FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 17J4Z

Calculation Name: 5INT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5INT

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0F7

Base Structure: X-ray

Registration Date: 2023-06-21

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2191654.985703
FMO2-HF: Nuclear repulsion 2114568.944377
FMO2-HF: Total energy -77086.041326
FMO2-MP2: Total energy -77309.156663


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:182:SER)


Summations of interaction energy for fragment #1(A:182: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.
-9.819-4.3684.358-4.507-5.304-0.027
Interaction energy analysis for fragmet #1(A:182:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / 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].
3A184ALA00.0150.0203.031-2.1041.2080.003-1.759-1.556-0.001
4A185LEU00.001-0.0014.9890.1520.269-0.001-0.007-0.1090.000
5A186GLN00.0230.0106.145-0.882-0.8820.0000.0000.0000.000
6A187GLY0-0.034-0.0038.1200.4960.4960.0000.0000.0000.000
7A188LYS10.8250.90610.4680.7100.7100.0000.0000.0000.000
8A189ARG10.7880.88112.1220.4290.4290.0000.0000.0000.000
9A190ILE0-0.005-0.00910.8640.0840.0840.0000.0000.0000.000
10A191LEU0-0.0020.01114.894-0.023-0.0230.0000.0000.0000.000
11A192ILE0-0.016-0.00914.0060.0220.0220.0000.0000.0000.000
12A193THR00.0370.01418.5380.0290.0290.0000.0000.0000.000
13A194ALA0-0.0340.00520.420-0.001-0.0010.0000.0000.0000.000
14A195GLY00.0240.00922.5600.0140.0140.0000.0000.0000.000
15A196PRO0-0.061-0.00925.5710.0010.0010.0000.0000.0000.000
16A197THR00.0350.00529.2990.0000.0000.0000.0000.0000.000
17A198ARG10.8150.88931.6940.1720.1720.0000.0000.0000.000
18A199GLU-1-0.786-0.89134.729-0.159-0.1590.0000.0000.0000.000
19A200LYS10.8830.91436.7510.1480.1480.0000.0000.0000.000
20A201ILE0-0.0020.00640.8540.0010.0010.0000.0000.0000.000
21A202ASP-1-0.799-0.87844.475-0.084-0.0840.0000.0000.0000.000
22A203PRO0-0.011-0.01144.291-0.005-0.0050.0000.0000.0000.000
23A204VAL0-0.047-0.02044.030-0.002-0.0020.0000.0000.0000.000
24A205ARG10.8520.91743.1220.0830.0830.0000.0000.0000.000
25A206PHE00.0240.00137.250-0.002-0.0020.0000.0000.0000.000
26A207MET00.0250.03637.8280.0060.0060.0000.0000.0000.000
27A208THR0-0.056-0.06733.175-0.007-0.0070.0000.0000.0000.000
28A209ASN0-0.048-0.01032.8970.0120.0120.0000.0000.0000.000
29A210PHE00.0480.00929.222-0.016-0.0160.0000.0000.0000.000
30A211SER00.0510.00426.207-0.004-0.0040.0000.0000.0000.000
31A212SER0-0.028-0.01025.095-0.008-0.0080.0000.0000.0000.000
32A213GLY00.0540.03322.7080.0000.0000.0000.0000.0000.000
33A214LYS10.9380.95720.3450.2250.2250.0000.0000.0000.000
34A215MET00.0140.02717.867-0.048-0.0480.0000.0000.0000.000
35A216GLY00.0780.04216.694-0.058-0.0580.0000.0000.0000.000
36A217TYR0-0.011-0.03216.200-0.080-0.0800.0000.0000.0000.000
37A218ALA0-0.008-0.00214.200-0.079-0.0790.0000.0000.0000.000
38A219ILE00.006-0.00112.331-0.134-0.1340.0000.0000.0000.000
39A220ALA00.0330.01111.453-0.190-0.1900.0000.0000.0000.000
40A221GLU-1-0.808-0.88610.229-1.059-1.0590.0000.0000.0000.000
41A222VAL0-0.028-0.0127.274-0.300-0.3000.0000.0000.0000.000
