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: MNG1Z

Calculation Name: 4MEM-A-Xray372

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: 2023-09-24

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2377083.37046
FMO2-HF: Nuclear repulsion 2291580.758178
FMO2-HF: Total energy -85502.612282
FMO2-MP2: Total energy -85754.109506


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:26:ALA)


Summations of interaction energy for fragment #1(A:26:ALA)
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.
1.1672.513-0.023-0.578-0.7450
Interaction energy analysis for fragmet #1(A:26:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.025
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].
3A28PRO0-0.035-0.0133.8080.2951.641-0.023-0.578-0.7450.000
4A29ASP-1-0.803-0.8996.4640.6760.6760.0000.0000.0000.000
5A30LEU00.0210.0199.567-0.169-0.1690.0000.0000.0000.000
6A31ASP-1-0.842-0.92712.4680.0090.0090.0000.0000.0000.000
7A32GLN0-0.015-0.0188.4140.0470.0470.0000.0000.0000.000
8A33GLN00.0580.0538.605-0.114-0.1140.0000.0000.0000.000
9A34TRP00.0090.00112.237-0.018-0.0180.0000.0000.0000.000
10A35ARG10.8440.92315.6800.0050.0050.0000.0000.0000.000
11A36GLN00.0080.01110.253-0.029-0.0290.0000.0000.0000.000
12A37ILE0-0.008-0.00212.9870.0010.0010.0000.0000.0000.000
13A38GLY0-0.002-0.00616.2040.0160.0160.0000.0000.0000.000
14A39ASN0-0.010-0.01818.1220.0240.0240.0000.0000.0000.000
15A40GLY0-0.020-0.00118.2300.0010.0010.0000.0000.0000.000
16A41ARG10.9020.93219.0270.1060.1060.0000.0000.0000.000
17A42GLU-1-0.953-0.94422.076-0.073-0.0730.0000.0000.0000.000
18A43ARG10.7600.86820.4550.1800.1800.0000.0000.0000.000
19A44PRO0-0.018-0.01223.8930.0050.0050.0000.0000.0000.000
20A45LEU00.0330.01226.439-0.009-0.0090.0000.0000.0000.000
21A46ARG10.9240.95624.1550.1350.1350.0000.0000.0000.000
22A47ALA00.0660.03128.309-0.006-0.0060.0000.0000.0000.000
23A48GLY00.0480.03329.000-0.003-0.0030.0000.0000.0000.000
24A49GLU-1-0.821-0.88124.110-0.169-0.1690.0000.0000.0000.000
25A50SER0-0.060-0.09021.8930.0140.0140.0000.0000.0000.000
26A51TRP0-0.031-0.02121.892-0.019-0.0190.0000.0000.0000.000
27A52PHE00.0350.01319.2760.0000.0000.0000.0000.0000.000
28A53LEU00.0000.01221.4350.0020.0020.0000.0000.0000.000
29A54VAL0-0.035-0.01018.440-0.013-0.0130.0000.0000.0000.000
30A55GLU-1-0.732-0.85621.297-0.036-0.0360.0000.0000.0000.000
31A56LYS10.8820.93522.3290.0420.0420.0000.0000.0000.000
32A57HIS10.8300.87523.6020.0370.0370.0000.0000.0000.000
33A58TRP00.0330.03013.8960.0060.0060.0000.0000.0000.000
34A59TYR00.0660.02919.0150.0150.0150.0000.0000.0000.000
35A60LYS10.8570.92319.8840.0240.0240.0000.0000.0000.000
