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: 4LLYN

Calculation Name: 4MCK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MCK

Chain ID: A

ChEMBL ID:

UniProt ID: P29022

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2284108.79338
FMO2-HF: Nuclear repulsion 2205304.578527
FMO2-HF: Total energy -78804.214853
FMO2-MP2: Total energy -79031.080519


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:-4:PHE)


Summations of interaction energy for fragment #1(A:-4:PHE)
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.
-20.459-13.1619.025-10.267-16.06-0.06
Interaction energy analysis for fragmet #1(A:-4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.003
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].
3A-2ALA00.0440.0063.652-1.4180.7900.045-0.881-1.3720.006
4A-1GLU-1-0.848-0.9055.4570.1620.1620.0000.0000.0000.000
5A0PHE0-0.020-0.0172.495-2.800-1.1932.343-0.902-3.0490.002
6A1VAL0-0.035-0.0073.425-0.4830.1410.019-0.107-0.5370.000
7A2VAL0-0.0170.0075.7970.1230.1230.0000.0000.0000.000
8A3SER00.0620.0408.913-0.041-0.0410.0000.0000.0000.000
9A4ASP-1-0.782-0.92011.256-0.140-0.1400.0000.0000.0000.000
10A5ALA0-0.034-0.00614.837-0.003-0.0030.0000.0000.0000.000
11A6PHE0-0.0120.00211.3310.0160.0160.0000.0000.0000.000
12A7PHE00.0380.01412.991-0.003-0.0030.0000.0000.0000.000
13A8ASN0-0.020-0.03514.920-0.007-0.0070.0000.0000.0000.000
14A9GLY00.0040.02017.5920.0050.0050.0000.0000.0000.000
15A10ILE0-0.0110.00714.0010.0020.0020.0000.0000.0000.000
16A11LYS10.9330.97618.4450.0980.0980.0000.0000.0000.000
17A12ASN0-0.031-0.00920.592-0.008-0.0080.0000.0000.0000.000
18A13GLN0-0.032-0.00221.8030.0070.0070.0000.0000.0000.000
19A14ALA00.0250.00924.150-0.010-0.0100.0000.0000.0000.000
20A15GLY00.0110.02025.970-0.010-0.0100.0000.0000.0000.000
21A16SER00.015-0.02427.9210.0040.0040.0000.0000.0000.000
22A17GLY0-0.014-0.01030.105-0.003-0.0030.0000.0000.0000.000
23A18CYS0-0.0710.01121.2200.0010.0010.0000.0000.0000.000
24A19GLU-1-0.773-0.88327.400-0.098-0.0980.0000.0000.0000.000
25A20GLY0-0.003-0.00524.300-0.007-0.0070.0000.0000.0000.000
26A21LYS10.8400.91123.5620.0410.0410.0000.0000.0000.000
27A22ASN0-0.037-0.02824.2120.0000.0000.0000.0000.0000.000
28A23PHE0-0.0030.02221.792-0.005-0.0050.0000.0000.0000.000
29A24TYR0-0.022-0.03918.548-0.029-0.0290.0000.0000.0000.000
30A25THR00.022-0.00118.2980.0100.0100.0000.0000.0000.000
31A26ARG10.8290.8919.6160.1680.1680.0000.0000.0000.000
32A27SER00.0570.02613.981-0.045-0.0450.0000.0000.0000.000
33A28ALA0-0.017-0.00115.746-0.028-0.0280.0000.0000.0000.000
34A29PHE00.0190.0007.654-0.022-0.0220.0000.0000.0000.000
35A30LEU00.0170.0049.303-0.121-0.1210.0000.0000.0000.000
36A31SER0-0.032-0.02111.886-0.021-0.0210.0000.0000.0000.000
37A32ALA0-0.045-0.02713.318-0.010-0.0100.0000.0000.0000.000
38A33VAL00.016-0.0017.184-0.059-0.0590.0000.0000.0000.000
39A34ASN0-0.031-0.00510.006-0.118-0.1180.0000.0000.0000.000
40A35ALA0-0.057-0.01711.7350.0240.0240.0000.0000.0000.000
41A36TYR0-0.070-0.06410.7570.0600.0600.0000.0000.0000.000
42A37PRO00.0510.0258.276-0.299-0.2990.0000.0000.0000.000
