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: Z6Q4N

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2037019.346285
FMO2-HF: Nuclear repulsion 1964867.273052
FMO2-HF: Total energy -72152.073233
FMO2-MP2: Total energy -72369.353317


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.
-115.323-118.11925.617-7.932-14.890.121
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 : -0.795 / q_NPA : -0.913
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].
3A163ASN0-0.050-0.0281.852-34.212-37.11017.665-7.322-7.4450.079
4A164SER00.0050.0191.901-11.783-13.1057.631-0.493-5.8160.028
5A165LEU00.040-0.0013.211-10.968-11.3390.3200.806-0.7560.012
6A166ARG10.9450.9776.334-30.956-30.9560.0000.0000.0000.000
7A167HIS0-0.051-0.0453.552-9.570-7.7750.001-0.923-0.8730.002
8A168LYS10.9380.9836.676-44.190-44.1900.0000.0000.0000.000
9A169TYR00.010-0.0108.657-1.925-1.9250.0000.0000.0000.000
10A170ASN0-0.060-0.02010.282-3.158-3.1580.0000.0000.0000.000
11A171PHE00.0940.03813.073-0.576-0.5760.0000.0000.0000.000
12A172ILE00.0120.00815.880-0.832-0.8320.0000.0000.0000.000
13A173ALA0-0.025-0.02614.712-0.879-0.8790.0000.0000.0000.000
14A174ASP-1-0.844-0.92614.08621.17721.1770.0000.0000.0000.000
15A175VAL0-0.033-0.00516.780-0.884-0.8840.0000.0000.0000.000
16A176VAL0-0.044-0.01119.114-0.793-0.7930.0000.0000.0000.000
17A177GLU-1-0.985-0.99315.92916.79616.7960.0000.0000.0000.000
18A178LYS10.9390.97919.826-13.822-13.8220.0000.0000.0000.000
19A179ILE0-0.004-0.01022.057-0.638-0.6380.0000.0000.0000.000
20A180ALA00.0090.00123.536-0.530-0.5300.0000.0000.0000.000
21A181PRO0-0.060-0.04724.013-0.477-0.4770.0000.0000.0000.000
22A182ALA0-0.0020.01227.167-0.366-0.3660.0000.0000.0000.000
23A183VAL0-0.028-0.00228.010-0.380-0.3800.0000.0000.0000.000
24A184VAL0-0.055-0.02830.5510.0460.0460.0000.0000.0000.000
25A185HIS00.0370.01433.260-0.022-0.0220.0000.0000.0000.000
26A186ILE0-0.025-0.02135.214-0.190-0.1900.0000.0000.0000.000
27A187GLU-1-0.915-0.96838.9167.5567.5560.0000.0000.0000.000
28A188LEU0-0.0010.00941.713-0.167-0.1670.0000.0000.0000.000
29A189PHE00.0460.02543.920-0.069-0.0690.0000.0000.0000.000
30A190ARG10.9300.95548.063-5.998-5.9980.0000.0000.0000.000
31A191LYS11.0030.99851.717-5.573-5.5730.0000.0000.0000.000
32A192LEU0-0.025-0.00853.746-0.041-0.0410.0000.0000.0000.000
33A193PRO00.005-0.01256.373-0.050-0.0500.0000.0000.0000.000
34A194PHE00.0630.04259.778-0.048-0.0480.0000.0000.0000.000
35A195SER0-0.070-0.02457.861-0.034-0.0340.0000.0000.0000.000
36A196LYS10.9870.99357.379-5.269-5.2690.0000.0000.0000.000
37A197ARG10.9480.96653.744-5.515-5.5150.0000.0000.0000.000
38A198GLU-1-0.876-0.95550.4615.9865.9860.0000.0000.0000.000
39A199VAL0-0.037-0.03048.9780.0200.0200.0000.0000.0000.000
40A200PRO00.0260.03344.446-0.097-0.0970.0000.0000.0000.000
41A201VAL0-0.089-0.06046.433-0.066-0.0660.0000.0000.0000.000
42A202ALA00.0270.00344.1050.0410.0410.0000.0000.0000.000
43A203SER00.0090.02038.8200.0760.0760.0000.0000.0000.000
44A204GLY00.0300.00737.568-0.050-0.0500.0000.0000.0000.000
