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: VRG31

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2219529.440854
FMO2-HF: Nuclear repulsion 2140669.789454
FMO2-HF: Total energy -78859.6514
FMO2-MP2: Total energy -79087.416881


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.
-19.705-6.6499.096-8.357-13.79-0.057
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 : -0.064 / q_NPA : -0.025
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].
3A150ILE00.0190.0313.784-1.2750.976-0.033-1.095-1.1240.001
4A151GLY00.0940.0406.0410.1800.1800.0000.0000.0000.000
5A152ASN0-0.051-0.0208.8520.0390.0390.0000.0000.0000.000
6A153SER0-0.031-0.03110.5770.0090.0090.0000.0000.0000.000
7A154THR0-0.021-0.02412.6250.0250.0250.0000.0000.0000.000
8A155PRO00.0820.02012.806-0.006-0.0060.0000.0000.0000.000
9A156ASN00.0070.00513.290-0.002-0.0020.0000.0000.0000.000
10A157GLU-1-0.763-0.82912.8760.1060.1060.0000.0000.0000.000
11A158GLN0-0.017-0.0238.3270.0780.0780.0000.0000.0000.000
12A159GLU-1-0.870-0.9319.6750.2050.2050.0000.0000.0000.000
13A160THR0-0.056-0.04712.1580.0340.0340.0000.0000.0000.000
14A161PHE00.0010.0006.043-0.029-0.0290.0000.0000.0000.000
15A162ARG10.8760.9335.3770.3310.3310.0000.0000.0000.000
16A163ALA00.0360.0249.5230.0810.0810.0000.0000.0000.000
17A164LYS10.8430.90512.629-0.280-0.2800.0000.0000.0000.000
18A165VAL0-0.014-0.0027.6390.0270.0270.0000.0000.0000.000
19A166ASP-1-0.862-0.93210.9310.5800.5800.0000.0000.0000.000
20A167GLU-1-0.876-0.91112.6910.2200.2200.0000.0000.0000.000
21A168ILE00.006-0.01213.440-0.048-0.0480.0000.0000.0000.000
22A169TRP00.0060.00311.1620.0200.0200.0000.0000.0000.000
23A170PHE0-0.040-0.00413.575-0.070-0.0700.0000.0000.0000.000
24A171ARG10.8910.94016.846-0.224-0.2240.0000.0000.0000.000
25A172LEU0-0.0190.00514.773-0.029-0.0290.0000.0000.0000.000
26A173THR0-0.017-0.02714.489-0.044-0.0440.0000.0000.0000.000
27A174GLN0-0.029-0.01017.718-0.015-0.0150.0000.0000.0000.000
28A175LYS10.8740.94716.359-0.181-0.1810.0000.0000.0000.000
29A176THR00.0340.00615.6710.0300.0300.0000.0000.0000.000
30A177ASP-1-0.854-0.93811.1100.5920.5920.0000.0000.0000.000
31A178GLY0-0.0180.00713.117-0.041-0.0410.0000.0000.0000.000
32A179THR0-0.006-0.01311.2400.0690.0690.0000.0000.0000.000
33A180VAL0-0.036-0.01013.209-0.020-0.0200.0000.0000.0000.000
34A181MET00.0500.02214.444-0.024-0.0240.0000.0000.0000.000
35A182ARG10.8590.91312.9740.1250.1250.0000.0000.0000.000
36A183ASP-1-0.880-0.94715.0600.0160.0160.0000.0000.0000.000
37A184PHE0-0.060-0.02617.4930.0090.0090.0000.0000.0000.000
38A185LEU00.018-0.00311.1470.0150.0150.0000.0000.0000.000
39A186ILE00.0080.01213.6500.0230.0230.0000.0000.0000.000
40A187GLU-1-0.811-0.88316.3740.0700.0700.0000.0000.0000.000
41A188LYS10.8180.89617.939-0.111-0.1110.0000.0000.0000.000
42A189ALA00.0140.00514.9800.0080.0080.0000.0000.0000.000
43A190ALA00.0030.00217.032-0.006-0.0060.0000.0000.0000.000
44A191GLU-1-0.873-0.92719.6400.0820.0820.0000.0000.0000.000
