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: 7GJYK

Calculation Name: 4MEM-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MEM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5D006

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2384386.365453
FMO2-HF: Nuclear repulsion 2298712.897176
FMO2-HF: Total energy -85673.468277
FMO2-MP2: Total energy -85925.481014


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:25:ACE )


Summations of interaction energy for fragment #1(A:25:ACE )
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.
1.2012.485-0.004-0.6-0.68-0.001
Interaction energy analysis for fragmet #1(A:25:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / 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].
3A27MET 0-0.0270.0033.6740.5471.831-0.004-0.600-0.680-0.001
4A28PRO 0-0.031-0.0105.6840.0550.0550.0000.0000.0000.000
5A29ASP -1-0.801-0.8998.871-0.127-0.1270.0000.0000.0000.000
6A30LEU 00.0110.01611.138-0.007-0.0070.0000.0000.0000.000
7A31ASP -1-0.833-0.92413.386-0.097-0.0970.0000.0000.0000.000
8A32GLN 0-0.011-0.01612.375-0.001-0.0010.0000.0000.0000.000
9A33GLN 00.0530.0519.8130.0480.0480.0000.0000.0000.000
10A34TRP 00.0090.00014.3920.0190.0190.0000.0000.0000.000
11A35ARG 10.8430.92417.8580.1190.1190.0000.0000.0000.000
12A36GLN 00.0110.01114.464-0.009-0.0090.0000.0000.0000.000
13A37ILE 0-0.014-0.00315.7400.0090.0090.0000.0000.0000.000
14A38GLY 0-0.005-0.00718.9640.0140.0140.0000.0000.0000.000
15A39ASN 00.000-0.01521.7020.0160.0160.0000.0000.0000.000
16A40GLY 0-0.022-0.00221.6340.0020.0020.0000.0000.0000.000
17A41ARG 10.9040.93422.6770.0500.0500.0000.0000.0000.000
18A42GLU -1-0.955-0.94525.200-0.050-0.0500.0000.0000.0000.000
19A43ARG 10.7580.86725.0640.0970.0970.0000.0000.0000.000
20A44PRO 0-0.019-0.01327.8800.0060.0060.0000.0000.0000.000
21A45LEU 00.0310.01130.550-0.004-0.0040.0000.0000.0000.000
22A46ARG 10.9230.95528.7810.0800.0800.0000.0000.0000.000
23A47ALA 00.0650.03132.270-0.001-0.0010.0000.0000.0000.000
24A48GLY 00.0510.03432.790-0.003-0.0030.0000.0000.0000.000
25A49GLU -1-0.819-0.88028.142-0.088-0.0880.0000.0000.0000.000
26A50SER 0-0.057-0.09025.4530.0060.0060.0000.0000.0000.000
27A51TRP 0-0.030-0.02025.157-0.010-0.0100.0000.0000.0000.000
28A52PHE 00.0320.01222.1070.0020.0020.0000.0000.0000.000
29A53LEU 00.0010.01224.151-0.002-0.0020.0000.0000.0000.000
30A54VAL 0-0.033-0.01120.3770.0020.0020.0000.0000.0000.000
31A55GLU -1-0.737-0.85822.9970.0320.0320.0000.0000.0000.000
32A56LYS 10.8820.93623.5190.0010.0010.0000.0000.0000.000
33A57HIS 10.8290.87424.726-0.031-0.0310.0000.0000.0000.000
34A58TRP 00.0320.02914.891-0.014-0.0140.0000.0000.0000.000
35A59TYR 00.0690.03019.9780.0040.0040.0000.0000.0000.000
