FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 7MM2K

Calculation Name: 3LYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYP

Chain ID: A

ChEMBL ID:

UniProt ID: Q4K6H7

Base Structure: X-ray

Registration Date: 2023-09-27

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2366604.92191
FMO2-HF: Nuclear repulsion 2286524.497356
FMO2-HF: Total energy -80080.424554
FMO2-MP2: Total energy -80314.917982


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:8:ARG)


Summations of interaction energy for fragment #1(A:8:ARG)
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.
-174.1-166.07815.69-11.912-11.796-0.103
Interaction energy analysis for fragmet #1(A:8:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.899 / q_NPA : 0.936
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].
3A10ALA00.0330.0163.260-10.397-7.5900.057-1.420-1.443-0.001
4A11CYS0-0.013-0.0115.5024.8244.8240.0000.0000.0000.000
5A12TYR00.0010.0158.2191.0601.0600.0000.0000.0000.000
6A13SER00.0580.00411.8760.7530.7530.0000.0000.0000.000
7A14ASP-1-0.794-0.89214.473-15.233-15.2330.0000.0000.0000.000
8A15PRO0-0.057-0.03517.219-0.203-0.2030.0000.0000.0000.000
9A16ALA00.0970.04818.1540.2980.2980.0000.0000.0000.000
10A17ASP-1-0.747-0.84220.031-14.760-14.7600.0000.0000.0000.000
11A18HIS0-0.080-0.05719.670-1.213-1.2130.0000.0000.0000.000
12A19TYR0-0.051-0.05420.035-0.498-0.4980.0000.0000.0000.000
13A20SER0-0.025-0.04315.835-1.327-1.3270.0000.0000.0000.000
14A21HIS0-0.0030.01515.167-0.712-0.7120.0000.0000.0000.000
15A22ARG10.8750.92416.04713.58813.5880.0000.0000.0000.000
16A23VAL00.0080.00511.427-0.514-0.5140.0000.0000.0000.000
17A24ARG10.7590.83711.38017.79817.7980.0000.0000.0000.000
18A25ILE00.0040.00711.984-1.023-1.0230.0000.0000.0000.000
19A26VAL00.0150.00611.720-0.503-0.5030.0000.0000.0000.000
20A27LEU0-0.041-0.0266.732-1.339-1.3390.0000.0000.0000.000
21A28ALA0-0.0060.0018.747-2.328-2.3280.0000.0000.0000.000
22A29GLU-1-0.789-0.87010.751-17.613-17.6130.0000.0000.0000.000
23A30LYS10.7160.8459.12821.88221.8820.0000.0000.0000.000
24A31GLY00.0120.0348.461-0.845-0.8450.0000.0000.0000.000
25A32VAL0-0.031-0.0304.398-2.200-2.083-0.001-0.018-0.0970.000
26A33SER0-0.023-0.0142.616-17.874-14.7760.991-1.899-2.190-0.016
27A34ALA0-0.0240.0071.750-35.007-38.11514.244-6.507-4.628-0.069
28A35GLU-1-0.900-0.9392.908-58.884-55.6590.181-1.359-2.047-0.012
29A36ILE0-0.010-0.0085.1373.8873.907-0.001-0.001-0.0170.000
30A37ILE0-0.011-0.0116.9561.6961.6960.0000.0000.0000.000
31A38SER00.000-0.01110.7101.1311.1310.0000.0000.0000.000
32A39VAL0-0.072-0.04514.3360.3500.3500.0000.0000.0000.000
33A40GLU-1-0.841-0.91716.878-13.245-13.2450.0000.0000.0000.000
34A41ALA0-0.054-0.01419.5820.7620.7620.0000.0000.0000.000
35A42GLY00.0560.01920.851-0.229-0.2290.0000.0000.0000.000
36A43ARG10.8420.89918.54013.94213.9420.0000.0000.0000.000
37A44GLN00.0220.02317.792-0.381-0.3810.0000.0000.0000.000
38A45PRO00.0610.03713.2340.4980.4980.0000.0000.0000.000
39A46PRO00.018-0.00614.702-0.084-0.0840.0000.0000.0000.000
40A47LYS10.8790.9367.47122.21322.2130.0000.0000.0000.000
41A48LEU00.0030.00411.305-0.590-0.5900.0000.0000.0000.000
42A49ILE0-0.003-0.00612.6620.2970.2970.0000.0000.0000.000
