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: M99VZ

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2365567.460861
FMO2-HF: Nuclear repulsion 2285487.608168
FMO2-HF: Total energy -80079.852693
FMO2-MP2: Total energy -80314.373209


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.
-150.384-145.67514.909-9.578-10.041-0.092
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 : 0.900 / q_NPA : 0.922
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].
3A10ALA00.0370.0173.323-7.394-5.2870.035-0.969-1.174-0.003
4A11CYS0-0.036-0.0145.6684.3224.3220.0000.0000.0000.000
5A12TYR00.0030.0118.1550.9970.9970.0000.0000.0000.000
6A13SER00.0810.01511.6140.7970.7970.0000.0000.0000.000
7A14ASP-1-0.803-0.90014.629-14.888-14.8880.0000.0000.0000.000
8A15PRO0-0.061-0.03317.318-0.156-0.1560.0000.0000.0000.000
9A16ALA00.0970.04418.2100.2920.2920.0000.0000.0000.000
10A17ASP-1-0.827-0.89820.282-13.713-13.7130.0000.0000.0000.000
11A18HIS0-0.067-0.05519.731-1.218-1.2180.0000.0000.0000.000
12A19TYR0-0.020-0.03120.095-0.540-0.5400.0000.0000.0000.000
13A20SER00.020-0.00215.866-1.314-1.3140.0000.0000.0000.000
14A21HIS00.0250.03015.228-0.780-0.7800.0000.0000.0000.000
15A22ARG10.9000.93816.10313.63613.6360.0000.0000.0000.000
16A23VAL00.0060.00211.525-0.522-0.5220.0000.0000.0000.000
17A24ARG10.7580.84211.43617.47117.4710.0000.0000.0000.000
18A25ILE00.0040.00912.032-1.007-1.0070.0000.0000.0000.000
19A26VAL00.0160.00511.481-0.510-0.5100.0000.0000.0000.000
20A27LEU0-0.036-0.0256.760-1.348-1.3480.0000.0000.0000.000
21A28ALA0-0.0090.0008.671-2.353-2.3530.0000.0000.0000.000
22A29GLU-1-0.796-0.88210.784-17.744-17.7440.0000.0000.0000.000
23A30LYS10.7230.8498.87822.06522.0650.0000.0000.0000.000
24A31GLY00.0180.0368.336-0.923-0.9230.0000.0000.0000.000
25A32VAL0-0.029-0.0264.141-2.367-2.219-0.001-0.033-0.1150.000
26A33SER0-0.034-0.0232.459-19.157-16.4691.785-2.004-2.469-0.019
27A34ALA0-0.0250.0071.768-33.296-35.91312.949-5.961-4.371-0.066
28A35GLU-1-0.910-0.9453.422-41.432-40.6480.015-0.061-0.738-0.001
29A36ILE0-0.004-0.0045.5323.0233.0230.0000.0000.0000.000
30A37ILE0-0.010-0.0116.8261.6571.6570.0000.0000.0000.000
31A38SER00.008-0.01310.9290.8910.8910.0000.0000.0000.000
32A39VAL0-0.076-0.04214.0120.3370.3370.0000.0000.0000.000
33A40GLU-1-0.837-0.91716.653-12.884-12.8840.0000.0000.0000.000
34A41ALA0-0.057-0.01419.3320.7130.7130.0000.0000.0000.000
35A42GLY00.0510.01720.555-0.235-0.2350.0000.0000.0000.000
36A43ARG10.8440.89918.46313.84213.8420.0000.0000.0000.000
37A44GLN00.0210.02817.574-0.335-0.3350.0000.0000.0000.000
38A45PRO00.0650.03912.9680.4700.4700.0000.0000.0000.000
39A46PRO00.019-0.00614.450-0.112-0.1120.0000.0000.0000.000
40A47LYS10.9601.0057.65823.87323.8730.0000.0000.0000.000
41A48LEU00.0000.00411.329-0.688-0.6880.0000.0000.0000.000
42A49ILE0-0.004-0.00712.5600.2360.2360.0000.0000.0000.000
43A50GLU-1-0.980-0.98711.851-18.784-18.7840.0000.0000.0000.000
44A51VAL0-0.041-0.0209.5710.0820.0820.0000.0000.0000.000
45A52ASN00.006-0.01412.9331.0301.0300.0000.0000.0000.000
46A53PRO00.0020.01315.4960.2510.2510.0000.0000.0000.000