36A61GLN00.0120.01318.3180.0290.0290.0000.0000.0000.000
37A62TRP00.0250.01612.8720.0320.0320.0000.0000.0000.000
38A63GLU-1-0.852-0.92916.493-0.006-0.0060.0000.0000.0000.000
39A64ALA0-0.065-0.03919.0370.0140.0140.0000.0000.0000.000
40A65TYR0-0.077-0.05411.0770.0140.0140.0000.0000.0000.000
41A66VAL0-0.018-0.00813.4720.0320.0320.0000.0000.0000.000
42A67LYS10.8210.89915.8430.0100.0100.0000.0000.0000.000
43A68GLY0-0.0190.00718.5330.0000.0000.0000.0000.0000.000
44A69GLY0-0.029-0.00816.9540.0020.0020.0000.0000.0000.000
45A70ASP-1-0.875-0.94215.8430.4060.4060.0000.0000.0000.000
46A71GLN0-0.022-0.0208.305-0.107-0.1070.0000.0000.0000.000
47A72ASP-1-0.915-0.93511.9380.8130.8130.0000.0000.0000.000
48A73ALA0-0.0030.01114.017-0.068-0.0680.0000.0000.0000.000
49A74SER0-0.025-0.03215.6770.0110.0110.0000.0000.0000.000
50A75THR0-0.039-0.02117.673-0.011-0.0110.0000.0000.0000.000
51A76PHE00.0680.0379.186-0.066-0.0660.0000.0000.0000.000
52A77PRO0-0.031-0.00813.128-0.021-0.0210.0000.0000.0000.000
53A78GLY0-0.016-0.00413.539-0.017-0.0170.0000.0000.0000.000
54A79SER0-0.032-0.01912.893-0.018-0.0180.0000.0000.0000.000
55A80ILE0-0.030-0.01513.5420.0340.0340.0000.0000.0000.000
56A81ASN00.0020.00216.340-0.006-0.0060.0000.0000.0000.000
57A82ASN00.0330.01019.8990.0160.0160.0000.0000.0000.000
58A83SER00.0240.01422.7700.0060.0060.0000.0000.0000.000
59A84GLY00.0050.01125.3200.0030.0030.0000.0000.0000.000
60A85LEU0-0.047-0.03124.4040.0030.0030.0000.0000.0000.000
61A86PHE0-0.017-0.00323.663-0.002-0.0020.0000.0000.0000.000
62A87GLU-1-0.957-0.97829.135-0.042-0.0420.0000.0000.0000.000
63A88ASP-1-0.797-0.90131.916-0.054-0.0540.0000.0000.0000.000
64A89GLN0-0.050-0.03426.442-0.003-0.0030.0000.0000.0000.000
65A90ILE0-0.0330.00029.099-0.001-0.0010.0000.0000.0000.000
66A91SER0-0.057-0.05130.612-0.004-0.0040.0000.0000.0000.000
67A92TRP00.0040.00225.212-0.007-0.0070.0000.0000.0000.000
68A93HIS10.9330.97628.6780.0630.0630.0000.0000.0000.000
69A94LEU0-0.021-0.01327.184-0.001-0.0010.0000.0000.0000.000
70A95ARG10.9861.00730.7180.0460.0460.0000.0000.0000.000
71A96GLU-1-0.866-0.94133.109-0.047-0.0470.0000.0000.0000.000
72A97ARG10.8410.91335.6650.0440.0440.0000.0000.0000.000
73A98LEU00.0010.02429.3870.0020.0020.0000.0000.0000.000
74A99VAL00.002-0.01432.655-0.003-0.0030.0000.0000.0000.000
75A100GLU-1-0.939-0.96627.951-0.084-0.0840.0000.0000.0000.000
76A101GLY0-0.029-0.01528.5260.0050.0050.0000.0000.0000.000
77A102ASP-1-0.931-0.95629.640-0.032-0.0320.0000.0000.0000.000
78A103ASP-1-0.870-0.93729.277-0.044-0.0440.0000.0000.0000.000
79A104TYR0-0.019-0.01925.157-0.007-0.0070.0000.0000.0000.000
80A105VAL0-0.050-0.02222.2510.0080.0080.0000.0000.0000.000