36A60LYS 10.8610.92420.944-0.009-0.0090.0000.0000.0000.000
37A61GLN 00.0110.01218.5760.0040.0040.0000.0000.0000.000
38A62TRP 00.0240.01414.1420.0080.0080.0000.0000.0000.000
39A63GLU -1-0.856-0.93017.145-0.017-0.0170.0000.0000.0000.000
40A64ALA 0-0.061-0.03719.731-0.005-0.0050.0000.0000.0000.000
41A65TYR 0-0.079-0.05610.594-0.013-0.0130.0000.0000.0000.000
42A66VAL 0-0.028-0.01014.268-0.004-0.0040.0000.0000.0000.000
43A67LYS 10.8270.90216.2420.0020.0020.0000.0000.0000.000
44A68GLY 0-0.0140.00918.472-0.001-0.0010.0000.0000.0000.000
45A69GLY 0-0.030-0.00916.9780.0020.0020.0000.0000.0000.000
46A70ASP -1-0.876-0.94314.6850.1340.1340.0000.0000.0000.000
47A71GLN 0-0.023-0.0217.762-0.061-0.0610.0000.0000.0000.000
48A72ASP -1-0.913-0.93410.5670.4170.4170.0000.0000.0000.000
49A73ALA 0-0.0020.01112.498-0.002-0.0020.0000.0000.0000.000
50A74SER 0-0.024-0.03214.6660.0220.0220.0000.0000.0000.000
51A75THR 0-0.037-0.01917.0330.0050.0050.0000.0000.0000.000
52A76PHE 00.0600.0369.003-0.023-0.0230.0000.0000.0000.000
53A77PRO 0-0.029-0.00913.3520.0000.0000.0000.0000.0000.000
54A78GLY 0-0.013-0.00413.600-0.005-0.0050.0000.0000.0000.000
55A79SER 0-0.035-0.01913.083-0.019-0.0190.0000.0000.0000.000
56A80ILE 0-0.029-0.01314.683-0.010-0.0100.0000.0000.0000.000
57A81ASN 00.0060.00317.181-0.001-0.0010.0000.0000.0000.000
58A82ASN 00.0310.00920.550-0.004-0.0040.0000.0000.0000.000
59A83SER 00.0230.01423.628-0.005-0.0050.0000.0000.0000.000
60A84GLY 00.0060.01225.899-0.003-0.0030.0000.0000.0000.000
61A85LEU 0-0.051-0.03425.822-0.004-0.0040.0000.0000.0000.000
62A86PHE 0-0.015-0.00224.587-0.004-0.0040.0000.0000.0000.000
63A87GLU -1-0.959-0.97730.0790.0130.0130.0000.0000.0000.000
64A88ASP -1-0.794-0.90032.7750.0210.0210.0000.0000.0000.000
65A89GLN 0-0.051-0.03426.532-0.001-0.0010.0000.0000.0000.000
66A90ILE 0-0.0320.00029.4650.0030.0030.0000.0000.0000.000
67A91SER 0-0.060-0.05231.471-0.003-0.0030.0000.0000.0000.000
68A92TRP 00.0070.00325.505-0.002-0.0020.0000.0000.0000.000
69A93HIS 10.9320.97630.027-0.007-0.0070.0000.0000.0000.000
70A94LEU 0-0.020-0.01328.8750.0020.0020.0000.0000.0000.000
71A95ARG 10.9871.00632.266-0.017-0.0170.0000.0000.0000.000
72A96GLU -1-0.866-0.94234.405-0.001-0.0010.0000.0000.0000.000
73A97ARG 10.8410.91437.0560.0020.0020.0000.0000.0000.000
74A98LEU 0-0.0020.02330.9220.0010.0010.0000.0000.0000.000
75A99VAL 00.004-0.01534.215-0.003-0.0030.0000.0000.0000.000
76A100GLU -1-0.940-0.96630.220-0.027-0.0270.0000.0000.0000.000
77A101GLY 0-0.026-0.01430.3990.0000.0000.0000.0000.0000.000
78A102ASP -1-0.931-0.95531.1770.0010.0010.0000.0000.0000.000
79A103ASP -1-0.869-0.93730.4770.0100.0100.0000.0000.0000.000
80A104TYR 0-0.018-0.01926.9500.0020.0020.0000.0000.0000.000
81A105VAL 0-0.048-0.02224.277-0.002-0.0020.0000.0000.0000.000
