Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 49LJN

Calculation Name: 3K66-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K66

Chain ID: A

ChEMBL ID:

UniProt ID: Q10651

Base Structure: X-ray

Registration Date: 2023-06-22

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2443279.704893
FMO2-HF: Nuclear repulsion 2351824.307896
FMO2-HF: Total energy -91455.396997
FMO2-MP2: Total energy -91721.798193


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:234:SER)


Summations of interaction energy for fragment #1(A:234:SER)
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.
0.7422.959-0.006-1.172-1.0380.004
Interaction energy analysis for fragmet #1(A:234:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.022
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].
3A236ASP-1-0.756-0.8333.9102.0864.236-0.005-1.168-0.9760.004
4A237PRO00.011-0.0025.789-0.188-0.1880.0000.0000.0000.000
5A238TYR00.014-0.0207.780-0.253-0.2530.0000.0000.0000.000
6A239PHE00.006-0.0098.120-0.082-0.0820.0000.0000.0000.000
7A240LYS10.8240.9034.617-1.608-1.541-0.001-0.004-0.0620.000
8A241ILE0-0.0270.01410.1440.0160.0160.0000.0000.0000.000
9A242ALA00.0240.01713.124-0.057-0.0570.0000.0000.0000.000
10A243ASN00.0150.01616.084-0.032-0.0320.0000.0000.0000.000
11A244TRP00.042-0.00515.625-0.032-0.0320.0000.0000.0000.000
12A245THR00.0450.02419.650-0.024-0.0240.0000.0000.0000.000
13A246ASN0-0.001-0.00220.071-0.024-0.0240.0000.0000.0000.000
14A247GLU-1-0.665-0.79317.4080.1200.1200.0000.0000.0000.000
15A248HIS0-0.023-0.01319.317-0.008-0.0080.0000.0000.0000.000
16A249ASP-1-0.810-0.89919.9160.1500.1500.0000.0000.0000.000
17A250ASP-1-0.899-0.96115.4480.2840.2840.0000.0000.0000.000
18A251PHE0-0.013-0.00215.2990.0260.0260.0000.0000.0000.000
19A252LYS10.9140.96316.653-0.111-0.1110.0000.0000.0000.000
20A253LYS10.8580.91314.594-0.267-0.2670.0000.0000.0000.000
21A254ALA0-0.013-0.00112.4320.0160.0160.0000.0000.0000.000
22A255GLU-1-0.834-0.89513.528-0.120-0.1200.0000.0000.0000.000
23A256MET0-0.009-0.01116.368-0.033-0.0330.0000.0000.0000.000
24A257ARG10.8040.8728.955-0.454-0.4540.0000.0000.0000.000
25A258MET0-0.031-0.00512.623-0.094-0.0940.0000.0000.0000.000
26A259ASP-1-0.814-0.90213.591-0.205-0.2050.0000.0000.0000.000
27A260GLU-1-0.860-0.91515.472-0.126-0.1260.0000.0000.0000.000
28A261LYS10.9440.9777.3931.3051.3050.0000.0000.0000.000
29A262HIS00.0030.00113.521-0.077-0.0770.0000.0000.0000.000
30A263ARG10.9120.93915.9600.1130.1130.0000.0000.0000.000
31A264LYS10.8480.91314.5590.2110.2110.0000.0000.0000.000
32A265LYS10.7880.87811.6610.7370.7370.0000.0000.0000.000
33A266VAL00.0120.00417.0450.0200.0200.0000.0000.0000.000
34A267ASP-1-0.877-0.93820.449-0.149-0.1490.0000.0000.0000.000
