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: 17KKZ

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1950838.887397
FMO2-HF: Nuclear repulsion 1872045.123266
FMO2-HF: Total energy -78793.764131
FMO2-MP2: Total energy -79023.057987


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.
-0.2535.60.403-2.481-3.773-0.011
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 : 1.036 / q_NPA : 1.001
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].
3A59HIS00.051-0.0053.100-6.476-2.4880.175-1.818-2.345-0.011
4A60VAL0-0.032-0.0062.9332.0783.8050.229-0.655-1.3000.000
5A61LEU0-0.020-0.0145.2074.6114.749-0.001-0.008-0.1280.000
6A62ALA00.0260.0107.2932.9362.9360.0000.0000.0000.000
7A63ALA00.0330.0187.9662.2962.2960.0000.0000.0000.000
8A64SER00.0000.0029.3592.2782.2780.0000.0000.0000.000
9A65VAL0-0.023-0.00711.6531.7901.7900.0000.0000.0000.000
10A66GLU-1-0.812-0.88312.750-18.712-18.7120.0000.0000.0000.000
11A67GLN00.0310.01713.6510.1540.1540.0000.0000.0000.000
12A68ALA0-0.035-0.02715.4581.2161.2160.0000.0000.0000.000
13A69THR0-0.025-0.02717.1501.2041.2040.0000.0000.0000.000
14A70GLU-1-0.922-0.95817.687-15.593-15.5930.0000.0000.0000.000
15A71ASN0-0.012-0.00119.6291.0791.0790.0000.0000.0000.000
16A72PHE0-0.006-0.01521.4450.7240.7240.0000.0000.0000.000
17A73LEU00.0290.00922.0950.6150.6150.0000.0000.0000.000
18A74GLU-1-0.799-0.85124.169-11.275-11.2750.0000.0000.0000.000
19A75LYS10.7720.86524.16712.66712.6670.0000.0000.0000.000
20A76GLY00.0450.02327.4470.4200.4200.0000.0000.0000.000
21A77ASP-1-0.769-0.85827.631-10.422-10.4220.0000.0000.0000.000
22A78LYS10.8140.89328.60410.92810.9280.0000.0000.0000.000
23A79ILE00.0340.02331.3640.3190.3190.0000.0000.0000.000
24A80ALA00.0130.00733.2620.3220.3220.0000.0000.0000.000
25A81LYS10.8540.91934.5948.9798.9790.0000.0000.0000.000
26A82GLU-1-0.899-0.95035.758-8.498-8.4980.0000.0000.0000.000
27A83SER0-0.0120.00738.0170.2540.2540.0000.0000.0000.000
28A84GLN0-0.025-0.01939.7290.0530.0530.0000.0000.0000.000
29A85PHE0-0.011-0.01941.9800.2030.2030.0000.0000.0000.000
30A86LEU00.0480.04239.943-0.187-0.1870.0000.0000.0000.000
31A87LYS10.8880.95638.9417.5507.5500.0000.0000.0000.000
32A88GLU-1-0.899-0.95138.190-7.315-7.3150.0000.0000.0000.000
33A89GLU-1-0.844-0.94137.917-7.573-7.5730.0000.0000.0000.000
34A90LEU0-0.039-0.02134.663-0.285-0.2850.0000.0000.0000.000
35A91VAL00.0090.00233.581-0.340-0.3400.0000.0000.0000.000
36A92VAL00.0290.03033.079-0.284-0.2840.0000.0000.0000.000
37A93ALA0-0.044-0.01932.217-0.271-0.2710.0000.0000.0000.000
38A94VAL0-0.016-0.02228.287-0.398-0.3980.0000.0000.0000.000
39A95GLU-1-0.927-0.95928.204-9.474-9.4740.0000.0000.0000.000
40A96ASP-1-0.872-0.93528.256-10.549-10.5490.0000.0000.0000.000
41A97VAL0-0.031-0.01324.176-0.433-0.4330.0000.0000.0000.000
42A98ARG10.8490.88523.90610.82110.8210.0000.0000.0000.000
43A99LYS10.9630.99423.5569.6429.6420.0000.0000.0000.000
44A100GLN0-0.101-0.08123.449-0.645-0.6450.0000.0000.0000.000
45A101GLY00.0110.00220.399-0.571-0.5710.0000.0000.0000.000
46A102ASP-1-0.879-0.93818.949-14.375-14.3750.0000.0000.0000.000
47A103LEU0-0.076-0.03518.793-0.546-0.5460.0000.0000.0000.000
