Manual

About

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: ZVR2N

Calculation Name: 1UDD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UDD

Chain ID: A

ChEMBL ID:

UniProt ID: O58873

Base Structure: X-ray

Registration Date: 2023-09-20

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2809410.792021
FMO2-HF: Nuclear repulsion 2721885.424433
FMO2-HF: Total energy -87525.367588
FMO2-MP2: Total energy -87782.866288


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.799-3.3060.335-1.427-1.402-0.007
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.001
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].
3A3VAL00.0200.0182.800-5.191-2.6980.335-1.427-1.402-0.007
4A4MET0-0.0030.0075.6600.1780.1780.0000.0000.0000.000
5A5ILE0-0.020-0.0089.0530.1120.1120.0000.0000.0000.000
6A6THR0-0.020-0.05512.1550.0520.0520.0000.0000.0000.000
7A7ASP-1-0.786-0.8959.135-0.039-0.0390.0000.0000.0000.000
8A8LYS10.8180.9289.404-0.373-0.3730.0000.0000.0000.000
9A9LEU0-0.0140.00711.9770.0200.0200.0000.0000.0000.000
10A10ARG10.8640.94714.603-0.072-0.0720.0000.0000.0000.000
11A11ARG10.9520.9668.875-0.585-0.5850.0000.0000.0000.000
12A12ASP-1-0.867-0.90414.4710.3740.3740.0000.0000.0000.000
13A13SER0-0.031-0.04016.364-0.019-0.0190.0000.0000.0000.000
14A14GLU-1-0.880-0.92915.1410.1150.1150.0000.0000.0000.000
15A15GLN0-0.0040.00119.538-0.023-0.0230.0000.0000.0000.000
16A16ILE0-0.047-0.03222.319-0.008-0.0080.0000.0000.0000.000
17A17TRP00.0640.01121.207-0.009-0.0090.0000.0000.0000.000
18A18LYS10.8580.91823.364-0.051-0.0510.0000.0000.0000.000
19A19LYS10.8640.92424.957-0.077-0.0770.0000.0000.0000.000
20A20ILE00.0130.01425.741-0.004-0.0040.0000.0000.0000.000
21A21PHE0-0.018-0.00622.133-0.004-0.0040.0000.0000.0000.000
22A22GLU-1-0.824-0.89427.8810.0340.0340.0000.0000.0000.000
23A23HIS00.0020.00730.602-0.003-0.0030.0000.0000.0000.000
24A24PRO00.002-0.01032.972-0.003-0.0030.0000.0000.0000.000
25A25PHE00.0380.01636.027-0.002-0.0020.0000.0000.0000.000
26A26VAL00.0270.02230.627-0.003-0.0030.0000.0000.0000.000
27A27VAL00.0140.00932.724-0.003-0.0030.0000.0000.0000.000
28A28GLN00.0190.01334.812-0.003-0.0030.0000.0000.0000.000
29A29LEU0-0.0410.00235.493-0.002-0.0020.0000.0000.0000.000
30A30TYR00.0610.00131.374-0.003-0.0030.0000.0000.0000.000
31A31SER0-0.021-0.02335.607-0.002-0.0020.0000.0000.0000.000
32A32GLY0-0.0110.00337.992-0.002-0.0020.0000.0000.0000.000
33A33THR0-0.054-0.03240.379-0.001-0.0010.0000.0000.0000.000
34A34LEU0-0.0250.00839.5230.0000.0000.0000.0000.0000.000
35A35PRO00.0120.00442.354-0.001-0.0010.0000.0000.0000.000
36A36LEU00.0650.03345.0250.0010.0010.0000.0000.0000.000
37A37GLU-1-0.801-0.90045.9360.0150.0150.0000.0000.0000.000
