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: GYQZ1

Calculation Name: 1QQG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QQG

Chain ID: A

ChEMBL ID:

UniProt ID: P35568

Base Structure: X-ray

Registration Date: 2023-09-26

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2421925.714104
FMO2-HF: Nuclear repulsion 2338459.226221
FMO2-HF: Total energy -83466.487883
FMO2-MP2: Total energy -83708.864179


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:12:ASP)


Summations of interaction energy for fragment #1(A:12:ASP)
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.
-247.739-236.1219.302-9.629-11.2890.083
Interaction energy analysis for fragmet #1(A:12:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.821 / q_NPA : -0.918
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].
3A14ARG10.9330.9732.504-54.620-52.5050.725-1.241-1.5980.002
4A15LYS10.9480.9876.280-26.084-26.0840.0000.0000.0000.000
5A16VAL0-0.0150.0008.5372.5782.5780.0000.0000.0000.000
6A17GLY00.0520.03111.031-1.995-1.9950.0000.0000.0000.000
7A18TYR0-0.033-0.01514.4980.4120.4120.0000.0000.0000.000
8A19LEU00.0860.06916.068-0.423-0.4230.0000.0000.0000.000
9A20ARG10.9030.92719.188-12.842-12.8420.0000.0000.0000.000
10A21LYS10.8610.93618.798-15.584-15.5840.0000.0000.0000.000
11A22PRO00.0710.04222.091-0.557-0.5570.0000.0000.0000.000
12A23LYS10.9650.98225.099-10.912-10.9120.0000.0000.0000.000
13A24SER0-0.019-0.03124.861-0.252-0.2520.0000.0000.0000.000
14A25MET00.0710.04225.7100.0550.0550.0000.0000.0000.000
15A26HIS0-0.0080.02423.0730.5230.5230.0000.0000.0000.000
16A27LYS10.9770.99520.768-14.500-14.5000.0000.0000.0000.000
17A28ARG10.8280.92717.002-15.903-15.9030.0000.0000.0000.000
18A29PHE00.0470.01710.607-0.598-0.5980.0000.0000.0000.000
19A30PHE00.0430.00912.4800.9510.9510.0000.0000.0000.000
20A31VAL0-0.002-0.0096.2950.1210.1210.0000.0000.0000.000
21A32LEU0-0.0020.0067.9220.1580.1580.0000.0000.0000.000
22A33ARG10.8410.9222.021-105.689-100.2617.996-6.665-6.7580.092
23A34ALA00.0380.0082.947-8.423-7.2410.128-0.444-0.8660.000
24A35ALA0-0.007-0.0082.7965.3557.2310.341-0.965-1.251-0.012
25A36SER0-0.012-0.0012.9351.3491.7850.109-0.151-0.3940.000
26A37GLU-1-0.888-0.9445.07027.86027.915-0.001-0.006-0.0480.000
27A38ALA0-0.038-0.0386.358-1.858-1.8580.0000.0000.0000.000
28A39GLY00.0020.0114.358-1.476-1.369-0.001-0.020-0.0860.000
29A40GLY0-0.0070.0075.3721.0951.151-0.0010.000-0.0550.000
30A41PRO00.0730.0295.7643.9763.9760.0000.0000.0000.000
31A42ALA00.0480.0385.9325.4345.4340.0000.0000.0000.000
32A43ARG10.8090.9053.614-58.896-58.5330.006-0.137-0.2330.001