47A54TYR0-0.032-0.01618.8240.9170.9170.0000.0000.0000.000
48A55GLY0-0.026-0.00917.1830.3520.3520.0000.0000.0000.000
49A56SER0-0.024-0.00118.132-0.144-0.1440.0000.0000.0000.000
50A57LEU00.0040.01815.028-1.221-1.2210.0000.0000.0000.000
51A58PRO0-0.013-0.01014.0890.8280.8280.0000.0000.0000.000
52A59THR0-0.014-0.03111.0251.1171.1170.0000.0000.0000.000
53A60LEU0-0.037-0.0097.892-1.558-1.5580.0000.0000.0000.000
54A61VAL0-0.001-0.0155.8562.7932.7930.0000.0000.0000.000
55A62ASP-1-0.763-0.8633.275-55.468-54.5740.082-0.416-0.560-0.003
56A63ARG10.7090.7953.09839.67640.3540.045-0.133-0.5890.000
57A64ASP-1-0.880-0.9165.363-26.404-26.377-0.001-0.001-0.0250.000
58A65LEU0-0.0410.0157.5792.1032.1030.0000.0000.0000.000
59A66ALA00.023-0.0038.745-1.592-1.5920.0000.0000.0000.000
60A67LEU0-0.0210.00211.3181.5261.5260.0000.0000.0000.000
61A68TRP00.0540.01713.346-1.153-1.1530.0000.0000.0000.000
62A69GLU-1-0.730-0.80116.057-14.430-14.4300.0000.0000.0000.000
63A70SER00.0120.01617.170-0.506-0.5060.0000.0000.0000.000
64A71THR0-0.086-0.12217.166-0.656-0.6560.0000.0000.0000.000
65A72VAL00.0390.02616.542-0.337-0.3370.0000.0000.0000.000
66A73VAL0-0.019-0.00712.147-0.944-0.9440.0000.0000.0000.000
67A74MET0-0.040-0.02413.222-1.259-1.2590.0000.0000.0000.000
68A75GLU-1-0.805-0.90514.682-15.237-15.2370.0000.0000.0000.000
69A76TYR00.0390.0258.6940.0870.0870.0000.0000.0000.000
70A77LEU0-0.035-0.0278.176-1.370-1.3700.0000.0000.0000.000
71A78ASP-1-0.828-0.92311.245-18.847-18.8470.0000.0000.0000.000
72A79GLU-1-0.971-0.97814.028-16.423-16.4230.0000.0000.0000.000
73A80ARG10.8720.9506.80032.41632.4160.0000.0000.0000.000
74A81TYR0-0.038-0.0265.374-3.654-3.6540.0000.0000.0000.000
75A82PRO00.0480.02410.4060.7600.7600.0000.0000.0000.000
76A83HIS0-0.0240.02612.8191.4981.4980.0000.0000.0000.000
77A84PRO00.0400.00912.188-1.670-1.6700.0000.0000.0000.000
78A85PRO00.0320.01715.239-0.776-0.7760.0000.0000.0000.000
79A86LEU00.0070.00914.2910.5290.5290.0000.0000.0000.000
80A87LEU00.0020.00218.1290.8500.8500.0000.0000.0000.000
81A88PRO0-0.012-0.00520.969-0.010-0.0100.0000.0000.0000.000
82A89VAL00.0730.03122.708-0.268-0.2680.0000.0000.0000.000
83A90TYR00.005-0.00124.5290.0610.0610.0000.0000.0000.000
84A91PRO00.035-0.00127.686-0.092-0.0920.0000.0000.0000.000
85A92VAL00.0570.03328.987-0.098-0.0980.0000.0000.0000.000
86A93ALA00.0170.01128.192-0.004-0.0040.0000.0000.0000.000
87A94ARG10.9680.99620.82713.66213.6620.0000.0000.0000.000
88A95ALA0-0.0040.00426.282-0.235-0.2350.0000.0000.0000.000
89A96ASN00.022-0.00128.8340.1290.1290.0000.0000.0000.000
90A97SER0-0.0010.00024.535-0.023-0.0230.0000.0000.0000.000
91A98ARG10.8830.94022.26913.05913.0590.0000.0000.0000.000
92A99LEU0-0.021-0.01226.1030.0300.0300.0000.0000.0000.000
93A100LEU0-0.012-0.01127.7190.2190.2190.0000.0000.0000.000
94A101ILE00.0430.02621.9800.1230.1230.0000.0000.0000.000
95A102HIS00.0120.01026.091-0.155-0.1550.0000.0000.0000.000
96A103ARG10.9400.96128.5769.4279.4270.0000.0000.0000.000
97A104ILE00.0300.03026.3890.2140.2140.0000.0000.0000.000
98A105GLN00.024-0.00425.641-0.330-0.3300.0000.0000.0000.000
99A106ARG10.8450.90728.3418.9658.9650.0000.0000.0000.000
