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: 5NN5Z

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287071.582248
FMO2-HF: Nuclear repulsion 2208267.107228
FMO2-HF: Total energy -78804.475021
FMO2-MP2: Total energy -79031.298433


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.
-19.456-11.97318.262-9.848-15.899-0.056
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 : 0.028 / q_NPA : 0.006
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-2ALA00.0430.0063.688-1.5880.5910.033-0.846-1.3660.007
4A-1GLU-1-0.831-0.8955.4360.0480.0480.0000.0000.0000.000
5A0PHE0-0.025-0.0212.501-2.741-1.1082.227-0.887-2.9730.001
6A1VAL0-0.0190.0023.467-0.4560.1380.014-0.096-0.5120.000
7A2VAL0-0.0160.0065.8920.2010.2010.0000.0000.0000.000
8A3SER00.0600.0408.759-0.016-0.0160.0000.0000.0000.000
9A4ASP-1-0.797-0.92311.026-0.210-0.2100.0000.0000.0000.000
10A5ALA0-0.019-0.00214.4800.0090.0090.0000.0000.0000.000
11A6PHE0-0.0080.00311.0970.0260.0260.0000.0000.0000.000
12A7PHE00.0260.00812.8440.0050.0050.0000.0000.0000.000
13A8ASN0-0.022-0.03314.8070.0030.0030.0000.0000.0000.000
14A9GLY00.0050.01717.5070.0120.0120.0000.0000.0000.000
15A10ILE0-0.026-0.00113.8460.0080.0080.0000.0000.0000.000
16A11LYS10.8900.95718.2130.1420.1420.0000.0000.0000.000
17A12ASN00.0010.00620.320-0.006-0.0060.0000.0000.0000.000
18A13GLN00.0190.02321.8770.0060.0060.0000.0000.0000.000
19A14ALA00.0440.01624.118-0.010-0.0100.0000.0000.0000.000
20A15GLY00.0250.02326.202-0.011-0.0110.0000.0000.0000.000
21A16SER00.016-0.01528.5060.0050.0050.0000.0000.0000.000
22A17GLY0-0.0070.00330.327-0.003-0.0030.0000.0000.0000.000
23A18CYS0-0.0620.00721.1970.0030.0030.0000.0000.0000.000
24A19GLU-1-0.772-0.87727.381-0.110-0.1100.0000.0000.0000.000
25A20GLY0-0.005-0.01124.143-0.007-0.0070.0000.0000.0000.000
26A21LYS10.7510.86123.4660.0610.0610.0000.0000.0000.000
27A22ASN0-0.014-0.01524.107-0.003-0.0030.0000.0000.0000.000
28A23PHE0-0.0090.01322.025-0.005-0.0050.0000.0000.0000.000
29A24TYR0-0.022-0.03818.580-0.031-0.0310.0000.0000.0000.000
30A25THR00.031-0.00418.1950.0080.0080.0000.0000.0000.000
31A26ARG10.8040.8879.2660.2900.2900.0000.0000.0000.000
32A27SER00.0670.03113.879-0.051-0.0510.0000.0000.0000.000
33A28ALA0-0.0190.00715.878-0.023-0.0230.0000.0000.0000.000
34A29PHE00.027-0.0047.760-0.014-0.0140.0000.0000.0000.000
35A30LEU00.0100.0019.155-0.110-0.1100.0000.0000.0000.000
36A31SER0-0.031-0.03111.864-0.013-0.0130.0000.0000.0000.000
37A32ALA0-0.034-0.00913.6860.0150.0150.0000.0000.0000.000
38A33VAL0-0.004-0.0097.252-0.051-0.0510.0000.0000.0000.000
39A34ASN0-0.035-0.01510.234-0.096-0.0960.0000.0000.0000.000
40A35ALA0-0.041-0.00811.8490.0510.0510.0000.0000.0000.000
41A36TYR0-0.076-0.06510.9610.0620.0620.0000.0000.0000.000
42A37PRO00.0500.0198.256-0.248-0.2480.0000.0000.0000.000
43A38GLY00.0210.0117.021-0.278-0.2780.0000.0000.0000.000
44A39PHE00.030-0.0106.483-0.132-0.1320.0000.0000.0000.000
45A40ALA0-0.094-0.0432.256-1.028-1.1712.610-1.170-1.2970.003
46A41HIS00.015-0.0061.896-9.728-8.87411.223-5.537-6.540-0.070