48A104MET0-0.045-0.01514.789-0.465-0.4650.0000.0000.0000.000
49A105LYS10.8770.94014.48116.67016.6700.0000.0000.0000.000
50A106SER0-0.013-0.00313.683-1.174-1.1740.0000.0000.0000.000
51A107ALA0-0.025-0.01313.936-0.725-0.7250.0000.0000.0000.000
52A108ALA0-0.018-0.02111.645-0.689-0.6890.0000.0000.0000.000
53A109GLY00.0240.0149.485-1.935-1.9350.0000.0000.0000.000
54A110GLU-1-0.804-0.8989.177-19.455-19.4550.0000.0000.0000.000
55A111PHE0-0.045-0.0339.817-0.624-0.6240.0000.0000.0000.000
56A112ALA0-0.024-0.0265.574-0.940-0.9400.0000.0000.0000.000
57A113ASP-1-0.840-0.9045.268-32.648-32.6480.0000.0000.0000.000
58A114ASP-1-0.936-0.9657.114-19.172-19.1720.0000.0000.0000.000
59A115PRO0-0.006-0.0035.7782.0642.0640.0000.0000.0000.000
60A116CYS0-0.021-0.0238.9981.3651.3650.0000.0000.0000.000
61A117SER00.0480.04811.9091.8111.8110.0000.0000.0000.000
62A118SER00.015-0.01914.3270.0550.0550.0000.0000.0000.000
63A119VAL0-0.0110.00516.9400.3670.3670.0000.0000.0000.000
64A120LYS10.8410.92012.50319.06619.0660.0000.0000.0000.000
65A121ARG10.9580.99112.50717.85517.8550.0000.0000.0000.000
66A122GLY00.0070.00114.8590.2630.2630.0000.0000.0000.000
67A123ASN0-0.009-0.01317.1790.9740.9740.0000.0000.0000.000
68A124MET00.0030.03112.8290.5950.5950.0000.0000.0000.000
69A125VAL00.0310.00616.0370.3910.3910.0000.0000.0000.000
70A126ARG10.8660.92018.40812.98312.9830.0000.0000.0000.000
71A127ALA00.0340.02718.1850.5000.5000.0000.0000.0000.000
72A128ALA00.0440.01517.6230.2270.2270.0000.0000.0000.000
73A129ARG10.9300.96419.55311.69911.6990.0000.0000.0000.000
74A130ALA00.0000.00923.1080.4340.4340.0000.0000.0000.000
75A131LEU00.0490.02819.1830.3640.3640.0000.0000.0000.000
76A132LEU00.0370.00620.6140.3300.3300.0000.0000.0000.000
77A133SER0-0.057-0.03123.9570.5330.5330.0000.0000.0000.000
78A134ALA00.0100.00726.1710.4060.4060.0000.0000.0000.000
79A135VAL0-0.0060.00323.4000.2580.2580.0000.0000.0000.000
80A136THR0-0.030-0.02526.8070.2990.2990.0000.0000.0000.000
81A137ARG10.9190.96329.4229.8219.8210.0000.0000.0000.000
82A138LEU00.0370.02928.4260.2670.2670.0000.0000.0000.000
83A139LEU0-0.024-0.01527.4360.2050.2050.0000.0000.0000.000
84A140ILE0-0.0030.00131.6940.2390.2390.0000.0000.0000.000
85A141LEU00.0240.00934.7370.2380.2380.0000.0000.0000.000
86A142ALA0-0.007-0.01033.4930.1980.1980.0000.0000.0000.000
87A143ASP-1-0.813-0.86635.513-7.857-7.8570.0000.0000.0000.000
88A144MET00.000-0.00737.1250.1920.1920.0000.0000.0000.000
89A145ALA0-0.0160.00038.5780.2380.2380.0000.0000.0000.000
90A146ASP-1-0.903-0.94737.370-7.917-7.9170.0000.0000.0000.000
91A147VAL0-0.046-0.02740.6720.2390.2390.0000.0000.0000.000
92A148TYR00.000-0.00843.3430.2080.2080.0000.0000.0000.000
93A149LYS10.9360.97942.6867.2557.2550.0000.0000.0000.000
94A150LEU0-0.028-0.02244.9960.1640.1640.0000.0000.0000.000
95A151LEU00.016-0.00146.7070.1790.1790.0000.0000.0000.000
96A152VAL0-0.0090.00348.7260.1690.1690.0000.0000.0000.000
97A153GLN0-0.051-0.04249.2800.0810.0810.0000.0000.0000.000
98A154LEU0-0.013-0.01250.9150.1210.1210.0000.0000.0000.000
99A155LYS10.8270.90952.7075.4775.4770.0000.0000.0000.000
100A156VAL00.0000.00553.7520.1370.1370.0000.0000.0000.000
101A157VAL0-0.020-0.01254.3800.1180.1180.0000.0000.0000.000