100A107ASP-1-0.883-0.93431.975-8.882-8.8820.0000.0000.0000.000
101A108TRP0-0.036-0.04729.4870.0590.0590.0000.0000.0000.000
102A109CYS0-0.0260.00026.647-0.167-0.1670.0000.0000.0000.000
103A110GLY00.0380.03928.952-0.016-0.0160.0000.0000.0000.000
104A111GLN0-0.014-0.02231.8630.1490.1490.0000.0000.0000.000
105A112VAL0-0.024-0.01527.2820.1470.1470.0000.0000.0000.000
106A113ASP-1-0.748-0.85327.616-11.602-11.6020.0000.0000.0000.000
107A114LEU0-0.036-0.00830.2460.1570.1570.0000.0000.0000.000
108A115ILE0-0.045-0.03532.8230.2470.2470.0000.0000.0000.000
109A116LEU00.0180.00127.4810.1460.1460.0000.0000.0000.000
110A117ASP-1-0.774-0.81931.474-9.724-9.7240.0000.0000.0000.000
111A118PRO00.0330.01031.5680.3750.3750.0000.0000.0000.000
112A119ARG10.7660.83832.9909.6379.6370.0000.0000.0000.000
113A120THR0-0.049-0.02235.8140.3120.3120.0000.0000.0000.000
114A121LYS10.9460.97238.4647.1377.1370.0000.0000.0000.000
115A122GLU-1-0.737-0.87739.958-8.119-8.1190.0000.0000.0000.000
116A123ALA00.000-0.00841.824-0.038-0.0380.0000.0000.0000.000
117A124ALA0-0.010-0.00540.6840.0300.0300.0000.0000.0000.000
118A125ARG10.8750.95435.8238.5698.5690.0000.0000.0000.000
119A126VAL0-0.032-0.01138.819-0.101-0.1010.0000.0000.0000.000
120A127GLN0-0.072-0.06241.1750.0800.0800.0000.0000.0000.000
121A128ALA00.0680.03836.475-0.012-0.0120.0000.0000.0000.000
122A129ARG10.8340.91036.0418.4068.4060.0000.0000.0000.000
123A130LYS10.8520.93737.7737.0697.0690.0000.0000.0000.000
124A131GLU-1-0.815-0.88539.093-7.842-7.8420.0000.0000.0000.000
125A132LEU00.0170.01931.814-0.029-0.0290.0000.0000.0000.000
126A133ARG10.9600.98535.9657.7207.7200.0000.0000.0000.000
127A134GLU-1-0.916-0.95737.479-7.296-7.2960.0000.0000.0000.000
128A135SER0-0.0120.02236.304-0.055-0.0550.0000.0000.0000.000
129A136LEU00.011-0.00731.397-0.035-0.0350.0000.0000.0000.000
130A137THR0-0.018-0.03435.326-0.007-0.0070.0000.0000.0000.000
131A138GLY0-0.0180.01438.3920.0920.0920.0000.0000.0000.000
132A139VAL0-0.0080.01033.4820.0920.0920.0000.0000.0000.000
133A140SER0-0.039-0.04435.271-0.079-0.0790.0000.0000.0000.000
134A141PRO0-0.007-0.01036.146-0.130-0.1300.0000.0000.0000.000
135A142LEU00.0280.01734.404-0.012-0.0120.0000.0000.0000.000
136A143PHE0-0.073-0.03628.838-0.206-0.2060.0000.0000.0000.000
137A144ALA0-0.046-0.02233.502-0.108-0.1080.0000.0000.0000.000
138A145ASP-1-0.930-0.95135.365-8.263-8.2630.0000.0000.0000.000
139A146LYS10.8420.92730.3859.5449.5440.0000.0000.0000.000
140A147PRO0-0.0050.01628.0810.0100.0100.0000.0000.0000.000
141A148PHE00.0110.01622.820-0.372-0.3720.0000.0000.0000.000
142A149PHE00.000-0.01726.2580.5140.5140.0000.0000.0000.000
143A150LEU0-0.037-0.02127.661-0.130-0.1300.0000.0000.0000.000
144A151SER0-0.049-0.04724.7250.0650.0650.0000.0000.0000.000
145A152GLU-1-0.864-0.95927.603-9.930-9.9300.0000.0000.0000.000
146A153GLU-1-0.952-0.95522.114-13.054-13.0540.0000.0000.0000.000
147A154GLN00.0110.03218.4820.9000.9000.0000.0000.0000.000
148A155SER00.000-0.01119.898-0.366-0.3660.0000.0000.0000.000
149A156LEU00.044-0.00616.137-0.091-0.0910.0000.0000.0000.000