35A268LYS10.8520.91618.4160.2910.2910.0000.0000.0000.000
36A269VAL0-0.007-0.01119.9310.0130.0130.0000.0000.0000.000
37A270MET00.0080.00222.4790.0190.0190.0000.0000.0000.000
38A271LYS10.8550.91323.9680.1260.1260.0000.0000.0000.000
39A272GLU-1-0.802-0.87121.772-0.222-0.2220.0000.0000.0000.000
40A273TRP0-0.009-0.00425.9290.0110.0110.0000.0000.0000.000
41A274GLY00.0610.03628.6040.0100.0100.0000.0000.0000.000
42A275ASP-1-0.820-0.87228.391-0.101-0.1010.0000.0000.0000.000
43A276LEU0-0.045-0.02727.7330.0070.0070.0000.0000.0000.000
44A277GLU-1-0.768-0.87831.691-0.078-0.0780.0000.0000.0000.000
45A278THR0-0.017-0.01833.7770.0090.0090.0000.0000.0000.000
46A279ARG10.7810.86834.0580.0800.0800.0000.0000.0000.000
47A280TYR0-0.063-0.06835.8350.0040.0040.0000.0000.0000.000
48A281ASN0-0.058-0.05037.7170.0080.0080.0000.0000.0000.000
49A282GLU-1-0.786-0.85338.956-0.059-0.0590.0000.0000.0000.000
50A283GLN00.0230.01139.5560.0040.0040.0000.0000.0000.000
51A284LYS10.8870.94841.5850.0650.0650.0000.0000.0000.000
52A285ALA00.0170.00343.7310.0010.0010.0000.0000.0000.000
53A286LYS10.8160.91741.5920.0590.0590.0000.0000.0000.000
54A287ASP-1-0.822-0.92142.581-0.060-0.0600.0000.0000.0000.000
55A288PRO00.0470.03343.333-0.004-0.0040.0000.0000.0000.000
56A289LYS10.9250.96443.8220.0500.0500.0000.0000.0000.000
57A290GLY00.0030.00141.093-0.003-0.0030.0000.0000.0000.000
58A291ALA0-0.016-0.00439.375-0.006-0.0060.0000.0000.0000.000
59A292GLU-1-0.763-0.87038.770-0.076-0.0760.0000.0000.0000.000
60A293LYS10.9210.97938.5850.0690.0690.0000.0000.0000.000
61A294PHE00.0030.00132.658-0.007-0.0070.0000.0000.0000.000
62A295LYS10.8990.94234.2870.0760.0760.0000.0000.0000.000
63A296SER0-0.025-0.01634.520-0.006-0.0060.0000.0000.0000.000
64A297GLN0-0.046-0.03332.520-0.002-0.0020.0000.0000.0000.000
65A298MET0-0.008-0.00229.363-0.016-0.0160.0000.0000.0000.000
66A299ASN00.0040.00829.659-0.013-0.0130.0000.0000.0000.000
67A300ALA00.0400.02729.956-0.009-0.0090.0000.0000.0000.000
68A301ARG10.8120.88423.0610.1830.1830.0000.0000.0000.000
69A302PHE00.0200.01625.557-0.020-0.0200.0000.0000.0000.000
70A303GLN00.0450.00925.727-0.011-0.0110.0000.0000.0000.000
71A304LYS10.9640.98524.6320.1610.1610.0000.0000.0000.000
72A305THR0-0.035-0.02520.563-0.024-0.0240.0000.0000.0000.000
73A306VAL0-0.004-0.00121.241-0.027-0.0270.0000.0000.0000.000
74A307SER00.0500.01822.352-0.010-0.0100.0000.0000.0000.000
75A308SER0-0.0060.01518.522-0.024-0.0240.0000.0000.0000.000
76A309LEU00.008-0.00816.783-0.043-0.0430.0000.0000.0000.000
77A310GLU-1-0.885-0.92618.493-0.211-0.2110.0000.0000.0000.000
78A311GLU-1-0.958-0.98319.407-0.262-0.2620.0000.0000.0000.000
79A312GLU-1-0.822-0.88612.495-0.761-0.7610.0000.0000.0000.000
80A313HIS00.006-0.00215.488-0.009-0.0090.0000.0000.0000.000
