FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZV71N

Calculation Name: 3MDN-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3MDN

Chain ID: A

ChEMBL ID:
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UniProt ID: Q5LRU5

Base Structure: X-ray

Registration Date: 2023-09-22

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 220
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2697979.173249
FMO2-HF: Nuclear repulsion 2611472.302743
FMO2-HF: Total energy -86506.870506
FMO2-MP2: Total energy -86760.21991


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-12.168-10.28913.017-5.766-9.13-0.032
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / 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].
3A4TRP00.008-0.0023.7130.1982.019-0.004-0.813-1.0030.003
4A5ALA00.009-0.0015.7140.2350.2350.0000.0000.0000.000
5A6ALA00.0030.0139.5060.2120.2120.0000.0000.0000.000
6A7TYR0-0.016-0.03012.263-0.040-0.0400.0000.0000.0000.000
7A8HIS0-0.004-0.01316.0980.0270.0270.0000.0000.0000.000
8A9GLY00.0290.00719.432-0.010-0.0100.0000.0000.0000.000
9A10THR0-0.023-0.01122.8470.0320.0320.0000.0000.0000.000
10A11PRO0-0.047-0.02923.096-0.027-0.0270.0000.0000.0000.000
11A12ILE0-0.0300.01818.7280.0170.0170.0000.0000.0000.000
12A13PHE0-0.007-0.01821.0130.0230.0230.0000.0000.0000.000
13A14LEU00.0030.00815.775-0.045-0.0450.0000.0000.0000.000
14A15GLU-1-0.740-0.84815.783-0.307-0.3070.0000.0000.0000.000
15A16ASP-1-0.873-0.91417.436-0.366-0.3660.0000.0000.0000.000
16A17VAL0-0.076-0.03812.928-0.040-0.0400.0000.0000.0000.000
17A18ILE0-0.040-0.00911.484-0.105-0.1050.0000.0000.0000.000
18A43GLY00.0250.0117.3650.0670.0670.0000.0000.0000.000
19A44PHE0-0.061-0.0517.1640.1060.1060.0000.0000.0000.000
20A45GLY00.0470.0188.0210.0620.0620.0000.0000.0000.000
21A46VAL0-0.043-0.0329.158-0.312-0.3120.0000.0000.0000.000
22A47ALA0-0.0040.00611.7380.1250.1250.0000.0000.0000.000
23A48TRP0-0.012-0.01414.149-0.099-0.0990.0000.0000.0000.000
24A49TYR00.0420.02717.1930.0360.0360.0000.0000.0000.000
25A50ASP-1-0.847-0.92020.628-0.143-0.1430.0000.0000.0000.000
26A51ALA0-0.068-0.02423.8820.0020.0020.0000.0000.0000.000
27A52ARG10.8370.91224.3980.0400.0400.0000.0000.0000.000
28A53PRO00.0130.00924.379-0.017-0.0170.0000.0000.0000.000
29A54GLU-1-0.860-0.93122.334-0.046-0.0460.0000.0000.0000.000
30A55PRO0-0.0200.00817.298-0.008-0.0080.0000.0000.0000.000
31A56GLY0-0.019-0.00119.1570.0410.0410.0000.0000.0000.000
32A57LEU0-0.031-0.03712.690-0.040-0.0400.0000.0000.0000.000
33A58TYR0-0.061-0.04714.2470.0200.0200.0000.0000.0000.000
34A59ARG10.8700.92011.128-0.662-0.6620.0000.0000.0000.000
35A60ASP-1-0.867-0.92611.7110.4870.4870.0000.0000.0000.000
36A61VAL00.0340.00411.0770.1390.1390.0000.0000.0000.000
37A62TYR0-0.056-0.00811.9970.0870.0870.0000.0000.0000.000
38A63PRO00.015-0.00110.4670.0310.0310.0000.0000.0000.000
39A64ALA00.0560.0299.848-0.114-0.1140.0000.0000.0000.000
40A65TRP0-0.036-0.0287.432-0.010-0.0100.0000.0000.0000.000
41A66SER0-0.058-0.03514.057-0.021-0.0210.0000.0000.0000.000
42A67ASP-1-0.699-0.80715.7850.2160.2160.0000.0000.0000.000
43A68PRO0-0.015-0.01417.344-0.053-0.0530.0000.0000.0000.000