82A106LEU 00.0340.02425.1250.0000.0000.0000.0000.0000.000
83A107LEU 0-0.035-0.02219.369-0.006-0.0060.0000.0000.0000.000
84A108PRO 00.0170.02322.5000.0020.0020.0000.0000.0000.000
85A109ALA 00.0720.02421.374-0.008-0.0080.0000.0000.0000.000
86A110PRO 0-0.053-0.01519.007-0.011-0.0110.0000.0000.0000.000
87A111ALA 00.0310.00717.355-0.025-0.0250.0000.0000.0000.000
88A112TRP 00.0390.01816.833-0.006-0.0060.0000.0000.0000.000
89A113ASN 00.0310.00215.7820.0180.0180.0000.0000.0000.000
90A114TYR 0-0.034-0.00812.258-0.031-0.0310.0000.0000.0000.000
91A115LEU 00.0470.04711.835-0.025-0.0250.0000.0000.0000.000
92A116VAL 00.0090.00312.5180.0330.0330.0000.0000.0000.000
93A117SER 0-0.111-0.0699.474-0.001-0.0010.0000.0000.0000.000
94A118TRP 0-0.024-0.0167.7430.0210.0210.0000.0000.0000.000
95A119TYR 0-0.018-0.0358.1220.1590.1590.0000.0000.0000.000
96A120GLY 00.0190.02210.8010.0610.0610.0000.0000.0000.000
97A121LEU 0-0.025-0.02112.400-0.011-0.0110.0000.0000.0000.000
98A122LYS 10.9350.96416.106-0.110-0.1100.0000.0000.0000.000
99A123ASP -1-0.945-0.96818.0590.0950.0950.0000.0000.0000.000
100A124ASP -1-0.908-0.95519.0280.0720.0720.0000.0000.0000.000
101A125GLN 0-0.050-0.03120.797-0.018-0.0180.0000.0000.0000.000
102A126PRO 00.0160.02920.679-0.003-0.0030.0000.0000.0000.000
103A127PRO 0-0.009-0.02020.3360.0010.0010.0000.0000.0000.000
104A128ILE 0-0.002-0.00122.0800.0000.0000.0000.0000.0000.000
105A129GLU -1-0.833-0.85624.676-0.059-0.0590.0000.0000.0000.000
106A130ARG 10.8670.93526.1430.0220.0220.0000.0000.0000.000
107A131LYS 10.9150.93928.2690.0510.0510.0000.0000.0000.000
108A132VAL 0-0.055-0.01030.4900.0040.0040.0000.0000.0000.000
109A133ILE 00.0000.00232.944-0.001-0.0010.0000.0000.0000.000
110A134GLU -1-0.861-0.95936.631-0.040-0.0400.0000.0000.0000.000
111A135LEU 00.0110.00139.7550.0020.0020.0000.0000.0000.000
112A136PRO 00.0310.01342.890-0.001-0.0010.0000.0000.0000.000
113A137GLY 0-0.0110.00245.1570.0010.0010.0000.0000.0000.000
114A138ILE 0-0.053-0.02939.762-0.001-0.0010.0000.0000.0000.000
115A139ARG 10.8670.95935.4840.0420.0420.0000.0000.0000.000
116A140LYS 10.9640.97135.4050.0210.0210.0000.0000.0000.000
117A141VAL 00.0450.02929.702-0.001-0.0010.0000.0000.0000.000
118A142GLU -1-0.765-0.86232.847-0.019-0.0190.0000.0000.0000.000
119A143VAL 00.007-0.00731.2890.0000.0000.0000.0000.0000.000
120A144TYR 0-0.058-0.03733.0760.0010.0010.0000.0000.0000.000
121A145PRO 00.0020.02333.9410.0000.0000.0000.0000.0000.000
122A146ILE 0-0.0150.01537.0160.0020.0020.0000.0000.0000.000
123A147GLU -1-0.900-0.96536.587-0.005-0.0050.0000.0000.0000.000
124A148LEU 0-0.0120.00240.2960.0010.0010.0000.0000.0000.000
125A149LEU 00.0080.00942.7380.0000.0000.0000.0000.0000.000