38A38LYS10.8200.91342.625-0.023-0.0230.0000.0000.0000.000
39A39PHE00.0280.01538.5020.0010.0010.0000.0000.0000.000
40A40LYS10.8570.92942.575-0.014-0.0140.0000.0000.0000.000
41A41PHE00.0100.01442.2330.0010.0010.0000.0000.0000.000
42A42TYR0-0.059-0.06735.8520.0010.0010.0000.0000.0000.000
43A43VAL00.0520.02240.4070.0010.0010.0000.0000.0000.000
44A44LEU0-0.0020.01741.7630.0000.0000.0000.0000.0000.000
45A45GLN0-0.0150.00640.2000.0020.0020.0000.0000.0000.000
46A46ASP-1-0.762-0.86836.8660.0300.0300.0000.0000.0000.000
47A47PHE0-0.0110.01938.8150.0000.0000.0000.0000.0000.000
48A48ASN0-0.025-0.02939.320-0.001-0.0010.0000.0000.0000.000
49A49TYR00.023-0.02530.5060.0010.0010.0000.0000.0000.000
50A50LEU00.0460.02935.6990.0010.0010.0000.0000.0000.000
51A51VAL00.0110.01336.9100.0000.0000.0000.0000.0000.000
52A52GLY0-0.014-0.02236.6220.0000.0000.0000.0000.0000.000
53A53LEU00.0300.00330.1120.0020.0020.0000.0000.0000.000
54A54THR00.002-0.01033.2140.0000.0000.0000.0000.0000.000
55A55ARG10.8960.95035.491-0.029-0.0290.0000.0000.0000.000
56A56ALA0-0.0010.00031.3180.0010.0010.0000.0000.0000.000
57A57LEU00.0250.00929.1170.0010.0010.0000.0000.0000.000
58A58ALA00.0270.02631.986-0.001-0.0010.0000.0000.0000.000
59A59VAL0-0.0080.01033.0480.0000.0000.0000.0000.0000.000
60A60ILE0-0.035-0.00927.4020.0010.0010.0000.0000.0000.000
61A61SER0-0.041-0.02830.686-0.001-0.0010.0000.0000.0000.000
62A62SER0-0.053-0.04532.198-0.001-0.0010.0000.0000.0000.000
63A63LYS10.7880.87930.411-0.050-0.0500.0000.0000.0000.000
64A64ALA0-0.039-0.01228.7390.0020.0020.0000.0000.0000.000
65A65GLU-1-0.838-0.91828.3790.0190.0190.0000.0000.0000.000
66A66TYR0-0.0100.01329.8710.0000.0000.0000.0000.0000.000
67A67PRO0-0.012-0.02028.140-0.001-0.0010.0000.0000.0000.000
68A68LEU00.000-0.00724.8140.0010.0010.0000.0000.0000.000
69A69MET0-0.019-0.01328.3170.0010.0010.0000.0000.0000.000
70A70ALA00.0130.00231.6440.0010.0010.0000.0000.0000.000
71A71GLU-1-0.831-0.89426.0950.0160.0160.0000.0000.0000.000
72A72LEU0-0.024-0.02226.5200.0010.0010.0000.0000.0000.000
73A73ILE0-0.010-0.00330.5170.0010.0010.0000.0000.0000.000
74A74GLU-1-0.830-0.89533.2100.0140.0140.0000.0000.0000.000
75A75LEU0-0.019-0.00628.5500.0000.0000.0000.0000.0000.000
76A76ALA0-0.004-0.01032.6010.0000.0000.0000.0000.0000.000
77A77ARG10.7550.86235.058-0.015-0.0150.0000.0000.0000.000
78A78ASP-1-0.826-0.89434.6060.0140.0140.0000.0000.0000.000
79A79GLU-1-0.901-0.95333.0720.0250.0250.0000.0000.0000.000
80A80VAL0-0.043-0.03336.749-0.001-0.0010.0000.0000.0000.000
81A81THR0-0.055-0.05239.849-0.001-0.0010.0000.0000.0000.000
82A82VAL00.0200.02438.149-0.001-0.0010.0000.0000.0000.000