44A69ASN0-0.050-0.03319.814-0.054-0.0540.0000.0000.0000.000
45A70LEU00.0410.02812.994-0.037-0.0370.0000.0000.0000.000
46A71ARG10.7890.88617.3830.1030.1030.0000.0000.0000.000
47A72ALA00.001-0.00518.854-0.040-0.0400.0000.0000.0000.000
48A73VAL00.014-0.00217.967-0.026-0.0260.0000.0000.0000.000
49A74ALA00.0260.00416.341-0.027-0.0270.0000.0000.0000.000
50A75HIS10.8140.90118.2930.1130.1130.0000.0000.0000.000
51A76HIS0-0.050-0.03021.7020.0130.0130.0000.0000.0000.000
52A77VAL00.0020.01020.1260.0040.0040.0000.0000.0000.000
53A78ARG10.9130.95721.1940.1400.1400.0000.0000.0000.000
54A79SER00.004-0.02519.0910.0070.0070.0000.0000.0000.000
55A80GLY00.0320.02720.890-0.024-0.0240.0000.0000.0000.000
56A81LEU0-0.043-0.01416.849-0.032-0.0320.0000.0000.0000.000
57A82PHE00.0010.00613.9840.0510.0510.0000.0000.0000.000
58A83LEU00.0080.00710.690-0.117-0.1170.0000.0000.0000.000
59A84SER0-0.046-0.0349.2680.2090.2090.0000.0000.0000.000
60A85HIS00.051-0.0012.701-4.444-4.9344.186-1.193-2.504-0.009
61A86VAL00.0110.0092.438-2.109-3.8427.786-2.639-3.414-0.014
62A99CYM-1-0.876-0.9247.1591.9741.9740.0000.0000.0000.000
63A100HIS0-0.069-0.0434.892-0.653-0.4600.003-0.055-0.1410.000
64A101PRO00.008-0.0037.660-0.040-0.0400.0000.0000.0000.000
65A102PHE0-0.021-0.0038.8290.1470.1470.0000.0000.0000.000
66A103ALA00.0300.00112.467-0.116-0.1160.0000.0000.0000.000
67A104ALA0-0.022-0.00715.9670.0530.0530.0000.0000.0000.000
68A105ARG10.7780.86519.520-0.053-0.0530.0000.0000.0000.000
69A106ARG10.9080.94021.7270.1320.1320.0000.0000.0000.000
70A107TRP00.0010.03017.936-0.044-0.0440.0000.0000.0000.000
71A108CYS0-0.032-0.01413.8370.0240.0240.0000.0000.0000.000
72A109PHE00.016-0.00310.479-0.100-0.1000.0000.0000.0000.000
73A110MET0-0.0200.0136.4460.0430.0430.0000.0000.0000.000
74A111HIS0-0.021-0.0116.2250.0680.0680.0000.0000.0000.000
75A112ASN00.0500.0322.564-1.1090.8321.048-1.028-1.961-0.012
76A113GLY00.015-0.0024.438-0.403-0.315-0.001-0.010-0.0780.000
77A114GLN0-0.043-0.0196.3100.5190.5190.0000.0000.0000.000
78A115VAL00.0000.0039.210-0.215-0.2150.0000.0000.0000.000
79A116GLY00.0240.02512.9530.1050.1050.0000.0000.0000.000
80A117GLY00.0560.01814.703-0.041-0.0410.0000.0000.0000.000
81A118PHE0-0.017-0.01114.186-0.017-0.0170.0000.0000.0000.000
82A119GLU-1-0.916-0.96614.4000.7380.7380.0000.0000.0000.000
83A120ALA0-0.0240.00017.407-0.032-0.0320.0000.0000.0000.000
84A121PHE0-0.029-0.02617.717-0.039-0.0390.0000.0000.0000.000
85A122ARG10.8720.94116.767-0.486-0.4860.0000.0000.0000.000
86A123LYS10.9810.99019.400-0.225-0.2250.0000.0000.0000.000
87A124GLN00.007-0.00422.858-0.004-0.0040.0000.0000.0000.000
88A125ALA00.0000.00918.783-0.024-0.0240.0000.0000.0000.000
89A126ASP-1-0.743-0.85119.1050.3670.3670.0000.0000.0000.000
90A127MET0-0.087-0.04021.236-0.025-0.0250.0000.0000.0000.000
91A128ALA00.0040.00122.915-0.021-0.0210.0000.0000.0000.000
92A129ILE0-0.075-0.02218.904-0.016-0.0160.0000.0000.0000.000
93A130ALA00.0630.02923.0330.0030.0030.0000.0000.0000.000
94A131ASP-1-0.872-0.94425.4230.1010.1010.0000.0000.0000.000
95A132GLU-1-0.915-0.93627.0740.0330.0330.0000.0000.0000.000
96A133PHE00.011-0.01421.808-0.001-0.0010.0000.0000.0000.000
