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: R9J78

Calculation Name: 3NUM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NUM

Chain ID: A

ChEMBL ID:

UniProt ID: Q92743

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2038296.224796
FMO2-HF: Nuclear repulsion 1966142.70078
FMO2-HF: Total energy -72153.524015
FMO2-MP2: Total energy -72370.739849


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:161:ASP)


Summations of interaction energy for fragment #1(A:161: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.
-122.862-122.69920.495-6.867-13.7910.116
Interaction energy analysis for fragmet #1(A:161:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.808 / q_NPA : -0.925
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].
3A163ASN0-0.008-0.0011.847-36.193-37.17814.907-6.909-7.0130.073
4A164SER0-0.0100.0012.115-14.114-13.7865.303-0.022-5.6090.031
5A165LEU00.028-0.0063.248-11.199-11.2920.2850.509-0.7010.011
6A166ARG10.9540.9786.546-31.047-31.0470.0000.0000.0000.000
7A167HIS0-0.026-0.0263.623-9.061-8.1480.000-0.445-0.4680.001
8A168LYS10.9000.9716.568-46.640-46.6400.0000.0000.0000.000
9A169TYR00.021-0.0108.715-1.604-1.6040.0000.0000.0000.000
10A170ASN0-0.076-0.03110.483-3.355-3.3550.0000.0000.0000.000
11A171PHE00.0920.04413.290-0.674-0.6740.0000.0000.0000.000
12A172ILE0-0.012-0.00316.096-0.916-0.9160.0000.0000.0000.000
13A173ALA0-0.016-0.01514.723-0.890-0.8900.0000.0000.0000.000
14A174ASP-1-0.828-0.91814.02321.34721.3470.0000.0000.0000.000
15A175VAL0-0.041-0.00816.804-0.924-0.9240.0000.0000.0000.000
16A176VAL0-0.033-0.02119.386-0.805-0.8050.0000.0000.0000.000
17A177GLU-1-0.971-0.98615.96416.64816.6480.0000.0000.0000.000
18A178LYS10.8650.93819.851-13.838-13.8380.0000.0000.0000.000
19A179ILE0-0.012-0.01222.084-0.651-0.6510.0000.0000.0000.000
20A180ALA00.0160.00323.628-0.531-0.5310.0000.0000.0000.000
21A181PRO0-0.044-0.03624.063-0.482-0.4820.0000.0000.0000.000
22A182ALA0-0.0090.01127.193-0.372-0.3720.0000.0000.0000.000
23A183VAL0-0.038-0.00828.688-0.384-0.3840.0000.0000.0000.000
24A184VAL0-0.048-0.02730.5740.0430.0430.0000.0000.0000.000
25A185HIS00.0190.01133.2820.0150.0150.0000.0000.0000.000
26A186ILE0-0.034-0.02835.234-0.194-0.1940.0000.0000.0000.000
27A187GLU-1-0.857-0.92438.9367.6347.6340.0000.0000.0000.000
28A188LEU0-0.0050.01041.732-0.169-0.1690.0000.0000.0000.000
29A189PHE00.0290.01143.567-0.083-0.0830.0000.0000.0000.000
30A190ARG10.9560.97448.082-5.981-5.9810.0000.0000.0000.000
31A191LYS10.9500.98151.735-5.687-5.6870.0000.0000.0000.000
32A192LEU0-0.011-0.00553.889-0.045-0.0450.0000.0000.0000.000
33A193PRO00.005-0.01256.389-0.044-0.0440.0000.0000.0000.000
34A194PHE00.0570.04159.794-0.046-0.0460.0000.0000.0000.000
35A195SER0-0.068-0.02558.141-0.039-0.0390.0000.0000.0000.000
36A196LYS11.0010.99857.552-5.282-5.2820.0000.0000.0000.000
37A197ARG10.9410.96653.598-5.538-5.5380.0000.0000.0000.000
38A198GLU-1-0.822-0.91950.5315.9895.9890.0000.0000.0000.000
39A199VAL0-0.030-0.02448.9970.0170.0170.0000.0000.0000.000
40A200PRO00.0290.02744.403-0.092-0.0920.0000.0000.0000.000
41A201VAL0-0.090-0.05346.449-0.065-0.0650.0000.0000.0000.000