42A223ALA00.0490.0246.616-0.672-0.6720.0000.0000.0000.000
43A224VAL00.0200.0176.986-0.636-0.6360.0000.0000.0000.000
44A225ASN0-0.120-0.0714.535-0.546-0.442-0.001-0.035-0.0690.000
45A226LEU0-0.045-0.0242.043-6.208-4.3404.358-2.765-3.461-0.026
46A227GLY00.0670.0333.7200.5320.582-0.0010.059-0.1090.000
47A228ALA0-0.0140.0085.8181.1511.1510.0000.0000.0000.000
48A229GLU-1-0.938-0.9649.108-0.773-0.7730.0000.0000.0000.000
49A230VAL0-0.028-0.01710.7960.1450.1450.0000.0000.0000.000
50A231ILE00.0160.00613.6320.0820.0820.0000.0000.0000.000
51A232LEU0-0.028-0.01916.996-0.009-0.0090.0000.0000.0000.000
52A233VAL00.0250.02418.9260.0400.0400.0000.0000.0000.000
53A234SER00.0030.00622.060-0.014-0.0140.0000.0000.0000.000
54A235GLY00.0590.04423.9070.0200.0200.0000.0000.0000.000
55A236PRO0-0.038-0.03926.458-0.010-0.0100.0000.0000.0000.000
56A237THR0-0.038-0.01124.5880.0000.0000.0000.0000.0000.000
57A238ALA0-0.008-0.00526.7400.0020.0020.0000.0000.0000.000
58A239LEU0-0.054-0.02621.0960.0060.0060.0000.0000.0000.000
59A240ASN00.0260.01620.7310.0010.0010.0000.0000.0000.000
60A241PRO00.005-0.00317.942-0.015-0.0150.0000.0000.0000.000
61A242PRO0-0.0110.00612.7060.0380.0380.0000.0000.0000.000
62A243LEU00.0240.00312.5450.0170.0170.0000.0000.0000.000
63A244HIS00.010-0.0099.793-0.108-0.1080.0000.0000.0000.000
64A245VAL0-0.0120.02012.922-0.042-0.0420.0000.0000.0000.000
65A246THR00.0350.01914.7460.1310.1310.0000.0000.0000.000
66A247THR0-0.041-0.02617.9130.0060.0060.0000.0000.0000.000
67A248VAL0-0.014-0.00820.2000.0350.0350.0000.0000.0000.000
68A249GLN00.0070.00023.1750.0100.0100.0000.0000.0000.000
69A250VAL0-0.0170.00226.0090.0150.0150.0000.0000.0000.000
70A251GLU-1-0.842-0.91229.056-0.157-0.1570.0000.0000.0000.000
71A252SER0-0.031-0.02931.898-0.001-0.0010.0000.0000.0000.000
72A253ALA00.021-0.02331.328-0.013-0.0130.0000.0000.0000.000
73A254GLN00.0040.01831.717-0.003-0.0030.0000.0000.0000.000
74A255ASP-1-0.760-0.86031.272-0.186-0.1860.0000.0000.0000.000
75A256MET0-0.026-0.00926.173-0.016-0.0160.0000.0000.0000.000
76A257LEU0-0.004-0.01027.627-0.018-0.0180.0000.0000.0000.000
77A258GLU-1-0.943-0.96329.020-0.191-0.1910.0000.0000.0000.000
78A259ALA00.0270.01325.904-0.010-0.0100.0000.0000.0000.000
79A260VAL0-0.027-0.01123.613-0.030-0.0300.0000.0000.0000.000
80A261ILE00.012-0.00325.248-0.014-0.0140.0000.0000.0000.000
81A262GLN0-0.075-0.02725.5720.0180.0180.0000.0000.0000.000
82A263HIS0-0.017-0.02821.816-0.007-0.0070.0000.0000.0000.000
83A264TYR00.004-0.01222.837-0.033-0.0330.0000.0000.0000.000
84A265GLN00.0340.01623.140-0.021-0.0210.0000.0000.0000.000
85A266ASN0-0.0100.00421.8660.0170.0170.0000.0000.0000.000
86A267VAL0-0.0300.00218.083-0.045-0.0450.0000.0000.0000.000
87A268ASP-1-0.754-0.85315.755-0.518-0.5180.0000.0000.0000.000
88A269VAL0-0.0050.00614.0670.0360.0360.0000.0000.0000.000
89A270VAL0-0.017-0.00217.254-0.025-0.0250.0000.0000.0000.000
90A271ILE00.0100.00514.4520.0300.0300.0000.0000.0000.000
91A272LYS10.9170.97219.1180.2300.2300.0000.0000.0000.000
92A273THR0-0.080-0.05818.3340.0150.0150.0000.0000.0000.000
93A274ALA0-0.012-0.01921.6460.0110.0110.0000.0000.0000.000