83A83GLU-1-0.812-0.90135.2620.0160.0160.0000.0000.0000.000
84A84VAL00.0000.00938.7400.0000.0000.0000.0000.0000.000
85A85GLU-1-0.869-0.91641.9990.0100.0100.0000.0000.0000.000
86A86ASN0-0.056-0.05538.091-0.002-0.0020.0000.0000.0000.000
87A87TYR0-0.030-0.03540.661-0.001-0.0010.0000.0000.0000.000
88A88VAL00.009-0.00242.2020.0000.0000.0000.0000.0000.000
89A89LYS10.7450.85842.669-0.012-0.0120.0000.0000.0000.000
90A90LEU0-0.004-0.00440.041-0.001-0.0010.0000.0000.0000.000
91A91LEU00.002-0.00144.0460.0000.0000.0000.0000.0000.000
92A92LYS10.9871.00146.653-0.010-0.0100.0000.0000.0000.000
93A93GLH0-0.148-0.09744.2910.0000.0000.0000.0000.0000.000
94A94LEU0-0.060-0.03144.0960.0000.0000.0000.0000.0000.000
95A95ASP-1-0.947-0.96248.7590.0110.0110.0000.0000.0000.000
96A96LEU0-0.026-0.00647.8880.0000.0000.0000.0000.0000.000
97A97THR0-0.022-0.04650.4970.0000.0000.0000.0000.0000.000
98A98LEU00.045-0.00145.8010.0010.0010.0000.0000.0000.000
99A99GLU-1-0.857-0.90948.7330.0150.0150.0000.0000.0000.000
100A100ASP-1-0.810-0.88950.1920.0160.0160.0000.0000.0000.000
101A101ALA00.0190.03145.2090.0010.0010.0000.0000.0000.000
102A102ILE0-0.056-0.02846.7560.0010.0010.0000.0000.0000.000
103A103LYS10.7600.86648.460-0.015-0.0150.0000.0000.0000.000
104A104THR0-0.044-0.02145.4970.0000.0000.0000.0000.0000.000
105A105GLU-1-0.944-0.96246.9630.0270.0270.0000.0000.0000.000
106A106PRO0-0.0050.00242.0580.0010.0010.0000.0000.0000.000
107A107THR00.027-0.02740.7000.0010.0010.0000.0000.0000.000
108A108LEU00.0190.01239.7080.0010.0010.0000.0000.0000.000
109A109VAL0-0.020-0.02035.8870.0020.0020.0000.0000.0000.000
110A110ASN0-0.021-0.01636.7290.0030.0030.0000.0000.0000.000
111A111SER00.0240.00237.3640.0000.0000.0000.0000.0000.000
112A112ALA00.0260.00936.4700.0010.0010.0000.0000.0000.000
113A113TYR0-0.067-0.05029.2330.0060.0060.0000.0000.0000.000
114A114MET00.0020.04133.1230.0020.0020.0000.0000.0000.000
115A115ASP-1-0.889-0.94434.8450.0420.0420.0000.0000.0000.000
116A116PHE0-0.066-0.03526.6800.0040.0040.0000.0000.0000.000
117A117MET0-0.0170.01029.5930.0040.0040.0000.0000.0000.000
118A118LEU00.0450.03231.1660.0010.0010.0000.0000.0000.000
119A119ALA00.0430.01033.6390.0000.0000.0000.0000.0000.000
120A120THR0-0.100-0.06127.0400.0060.0060.0000.0000.0000.000
121A121ALA00.0250.01629.2380.0020.0020.0000.0000.0000.000
122A122TYR0-0.0180.01030.4710.0000.0000.0000.0000.0000.000
123A123LYS10.8450.91129.276-0.073-0.0730.0000.0000.0000.000
124A124GLY00.0270.03727.2320.0030.0030.0000.0000.0000.000
125A125ASN00.005-0.00723.472-0.007-0.0070.0000.0000.0000.000
126A126ILE00.1010.02523.9750.0040.0040.0000.0000.0000.000
127A127ILE00.0120.02318.9730.0000.0000.0000.0000.0000.000
