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: M3R4Z

Calculation Name: 1D02-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D02

Chain ID: A

ChEMBL ID:

UniProt ID: P43642

Base Structure: X-ray

Registration Date: 2023-03-13

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 OptAll
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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2230034.411672
FMO2-HF: Nuclear repulsion 2151569.607455
FMO2-HF: Total energy -78464.804217
FMO2-MP2: Total energy -78699.456829


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-18.897-13.76610.711-6.626-9.215-0.056
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / 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].
3A8GLY00.0950.0463.869-1.689-0.112-0.009-0.751-0.8170.004
4A9ARG10.8830.9416.128-0.442-0.4420.0000.0000.0000.000
5A10LEU00.0370.0187.650-0.090-0.0900.0000.0000.0000.000
6A11ASN0-0.0090.00210.4600.1030.1030.0000.0000.0000.000
7A12TRP00.038-0.01212.571-0.033-0.0330.0000.0000.0000.000
8A13GLN0-0.028-0.00315.460-0.009-0.0090.0000.0000.0000.000
9A14ALA00.0620.04615.539-0.007-0.0070.0000.0000.0000.000
10A15LEU0-0.021-0.00116.887-0.011-0.0110.0000.0000.0000.000
11A16ALA0-0.014-0.01018.714-0.005-0.0050.0000.0000.0000.000
12A17GLY00.0240.01120.528-0.002-0.0020.0000.0000.0000.000
13A18LEU0-0.014-0.00220.810-0.004-0.0040.0000.0000.0000.000
14A19LYS10.9150.96322.831-0.001-0.0010.0000.0000.0000.000
15A20ALA0-0.033-0.02024.8070.0000.0000.0000.0000.0000.000
16A21SER0-0.067-0.04525.775-0.002-0.0020.0000.0000.0000.000
17A22GLY0-0.012-0.00127.585-0.002-0.0020.0000.0000.0000.000
18A23ALA0-0.0060.01026.237-0.003-0.0030.0000.0000.0000.000
19A24GLU-1-0.892-0.95227.586-0.055-0.0550.0000.0000.0000.000
20A25GLN0-0.0100.00022.676-0.008-0.0080.0000.0000.0000.000
21A26ASN00.004-0.00724.159-0.012-0.0120.0000.0000.0000.000
22A27LEU00.0360.01020.064-0.002-0.0020.0000.0000.0000.000
23A28TYR00.017-0.01419.930-0.009-0.0090.0000.0000.0000.000
24A29ASN00.0410.01219.193-0.014-0.0140.0000.0000.0000.000
25A30VAL0-0.0110.00218.9990.0050.0050.0000.0000.0000.000
26A31PHE00.030-0.00414.7920.0050.0050.0000.0000.0000.000
27A32ASN0-0.037-0.02614.585-0.041-0.0410.0000.0000.0000.000
28A33ALA00.0480.04114.251-0.004-0.0040.0000.0000.0000.000
29A34VAL0-0.040-0.01813.1810.0200.0200.0000.0000.0000.000
30A35PHE00.003-0.01110.393-0.014-0.0140.0000.0000.0000.000
31A36GLU-1-0.880-0.9319.600-0.074-0.0740.0000.0000.0000.000
32A37GLY0-0.0030.0018.3150.0660.0660.0000.0000.0000.000
33A38THR0-0.087-0.0245.9800.0780.0780.0000.0000.0000.000
34A39LYS10.7960.8882.2842.8833.7792.960-1.072-2.783-0.002
35A40TYR0-0.036-0.0204.123-0.450-0.2690.000-0.027-0.1540.000
36A41VAL00.0330.0237.7970.1110.1110.0000.0000.0000.000
37A42LEU0-0.015-0.00310.618-0.015-0.0150.0000.0000.0000.000
38A43TYR0-0.073-0.06112.7320.0380.0380.0000.0000.0000.000
39A44GLU-1-0.886-0.95217.149-0.141-0.1410.0000.0000.0000.000
40A45LYS10.9030.95620.8050.1390.1390.0000.0000.0000.000
41A46PRO0-0.0080.00618.585-0.001-0.0010.0000.0000.0000.000
42A47LYS10.9830.96920.2960.2200.2200.0000.0000.0000.000
