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: V5LL1

Calculation Name: 1DOW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DOW

Chain ID: A

ChEMBL ID:

UniProt ID: P26231

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1949778.444418
FMO2-HF: Nuclear repulsion 1870985.680878
FMO2-HF: Total energy -78792.76354
FMO2-MP2: Total energy -79022.104973


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:57:LYS)


Summations of interaction energy for fragment #1(A:57:LYS)
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.
0.429000000000024.9680.44-1.772-3.206-0.007
Interaction energy analysis for fragmet #1(A:57:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.015 / q_NPA : 0.979
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].
3A59HIS00.029-0.0193.176-5.995-3.0940.043-1.254-1.689-0.005
4A60VAL0-0.040-0.0072.8051.6653.1590.398-0.510-1.383-0.002
5A61LEU0-0.026-0.0215.1854.6244.768-0.001-0.008-0.1340.000
6A62ALA00.0240.0097.2872.8932.8930.0000.0000.0000.000
7A63ALA00.0370.0197.9572.2192.2190.0000.0000.0000.000
8A64SER00.0120.0099.6132.4342.4340.0000.0000.0000.000
9A65VAL0-0.027-0.00411.6381.8041.8040.0000.0000.0000.000
10A66GLU-1-0.855-0.91512.740-18.925-18.9250.0000.0000.0000.000
11A67GLN00.0310.01913.6230.0720.0720.0000.0000.0000.000
12A68ALA0-0.040-0.03015.4431.2411.2410.0000.0000.0000.000
13A69THR0-0.030-0.03317.0871.2291.2290.0000.0000.0000.000
14A70GLU-1-0.914-0.95717.305-16.079-16.0790.0000.0000.0000.000
15A71ASN0-0.014-0.00719.6101.0981.0980.0000.0000.0000.000
16A72PHE0-0.031-0.02221.4290.7470.7470.0000.0000.0000.000
17A73LEU00.0330.00422.0960.6380.6380.0000.0000.0000.000
18A74GLU-1-0.902-0.92724.156-11.751-11.7510.0000.0000.0000.000
19A75LYS10.8330.90924.74412.70112.7010.0000.0000.0000.000
20A76GLY00.0440.02327.4330.4260.4260.0000.0000.0000.000
21A77ASP-1-0.771-0.88027.944-10.380-10.3800.0000.0000.0000.000
22A78LYS10.8550.92928.87510.99710.9970.0000.0000.0000.000
23A79ILE00.0550.03431.5250.3150.3150.0000.0000.0000.000
24A80ALA00.0170.00833.2510.3290.3290.0000.0000.0000.000
25A81LYS10.9270.96434.6449.0579.0570.0000.0000.0000.000
26A82GLU-1-1.011-1.02035.932-8.449-8.4490.0000.0000.0000.000
27A83SER0-0.028-0.01237.9880.2510.2510.0000.0000.0000.000
28A84GLN0-0.053-0.03539.7160.0570.0570.0000.0000.0000.000
29A85PHE0-0.003-0.01441.9610.2070.2070.0000.0000.0000.000
30A86LEU00.0530.05339.841-0.189-0.1890.0000.0000.0000.000
31A87LYS10.9140.97839.0607.5807.5800.0000.0000.0000.000
32A88GLU-1-0.901-0.95638.183-7.326-7.3260.0000.0000.0000.000
33A89GLU-1-0.848-0.94037.913-7.591-7.5910.0000.0000.0000.000
34A90LEU0-0.041-0.02234.675-0.284-0.2840.0000.0000.0000.000
35A91VAL00.0110.00433.574-0.343-0.3430.0000.0000.0000.000
36A92VAL00.0220.02733.076-0.284-0.2840.0000.0000.0000.000
37A93ALA0-0.044-0.01932.135-0.262-0.2620.0000.0000.0000.000
38A94VAL0-0.018-0.02128.184-0.394-0.3940.0000.0000.0000.000
39A95GLU-1-0.942-0.96928.200-9.469-9.4690.0000.0000.0000.000
40A96ASP-1-0.878-0.94628.257-10.532-10.5320.0000.0000.0000.000
41A97VAL0-0.036-0.01524.229-0.435-0.4350.0000.0000.0000.000
42A98ARG10.8670.91723.90410.84010.8400.0000.0000.0000.000
43A99LYS10.9630.99523.5599.6799.6790.0000.0000.0000.000
44A100GLN0-0.087-0.06523.486-0.642-0.6420.0000.0000.0000.000