102A158GLU-1-0.843-0.91256.815-5.243-5.2430.0000.0000.0000.000
103A159ASP-1-0.843-0.92558.791-5.159-5.1590.0000.0000.0000.000
104A160GLY0-0.038-0.02759.7480.1050.1050.0000.0000.0000.000
105A161ILE00.0210.00459.0380.0950.0950.0000.0000.0000.000
106A162LEU0-0.0190.00462.6620.1060.1060.0000.0000.0000.000
107A163LYS10.9250.96062.1995.1385.1380.0000.0000.0000.000
108A164LEU0-0.023-0.00564.4300.0690.0690.0000.0000.0000.000
109A165ARG10.8170.88966.6694.5994.5990.0000.0000.0000.000
110A166ASN0-0.036-0.03168.6780.1080.1080.0000.0000.0000.000
111A167ALA00.0380.05169.9780.0410.0410.0000.0000.0000.000
112A168GLY00.0270.00471.6410.0380.0380.0000.0000.0000.000
113A169ASN0-0.020-0.01974.5780.0500.0500.0000.0000.0000.000
114A170GLU-1-0.784-0.90774.093-4.237-4.2370.0000.0000.0000.000
115A171GLN00.0140.02473.013-0.083-0.0830.0000.0000.0000.000
116A172ASP-1-0.855-0.93071.021-4.496-4.4960.0000.0000.0000.000
117A173LEU0-0.053-0.01169.448-0.091-0.0910.0000.0000.0000.000
118A174GLY00.0360.01768.298-0.083-0.0830.0000.0000.0000.000
119A175ILE0-0.023-0.01366.534-0.101-0.1010.0000.0000.0000.000
120A176GLN00.022-0.00465.129-0.162-0.1620.0000.0000.0000.000
121A177TYR0-0.0290.00062.843-0.123-0.1230.0000.0000.0000.000
122A178LYS10.9150.94562.5604.8164.8160.0000.0000.0000.000
123A179ALA0-0.014-0.00260.894-0.100-0.1000.0000.0000.0000.000
124A180LEU0-0.0180.01158.752-0.102-0.1020.0000.0000.0000.000
125A181LYS10.8270.88656.4545.4715.4710.0000.0000.0000.000
126A182PRO00.0390.01455.474-0.092-0.0920.0000.0000.0000.000
127A183GLU-1-0.754-0.84753.621-6.081-6.0810.0000.0000.0000.000
128A184VAL00.0130.00453.320-0.106-0.1060.0000.0000.0000.000
129A185ASP-1-0.820-0.88652.453-5.850-5.8500.0000.0000.0000.000
130A186LYS10.7940.88348.6035.9895.9890.0000.0000.0000.000
131A187LEU00.0320.01948.439-0.152-0.1520.0000.0000.0000.000
132A188ASN00.0300.02048.699-0.144-0.1440.0000.0000.0000.000
133A189ILE0-0.0060.00544.534-0.140-0.1400.0000.0000.0000.000
134A190MET0-0.044-0.01644.138-0.149-0.1490.0000.0000.0000.000
135A191ALA00.0530.01844.115-0.121-0.1210.0000.0000.0000.000
136A192ALA0-0.049-0.02245.050-0.049-0.0490.0000.0000.0000.000
137A193LYS10.9380.96040.1867.4517.4510.0000.0000.0000.000
138A194ARG10.8560.90438.2397.5887.5880.0000.0000.0000.000
139A195GLN00.0490.03041.5650.0320.0320.0000.0000.0000.000
140A196GLN0-0.075-0.03337.3420.0400.0400.0000.0000.0000.000
141A197GLU-1-0.873-0.92136.316-8.273-8.2730.0000.0000.0000.000
142A198LEU0-0.040-0.00338.121-0.079-0.0790.0000.0000.0000.000
143A199LYS10.9750.97233.3548.6848.6840.0000.0000.0000.000
144A200ASP-1-0.800-0.88739.603-6.714-6.7140.0000.0000.0000.000
145A201VAL0-0.005-0.01743.0010.0330.0330.0000.0000.0000.000
146A202GLY00.0520.04044.8740.1130.1130.0000.0000.0000.000
147A203ASN0-0.017-0.03445.289-0.007-0.0070.0000.0000.0000.000
148A204ARG10.8440.92240.7037.3767.3760.0000.0000.0000.000
149A205ASP-1-0.868-0.93145.861-6.333-6.3330.0000.0000.0000.000
150A206GLN0-0.039-0.01049.2220.0310.0310.0000.0000.0000.000
151A207MET00.0100.01246.3590.1410.1410.0000.0000.0000.000
152A208ALA0-0.042-0.01348.4440.0570.0570.0000.0000.0000.000
153A209ALA0-0.002-0.00949.9530.0980.0980.0000.0000.0000.000