97A134TYR00.0000.00422.1160.0330.0330.0000.0000.0000.000
98A135THR0-0.023-0.00822.6230.0340.0340.0000.0000.0000.000
99A136TYR0-0.023-0.01219.4870.0040.0040.0000.0000.0000.000
100A137ARG10.7260.85414.371-0.484-0.4840.0000.0000.0000.000
101A138LYS10.8270.90317.075-0.267-0.2670.0000.0000.0000.000
102A139GLY00.0170.02114.4220.0230.0230.0000.0000.0000.000
103A140SER0-0.041-0.03513.915-0.039-0.0390.0000.0000.0000.000
104A141THR00.0400.0148.913-0.153-0.1530.0000.0000.0000.000
105A142ASP-1-0.703-0.8659.8200.8200.8200.0000.0000.0000.000
106A143SER00.000-0.0238.0020.0520.0520.0000.0000.0000.000
107A144GLU-1-0.781-0.85310.3740.3760.3760.0000.0000.0000.000
108A145VAL00.0200.00013.016-0.109-0.1090.0000.0000.0000.000
109A146LEU0-0.006-0.00511.465-0.082-0.0820.0000.0000.0000.000
110A147PHE0-0.0110.01013.287-0.076-0.0760.0000.0000.0000.000
111A148LEU00.0340.01615.106-0.041-0.0410.0000.0000.0000.000
112A149LEU0-0.0170.00618.011-0.029-0.0290.0000.0000.0000.000
113A150ALA00.0140.00417.459-0.024-0.0240.0000.0000.0000.000
114A151LEU0-0.029-0.01718.442-0.020-0.0200.0000.0000.0000.000
115A152SER0-0.027-0.02421.038-0.004-0.0040.0000.0000.0000.000
116A153GLU-1-0.819-0.86722.265-0.012-0.0120.0000.0000.0000.000
117A154GLY00.0380.02723.895-0.016-0.0160.0000.0000.0000.000
118A155LEU0-0.038-0.02217.560-0.017-0.0170.0000.0000.0000.000
119A156GLU-1-0.892-0.95821.809-0.056-0.0560.0000.0000.0000.000
120A157HIS0-0.032-0.01523.9150.0060.0060.0000.0000.0000.000
121A158ASP-1-0.832-0.90724.793-0.139-0.1390.0000.0000.0000.000
122A159PRO00.0430.02120.1920.0010.0010.0000.0000.0000.000
123A160HIS0-0.034-0.02519.8300.0060.0060.0000.0000.0000.000
124A161GLY00.0450.01221.117-0.003-0.0030.0000.0000.0000.000
125A162ALA00.0000.00421.6410.0140.0140.0000.0000.0000.000
126A163LEU00.0320.00914.5460.0250.0250.0000.0000.0000.000
127A164ALA00.0160.01318.5090.0150.0150.0000.0000.0000.000
128A165ARG10.7670.86520.4340.0950.0950.0000.0000.0000.000
129A166ALA0-0.0020.00718.3300.0250.0250.0000.0000.0000.000
130A167ILE0-0.003-0.01014.9350.0380.0380.0000.0000.0000.000
131A168ALA00.0070.00117.7490.0260.0260.0000.0000.0000.000
132A169ARG10.8130.90021.146-0.026-0.0260.0000.0000.0000.000
133A170LEU00.0210.00815.3170.0250.0250.0000.0000.0000.000
134A171GLU-1-0.749-0.84917.663-0.062-0.0620.0000.0000.0000.000
135A172GLY0-0.009-0.00618.7480.0070.0070.0000.0000.0000.000
136A173LEU0-0.043-0.02720.6300.0080.0080.0000.0000.0000.000
137A174SER00.027-0.00317.4650.0000.0000.0000.0000.0000.000
138A175ARG10.8020.87919.7220.0240.0240.0000.0000.0000.000
139A176ALA0-0.045-0.00422.559-0.003-0.0030.0000.0000.0000.000
140A177HIS0-0.047-0.02722.6150.0070.0070.0000.0000.0000.000
141A178GLY00.0200.02519.4740.0320.0320.0000.0000.0000.000
142A179THR0-0.077-0.04517.6270.0010.0010.0000.0000.0000.000
143A180THR0-0.0110.01917.309-0.006-0.0060.0000.0000.0000.000
144A181PRO0-0.009-0.00312.4850.0360.0360.0000.0000.0000.000
145A182HIS00.026-0.01514.2580.0130.0130.0000.0000.0000.000
146A183MET0-0.026-0.00413.4900.0470.0470.0000.0000.0000.000
147A184ARG10.8340.9149.1090.1160.1160.0000.0000.0000.000
148A185LEU00.008-0.0048.9280.1140.1140.0000.0000.0000.000
