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: ZVYGN

Calculation Name: 1Q5Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Q5Q

Chain ID: A

ChEMBL ID:

UniProt ID: Q53080

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2569552.813782
FMO2-HF: Nuclear repulsion 2485376.546222
FMO2-HF: Total energy -84176.267559
FMO2-MP2: Total energy -84423.600871


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:9:ALA)


Summations of interaction energy for fragment #1(A:9:ALA)
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.
-7.164-2.8951.215-2.232-3.2530.011
Interaction energy analysis for fragmet #1(A:9:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.009
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].
3A11GLN0-0.018-0.0292.774-2.736-0.0220.245-1.337-1.6230.007
4A12ILE00.0150.0232.607-3.502-1.9470.970-0.895-1.6300.004
5A13MET00.0500.0174.905-0.469-0.4690.0000.0000.0000.000
6A14ARG10.9590.9976.704-0.550-0.5500.0000.0000.0000.000
7A15ASP-1-0.838-0.9348.1321.4631.4630.0000.0000.0000.000
8A16ARG10.7590.8598.034-0.458-0.4580.0000.0000.0000.000
9A17SER00.0530.02210.701-0.128-0.1280.0000.0000.0000.000
10A18GLU-1-0.844-0.89212.6430.2400.2400.0000.0000.0000.000
11A19LEU0-0.025-0.00613.860-0.054-0.0540.0000.0000.0000.000
12A20ALA00.0180.00415.248-0.042-0.0420.0000.0000.0000.000
13A21ARG10.8910.92516.837-0.233-0.2330.0000.0000.0000.000
14A22LYS10.8660.92616.089-0.385-0.3850.0000.0000.0000.000
15A23GLY0-0.002-0.00319.821-0.017-0.0170.0000.0000.0000.000
16A24ILE0-0.025-0.01220.373-0.016-0.0160.0000.0000.0000.000
17A25ALA0-0.0230.00022.869-0.012-0.0120.0000.0000.0000.000
18A26ARG10.9060.97821.227-0.179-0.1790.0000.0000.0000.000
19A27GLY0-0.036-0.00726.260-0.005-0.0050.0000.0000.0000.000
20A28ARG10.8650.92228.276-0.057-0.0570.0000.0000.0000.000
21A29SER0-0.013-0.02129.9020.0030.0030.0000.0000.0000.000
22A30VAL0-0.071-0.04631.481-0.002-0.0020.0000.0000.0000.000
23A31VAL00.0070.00332.5350.0000.0000.0000.0000.0000.000
24A32VAL0-0.023-0.00833.293-0.001-0.0010.0000.0000.0000.000
25A33LEU0-0.0030.00435.600-0.001-0.0010.0000.0000.0000.000
26A34THR00.0250.01838.2290.0000.0000.0000.0000.0000.000
27A35PHE0-0.051-0.03140.5790.0010.0010.0000.0000.0000.000
28A36ARG10.8360.91844.319-0.005-0.0050.0000.0000.0000.000
29A37ASP-1-0.891-0.93747.2410.0040.0040.0000.0000.0000.000
30A38GLY0-0.006-0.01944.011-0.001-0.0010.0000.0000.0000.000
31A39VAL0-0.055-0.01737.6130.0000.0000.0000.0000.0000.000
32A40LEU00.0130.01540.2760.0000.0000.0000.0000.0000.000
33A41PHE0-0.031-0.02234.7430.0000.0000.0000.0000.0000.000
34A42VAL00.0830.03737.4810.0000.0000.0000.0000.0000.000
35A43ALA00.0120.00335.0000.0020.0020.0000.0000.0000.000
36A44GLU-1-0.738-0.85334.4690.0530.0530.0000.0000.0000.000