128A128GLU-1-0.848-0.90922.0440.0980.0980.0000.0000.0000.000
129A129GLY00.0490.02423.7710.0010.0010.0000.0000.0000.000
130A130LEU00.0520.01722.9240.0000.0000.0000.0000.0000.000
131A131THR0-0.058-0.05020.2760.0030.0030.0000.0000.0000.000
132A132ALA0-0.037-0.03222.2980.0050.0050.0000.0000.0000.000
133A133LEU00.0330.01725.490-0.001-0.0010.0000.0000.0000.000
134A134LEU0-0.0330.00418.383-0.002-0.0020.0000.0000.0000.000
135A135PRO0-0.040-0.02122.596-0.002-0.0020.0000.0000.0000.000
136A136CYS00.0520.05824.025-0.003-0.0030.0000.0000.0000.000
137A137PHE00.0700.02524.822-0.002-0.0020.0000.0000.0000.000
138A138TRP0-0.051-0.04715.125-0.001-0.0010.0000.0000.0000.000
139A139SER0-0.028-0.03522.925-0.003-0.0030.0000.0000.0000.000
140A140TYR00.0290.00924.628-0.002-0.0020.0000.0000.0000.000
141A141ALA00.0120.01623.614-0.003-0.0030.0000.0000.0000.000
142A142GLU-1-0.810-0.89318.9690.0460.0460.0000.0000.0000.000
143A143ILE0-0.038-0.01923.800-0.002-0.0020.0000.0000.0000.000
144A144ALA00.0180.01627.178-0.003-0.0030.0000.0000.0000.000
145A145GLU-1-0.808-0.89922.8820.0070.0070.0000.0000.0000.000
146A146TYR0-0.071-0.03924.164-0.003-0.0030.0000.0000.0000.000
147A147HIS0-0.048-0.02926.632-0.004-0.0040.0000.0000.0000.000
148A148LYS10.8540.92625.683-0.009-0.0090.0000.0000.0000.000
149A149ASP-1-0.890-0.93630.4380.0070.0070.0000.0000.0000.000
150A150LYS10.8750.91530.700-0.014-0.0140.0000.0000.0000.000
151A151LEU00.0080.01432.258-0.001-0.0010.0000.0000.0000.000
152A152ARG10.8520.91930.790-0.001-0.0010.0000.0000.0000.000
153A153ASP-1-0.930-0.95336.7760.0010.0010.0000.0000.0000.000
154A154ASN0-0.046-0.00937.6510.0000.0000.0000.0000.0000.000
155A155PRO00.0600.02940.1070.0000.0000.0000.0000.0000.000
156A156ILE0-0.0130.01542.707-0.001-0.0010.0000.0000.0000.000
157A157LYS10.8420.90542.127-0.007-0.0070.0000.0000.0000.000
158A158ILE00.0620.03041.9970.0000.0000.0000.0000.0000.000
159A159TYR00.000-0.01738.9020.0010.0010.0000.0000.0000.000
160A160ARG10.8770.93437.698-0.006-0.0060.0000.0000.0000.000
161A161GLU-1-0.883-0.92637.4470.0080.0080.0000.0000.0000.000
162A162TRP00.0450.02033.577-0.001-0.0010.0000.0000.0000.000
163A163GLY00.0460.02233.9260.0010.0010.0000.0000.0000.000
164A164LYS10.8700.92332.539-0.008-0.0080.0000.0000.0000.000
165A165VAL00.0220.03432.288-0.001-0.0010.0000.0000.0000.000
166A166TYR00.0430.01928.4450.0000.0000.0000.0000.0000.000
167A167LEU0-0.046-0.02227.2020.0010.0010.0000.0000.0000.000
168A168SER0-0.0210.00028.481-0.002-0.0020.0000.0000.0000.000
169A169ASN0-0.007-0.02626.5780.0010.0010.0000.0000.0000.000
170A170GLU-1-0.844-0.91426.3680.0080.0080.0000.0000.0000.000
171A171TYR00.0060.00326.5670.0010.0010.0000.0000.0000.000