45A101GLY00.0120.00420.397-0.550-0.5500.0000.0000.0000.000
46A102ASP-1-0.884-0.93818.952-14.203-14.2030.0000.0000.0000.000
47A103LEU0-0.083-0.04018.825-0.517-0.5170.0000.0000.0000.000
48A104MET0-0.044-0.01514.813-0.407-0.4070.0000.0000.0000.000
49A105LYS10.9180.97214.50217.02317.0230.0000.0000.0000.000
50A106SER0-0.008-0.00313.717-1.180-1.1800.0000.0000.0000.000
51A107ALA0-0.021-0.00813.976-0.640-0.6400.0000.0000.0000.000
52A108ALA0-0.015-0.02211.643-0.554-0.5540.0000.0000.0000.000
53A109GLY00.0140.0089.520-1.746-1.7460.0000.0000.0000.000
54A110GLU-1-0.885-0.9379.215-18.949-18.9490.0000.0000.0000.000
55A111PHE0-0.062-0.04810.187-0.322-0.3220.0000.0000.0000.000
56A112ALA0-0.025-0.0275.577-0.627-0.6270.0000.0000.0000.000
57A113ASP-1-0.836-0.8945.327-30.380-30.3800.0000.0000.0000.000
58A114ASP-1-0.926-0.9537.153-18.451-18.4510.0000.0000.0000.000
59A115PRO0-0.008-0.0086.3241.8031.8030.0000.0000.0000.000
60A116CYS0-0.015-0.0209.3671.0671.0670.0000.0000.0000.000
61A117SER00.0420.04812.4481.5051.5050.0000.0000.0000.000
62A118SER00.025-0.01514.5400.0450.0450.0000.0000.0000.000
63A119VAL0-0.0060.00817.2720.3060.3060.0000.0000.0000.000
64A120LYS10.9090.95712.72917.92117.9210.0000.0000.0000.000
65A121ARG10.9741.00012.62617.06717.0670.0000.0000.0000.000
66A122GLY0-0.005-0.00614.9450.2160.2160.0000.0000.0000.000
67A123ASN0-0.030-0.03417.1220.8790.8790.0000.0000.0000.000
68A124MET00.0070.03112.8810.5200.5200.0000.0000.0000.000
69A125VAL00.0310.00816.1040.3540.3540.0000.0000.0000.000
70A126ARG10.8800.93618.47912.62512.6250.0000.0000.0000.000
71A127ALA00.0380.03218.2330.4730.4730.0000.0000.0000.000
72A128ALA00.0430.01417.6830.1920.1920.0000.0000.0000.000
73A129ARG10.9320.96419.58511.58211.5820.0000.0000.0000.000
74A130ALA0-0.014-0.00723.1150.4020.4020.0000.0000.0000.000
75A131LEU00.0590.03119.2230.3480.3480.0000.0000.0000.000
76A132LEU00.0350.00320.5580.3190.3190.0000.0000.0000.000
77A133SER0-0.054-0.02323.9570.5470.5470.0000.0000.0000.000
78A134ALA00.0080.00826.1620.4010.4010.0000.0000.0000.000
79A135VAL0-0.0030.00623.4060.2480.2480.0000.0000.0000.000
80A136THR0-0.017-0.01226.7960.2990.2990.0000.0000.0000.000
81A137ARG10.9390.96329.3299.5859.5850.0000.0000.0000.000
82A138LEU00.0410.03328.3940.2620.2620.0000.0000.0000.000
83A139LEU0-0.034-0.02027.4210.1980.1980.0000.0000.0000.000
84A140ILE00.0000.00431.6100.2390.2390.0000.0000.0000.000
85A141LEU00.0250.00634.7260.2350.2350.0000.0000.0000.000
86A142ALA0-0.008-0.00833.4590.1940.1940.0000.0000.0000.000
87A143ASP-1-0.826-0.88935.481-7.919-7.9190.0000.0000.0000.000
88A144MET00.013-0.00837.0490.1990.1990.0000.0000.0000.000
89A145ALA0-0.0150.00438.5890.2420.2420.0000.0000.0000.000
90A146ASP-1-0.911-0.95037.345-8.017-8.0170.0000.0000.0000.000
91A147VAL0-0.048-0.03240.6150.2400.2400.0000.0000.0000.000
92A148TYR00.002-0.00343.2730.1980.1980.0000.0000.0000.000
93A149LYS10.9670.99442.6747.3027.3020.0000.0000.0000.000
94A150LEU0-0.032-0.02744.9460.1550.1550.0000.0000.0000.000
95A151LEU00.009-0.00246.6520.1770.1770.0000.0000.0000.000
96A152VAL0-0.0100.00548.6720.1670.1670.0000.0000.0000.000
97A153GLN0-0.072-0.05049.3010.0790.0790.0000.0000.0000.000
98A154LEU0-0.023-0.01450.8580.1140.1140.0000.0000.0000.000