81A106LEU00.0340.02422.955-0.012-0.0120.0000.0000.0000.000
82A107LEU0-0.033-0.02116.754-0.001-0.0010.0000.0000.0000.000
83A108PRO00.0130.02219.169-0.004-0.0040.0000.0000.0000.000
84A109ALA00.0730.02517.971-0.026-0.0260.0000.0000.0000.000
85A110PRO0-0.052-0.01414.963-0.036-0.0360.0000.0000.0000.000
86A111ALA00.0320.00613.566-0.068-0.0680.0000.0000.0000.000
87A112TRP00.0380.01813.690-0.047-0.0470.0000.0000.0000.000
88A113ASN00.0260.00012.078-0.015-0.0150.0000.0000.0000.000
89A114TYR0-0.037-0.0098.078-0.074-0.0740.0000.0000.0000.000
90A115LEU00.0560.0508.940-0.161-0.1610.0000.0000.0000.000
91A116VAL00.0100.00310.682-0.008-0.0080.0000.0000.0000.000
92A117SER0-0.115-0.0706.188-0.116-0.1160.0000.0000.0000.000
93A118TRP0-0.024-0.0175.517-0.049-0.0490.0000.0000.0000.000
94A119TYR0-0.015-0.0337.1800.2160.2160.0000.0000.0000.000
95A120GLY00.0130.0199.9410.0950.0950.0000.0000.0000.000
96A121LEU0-0.019-0.01911.7440.0400.0400.0000.0000.0000.000
97A122LYS10.9330.96515.4910.0460.0460.0000.0000.0000.000
98A123ASP-1-0.944-0.96717.861-0.062-0.0620.0000.0000.0000.000
99A124ASP-1-0.910-0.95619.019-0.116-0.1160.0000.0000.0000.000
100A125GLN0-0.046-0.03120.188-0.006-0.0060.0000.0000.0000.000
101A126PRO00.0160.03019.675-0.023-0.0230.0000.0000.0000.000
102A127PRO0-0.014-0.02118.1480.0040.0040.0000.0000.0000.000
103A128ILE0-0.003-0.00220.1060.0130.0130.0000.0000.0000.000
104A129GLU-1-0.831-0.85621.905-0.184-0.1840.0000.0000.0000.000
105A130ARG10.8640.93523.4300.1210.1210.0000.0000.0000.000
106A131LYS10.9170.94024.6810.1360.1360.0000.0000.0000.000
107A132VAL0-0.053-0.01126.9890.0080.0080.0000.0000.0000.000
108A133ILE0-0.0030.00229.475-0.001-0.0010.0000.0000.0000.000
109A134GLU-1-0.859-0.95933.153-0.075-0.0750.0000.0000.0000.000
110A135LEU00.0080.00336.1580.0020.0020.0000.0000.0000.000
111A136PRO00.0320.01239.433-0.001-0.0010.0000.0000.0000.000
112A137GLY0-0.0080.00241.4670.0020.0020.0000.0000.0000.000
113A138ILE0-0.052-0.02736.5540.0000.0000.0000.0000.0000.000
114A139ARG10.8640.95831.5570.0760.0760.0000.0000.0000.000
115A140LYS10.9600.97132.1490.0670.0670.0000.0000.0000.000
116A141VAL00.0450.02926.760-0.003-0.0030.0000.0000.0000.000
117A142GLU-1-0.766-0.86329.728-0.070-0.0700.0000.0000.0000.000
118A143VAL00.013-0.00528.748-0.005-0.0050.0000.0000.0000.000
119A144TYR0-0.059-0.03830.525-0.002-0.0020.0000.0000.0000.000
120A145PRO00.0050.02531.3230.0040.0040.0000.0000.0000.000
121A146ILE0-0.0200.01434.3720.0020.0020.0000.0000.0000.000
122A147GLU-1-0.899-0.96434.587-0.070-0.0700.0000.0000.0000.000
123A148LEU0-0.0110.00237.9570.0040.0040.0000.0000.0000.000
124A149LEU00.0070.01040.424-0.002-0.0020.0000.0000.0000.000
125A150LEU00.0260.00741.0810.0030.0030.0000.0000.0000.000