43A38GLY00.0180.0077.115-0.298-0.2980.0000.0000.0000.000
44A39PHE00.021-0.0166.318-0.126-0.1260.0000.0000.0000.000
45A40ALA0-0.075-0.0252.195-1.100-1.4623.120-1.371-1.3880.002
46A41HIS0-0.007-0.0191.883-10.483-10.03011.789-5.701-6.542-0.070
47A42GLY00.0140.0174.5650.5890.674-0.001-0.033-0.0520.000
48A43GLY0-0.0030.0016.2790.1200.1200.0000.0000.0000.000
49A44THR0-0.049-0.0506.9540.2190.2190.0000.0000.0000.000
50A45GLU-1-0.813-0.9102.3023.7304.6680.745-0.450-1.232-0.001
51A46VAL0-0.006-0.0024.4701.7531.938-0.001-0.011-0.1730.000
52A47GLU-1-0.826-0.8866.9880.6340.6340.0000.0000.0000.000
53A48GLY00.0380.0292.485-2.032-1.4420.663-0.665-0.5880.002
54A49LYS10.8970.9273.373-5.863-5.4500.0350.121-0.5690.000
55A50ARG10.8820.9304.864-1.942-1.945-0.001-0.0040.0090.000
56A51GLU-1-0.739-0.8445.442-1.542-1.5420.0000.0000.0000.000
57A52ILE00.0080.0072.562-0.5460.0150.269-0.263-0.567-0.001
58A53ALA00.001-0.0016.335-0.005-0.0050.0000.0000.0000.000
59A54ALA0-0.017-0.0259.429-0.051-0.0510.0000.0000.0000.000
60A55PHE00.0040.0059.194-0.011-0.0110.0000.0000.0000.000
61A56PHE00.0300.0028.8570.0510.0510.0000.0000.0000.000
62A57ALA0-0.0380.01512.3580.0350.0350.0000.0000.0000.000
63A58HIS00.0200.00414.1490.0150.0150.0000.0000.0000.000
64A59VAL00.0360.02414.0820.0140.0140.0000.0000.0000.000
65A60THR0-0.0450.00115.8560.0220.0220.0000.0000.0000.000
66A61HIS00.009-0.00118.1450.0170.0170.0000.0000.0000.000
67A62GLN0-0.0010.00519.4360.0070.0070.0000.0000.0000.000
68A63THR0-0.021-0.00619.5010.0040.0040.0000.0000.0000.000
69A64GLY00.0160.01222.0500.0070.0070.0000.0000.0000.000
70A65HIS0-0.042-0.04720.0330.0030.0030.0000.0000.0000.000
71A66PHE0-0.013-0.00815.006-0.005-0.0050.0000.0000.0000.000
72A68TYR00.011-0.00824.1840.0030.0030.0000.0000.0000.000
73A69ILE0-0.0170.01623.499-0.016-0.0160.0000.0000.0000.000
74A70SER0-0.030-0.02824.769-0.014-0.0140.0000.0000.0000.000
75A71GLU-1-0.766-0.84627.435-0.085-0.0850.0000.0000.0000.000
76A72ILE00.0100.01028.7820.0020.0020.0000.0000.0000.000
77A73ASN0-0.0100.00731.7860.0070.0070.0000.0000.0000.000
78A74LYS10.9350.94731.1830.0800.0800.0000.0000.0000.000
79A75SER00.007-0.00434.426-0.001-0.0010.0000.0000.0000.000
80A76ASN00.0060.01134.0850.0030.0030.0000.0000.0000.000
81A77ALA00.0680.01734.122-0.005-0.0050.0000.0000.0000.000
82A78TYR0-0.054-0.03230.188-0.006-0.0060.0000.0000.0000.000
83A79CYS0-0.021-0.03231.894-0.014-0.0140.0000.0000.0000.000
84A80ASP-1-0.803-0.89532.267-0.086-0.0860.0000.0000.0000.000
85A81ALA00.008-0.02334.140-0.006-0.0060.0000.0000.0000.000
86A82SER0-0.016-0.00335.3520.0040.0040.0000.0000.0000.000
87A83ASN0-0.034-0.01831.045-0.010-0.0100.0000.0000.0000.000
88A84ARG10.9550.97230.7680.1160.1160.0000.0000.0000.000
89A86TRP00.0060.01926.661-0.009-0.0090.0000.0000.0000.000
90A87PRO00.0110.01631.7120.0020.0020.0000.0000.0000.000
91A89ALA00.0300.02434.9130.0050.0050.0000.0000.0000.000
92A90ALA00.0390.00736.7360.0010.0010.0000.0000.0000.000
93A91GLY0-0.0100.00039.201-0.001-0.0010.0000.0000.0000.000
94A92GLN0-0.029-0.00233.676-0.002-0.0020.0000.0000.0000.000
95A93LYS10.8550.93633.5360.0780.0780.0000.0000.0000.000