42A202ALA00.0310.00044.0530.0400.0400.0000.0000.0000.000
43A203SER00.003-0.00239.2500.0720.0720.0000.0000.0000.000
44A204GLY00.0210.00837.589-0.045-0.0450.0000.0000.0000.000
45A205SER00.0200.03333.3290.1930.1930.0000.0000.0000.000
46A206GLY00.0340.01834.775-0.269-0.2690.0000.0000.0000.000
47A207PHE00.0150.00632.5160.3290.3290.0000.0000.0000.000
48A208ILE0-0.0100.01632.696-0.340-0.3400.0000.0000.0000.000
49A209VAL00.003-0.01034.1340.2480.2480.0000.0000.0000.000
50A210SER00.019-0.03336.497-0.096-0.0960.0000.0000.0000.000
51A211GLU-1-0.775-0.86435.2448.5158.5150.0000.0000.0000.000
52A212ASP-1-0.798-0.87137.0007.5757.5750.0000.0000.0000.000
53A213GLY0-0.0010.00538.223-0.120-0.1200.0000.0000.0000.000
54A214LEU0-0.019-0.00339.291-0.187-0.1870.0000.0000.0000.000
55A215ILE0-0.019-0.02136.9030.2680.2680.0000.0000.0000.000
56A216VAL00.0130.01337.851-0.268-0.2680.0000.0000.0000.000
57A217THR0-0.002-0.02237.6760.2040.2040.0000.0000.0000.000
58A218ASN00.0280.02339.498-0.241-0.2410.0000.0000.0000.000
59A219ALA0-0.0130.00141.709-0.046-0.0460.0000.0000.0000.000
60A220HIS0-0.086-0.05243.027-0.244-0.2440.0000.0000.0000.000
61A221VAL0-0.057-0.00539.063-0.051-0.0510.0000.0000.0000.000
62A222VAL0-0.011-0.01642.496-0.115-0.1150.0000.0000.0000.000
63A223THR00.005-0.00945.151-0.068-0.0680.0000.0000.0000.000
64A224ASN00.001-0.01548.8480.0190.0190.0000.0000.0000.000
65A225LYS10.7940.90251.516-6.145-6.1450.0000.0000.0000.000
66A226HIS0-0.029-0.00549.139-0.072-0.0720.0000.0000.0000.000
67A227ARG10.7760.86548.065-6.360-6.3600.0000.0000.0000.000
68A228VAL00.0400.01842.9670.0650.0650.0000.0000.0000.000
69A229LYS10.8830.96542.359-6.956-6.9560.0000.0000.0000.000
70A230VAL00.0360.01337.2620.0950.0950.0000.0000.0000.000
71A231GLU-1-0.841-0.92334.2428.5828.5820.0000.0000.0000.000
72A232LEU0-0.010-0.00132.6450.1920.1920.0000.0000.0000.000
73A233LYS11.0181.02022.751-12.426-12.4260.0000.0000.0000.000
74A234ASN0-0.027-0.03729.2540.0490.0490.0000.0000.0000.000
75A235GLY00.0560.03630.2270.0230.0230.0000.0000.0000.000
76A236ALA0-0.075-0.01733.234-0.254-0.2540.0000.0000.0000.000
77A237THR0-0.003-0.01136.3650.0020.0020.0000.0000.0000.000
78A238TYR0-0.026-0.04536.815-0.029-0.0290.0000.0000.0000.000
79A239GLU-1-0.818-0.87341.4806.6016.6010.0000.0000.0000.000
80A240ALA0-0.022-0.00542.4150.0410.0410.0000.0000.0000.000
81A241LYS10.7950.87244.387-6.803-6.8030.0000.0000.0000.000
82A242ILE00.0330.01346.1620.1490.1490.0000.0000.0000.000
83A243LYS10.8690.93646.534-6.552-6.5520.0000.0000.0000.000
84A244ASP-1-0.771-0.86847.7436.3666.3660.0000.0000.0000.000
85A245VAL0-0.039-0.02347.2150.1760.1760.0000.0000.0000.000
86A246ASP-1-0.767-0.84947.8846.3456.3450.0000.0000.0000.000
87A247GLU-1-0.798-0.92248.0676.2766.2760.0000.0000.0000.000
88A248LYS10.8110.89249.239-6.249-6.2490.0000.0000.0000.000
89A249ALA0-0.042-0.01146.3950.0640.0640.0000.0000.0000.000
90A250ASP-1-0.813-0.91343.7097.5807.5800.0000.0000.0000.000
91A251ILE0-0.024-0.01341.6360.2490.2490.0000.0000.0000.000
92A252ALA00.0090.00642.965-0.225-0.2250.0000.0000.0000.000
93A253LEU0-0.0070.00042.1290.2270.2270.0000.0000.0000.000