94A275ALA0-0.0030.00125.4470.0060.0060.0000.0000.0000.000
95A276VAL00.0080.00927.4300.0130.0130.0000.0000.0000.000
96A277ALA00.0050.00930.258-0.011-0.0110.0000.0000.0000.000
97A278ASP-1-0.831-0.89731.039-0.192-0.1920.0000.0000.0000.000
98A279TYR0-0.001-0.00834.0380.0080.0080.0000.0000.0000.000
99A280ARG10.8690.92437.6880.1270.1270.0000.0000.0000.000
100A281PRO00.012-0.00239.9140.0050.0050.0000.0000.0000.000
101A282LYS10.8690.93143.4190.0870.0870.0000.0000.0000.000
102A283TYR0-0.068-0.02945.9290.0020.0020.0000.0000.0000.000
103A284VAL00.0380.01143.523-0.003-0.0030.0000.0000.0000.000
104A285HIS0-0.013-0.00146.1270.0040.0040.0000.0000.0000.000
105A297VAL0-0.006-0.01451.3990.0000.0000.0000.0000.0000.000
106A298ILE00.0180.01545.294-0.002-0.0020.0000.0000.0000.000
107A299GLU-1-0.879-0.94047.100-0.081-0.0810.0000.0000.0000.000
108A300LEU00.0170.02141.947-0.003-0.0030.0000.0000.0000.000
109A301GLU-1-0.853-0.91641.863-0.107-0.1070.0000.0000.0000.000
110A302ARG10.8140.89335.5470.1350.1350.0000.0000.0000.000
111A303THR00.0380.02635.1070.0000.0000.0000.0000.0000.000
112A304VAL00.0400.02033.6080.0020.0020.0000.0000.0000.000
113A305ASP-1-0.828-0.89931.260-0.185-0.1850.0000.0000.0000.000
114A306ILE00.0490.02227.0770.0000.0000.0000.0000.0000.000
115A307LEU00.0390.01924.218-0.006-0.0060.0000.0000.0000.000
116A308LYS10.7790.86827.9450.1460.1460.0000.0000.0000.000
117A309THR0-0.007-0.01230.8040.0060.0060.0000.0000.0000.000
118A310LEU0-0.001-0.00124.5070.0020.0020.0000.0000.0000.000
119A311GLY00.0280.02927.487-0.006-0.0060.0000.0000.0000.000
120A312GLU-1-0.837-0.90028.534-0.137-0.1370.0000.0000.0000.000
121A313MET0-0.075-0.03428.9070.0060.0060.0000.0000.0000.000
122A314LYS10.7870.90723.4550.2360.2360.0000.0000.0000.000
123A315ASP-1-0.864-0.93225.630-0.203-0.2030.0000.0000.0000.000
124A316LYS10.8220.89821.2250.3180.3180.0000.0000.0000.000
125A317GLN0-0.024-0.00320.450-0.005-0.0050.0000.0000.0000.000
126A318LEU00.0180.01015.6770.0250.0250.0000.0000.0000.000
127A319LEU0-0.051-0.02019.648-0.028-0.0280.0000.0000.0000.000
128A320ILE00.0240.01416.9230.0240.0240.0000.0000.0000.000
129A321GLY00.0230.01020.393-0.008-0.0080.0000.0000.0000.000
130A322PHE00.0250.01418.7890.0000.0000.0000.0000.0000.000
131A323ALA0-0.002-0.01124.1480.0180.0180.0000.0000.0000.000
132A324ALA00.003-0.01126.369-0.010-0.0100.0000.0000.0000.000
133A325GLU-1-0.836-0.88328.889-0.141-0.1410.0000.0000.0000.000
134A326THR0-0.007-0.01232.2730.0020.0020.0000.0000.0000.000
135A327THR0-0.019-0.02634.8860.0090.0090.0000.0000.0000.000
136A328ASN0-0.055-0.02335.083-0.006-0.0060.0000.0000.0000.000
137A329VAL00.0510.02929.209-0.004-0.0040.0000.0000.0000.000
138A330GLU-1-0.802-0.86130.040-0.108-0.1080.0000.0000.0000.000
139A331GLU-1-0.816-0.90131.081-0.097-0.0970.0000.0000.0000.000
140A332TYR0-0.043-0.03529.706-0.008-0.0080.0000.0000.0000.000
141A333ALA00.0020.00127.070-0.007-0.0070.0000.0000.0000.000
142A334THR00.002-0.01528.499-0.009-0.0090.0000.0000.0000.000
143A335LYS10.7980.88330.1220.1200.1200.0000.0000.0000.000
144A336LYS10.8010.89028.2490.1880.1880.0000.0000.0000.000
145A337LEU0-0.018-0.00824.559-0.008-0.0080.0000.0000.0000.000