81A314LYS10.8560.91617.1580.2440.2440.0000.0000.0000.000
82A315ARG10.8110.87611.8490.6940.6940.0000.0000.0000.000
83A316MET0-0.082-0.05110.034-0.004-0.0040.0000.0000.0000.000
84A317ARG10.7910.87814.5690.1700.1700.0000.0000.0000.000
85A318LYS10.8570.90717.7170.1790.1790.0000.0000.0000.000
86A319GLU-1-0.826-0.86511.824-0.681-0.6810.0000.0000.0000.000
87A320ILE0-0.029-0.02013.0800.0480.0480.0000.0000.0000.000
88A321GLU-1-0.857-0.93415.656-0.073-0.0730.0000.0000.0000.000
89A322ALA0-0.028-0.00818.4670.0280.0280.0000.0000.0000.000
90A323VAL00.0100.00414.0440.0220.0220.0000.0000.0000.000
91A324HIS10.8530.92817.2530.0090.0090.0000.0000.0000.000
92A325GLU-1-0.866-0.94819.028-0.004-0.0040.0000.0000.0000.000
93A326GLU-1-0.927-0.95418.7140.0340.0340.0000.0000.0000.000
94A327ARG10.8810.94312.916-0.164-0.1640.0000.0000.0000.000
95A328VAL0-0.058-0.02220.8770.0090.0090.0000.0000.0000.000
96A329GLN00.0250.00823.772-0.006-0.0060.0000.0000.0000.000
97A330ALA00.0100.02922.9290.0010.0010.0000.0000.0000.000
98A331MET00.0310.01622.8450.0010.0010.0000.0000.0000.000
99A332LEU0-0.081-0.03625.712-0.001-0.0010.0000.0000.0000.000
100A333ASN0-0.033-0.04828.505-0.003-0.0030.0000.0000.0000.000
101A334GLU-1-0.909-0.94126.5450.0800.0800.0000.0000.0000.000
102A335LYS10.8720.93329.457-0.042-0.0420.0000.0000.0000.000
103A336LYS10.7650.87031.554-0.014-0.0140.0000.0000.0000.000
104A337ARG10.8810.94730.991-0.055-0.0550.0000.0000.0000.000
105A338ASP-1-0.802-0.88631.9710.0540.0540.0000.0000.0000.000
106A339ALA00.0230.01534.671-0.001-0.0010.0000.0000.0000.000
107A340THR0-0.051-0.04837.064-0.004-0.0040.0000.0000.0000.000
108A341HIS0-0.046-0.01437.422-0.003-0.0030.0000.0000.0000.000
109A342ASP-1-0.848-0.93637.9680.0440.0440.0000.0000.0000.000
110A343TYR0-0.056-0.05540.532-0.002-0.0020.0000.0000.0000.000
111A344ARG10.9160.92542.538-0.021-0.0210.0000.0000.0000.000
112A345GLN00.0310.04140.434-0.001-0.0010.0000.0000.0000.000
113A346ALA0-0.014-0.00244.460-0.001-0.0010.0000.0000.0000.000
114A347LEU00.012-0.00446.322-0.001-0.0010.0000.0000.0000.000
115A348ALA00.0230.01247.490-0.001-0.0010.0000.0000.0000.000
116A349THR0-0.070-0.04647.3650.0000.0000.0000.0000.0000.000
117A350HIS0-0.066-0.06350.0170.0010.0010.0000.0000.0000.000
118A351VAL0-0.0270.00052.438-0.001-0.0010.0000.0000.0000.000
119A352ASN0-0.074-0.01752.499-0.001-0.0010.0000.0000.0000.000
120A353LYS10.9840.98651.045-0.028-0.0280.0000.0000.0000.000
121A354PRO00.0230.00353.9200.0010.0010.0000.0000.0000.000
122A355ASN00.0350.03847.3340.0010.0010.0000.0000.0000.000
123A356LYS10.8960.93550.213-0.021-0.0210.0000.0000.0000.000
124A357HIS00.0310.01946.152-0.001-0.0010.0000.0000.0000.000
125A358SER00.0250.02544.8680.0000.0000.0000.0000.0000.000
126A359VAL00.0620.03845.1980.0010.0010.0000.0000.0000.000