94A254ILE0-0.011-0.01740.719-0.229-0.2290.0000.0000.0000.000
95A255LYS10.8720.92142.282-6.997-6.9970.0000.0000.0000.000
96A256ILE0-0.028-0.00337.630-0.151-0.1510.0000.0000.0000.000
97A257ASP-1-0.813-0.88741.8176.8416.8410.0000.0000.0000.000
98A258HIS10.8790.93935.316-8.463-8.4630.0000.0000.0000.000
99A259GLN00.0640.04039.0810.0650.0650.0000.0000.0000.000
100A260GLY00.0090.00037.2240.1950.1950.0000.0000.0000.000
101A261LYS10.7950.88634.790-8.333-8.3330.0000.0000.0000.000
102A262LEU0-0.0190.00433.4870.2090.2090.0000.0000.0000.000
103A263PRO0-0.007-0.00129.117-0.001-0.0010.0000.0000.0000.000
104A264VAL0-0.019-0.01530.818-0.194-0.1940.0000.0000.0000.000
105A265LEU0-0.0120.00928.0770.3570.3570.0000.0000.0000.000
106A266LEU0-0.0050.00130.187-0.357-0.3570.0000.0000.0000.000
107A267LEU0-0.006-0.01432.1250.1620.1620.0000.0000.0000.000
108A268GLY00.1070.07432.638-0.004-0.0040.0000.0000.0000.000
109A269ARG10.7480.85833.482-8.799-8.7990.0000.0000.0000.000
110A270SER00.0290.00335.0970.1430.1430.0000.0000.0000.000
111A271SER0-0.074-0.04636.171-0.125-0.1250.0000.0000.0000.000
112A272GLU-1-0.827-0.88333.4538.8708.8700.0000.0000.0000.000
113A273LEU0-0.0400.00331.0820.2890.2890.0000.0000.0000.000
114A274ARG10.8480.91726.268-11.928-11.9280.0000.0000.0000.000
115A275PRO0-0.001-0.01230.6550.2860.2860.0000.0000.0000.000
116A276GLY0-0.013-0.00628.5210.1510.1510.0000.0000.0000.000
117A277GLU-1-0.835-0.90726.40211.97211.9720.0000.0000.0000.000
118A278PHE00.012-0.00520.917-0.104-0.1040.0000.0000.0000.000
119A279VAL0-0.001-0.00724.887-0.118-0.1180.0000.0000.0000.000
120A280VAL0-0.028-0.01422.8110.2710.2710.0000.0000.0000.000
121A281ALA00.0120.01325.848-0.385-0.3850.0000.0000.0000.000
122A282ILE00.0070.00325.1000.1950.1950.0000.0000.0000.000
123A283GLY00.0350.01028.331-0.365-0.3650.0000.0000.0000.000
124A284SER0-0.029-0.03029.1930.2870.2870.0000.0000.0000.000
125A285PRO0-0.090-0.00929.682-0.135-0.1350.0000.0000.0000.000
126A286PHE00.0680.04130.9930.2300.2300.0000.0000.0000.000
127A287SER0-0.043-0.03731.0580.1710.1710.0000.0000.0000.000
128A288LEU0-0.057-0.02124.6780.2610.2610.0000.0000.0000.000
129A289GLN0-0.063-0.01025.7100.5530.5530.0000.0000.0000.000
130A290ASN00.005-0.01925.4770.3480.3480.0000.0000.0000.000
131A291THR0-0.031-0.01326.5470.0550.0550.0000.0000.0000.000
132A292VAL00.0050.00122.359-0.216-0.2160.0000.0000.0000.000
133A293THR0-0.038-0.03624.9960.3060.3060.0000.0000.0000.000
134A294THR0-0.007-0.02721.5880.1350.1350.0000.0000.0000.000
135A295GLY00.0380.01825.026-0.134-0.1340.0000.0000.0000.000
136A296ILE00.0270.02225.6050.3930.3930.0000.0000.0000.000
137A297VAL00.0000.02827.884-0.440-0.4400.0000.0000.0000.000
138A298SER00.024-0.00431.2070.0210.0210.0000.0000.0000.000
139A299THR0-0.072-0.04033.434-0.345-0.3450.0000.0000.0000.000
140A300THR00.0300.03536.3070.0100.0100.0000.0000.0000.000
141A315ASP-1-0.833-0.89743.1637.4327.4320.0000.0000.0000.000
142A316TYR0-0.046-0.05140.132-0.070-0.0700.0000.0000.0000.000
143A317ILE00.0070.02634.061-0.011-0.0110.0000.0000.0000.000
144A318GLN0-0.018-0.03136.183-0.145-0.1450.0000.0000.0000.000
