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: NNV3Q

Calculation Name: 1ULY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ULY

Chain ID: A

ChEMBL ID:

UniProt ID: O59595

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2131079.641931
FMO2-HF: Nuclear repulsion 2052979.792799
FMO2-HF: Total energy -78099.849131
FMO2-MP2: Total energy -78329.910138


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:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-15.285-17.1422.569-11.205-9.51-0.068
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : 0.008
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].
3A4LYS10.8210.9193.6370.7013.482-0.014-1.591-1.1760.005
4A5VAL0-0.038-0.0292.9370.7812.0370.034-0.621-0.6690.003
5A6LYS10.9170.9681.906-3.244-7.7199.597-3.116-2.006-0.026
6A7VAL0-0.018-0.0114.1910.0950.204-0.001-0.037-0.0710.000
7A8ILE0-0.048-0.0246.9840.3600.3600.0000.0000.0000.000
8A9THR00.032-0.0119.7180.0140.0140.0000.0000.0000.000
9A10ASP-1-0.849-0.90712.8440.1020.1020.0000.0000.0000.000
10A11PRO00.041-0.00914.850-0.054-0.0540.0000.0000.0000.000
11A12GLU-1-0.777-0.86917.862-0.015-0.0150.0000.0000.0000.000
12A13VAL0-0.004-0.00212.748-0.042-0.0420.0000.0000.0000.000
13A14ILE0-0.040-0.02013.711-0.065-0.0650.0000.0000.0000.000
14A15LYS10.7650.85616.003-0.049-0.0490.0000.0000.0000.000
15A16VAL0-0.0360.00217.848-0.018-0.0180.0000.0000.0000.000
16A17MET0-0.026-0.01312.365-0.016-0.0160.0000.0000.0000.000
17A18LEU0-0.020-0.00617.215-0.026-0.0260.0000.0000.0000.000
18A19GLU-1-0.780-0.84519.535-0.158-0.1580.0000.0000.0000.000
19A20ASP-1-0.804-0.90221.293-0.195-0.1950.0000.0000.0000.000
20A21THR0-0.054-0.05422.938-0.015-0.0150.0000.0000.0000.000
21A22ARG10.8680.91218.6070.1350.1350.0000.0000.0000.000
22A23ARG10.8960.95718.0070.1660.1660.0000.0000.0000.000
23A24LYS10.8190.89518.4570.1450.1450.0000.0000.0000.000
24A25ILE00.0250.01417.967-0.021-0.0210.0000.0000.0000.000
25A26LEU00.0130.00613.238-0.043-0.0430.0000.0000.0000.000
26A27LYS10.9360.97914.9830.2560.2560.0000.0000.0000.000
27A28LEU00.0170.01017.238-0.032-0.0320.0000.0000.0000.000
28A29LEU0-0.023-0.00914.966-0.015-0.0150.0000.0000.0000.000
29A30ARG10.8800.93911.5870.7550.7550.0000.0000.0000.000
30A31ASN0-0.076-0.03214.659-0.017-0.0170.0000.0000.0000.000
31A32LYS10.9090.95117.1550.3290.3290.0000.0000.0000.000
32A33GLU-1-0.820-0.90016.208-0.427-0.4270.0000.0000.0000.000
33A34MET0-0.081-0.04217.6360.0550.0550.0000.0000.0000.000
34A35THR0-0.019-0.02520.682-0.008-0.0080.0000.0000.0000.000
35A36ILE00.0100.00123.449-0.003-0.0030.0000.0000.0000.000
36A37SER0-0.001-0.03125.1870.0070.0070.0000.0000.0000.000
37A38GLN00.0070.00624.162-0.019-0.0190.0000.0000.0000.000
38A39LEU00.0100.00020.528-0.004-0.0040.0000.0000.0000.000
39A40SER0-0.108-0.06424.5820.0090.0090.0000.0000.0000.000
40A41GLU-1-0.886-0.94328.086-0.135-0.1350.0000.0000.0000.000
41A42ILE0-0.027-0.01324.5860.0020.0020.0000.0000.0000.000
42A43LEU0-0.060-0.04123.187-0.001-0.0010.0000.0000.0000.000