33A44LEU00.0210.0267.5833.5023.5020.0000.0000.0000.000
34A45GLU-1-0.808-0.8936.77241.05241.0520.0000.0000.0000.000
35A46TYR0-0.0050.00810.284-1.117-1.1170.0000.0000.0000.000
36A47TYR00.0420.0157.774-0.873-0.8730.0000.0000.0000.000
37A48GLU-1-1.005-1.01314.16514.67614.6760.0000.0000.0000.000
38A49ASN00.031-0.01016.465-0.170-0.1700.0000.0000.0000.000
39A50GLU-1-0.869-0.94213.32922.36422.3640.0000.0000.0000.000
40A51LYN0-0.0020.00613.5231.9521.9520.0000.0000.0000.000
41A52LYS10.9130.96314.674-16.348-16.3480.0000.0000.0000.000
42A53TRP00.0270.0216.091-1.977-1.9770.0000.0000.0000.000
43A54ARG10.9320.9669.795-17.962-17.9620.0000.0000.0000.000
44A55HIS0-0.014-0.02211.5791.4521.4520.0000.0000.0000.000
45A56LYS10.9580.9897.367-36.871-36.8710.0000.0000.0000.000
46A57SER00.0270.02311.775-0.857-0.8570.0000.0000.0000.000
47A58SER0-0.050-0.04613.713-2.111-2.1110.0000.0000.0000.000
48A59ALA00.0450.04712.2282.1172.1170.0000.0000.0000.000
49A60PRO0-0.0180.0009.560-1.867-1.8670.0000.0000.0000.000
50A61LYS10.9250.94812.344-18.259-18.2590.0000.0000.0000.000
51A62ARG10.8090.87513.927-18.684-18.6840.0000.0000.0000.000
52A63SER00.005-0.0239.1051.3811.3810.0000.0000.0000.000
53A64ILE0-0.003-0.00411.634-1.505-1.5050.0000.0000.0000.000
54A65PRO00.0590.03010.7271.8021.8020.0000.0000.0000.000
55A66LEU00.0330.0129.621-1.859-1.8590.0000.0000.0000.000
56A67GLU-1-0.894-0.93012.38420.46620.4660.0000.0000.0000.000
57A68SER0-0.073-0.04314.328-1.492-1.4920.0000.0000.0000.000
58A69CYS0-0.083-0.04515.410-0.999-0.9990.0000.0000.0000.000
59A70PHE00.0310.01217.7540.0570.0570.0000.0000.0000.000
60A71ASN0-0.056-0.05320.436-0.502-0.5020.0000.0000.0000.000
61A72ILE00.0240.01615.8490.4100.4100.0000.0000.0000.000
62A73ASN00.0500.03420.150-0.683-0.6830.0000.0000.0000.000
63A74LYS10.8840.96122.387-12.842-12.8420.0000.0000.0000.000
64A75ARG10.7940.86024.207-11.870-11.8700.0000.0000.0000.000
65A76ALA00.006-0.01526.9150.2300.2300.0000.0000.0000.000
66A77ASP-1-0.838-0.91629.50410.59910.5990.0000.0000.0000.000
67A78SER0-0.099-0.07432.012-0.050-0.0500.0000.0000.0000.000
68A79LYS10.8520.94431.085-10.247-10.2470.0000.0000.0000.000
69A80ASN0-0.030-0.02227.0840.3740.3740.0000.0000.0000.000
70A81LYS11.0271.00029.229-9.678-9.6780.0000.0000.0000.000
71A82HIS00.0130.02725.057-0.241-0.2410.0000.0000.0000.000
72A83LEU0-0.0110.01523.5490.7300.7300.0000.0000.0000.000
73A84VAL00.0220.03518.138-0.258-0.2580.0000.0000.0000.000
74A85ALA0-0.029-0.02420.5260.3590.3590.0000.0000.0000.000
75A86LEU00.0100.01114.9160.0490.0490.0000.0000.0000.000
76A87TYR00.019-0.00719.451-0.597-0.5970.0000.0000.0000.000
77A88THR00.0790.04117.876-0.061-0.0610.0000.0000.0000.000