45A205SER00.0210.02733.2700.1760.1760.0000.0000.0000.000
46A206GLY00.0260.00934.738-0.262-0.2620.0000.0000.0000.000
47A207PHE00.0240.00832.4870.3170.3170.0000.0000.0000.000
48A208ILE0-0.0280.01532.452-0.335-0.3350.0000.0000.0000.000
49A209VAL00.008-0.00834.1080.2490.2490.0000.0000.0000.000
50A210SER0-0.009-0.05936.470-0.092-0.0920.0000.0000.0000.000
51A211GLU-1-0.802-0.88635.2178.5908.5900.0000.0000.0000.000
52A212ASP-1-0.823-0.88636.9717.5897.5890.0000.0000.0000.000
53A213GLY00.0000.00538.199-0.115-0.1150.0000.0000.0000.000
54A214LEU0-0.028-0.01039.264-0.190-0.1900.0000.0000.0000.000
55A215ILE0-0.011-0.02236.9000.2590.2590.0000.0000.0000.000
56A216VAL00.0220.02137.826-0.267-0.2670.0000.0000.0000.000
57A217THR00.0090.00437.6530.2040.2040.0000.0000.0000.000
58A218ASN00.0200.02739.318-0.263-0.2630.0000.0000.0000.000
59A219ALA00.0090.00641.689-0.036-0.0360.0000.0000.0000.000
60A220HIS0-0.088-0.04843.025-0.234-0.2340.0000.0000.0000.000
61A221VAL0-0.070-0.01639.105-0.044-0.0440.0000.0000.0000.000
62A222VAL0-0.014-0.02342.477-0.115-0.1150.0000.0000.0000.000
63A223THR00.0410.01045.130-0.078-0.0780.0000.0000.0000.000
64A224ASN00.010-0.01948.828-0.011-0.0110.0000.0000.0000.000
65A225LYS10.8720.96051.494-6.107-6.1070.0000.0000.0000.000
66A226HIS0-0.035-0.00549.167-0.093-0.0930.0000.0000.0000.000
67A227ARG10.8670.95947.901-6.375-6.3750.0000.0000.0000.000
68A228VAL00.0330.01542.8670.0630.0630.0000.0000.0000.000
69A229LYS10.9000.96942.462-6.908-6.9080.0000.0000.0000.000
70A230VAL00.0370.01637.2870.1010.1010.0000.0000.0000.000
71A231GLU-1-0.835-0.91234.4548.5118.5110.0000.0000.0000.000
72A232LEU0-0.014-0.00832.5820.1950.1950.0000.0000.0000.000
73A233LYS11.0401.02622.838-12.335-12.3350.0000.0000.0000.000
74A234ASN0-0.033-0.03629.2310.0620.0620.0000.0000.0000.000
75A235GLY00.0610.03730.2050.0250.0250.0000.0000.0000.000
76A236ALA0-0.072-0.01933.213-0.251-0.2510.0000.0000.0000.000
77A237THR0-0.001-0.00436.3430.0060.0060.0000.0000.0000.000
78A238TYR0-0.025-0.04636.868-0.033-0.0330.0000.0000.0000.000
79A239GLU-1-0.857-0.92541.4576.6066.6060.0000.0000.0000.000
80A240ALA0-0.027-0.00542.4060.0440.0440.0000.0000.0000.000
81A241LYS10.8080.88244.363-6.773-6.7730.0000.0000.0000.000
82A242ILE00.0380.01246.1370.1530.1530.0000.0000.0000.000
83A243LYS10.8590.93146.361-6.617-6.6170.0000.0000.0000.000
84A244ASP-1-0.818-0.91547.7076.3516.3510.0000.0000.0000.000
85A245VAL0-0.049-0.02047.1910.1790.1790.0000.0000.0000.000
86A246ASP-1-0.774-0.85347.8416.3376.3370.0000.0000.0000.000
87A247GLU-1-0.864-0.95848.0466.3506.3500.0000.0000.0000.000
88A248LYS10.8020.88649.074-6.224-6.2240.0000.0000.0000.000
89A249ALA0-0.065-0.02346.2390.0670.0670.0000.0000.0000.000
90A250ASP-1-0.809-0.91143.5127.5057.5050.0000.0000.0000.000
91A251ILE0-0.039-0.01741.8440.2560.2560.0000.0000.0000.000
92A252ALA00.0030.00342.944-0.221-0.2210.0000.0000.0000.000
93A253LEU0-0.003-0.00142.1630.2200.2200.0000.0000.0000.000
94A254ILE0-0.014-0.01340.736-0.230-0.2300.0000.0000.0000.000
95A255LYS10.9000.94942.256-6.944-6.9440.0000.0000.0000.000
