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: YYG52

Calculation Name: 1Q88-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1Q88

Chain ID: A

ChEMBL ID:
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UniProt ID: Q95VR4

Base Structure: X-ray

Registration Date: 2023-06-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2217794.394658
FMO2-HF: Nuclear repulsion 2138936.069934
FMO2-HF: Total energy -78858.324724
FMO2-MP2: Total energy -79086.131089


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:148:MET)


Summations of interaction energy for fragment #1(A:148:MET)
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.
-21.862-7.2739.262-9-14.849-0.062
Interaction energy analysis for fragmet #1(A:148:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.017
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].
3A150ILE00.0280.0273.815-1.6840.720-0.035-1.200-1.1690.001
4A151GLY00.0960.0386.0230.1940.1940.0000.0000.0000.000
5A152ASN0-0.047-0.0058.8590.0520.0520.0000.0000.0000.000
6A153SER0-0.030-0.04010.6870.0040.0040.0000.0000.0000.000
7A154THR0-0.0100.00012.6280.0320.0320.0000.0000.0000.000
8A155PRO00.0970.02912.8140.0000.0000.0000.0000.0000.000
9A156ASN00.0000.00213.3980.0070.0070.0000.0000.0000.000
10A157GLU-1-0.865-0.91612.9590.1390.1390.0000.0000.0000.000
11A158GLN00.007-0.0208.0780.0680.0680.0000.0000.0000.000
12A159GLU-1-0.941-0.9739.8130.3960.3960.0000.0000.0000.000
13A160THR0-0.058-0.04112.3060.0360.0360.0000.0000.0000.000
14A161PHE0-0.012-0.0026.078-0.030-0.0300.0000.0000.0000.000
15A162ARG10.9460.9764.428-0.0190.156-0.001-0.034-0.1390.000
16A163ALA00.0500.0319.6960.0730.0730.0000.0000.0000.000
17A164LYS10.8830.94912.788-0.326-0.3260.0000.0000.0000.000
18A165VAL00.0010.0027.5690.0040.0040.0000.0000.0000.000
19A166ASP-1-0.873-0.94010.8100.7040.7040.0000.0000.0000.000
20A167GLU-1-0.923-0.96112.5700.2310.2310.0000.0000.0000.000
21A168ILE0-0.002-0.01413.237-0.059-0.0590.0000.0000.0000.000
22A169TRP00.0040.00510.5570.0120.0120.0000.0000.0000.000
23A170PHE0-0.0290.00113.472-0.076-0.0760.0000.0000.0000.000
24A171ARG10.8860.94116.740-0.235-0.2350.0000.0000.0000.000
25A172LEU0-0.0300.00013.901-0.036-0.0360.0000.0000.0000.000
26A173THR0-0.017-0.02814.215-0.046-0.0460.0000.0000.0000.000
27A174GLN0-0.024-0.00617.357-0.015-0.0150.0000.0000.0000.000
28A175LYS10.8950.96516.172-0.194-0.1940.0000.0000.0000.000
29A176THR00.0340.00815.5650.0290.0290.0000.0000.0000.000
30A177ASP-1-0.869-0.95111.3790.6930.6930.0000.0000.0000.000
31A178GLY0-0.0310.00313.070-0.057-0.0570.0000.0000.0000.000
32A179THR0-0.014-0.01711.3840.0670.0670.0000.0000.0000.000
33A180VAL0-0.028-0.01713.029-0.016-0.0160.0000.0000.0000.000
34A181MET00.0170.01014.253-0.030-0.0300.0000.0000.0000.000
35A182ARG10.8740.92012.7590.1850.1850.0000.0000.0000.000
36A183ASP-1-0.877-0.94614.774-0.012-0.0120.0000.0000.0000.000
37A184PHE0-0.061-0.02617.0120.0100.0100.0000.0000.0000.000
38A185LEU00.015-0.01010.4990.0160.0160.0000.0000.0000.000
39A186ILE00.0040.00813.1990.0200.0200.0000.0000.0000.000