45A192TYR0-0.062-0.01318.006-0.012-0.0120.0000.0000.0000.000
46A193PHE00.010-0.00913.7730.0180.0180.0000.0000.0000.000
47A194LYS10.8140.92719.551-0.077-0.0770.0000.0000.0000.000
48A195GLN00.0260.01922.3360.0120.0120.0000.0000.0000.000
49A196PRO0-0.010-0.01225.364-0.003-0.0030.0000.0000.0000.000
50A197GLU-1-0.861-0.94428.7620.0420.0420.0000.0000.0000.000
51A198GLN0-0.002-0.00322.0310.0040.0040.0000.0000.0000.000
52A199PRO00.0150.00427.0620.0060.0060.0000.0000.0000.000
53A200LYS10.8460.88523.756-0.060-0.0600.0000.0000.0000.000
54A201GLN0-0.021-0.03223.5530.0090.0090.0000.0000.0000.000
55A202ASN00.0220.03223.7190.0020.0020.0000.0000.0000.000
56A203ALA00.0280.01920.613-0.005-0.0050.0000.0000.0000.000
57A204ILE0-0.008-0.01019.2630.0060.0060.0000.0000.0000.000
58A205GLU-1-0.889-0.94318.750-0.017-0.0170.0000.0000.0000.000
59A206VAL0-0.0080.00217.572-0.018-0.0180.0000.0000.0000.000
60A207ILE00.0130.00613.821-0.013-0.0130.0000.0000.0000.000
61A208SER0-0.0110.00113.940-0.016-0.0160.0000.0000.0000.000
62A209ALA00.0140.01114.605-0.034-0.0340.0000.0000.0000.000
63A210ILE0-0.0120.00810.956-0.037-0.0370.0000.0000.0000.000
64A211MET0-0.0370.0079.757-0.034-0.0340.0000.0000.0000.000
65A212ALA0-0.029-0.01710.3780.0160.0160.0000.0000.0000.000
66A213PRO0-0.021-0.0129.046-0.109-0.1090.0000.0000.0000.000
67A214GLN0-0.013-0.02211.9850.0700.0700.0000.0000.0000.000
68A215GLU-1-0.913-0.95015.175-0.260-0.2600.0000.0000.0000.000
69A216GLU-1-0.891-0.9349.541-0.459-0.4590.0000.0000.0000.000
70A217GLN00.012-0.01013.9110.0480.0480.0000.0000.0000.000
71A218THR0-0.0140.00912.5690.0330.0330.0000.0000.0000.000
72A219LYS10.8510.9087.9580.1810.1810.0000.0000.0000.000
73A220SER00.0060.0017.0180.1120.1120.0000.0000.0000.000
74A221LYS10.8850.9358.055-0.605-0.6050.0000.0000.0000.000
75A222ALA00.0170.0103.2270.0490.5600.074-0.115-0.4690.001
76A223ASP-1-0.793-0.9053.670-0.3200.7600.070-0.488-0.662-0.004
77A224LEU00.0350.0165.5670.0260.0260.0000.0000.0000.000
78A225TYR00.0060.0022.674-2.790-1.5841.905-0.857-2.2530.001
79A226LYS10.9550.9653.022-0.2401.0620.361-0.349-1.3130.000
80A227PHE00.000-0.0074.841-1.046-0.9820.010-0.024-0.0490.000
81A228LEU0-0.008-0.0138.313-0.220-0.2200.0000.0000.0000.000
82A229ALA0-0.0230.0036.125-0.216-0.2160.0000.0000.0000.000
83A230MET0-0.043-0.0027.561-0.331-0.3310.0000.0000.0000.000
84A231PHE0-0.018-0.02010.068-0.095-0.0950.0000.0000.0000.000
85A232GLY0-0.077-0.02113.4050.0140.0140.0000.0000.0000.000
86A233PRO00.0660.05413.5710.0570.0570.0000.0000.0000.000
87A234TYR00.006-0.01515.464-0.015-0.0150.0000.0000.0000.000
88A235GLU-1-0.879-0.94316.6670.1850.1850.0000.0000.0000.000
89A236THR00.0170.00819.183-0.023-0.0230.0000.0000.0000.000
90A237ILE00.0100.02013.307-0.022-0.0220.0000.0000.0000.000
91A238MET00.0160.01417.555-0.027-0.0270.0000.0000.0000.000
92A239LEU0-0.012-0.00519.974-0.020-0.0200.0000.0000.0000.000
93A240LYS10.8710.93815.676-0.116-0.1160.0000.0000.0000.000
94A241ILE0-0.022-0.00115.090-0.026-0.0260.0000.0000.0000.000