43A44GLY00.0280.03927.2880.0090.0090.0000.0000.0000.000
44A45LYS10.8880.95127.2370.1580.1580.0000.0000.0000.000
45A46THR00.0590.04529.793-0.008-0.0080.0000.0000.0000.000
46A47PRO00.0880.03029.205-0.004-0.0040.0000.0000.0000.000
47A48GLN00.0510.02128.667-0.013-0.0130.0000.0000.0000.000
48A49THR0-0.0120.00128.100-0.001-0.0010.0000.0000.0000.000
49A50ILE00.0150.00424.019-0.007-0.0070.0000.0000.0000.000
50A51TYR00.0140.00424.247-0.017-0.0170.0000.0000.0000.000
51A52HIS00.0240.01524.313-0.009-0.0090.0000.0000.0000.000
52A53HIS00.0220.01722.318-0.005-0.0050.0000.0000.0000.000
53A54ILE00.000-0.00119.469-0.018-0.0180.0000.0000.0000.000
54A55GLU-1-0.787-0.89319.403-0.160-0.1600.0000.0000.0000.000
55A56LYS10.8540.91220.1930.0920.0920.0000.0000.0000.000
56A57LEU0-0.0030.00215.5640.0010.0010.0000.0000.0000.000
57A58LYS10.8390.91615.2890.1050.1050.0000.0000.0000.000
58A59GLU-1-0.880-0.91615.758-0.070-0.0700.0000.0000.0000.000
59A60ALA00.0060.00515.3190.0280.0280.0000.0000.0000.000
60A61GLY00.0300.02412.0960.0040.0040.0000.0000.0000.000
61A62LEU0-0.062-0.03310.496-0.110-0.1100.0000.0000.0000.000
62A63VAL00.001-0.01811.635-0.149-0.1490.0000.0000.0000.000
63A64GLU-1-0.772-0.85510.789-0.663-0.6630.0000.0000.0000.000
64A65VAL0-0.054-0.04114.485-0.034-0.0340.0000.0000.0000.000
65A66LYS10.8570.94711.3820.7750.7750.0000.0000.0000.000
66A67ARG10.8630.91816.4210.2930.2930.0000.0000.0000.000
67A68THR0-0.005-0.00920.056-0.004-0.0040.0000.0000.0000.000
68A69GLU-1-0.777-0.86523.697-0.194-0.1940.0000.0000.0000.000
69A70MET00.0240.01226.6880.0010.0010.0000.0000.0000.000
70A71LYS10.8330.92826.1950.1900.1900.0000.0000.0000.000
71A72GLY00.0240.01631.7970.0030.0030.0000.0000.0000.000
72A73ASN0-0.033-0.02435.3230.0040.0040.0000.0000.0000.000
73A74LEU00.0050.00530.3520.0040.0040.0000.0000.0000.000
74A75VAL00.0320.01427.134-0.007-0.0070.0000.0000.0000.000
75A76GLU-1-0.757-0.82526.017-0.183-0.1830.0000.0000.0000.000
76A77LYS10.9010.95121.5860.1490.1490.0000.0000.0000.000
77A78TYR0-0.077-0.06519.7580.0000.0000.0000.0000.0000.000
78A79TYR00.006-0.01117.2630.0040.0040.0000.0000.0000.000
79A80GLY00.0460.00314.4500.0050.0050.0000.0000.0000.000
80A81ARG10.7700.8749.1831.1321.1320.0000.0000.0000.000
81A82THR0-0.022-0.0286.623-0.009-0.0090.0000.0000.0000.000
82A83ALA00.0280.0184.757-0.401-0.413-0.001-0.0150.0290.000
83A84ASP-1-0.810-0.8726.634-1.141-1.1410.0000.0000.0000.000
84A85VAL0-0.038-0.0137.0940.5460.5460.0000.0000.0000.000
85A86PHE0-0.046-0.0266.603-0.339-0.3390.0000.0000.0000.000
86A87TYR00.0570.0287.6510.0880.0880.0000.0000.0000.000
87A88ILE00.0060.0059.7490.0400.0400.0000.0000.0000.000
88A89ASN00.064-0.00412.551-0.022-0.0220.0000.0000.0000.000
89A90LEU0-0.035-0.00815.469-0.007-0.0070.0000.0000.0000.000
90A91TYR0-0.021-0.01218.630-0.007-0.0070.0000.0000.0000.000
91A92LEU0-0.0320.00514.9930.0180.0180.0000.0000.0000.000
92A93GLY0-0.004-0.00319.1580.0090.0090.0000.0000.0000.000