96A94TYR0-0.062-0.03228.935-0.004-0.0040.0000.0000.0000.000
97A95TYR00.0670.02728.813-0.001-0.0010.0000.0000.0000.000
98A96GLY00.0330.02025.570-0.010-0.0100.0000.0000.0000.000
99A97ARG10.7850.86724.3730.1400.1400.0000.0000.0000.000
100A98GLY00.0590.03320.886-0.019-0.0190.0000.0000.0000.000
101A99PRO0-0.024-0.00616.2390.0180.0180.0000.0000.0000.000
102A100LEU0-0.005-0.00714.2840.0100.0100.0000.0000.0000.000
103A101GLN0-0.100-0.05418.6270.0230.0230.0000.0000.0000.000
104A102ILE00.0250.03720.4430.0120.0120.0000.0000.0000.000
105A103SER00.023-0.00922.4780.0190.0190.0000.0000.0000.000
106A104TRP00.0110.00225.802-0.005-0.0050.0000.0000.0000.000
107A105ASN00.0060.00227.477-0.013-0.0130.0000.0000.0000.000
108A106TYR0-0.030-0.01725.874-0.011-0.0110.0000.0000.0000.000
109A107ASN0-0.024-0.02123.010-0.022-0.0220.0000.0000.0000.000
110A108TYR00.001-0.00523.778-0.019-0.0190.0000.0000.0000.000
111A109GLY0-0.016-0.00525.581-0.007-0.0070.0000.0000.0000.000
112A110PRO0-0.036-0.01422.900-0.005-0.0050.0000.0000.0000.000
113A111ALA00.0510.03020.925-0.018-0.0180.0000.0000.0000.000
114A112GLY00.000-0.00321.778-0.016-0.0160.0000.0000.0000.000
115A113ARG10.8910.94524.4730.1720.1720.0000.0000.0000.000
116A114ASP-1-0.837-0.89617.881-0.415-0.4150.0000.0000.0000.000
117A115ILE0-0.042-0.01618.791-0.007-0.0070.0000.0000.0000.000
118A116GLY0-0.0050.00721.0140.0020.0020.0000.0000.0000.000
119A117PHE0-0.062-0.03722.8030.0170.0170.0000.0000.0000.000
120A118ASN00.0400.01926.685-0.006-0.0060.0000.0000.0000.000
121A119GLY00.0530.03027.0170.0050.0050.0000.0000.0000.000
122A120LEU0-0.032-0.01627.7670.0050.0050.0000.0000.0000.000
123A121ALA00.0030.00431.1670.0080.0080.0000.0000.0000.000
124A122ASP-1-0.867-0.94030.007-0.121-0.1210.0000.0000.0000.000
125A123PRO00.0200.01928.004-0.011-0.0110.0000.0000.0000.000
126A124ASN00.030-0.00227.500-0.009-0.0090.0000.0000.0000.000
127A125ARG10.9941.00526.4360.1640.1640.0000.0000.0000.000
128A126VAL0-0.038-0.01222.032-0.008-0.0080.0000.0000.0000.000
129A127ALA0-0.011-0.02123.594-0.007-0.0070.0000.0000.0000.000
130A128GLN0-0.036-0.01126.1640.0020.0020.0000.0000.0000.000
131A129ASP-1-0.822-0.90222.421-0.211-0.2110.0000.0000.0000.000
132A130ALA00.0490.02119.959-0.017-0.0170.0000.0000.0000.000
133A131VAL00.0030.00117.530-0.036-0.0360.0000.0000.0000.000
134A132ILE0-0.015-0.00318.044-0.042-0.0420.0000.0000.0000.000
135A133ALA00.0060.00819.527-0.021-0.0210.0000.0000.0000.000
136A134PHE0-0.011-0.02113.924-0.016-0.0160.0000.0000.0000.000
137A135LYS10.9821.00314.8860.2990.2990.0000.0000.0000.000
138A136THR0-0.028-0.01416.279-0.015-0.0150.0000.0000.0000.000
139A137ALA0-0.0240.00115.1900.0040.0040.0000.0000.0000.000
140A138LEU00.0240.0089.693-0.006-0.0060.0000.0000.0000.000
141A139TRP00.0370.03513.180-0.023-0.0230.0000.0000.0000.000
142A140PHE0-0.005-0.00915.8890.0060.0060.0000.0000.0000.000
143A141TRP0-0.002-0.0389.6460.0870.0870.0000.0000.0000.000
144A142MET0-0.0130.0089.394-0.029-0.0290.0000.0000.0000.000
145A143ASN0-0.065-0.03012.9860.0590.0590.0000.0000.0000.000
146A144ASN0-0.078-0.03216.1480.0690.0690.0000.0000.0000.000