150A157VAL0-0.0040.00119.7580.1170.1170.0000.0000.0000.000
151A158ASP-1-0.716-0.83121.446-12.556-12.5560.0000.0000.0000.000
152A159CYS0-0.055-0.01117.499-0.300-0.3000.0000.0000.0000.000
153A160CYS0-0.034-0.00819.626-0.247-0.2470.0000.0000.0000.000
154A161LEU00.0050.00622.1460.3320.3320.0000.0000.0000.000
155A162LEU0-0.003-0.00720.6800.3400.3400.0000.0000.0000.000
156A163PRO00.0060.01419.7870.3870.3870.0000.0000.0000.000
157A164ILE00.0310.01522.4590.3540.3540.0000.0000.0000.000
158A165LEU00.007-0.00926.1010.3920.3920.0000.0000.0000.000
159A166TRP0-0.027-0.02423.5590.4260.4260.0000.0000.0000.000
160A167ARG10.7900.85820.74414.15414.1540.0000.0000.0000.000
161A168LEU0-0.0170.00327.3650.3470.3470.0000.0000.0000.000
162A169PRO00.0370.01229.4970.2950.2950.0000.0000.0000.000
163A170VAL00.0260.02027.8200.2880.2880.0000.0000.0000.000
164A171LEU0-0.031-0.00229.1770.1720.1720.0000.0000.0000.000
165A172GLY0-0.0030.00632.5060.2990.2990.0000.0000.0000.000
166A173ILE0-0.076-0.04033.4400.3330.3330.0000.0000.0000.000
167A174GLU-1-0.889-0.94734.732-8.375-8.3750.0000.0000.0000.000
168A175LEU0-0.047-0.02633.1930.2140.2140.0000.0000.0000.000
169A176PRO00.0330.02637.3050.1110.1110.0000.0000.0000.000
170A177ARG11.0180.98339.4917.2927.2920.0000.0000.0000.000
171A178GLN0-0.029-0.01640.815-0.091-0.0910.0000.0000.0000.000
172A179ALA00.0140.01536.6450.0000.0000.0000.0000.0000.000
173A180LYS10.8870.93936.3498.1148.1140.0000.0000.0000.000
174A181PRO00.0470.03335.641-0.198-0.1980.0000.0000.0000.000
175A182LEU00.0020.00930.635-0.281-0.2810.0000.0000.0000.000
176A183LEU0-0.007-0.01731.448-0.340-0.3400.0000.0000.0000.000
177A184ASP-1-0.803-0.90631.758-9.085-9.0850.0000.0000.0000.000
178A185TYR0-0.111-0.08924.991-0.364-0.3640.0000.0000.0000.000
179A186MET0-0.050-0.02227.352-0.339-0.3390.0000.0000.0000.000
180A187GLU-1-0.956-0.95926.918-10.089-10.0890.0000.0000.0000.000
181A188ARG10.8670.92526.99710.23710.2370.0000.0000.0000.000
182A189GLN0-0.014-0.02922.699-0.712-0.7120.0000.0000.0000.000
183A190PHE0-0.034-0.02522.213-0.613-0.6130.0000.0000.0000.000
184A191ALA00.0120.01222.432-0.435-0.4350.0000.0000.0000.000
185A192ARG10.7920.88617.97315.39915.3990.0000.0000.0000.000
186A193GLU-1-0.899-0.94815.560-17.860-17.8600.0000.0000.0000.000
187A194ALA00.0340.01614.469-0.670-0.6700.0000.0000.0000.000
188A195PHE00.0250.01915.018-0.670-0.6700.0000.0000.0000.000
189A196GLN00.0200.00617.388-0.403-0.4030.0000.0000.0000.000
190A197ALA00.000-0.00212.416-0.084-0.0840.0000.0000.0000.000
191A198SER0-0.086-0.04313.295-0.863-0.8630.0000.0000.0000.000
192A199LEU0-0.068-0.01114.349-0.076-0.0760.0000.0000.0000.000
193A200SER00.004-0.01616.438-0.388-0.3880.0000.0000.0000.000
194A201GLY0-0.001-0.02017.3590.7450.7450.0000.0000.0000.000
195A202VAL00.0710.02920.1750.5620.5620.0000.0000.0000.000
196A203GLU-1-0.695-0.81618.338-16.052-16.0520.0000.0000.0000.000
197A204ARG10.8450.93117.93716.09416.0940.0000.0000.0000.000
198A205ASP-1-0.892-0.93323.036-11.804-11.8040.0000.0000.0000.000
199A206MET0-0.141-0.05023.4480.5250.5250.0000.0000.0000.000
200A207ARG10.8150.91426.29511.42911.4290.0000.0000.0000.000