78A89ARG10.9120.95220.721-13.760-13.7600.0000.0000.0000.000
79A90ASP-1-0.800-0.90922.19212.61812.6180.0000.0000.0000.000
80A91GLU-1-0.834-0.89219.48915.49415.4940.0000.0000.0000.000
81A92HIS00.0030.01722.4400.2970.2970.0000.0000.0000.000
82A93PHE0-0.032-0.00916.166-0.060-0.0600.0000.0000.0000.000
83A94ALA00.0310.01919.7890.3700.3700.0000.0000.0000.000
84A95ILE0-0.057-0.02916.5550.1020.1020.0000.0000.0000.000
85A96ALA0-0.017-0.02020.083-0.384-0.3840.0000.0000.0000.000
86A97ALA0-0.002-0.00221.1780.4150.4150.0000.0000.0000.000
87A98ASP-1-0.929-0.97222.51113.35613.3560.0000.0000.0000.000
88A99SER00.0230.00623.933-0.573-0.5730.0000.0000.0000.000
89A100GLU-1-0.900-0.96224.30211.72711.7270.0000.0000.0000.000
90A101ALA00.0320.02723.3140.3530.3530.0000.0000.0000.000
91A102GLU-1-0.882-0.94819.06316.81716.8170.0000.0000.0000.000
92A103GLN0-0.029-0.04219.2670.7880.7880.0000.0000.0000.000
93A104ASP-1-0.821-0.91520.07014.90814.9080.0000.0000.0000.000
94A105SER00.0070.01016.7141.0521.0520.0000.0000.0000.000
95A106TRP0-0.012-0.03211.9451.8601.8600.0000.0000.0000.000
96A107TYR0-0.028-0.00915.4450.8150.8150.0000.0000.0000.000
97A108GLN00.0210.00616.6760.5470.5470.0000.0000.0000.000
98A109ALA0-0.0220.00011.3950.5960.5960.0000.0000.0000.000
99A110LEU0-0.052-0.05111.9321.2601.2600.0000.0000.0000.000
100A111LEU00.0030.00213.3360.2760.2760.0000.0000.0000.000
101A112GLN0-0.053-0.01311.8091.1381.1380.0000.0000.0000.000
102A113LEU0-0.064-0.0316.8301.1151.1150.0000.0000.0000.000
103A114HIS0-0.0330.00910.5980.5760.5760.0000.0000.0000.000
104A159ALA00.0030.00524.094-0.064-0.0640.0000.0000.0000.000
105A160PHE0-0.036-0.03825.296-0.572-0.5720.0000.0000.0000.000
106A161LYS10.9200.97425.973-9.473-9.4730.0000.0000.0000.000
107A162GLU-1-0.872-0.92127.14411.27211.2720.0000.0000.0000.000
108A163VAL0-0.0010.00625.615-0.215-0.2150.0000.0000.0000.000
109A164TRP00.0660.05627.4450.2870.2870.0000.0000.0000.000
110A165GLN00.0230.00726.8530.1720.1720.0000.0000.0000.000
111A166VAL0-0.011-0.00629.747-0.116-0.1160.0000.0000.0000.000
112A167ILE00.004-0.01033.3210.0510.0510.0000.0000.0000.000
113A168LEU00.0070.01035.821-0.241-0.2410.0000.0000.0000.000
114A169LYS10.9390.95938.337-7.963-7.9630.0000.0000.0000.000
115A170PRO00.0180.00741.627-0.010-0.0100.0000.0000.0000.000
116A171LYS10.9410.97844.550-7.295-7.2950.0000.0000.0000.000
117A172GLY00.0550.02345.8470.1180.1180.0000.0000.0000.000
118A173LEU0-0.015-0.01844.656-0.054-0.0540.0000.0000.0000.000
119A174GLY0-0.0050.01943.0100.1100.1100.0000.0000.0000.000
120A175GLN00.012-0.00243.9180.1290.1290.0000.0000.0000.000
121A176THR0-0.0020.00946.391-0.039-0.0390.0000.0000.0000.000