147A145VAL0-0.015-0.00113.7880.0450.0450.0000.0000.0000.000
148A146HIS0-0.026-0.0257.6770.1500.1500.0000.0000.0000.000
149A147ARG10.9190.94911.8180.2730.2730.0000.0000.0000.000
150A148LEU0-0.017-0.01814.2960.0540.0540.0000.0000.0000.000
151A149MET00.0070.0278.9410.0570.0570.0000.0000.0000.000
152A150PRO0-0.0070.00111.4510.1000.1000.0000.0000.0000.000
153A151GLN0-0.046-0.01613.0690.0430.0430.0000.0000.0000.000
154A152GLY00.0270.02914.5750.0210.0210.0000.0000.0000.000
155A153PHE00.0340.01413.606-0.045-0.0450.0000.0000.0000.000
156A154GLY00.0660.04015.539-0.044-0.0440.0000.0000.0000.000
157A155ALA0-0.051-0.02717.157-0.022-0.0220.0000.0000.0000.000
158A156THR0-0.028-0.03413.334-0.032-0.0320.0000.0000.0000.000
159A157ILE00.000-0.00816.788-0.022-0.0220.0000.0000.0000.000
160A158ARG10.8490.90319.7540.0100.0100.0000.0000.0000.000
161A159ALA0-0.0230.00017.968-0.004-0.0040.0000.0000.0000.000
162A160ILE0-0.0290.00216.115-0.018-0.0180.0000.0000.0000.000
163A161ASN00.018-0.01420.520-0.001-0.0010.0000.0000.0000.000
164A162GLY00.0360.02224.1810.0000.0000.0000.0000.0000.000
165A164LEU0-0.070-0.02626.6870.0100.0100.0000.0000.0000.000
166A165GLU-1-0.783-0.85824.115-0.052-0.0520.0000.0000.0000.000
167A198CYS0-0.0180.01222.2430.0020.0020.0000.0000.0000.000
168A167ASN00.005-0.02526.925-0.005-0.0050.0000.0000.0000.000
169A168GLY00.0620.03329.677-0.001-0.0010.0000.0000.0000.000
170A169ASN0-0.041-0.00730.1980.0000.0000.0000.0000.0000.000
171A170ASN00.010-0.00128.6120.0000.0000.0000.0000.0000.000
172A171PRO00.0220.01327.7840.0000.0000.0000.0000.0000.000
173A172ALA00.0380.02827.1610.0060.0060.0000.0000.0000.000
174A173GLN00.0640.02925.2820.0090.0090.0000.0000.0000.000
175A174MET0-0.0130.04023.2830.0050.0050.0000.0000.0000.000
176A175ASN0-0.023-0.05322.3030.0170.0170.0000.0000.0000.000
177A176ALA0-0.0120.01922.7590.0130.0130.0000.0000.0000.000
178A177ARG10.7830.84418.7290.0880.0880.0000.0000.0000.000
179A178VAL0-0.009-0.00817.9390.0150.0150.0000.0000.0000.000
180A179GLY0-0.012-0.00218.3720.0320.0320.0000.0000.0000.000
181A180TYR00.0350.01616.7820.0230.0230.0000.0000.0000.000
182A181TYR0-0.023-0.01711.0480.0380.0380.0000.0000.0000.000
183A182LYS10.9500.97314.025-0.093-0.0930.0000.0000.0000.000
184A183GLN0-0.030-0.00715.9150.0410.0410.0000.0000.0000.000
185A184TYR0-0.005-0.03611.5380.0440.0440.0000.0000.0000.000
186A185CYS0-0.025-0.00111.1680.1090.1090.0000.0000.0000.000
187A186GLN0-0.009-0.00112.2450.1160.1160.0000.0000.0000.000
188A187GLN0-0.029-0.01213.2750.0150.0150.0000.0000.0000.000
189A188LEU0-0.064-0.0267.073-0.014-0.0140.0000.0000.0000.000
190A189ARG10.8970.9579.162-0.235-0.2350.0000.0000.0000.000
191A190VAL0-0.0060.0098.6420.1780.1780.0000.0000.0000.000
192A191ASP-1-0.850-0.91711.2820.4630.4630.0000.0000.0000.000
193A192PRO00.008-0.00112.4890.0880.0880.0000.0000.0000.000
194A193GLY00.0170.02514.116-0.020-0.0200.0000.0000.0000.000
195A194PRO00.0260.00715.489-0.037-0.0370.0000.0000.0000.000
196A195ASN0-0.046-0.03417.463-0.011-0.0110.0000.0000.0000.000
197A196LEU00.0090.01416.548-0.017-0.0170.0000.0000.0000.000
198A197THR00.0860.02519.271-0.017-0.0170.0000.0000.0000.000