127A360LEU00.0290.01445.9200.0000.0000.0000.0000.0000.000
128A361GLN0-0.010-0.01842.035-0.001-0.0010.0000.0000.0000.000
129A362SER00.0190.00741.1970.0020.0020.0000.0000.0000.000
130A363LEU00.0120.01541.1070.0000.0000.0000.0000.0000.000
131A364LYS10.8910.96042.244-0.026-0.0260.0000.0000.0000.000
132A365ALA0-0.022-0.00537.7920.0000.0000.0000.0000.0000.000
133A366TYR00.020-0.01637.3000.0010.0010.0000.0000.0000.000
134A367ILE00.0210.01537.848-0.001-0.0010.0000.0000.0000.000
135A368ARG10.8800.93036.484-0.034-0.0340.0000.0000.0000.000
136A369ALA0-0.062-0.01433.6040.0030.0030.0000.0000.0000.000
137A370GLU-1-0.673-0.79933.9270.0080.0080.0000.0000.0000.000
138A371GLU-1-0.699-0.80635.9090.0010.0010.0000.0000.0000.000
139A372LYS10.9270.96428.265-0.039-0.0390.0000.0000.0000.000
140A373ASP-1-0.789-0.88931.1320.0000.0000.0000.0000.0000.000
141A374ARG10.8210.92132.527-0.003-0.0030.0000.0000.0000.000
142A375MET0-0.0020.01030.483-0.003-0.0030.0000.0000.0000.000
143A376HIS00.0180.00726.6290.0040.0040.0000.0000.0000.000
144A377THR0-0.026-0.01430.445-0.009-0.0090.0000.0000.0000.000
145A378LEU00.0300.00932.147-0.007-0.0070.0000.0000.0000.000
146A379ASN00.0210.00330.704-0.007-0.0070.0000.0000.0000.000
147A380ARG10.8890.95224.1240.0520.0520.0000.0000.0000.000
148A381TYR00.0260.00729.686-0.007-0.0070.0000.0000.0000.000
149A382ARG10.8490.91232.7510.0290.0290.0000.0000.0000.000
150A383HIS00.0370.01927.494-0.006-0.0060.0000.0000.0000.000
151A384LEU00.0090.00727.261-0.007-0.0070.0000.0000.0000.000
152A385LEU0-0.032-0.03130.378-0.005-0.0050.0000.0000.0000.000
153A386LYS10.7840.88132.0370.0500.0500.0000.0000.0000.000
154A387ALA0-0.0120.01727.052-0.004-0.0040.0000.0000.0000.000
155A388ASP-1-0.804-0.90026.919-0.136-0.1360.0000.0000.0000.000
156A389SER00.0280.00530.2770.0050.0050.0000.0000.0000.000
157A390LYS10.8710.93729.6650.1150.1150.0000.0000.0000.000
158A391GLU-1-0.809-0.91026.754-0.124-0.1240.0000.0000.0000.000
159A392ALA0-0.0050.00431.1290.0060.0060.0000.0000.0000.000
160A393ALA0-0.007-0.00633.3300.0060.0060.0000.0000.0000.000
161A394ALA0-0.011-0.00732.2680.0040.0040.0000.0000.0000.000
162A395TYR0-0.024-0.00230.8530.0020.0020.0000.0000.0000.000
163A396LYS10.9730.98533.3380.0410.0410.0000.0000.0000.000
164A397PRO00.0290.01236.4110.0050.0050.0000.0000.0000.000
165A398THR00.0230.00332.1850.0040.0040.0000.0000.0000.000
166A399VAL0-0.0100.00534.1490.0050.0050.0000.0000.0000.000
167A400ILE00.0090.00236.0170.0050.0050.0000.0000.0000.000
168A401HIS0-0.025-0.00737.2200.0030.0030.0000.0000.0000.000
169A402ARG10.9020.92428.5090.0230.0230.0000.0000.0000.000
170A403LEU00.0040.00336.7160.0040.0040.0000.0000.0000.000
171A404ARG10.9690.99039.3000.0200.0200.0000.0000.0000.000
172A405TYR00.013-0.00738.7710.0020.0020.0000.0000.0000.000