37A45ASN0-0.101-0.09534.9420.0070.0070.0000.0000.0000.000
38A46PRO00.0370.03136.410-0.002-0.0020.0000.0000.0000.000
39A47SER0-0.0170.00337.878-0.003-0.0030.0000.0000.0000.000
40A48THR00.0540.01739.756-0.001-0.0010.0000.0000.0000.000
41A49ALA0-0.041-0.01540.427-0.002-0.0020.0000.0000.0000.000
42A50LEU0-0.054-0.02534.542-0.001-0.0010.0000.0000.0000.000
43A51HIS00.0070.01636.2420.0010.0010.0000.0000.0000.000
44A52LYS10.8820.93631.339-0.045-0.0450.0000.0000.0000.000
45A53VAL0-0.019-0.00232.994-0.002-0.0020.0000.0000.0000.000
46A54SER0-0.036-0.01935.0640.0010.0010.0000.0000.0000.000
47A55GLU-1-0.838-0.87636.5570.0020.0020.0000.0000.0000.000
48A56LEU0-0.043-0.01532.3850.0010.0010.0000.0000.0000.000
49A57TYR00.0570.00036.471-0.002-0.0020.0000.0000.0000.000
50A58ASP-1-0.797-0.86239.242-0.005-0.0050.0000.0000.0000.000
51A59ARG10.7690.86140.9270.0060.0060.0000.0000.0000.000
52A60LEU00.0120.02735.041-0.001-0.0010.0000.0000.0000.000
53A61GLY00.0420.01336.4220.0020.0020.0000.0000.0000.000
54A62PHE00.000-0.00728.580-0.002-0.0020.0000.0000.0000.000
55A63ALA00.0590.02431.6500.0020.0020.0000.0000.0000.000
56A64ALA0-0.0200.00427.404-0.003-0.0030.0000.0000.0000.000
57A65VAL00.0130.00725.7850.0020.0020.0000.0000.0000.000
58A66GLY00.0600.02224.4880.0010.0010.0000.0000.0000.000
59A67LYS10.8730.93122.320-0.112-0.1120.0000.0000.0000.000
60A68TYR00.0460.01625.284-0.005-0.0050.0000.0000.0000.000
61A69ASN00.0240.00724.4840.0020.0020.0000.0000.0000.000
62A70GLU-1-0.800-0.88321.0960.1060.1060.0000.0000.0000.000
63A71PHE00.0860.03724.812-0.010-0.0100.0000.0000.0000.000
64A72GLU-1-0.757-0.82226.6110.0180.0180.0000.0000.0000.000
65A73ASN0-0.045-0.02525.102-0.007-0.0070.0000.0000.0000.000
66A74LEU00.0600.02522.455-0.006-0.0060.0000.0000.0000.000
67A75ARG10.8300.90426.927-0.026-0.0260.0000.0000.0000.000
68A76ARG10.8450.89930.511-0.025-0.0250.0000.0000.0000.000
69A77ALA00.0210.01827.852-0.003-0.0030.0000.0000.0000.000
70A78GLY00.0410.02429.810-0.005-0.0050.0000.0000.0000.000
71A79ILE0-0.001-0.00431.002-0.002-0.0020.0000.0000.0000.000
72A80VAL0-0.027-0.00832.386-0.002-0.0020.0000.0000.0000.000
73A81HIS00.001-0.00130.204-0.002-0.0020.0000.0000.0000.000
74A82ALA0-0.007-0.01332.795-0.002-0.0020.0000.0000.0000.000
75A83ASP-1-0.865-0.96235.543-0.007-0.0070.0000.0000.0000.000
76A84MET0-0.0230.01132.806-0.002-0.0020.0000.0000.0000.000
77A85ARG10.9020.94833.1390.0290.0290.0000.0000.0000.000
78A86GLY00.010-0.00437.244-0.001-0.0010.0000.0000.0000.000
79A87TYR0-0.076-0.02940.4400.0010.0010.0000.0000.0000.000
80A88SER0-0.045-0.02838.744-0.001-0.0010.0000.0000.0000.000
81A89TYR0-0.078-0.02836.723-0.002-0.0020.0000.0000.0000.000
82A90ASP-1-0.749-0.84242.189-0.013-0.0130.0000.0000.0000.000
83A91ARG10.8610.90342.1380.0070.0070.0000.0000.0000.000