95A242ALA0-0.016-0.01217.817-0.024-0.0240.0000.0000.0000.000
96A243SER0-0.034-0.01520.938-0.013-0.0130.0000.0000.0000.000
97A244LEU00.0320.01015.231-0.012-0.0120.0000.0000.0000.000
98A245LEU00.004-0.01516.288-0.018-0.0180.0000.0000.0000.000
99A246LEU0-0.0360.01619.922-0.008-0.0080.0000.0000.0000.000
100A247ILE00.0180.00321.948-0.006-0.0060.0000.0000.0000.000
101A248SER00.0180.01319.423-0.012-0.0120.0000.0000.0000.000
102A249ASN0-0.030-0.02621.555-0.015-0.0150.0000.0000.0000.000
103A250ASN0-0.0120.00124.0030.0020.0020.0000.0000.0000.000
104A251LYS10.8410.91224.4370.0700.0700.0000.0000.0000.000
105A252GLY00.0210.01025.164-0.005-0.0050.0000.0000.0000.000
106A253HIS0-0.050-0.00921.844-0.010-0.0100.0000.0000.0000.000
107A254TRP00.0070.01616.772-0.018-0.0180.0000.0000.0000.000
108A255LEU0-0.032-0.00913.500-0.031-0.0310.0000.0000.0000.000
109A256THR0-0.040-0.01913.2480.0290.0290.0000.0000.0000.000
110A257PHE00.029-0.01210.545-0.029-0.0290.0000.0000.0000.000
111A258ASP-1-0.920-0.93010.095-0.543-0.5430.0000.0000.0000.000
112A259PRO00.0470.0058.105-0.078-0.0780.0000.0000.0000.000
113A260GLN0-0.072-0.0449.7050.0530.0530.0000.0000.0000.000
114A261ALA00.1080.05711.2400.1010.1010.0000.0000.0000.000
115A262GLU-1-0.926-0.94911.146-0.645-0.6450.0000.0000.0000.000
116A263LYS10.9000.94312.3910.6840.6840.0000.0000.0000.000
117A264ASN00.0330.01915.6770.0620.0620.0000.0000.0000.000
118A265ALA00.0120.02016.3440.0440.0440.0000.0000.0000.000
119A266ASN0-0.023-0.02318.0680.0130.0130.0000.0000.0000.000
120A267ASN0-0.055-0.02020.2330.0180.0180.0000.0000.0000.000
121A268GLN0-0.0090.02919.9040.0370.0370.0000.0000.0000.000
122A269ARG10.9760.95823.8800.1080.1080.0000.0000.0000.000
123A270ASP-1-0.931-0.95025.284-0.102-0.1020.0000.0000.0000.000
124A271SER0-0.030-0.02722.7240.0050.0050.0000.0000.0000.000
125A272ILE00.011-0.01321.6770.0010.0010.0000.0000.0000.000
126A273SER0-0.0110.00717.5090.0100.0100.0000.0000.0000.000
127A274GLY00.0310.01315.7980.0100.0100.0000.0000.0000.000
128A275TRP0-0.018-0.0189.7950.0890.0890.0000.0000.0000.000
129A276PHE00.0520.0197.7600.0890.0890.0000.0000.0000.000
130A277ASP-1-0.795-0.8976.752-1.450-1.4500.0000.0000.0000.000
131A278GLN00.003-0.0173.299-0.735-0.2670.017-0.076-0.4090.000
132A279ASN0-0.040-0.0212.489-8.068-5.2681.985-1.963-2.823-0.025
133A280GLU-1-0.836-0.9172.382-3.602-1.3592.935-2.802-2.375-0.031
134A281PRO00.0280.0042.458-0.5870.4971.773-0.584-2.2720.000
135A282ASN00.0070.0125.3030.0380.085-0.001-0.004-0.0410.000
136A283CYS0-0.062-0.0197.9390.1220.1220.0000.0000.0000.000
137A284LEU0-0.0090.0099.711-0.140-0.1400.0000.0000.0000.000
138A285ILE0-0.006-0.01810.7510.0750.0750.0000.0000.0000.000
139A286LEU00.004-0.00814.033-0.008-0.0080.0000.0000.0000.000
140A287LYS10.8390.93517.6310.2330.2330.0000.0000.0000.000
141A288THR0-0.007-0.03319.3090.0090.0090.0000.0000.0000.000
142A289PRO00.0400.01222.995-0.003-0.0030.0000.0000.0000.000
143A290THR0-0.045-0.00625.4220.0030.0030.0000.0000.0000.000