40A187GLU-1-0.873-0.92915.8960.0510.0510.0000.0000.0000.000
41A188LYS10.9410.96517.482-0.107-0.1070.0000.0000.0000.000
42A189ALA00.0060.00514.4210.0110.0110.0000.0000.0000.000
43A190ALA00.0030.00216.473-0.005-0.0050.0000.0000.0000.000
44A191GLU-1-0.930-0.97119.0720.0720.0720.0000.0000.0000.000
45A192TYR0-0.049-0.00917.749-0.011-0.0110.0000.0000.0000.000
46A193PHE00.012-0.00813.4300.0190.0190.0000.0000.0000.000
47A194LYS10.8120.92519.026-0.061-0.0610.0000.0000.0000.000
48A195GLN00.0500.02621.7270.0160.0160.0000.0000.0000.000
49A196PRO0-0.008-0.01924.795-0.003-0.0030.0000.0000.0000.000
50A197GLU-1-0.894-0.95628.1880.0270.0270.0000.0000.0000.000
51A198GLN00.0030.00821.3350.0040.0040.0000.0000.0000.000
52A199PRO00.0130.00726.4700.0070.0070.0000.0000.0000.000
53A200LYS10.8710.91423.243-0.049-0.0490.0000.0000.0000.000
54A201GLN00.019-0.00223.0110.0070.0070.0000.0000.0000.000
55A202ASN00.0300.03823.2100.0000.0000.0000.0000.0000.000
56A203ALA00.0360.02019.971-0.008-0.0080.0000.0000.0000.000
57A204ILE0-0.011-0.00818.7170.0000.0000.0000.0000.0000.000
58A205GLU-1-0.940-0.97518.262-0.058-0.0580.0000.0000.0000.000
59A206VAL0-0.0090.00416.902-0.022-0.0220.0000.0000.0000.000
60A207ILE00.0310.00913.228-0.023-0.0230.0000.0000.0000.000
61A208SER0-0.035-0.01413.449-0.033-0.0330.0000.0000.0000.000
62A209ALA00.0150.00314.217-0.039-0.0390.0000.0000.0000.000
63A210ILE0-0.0110.01110.442-0.043-0.0430.0000.0000.0000.000
64A211MET0-0.0380.0079.105-0.079-0.0790.0000.0000.0000.000
65A212ALA0-0.024-0.02210.0380.0370.0370.0000.0000.0000.000
66A213PRO0-0.027-0.0228.843-0.133-0.1330.0000.0000.0000.000
67A214GLN00.0140.01111.8650.0730.0730.0000.0000.0000.000
68A215GLU-1-0.930-0.96415.019-0.302-0.3020.0000.0000.0000.000
69A216GLU-1-0.905-0.9479.168-0.471-0.4710.0000.0000.0000.000
70A217GLN00.009-0.02013.8550.0470.0470.0000.0000.0000.000
71A218THR0-0.051-0.00813.1720.0270.0270.0000.0000.0000.000
72A219LYS10.9470.9818.5760.2190.2190.0000.0000.0000.000
73A220SER0-0.012-0.0157.1970.1350.1350.0000.0000.0000.000
74A221LYS10.9020.9537.737-0.797-0.7970.0000.0000.0000.000
75A222ALA00.0080.0073.1990.0660.6150.094-0.122-0.5220.001
76A223ASP-1-0.817-0.9143.180-1.598-0.1060.134-0.767-0.859-0.007
77A224LEU00.0140.0065.109-0.0360.004-0.001-0.001-0.0370.000
78A225TYR00.0000.0053.040-2.508-1.4191.935-0.813-2.2120.000
79A226LYS10.9930.9832.4780.8252.0601.391-0.559-2.0660.000
80A227PHE00.002-0.0094.481-0.922-0.8300.010-0.024-0.0770.000
81A228LEU00.001-0.0097.902-0.174-0.1740.0000.0000.0000.000
82A229ALA0-0.0210.0036.114-0.171-0.1710.0000.0000.0000.000
83A230MET0-0.053-0.0096.722-0.293-0.2930.0000.0000.0000.000
84A231PHE0-0.020-0.0209.639-0.070-0.0700.0000.0000.0000.000
85A232GLY0-0.078-0.03112.9980.0230.0230.0000.0000.0000.000
86A233PRO00.0680.05913.5920.0550.0550.0000.0000.0000.000
87A234TYR00.010-0.01315.441-0.017-0.0170.0000.0000.0000.000
88A235GLU-1-0.881-0.94016.5830.1720.1720.0000.0000.0000.000
89A236THR0-0.0040.00319.108-0.027-0.0270.0000.0000.0000.000
90A237ILE00.0250.02012.938-0.025-0.0250.0000.0000.0000.000
91A238MET00.009-0.00217.223-0.034-0.0340.0000.0000.0000.000