122A177LYS10.8900.95443.667-6.898-6.8980.0000.0000.0000.000
123A178ASN0-0.0080.00242.1920.1030.1030.0000.0000.0000.000
124A179LEU0-0.061-0.01438.4440.2240.2240.0000.0000.0000.000
125A180ILE00.013-0.00539.505-0.066-0.0660.0000.0000.0000.000
126A181GLY00.0000.00536.4690.1480.1480.0000.0000.0000.000
127A182ILE0-0.025-0.01929.870-0.036-0.0360.0000.0000.0000.000
128A183TYR00.0190.01932.1390.0620.0620.0000.0000.0000.000
129A184ARG10.7820.88224.238-12.135-12.1350.0000.0000.0000.000
130A185LEU00.0060.01830.454-0.156-0.1560.0000.0000.0000.000
131A186CYS0-0.040-0.02329.2370.3960.3960.0000.0000.0000.000
132A187LEU00.0250.02030.522-0.307-0.3070.0000.0000.0000.000
133A188THR00.0330.00830.4190.2740.2740.0000.0000.0000.000
134A189SER00.001-0.02432.138-0.094-0.0940.0000.0000.0000.000
135A190LYS11.0431.02633.644-9.144-9.1440.0000.0000.0000.000
136A191THR0-0.038-0.00734.616-0.157-0.1570.0000.0000.0000.000
137A192ILE00.0450.02634.7340.2270.2270.0000.0000.0000.000
138A193SER0-0.021-0.00332.370-0.311-0.3110.0000.0000.0000.000
139A194PHE00.0470.02533.1390.2380.2380.0000.0000.0000.000
140A195VAL00.0480.02028.670-0.174-0.1740.0000.0000.0000.000
141A196LYS10.9390.97831.014-9.414-9.4140.0000.0000.0000.000
142A197LEU0-0.010-0.01526.1480.2440.2440.0000.0000.0000.000
143A198ASN0-0.073-0.05526.022-0.772-0.7720.0000.0000.0000.000
144A199SER0-0.061-0.01827.523-0.110-0.1100.0000.0000.0000.000
145A200GLU-1-0.883-0.95424.94812.56612.5660.0000.0000.0000.000
146A201ALA0-0.0050.00927.9620.0270.0270.0000.0000.0000.000
147A202ALA0-0.039-0.03331.2030.0210.0210.0000.0000.0000.000
148A203ALA0-0.043-0.00233.264-0.185-0.1850.0000.0000.0000.000
149A204VAL00.005-0.00736.482-0.211-0.2110.0000.0000.0000.000
150A205VAL00.010-0.00235.2550.2480.2480.0000.0000.0000.000
151A206LEU0-0.007-0.00237.789-0.253-0.2530.0000.0000.0000.000
152A207GLN00.0430.01238.6860.2400.2400.0000.0000.0000.000
153A208LEU00.0450.01137.081-0.143-0.1430.0000.0000.0000.000
154A209MET00.0170.01040.983-0.124-0.1240.0000.0000.0000.000
155A210ASN0-0.071-0.03343.881-0.147-0.1470.0000.0000.0000.000
156A211ILE00.0160.01340.267-0.101-0.1010.0000.0000.0000.000
157A212ARG10.9110.96544.905-6.187-6.1870.0000.0000.0000.000
158A213ARG10.9390.97046.335-6.541-6.5410.0000.0000.0000.000
159A214CYS0-0.0260.00941.8100.0780.0780.0000.0000.0000.000
160A215GLY00.0130.00243.384-0.120-0.1200.0000.0000.0000.000
161A216HIS0-0.028-0.01741.2340.1430.1430.0000.0000.0000.000
162A217SER00.0160.01743.229-0.224-0.2240.0000.0000.0000.000
163A218GLU-1-0.900-0.94543.3917.1717.1710.0000.0000.0000.000
164A219ASN0-0.052-0.02238.009-0.066-0.0660.0000.0000.0000.000
