Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Z69KN

Calculation Name: 3DMP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMP

Chain ID: A

ChEMBL ID:

UniProt ID: Q63VS8

Base Structure: X-ray

Registration Date: 2023-06-26

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2478954.905889
FMO2-HF: Nuclear repulsion 2395796.948702
FMO2-HF: Total energy -83157.957187
FMO2-MP2: Total energy -83401.578315


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-14.287-6.5390.204-4.014-3.938-0.019
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.004
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].
3A2LYS10.9290.9923.8152.0664.819-0.027-1.510-1.2160.001
4A3GLN0-0.015-0.0186.8520.2330.2330.0000.0000.0000.000
5A4ASP-1-0.779-0.8499.898-0.619-0.6190.0000.0000.0000.000
6A5SER00.003-0.01413.5910.0510.0510.0000.0000.0000.000
7A6ARG10.8130.88215.9920.6470.6470.0000.0000.0000.000
8A7PHE0-0.026-0.01715.2750.0350.0350.0000.0000.0000.000
9A8PRO00.0240.02014.300-0.095-0.0950.0000.0000.0000.000
10A9ASN0-0.021-0.02413.7150.0100.0100.0000.0000.0000.000
11A10LEU0-0.0030.01412.382-0.036-0.0360.0000.0000.0000.000
12A11PHE0-0.031-0.0207.7040.0220.0220.0000.0000.0000.000
13A12ILE0-0.018-0.0057.9760.1220.1220.0000.0000.0000.000
14A13LEU00.0020.0014.888-1.438-1.387-0.001-0.025-0.0240.000
15A14ASP-1-0.848-0.9343.064-9.460-8.1710.051-0.708-0.633-0.006
16A15HIS00.0840.0523.0910.2421.0410.038-0.224-0.6130.000
17A16PRO00.0440.0064.0790.7000.8080.003-0.026-0.0860.000
18A17LEU0-0.014-0.0197.4160.2160.2160.0000.0000.0000.000
19A18ILE00.0090.0245.4350.3110.3110.0000.0000.0000.000
20A19GLN0-0.014-0.0256.2950.9220.9220.0000.0000.0000.000
21A20HIS0-0.0090.0029.8860.2450.2450.0000.0000.0000.000
22A21LYS10.8860.91912.0520.8450.8450.0000.0000.0000.000
23A22LEU00.0370.01712.1090.1260.1260.0000.0000.0000.000
24A23THR0-0.025-0.00314.0410.1350.1350.0000.0000.0000.000
25A24HIS0-0.016-0.00816.1670.1370.1370.0000.0000.0000.000
26A25MET0-0.0180.03515.3320.0800.0800.0000.0000.0000.000
27A26ARG10.7560.83314.2121.0061.0060.0000.0000.0000.000
28A27ASP-1-0.884-0.91619.763-0.350-0.3500.0000.0000.0000.000
29A28LYS10.9690.97522.3920.3010.3010.0000.0000.0000.000
30A29ASP-1-0.928-0.95925.760-0.270-0.2700.0000.0000.0000.000
31A30THR0-0.123-0.07721.7680.0310.0310.0000.0000.0000.000
32A31SER00.005-0.00724.825-0.001-0.0010.0000.0000.0000.000
33A32THR00.0760.02225.378-0.017-0.0170.0000.0000.0000.000
34A33ARG10.9200.95925.6680.2120.2120.0000.0000.0000.000
35A34THR00.0120.00021.3570.0020.0020.0000.0000.0000.000
36A35PHE00.0350.03121.273-0.038-0.0380.0000.0000.0000.000
37A36ARG10.8890.93820.6900.2510.2510.0000.0000.0000.000