92A239LEU0-0.022-0.00619.504-0.021-0.0210.0000.0000.0000.000
93A240LYS10.8600.94615.498-0.084-0.0840.0000.0000.0000.000
94A241ILE0-0.0180.00414.852-0.029-0.0290.0000.0000.0000.000
95A242ALA0-0.013-0.01317.383-0.025-0.0250.0000.0000.0000.000
96A243SER0-0.0140.00420.428-0.015-0.0150.0000.0000.0000.000
97A244LEU00.0360.01014.667-0.011-0.0110.0000.0000.0000.000
98A245LEU00.010-0.01516.130-0.017-0.0170.0000.0000.0000.000
99A246LEU0-0.0400.01419.571-0.006-0.0060.0000.0000.0000.000
100A247ILE00.0220.00921.554-0.004-0.0040.0000.0000.0000.000
101A248SER00.0060.00619.157-0.011-0.0110.0000.0000.0000.000
102A249ASN0-0.021-0.01921.283-0.015-0.0150.0000.0000.0000.000
103A250ASN0-0.010-0.00123.7210.0040.0040.0000.0000.0000.000
104A251LYS10.8370.91724.1100.0990.0990.0000.0000.0000.000
105A252GLY00.0310.01424.995-0.005-0.0050.0000.0000.0000.000
106A253HIS0-0.042-0.00821.650-0.012-0.0120.0000.0000.0000.000
107A254TRP00.0080.01616.688-0.023-0.0230.0000.0000.0000.000
108A255LEU0-0.028-0.01313.406-0.035-0.0350.0000.0000.0000.000
109A256THR0-0.045-0.00813.0710.0170.0170.0000.0000.0000.000
110A257PHE00.045-0.00710.350-0.037-0.0370.0000.0000.0000.000
111A258ASP-1-0.941-0.9529.949-0.662-0.6620.0000.0000.0000.000
112A259PRO00.0360.0018.082-0.119-0.1190.0000.0000.0000.000
113A260GLN0-0.059-0.0369.7940.0930.0930.0000.0000.0000.000
114A261ALA00.1000.05111.3010.1090.1090.0000.0000.0000.000
115A262GLU-1-0.953-0.97311.330-0.696-0.6960.0000.0000.0000.000
116A263LYS10.8720.93012.2030.7640.7640.0000.0000.0000.000
117A264ASN00.0430.02715.8190.0820.0820.0000.0000.0000.000
118A265ALA00.0130.01916.4240.0480.0480.0000.0000.0000.000
119A266ASN0-0.028-0.03318.1710.0210.0210.0000.0000.0000.000
120A267ASN0-0.030-0.00320.4000.0050.0050.0000.0000.0000.000
121A268GLN0-0.0140.02420.2220.0410.0410.0000.0000.0000.000
122A269ARG10.9680.95323.9850.1300.1300.0000.0000.0000.000
123A270ASP-1-0.950-0.95825.344-0.126-0.1260.0000.0000.0000.000
124A271SER0-0.039-0.02222.8590.0050.0050.0000.0000.0000.000
125A272ILE00.021-0.00821.6330.0010.0010.0000.0000.0000.000
126A273SER0-0.0060.00317.0840.0080.0080.0000.0000.0000.000
127A274GLY00.0110.00115.7130.0110.0110.0000.0000.0000.000
128A275TRP00.0110.0109.7010.1070.1070.0000.0000.0000.000
129A276PHE00.0540.0207.4950.1130.1130.0000.0000.0000.000
130A277ASP-1-0.824-0.8956.395-1.886-1.8860.0000.0000.0000.000
131A278GLN00.007-0.0163.427-0.754-0.3200.015-0.067-0.3810.000
132A279ASN0-0.047-0.0372.672-9.204-5.7061.426-2.085-2.839-0.025
133A280GLU-1-0.879-0.9462.376-3.901-1.5242.881-2.848-2.410-0.032
134A281PRO00.0070.0032.692-0.5160.6881.413-0.480-2.1380.000
135A282ASN0-0.0040.0055.4120.1460.1460.0000.0000.0000.000
136A283CYS0-0.072-0.0278.1050.1580.1580.0000.0000.0000.000
137A284LEU0-0.0090.0119.821-0.162-0.1620.0000.0000.0000.000
138A285ILE0-0.012-0.02010.9410.0980.0980.0000.0000.0000.000
139A286LEU00.005-0.01314.097-0.008-0.0080.0000.0000.0000.000
140A287LYS10.8790.94817.5500.2980.2980.0000.0000.0000.000
141A288THR0-0.009-0.02419.3080.0110.0110.0000.0000.0000.000
142A289PRO00.0350.00822.972-0.003-0.0030.0000.0000.0000.000