165A220PHE0-0.028-0.02939.1060.1990.1990.0000.0000.0000.000
166A221PHE00.0900.01837.955-0.040-0.0400.0000.0000.0000.000
167A222PHE0-0.0170.00340.7380.0310.0310.0000.0000.0000.000
168A223ILE00.0160.00238.5080.0560.0560.0000.0000.0000.000
169A224GLU-1-0.863-0.92943.0596.3536.3530.0000.0000.0000.000
170A225VAL0-0.009-0.00643.5620.0350.0350.0000.0000.0000.000
171A226GLY00.033-0.00246.464-0.166-0.1660.0000.0000.0000.000
172A227ARG10.9570.94649.092-5.634-5.6340.0000.0000.0000.000
173A228SER0-0.043-0.01148.4190.0070.0070.0000.0000.0000.000
174A229ALA00.0470.04945.4740.1000.1000.0000.0000.0000.000
175A230VAL00.0410.02242.060-0.116-0.1160.0000.0000.0000.000
176A231THR0-0.069-0.03843.2280.0120.0120.0000.0000.0000.000
177A232GLY00.0000.00946.115-0.086-0.0860.0000.0000.0000.000
178A233PRO0-0.030-0.02148.1900.1090.1090.0000.0000.0000.000
179A234GLY00.0570.01948.962-0.043-0.0430.0000.0000.0000.000
180A235GLU-1-0.854-0.93045.9386.6926.6920.0000.0000.0000.000
181A236PHE00.0080.01041.020-0.010-0.0100.0000.0000.0000.000
182A237TRP0-0.011-0.01942.6560.1540.1540.0000.0000.0000.000
183A238MET0-0.041-0.00537.2710.2060.2060.0000.0000.0000.000
184A239GLN0-0.037-0.00537.557-0.252-0.2520.0000.0000.0000.000
185A240VAL0-0.005-0.00334.2460.2730.2730.0000.0000.0000.000
186A241ASP-1-0.926-0.96530.39410.24710.2470.0000.0000.0000.000
187A242ASP-1-0.733-0.87834.0359.3199.3190.0000.0000.0000.000
188A243SER00.0550.00336.6020.1190.1190.0000.0000.0000.000
189A244VAL0-0.0150.01734.322-0.081-0.0810.0000.0000.0000.000
190A245VAL00.0150.00332.2950.0610.0610.0000.0000.0000.000
191A246ALA0-0.003-0.00134.6160.0280.0280.0000.0000.0000.000
192A247GLN0-0.0160.00137.704-0.092-0.0920.0000.0000.0000.000
193A248ASN00.0190.00832.6900.1780.1780.0000.0000.0000.000
194A249MET0-0.0290.02333.7330.0540.0540.0000.0000.0000.000
195A250HIS00.000-0.00935.720-0.050-0.0500.0000.0000.0000.000
196A251GLU-1-0.897-0.94937.4608.2528.2520.0000.0000.0000.000
197A252THR00.001-0.02232.456-0.003-0.0030.0000.0000.0000.000
198A253ILE0-0.024-0.02335.518-0.002-0.0020.0000.0000.0000.000
199A254LEU0-0.036-0.01637.412-0.157-0.1570.0000.0000.0000.000
200A255GLU-1-0.905-0.96237.4647.8147.8140.0000.0000.0000.000
201A256ALA0-0.014-0.00136.4350.0010.0010.0000.0000.0000.000
202A257MET0-0.083-0.04738.133-0.057-0.0570.0000.0000.0000.000
203A258ARG10.9580.96341.641-7.258-7.2580.0000.0000.0000.000
204A259ALA00.0580.04538.884-0.117-0.1170.0000.0000.0000.000
205A260MET0-0.097-0.04840.3110.0270.0270.0000.0000.0000.000
206A261SER0-0.137-0.04642.097-0.144-0.1440.0000.0000.0000.000
207A262ASP-1-0.925-0.96041.5267.2617.2610.0000.0000.0000.000