126A151VAL00.0340.01843.9320.0000.0000.0000.0000.0000.000
127A152GLN00.0480.02946.7880.0010.0010.0000.0000.0000.000
128A153HIS0-0.008-0.02649.0030.0010.0010.0000.0000.0000.000
129A154SER0-0.044-0.03952.4150.0010.0010.0000.0000.0000.000
130A155ASP-1-0.894-0.94147.986-0.039-0.0390.0000.0000.0000.000
131A156MET0-0.041-0.02748.902-0.001-0.0010.0000.0000.0000.000
132A157GLU-1-0.975-0.96948.705-0.033-0.0330.0000.0000.0000.000
133A158THR0-0.048-0.02343.675-0.001-0.0010.0000.0000.0000.000
134A159ALA0-0.026-0.01044.1080.0000.0000.0000.0000.0000.000
135A160LEU0-0.015-0.00438.938-0.002-0.0020.0000.0000.0000.000
136A161THR0-0.010-0.00836.8310.0020.0020.0000.0000.0000.000
137A162ILE0-0.022-0.00635.932-0.004-0.0040.0000.0000.0000.000
138A163GLN0-0.023-0.00930.604-0.002-0.0020.0000.0000.0000.000
139A164PHE00.010-0.00134.588-0.002-0.0020.0000.0000.0000.000
140A165SER0-0.046-0.06034.1930.0000.0000.0000.0000.0000.000
141A166TYR0-0.036-0.02935.9400.0030.0030.0000.0000.0000.000
142A167SER0-0.077-0.05436.3410.0030.0030.0000.0000.0000.000
143A168ASP-1-0.792-0.88336.424-0.074-0.0740.0000.0000.0000.000
144A169SER00.0220.00839.2730.0030.0030.0000.0000.0000.000
145A170VAL00.0360.01042.385-0.001-0.0010.0000.0000.0000.000
146A171ASP-1-0.950-0.98044.710-0.050-0.0500.0000.0000.0000.000
147A172LEU00.0250.02136.8230.0000.0000.0000.0000.0000.000
148A173VAL00.0000.00540.609-0.002-0.0020.0000.0000.0000.000
149A174LEU0-0.047-0.02241.9190.0000.0000.0000.0000.0000.000
150A175GLN0-0.006-0.01341.048-0.002-0.0020.0000.0000.0000.000
151A176THR00.0320.02537.238-0.002-0.0020.0000.0000.0000.000
152A177ALA0-0.004-0.01039.704-0.001-0.0010.0000.0000.0000.000
153A178ARG10.7790.86842.3120.0460.0460.0000.0000.0000.000
154A179GLU-1-0.945-0.95837.362-0.069-0.0690.0000.0000.0000.000
155A180GLN0-0.029-0.02035.532-0.002-0.0020.0000.0000.0000.000
156A181PHE0-0.081-0.04439.8130.0010.0010.0000.0000.0000.000
157A182LEU0-0.079-0.03141.3420.0020.0020.0000.0000.0000.000
158A183VAL0-0.0100.00343.6190.0020.0020.0000.0000.0000.000
159A184GLU-1-0.874-0.90045.598-0.042-0.0420.0000.0000.0000.000
160A185PRO0-0.016-0.02446.3130.0010.0010.0000.0000.0000.000
161A186GLN0-0.072-0.07047.976-0.001-0.0010.0000.0000.0000.000
162A187GLU-1-0.934-0.95450.651-0.037-0.0370.0000.0000.0000.000
163A188ASP-1-0.827-0.89051.024-0.037-0.0370.0000.0000.0000.000
164A189THR00.0480.00648.8240.0000.0000.0000.0000.0000.000
165A190ARG10.7900.91450.9850.0310.0310.0000.0000.0000.000
166A191LEU00.0530.02946.1960.0000.0000.0000.0000.0000.000
167A192TRP0-0.035-0.01450.5180.0020.0020.0000.0000.0000.000
168A193THR00.0140.00448.865-0.001-0.0010.0000.0000.0000.000