143A290THR0-0.042-0.00525.5610.0020.0020.0000.0000.0000.000
144A291GLY00.0640.02623.4610.0080.0080.0000.0000.0000.000
145A292ILE0-0.044-0.01316.542-0.011-0.0110.0000.0000.0000.000
146A293ARG10.9330.98318.6870.1670.1670.0000.0000.0000.000
147A294LYS10.9650.98111.7020.2550.2550.0000.0000.0000.000
148A295ILE0-0.0080.02014.8900.0440.0440.0000.0000.0000.000
149A296TRP0-0.040-0.02510.277-0.034-0.0340.0000.0000.0000.000
150A297ASN00.0320.00211.2890.0340.0340.0000.0000.0000.000
151A298LYS10.8960.95411.864-0.045-0.0450.0000.0000.0000.000
152A299PRO0-0.020-0.0199.4360.0040.0040.0000.0000.0000.000
153A300LEU00.015-0.00112.3690.0290.0290.0000.0000.0000.000
154A301ILE0-0.0310.00215.200-0.008-0.0080.0000.0000.0000.000
155A302GLU-1-0.893-0.95817.7410.1020.1020.0000.0000.0000.000
156A303ALA0-0.013-0.02420.024-0.013-0.0130.0000.0000.0000.000
157A304THR0-0.016-0.00121.487-0.008-0.0080.0000.0000.0000.000
158A305GLY0-0.0080.00722.662-0.004-0.0040.0000.0000.0000.000
159A306GLN0-0.034-0.03622.221-0.001-0.0010.0000.0000.0000.000
160A307TYR0-0.022-0.01316.9430.0110.0110.0000.0000.0000.000
161A308LEU00.0120.01816.482-0.007-0.0070.0000.0000.0000.000
162A309MET0-0.049-0.02415.8880.0240.0240.0000.0000.0000.000
163A310ASP-1-0.773-0.88816.702-0.070-0.0700.0000.0000.0000.000
164A311GLU-1-0.891-0.96917.214-0.068-0.0680.0000.0000.0000.000
165A312ASN0-0.089-0.03418.1210.0250.0250.0000.0000.0000.000
166A313GLY0-0.0120.00119.9370.0110.0110.0000.0000.0000.000
167A314GLU-1-0.977-0.98120.912-0.001-0.0010.0000.0000.0000.000
168A315LYS10.9110.94520.669-0.029-0.0290.0000.0000.0000.000
169A316TYR0-0.019-0.01820.831-0.005-0.0050.0000.0000.0000.000
170A317ASP-1-0.794-0.92121.9560.0030.0030.0000.0000.0000.000
171A318SER00.000-0.00721.5140.0060.0060.0000.0000.0000.000
172A319TRP00.0150.00014.582-0.014-0.0140.0000.0000.0000.000
173A320ASP-1-0.876-0.95021.110-0.054-0.0540.0000.0000.0000.000
174A321LYN00.0660.06524.752-0.004-0.0040.0000.0000.0000.000
175A322TYR0-0.007-0.00220.458-0.012-0.0120.0000.0000.0000.000
176A323PHE0-0.046-0.03819.145-0.009-0.0090.0000.0000.0000.000
177A324GLU-1-0.957-0.96424.683-0.037-0.0370.0000.0000.0000.000
178A325MET0-0.045-0.01426.3230.0050.0050.0000.0000.0000.000
179A326LYS10.8430.91224.0500.0590.0590.0000.0000.0000.000
180A327PRO00.0120.00925.077-0.014-0.0140.0000.0000.0000.000
181A328ILE00.0290.03822.236-0.003-0.0030.0000.0000.0000.000
182A329GLU-1-0.930-0.97125.242-0.103-0.1030.0000.0000.0000.000
183A330THR0-0.067-0.06429.1140.0060.0060.0000.0000.0000.000
184A331TYR00.0310.01732.470-0.001-0.0010.0000.0000.0000.000
185A332LEU0-0.045-0.04631.0280.0030.0030.0000.0000.0000.000
186A333THR0-0.0360.00133.813-0.002-0.0020.0000.0000.0000.000
187A334ALA0-0.0010.02436.3580.0010.0010.0000.0000.0000.000
188A335TYR00.028-0.00939.014-0.002-0.0020.0000.0000.0000.000
189A336PRO0-0.031-0.01440.9850.0020.0020.0000.0000.0000.000
190A337THR00.0280.02543.1110.0010.0010.0000.0000.0000.000
191A338PHE0-0.050-0.02645.3520.0000.0000.0000.0000.0000.000
192A339ALA00.0220.01947.9980.0020.0020.0000.0000.0000.000