47A42GLY0-0.0060.0044.6290.5620.641-0.001-0.025-0.0530.000
48A43GLY0-0.023-0.0076.5970.1510.1510.0000.0000.0000.000
49A44THR0-0.057-0.0596.5370.1390.1390.0000.0000.0000.000
50A45GLU-1-0.818-0.9152.2363.4604.4360.895-0.581-1.2910.001
51A46VAL0-0.017-0.0014.3481.2431.402-0.001-0.011-0.1480.000
52A47GLU-1-0.795-0.8766.8470.8580.8580.0000.0000.0000.000
53A48GLY00.0420.0332.397-2.261-1.7071.070-0.914-0.7110.003
54A49LYS10.8850.9263.227-5.585-5.4840.0510.413-0.5650.000
55A50ARG10.8820.9404.860-1.873-1.875-0.001-0.0030.0060.000
56A51GLU-1-0.724-0.8405.411-1.426-1.4260.0000.0000.0000.000
57A52ILE00.0040.0072.809-0.4640.0350.142-0.191-0.449-0.001
58A53ALA00.005-0.0046.4470.0450.0450.0000.0000.0000.000
59A54ALA0-0.017-0.0259.410-0.022-0.0220.0000.0000.0000.000
60A55PHE00.0050.0059.3350.0020.0020.0000.0000.0000.000
61A56PHE00.0310.0068.9870.0690.0690.0000.0000.0000.000
62A57ALA0-0.0350.01512.3890.0440.0440.0000.0000.0000.000
63A58HIS00.0250.00514.1580.0200.0200.0000.0000.0000.000
64A59VAL00.0320.02114.0820.0150.0150.0000.0000.0000.000
65A60THR0-0.0460.00115.8920.0230.0230.0000.0000.0000.000
66A61HIS0-0.045-0.01418.2000.0180.0180.0000.0000.0000.000
67A62GLN00.0200.00919.8810.0110.0110.0000.0000.0000.000
68A63THR0-0.023-0.00319.5050.0020.0020.0000.0000.0000.000
69A64GLY00.0120.00922.0260.0070.0070.0000.0000.0000.000
70A65HIS0-0.042-0.05020.1760.0020.0020.0000.0000.0000.000
71A66PHE0-0.014-0.01415.015-0.005-0.0050.0000.0000.0000.000
72A68TYR00.002-0.01024.2250.0040.0040.0000.0000.0000.000
73A69ILE0-0.0130.01823.489-0.017-0.0170.0000.0000.0000.000
74A70SER0-0.007-0.01724.699-0.014-0.0140.0000.0000.0000.000
75A71GLU-1-0.756-0.84227.354-0.085-0.0850.0000.0000.0000.000
76A72ILE00.0140.01228.8690.0020.0020.0000.0000.0000.000
77A73ASN00.0220.02232.0440.0060.0060.0000.0000.0000.000
78A74LYS10.8780.93430.7000.0920.0920.0000.0000.0000.000
79A75SER0-0.017-0.01234.437-0.001-0.0010.0000.0000.0000.000
80A76ASN00.0070.00633.8540.0030.0030.0000.0000.0000.000
81A77ALA00.0610.01734.406-0.005-0.0050.0000.0000.0000.000
82A78TYR0-0.069-0.04830.753-0.005-0.0050.0000.0000.0000.000
83A79CYS00.011-0.02131.934-0.013-0.0130.0000.0000.0000.000
84A80ASP-1-0.768-0.85932.611-0.082-0.0820.0000.0000.0000.000
85A81ALA00.0330.00234.552-0.005-0.0050.0000.0000.0000.000
86A82SER0-0.043-0.02835.3710.0030.0030.0000.0000.0000.000
87A83ASN0-0.050-0.03830.837-0.009-0.0090.0000.0000.0000.000
88A84ARG10.9470.96031.0630.1050.1050.0000.0000.0000.000
89A86TRP0-0.0100.01226.944-0.008-0.0080.0000.0000.0000.000
90A87PRO00.0190.01931.7910.0010.0010.0000.0000.0000.000
91A89ALA00.0380.02935.1280.0050.0050.0000.0000.0000.000
92A90ALA00.0240.00137.0420.0010.0010.0000.0000.0000.000
93A91GLY0-0.0050.00339.792-0.001-0.0010.0000.0000.0000.000
94A92GLN0-0.032-0.01134.089-0.001-0.0010.0000.0000.0000.000
95A93LYS10.8520.93933.7100.0790.0790.0000.0000.0000.000
96A94TYR0-0.062-0.03529.157-0.005-0.0050.0000.0000.0000.000
97A95TYR00.0500.02028.874-0.002-0.0020.0000.0000.0000.000
98A96GLY00.0300.01625.631-0.009-0.0090.0000.0000.0000.000