43A50GLU-1-0.914-0.92511.234-19.053-19.0530.0000.0000.0000.000
44A51VAL0-0.027-0.0139.3670.2340.2340.0000.0000.0000.000
45A52ASN00.001-0.01412.7781.0701.0700.0000.0000.0000.000
46A53PRO00.0050.01015.4540.2310.2310.0000.0000.0000.000
47A54TYR0-0.032-0.01318.7650.6950.6950.0000.0000.0000.000
48A55GLY0-0.022-0.00617.3100.3330.3330.0000.0000.0000.000
49A56SER0-0.0010.01018.0660.2270.2270.0000.0000.0000.000
50A57LEU0-0.039-0.00115.305-1.219-1.2190.0000.0000.0000.000
51A58PRO00.0130.00313.9670.8050.8050.0000.0000.0000.000
52A59THR0-0.027-0.03411.2311.2041.2040.0000.0000.0000.000
53A60LEU0-0.029-0.0067.903-1.635-1.6350.0000.0000.0000.000
54A61VAL00.005-0.0145.8642.9502.9500.0000.0000.0000.000
55A62ASP-1-0.756-0.8563.044-55.903-54.6880.192-0.595-0.812-0.005
56A63ARG10.7210.7953.17938.72639.3510.028-0.113-0.5400.000
57A64ASP-1-0.893-0.9235.391-26.090-26.067-0.0010.000-0.0220.000
58A65LEU0-0.0320.0187.6242.0072.0070.0000.0000.0000.000
59A66ALA00.016-0.0038.710-1.596-1.5960.0000.0000.0000.000
60A67LEU0-0.0150.00411.1731.5131.5130.0000.0000.0000.000
61A68TRP00.0420.01013.429-1.244-1.2440.0000.0000.0000.000
62A69GLU-1-0.718-0.83516.151-14.535-14.5350.0000.0000.0000.000
63A70SER0-0.0160.00817.179-0.562-0.5620.0000.0000.0000.000
64A71THR0-0.057-0.08117.370-0.711-0.7110.0000.0000.0000.000
65A72VAL00.0340.02616.814-0.264-0.2640.0000.0000.0000.000
66A73VAL0-0.012-0.00312.313-0.890-0.8900.0000.0000.0000.000
67A74MET0-0.031-0.01913.422-1.240-1.2400.0000.0000.0000.000
68A75GLU-1-0.756-0.84214.858-15.023-15.0230.0000.0000.0000.000
69A76TYR00.0280.0219.290-0.167-0.1670.0000.0000.0000.000
70A77LEU0-0.028-0.0248.443-1.244-1.2440.0000.0000.0000.000
71A78ASP-1-0.812-0.90911.439-18.699-18.6990.0000.0000.0000.000
72A79GLU-1-0.971-0.98214.215-15.865-15.8650.0000.0000.0000.000
73A80ARG10.8620.9497.54430.92930.9290.0000.0000.0000.000
74A81TYR0-0.025-0.0225.557-3.006-3.0060.0000.0000.0000.000
75A82PRO00.0390.02210.5490.7160.7160.0000.0000.0000.000
76A83HIS0-0.0270.02212.9411.5291.5290.0000.0000.0000.000
77A84PRO00.0490.01312.326-1.668-1.6680.0000.0000.0000.000
78A85PRO00.0250.01315.407-0.737-0.7370.0000.0000.0000.000
79A86LEU00.0120.00914.4390.5030.5030.0000.0000.0000.000
80A87LEU0-0.010-0.00118.3190.8060.8060.0000.0000.0000.000
81A88PRO00.0020.00221.157-0.031-0.0310.0000.0000.0000.000
82A89VAL00.0590.02822.935-0.280-0.2800.0000.0000.0000.000
83A90TYR00.0070.00024.6910.0600.0600.0000.0000.0000.000
84A91PRO00.0450.00727.862-0.093-0.0930.0000.0000.0000.000
85A92VAL00.0390.02129.161-0.090-0.0900.0000.0000.0000.000
86A93ALA00.0110.00628.413-0.008-0.0080.0000.0000.0000.000
87A94ARG10.9630.99620.46213.88513.8850.0000.0000.0000.000
88A95ALA0-0.0060.00326.471-0.234-0.2340.0000.0000.0000.000
89A96ASN00.015-0.00529.0290.1300.1300.0000.0000.0000.000
90A97SER00.0150.00624.7460.0270.0270.0000.0000.0000.000
91A98ARG10.8330.87121.81013.28513.2850.0000.0000.0000.000
92A99LEU0-0.018-0.00626.3090.0230.0230.0000.0000.0000.000
93A100LEU0-0.006-0.00927.9910.1920.1920.0000.0000.0000.000
94A101ILE00.0380.02322.1910.1120.1120.0000.0000.0000.000
95A102HIS00.0040.00526.304-0.173-0.1730.0000.0000.0000.000
96A103ARG10.8920.93928.7869.3999.3990.0000.0000.0000.000