149A186SER00.0220.0367.267-0.135-0.1350.0000.0000.0000.000
150A187ALA00.014-0.0037.799-0.066-0.0660.0000.0000.0000.000
151A188ALA00.0290.0149.567-0.011-0.0110.0000.0000.0000.000
152A189PHE0-0.002-0.02411.0720.0990.0990.0000.0000.0000.000
153A190SER00.000-0.01413.866-0.023-0.0230.0000.0000.0000.000
154A191ASP-1-0.727-0.84717.114-0.176-0.1760.0000.0000.0000.000
155A192GLY00.0300.01219.8770.0350.0350.0000.0000.0000.000
156A193GLN0-0.080-0.03721.4490.0090.0090.0000.0000.0000.000
157A194THR0-0.014-0.01520.865-0.007-0.0070.0000.0000.0000.000
158A195LEU0-0.0400.00413.8610.0020.0020.0000.0000.0000.000
159A196TYR0-0.014-0.01016.3560.0100.0100.0000.0000.0000.000
160A197ALA00.0360.00912.746-0.088-0.0880.0000.0000.0000.000
161A198ALA0-0.022-0.00312.7710.1090.1090.0000.0000.0000.000
162A199ARG10.7670.86011.4910.9300.9300.0000.0000.0000.000
163A200TYR0-0.042-0.06312.4790.0970.0970.0000.0000.0000.000
164A201SER00.005-0.02312.506-0.044-0.0440.0000.0000.0000.000
165A202SER0-0.0430.00514.4160.0380.0380.0000.0000.0000.000
166A203ASP-1-0.799-0.86314.650-0.172-0.1720.0000.0000.0000.000
167A204HIS00.0310.00316.404-0.051-0.0510.0000.0000.0000.000
168A205ILE0-0.043-0.01610.656-0.044-0.0440.0000.0000.0000.000
169A206ALA00.0180.00411.388-0.015-0.0150.0000.0000.0000.000
170A207PRO0-0.015-0.0086.249-0.016-0.0160.0000.0000.0000.000
171A208SER00.004-0.0087.6080.2160.2160.0000.0000.0000.000
172A209VAL0-0.012-0.0178.587-0.431-0.4310.0000.0000.0000.000
173A210TYR0-0.042-0.03010.2080.2220.2220.0000.0000.0000.000
174A211TYR0-0.059-0.06113.674-0.085-0.0850.0000.0000.0000.000
175A212ARG10.8460.92216.4460.7090.7090.0000.0000.0000.000
176A213TYR00.0230.02819.274-0.013-0.0130.0000.0000.0000.000
177A214SER0-0.041-0.04320.5510.0010.0010.0000.0000.0000.000
178A215HIS00.0600.00422.4980.0340.0340.0000.0000.0000.000
179A216ALA0-0.033-0.01323.9590.0280.0280.0000.0000.0000.000
180A217ARG10.8240.88318.2810.5760.5760.0000.0000.0000.000
181A218GLN0-0.0110.00923.7370.0240.0240.0000.0000.0000.000
182A219GLY00.0410.02322.1220.0290.0290.0000.0000.0000.000
183A220TRP0-0.0180.00019.113-0.031-0.0310.0000.0000.0000.000
184A221ALA00.0190.01215.2590.0020.0020.0000.0000.0000.000
185A222VAL0-0.017-0.02012.1550.0320.0320.0000.0000.0000.000
186A223VAL00.0040.0029.760-0.062-0.0620.0000.0000.0000.000
187A224SER00.0540.0375.5410.0080.0080.0000.0000.0000.000
188A225GLU-1-0.848-0.9114.325-5.207-5.148-0.001-0.028-0.0290.000
189A226PRO00.0210.0198.5740.0660.0660.0000.0000.0000.000
190A227LEU0-0.011-0.00710.645-0.113-0.1130.0000.0000.0000.000
191A228GLU-1-0.913-0.96312.750-0.841-0.8410.0000.0000.0000.000
192A229THR0-0.057-0.00515.4230.0480.0480.0000.0000.0000.000
193A230ASP-1-0.872-0.93918.579-0.431-0.4310.0000.0000.0000.000
194A231GLU-1-0.799-0.86521.315-0.477-0.4770.0000.0000.0000.000
195A232GLY0-0.006-0.00122.0680.0370.0370.0000.0000.0000.000
196A233ASP-1-0.906-0.94820.236-0.524-0.5240.0000.0000.0000.000
197A234TRP0-0.068-0.04814.995-0.055-0.0550.0000.0000.0000.000
198A235THR0-0.0100.00218.1570.0470.0470.0000.0000.0000.000
199A236GLU-1-0.812-0.87613.806-1.056-1.0560.0000.0000.0000.000
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