96A256ILE0-0.026-0.01137.954-0.146-0.1460.0000.0000.0000.000
97A257ASP-1-0.841-0.89541.7906.8526.8520.0000.0000.0000.000
98A258HIS10.8880.94835.162-8.455-8.4550.0000.0000.0000.000
99A259GLN00.0630.03539.0470.0080.0080.0000.0000.0000.000
100A260GLY0-0.010-0.01137.1950.1990.1990.0000.0000.0000.000
101A261LYS10.8450.91634.729-8.149-8.1490.0000.0000.0000.000
102A262LEU0-0.029-0.00333.4630.2090.2090.0000.0000.0000.000
103A263PRO00.0060.00128.8880.0130.0130.0000.0000.0000.000
104A264VAL0-0.014-0.00530.816-0.189-0.1890.0000.0000.0000.000
105A265LEU0-0.0140.00528.0950.3520.3520.0000.0000.0000.000
106A266LEU0-0.0040.00130.158-0.368-0.3680.0000.0000.0000.000
107A267LEU0-0.007-0.01132.0990.1540.1540.0000.0000.0000.000
108A268GLY00.0790.05432.6410.0060.0060.0000.0000.0000.000
109A269ARG10.7480.86233.482-8.761-8.7610.0000.0000.0000.000
110A270SER00.0830.03035.0370.1300.1300.0000.0000.0000.000
111A271SER0-0.096-0.05736.116-0.117-0.1170.0000.0000.0000.000
112A272GLU-1-0.802-0.87233.4848.8598.8590.0000.0000.0000.000
113A273LEU0-0.0480.00030.7870.2590.2590.0000.0000.0000.000
114A274ARG10.9510.97026.251-11.923-11.9230.0000.0000.0000.000
115A275PRO0-0.012-0.01030.5840.2560.2560.0000.0000.0000.000
116A276GLY0-0.023-0.01628.4460.1540.1540.0000.0000.0000.000
117A277GLU-1-0.893-0.95426.38912.01512.0150.0000.0000.0000.000
118A278PHE0-0.010-0.00920.534-0.093-0.0930.0000.0000.0000.000
119A279VAL00.0160.00324.831-0.120-0.1200.0000.0000.0000.000
120A280VAL0-0.040-0.01622.6120.2540.2540.0000.0000.0000.000
121A281ALA00.0120.00125.634-0.383-0.3830.0000.0000.0000.000
122A282ILE0-0.0090.00024.8700.1870.1870.0000.0000.0000.000
123A283GLY00.0260.00728.312-0.365-0.3650.0000.0000.0000.000
124A284SER0-0.027-0.03129.1730.2710.2710.0000.0000.0000.000
125A285PRO0-0.100-0.01829.752-0.121-0.1210.0000.0000.0000.000
126A286PHE00.0770.05031.3250.1920.1920.0000.0000.0000.000
127A287SER0-0.061-0.04731.3400.1660.1660.0000.0000.0000.000
128A288LEU0-0.033-0.01324.7100.2780.2780.0000.0000.0000.000
129A289GLN0-0.077-0.02426.0950.5560.5560.0000.0000.0000.000
130A290ASN00.0370.00425.4550.1740.1740.0000.0000.0000.000
131A291THR0-0.050-0.02426.5120.0600.0600.0000.0000.0000.000
132A292VAL00.0180.00522.299-0.233-0.2330.0000.0000.0000.000
133A293THR0-0.013-0.00924.8040.3250.3250.0000.0000.0000.000
134A294THR00.008-0.02421.6690.1360.1360.0000.0000.0000.000
135A295GLY00.0230.01024.813-0.129-0.1290.0000.0000.0000.000
136A296ILE00.0190.01825.5470.3600.3600.0000.0000.0000.000
137A297VAL00.0010.01927.829-0.442-0.4420.0000.0000.0000.000
138A298SER00.034-0.00531.1490.0950.0950.0000.0000.0000.000
139A299THR0-0.088-0.05233.374-0.330-0.3300.0000.0000.0000.000
140A300THR00.0320.03736.2630.0140.0140.0000.0000.0000.000
141A315ASP-1-0.951-0.97343.0767.4817.4810.0000.0000.0000.000
142A316TYR0-0.050-0.05639.943-0.082-0.0820.0000.0000.0000.000
143A317ILE00.0060.02734.005-0.003-0.0030.0000.0000.0000.000
144A318GLN00.021-0.01036.135-0.076-0.0760.0000.0000.0000.000
145A319THR0-0.029-0.02230.1930.2670.2670.0000.0000.0000.000