38A37GLU-1-0.886-0.92920.536-0.384-0.3840.0000.0000.0000.000
39A38LEU00.0250.00416.202-0.029-0.0290.0000.0000.0000.000
40A39LEU00.0080.01115.954-0.105-0.1050.0000.0000.0000.000
41A40ARG10.8270.91916.3860.2780.2780.0000.0000.0000.000
42A41GLU-1-0.820-0.92514.600-0.599-0.5990.0000.0000.0000.000
43A42ILE0-0.008-0.00110.934-0.077-0.0770.0000.0000.0000.000
44A43THR0-0.006-0.00711.045-0.192-0.1920.0000.0000.0000.000
45A44LEU00.0330.04112.377-0.038-0.0380.0000.0000.0000.000
46A45LEU0-0.036-0.0348.2380.0310.0310.0000.0000.0000.000
47A46MET0-0.034-0.0108.019-0.193-0.1930.0000.0000.0000.000
48A47GLY00.0520.0078.851-0.001-0.0010.0000.0000.0000.000
49A48TYR0-0.0320.0137.3510.3290.3290.0000.0000.0000.000
50A49GLU-1-0.893-0.9513.171-6.007-3.3590.141-1.520-1.269-0.014
51A50ILE0-0.069-0.0146.2740.5600.5600.0000.0000.0000.000
52A51THR0-0.060-0.0678.7560.2620.2620.0000.0000.0000.000
53A52ARG10.8950.9524.341-1.533-1.433-0.001-0.001-0.0970.000
54A53ASN0-0.031-0.0149.5990.2360.2360.0000.0000.0000.000
55A54LEU0-0.0070.00112.317-0.076-0.0760.0000.0000.0000.000
56A55PRO0-0.0120.00015.2030.0560.0560.0000.0000.0000.000
57A56ILE0-0.0070.00417.621-0.041-0.0410.0000.0000.0000.000
58A57THR0-0.038-0.01520.261-0.002-0.0020.0000.0000.0000.000
59A58THR00.0120.00023.8510.0080.0080.0000.0000.0000.000
60A59LYS10.9220.97826.558-0.076-0.0760.0000.0000.0000.000
61A60ARG10.9080.95429.013-0.107-0.1070.0000.0000.0000.000
62A61VAL0-0.040-0.02828.954-0.012-0.0120.0000.0000.0000.000
63A62GLU-1-0.909-0.94331.9100.0810.0810.0000.0000.0000.000
64A63THR0-0.048-0.01530.427-0.007-0.0070.0000.0000.0000.000
65A64PRO00.000-0.02432.910-0.003-0.0030.0000.0000.0000.000
66A65LEU0-0.041-0.01033.186-0.002-0.0020.0000.0000.0000.000
67A66VAL0-0.0050.00433.413-0.001-0.0010.0000.0000.0000.000
68A67GLU-1-0.871-0.93334.2920.0940.0940.0000.0000.0000.000
69A68ILE0-0.045-0.02828.1430.0110.0110.0000.0000.0000.000
70A69ASP-1-0.831-0.91729.1530.1410.1410.0000.0000.0000.000
71A70ALA0-0.007-0.01025.9590.0230.0230.0000.0000.0000.000
72A71PRO00.0090.00320.970-0.016-0.0160.0000.0000.0000.000
73A72VAL0-0.031-0.01722.049-0.022-0.0220.0000.0000.0000.000
74A73ILE00.0960.03816.5630.0200.0200.0000.0000.0000.000
75A74ALA0-0.036-0.02120.906-0.022-0.0220.0000.0000.0000.000
76A75GLY00.0520.02120.898-0.015-0.0150.0000.0000.0000.000
77A76LYS10.9750.97521.946-0.009-0.0090.0000.0000.0000.000
78A77LYS10.8870.96322.454-0.055-0.0550.0000.0000.0000.000
79A78LEU00.0730.03616.9420.0010.0010.0000.0000.0000.000
80A79ALA0-0.034-0.01121.4250.0090.0090.0000.0000.0000.000
81A80ILE00.0290.03818.181-0.025-0.0250.0000.0000.0000.000
82A81VAL0-0.032-0.04021.1320.0370.0370.0000.0000.0000.000
