135A175ALA00.0160.01812.746-0.327-0.3270.0000.0000.0000.000
136A176ARG10.8680.90215.49913.89813.8980.0000.0000.0000.000
137A177SER0-0.091-0.05213.261-0.074-0.0740.0000.0000.0000.000
138A178LYS10.8570.92710.30921.74721.7470.0000.0000.0000.000
139A179GLY00.0220.01816.1320.1490.1490.0000.0000.0000.000
140A180ILE0-0.066-0.01615.2990.1610.1610.0000.0000.0000.000
141A181THR0-0.096-0.05119.6400.4550.4550.0000.0000.0000.000
142A182ALA00.0020.01022.9520.4850.4850.0000.0000.0000.000
143A183THR00.0160.03421.116-0.551-0.5510.0000.0000.0000.000
144A184PRO00.016-0.01120.2470.6610.6610.0000.0000.0000.000
145A185THR0-0.033-0.03217.3170.4550.4550.0000.0000.0000.000
146A186LEU0-0.0180.00714.901-0.930-0.9300.0000.0000.0000.000
147A187VAL0-0.017-0.02010.1860.3530.3530.0000.0000.0000.000
148A188ILE00.0200.02710.518-2.565-2.5650.0000.0000.0000.000
149A189ARG10.8780.9193.86041.26241.4720.000-0.023-0.1880.000
150A190ASP-1-0.704-0.8286.528-39.362-39.3620.0000.0000.0000.000
151A191ASN0-0.034-0.0372.004-41.361-38.9945.142-3.835-3.674-0.057
152A192GLN00.0200.0231.904-35.375-34.1456.947-4.666-3.511-0.074
153A193THR0-0.040-0.0334.8143.3973.452-0.001-0.002-0.0510.000
154A194GLY0-0.0090.0053.6611.3511.5230.003-0.036-0.1380.000
155A195ARG10.8490.9504.58625.73325.791-0.001-0.003-0.0530.000
156A196SER00.009-0.0147.822-3.094-3.0940.0000.0000.0000.000
157A197VAL00.0000.0059.7011.7401.7400.0000.0000.0000.000
158A198LYS10.7920.89213.18614.62614.6260.0000.0000.0000.000
159A199LEU0-0.005-0.00615.5750.8920.8920.0000.0000.0000.000
160A200GLU-1-0.692-0.84618.518-14.519-14.5190.0000.0000.0000.000
161A201GLY00.0320.01821.2470.6120.6120.0000.0000.0000.000
162A202MET0-0.062-0.02021.400-0.545-0.5450.0000.0000.0000.000
163A203ALA00.0020.01119.6770.4300.4300.0000.0000.0000.000
164A204ASP-1-0.734-0.81621.658-12.973-12.9730.0000.0000.0000.000
165A205GLU-1-0.850-0.92221.001-13.813-13.8130.0000.0000.0000.000
166A206THR0-0.004-0.01621.165-0.460-0.4600.0000.0000.0000.000
167A207THR0-0.042-0.02419.973-0.355-0.3550.0000.0000.0000.000
168A208LEU0-0.040-0.01516.354-0.852-0.8520.0000.0000.0000.000
169A209LEU0-0.004-0.00416.704-1.163-1.1630.0000.0000.0000.000
170A210SER0-0.019-0.03018.174-0.558-0.5580.0000.0000.0000.000
171A211ALA00.0040.00615.472-0.311-0.3110.0000.0000.0000.000
172A212ILE00.0200.00512.738-1.107-1.1070.0000.0000.0000.000
173A213ASP-1-0.808-0.89314.475-16.088-16.0880.0000.0000.0000.000
174A214TRP0-0.0060.00013.565-0.439-0.4390.0000.0000.0000.000
175A215LEU0-0.086-0.05010.355-0.323-0.3230.0000.0000.0000.000
176A216ALA0-0.009-0.01611.132-1.054-1.0540.0000.0000.0000.000
177A217LYS10.8420.91713.08315.87215.8720.0000.0000.0000.000
178A218ASP-1-0.913-0.95116.506-16.088-16.0880.0000.0000.0000.000
179A219LEU0-0.089-0.04310.623-0.126-0.1260.0000.0000.0000.000
180A220LEU0-0.010-0.00612.945-1.900-1.9000.0000.0000.0000.000
181A221GLU-1-0.978-0.96714.878-18.505-18.5050.0000.0000.0000.000