84A92ARG10.7920.87241.7930.0140.0140.0000.0000.0000.000
85A93ASP-1-0.851-0.92839.541-0.023-0.0230.0000.0000.0000.000
86A94VAL0-0.097-0.03436.296-0.003-0.0030.0000.0000.0000.000
87A95THR0-0.015-0.01235.0920.0000.0000.0000.0000.0000.000
88A96GLY00.042-0.00434.033-0.001-0.0010.0000.0000.0000.000
89A97ARG10.9690.99230.3720.0400.0400.0000.0000.0000.000
90A98SER0-0.0300.00829.797-0.004-0.0040.0000.0000.0000.000
91A99LEU00.0310.00629.383-0.003-0.0030.0000.0000.0000.000
92A100ALA00.0070.01727.7270.0000.0000.0000.0000.0000.000
93A101ASN0-0.002-0.02725.269-0.008-0.0080.0000.0000.0000.000
94A102ALA00.0220.02524.308-0.007-0.0070.0000.0000.0000.000
95A103TYR0-0.026-0.02723.901-0.002-0.0020.0000.0000.0000.000
96A104ALA00.0190.01321.3850.0020.0020.0000.0000.0000.000
97A105GLN00.0130.01219.048-0.004-0.0040.0000.0000.0000.000
98A106THR0-0.027-0.03319.145-0.009-0.0090.0000.0000.0000.000
99A107LEU0-0.025-0.02118.7520.0030.0030.0000.0000.0000.000
100A108GLY00.0730.04715.6940.0070.0070.0000.0000.0000.000
101A109THR0-0.044-0.02014.271-0.029-0.0290.0000.0000.0000.000
102A110ILE0-0.047-0.02114.4490.0010.0010.0000.0000.0000.000
103A111PHE0-0.029-0.0209.9930.0560.0560.0000.0000.0000.000
104A112THR0-0.036-0.0059.2480.0050.0050.0000.0000.0000.000
105A113GLU-1-0.933-0.9649.851-0.161-0.1610.0000.0000.0000.000
106A114GLN0-0.0210.01112.4320.0330.0330.0000.0000.0000.000
107A115PRO00.0220.01212.5350.0340.0340.0000.0000.0000.000
108A116LYS10.7220.82913.036-0.083-0.0830.0000.0000.0000.000
109A117PRO00.0180.03412.563-0.041-0.0410.0000.0000.0000.000
110A118TYR00.027-0.00314.9600.0130.0130.0000.0000.0000.000
111A119GLU-1-0.863-0.91418.5360.1720.1720.0000.0000.0000.000
112A120VAL0-0.065-0.04420.072-0.007-0.0070.0000.0000.0000.000
113A121GLU-1-0.828-0.90921.3640.0410.0410.0000.0000.0000.000
114A122ILE0-0.035-0.02523.8800.0020.0020.0000.0000.0000.000
115A123CYS0-0.0170.00126.475-0.005-0.0050.0000.0000.0000.000
116A124VAL0-0.032-0.01229.1780.0010.0010.0000.0000.0000.000
117A125ALA00.0110.01231.656-0.002-0.0020.0000.0000.0000.000
118A126GLU-1-0.833-0.93035.145-0.018-0.0180.0000.0000.0000.000
119A127VAL00.0230.02537.6700.0000.0000.0000.0000.0000.000
120A128GLY00.0390.03041.330-0.001-0.0010.0000.0000.0000.000
121A129ARG10.9080.93542.7170.0170.0170.0000.0000.0000.000
122A130VAL00.0190.01146.4180.0000.0000.0000.0000.0000.000
123A131GLY00.0100.01849.7300.0000.0000.0000.0000.0000.000
124A132SER0-0.046-0.03246.2860.0000.0000.0000.0000.0000.000
125A133PRO00.0830.05147.9790.0010.0010.0000.0000.0000.000
126A134LYS10.8460.92238.5090.0160.0160.0000.0000.0000.000
127A135ALA00.0510.02641.6440.0010.0010.0000.0000.0000.000
128A136PRO00.0100.00539.671-0.002-0.0020.0000.0000.0000.000