43A48HIS00.0300.01715.0870.0590.0590.0000.0000.0000.000
44A49LEU00.0470.03320.4460.0040.0040.0000.0000.0000.000
45A50LYS10.8440.91923.6970.1820.1820.0000.0000.0000.000
46A51ASN00.0090.00626.1710.0220.0220.0000.0000.0000.000
47A52LEU0-0.044-0.01625.369-0.008-0.0080.0000.0000.0000.000
48A53TYR00.012-0.01629.2660.0040.0040.0000.0000.0000.000
49A54ALA00.0090.02432.7720.0070.0070.0000.0000.0000.000
50A55GLN00.0420.00729.0770.0110.0110.0000.0000.0000.000
51A56VAL0-0.056-0.02434.2360.0000.0000.0000.0000.0000.000
52A57VAL00.0290.01036.2130.0050.0050.0000.0000.0000.000
53A58LEU0-0.024-0.00339.1670.0010.0010.0000.0000.0000.000
54A59PRO00.0180.00241.9420.0010.0010.0000.0000.0000.000
55A60ASP-1-0.824-0.90745.125-0.070-0.0700.0000.0000.0000.000
56A61ASP-1-0.866-0.93848.145-0.056-0.0560.0000.0000.0000.000
57A62VAL0-0.043-0.01144.3860.0010.0010.0000.0000.0000.000
58A63ILE0-0.015-0.01143.4350.0000.0000.0000.0000.0000.000
59A64LYS10.8130.89447.2660.0580.0580.0000.0000.0000.000
60A65GLU-1-0.928-0.94649.970-0.053-0.0530.0000.0000.0000.000
61A66ILE0-0.059-0.02144.410-0.001-0.0010.0000.0000.0000.000
62A67PHE0-0.021-0.02045.6590.0010.0010.0000.0000.0000.000
63A68ASN0-0.024-0.01945.756-0.006-0.0060.0000.0000.0000.000
64A69PRO0-0.037-0.00942.8910.0020.0020.0000.0000.0000.000
65A70LEU00.0200.00444.689-0.002-0.0020.0000.0000.0000.000
66A71ILE0-0.038-0.02238.380-0.001-0.0010.0000.0000.0000.000
67A72ASP-1-0.734-0.81437.465-0.108-0.1080.0000.0000.0000.000
68A73LEU0-0.014-0.00437.118-0.006-0.0060.0000.0000.0000.000
69A74SER0-0.085-0.05335.046-0.007-0.0070.0000.0000.0000.000
70A75THR0-0.042-0.04532.858-0.008-0.0080.0000.0000.0000.000
71A76THR0-0.053-0.03232.701-0.004-0.0040.0000.0000.0000.000
72A77GLN0-0.028-0.00827.231-0.011-0.0110.0000.0000.0000.000
73A78TRP00.0230.01131.2520.0010.0010.0000.0000.0000.000
74A79GLY00.0620.02428.671-0.006-0.0060.0000.0000.0000.000
75A80VAL0-0.059-0.02625.5270.0120.0120.0000.0000.0000.000
76A81SER0-0.053-0.05124.855-0.006-0.0060.0000.0000.0000.000
77A82PRO00.0060.03022.1430.0130.0130.0000.0000.0000.000
78A83ALA00.0180.02323.951-0.002-0.0020.0000.0000.0000.000
79A84PHE00.0160.00518.4410.0050.0050.0000.0000.0000.000
80A85ALA0-0.006-0.00216.5570.0010.0010.0000.0000.0000.000
81A86ILE0-0.0010.01912.1570.0110.0110.0000.0000.0000.000
82A87GLU-1-0.792-0.8579.277-0.757-0.7570.0000.0000.0000.000
83A88ASN0-0.006-0.0125.246-0.211-0.2110.0000.0000.0000.000
84A89THR0-0.047-0.0504.652-0.205-0.085-0.001-0.012-0.1070.000
85A90GLU-1-0.826-0.9002.031-18.848-16.6317.758-4.722-5.253-0.058
86A91THR0-0.040-0.0413.9940.3310.4710.003-0.042-0.1010.000
87A92HIS10.8170.9047.0531.5321.5320.0000.0000.0000.000
88A93LYS10.8740.9649.5880.8800.8800.0000.0000.0000.000
89A94ILE0-0.044-0.04211.164-0.049-0.0490.0000.0000.0000.000
90A95LEU00.0060.02013.9590.0440.0440.0000.0000.0000.000
91A96PHE00.018-0.01116.4300.0160.0160.0000.0000.0000.000
92A97GLY00.0330.00719.3170.0090.0090.0000.0000.0000.000
93A98GLU-1-0.855-0.92721.742-0.147-0.1470.0000.0000.0000.000
94A99ILE00.0300.03023.9310.0040.0040.0000.0000.0000.000
95A100LYS10.7370.84627.2690.1280.1280.0000.0000.0000.000