172A172LEU00.0070.00223.0410.0030.0030.0000.0000.0000.000
173A173ASN0-0.031-0.03222.6000.0020.0020.0000.0000.0000.000
174A174LEU0-0.0270.01123.3070.0000.0000.0000.0000.0000.000
175A175VAL00.0200.01020.3790.0020.0020.0000.0000.0000.000
176A176GLY0-0.007-0.00519.0270.0020.0020.0000.0000.0000.000
177A177ARG10.8060.87819.014-0.017-0.0170.0000.0000.0000.000
178A178LEU00.0340.01920.762-0.001-0.0010.0000.0000.0000.000
179A179ARG10.8490.92013.055-0.024-0.0240.0000.0000.0000.000
180A180LYS10.9800.99216.195-0.005-0.0050.0000.0000.0000.000
181A181ILE00.0100.01217.155-0.006-0.0060.0000.0000.0000.000
182A182ILE00.0050.01016.1960.0010.0010.0000.0000.0000.000
183A183ASP-1-0.757-0.85312.6900.0060.0060.0000.0000.0000.000
184A184SER0-0.119-0.04413.355-0.026-0.0260.0000.0000.0000.000
185A185SER0-0.017-0.02215.5950.0090.0090.0000.0000.0000.000
186A186GLY00.0130.00114.956-0.013-0.0130.0000.0000.0000.000
187A187HIS00.0390.0149.0840.0770.0770.0000.0000.0000.000
188A188SER0-0.036-0.01113.1320.0640.0640.0000.0000.0000.000
189A189GLY00.0550.02015.630-0.020-0.0200.0000.0000.0000.000
190A190TYR00.040-0.01814.183-0.017-0.0170.0000.0000.0000.000
191A191ASP-1-0.773-0.88916.3050.3210.3210.0000.0000.0000.000
192A192ARG10.7520.89018.628-0.128-0.1280.0000.0000.0000.000
193A193LEU00.0660.03417.128-0.007-0.0070.0000.0000.0000.000
194A194ARG10.8620.92416.099-0.294-0.2940.0000.0000.0000.000
195A195ARG10.8990.93918.945-0.164-0.1640.0000.0000.0000.000
196A196ILE00.0070.03322.615-0.010-0.0100.0000.0000.0000.000
197A197PHE00.0880.04119.640-0.007-0.0070.0000.0000.0000.000
198A198ILE0-0.0250.00019.376-0.010-0.0100.0000.0000.0000.000
199A199THR0-0.071-0.04523.015-0.008-0.0080.0000.0000.0000.000
200A200GLY00.0670.03425.882-0.007-0.0070.0000.0000.0000.000
201A201SER00.006-0.00923.248-0.006-0.0060.0000.0000.0000.000
202A202LYS10.9000.94025.596-0.111-0.1110.0000.0000.0000.000
203A203PHE00.0040.00828.273-0.004-0.0040.0000.0000.0000.000
204A204GLU-1-0.712-0.81327.4490.0420.0420.0000.0000.0000.000
205A205LEU0-0.045-0.01928.524-0.004-0.0040.0000.0000.0000.000
206A206ALA0-0.022-0.01430.831-0.004-0.0040.0000.0000.0000.000
207A207PHE00.0300.02133.341-0.003-0.0030.0000.0000.0000.000
208A208TRP00.0220.00630.881-0.005-0.0050.0000.0000.0000.000
209A209GLU-1-0.822-0.88135.0370.0360.0360.0000.0000.0000.000
210A210MET0-0.0550.01036.814-0.003-0.0030.0000.0000.0000.000
211A211ALA00.0490.02838.215-0.002-0.0020.0000.0000.0000.000
212A212TRP0-0.048-0.01738.639-0.003-0.0030.0000.0000.0000.000
213A213ARG10.8290.88539.256-0.038-0.0380.0000.0000.0000.000
214A214GLY00.0090.03442.952-0.001-0.0010.0000.0000.0000.000
215A215GLY0-0.024-0.01342.5740.0000.0000.0000.0000.0000.000