129A137GLN0-0.040-0.01733.4680.0020.0020.0000.0000.0000.000
130A138LEU0-0.0070.00733.1630.0020.0020.0000.0000.0000.000
131A139TYR00.0370.01328.600-0.004-0.0040.0000.0000.0000.000
132A140ARG10.8940.94124.080-0.006-0.0060.0000.0000.0000.000
133A141ILE0-0.034-0.01521.840-0.008-0.0080.0000.0000.0000.000
134A142THR00.000-0.02018.9500.0110.0110.0000.0000.0000.000
135A143TYR00.003-0.02414.535-0.009-0.0090.0000.0000.0000.000
136A144ASP-1-0.803-0.87414.176-0.035-0.0350.0000.0000.0000.000
137A145GLY0-0.0120.00115.441-0.037-0.0370.0000.0000.0000.000
138A146SER0-0.063-0.03217.401-0.018-0.0180.0000.0000.0000.000
139A147ILE0-0.035-0.03819.6870.0140.0140.0000.0000.0000.000
140A148VAL0-0.0280.00123.382-0.007-0.0070.0000.0000.0000.000
141A149ASP-1-0.932-0.97126.223-0.026-0.0260.0000.0000.0000.000
142A150GLU-1-0.822-0.91029.209-0.002-0.0020.0000.0000.0000.000
143A151GLN0-0.016-0.01732.445-0.001-0.0010.0000.0000.0000.000
144A152HIS0-0.087-0.04035.6230.0000.0000.0000.0000.0000.000
145A153PHE00.0440.00433.7390.0010.0010.0000.0000.0000.000
146A154VAL0-0.0110.00629.665-0.001-0.0010.0000.0000.0000.000
147A155VAL00.004-0.00130.5340.0020.0020.0000.0000.0000.000
148A156MET0-0.027-0.00126.898-0.001-0.0010.0000.0000.0000.000
149A157GLY00.0240.01026.674-0.001-0.0010.0000.0000.0000.000
150A158GLY00.0510.05027.175-0.005-0.0050.0000.0000.0000.000
151A159THR0-0.040-0.04226.8950.0040.0040.0000.0000.0000.000
152A160THR00.0640.02826.561-0.004-0.0040.0000.0000.0000.000
153A161GLU-1-0.933-0.95226.6620.0590.0590.0000.0000.0000.000
154A162PRO0-0.0010.00330.056-0.006-0.0060.0000.0000.0000.000
155A163ILE00.0570.03432.280-0.004-0.0040.0000.0000.0000.000
156A164ALA0-0.028-0.02431.058-0.005-0.0050.0000.0000.0000.000
157A165THR0-0.039-0.03633.069-0.005-0.0050.0000.0000.0000.000
158A166ALA00.0810.05935.250-0.003-0.0030.0000.0000.0000.000
159A167MET00.0070.02835.926-0.003-0.0030.0000.0000.0000.000
160A168ARG10.8370.90131.500-0.021-0.0210.0000.0000.0000.000
161A169GLU-1-0.963-0.96237.4170.0160.0160.0000.0000.0000.000
162A170SER0-0.070-0.04340.766-0.001-0.0010.0000.0000.0000.000
163A171TYR0-0.032-0.03239.845-0.001-0.0010.0000.0000.0000.000
164A172ARG10.9510.96941.930-0.012-0.0120.0000.0000.0000.000
165A173ALA00.0160.00644.4230.0000.0000.0000.0000.0000.000
166A174ASP-1-0.854-0.91845.2800.0020.0020.0000.0000.0000.000
167A175LEU00.0030.01644.0110.0010.0010.0000.0000.0000.000
168A176ASP-1-0.814-0.92847.6380.0070.0070.0000.0000.0000.000
169A177LEU00.0280.01346.4890.0010.0010.0000.0000.0000.000
170A178GLU-1-0.902-0.95647.3890.0140.0140.0000.0000.0000.000
171A179ALA0-0.028-0.01348.4660.0010.0010.0000.0000.0000.000
172A180ALA0-0.026-0.01343.8790.0010.0010.0000.0000.0000.000
173A181VAL00.0230.00143.3500.0020.0020.0000.0000.0000.000