144A291GLY00.0480.01623.4600.0070.0070.0000.0000.0000.000
145A292ILE0-0.051-0.01516.557-0.009-0.0090.0000.0000.0000.000
146A293ARG10.9140.96518.5940.1220.1220.0000.0000.0000.000
147A294LYS10.8500.9259.5610.3380.3380.0000.0000.0000.000
148A295ILE0-0.0300.01114.7480.0360.0360.0000.0000.0000.000
149A296TRP0-0.037-0.02510.341-0.027-0.0270.0000.0000.0000.000
150A297ASN00.0410.00711.2290.0210.0210.0000.0000.0000.000
151A298LYS10.8300.90911.913-0.052-0.0520.0000.0000.0000.000
152A299PRO0-0.021-0.0159.3630.0020.0020.0000.0000.0000.000
153A300LEU0-0.011-0.01212.3520.0260.0260.0000.0000.0000.000
154A301ILE0-0.0300.00115.150-0.007-0.0070.0000.0000.0000.000
155A302GLU-1-0.874-0.94417.7360.1060.1060.0000.0000.0000.000
156A303ALA0-0.028-0.03220.007-0.012-0.0120.0000.0000.0000.000
157A304THR0-0.033-0.00621.503-0.009-0.0090.0000.0000.0000.000
158A305GLY00.0030.01122.677-0.006-0.0060.0000.0000.0000.000
159A306GLN0-0.031-0.03022.2560.0000.0000.0000.0000.0000.000
160A307TYR0-0.005-0.00817.0350.0040.0040.0000.0000.0000.000
161A308LEU00.0070.02016.539-0.002-0.0020.0000.0000.0000.000
162A309MET0-0.045-0.02016.0250.0150.0150.0000.0000.0000.000
163A310ASP-1-0.751-0.85016.802-0.047-0.0470.0000.0000.0000.000
164A311GLU-1-0.852-0.93117.194-0.043-0.0430.0000.0000.0000.000
165A312ASN0-0.139-0.07518.1120.0200.0200.0000.0000.0000.000
166A313GLY0-0.0070.00519.8990.0080.0080.0000.0000.0000.000
167A314GLU-1-0.925-0.96620.9050.0100.0100.0000.0000.0000.000
168A315LYS10.8530.92720.578-0.027-0.0270.0000.0000.0000.000
169A316TYR0-0.041-0.05220.973-0.005-0.0050.0000.0000.0000.000
170A317ASP-1-0.832-0.93722.0210.0160.0160.0000.0000.0000.000
171A318SER0-0.041-0.05221.6010.0070.0070.0000.0000.0000.000
172A319TRP00.041-0.00114.505-0.017-0.0170.0000.0000.0000.000
173A320ASP-1-0.815-0.88921.421-0.024-0.0240.0000.0000.0000.000
174A321LYN00.0910.07125.099-0.005-0.0050.0000.0000.0000.000
175A322TYR00.0060.00520.127-0.010-0.0100.0000.0000.0000.000
176A323PHE0-0.051-0.04219.164-0.008-0.0080.0000.0000.0000.000
177A324GLU-1-0.954-0.96224.849-0.021-0.0210.0000.0000.0000.000
178A325MET0-0.050-0.01526.1690.0030.0030.0000.0000.0000.000
179A326LYS10.8600.91924.0640.0370.0370.0000.0000.0000.000
180A327PRO00.0340.02825.071-0.011-0.0110.0000.0000.0000.000
181A328ILE00.0100.02721.958-0.003-0.0030.0000.0000.0000.000
182A329GLU-1-0.926-0.96425.410-0.083-0.0830.0000.0000.0000.000
183A330THR0-0.045-0.04829.2130.0060.0060.0000.0000.0000.000
184A331TYR00.005-0.01232.540-0.002-0.0020.0000.0000.0000.000
185A332LEU0-0.007-0.01731.3750.0020.0020.0000.0000.0000.000
186A333THR0-0.062-0.01034.077-0.002-0.0020.0000.0000.0000.000
187A334ALA0-0.0040.01936.6130.0020.0020.0000.0000.0000.000
188A335TYR00.037-0.00239.312-0.001-0.0010.0000.0000.0000.000
189A336PRO0-0.024-0.01341.2890.0010.0010.0000.0000.0000.000
190A337THR00.0210.02543.6300.0010.0010.0000.0000.0000.000
191A338PHE0-0.023-0.00945.6870.0000.0000.0000.0000.0000.000
192A339ALA0-0.007-0.00148.2280.0020.0020.0000.0000.0000.000