126A150LEU 00.0300.01043.7360.0000.0000.0000.0000.0000.000
127A151VAL 00.0320.01746.3100.0010.0010.0000.0000.0000.000
128A152GLN 00.0480.02949.054-0.001-0.0010.0000.0000.0000.000
129A153HIS 0-0.006-0.02451.3810.0010.0010.0000.0000.0000.000
130A154SER 0-0.049-0.04054.7990.0000.0000.0000.0000.0000.000
131A155ASP -1-0.893-0.94150.052-0.003-0.0030.0000.0000.0000.000
132A156MET 0-0.040-0.02650.9600.0000.0000.0000.0000.0000.000
133A157GLU -1-0.977-0.97050.2890.0010.0010.0000.0000.0000.000
134A158THR 0-0.047-0.02345.5840.0010.0010.0000.0000.0000.000
135A159ALA 0-0.025-0.01145.969-0.001-0.0010.0000.0000.0000.000
136A160LEU 0-0.014-0.00441.0240.0010.0010.0000.0000.0000.000
137A161THR 0-0.013-0.00938.9110.0000.0000.0000.0000.0000.000
138A162ILE 0-0.024-0.00738.542-0.001-0.0010.0000.0000.0000.000
139A163GLN 0-0.023-0.00832.954-0.002-0.0020.0000.0000.0000.000
140A164PHE 00.010-0.00237.402-0.002-0.0020.0000.0000.0000.000
141A165SER 0-0.044-0.06037.3690.0000.0000.0000.0000.0000.000
142A166TYR 0-0.036-0.02838.9990.0010.0010.0000.0000.0000.000
143A167SER 0-0.080-0.05439.6640.0000.0000.0000.0000.0000.000
144A168ASP -1-0.792-0.88539.639-0.026-0.0260.0000.0000.0000.000
145A169SER 00.0230.00942.6100.0020.0020.0000.0000.0000.000
146A170VAL 00.0290.00845.6520.0000.0000.0000.0000.0000.000
147A171ASP -1-0.952-0.98048.015-0.019-0.0190.0000.0000.0000.000
148A172LEU 00.0310.02340.2540.0000.0000.0000.0000.0000.000
149A173VAL 0-0.0010.00343.8290.0000.0000.0000.0000.0000.000
150A174LEU 0-0.048-0.02244.9990.0010.0010.0000.0000.0000.000
151A175GLN 0-0.002-0.01244.376-0.001-0.0010.0000.0000.0000.000
152A176THR 00.0330.02640.1970.0000.0000.0000.0000.0000.000
153A177ALA 0-0.013-0.01342.7650.0010.0010.0000.0000.0000.000
154A178ARG 10.7830.86945.1440.0160.0160.0000.0000.0000.000
155A179GLU -1-0.941-0.95540.535-0.023-0.0230.0000.0000.0000.000
156A180GLN 0-0.030-0.02038.0500.0000.0000.0000.0000.0000.000
157A181PHE 0-0.079-0.04542.4770.0010.0010.0000.0000.0000.000
158A182LEU 0-0.078-0.03043.7050.0010.0010.0000.0000.0000.000
159A183VAL 0-0.0130.00246.2860.0010.0010.0000.0000.0000.000
160A184GLU -1-0.874-0.90148.572-0.013-0.0130.0000.0000.0000.000
161A185PRO 0-0.016-0.02449.4540.0000.0000.0000.0000.0000.000
162A186GLN 0-0.072-0.06951.216-0.001-0.0010.0000.0000.0000.000
163A187GLU -1-0.935-0.95553.541-0.010-0.0100.0000.0000.0000.000
164A188ASP -1-0.829-0.89054.206-0.013-0.0130.0000.0000.0000.000
165A189THR 00.0450.00551.7660.0000.0000.0000.0000.0000.000
166A190ARG 10.7950.91554.0380.0080.0080.0000.0000.0000.000
167A191LEU 00.0520.02849.1930.0010.0010.0000.0000.0000.000
168A192TRP 0-0.036-0.01453.3740.0000.0000.0000.0000.0000.000
169A193THR 00.0130.00451.3470.0000.0000.0000.0000.0000.000
170A194LYS 10.9670.99253.4760.0020.0020.0000.0000.0000.000