97A104ILE00.0270.02626.4060.2180.2180.0000.0000.0000.000
98A105GLN00.0420.00825.574-0.335-0.3350.0000.0000.0000.000
99A106ARG10.8550.91228.3808.9748.9740.0000.0000.0000.000
100A107ASP-1-0.860-0.92332.028-8.930-8.9300.0000.0000.0000.000
101A108TRP0-0.020-0.03229.4030.0880.0880.0000.0000.0000.000
102A109CYS0-0.0200.00426.693-0.172-0.1720.0000.0000.0000.000
103A110GLY00.0380.03828.892-0.023-0.0230.0000.0000.0000.000
104A111GLN0-0.018-0.02631.8010.1400.1400.0000.0000.0000.000
105A112VAL0-0.017-0.00927.1570.1420.1420.0000.0000.0000.000
106A113ASP-1-0.757-0.84927.526-11.753-11.7530.0000.0000.0000.000
107A114LEU0-0.025-0.00330.1830.1530.1530.0000.0000.0000.000
108A115ILE0-0.041-0.02332.8070.2430.2430.0000.0000.0000.000
109A116LEU00.0220.00227.3500.1370.1370.0000.0000.0000.000
110A117ASP-1-0.772-0.81431.413-9.815-9.8150.0000.0000.0000.000
111A118PRO00.0360.01531.7130.3820.3820.0000.0000.0000.000
112A119ARG10.7700.83933.1029.7669.7660.0000.0000.0000.000
113A120THR0-0.056-0.02935.7930.3230.3230.0000.0000.0000.000
114A121LYS10.9540.97138.4007.1537.1530.0000.0000.0000.000
115A122GLU-1-0.695-0.83239.602-8.310-8.3100.0000.0000.0000.000
116A123ALA0-0.003-0.01041.763-0.037-0.0370.0000.0000.0000.000
117A124ALA0-0.004-0.00740.8470.0280.0280.0000.0000.0000.000
118A125ARG10.8550.92535.6208.6838.6830.0000.0000.0000.000
119A126VAL0-0.035-0.01538.759-0.101-0.1010.0000.0000.0000.000
120A127GLN0-0.061-0.04941.1170.0690.0690.0000.0000.0000.000
121A128ALA00.0680.03836.440-0.010-0.0100.0000.0000.0000.000
122A129ARG10.8140.90036.2068.4168.4160.0000.0000.0000.000
123A130LYS10.8140.90437.7157.1507.1500.0000.0000.0000.000
124A131GLU-1-0.833-0.89738.971-7.893-7.8930.0000.0000.0000.000
125A132LEU00.0090.01431.612-0.030-0.0300.0000.0000.0000.000
126A133ARG10.9110.95535.9117.6777.6770.0000.0000.0000.000
127A134GLU-1-0.817-0.88637.425-7.362-7.3620.0000.0000.0000.000
128A135SER0-0.0100.01836.183-0.039-0.0390.0000.0000.0000.000
129A136LEU00.012-0.00431.338-0.032-0.0320.0000.0000.0000.000
130A137THR0-0.023-0.03835.275-0.006-0.0060.0000.0000.0000.000
131A138GLY0-0.026-0.00138.3430.0980.0980.0000.0000.0000.000
132A139VAL0-0.0100.00433.6000.0940.0940.0000.0000.0000.000
133A140SER0-0.030-0.02435.278-0.090-0.0900.0000.0000.0000.000
134A141PRO0-0.011-0.01236.220-0.122-0.1220.0000.0000.0000.000
135A142LEU00.0310.02334.684-0.005-0.0050.0000.0000.0000.000
136A143PHE0-0.071-0.03828.935-0.207-0.2070.0000.0000.0000.000
137A144ALA0-0.048-0.02233.677-0.111-0.1110.0000.0000.0000.000
138A145ASP-1-0.927-0.95035.337-8.329-8.3290.0000.0000.0000.000
139A146LYS10.7870.88330.6109.4969.4960.0000.0000.0000.000
140A147PRO0-0.0100.01628.1430.0160.0160.0000.0000.0000.000
141A148PHE00.0280.02222.924-0.375-0.3750.0000.0000.0000.000
142A149PHE0-0.004-0.02026.4470.5230.5230.0000.0000.0000.000
143A150LEU0-0.030-0.01727.860-0.130-0.1300.0000.0000.0000.000
144A151SER0-0.037-0.03824.9180.0840.0840.0000.0000.0000.000
145A152GLU-1-0.814-0.91727.797-9.906-9.9060.0000.0000.0000.000
146A153GLU-1-0.952-0.96222.278-13.315-13.3150.0000.0000.0000.000
147A154GLN00.0070.02918.6010.9200.9200.0000.0000.0000.000
148A155SER0-0.004-0.01520.150-0.287-0.2870.0000.0000.0000.000