99A97ARG10.7940.87424.4450.1430.1430.0000.0000.0000.000
100A98GLY00.0810.04520.836-0.018-0.0180.0000.0000.0000.000
101A99PRO0-0.027-0.01116.2450.0180.0180.0000.0000.0000.000
102A100LEU0-0.004-0.00314.3970.0100.0100.0000.0000.0000.000
103A101GLN0-0.070-0.04218.7550.0280.0280.0000.0000.0000.000
104A102ILE00.0040.03020.4990.0140.0140.0000.0000.0000.000
105A103SER00.023-0.00822.6120.0170.0170.0000.0000.0000.000
106A104TRP00.0080.00225.819-0.003-0.0030.0000.0000.0000.000
107A105ASN0-0.0010.00027.426-0.013-0.0130.0000.0000.0000.000
108A106TYR0-0.020-0.01126.071-0.010-0.0100.0000.0000.0000.000
109A107ASN0-0.029-0.02023.139-0.018-0.0180.0000.0000.0000.000
110A108TYR0-0.005-0.01023.884-0.018-0.0180.0000.0000.0000.000
111A109GLY0-0.009-0.00525.773-0.007-0.0070.0000.0000.0000.000
112A110PRO0-0.051-0.01723.153-0.003-0.0030.0000.0000.0000.000
113A111ALA00.0600.03221.174-0.014-0.0140.0000.0000.0000.000
114A112GLY0-0.008-0.01322.078-0.014-0.0140.0000.0000.0000.000
115A113ARG10.8980.94824.5950.1560.1560.0000.0000.0000.000
116A114ASP-1-0.844-0.88918.452-0.383-0.3830.0000.0000.0000.000
117A115ILE0-0.014-0.00219.213-0.009-0.0090.0000.0000.0000.000
118A116GLY00.0060.00721.111-0.004-0.0040.0000.0000.0000.000
119A117PHE0-0.059-0.03923.4340.0150.0150.0000.0000.0000.000
120A118ASN00.0640.03527.019-0.005-0.0050.0000.0000.0000.000
121A119GLY00.0350.01827.1830.0060.0060.0000.0000.0000.000
122A120LEU0-0.027-0.00527.9800.0040.0040.0000.0000.0000.000
123A121ALA00.0100.00831.3870.0080.0080.0000.0000.0000.000
124A122ASP-1-0.803-0.90929.827-0.128-0.1280.0000.0000.0000.000
125A123PRO0-0.016-0.00228.385-0.010-0.0100.0000.0000.0000.000
126A124ASN00.027-0.00227.801-0.008-0.0080.0000.0000.0000.000
127A125ARG10.9680.99326.7730.1610.1610.0000.0000.0000.000
128A126VAL0-0.031-0.00922.121-0.008-0.0080.0000.0000.0000.000
129A127ALA0-0.017-0.02423.633-0.009-0.0090.0000.0000.0000.000
130A128GLN0-0.056-0.02426.2310.0060.0060.0000.0000.0000.000
131A129ASP-1-0.827-0.90522.562-0.222-0.2220.0000.0000.0000.000
132A130ALA00.0530.02420.258-0.014-0.0140.0000.0000.0000.000
133A131VAL00.0060.00217.623-0.036-0.0360.0000.0000.0000.000
134A132ILE0-0.010-0.00218.299-0.038-0.0380.0000.0000.0000.000
135A133ALA0-0.0140.00319.824-0.017-0.0170.0000.0000.0000.000
136A134PHE0-0.017-0.02213.988-0.016-0.0160.0000.0000.0000.000
137A135LYS10.9360.97915.0280.2850.2850.0000.0000.0000.000
138A136THR0-0.022-0.01416.419-0.014-0.0140.0000.0000.0000.000
139A137ALA0-0.028-0.00315.3010.0040.0040.0000.0000.0000.000
140A138LEU00.0220.0119.823-0.006-0.0060.0000.0000.0000.000
141A139TRP00.0540.03913.308-0.019-0.0190.0000.0000.0000.000
142A140PHE00.0080.00115.9340.0100.0100.0000.0000.0000.000
143A141TRP0-0.016-0.0389.6580.0690.0690.0000.0000.0000.000
144A142MET0-0.0120.0089.703-0.019-0.0190.0000.0000.0000.000
145A143ASN0-0.066-0.03513.1670.0720.0720.0000.0000.0000.000
146A144ASN0-0.046-0.02516.2210.0640.0640.0000.0000.0000.000
147A145VAL0-0.026-0.00213.7110.0420.0420.0000.0000.0000.000
148A146HIS0-0.014-0.0247.8180.1530.1530.0000.0000.0000.000