174A182GLY00.0500.03443.8180.0020.0020.0000.0000.0000.000
175A183ILE0-0.072-0.04241.1020.0020.0020.0000.0000.0000.000
176A184ALA00.015-0.00139.4590.0020.0020.0000.0000.0000.000
177A185VAL00.001-0.00239.7610.0030.0030.0000.0000.0000.000
178A186ASN0-0.022-0.02141.4670.0030.0030.0000.0000.0000.000
179A187ALA0-0.0020.00237.5660.0020.0020.0000.0000.0000.000
180A188LEU0-0.017-0.02135.3580.0030.0030.0000.0000.0000.000
181A189ARG10.7990.89437.395-0.026-0.0260.0000.0000.0000.000
182A190GLN0-0.073-0.01337.2650.0010.0010.0000.0000.0000.000
183A191GLY00.0190.00734.3890.0020.0020.0000.0000.0000.000
184A192GLY0-0.057-0.02132.7560.0010.0010.0000.0000.0000.000
185A201VAL0-0.009-0.01338.3360.0010.0010.0000.0000.0000.000
186A202ASP-1-0.845-0.92240.2070.0330.0330.0000.0000.0000.000
187A203VAL00.0730.04841.748-0.002-0.0020.0000.0000.0000.000
188A204ALA00.0470.02844.0770.0000.0000.0000.0000.0000.000
189A205SER0-0.111-0.06642.8110.0000.0000.0000.0000.0000.000
190A206LEU00.009-0.00339.7870.0030.0030.0000.0000.0000.000
191A207GLU-1-0.733-0.84336.7360.0270.0270.0000.0000.0000.000
192A208VAL00.0650.02839.2740.0000.0000.0000.0000.0000.000
193A209ALA0-0.062-0.03140.249-0.001-0.0010.0000.0000.0000.000
194A210VAL00.0230.01141.4720.0000.0000.0000.0000.0000.000
195A211LEU0-0.051-0.01938.7150.0000.0000.0000.0000.0000.000
196A212ASP-1-0.771-0.86242.5970.0020.0020.0000.0000.0000.000
197A213GLN00.0360.00845.7820.0000.0000.0000.0000.0000.000
198A214SER0-0.030-0.03046.906-0.001-0.0010.0000.0000.0000.000
199A215ARG10.8730.94346.953-0.005-0.0050.0000.0000.0000.000
200A216PRO00.0200.01149.251-0.001-0.0010.0000.0000.0000.000
201A217ARG10.8870.92845.5830.0030.0030.0000.0000.0000.000
202A218ARG10.8510.90643.343-0.004-0.0040.0000.0000.0000.000
203A219ALA00.0580.03043.4130.0010.0010.0000.0000.0000.000
204A220PHE0-0.0110.02238.8300.0010.0010.0000.0000.0000.000
205A221ARG10.8580.91343.133-0.007-0.0070.0000.0000.0000.000
206A222ARG10.8260.90338.548-0.019-0.0190.0000.0000.0000.000
207A223ILE0-0.004-0.00544.616-0.001-0.0010.0000.0000.0000.000
208A224ALA0-0.0050.00146.1120.0010.0010.0000.0000.0000.000
209A225GLY00.1010.03748.3080.0000.0000.0000.0000.0000.000
210A226THR00.0380.01949.7060.0000.0000.0000.0000.0000.000
211A227ALA0-0.018-0.01150.6480.0000.0000.0000.0000.0000.000
212A228LEU0-0.014-0.00844.3910.0000.0000.0000.0000.0000.000
213A229GLU-1-0.928-0.97749.0450.0210.0210.0000.0000.0000.000
214A230GLN0-0.088-0.03351.5120.0000.0000.0000.0000.0000.000
215A231LEU0-0.010-0.00248.165-0.001-0.0010.0000.0000.0000.000
216A232VAL0-0.021-0.00245.6140.0000.0000.0000.0000.0000.000
217A233PRO0-0.0050.01846.6480.0000.0000.0000.0000.0000.000
218A234ALA00.0200.00848.1800.0020.0020.0000.0000.0000.000
219A235GLU-1-0.968-0.98246.9630.0290.0290.0000.0000.0000.000