149A156LEU00.053-0.00416.283-0.104-0.1040.0000.0000.0000.000
150A157VAL00.0020.00719.9660.1090.1090.0000.0000.0000.000
151A158ASP-1-0.717-0.83021.676-12.627-12.6270.0000.0000.0000.000
152A159CYS0-0.058-0.01317.738-0.306-0.3060.0000.0000.0000.000
153A160CYS0-0.039-0.01619.691-0.293-0.2930.0000.0000.0000.000
154A161LEU0-0.002-0.00122.1490.3360.3360.0000.0000.0000.000
155A162LEU00.000-0.00420.6460.3360.3360.0000.0000.0000.000
156A163PRO00.0110.01519.7130.3750.3750.0000.0000.0000.000
157A164ILE00.0140.00522.4060.3610.3610.0000.0000.0000.000
158A165LEU00.013-0.00626.0400.3990.3990.0000.0000.0000.000
159A166TRP0-0.010-0.01523.5420.4190.4190.0000.0000.0000.000
160A167ARG10.7940.86620.61814.45114.4510.0000.0000.0000.000
161A168LEU0-0.0150.00227.3120.3550.3550.0000.0000.0000.000
162A169PRO00.0410.01729.4500.2950.2950.0000.0000.0000.000
163A170VAL00.0150.01427.6890.2900.2900.0000.0000.0000.000
164A171LEU0-0.037-0.00529.0630.1710.1710.0000.0000.0000.000
165A172GLY0-0.003-0.00132.4500.3000.3000.0000.0000.0000.000
166A173ILE0-0.077-0.04233.3510.3360.3360.0000.0000.0000.000
167A174GLU-1-0.902-0.94634.681-8.499-8.4990.0000.0000.0000.000
168A175LEU0-0.044-0.02833.1690.2200.2200.0000.0000.0000.000
169A176PRO00.0340.02637.2580.1080.1080.0000.0000.0000.000
170A177ARG11.0150.98239.4487.3697.3690.0000.0000.0000.000
171A178GLN0-0.026-0.01640.775-0.117-0.1170.0000.0000.0000.000
172A179ALA00.0140.01436.636-0.001-0.0010.0000.0000.0000.000
173A180LYS10.8440.89636.3088.2418.2410.0000.0000.0000.000
174A181PRO00.0530.03435.605-0.201-0.2010.0000.0000.0000.000
175A182LEU00.0010.00830.603-0.289-0.2890.0000.0000.0000.000
176A183LEU00.000-0.01331.408-0.346-0.3460.0000.0000.0000.000
177A184ASP-1-0.779-0.86931.722-9.105-9.1050.0000.0000.0000.000
178A185TYR0-0.097-0.07925.213-0.342-0.3420.0000.0000.0000.000
179A186MET0-0.050-0.01827.326-0.344-0.3440.0000.0000.0000.000
180A187GLU-1-0.958-0.96126.877-10.189-10.1890.0000.0000.0000.000
181A188ARG10.8610.92627.01610.24510.2450.0000.0000.0000.000
182A189GLN0-0.006-0.02822.697-0.847-0.8470.0000.0000.0000.000
183A190PHE0-0.033-0.02622.181-0.620-0.6200.0000.0000.0000.000
184A191ALA00.0120.01822.401-0.456-0.4560.0000.0000.0000.000
185A192ARG10.7710.87118.03015.51215.5120.0000.0000.0000.000
186A193GLU-1-0.892-0.95215.551-18.356-18.3560.0000.0000.0000.000
187A194ALA00.0280.02014.442-0.700-0.7000.0000.0000.0000.000
188A195PHE00.0340.01914.985-0.678-0.6780.0000.0000.0000.000
189A196GLN00.0190.01317.351-0.423-0.4230.0000.0000.0000.000
190A197ALA00.0070.00212.416-0.090-0.0900.0000.0000.0000.000
191A198SER0-0.074-0.04113.258-0.909-0.9090.0000.0000.0000.000
192A199LEU0-0.074-0.01214.307-0.103-0.1030.0000.0000.0000.000
193A200SER00.007-0.01716.398-0.420-0.4200.0000.0000.0000.000
194A201GLY00.004-0.01517.3140.7790.7790.0000.0000.0000.000
195A202VAL00.0800.03420.1350.5760.5760.0000.0000.0000.000
196A203GLU-1-0.702-0.80818.330-16.384-16.3840.0000.0000.0000.000
197A204ARG10.8200.91317.90816.55316.5530.0000.0000.0000.000
198A205ASP-1-0.886-0.93322.996-12.217-12.2170.0000.0000.0000.000
199A206MET0-0.139-0.04823.4170.5460.5460.0000.0000.0000.000
200A207ARG10.8090.90726.22711.62811.6280.0000.0000.0000.000