83A82PRO0-0.0010.01722.385-0.035-0.0350.0000.0000.0000.000
84A83VAL00.0110.01722.6880.0460.0460.0000.0000.0000.000
85A84LEU0-0.075-0.02424.967-0.014-0.0140.0000.0000.0000.000
86A85ARG10.9650.95427.7970.2600.2600.0000.0000.0000.000
87A86ALA00.0570.00723.8290.0050.0050.0000.0000.0000.000
88A87GLY00.0600.03721.647-0.030-0.0300.0000.0000.0000.000
89A88VAL0-0.045-0.02821.777-0.015-0.0150.0000.0000.0000.000
90A89GLY00.0400.01621.7990.0070.0070.0000.0000.0000.000
91A90MET0-0.049-0.01115.3900.0020.0020.0000.0000.0000.000
92A91SER00.0370.00418.202-0.004-0.0040.0000.0000.0000.000
93A92ASP-1-0.863-0.93020.512-0.297-0.2970.0000.0000.0000.000
94A93GLY00.0490.03617.0110.0310.0310.0000.0000.0000.000
95A94LEU0-0.005-0.01814.1770.0230.0230.0000.0000.0000.000
96A95LEU0-0.035-0.01617.1830.0560.0560.0000.0000.0000.000
97A96GLU-1-0.984-0.97618.485-0.263-0.2630.0000.0000.0000.000
98A97LEU0-0.049-0.01412.8230.0510.0510.0000.0000.0000.000
99A98ILE0-0.067-0.04215.4370.0790.0790.0000.0000.0000.000
100A99PRO00.0640.03919.269-0.004-0.0040.0000.0000.0000.000
101A100SER0-0.132-0.06622.8090.0100.0100.0000.0000.0000.000
102A101ALA00.0120.01721.1630.0170.0170.0000.0000.0000.000
103A102ARG10.8960.94823.3030.0760.0760.0000.0000.0000.000
104A103VAL00.0480.02924.151-0.017-0.0170.0000.0000.0000.000
105A104GLY0-0.047-0.02025.3640.0240.0240.0000.0000.0000.000
106A105HIS0-0.003-0.01326.122-0.031-0.0310.0000.0000.0000.000
107A106ILE00.0190.01025.5330.0250.0250.0000.0000.0000.000
108A107GLY00.006-0.00127.937-0.022-0.0220.0000.0000.0000.000
109A108VAL00.043-0.05429.1950.0210.0210.0000.0000.0000.000
110A109TYR0-0.0070.00029.550-0.006-0.0060.0000.0000.0000.000
111A110ARG10.9281.03031.1940.1680.1680.0000.0000.0000.000
112A111ALA0-0.113-0.01531.4710.0150.0150.0000.0000.0000.000
113A112ASP-1-0.869-0.93432.160-0.251-0.2510.0000.0000.0000.000
114A113ASP-1-0.899-0.94732.180-0.239-0.2390.0000.0000.0000.000
115A114HIS0-0.024-0.00833.602-0.003-0.0030.0000.0000.0000.000
116A115ARG10.9680.98234.6820.1550.1550.0000.0000.0000.000
117A116PRO00.0920.02931.183-0.006-0.0060.0000.0000.0000.000
118A117VAL0-0.128-0.07133.0060.0170.0170.0000.0000.0000.000
119A118GLU-1-0.722-0.86532.556-0.170-0.1700.0000.0000.0000.000
120A119TYR0-0.055-0.02831.2170.0150.0150.0000.0000.0000.000
121A120LEU0-0.029-0.01632.3870.0120.0120.0000.0000.0000.000
122A121VAL00.0440.04430.671-0.015-0.0150.0000.0000.0000.000
123A122ARG10.8480.91730.9590.1540.1540.0000.0000.0000.000
124A123LEU00.0620.03827.153-0.016-0.0160.0000.0000.0000.000
125A124PRO0-0.006-0.00226.4210.0130.0130.0000.0000.0000.000
126A125ASP-1-0.877-0.94629.616-0.070-0.0700.0000.0000.0000.000