96A101ARG10.8720.91426.9450.1040.1040.0000.0000.0000.000
97A102GLN0-0.024-0.02432.909-0.002-0.0020.0000.0000.0000.000
98A103ASP-1-0.801-0.88436.457-0.042-0.0420.0000.0000.0000.000
99A104GLY0-0.027-0.03239.304-0.003-0.0030.0000.0000.0000.000
100A105TRP0-0.073-0.02840.7320.0020.0020.0000.0000.0000.000
101A106VAL00.006-0.00539.561-0.001-0.0010.0000.0000.0000.000
102A107GLU-1-0.775-0.86041.807-0.023-0.0230.0000.0000.0000.000
103A108GLY0-0.013-0.00945.106-0.001-0.0010.0000.0000.0000.000
104A109LYS10.7670.86941.2550.0360.0360.0000.0000.0000.000
105A110ASP-1-0.753-0.84847.364-0.027-0.0270.0000.0000.0000.000
106A111PRO0-0.006-0.01647.142-0.002-0.0020.0000.0000.0000.000
107A112SER0-0.073-0.06146.935-0.003-0.0030.0000.0000.0000.000
108A113ALA00.0000.00044.549-0.002-0.0020.0000.0000.0000.000
109A114GLY00.0400.02642.451-0.003-0.0030.0000.0000.0000.000
110A115ARG10.8700.92343.1670.0390.0390.0000.0000.0000.000
111A116GLY0-0.034-0.00442.024-0.001-0.0010.0000.0000.0000.000
112A117ASN0-0.006-0.03140.0460.0010.0010.0000.0000.0000.000
113A118ALA00.0310.02837.855-0.004-0.0040.0000.0000.0000.000
114A119HIS00.0130.00634.184-0.008-0.0080.0000.0000.0000.000
115A120GLU-1-0.806-0.88834.020-0.074-0.0740.0000.0000.0000.000
116A121ARG10.8930.94633.9550.0900.0900.0000.0000.0000.000
117A122SER0-0.054-0.03829.917-0.007-0.0070.0000.0000.0000.000
118A123CYS00.0240.00930.293-0.009-0.0090.0000.0000.0000.000
119A124LYS10.9260.97830.1170.1320.1320.0000.0000.0000.000
120A125LEU0-0.0150.00025.282-0.003-0.0030.0000.0000.0000.000
121A126PHE00.0450.02727.881-0.011-0.0110.0000.0000.0000.000
122A127THR0-0.039-0.01830.2490.0030.0030.0000.0000.0000.000
123A128PRO00.0560.01530.073-0.011-0.0110.0000.0000.0000.000
124A129GLY0-0.019-0.00429.834-0.008-0.0080.0000.0000.0000.000
125A130LEU0-0.015-0.01427.392-0.012-0.0120.0000.0000.0000.000
126A131LEU00.0430.03725.645-0.019-0.0190.0000.0000.0000.000
127A132LYS11.0061.00524.5360.1350.1350.0000.0000.0000.000
128A133ALA0-0.0060.01024.251-0.018-0.0180.0000.0000.0000.000
129A134TYR00.029-0.00521.465-0.019-0.0190.0000.0000.0000.000
130A135ARG10.7390.84419.9190.1900.1900.0000.0000.0000.000
131A136THR0-0.052-0.03119.512-0.029-0.0290.0000.0000.0000.000
132A137ILE0-0.057-0.03618.889-0.032-0.0320.0000.0000.0000.000
133A138GLY00.0250.02716.020-0.033-0.0330.0000.0000.0000.000
134A139GLY00.0410.02115.066-0.071-0.0710.0000.0000.0000.000
135A140ILE0-0.029-0.01115.387-0.001-0.0010.0000.0000.0000.000
136A141ASN0-0.048-0.04717.4190.0730.0730.0000.0000.0000.000
137A142ASP-1-0.852-0.90818.256-0.195-0.1950.0000.0000.0000.000
138A143GLU-1-0.786-0.88720.281-0.176-0.1760.0000.0000.0000.000
139A144GLU-1-0.880-0.88820.305-0.118-0.1180.0000.0000.0000.000
140A145ILE0-0.077-0.02318.5170.0110.0110.0000.0000.0000.000
141A146LEU00.0240.02221.988-0.010-0.0100.0000.0000.0000.000
142A147PRO0-0.013-0.00419.879-0.014-0.0140.0000.0000.0000.000
143A148PHE0-0.024-0.02420.210-0.019-0.0190.0000.0000.0000.000
144A149TRP0-0.0040.00118.4770.0010.0010.0000.0000.0000.000
145A150VAL0-0.040-0.01722.129-0.002-0.0020.0000.0000.0000.000
146A151VAL00.0390.02522.7520.0110.0110.0000.0000.0000.000