154A210ALA0-0.017-0.00352.5360.1170.1170.0000.0000.0000.000
155A211ARG10.8860.92447.6266.5386.5380.0000.0000.0000.000
156A212GLY00.0150.02552.7840.0590.0590.0000.0000.0000.000
157A213ILE0-0.032-0.01755.0420.1070.1070.0000.0000.0000.000
158A214LEU00.0240.01353.9970.1040.1040.0000.0000.0000.000
159A215GLN0-0.047-0.04252.1680.0370.0370.0000.0000.0000.000
160A216LYS10.9280.97057.1575.1385.1380.0000.0000.0000.000
161A217ASN0-0.001-0.03460.0850.1620.1620.0000.0000.0000.000
162A218VAL00.0380.04759.2800.0840.0840.0000.0000.0000.000
163A219PRO00.0160.00361.0250.0810.0810.0000.0000.0000.000
164A220ILE00.0000.00264.1830.0910.0910.0000.0000.0000.000
165A221LEU00.0270.02264.9870.0880.0880.0000.0000.0000.000
166A222TYR0-0.028-0.00466.4760.0550.0550.0000.0000.0000.000
167A223THR00.010-0.00568.0880.0780.0780.0000.0000.0000.000
168A224ALA00.0080.00870.0950.0750.0750.0000.0000.0000.000
169A225SER00.005-0.02869.7700.0750.0750.0000.0000.0000.000
170A226GLN00.0200.02372.1990.0040.0040.0000.0000.0000.000
171A227ALA00.0040.01174.0210.0640.0640.0000.0000.0000.000
172A228CYS0-0.090-0.04775.0210.0640.0640.0000.0000.0000.000
173A229LEU0-0.060-0.02674.0800.0530.0530.0000.0000.0000.000
174A230GLN0-0.056-0.03177.1820.0690.0690.0000.0000.0000.000
175A231HIS0-0.034-0.00679.9450.0940.0940.0000.0000.0000.000
176A232PRO00.0710.03081.374-0.011-0.0110.0000.0000.0000.000
177A233ASP-1-0.880-0.92082.401-3.717-3.7170.0000.0000.0000.000
178A234VAL0-0.0210.00181.6070.0220.0220.0000.0000.0000.000
179A235ALA0-0.025-0.02481.030-0.063-0.0630.0000.0000.0000.000
180A236ALA00.0310.00979.461-0.053-0.0530.0000.0000.0000.000
181A237TYR00.0590.02376.945-0.071-0.0710.0000.0000.0000.000
182A238LYS10.8710.91775.4413.8863.8860.0000.0000.0000.000
183A239ALA00.0040.00774.603-0.063-0.0630.0000.0000.0000.000
184A240ASN0-0.023-0.00672.123-0.082-0.0820.0000.0000.0000.000
185A241ARG10.9670.97470.6874.2714.2710.0000.0000.0000.000
186A242ASP-1-0.879-0.92669.805-4.560-4.5600.0000.0000.0000.000
187A243LEU0-0.0170.00568.443-0.073-0.0730.0000.0000.0000.000
188A244ILE0-0.001-0.01265.766-0.081-0.0810.0000.0000.0000.000
189A245TYR00.0080.00164.202-0.068-0.0680.0000.0000.0000.000
190A246LYS10.9850.99264.4904.5404.5400.0000.0000.0000.000
191A247GLN0-0.044-0.02262.955-0.095-0.0950.0000.0000.0000.000
192A248LEU00.0000.00160.167-0.106-0.1060.0000.0000.0000.000
193A249GLN00.0150.00259.621-0.090-0.0900.0000.0000.0000.000
194A250GLN0-0.025-0.01359.414-0.053-0.0530.0000.0000.0000.000
195A251ALA0-0.0080.01256.588-0.088-0.0880.0000.0000.0000.000
196A252VAL00.0270.00855.197-0.132-0.1320.0000.0000.0000.000
197A253THR00.004-0.00954.572-0.115-0.1150.0000.0000.0000.000
198A254GLY00.0110.02254.105-0.088-0.0880.0000.0000.0000.000
199A255ILE00.003-0.01949.695-0.131-0.1310.0000.0000.0000.000
200A256SER00.003-0.00549.753-0.179-0.1790.0000.0000.0000.000
201A257ASN0-0.042-0.02949.807-0.124-0.1240.0000.0000.0000.000
202A258ALA00.0020.00948.109-0.095-0.0950.0000.0000.0000.000
203A259ALA0-0.027-0.02145.627-0.159-0.1590.0000.0000.0000.000
204A260GLN0-0.084-0.04544.409-0.202-0.2020.0000.0000.0000.000
205A261ALA0-0.0110.01742.767-0.080-0.0800.0000.0000.0000.000