146A338ARG10.8530.92627.5940.1240.1240.0000.0000.0000.000
147A339GLU-1-0.839-0.91930.557-0.128-0.1280.0000.0000.0000.000
148A340LYS10.8080.90128.0590.1590.1590.0000.0000.0000.000
149A341ASN0-0.016-0.00227.918-0.012-0.0120.0000.0000.0000.000
150A342ALA00.0190.02723.920-0.014-0.0140.0000.0000.0000.000
151A343ASN00.0400.00120.2640.0160.0160.0000.0000.0000.000
152A344MET00.0150.01116.4150.0190.0190.0000.0000.0000.000
153A345ILE0-0.050-0.01321.479-0.016-0.0160.0000.0000.0000.000
154A346VAL00.0110.00818.9010.0110.0110.0000.0000.0000.000
155A347ALA00.0150.00822.0020.0020.0020.0000.0000.0000.000
156A348ASN0-0.038-0.01922.784-0.024-0.0240.0000.0000.0000.000
157A349ASP-1-0.815-0.89025.363-0.164-0.1640.0000.0000.0000.000
158A361THR0-0.011-0.00721.671-0.008-0.0080.0000.0000.0000.000
159A362ASN0-0.094-0.05621.391-0.022-0.0220.0000.0000.0000.000
160A363ILE00.0340.03122.272-0.002-0.0020.0000.0000.0000.000
161A364VAL0-0.040-0.02419.541-0.008-0.0080.0000.0000.0000.000
162A365THR00.0410.02022.3490.0090.0090.0000.0000.0000.000
163A366MET0-0.055-0.01916.115-0.032-0.0320.0000.0000.0000.000
164A367TYR0-0.002-0.03121.4810.0160.0160.0000.0000.0000.000
165A368ARG10.8160.86718.5720.1090.1090.0000.0000.0000.000
166A369LYS10.9130.96022.5870.1840.1840.0000.0000.0000.000
167A370ASP-1-0.814-0.88822.051-0.121-0.1210.0000.0000.0000.000
168A371GLY0-0.020-0.01425.0810.0140.0140.0000.0000.0000.000
169A372GLU-1-0.883-0.91121.354-0.068-0.0680.0000.0000.0000.000
170A373VAL0-0.010-0.01823.667-0.019-0.0190.0000.0000.0000.000
171A374ILE0-0.019-0.00618.1330.0110.0110.0000.0000.0000.000
172A375GLU-1-0.937-0.95621.170-0.116-0.1160.0000.0000.0000.000
173A376LEU0-0.026-0.01817.170-0.003-0.0030.0000.0000.0000.000
174A377PRO00.0260.01019.9940.0050.0050.0000.0000.0000.000
175A378LEU0-0.026-0.01921.750-0.020-0.0200.0000.0000.0000.000
176A379LEU00.0170.02716.7040.0060.0060.0000.0000.0000.000
177A380THR0-0.057-0.08316.574-0.022-0.0220.0000.0000.0000.000
178A381LYS10.8550.88317.2330.2320.2320.0000.0000.0000.000
179A382LYS10.8440.90210.6250.7390.7390.0000.0000.0000.000
180A383GLU-1-0.802-0.86512.318-0.376-0.3760.0000.0000.0000.000
181A384VAL00.0360.01613.412-0.029-0.0290.0000.0000.0000.000
182A385ALA0-0.003-0.01112.541-0.014-0.0140.0000.0000.0000.000
183A386ARG10.8580.9247.3450.5460.5460.0000.0000.0000.000
184A387GLU-1-0.813-0.90110.173-0.411-0.4110.0000.0000.0000.000
185A388ILE00.003-0.01112.6320.0500.0500.0000.0000.0000.000
186A389LEU0-0.039-0.0258.7060.0270.0270.0000.0000.0000.000
187A390LYS10.8950.9659.429-0.015-0.0150.0000.0000.0000.000
188A391GLN00.0430.00710.5310.1150.1150.0000.0000.0000.000
189A392ILE0-0.018-0.00812.0820.0330.0330.0000.0000.0000.000
190A393GLU-1-0.883-0.9447.1180.0970.0970.0000.0000.0000.000
191A394MET0-0.043-0.01410.5050.0770.0770.0000.0000.0000.000
192A395MET00.0600.02913.5230.0060.0060.0000.0000.0000.000
193A396LEU0-0.060-0.03711.580-0.007-0.0070.0000.0000.0000.000
194A397GLU-1-0.877-0.91412.118-0.221-0.2210.0000.0000.0000.000
195A398ASP-1-0.939-0.95215.316-0.077-0.0770.0000.0000.0000.000
196A399ASP-1-1.079-1.03918.360-0.197-0.1970.0000.0000.0000.000