127A126LEU00.012-0.00128.275-0.007-0.0070.0000.0000.0000.000
128A127GLU-1-0.924-0.96827.733-0.052-0.0520.0000.0000.0000.000
129A128ASP-1-0.992-0.98526.1680.0220.0220.0000.0000.0000.000
130A129ARG10.8140.91423.6390.0880.0880.0000.0000.0000.000
131A130ILE00.0150.01617.473-0.005-0.0050.0000.0000.0000.000
132A131PHE0-0.013-0.01820.8530.0000.0000.0000.0000.0000.000
133A132ILE00.0290.00514.991-0.019-0.0190.0000.0000.0000.000
134A133LEU0-0.008-0.00218.4320.0160.0160.0000.0000.0000.000
135A134CYS0-0.040-0.00617.936-0.081-0.0810.0000.0000.0000.000
136A135ASP-1-0.810-0.94818.665-0.400-0.4000.0000.0000.0000.000
137A136PRO00.0320.01318.038-0.076-0.0760.0000.0000.0000.000
138A137MET0-0.0110.00417.944-0.110-0.1100.0000.0000.0000.000
139A138VAL0-0.0030.01118.8430.0560.0560.0000.0000.0000.000
140A139ALA00.0370.00820.817-0.030-0.0300.0000.0000.0000.000
141A140THR00.0910.03123.356-0.011-0.0110.0000.0000.0000.000
142A141GLY00.0710.03223.377-0.001-0.0010.0000.0000.0000.000
143A142TYR00.0200.00524.3710.0020.0020.0000.0000.0000.000
144A143SER00.0220.01225.5600.0170.0170.0000.0000.0000.000
145A144ALA00.0120.01121.4180.0140.0140.0000.0000.0000.000
146A145ALA00.0450.01823.4930.0110.0110.0000.0000.0000.000
147A146HIS00.0050.00625.1960.0310.0310.0000.0000.0000.000
148A147ALA0-0.010-0.01124.2120.0230.0230.0000.0000.0000.000
149A148ILE00.0230.00920.2930.0160.0160.0000.0000.0000.000
150A149ASP-1-0.854-0.93124.800-0.194-0.1940.0000.0000.0000.000
151A150VAL0-0.115-0.04728.2520.0250.0250.0000.0000.0000.000
152A151LEU00.0130.00724.1230.0200.0200.0000.0000.0000.000
153A152LYS10.9591.00124.3180.2310.2310.0000.0000.0000.000
154A153ARG10.8540.93028.3890.1770.1770.0000.0000.0000.000
155A154ARG10.7420.84830.7960.1580.1580.0000.0000.0000.000
156A155GLY00.0150.00931.1150.0090.0090.0000.0000.0000.000
157A156VAL0-0.065-0.02125.1160.0120.0120.0000.0000.0000.000
158A157PRO00.0360.01024.685-0.016-0.0160.0000.0000.0000.000
159A158GLY00.0470.01522.328-0.014-0.0140.0000.0000.0000.000
160A159GLU-1-0.857-0.93620.155-0.119-0.1190.0000.0000.0000.000
161A160ARG10.8070.91419.4060.0830.0830.0000.0000.0000.000
162A161LEU0-0.015-0.01219.883-0.007-0.0070.0000.0000.0000.000
163A162MET0-0.0160.00813.792-0.038-0.0380.0000.0000.0000.000
164A163PHE00.0180.00916.0980.0500.0500.0000.0000.0000.000
165A164LEU0-0.011-0.00711.558-0.113-0.1130.0000.0000.0000.000
166A165ALA00.0270.00914.2620.1310.1310.0000.0000.0000.000
167A166LEU0-0.044-0.01813.527-0.191-0.1910.0000.0000.0000.000
168A167VAL00.018-0.00313.642-0.200-0.2000.0000.0000.0000.000
169A168ALA0-0.0060.00615.9050.1000.1000.0000.0000.0000.000
170A169ALA00.0200.02117.414-0.052-0.0520.0000.0000.0000.000