173A406ILE0-0.043-0.00735.1630.0030.0030.0000.0000.0000.000
174A407ASP-1-0.734-0.83839.3490.0010.0010.0000.0000.0000.000
175A408LEU0-0.028-0.00542.9700.0020.0020.0000.0000.0000.000
176A409ARG10.8270.89636.410-0.003-0.0030.0000.0000.0000.000
177A410ILE00.0120.02740.0070.0020.0020.0000.0000.0000.000
178A411ASN0-0.027-0.03443.2670.0020.0020.0000.0000.0000.000
179A412GLY00.0060.00545.7680.0000.0000.0000.0000.0000.000
180A413THR0-0.028-0.03042.6600.0020.0020.0000.0000.0000.000
181A414LEU0-0.024-0.01745.2900.0010.0010.0000.0000.0000.000
182A415ALA0-0.029-0.01248.1750.0000.0000.0000.0000.0000.000
183A416MET00.0030.02444.2800.0010.0010.0000.0000.0000.000
184A417LEU0-0.013-0.00448.6440.0010.0010.0000.0000.0000.000
185A418ARG10.9370.97852.038-0.006-0.0060.0000.0000.0000.000
186A419ASP-1-0.900-0.93253.6780.0110.0110.0000.0000.0000.000
187A420PHE0-0.031-0.01151.5380.0010.0010.0000.0000.0000.000
188A421PRO00.0570.03356.1710.0000.0000.0000.0000.0000.000
189A422ASP-1-0.870-0.93057.5500.0150.0150.0000.0000.0000.000
190A423LEU0-0.011-0.01451.5200.0000.0000.0000.0000.0000.000
191A424GLU-1-0.820-0.92054.0230.0090.0090.0000.0000.0000.000
192A425LYS10.9120.95755.294-0.011-0.0110.0000.0000.0000.000
193A426TYR0-0.007-0.00556.263-0.001-0.0010.0000.0000.0000.000
194A427VAL0-0.004-0.00549.7970.0000.0000.0000.0000.0000.000
195A428ARG10.9120.95651.080-0.007-0.0070.0000.0000.0000.000
196A429PRO00.0280.02351.3790.0000.0000.0000.0000.0000.000
197A430ILE00.0170.01949.5450.0000.0000.0000.0000.0000.000
198A431ALA0-0.006-0.00947.0820.0000.0000.0000.0000.0000.000
199A432VAL0-0.012-0.00947.0170.0000.0000.0000.0000.0000.000
200A433THR0-0.007-0.00648.488-0.001-0.0010.0000.0000.0000.000
201A434TYR00.0260.01440.6970.0010.0010.0000.0000.0000.000
202A435TRP0-0.083-0.04841.8410.0000.0000.0000.0000.0000.000
203A436LYS10.8040.88544.170-0.006-0.0060.0000.0000.0000.000
204A437ASP-1-0.832-0.91146.0390.0080.0080.0000.0000.0000.000
205A438TYR00.004-0.01136.4700.0010.0010.0000.0000.0000.000
206A439ARG10.7100.78440.662-0.001-0.0010.0000.0000.0000.000
207A440ASP-1-0.829-0.90641.4710.0010.0010.0000.0000.0000.000
208A441GLU-1-0.961-0.98440.1950.0180.0180.0000.0000.0000.000
209A442VAL0-0.053-0.02535.2380.0000.0000.0000.0000.0000.000
210A443SER0-0.089-0.05936.540-0.002-0.0020.0000.0000.0000.000
211A444PRO00.0540.04038.591-0.001-0.0010.0000.0000.0000.000
212A445ASP-1-0.863-0.93142.084-0.012-0.0120.0000.0000.0000.000
213A446ILE0-0.126-0.05339.957-0.002-0.0020.0000.0000.0000.000
214A447SER00.0400.01143.318-0.001-0.0010.0000.0000.0000.000
215A448VAL0-0.042-0.00941.110-0.001-0.0010.0000.0000.0000.000
216A449GLU-1-0.759-0.85838.444-0.043-0.0430.0000.0000.0000.000
217A450ASP-1-0.961-0.96841.693-0.030-0.0300.0000.0000.0000.000