93A94ASP-1-0.801-0.90321.2720.0240.0240.0000.0000.0000.000
94A95GLU-1-0.811-0.88223.0600.0220.0220.0000.0000.0000.000
95A96GLU-1-0.872-0.92624.590-0.016-0.0160.0000.0000.0000.000
96A97LEU0-0.032-0.02618.645-0.017-0.0170.0000.0000.0000.000
97A98ARG10.8570.93522.800-0.051-0.0510.0000.0000.0000.000
98A99TYR0-0.034-0.04025.152-0.011-0.0110.0000.0000.0000.000
99A100ILE00.0010.01323.242-0.012-0.0120.0000.0000.0000.000
100A101ALA0-0.022-0.01222.901-0.013-0.0130.0000.0000.0000.000
101A102ARG10.8720.90324.527-0.015-0.0150.0000.0000.0000.000
102A103SER0-0.009-0.00628.017-0.003-0.0030.0000.0000.0000.000
103A104ARG10.8640.93519.9930.0930.0930.0000.0000.0000.000
104A105LEU00.0100.01525.416-0.007-0.0070.0000.0000.0000.000
105A106LYS10.8980.92828.4210.0340.0340.0000.0000.0000.000
106A107THR00.0100.00429.343-0.004-0.0040.0000.0000.0000.000
107A108LYS10.8150.91626.4680.0790.0790.0000.0000.0000.000
108A109ILE00.0470.04231.4950.0010.0010.0000.0000.0000.000
109A110ASP-1-0.821-0.90934.361-0.040-0.0400.0000.0000.0000.000
110A111ILE0-0.045-0.02131.8760.0000.0000.0000.0000.0000.000
111A112PHE00.015-0.00630.9570.0000.0000.0000.0000.0000.000
112A113LYS10.8640.92236.6780.0260.0260.0000.0000.0000.000
113A114ARG10.8630.94238.7280.0500.0500.0000.0000.0000.000
114A115LEU0-0.030-0.01435.9870.0000.0000.0000.0000.0000.000
115A116GLY00.0220.02140.2330.0010.0010.0000.0000.0000.000
116A117TYR0-0.046-0.02037.6160.0020.0020.0000.0000.0000.000
117A118GLN0-0.035-0.01640.9830.0020.0020.0000.0000.0000.000
118A119PHE00.007-0.00336.6480.0010.0010.0000.0000.0000.000
119A120GLU-1-0.747-0.85240.229-0.008-0.0080.0000.0000.0000.000
120A121GLU-1-0.822-0.91437.254-0.021-0.0210.0000.0000.0000.000
121A122ASN0-0.046-0.03936.0810.0000.0000.0000.0000.0000.000
122A123GLU-1-0.809-0.89235.8150.0030.0030.0000.0000.0000.000
123A124LEU00.0030.00833.2810.0010.0010.0000.0000.0000.000
124A125LEU00.013-0.00330.424-0.002-0.0020.0000.0000.0000.000
125A126ASN0-0.027-0.01730.6520.0040.0040.0000.0000.0000.000
126A127ILE00.0010.00830.4180.0050.0050.0000.0000.0000.000
127A128MET00.0190.00228.5110.0000.0000.0000.0000.0000.000
128A129ASP-1-0.779-0.85725.9980.0060.0060.0000.0000.0000.000
129A130ARG10.8780.94125.524-0.029-0.0290.0000.0000.0000.000
130A131MET0-0.040-0.00225.2400.0070.0070.0000.0000.0000.000
131A132SER00.0520.00922.596-0.004-0.0040.0000.0000.0000.000
132A133GLN0-0.011-0.01121.074-0.013-0.0130.0000.0000.0000.000
133A134LYS10.8050.89020.473-0.053-0.0530.0000.0000.0000.000
134A135GLU-1-0.792-0.88019.913-0.028-0.0280.0000.0000.0000.000
135A136PHE0-0.051-0.01815.648-0.019-0.0190.0000.0000.0000.000
136A137ASP-1-0.803-0.90115.6330.1420.1420.0000.0000.0000.000
137A138ALA0-0.0120.00015.9730.0520.0520.0000.0000.0000.000
138A139THR00.019-0.01012.6410.0180.0180.0000.0000.0000.000
139A140VAL0-0.0330.00511.3160.0100.0100.0000.0000.0000.000
140A141ARG10.8320.90510.875-0.135-0.1350.0000.0000.0000.000
141A142ILE0-0.037-0.01611.8840.1150.1150.0000.0000.0000.000