147A152PHE00.016-0.00525.8300.0030.0030.0000.0000.0000.000
148A153GLU-1-0.763-0.87027.304-0.093-0.0930.0000.0000.0000.000
149A154GLY00.0580.03030.8470.0010.0010.0000.0000.0000.000
150A155ASP-1-0.735-0.86534.371-0.038-0.0380.0000.0000.0000.000
151A156ILE0-0.0240.00133.8680.0020.0020.0000.0000.0000.000
152A157THR0-0.033-0.03730.9690.0010.0010.0000.0000.0000.000
153A158ARG10.7600.84733.7890.0320.0320.0000.0000.0000.000
154A159ASP-1-0.741-0.84636.771-0.040-0.0400.0000.0000.0000.000
155A160PRO0-0.0010.00938.833-0.002-0.0020.0000.0000.0000.000
156A161LYS10.9280.97540.8550.0410.0410.0000.0000.0000.000
157A162ARG10.8410.89337.5520.0530.0530.0000.0000.0000.000
158A163VAL00.0210.02034.004-0.004-0.0040.0000.0000.0000.000
159A164ARG10.8970.93935.1690.0300.0300.0000.0000.0000.000
160A165GLU-1-0.821-0.88337.135-0.061-0.0610.0000.0000.0000.000
161A166ILE00.0090.00831.426-0.003-0.0030.0000.0000.0000.000
162A167THR0-0.046-0.03532.416-0.003-0.0030.0000.0000.0000.000
163A168PHE0-0.021-0.00433.365-0.002-0.0020.0000.0000.0000.000
164A169TRP0-0.003-0.01733.215-0.004-0.0040.0000.0000.0000.000
165A170TYR00.0020.00126.776-0.010-0.0100.0000.0000.0000.000
166A171ASP-1-0.809-0.86430.023-0.079-0.0790.0000.0000.0000.000
167A172HIS10.8130.89327.7510.0980.0980.0000.0000.0000.000
168A173TYR0-0.013-0.01224.9360.0010.0010.0000.0000.0000.000
169A174GLN0-0.022-0.03726.328-0.007-0.0070.0000.0000.0000.000
170A175ASP-1-0.772-0.87321.743-0.098-0.0980.0000.0000.0000.000
171A176ASN0-0.007-0.00521.642-0.004-0.0040.0000.0000.0000.000
172A177TYR0-0.043-0.02723.731-0.004-0.0040.0000.0000.0000.000
173A178PHE00.0140.00623.6580.0000.0000.0000.0000.0000.000
174A179MET0-0.0100.00925.7690.0000.0000.0000.0000.0000.000
175A180TRP0-0.0060.00224.4510.0010.0010.0000.0000.0000.000
176A181ARG10.8670.92427.9350.0450.0450.0000.0000.0000.000
177A182PRO00.004-0.01430.5950.0010.0010.0000.0000.0000.000
178A183ASN0-0.001-0.00331.6930.0040.0040.0000.0000.0000.000
179A184GLU-1-0.794-0.86227.471-0.015-0.0150.0000.0000.0000.000
180A185SER0-0.030-0.02124.344-0.008-0.0080.0000.0000.0000.000
181A186GLY00.0550.01322.411-0.005-0.0050.0000.0000.0000.000
182A187GLU-1-0.897-0.94319.806-0.006-0.0060.0000.0000.0000.000
183A188LYS10.8680.91520.0230.0070.0070.0000.0000.0000.000
184A189LEU0-0.0280.00120.380-0.008-0.0080.0000.0000.0000.000
185A190VAL00.001-0.00815.159-0.022-0.0220.0000.0000.0000.000
186A191GLN0-0.029-0.01516.851-0.026-0.0260.0000.0000.0000.000
187A192HIS00.0250.02318.3370.0070.0070.0000.0000.0000.000
188A193PHE00.0450.00711.606-0.014-0.0140.0000.0000.0000.000
189A194ASN0-0.070-0.04513.124-0.062-0.0620.0000.0000.0000.000
190A195GLU-1-0.850-0.92614.378-0.047-0.0470.0000.0000.0000.000
191A196LYS10.7790.90017.0970.0850.0850.0000.0000.0000.000
192A197LEU0-0.013-0.00616.296-0.016-0.0160.0000.0000.0000.000
193A198LYS10.8370.9149.5530.1990.1990.0000.0000.0000.000
194A199LYS10.8900.93911.0650.0470.0470.0000.0000.0000.000
195A200TYR0-0.008-0.03411.966-0.077-0.0770.0000.0000.0000.000
196A201LEU0-0.009-0.00410.137-0.025-0.0250.0000.0000.0000.000
197A202ASP-1-0.822-0.8726.521-1.888-1.8880.0000.0000.0000.000