145A319THR0-0.020-0.03030.2900.2880.2880.0000.0000.0000.000
146A320ASP-1-0.859-0.92528.74810.66210.6620.0000.0000.0000.000
147A321ALA0-0.0280.01828.4640.1320.1320.0000.0000.0000.000
148A322ILE00.0320.01829.281-0.407-0.4070.0000.0000.0000.000
149A323ILE00.0090.03230.6820.2460.2460.0000.0000.0000.000
150A324ASN00.015-0.00131.509-0.271-0.2710.0000.0000.0000.000
151A325TYR00.024-0.00534.195-0.012-0.0120.0000.0000.0000.000
152A326GLY0-0.0050.01331.985-0.072-0.0720.0000.0000.0000.000
153A327ASN00.033-0.01829.546-0.200-0.2000.0000.0000.0000.000
154A328ALA00.0370.03032.431-0.013-0.0130.0000.0000.0000.000
155A329GLY0-0.012-0.00735.843-0.005-0.0050.0000.0000.0000.000
156A330GLY00.002-0.00232.767-0.032-0.0320.0000.0000.0000.000
157A331PRO0-0.0390.00229.894-0.164-0.1640.0000.0000.0000.000
158A332LEU00.0360.01629.6230.2810.2810.0000.0000.0000.000
159A333VAL0-0.010-0.02025.929-0.249-0.2490.0000.0000.0000.000
160A334ASN00.0680.03927.0580.5050.5050.0000.0000.0000.000
161A335LEU00.003-0.01820.6120.1930.1930.0000.0000.0000.000
162A336ASP-1-0.867-0.91322.57913.76513.7650.0000.0000.0000.000
163A337GLY0-0.080-0.04324.852-0.006-0.0060.0000.0000.0000.000
164A338GLU-1-0.897-0.93425.91610.25610.2560.0000.0000.0000.000
165A339VAL0-0.005-0.01129.5530.1040.1040.0000.0000.0000.000
166A340ILE0-0.041-0.03130.903-0.270-0.2700.0000.0000.0000.000
167A341GLY00.034-0.00233.458-0.272-0.2720.0000.0000.0000.000
168A342ILE0-0.048-0.00434.3060.2170.2170.0000.0000.0000.000
169A343ASN0-0.033-0.02631.372-0.082-0.0820.0000.0000.0000.000
170A344THR00.0480.00835.540-0.197-0.1970.0000.0000.0000.000
171A345LEU00.0270.01637.4320.1650.1650.0000.0000.0000.000
172A346LYS10.8380.95139.463-7.525-7.5250.0000.0000.0000.000
173A347VAL00.0340.00937.4430.1900.1900.0000.0000.0000.000
174A348THR0-0.084-0.05739.398-0.315-0.3150.0000.0000.0000.000
175A349ALA0-0.0060.00739.4840.1300.1300.0000.0000.0000.000
176A350GLY00.0160.01036.0610.1300.1300.0000.0000.0000.000
177A351ILE0-0.0010.01434.7540.2700.2700.0000.0000.0000.000
178A352SER00.0200.00233.550-0.430-0.4300.0000.0000.0000.000
179A353PHE00.026-0.00436.201-0.021-0.0210.0000.0000.0000.000
180A354ALA00.0270.01635.3920.0090.0090.0000.0000.0000.000
181A355ILE0-0.014-0.00137.507-0.092-0.0920.0000.0000.0000.000
182A356PRO00.0590.02837.8310.2210.2210.0000.0000.0000.000
183A357SER00.0320.00135.894-0.245-0.2450.0000.0000.0000.000
184A358ASP-1-0.779-0.89338.0118.3188.3180.0000.0000.0000.000
185A359LYS10.8250.89340.859-7.579-7.5790.0000.0000.0000.000
186A360ILE00.0220.02537.529-0.170-0.1700.0000.0000.0000.000
187A361LYS10.8350.91137.161-8.708-8.7080.0000.0000.0000.000
188A362LYS10.8370.90442.092-6.719-6.7190.0000.0000.0000.000
189A363PHE00.006-0.00243.481-0.100-0.1000.0000.0000.0000.000
190A364LEU00.010-0.00440.133-0.108-0.1080.0000.0000.0000.000
191A365THR0-0.092-0.05244.733-0.080-0.0800.0000.0000.0000.000
192A366GLU-1-0.878-0.92946.9726.3766.3760.0000.0000.0000.000
193A367SER0-0.028-0.01647.482-0.114-0.1140.0000.0000.0000.000
194A368HIS0-0.134-0.06945.8600.0340.0340.0000.0000.0000.000
195A369ASP-1-0.960-0.95449.2745.8135.8130.0000.0000.0000.000