99A155LYS10.9060.96352.6525.5105.5100.0000.0000.0000.000
100A156VAL00.0000.01053.5380.1370.1370.0000.0000.0000.000
101A157VAL0-0.014-0.01154.3160.1170.1170.0000.0000.0000.000
102A158GLU-1-0.918-0.95756.764-5.289-5.2890.0000.0000.0000.000
103A159ASP-1-0.857-0.93558.745-5.204-5.2040.0000.0000.0000.000
104A160GLY0-0.024-0.02659.7030.1060.1060.0000.0000.0000.000
105A161ILE00.0180.00559.1460.0980.0980.0000.0000.0000.000
106A162LEU0-0.022-0.00362.6160.1070.1070.0000.0000.0000.000
107A163LYS10.9350.96162.8265.1155.1150.0000.0000.0000.000
108A164LEU0-0.0260.00064.3330.0690.0690.0000.0000.0000.000
109A165ARG10.8050.90266.6324.6264.6260.0000.0000.0000.000
110A166ASN0-0.054-0.04768.6310.1130.1130.0000.0000.0000.000
111A167ALA00.0370.04970.0140.0400.0400.0000.0000.0000.000
112A168GLY00.0230.00471.6070.0390.0390.0000.0000.0000.000
113A169ASN0-0.010-0.00474.5500.0420.0420.0000.0000.0000.000
114A170GLU-1-0.824-0.94074.037-4.252-4.2520.0000.0000.0000.000
115A171GLN00.0310.03572.861-0.093-0.0930.0000.0000.0000.000
116A172ASP-1-0.875-0.95270.904-4.515-4.5150.0000.0000.0000.000
117A173LEU0-0.052-0.01369.372-0.093-0.0930.0000.0000.0000.000
118A174GLY00.0410.01968.208-0.084-0.0840.0000.0000.0000.000
119A175ILE0-0.020-0.01166.148-0.104-0.1040.0000.0000.0000.000
120A176GLN00.019-0.00864.986-0.161-0.1610.0000.0000.0000.000
121A177TYR0-0.019-0.00162.935-0.090-0.0900.0000.0000.0000.000
122A178LYS10.9050.94162.3534.8654.8650.0000.0000.0000.000
123A179ALA0-0.017-0.00460.700-0.100-0.1000.0000.0000.0000.000
124A180LEU0-0.0060.01858.741-0.099-0.0990.0000.0000.0000.000
125A181LYS10.8710.92556.3525.4875.4870.0000.0000.0000.000
126A182PRO00.0290.00055.245-0.096-0.0960.0000.0000.0000.000
127A183GLU-1-0.816-0.89453.647-6.025-6.0250.0000.0000.0000.000
128A184VAL0-0.012-0.01053.289-0.109-0.1090.0000.0000.0000.000
129A185ASP-1-0.854-0.91352.162-5.935-5.9350.0000.0000.0000.000
130A186LYS10.9140.96047.8756.3336.3330.0000.0000.0000.000
131A187LEU00.0310.01648.409-0.162-0.1620.0000.0000.0000.000
132A188ASN00.0370.02348.656-0.106-0.1060.0000.0000.0000.000
133A189ILE0-0.018-0.00344.398-0.144-0.1440.0000.0000.0000.000
134A190MET0-0.058-0.02544.091-0.163-0.1630.0000.0000.0000.000
135A191ALA00.0600.02244.075-0.121-0.1210.0000.0000.0000.000
136A192ALA0-0.045-0.02244.955-0.046-0.0460.0000.0000.0000.000
137A193LYS10.9390.95840.1187.5027.5020.0000.0000.0000.000
138A194ARG10.9330.96839.0777.5567.5560.0000.0000.0000.000
139A195GLN00.0520.02941.4900.0520.0520.0000.0000.0000.000
140A196GLN0-0.078-0.03436.9440.1040.1040.0000.0000.0000.000
141A197GLU-1-0.916-0.95035.945-8.487-8.4870.0000.0000.0000.000
142A198LEU0-0.067-0.01038.031-0.063-0.0630.0000.0000.0000.000
143A199LYS10.9590.95933.1258.7058.7050.0000.0000.0000.000
144A200ASP-1-0.848-0.90539.496-6.747-6.7470.0000.0000.0000.000
145A201VAL0-0.007-0.02742.7850.0260.0260.0000.0000.0000.000
146A202GLY00.0700.04844.7680.1070.1070.0000.0000.0000.000
147A203ASN00.008-0.00745.139-0.034-0.0340.0000.0000.0000.000
148A204ARG10.8940.94840.3797.3737.3730.0000.0000.0000.000
149A205ASP-1-0.878-0.93645.770-6.350-6.3500.0000.0000.0000.000
150A206GLN0-0.047-0.02549.1330.0480.0480.0000.0000.0000.000
151A207MET00.0090.01546.2260.1390.1390.0000.0000.0000.000