171A170PRO00.002-0.00918.840-0.006-0.0060.0000.0000.0000.000
172A171GLU-1-0.835-0.93020.297-0.427-0.4270.0000.0000.0000.000
173A172GLY00.0450.02222.3380.0320.0320.0000.0000.0000.000
174A173VAL0-0.059-0.04117.0670.0090.0090.0000.0000.0000.000
175A174GLN0-0.0250.00120.082-0.004-0.0040.0000.0000.0000.000
176A175VAL00.0230.02222.7880.0310.0310.0000.0000.0000.000
177A176PHE0-0.069-0.03618.3770.0240.0240.0000.0000.0000.000
178A177GLN00.020-0.01218.918-0.011-0.0110.0000.0000.0000.000
179A178ASP-1-0.911-0.94821.725-0.240-0.2400.0000.0000.0000.000
180A179ALA0-0.059-0.01325.3450.0280.0280.0000.0000.0000.000
181A180HIS0-0.092-0.07222.0750.0450.0450.0000.0000.0000.000
182A181PRO00.0600.04521.164-0.037-0.0370.0000.0000.0000.000
183A182ASP-1-0.920-0.95819.528-0.168-0.1680.0000.0000.0000.000
184A183VAL0-0.083-0.03718.3140.0150.0150.0000.0000.0000.000
185A184LYS10.9240.97912.3920.1530.1530.0000.0000.0000.000
186A185LEU00.0000.01214.4520.0140.0140.0000.0000.0000.000
187A186TYR00.001-0.0238.384-0.042-0.0420.0000.0000.0000.000
188A187VAL00.0220.01010.3570.1720.1720.0000.0000.0000.000
189A188ALA00.0200.0079.170-0.564-0.5640.0000.0000.0000.000
190A189SER0-0.079-0.0669.542-0.297-0.2970.0000.0000.0000.000
191A190LEU0-0.0270.00011.9370.1260.1260.0000.0000.0000.000
192A191ASP-1-0.736-0.81314.305-0.948-0.9480.0000.0000.0000.000
193A192SER0-0.036-0.07017.0420.0050.0050.0000.0000.0000.000
194A193HIS0-0.0130.03219.9480.0010.0010.0000.0000.0000.000
195A194LEU0-0.033-0.00223.179-0.029-0.0290.0000.0000.0000.000
196A195ASP-1-0.860-0.93025.749-0.324-0.3240.0000.0000.0000.000
197A196ASP-1-0.905-0.96628.634-0.248-0.2480.0000.0000.0000.000
198A197HIS0-0.091-0.04431.1030.0130.0130.0000.0000.0000.000
199A198ALA0-0.0240.00228.413-0.004-0.0040.0000.0000.0000.000
200A199TYR0-0.028-0.03726.040-0.026-0.0260.0000.0000.0000.000
201A200ILE0-0.048-0.02919.469-0.003-0.0030.0000.0000.0000.000
202A201VAL00.0020.04322.6030.0040.0040.0000.0000.0000.000
203A202PRO0-0.007-0.04018.686-0.031-0.0310.0000.0000.0000.000
204A203GLY00.0120.01419.2890.0340.0340.0000.0000.0000.000
205A204LEU00.000-0.02617.523-0.014-0.0140.0000.0000.0000.000
206A205GLY00.0320.03821.4020.0370.0370.0000.0000.0000.000
207A206ASP-1-0.765-0.85424.673-0.355-0.3550.0000.0000.0000.000
208A207ALA00.020-0.00722.9750.0040.0040.0000.0000.0000.000
209A208GLY0-0.020-0.01924.7450.0100.0100.0000.0000.0000.000
210A209ASP-1-0.847-0.92527.798-0.267-0.2670.0000.0000.0000.000
211A210ARG10.7630.86722.5620.4700.4700.0000.0000.0000.000
212A211LEU0-0.047-0.02522.2790.0060.0060.0000.0000.0000.000
213A212PHE0-0.098-0.05926.3340.0170.0170.0000.0000.0000.000
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