169A194LYS10.9710.99451.0890.0320.0320.0000.0000.0000.000
170A195ASN00.0820.05551.0290.0000.0000.0000.0000.0000.000
171A196SER0-0.019-0.04150.3800.0010.0010.0000.0000.0000.000
172A197GLU-1-0.962-0.92852.711-0.025-0.0250.0000.0000.0000.000
173A198GLY0-0.036-0.03455.7990.0010.0010.0000.0000.0000.000
174A199SER0-0.055-0.03955.8980.0020.0020.0000.0000.0000.000
175A200LEU0-0.047-0.01654.233-0.001-0.0010.0000.0000.0000.000
176A201ASP-1-0.862-0.92854.929-0.028-0.0280.0000.0000.0000.000
177A202ARG10.9140.94654.3090.0290.0290.0000.0000.0000.000
178A203LEU00.0190.00348.2140.0010.0010.0000.0000.0000.000
179A204CYS0-0.087-0.04351.860-0.001-0.0010.0000.0000.0000.000
180A205ASN00.0270.00651.794-0.001-0.0010.0000.0000.0000.000
181A206THR00.0290.00547.9110.0000.0000.0000.0000.0000.000
182A207GLN00.0140.00546.875-0.004-0.0040.0000.0000.0000.000
183A208ILE0-0.031-0.00246.9610.0000.0000.0000.0000.0000.000
184A209THR00.0050.00542.340-0.001-0.0010.0000.0000.0000.000
185A210LEU00.0220.00340.1110.0030.0030.0000.0000.0000.000
186A211LEU0-0.028-0.01141.4710.0020.0020.0000.0000.0000.000
187A212ASP-1-0.899-0.95443.933-0.041-0.0410.0000.0000.0000.000
188A213ALA0-0.089-0.03546.4630.0020.0020.0000.0000.0000.000
189A214CYS0-0.097-0.04146.9780.0020.0020.0000.0000.0000.000
190A215LEU0-0.024-0.00544.0370.0010.0010.0000.0000.0000.000
191A216GLU-1-0.917-0.96343.790-0.040-0.0400.0000.0000.0000.000
192A217THR00.009-0.00738.294-0.002-0.0020.0000.0000.0000.000
193A218GLY0-0.005-0.01540.9690.0020.0020.0000.0000.0000.000
194A219GLN0-0.038-0.00842.2450.0010.0010.0000.0000.0000.000
195A220LEU0-0.018-0.00844.665-0.001-0.0010.0000.0000.0000.000
196A221VAL0-0.029-0.01945.3120.0020.0020.0000.0000.0000.000
197A222ILE00.0070.00746.981-0.001-0.0010.0000.0000.0000.000
198A223MET0-0.0020.00946.8520.0000.0000.0000.0000.0000.000
199A224GLU-1-0.720-0.85849.334-0.030-0.0300.0000.0000.0000.000
200A225THR00.0800.02650.890-0.001-0.0010.0000.0000.0000.000
201A226ARG10.7770.89953.2210.0330.0330.0000.0000.0000.000
202A227ASN00.0170.01556.425-0.001-0.0010.0000.0000.0000.000
203A228LYS10.9800.96655.7700.0320.0320.0000.0000.0000.000
204A229ASP-1-0.845-0.89260.378-0.026-0.0260.0000.0000.0000.000
205A230GLY0-0.023-0.00961.0360.0010.0010.0000.0000.0000.000
206A231THR0-0.039-0.03761.7180.0000.0000.0000.0000.0000.000
207A232TRP00.007-0.01654.307-0.001-0.0010.0000.0000.0000.000
208A233PRO00.0430.03756.6080.0010.0010.0000.0000.0000.000
209A234SER0-0.088-0.04857.5130.0010.0010.0000.0000.0000.000
210A235ALA0-0.074-0.05059.5770.0010.0010.0000.0000.0000.000
211A236GLN0-0.041-0.03162.2460.0010.0010.0000.0000.0000.000
212A237LEU0-0.0310.00165.0390.0010.0010.0000.0000.0000.000