146A320ASP-1-0.844-0.91327.83111.03211.0320.0000.0000.0000.000
147A321ALA0-0.0470.00528.1700.1250.1250.0000.0000.0000.000
148A322ILE00.0320.02528.795-0.410-0.4100.0000.0000.0000.000
149A323ILE0-0.0150.01330.4780.2330.2330.0000.0000.0000.000
150A324ASN00.0190.00031.440-0.264-0.2640.0000.0000.0000.000
151A325TYR00.020-0.01033.950-0.012-0.0120.0000.0000.0000.000
152A326GLY0-0.0070.01131.957-0.073-0.0730.0000.0000.0000.000
153A327ASN00.034-0.00829.339-0.201-0.2010.0000.0000.0000.000
154A328ALA00.0370.03232.411-0.013-0.0130.0000.0000.0000.000
155A329GLY0-0.030-0.01835.824-0.010-0.0100.0000.0000.0000.000
156A330GLY00.0090.00132.748-0.038-0.0380.0000.0000.0000.000
157A331PRO0-0.0340.00429.784-0.181-0.1810.0000.0000.0000.000
158A332LEU00.0410.01129.1160.2740.2740.0000.0000.0000.000
159A333VAL0-0.013-0.01725.811-0.261-0.2610.0000.0000.0000.000
160A334ASN00.0840.06826.8810.5420.5420.0000.0000.0000.000
161A335LEU00.003-0.02920.4800.2280.2280.0000.0000.0000.000
162A336ASP-1-0.889-0.92422.57913.65813.6580.0000.0000.0000.000
163A337GLY0-0.110-0.05624.852-0.010-0.0100.0000.0000.0000.000
164A338GLU-1-0.954-0.96625.89110.34110.3410.0000.0000.0000.000
165A339VAL0-0.008-0.01629.5530.0960.0960.0000.0000.0000.000
166A340ILE0-0.031-0.02830.793-0.278-0.2780.0000.0000.0000.000
167A341GLY00.023-0.00433.257-0.272-0.2720.0000.0000.0000.000
168A342ILE0-0.048-0.00134.1630.2080.2080.0000.0000.0000.000
169A343ASN0-0.021-0.03231.329-0.114-0.1140.0000.0000.0000.000
170A344THR00.0300.01035.332-0.300-0.3000.0000.0000.0000.000
171A345LEU00.0300.00737.2240.1680.1680.0000.0000.0000.000
172A346LYS10.8870.96639.260-7.432-7.4320.0000.0000.0000.000
173A347VAL00.0490.01837.1580.1980.1980.0000.0000.0000.000
174A348THR0-0.085-0.05939.240-0.327-0.3270.0000.0000.0000.000
175A349ALA0-0.0140.00739.4430.1250.1250.0000.0000.0000.000
176A350GLY00.0050.00536.0250.1290.1290.0000.0000.0000.000
177A351ILE00.0030.01534.6440.2740.2740.0000.0000.0000.000
178A352SER00.013-0.01033.241-0.422-0.4220.0000.0000.0000.000
179A353PHE0-0.026-0.01935.9870.0020.0020.0000.0000.0000.000
180A354ALA00.0310.01535.2140.0080.0080.0000.0000.0000.000
181A355ILE0-0.0100.00437.291-0.083-0.0830.0000.0000.0000.000
182A356PRO00.0500.02237.6130.2260.2260.0000.0000.0000.000
183A357SER00.0330.00235.755-0.220-0.2200.0000.0000.0000.000
184A358ASP-1-0.837-0.92437.8158.1818.1810.0000.0000.0000.000
185A359LYS10.9030.95040.713-7.442-7.4420.0000.0000.0000.000
186A360ILE00.0310.03237.507-0.169-0.1690.0000.0000.0000.000
187A361LYS10.9640.97638.019-8.548-8.5480.0000.0000.0000.000
188A362LYS10.9370.97742.067-6.788-6.7880.0000.0000.0000.000
189A363PHE00.0110.00343.678-0.089-0.0890.0000.0000.0000.000
190A364LEU00.002-0.00940.140-0.104-0.1040.0000.0000.0000.000
191A365THR0-0.117-0.06444.707-0.089-0.0890.0000.0000.0000.000
192A366GLU-1-0.946-0.98746.9466.3896.3890.0000.0000.0000.000
193A367SER0-0.0120.02447.363-0.090-0.0900.0000.0000.0000.000
194A368HIS0-0.096-0.05146.2350.0130.0130.0000.0000.0000.000
195A369ASP-1-0.983-0.97549.2465.8385.8380.0000.0000.0000.000