149A147ARG10.8960.94011.8870.2560.2560.0000.0000.0000.000
150A148LEU0-0.025-0.01714.2270.0510.0510.0000.0000.0000.000
151A149MET00.0200.0369.0040.0420.0420.0000.0000.0000.000
152A150PRO00.0050.00011.2980.1070.1070.0000.0000.0000.000
153A151GLN0-0.067-0.02613.1290.0160.0160.0000.0000.0000.000
154A152GLY00.0280.03314.5600.0070.0070.0000.0000.0000.000
155A153PHE00.0400.01913.735-0.043-0.0430.0000.0000.0000.000
156A154GLY00.0380.02615.814-0.041-0.0410.0000.0000.0000.000
157A155ALA0-0.024-0.01017.170-0.021-0.0210.0000.0000.0000.000
158A156THR0-0.010-0.02213.254-0.031-0.0310.0000.0000.0000.000
159A157ILE0-0.014-0.01616.698-0.023-0.0230.0000.0000.0000.000
160A158ARG10.9020.93219.7760.0020.0020.0000.0000.0000.000
161A159ALA0-0.045-0.01117.767-0.003-0.0030.0000.0000.0000.000
162A160ILE0-0.046-0.00516.238-0.023-0.0230.0000.0000.0000.000
163A161ASN0-0.013-0.03020.6370.0030.0030.0000.0000.0000.000
164A162GLY00.0350.02824.1920.0080.0080.0000.0000.0000.000
165A164LEU0-0.013-0.01626.9520.0100.0100.0000.0000.0000.000
166A165GLU-1-0.742-0.83824.157-0.061-0.0610.0000.0000.0000.000
167A198CYS0-0.059-0.01122.2780.0040.0040.0000.0000.0000.000
168A167ASN00.000-0.02026.762-0.003-0.0030.0000.0000.0000.000
169A168GLY00.0690.04129.3710.0010.0010.0000.0000.0000.000
170A169ASN0-0.044-0.01530.2770.0000.0000.0000.0000.0000.000
171A170ASN00.0140.00228.658-0.001-0.0010.0000.0000.0000.000
172A171PRO00.0310.01727.832-0.001-0.0010.0000.0000.0000.000
173A172ALA00.0340.02827.3040.0070.0070.0000.0000.0000.000
174A173GLN00.0360.00825.4560.0100.0100.0000.0000.0000.000
175A174MET0-0.0030.03523.2950.0020.0020.0000.0000.0000.000
176A175ASN0-0.013-0.03822.2330.0160.0160.0000.0000.0000.000
177A176ALA0-0.0040.01422.4460.0120.0120.0000.0000.0000.000
178A177ARG10.7730.84418.7410.0950.0950.0000.0000.0000.000
179A178VAL00.0120.00017.7930.0110.0110.0000.0000.0000.000
180A179GLY0-0.020-0.00418.3770.0310.0310.0000.0000.0000.000
181A180TYR00.0370.01716.7130.0230.0230.0000.0000.0000.000
182A181TYR0-0.027-0.01910.9730.0270.0270.0000.0000.0000.000
183A182LYS10.9470.97513.827-0.079-0.0790.0000.0000.0000.000
184A183GLN0-0.026-0.00715.6340.0440.0440.0000.0000.0000.000
185A184TYR0-0.014-0.04011.2910.0360.0360.0000.0000.0000.000
186A185CYS0-0.0250.00510.9220.0940.0940.0000.0000.0000.000
187A186GLN0-0.0070.00511.9930.1220.1220.0000.0000.0000.000
188A187GLN0-0.020-0.01112.9840.0240.0240.0000.0000.0000.000
189A188LEU0-0.054-0.0316.951-0.025-0.0250.0000.0000.0000.000
190A189ARG10.8850.9538.614-0.134-0.1340.0000.0000.0000.000
191A190VAL00.0080.0128.5080.2290.2290.0000.0000.0000.000
192A191ASP-1-0.858-0.91911.0500.5060.5060.0000.0000.0000.000
193A192PRO00.008-0.00412.6720.0700.0700.0000.0000.0000.000
194A193GLY00.0270.02713.853-0.006-0.0060.0000.0000.0000.000
195A194PRO00.0270.00415.493-0.044-0.0440.0000.0000.0000.000
196A195ASN0-0.038-0.03617.350-0.008-0.0080.0000.0000.0000.000
197A196LEU00.0180.01216.466-0.021-0.0210.0000.0000.0000.000
198A197THR00.0460.02319.169-0.016-0.0160.0000.0000.0000.000