152A208ALA0-0.035-0.01148.3500.0670.0670.0000.0000.0000.000
153A209ALA0-0.001-0.00949.8810.0950.0950.0000.0000.0000.000
154A210ALA0-0.0150.00052.4630.1180.1180.0000.0000.0000.000
155A211ARG10.8720.91847.5526.5666.5660.0000.0000.0000.000
156A212GLY00.0090.01252.7240.0590.0590.0000.0000.0000.000
157A213ILE0-0.033-0.01354.9840.1030.1030.0000.0000.0000.000
158A214LEU00.0340.01554.1110.1050.1050.0000.0000.0000.000
159A215GLN0-0.026-0.02352.4900.0370.0370.0000.0000.0000.000
160A216LYS10.9450.97357.1145.1995.1990.0000.0000.0000.000
161A217ASN0-0.002-0.03660.0390.1700.1700.0000.0000.0000.000
162A218VAL00.0260.05258.8650.0860.0860.0000.0000.0000.000
163A219PRO0-0.007-0.01660.9330.0820.0820.0000.0000.0000.000
164A220ILE00.0140.01364.1440.0870.0870.0000.0000.0000.000
165A221LEU00.0230.02164.8000.0890.0890.0000.0000.0000.000
166A222TYR0-0.0050.01066.4060.0630.0630.0000.0000.0000.000
167A223THR00.010-0.00368.0540.0800.0800.0000.0000.0000.000
168A224ALA00.0100.00970.0550.0750.0750.0000.0000.0000.000
169A225SER0-0.003-0.02869.7310.0780.0780.0000.0000.0000.000
170A226GLN00.0110.00872.1590.0370.0370.0000.0000.0000.000
171A227ALA00.0010.00873.9890.0630.0630.0000.0000.0000.000
172A228CYS0-0.092-0.04175.0680.0650.0650.0000.0000.0000.000
173A229LEU0-0.066-0.02673.9930.0540.0540.0000.0000.0000.000
174A230GLN0-0.0220.00276.8200.0780.0780.0000.0000.0000.000
175A231HIS0-0.0260.00079.9970.0900.0900.0000.0000.0000.000
176A232PRO00.0230.00781.332-0.011-0.0110.0000.0000.0000.000
177A233ASP-1-0.888-0.95182.358-3.716-3.7160.0000.0000.0000.000
178A234VAL0-0.044-0.00681.5770.0240.0240.0000.0000.0000.000
179A235ALA00.006-0.00980.975-0.061-0.0610.0000.0000.0000.000
180A236ALA00.0220.00279.398-0.055-0.0550.0000.0000.0000.000
181A237TYR00.0580.02376.898-0.074-0.0740.0000.0000.0000.000
182A238LYS10.9300.96475.3853.9243.9240.0000.0000.0000.000
183A239ALA00.0090.01174.540-0.064-0.0640.0000.0000.0000.000
184A240ASN0-0.022-0.00571.799-0.070-0.0700.0000.0000.0000.000
185A241ARG11.0050.99570.7714.2614.2610.0000.0000.0000.000
186A242ASP-1-0.909-0.95569.744-4.570-4.5700.0000.0000.0000.000
187A243LEU0-0.0090.01368.263-0.072-0.0720.0000.0000.0000.000
188A244ILE0-0.012-0.01865.754-0.077-0.0770.0000.0000.0000.000
189A245TYR00.0420.01564.761-0.074-0.0740.0000.0000.0000.000
190A246LYS10.9830.99264.4224.5814.5810.0000.0000.0000.000
191A247GLN0-0.037-0.02162.903-0.130-0.1300.0000.0000.0000.000
192A248LEU00.0030.00260.164-0.104-0.1040.0000.0000.0000.000
193A249GLN0-0.014-0.00959.553-0.107-0.1070.0000.0000.0000.000
194A250GLN0-0.030-0.02159.335-0.076-0.0760.0000.0000.0000.000
195A251ALA0-0.0110.01056.489-0.088-0.0880.0000.0000.0000.000
196A252VAL00.0390.01755.122-0.135-0.1350.0000.0000.0000.000
197A253THR0-0.019-0.01554.495-0.116-0.1160.0000.0000.0000.000
198A254GLY00.0100.01154.015-0.085-0.0850.0000.0000.0000.000
199A255ILE00.003-0.01949.616-0.134-0.1340.0000.0000.0000.000
200A256SER0-0.009-0.01049.672-0.179-0.1790.0000.0000.0000.000
201A257ASN0-0.001-0.00349.717-0.140-0.1400.0000.0000.0000.000
202A258ALA0-0.0110.00547.939-0.095-0.0950.0000.0000.0000.000
203A259ALA0-0.034-0.03045.542-0.161-0.1610.0000.0000.0000.000
204A260GLN0-0.083-0.03644.321-0.215-0.2150.0000.0000.0000.000
205A261ALA0-0.0210.01242.614-0.081-0.0810.0000.0000.0000.000