142A143SER0-0.023-0.0328.2040.0560.0560.0000.0000.0000.000
143A144LYS10.8690.9146.415-1.677-1.6770.0000.0000.0000.000
144A145TYR00.0010.0097.4440.5060.5060.0000.0000.0000.000
145A146ILE0-0.002-0.0086.084-0.048-0.0480.0000.0000.0000.000
146A147GLU-1-0.844-0.9062.3690.9891.3121.687-0.827-1.1840.003
147A148GLU-1-0.866-0.9173.5452.5293.3030.081-0.279-0.576-0.001
148A149LYS10.8390.9025.897-1.314-1.3140.0000.0000.0000.000
149A150GLU-1-0.723-0.8361.890-15.548-18.15911.186-4.719-3.857-0.052
150A151ASP-1-0.882-0.9355.575-0.016-0.0160.0000.0000.0000.000
151A152ALA0-0.059-0.0337.900-0.003-0.0030.0000.0000.0000.000
152A153LEU00.023-0.0068.430-0.001-0.0010.0000.0000.0000.000
153A154LYS10.7760.8618.7200.1210.1210.0000.0000.0000.000
154A155ASP-1-0.855-0.9039.767-0.339-0.3390.0000.0000.0000.000
155A156PHE00.0080.02112.2140.0630.0630.0000.0000.0000.000
156A157SER0-0.018-0.04612.093-0.153-0.1530.0000.0000.0000.000
157A158ASN00.020-0.0289.216-0.046-0.0460.0000.0000.0000.000
158A159GLU-1-0.893-0.93811.471-0.414-0.4140.0000.0000.0000.000
159A160ASP-1-0.821-0.87214.361-0.355-0.3550.0000.0000.0000.000
160A161ILE0-0.015-0.0038.2120.0310.0310.0000.0000.0000.000
161A162ILE0-0.032-0.00811.3470.0490.0490.0000.0000.0000.000
162A163HIS10.8640.93112.8190.4070.4070.0000.0000.0000.000
163A164ALA00.0050.00913.2120.0570.0570.0000.0000.0000.000
164A165ILE0-0.011-0.0118.7970.0740.0740.0000.0000.0000.000
165A166GLU-1-0.879-0.95013.443-0.199-0.1990.0000.0000.0000.000
166A167TRP0-0.0030.01216.8740.0500.0500.0000.0000.0000.000
167A168LEU0-0.012-0.01113.6690.0320.0320.0000.0000.0000.000
168A169SER0-0.025-0.02115.7650.0490.0490.0000.0000.0000.000
169A170THR0-0.003-0.02317.5200.0190.0190.0000.0000.0000.000
170A171ALA0-0.042-0.02420.1540.0120.0120.0000.0000.0000.000
171A172GLU-1-0.789-0.85318.1380.1610.1610.0000.0000.0000.000
172A173LEU0-0.0010.00620.5670.0060.0060.0000.0000.0000.000
173A174ALA0-0.050-0.02523.2200.0010.0010.0000.0000.0000.000
174A175ARG10.8370.90120.773-0.079-0.0790.0000.0000.0000.000
175A176ASP-1-0.792-0.86924.7590.0780.0780.0000.0000.0000.000
176A177GLU-1-0.880-0.95826.8100.0380.0380.0000.0000.0000.000
177A178GLU-1-0.836-0.90028.7950.0450.0450.0000.0000.0000.000
178A179TYR0-0.075-0.06824.698-0.007-0.0070.0000.0000.0000.000
179A180LEU00.0410.01628.029-0.011-0.0110.0000.0000.0000.000
180A181GLU-1-0.912-0.93030.7040.0130.0130.0000.0000.0000.000
181A182LEU0-0.051-0.02928.521-0.006-0.0060.0000.0000.0000.000
182A183LEU00.0550.02928.836-0.006-0.0060.0000.0000.0000.000
183A184LYS10.8520.91031.339-0.018-0.0180.0000.0000.0000.000
184A185ARG10.8440.92034.458-0.003-0.0030.0000.0000.0000.000
185A186LEU00.0330.00529.981-0.003-0.0030.0000.0000.0000.000
186A187GLY00.0170.01134.024-0.004-0.0040.0000.0000.0000.000
187A188SER0-0.062-0.04936.1140.0000.0000.0000.0000.0000.000
188A189ILE0-0.034-0.00136.034-0.001-0.0010.0000.0000.0000.000
189A190LEU0-0.017-0.00733.395-0.001-0.0010.0000.0000.0000.000
190A191LYS10.8410.93037.5040.0180.0180.0000.0000.0000.000