171A195ASN 00.0830.05553.3590.0010.0010.0000.0000.0000.000
172A196SER 0-0.019-0.04252.6490.0010.0010.0000.0000.0000.000
173A197GLU -1-0.957-0.92554.924-0.004-0.0040.0000.0000.0000.000
174A198GLY 0-0.039-0.03558.0880.0010.0010.0000.0000.0000.000
175A199SER 0-0.055-0.04058.2640.0010.0010.0000.0000.0000.000
176A200LEU 0-0.044-0.01556.6410.0000.0000.0000.0000.0000.000
177A201ASP -1-0.863-0.92957.519-0.006-0.0060.0000.0000.0000.000
178A202ARG 10.9150.94657.0230.0080.0080.0000.0000.0000.000
179A203LEU 00.0220.00451.1570.0000.0000.0000.0000.0000.000
180A204CYS 0-0.089-0.04354.981-0.001-0.0010.0000.0000.0000.000
181A205ASN 00.0280.00655.256-0.001-0.0010.0000.0000.0000.000
182A206THR 00.0250.00451.2840.0000.0000.0000.0000.0000.000
183A207GLN 00.0170.00750.317-0.002-0.0020.0000.0000.0000.000
184A208ILE 0-0.030-0.00250.398-0.001-0.0010.0000.0000.0000.000
185A209THR 00.0070.00545.6040.0000.0000.0000.0000.0000.000
186A210LEU 00.0150.00243.0990.0010.0010.0000.0000.0000.000
187A211LEU 0-0.023-0.01044.5040.0010.0010.0000.0000.0000.000
188A212ASP -1-0.899-0.95546.921-0.015-0.0150.0000.0000.0000.000
189A213ALA 0-0.089-0.03549.4150.0010.0010.0000.0000.0000.000
190A214CYS 0-0.098-0.04049.7160.0010.0010.0000.0000.0000.000
191A215LEU 0-0.020-0.00546.7360.0010.0010.0000.0000.0000.000
192A216GLU -1-0.917-0.96546.250-0.005-0.0050.0000.0000.0000.000
193A217THR 00.010-0.00540.400-0.001-0.0010.0000.0000.0000.000
194A218GLY 0-0.005-0.01543.1520.0010.0010.0000.0000.0000.000
195A219GLN 0-0.041-0.00944.2730.0010.0010.0000.0000.0000.000
196A220LEU 0-0.020-0.01046.950-0.001-0.0010.0000.0000.0000.000
197A221VAL 0-0.027-0.01847.8920.0000.0000.0000.0000.0000.000
198A222ILE 00.0040.00549.4280.0000.0000.0000.0000.0000.000
199A223MET 00.0020.01049.567-0.001-0.0010.0000.0000.0000.000
200A224GLU -1-0.722-0.85652.009-0.006-0.0060.0000.0000.0000.000
201A225THR 00.0830.02553.626-0.001-0.0010.0000.0000.0000.000
202A226ARG 10.7710.89856.0260.0110.0110.0000.0000.0000.000
203A227ASN 00.0230.01759.2940.0000.0000.0000.0000.0000.000
204A228LYS 10.9810.96758.6880.0090.0090.0000.0000.0000.000
205A229ASP -1-0.846-0.89263.280-0.007-0.0070.0000.0000.0000.000
206A230GLY 0-0.022-0.00964.1010.0000.0000.0000.0000.0000.000
207A231THR 0-0.041-0.03864.7570.0000.0000.0000.0000.0000.000
208A232TRP 00.007-0.01657.2440.0000.0000.0000.0000.0000.000
209A233PRO 00.0390.03759.2150.0010.0010.0000.0000.0000.000
210A234SER 0-0.087-0.04860.0980.0010.0010.0000.0000.0000.000
211A235ALA 0-0.075-0.05262.1490.0000.0000.0000.0000.0000.000
212A236GLN 0-0.037-0.03264.8990.0000.0000.0000.0000.0000.000
213A237LEU 0-0.024-0.01067.6170.0000.0000.0000.0000.0000.000
214A238NME 0-0.0110.01070.5950.0000.0000.0000.0000.0000.000