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: YNY52

Calculation Name: 3URO-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3URO

Chain ID: R

ChEMBL ID:

UniProt ID: P15151

Base Structure: X-ray

Registration Date: 2023-09-26

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078457.109986
FMO2-HF: Nuclear repulsion 1996056.685451
FMO2-HF: Total energy -82400.424535
FMO2-MP2: Total energy -82641.067684


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(R:30:VAL)


Summations of interaction energy for fragment #1(R:30:VAL)
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.
-8.853-5.45.945-2.93-6.467-0.008
Interaction energy analysis for fragmet #1(R:30:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.030
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].
3R32GLN0-0.091-0.0913.831-2.311-0.113-0.013-1.061-1.125-0.003
4R33ALA0-0.088-0.0926.9030.4110.4110.0000.0000.0000.000
5R34PRO0-0.054-0.00910.4630.0460.0460.0000.0000.0000.000
6R35THR0-0.051-0.01911.7970.0730.0730.0000.0000.0000.000
7R36GLN00.127-0.05214.1990.0600.0600.0000.0000.0000.000
8R37VAL0-0.092-0.05618.0340.0050.0050.0000.0000.0000.000
9R38PRO0-0.0280.03220.7730.0180.0180.0000.0000.0000.000
10R39GLY00.053-0.00524.576-0.008-0.0080.0000.0000.0000.000
11R40PHE0-0.079-0.06326.2030.0000.0000.0000.0000.0000.000
12R41LEU00.0240.01230.0070.0010.0010.0000.0000.0000.000
13R42GLY0-0.0760.02132.129-0.005-0.0050.0000.0000.0000.000
14R43ASP-1-0.799-0.85029.368-0.018-0.0180.0000.0000.0000.000
15R44SER0-0.0470.00028.8060.0010.0010.0000.0000.0000.000
16R45VAL0-0.119-0.08424.743-0.004-0.0040.0000.0000.0000.000
17R46THR0-0.228-0.10720.1040.0140.0140.0000.0000.0000.000
18R47LEU00.0310.01517.627-0.028-0.0280.0000.0000.0000.000
19R48PRO00.0560.01113.7150.0460.0460.0000.0000.0000.000
20R49CYS00.0900.00910.584-0.057-0.0570.0000.0000.0000.000
21R50TYR0-0.0180.0058.8740.1680.1680.0000.0000.0000.000
22R51LEU00.2280.2602.149-1.719-2.0001.7480.170-1.637-0.006
23R52GLN0-0.0050.0344.0310.3850.571-0.001-0.027-0.1580.000
24R53VAL00.0310.0163.267-1.426-0.6760.028-0.384-0.393-0.003
25R54PRO0-0.128-0.0382.159-1.032-0.4601.701-0.763-1.5090.002
26R55ASN00.053-0.0375.4030.3600.3600.0000.0000.0000.000
27R56MET0-0.088-0.0238.0620.0720.0720.0000.0000.0000.000
28R57GLU-1-0.833-0.9276.1901.4671.4670.0000.0000.0000.000
29R58VAL0-0.002-0.0097.691-0.105-0.1050.0000.0000.0000.000
30R59THR0-0.0130.0097.138-0.308-0.3080.0000.0000.0000.000
31R60HIS00.0330.0759.788-0.031-0.0310.0000.0000.0000.000
32R61VAL00.016-0.04710.5890.2880.2880.0000.0000.0000.000
33R62SER0-0.046-0.0469.1010.0250.0250.0000.0000.0000.000
34R63GLN0-0.104-0.05610.523-0.265-0.2650.0000.0000.0000.000
35R64LEU00.0700.02012.1590.0160.0160.0000.0000.0000.000
36R65THR00.042-0.02513.257-0.065-0.0650.0000.0000.0000.000
37R66TRP0-0.032-0.00714.045-0.008-0.0080.0000.0000.0000.000
38R67ALA0-0.0160.00416.502-0.004-0.0040.0000.0000.0000.000
39R68ARG00.1550.06418.534-0.018-0.0180.0000.0000.0000.000
40R69HIS10.8920.97117.298-0.128-0.1280.0000.0000.0000.000
41R70GLY00.176-0.03820.527-0.012-0.0120.0000.0000.0000.000
42R71GLU-1-0.939-0.88922.8020.0870.0870.0000.0000.0000.000
43R72SER0-0.073-0.07019.2460.0010.0010.0000.0000.0000.000
44R73GLY0-0.1740.01922.3280.0150.0150.0000.0000.0000.000
45R74SER00.043-0.03422.257-0.021-0.0210.0000.0000.0000.000
46R75MET0-0.090-0.05320.3180.0250.0250.0000.0000.0000.000
47R76ALA00.0450.05221.955-0.004-0.0040.0000.0000.0000.000
48R77VAL0-0.060-0.00919.191-0.006-0.0060.0000.0000.0000.000
49R78PHE00.017-0.00817.958-0.013-0.0130.0000.0000.0000.000
50R79HIS00.0670.08716.1050.0840.0840.0000.0000.0000.000
51R80GLN00.032-0.01216.841-0.037-0.0370.0000.0000.0000.000
52R81THR0-0.030-0.02816.5780.0810.0810.0000.0000.0000.000
53R82GLN00.042-0.00318.4290.0270.0270.0000.0000.0000.000
54R83GLY0-0.023-0.01621.212-0.033-0.0330.0000.0000.0000.000
55R84PRO00.0230.02121.0410.0360.0360.0000.0000.0000.000
56R85SER0-0.022-0.00521.739-0.021-0.0210.0000.0000.0000.000
57R86TYR00.0640.04322.6110.0080.0080.0000.0000.0000.000
58R87SER00.0650.04024.2340.0010.0010.0000.0000.0000.000
59R88GLU-1-0.892-0.93726.4830.0910.0910.0000.0000.0000.000
60R89SER0-0.128-0.14026.456-0.017-0.0170.0000.0000.0000.000
61R90LYN00.0600.05127.2620.0050.0050.0000.0000.0000.000
62R91ARG10.8380.96828.833-0.054-0.0540.0000.0000.0000.000
63R92LEU00.0080.01325.5770.0070.0070.0000.0000.0000.000
64R93GLU-1-0.913-1.01024.5230.0230.0230.0000.0000.0000.000
65R94PHE0-0.022-0.02820.178-0.012-0.0120.0000.0000.0000.000
66R95VAL0-0.017-0.00917.959-0.012-0.0120.0000.0000.0000.000
67R96ALA0-0.0360.00815.4130.0040.0040.0000.0000.0000.000
68R97ALA0-0.026-0.02617.4750.0390.0390.0000.0000.0000.000
69R98ARG10.9351.01617.886-0.357-0.3570.0000.0000.0000.000
70R99LEU0-0.072-0.04018.864-0.014-0.0140.0000.0000.0000.000
71R100GLY00.0240.00120.311-0.023-0.0230.0000.0000.0000.000
72R101ALA0-0.059-0.02515.5130.0520.0520.0000.0000.0000.000
73R102GLU-1-0.863-0.91213.2430.2020.2020.0000.0000.0000.000
74R103LEU0-0.060-0.0478.714-0.104-0.1040.0000.0000.0000.000
75R104ARG0-0.024-0.05110.1990.0090.0090.0000.0000.0000.000
76R105ASP-1-0.694-0.8448.3090.0250.0250.0000.0000.0000.000
77R106ALA0-0.0150.01111.058-0.058-0.0580.0000.0000.0000.000
78R107SER0-0.0120.00113.384-0.066-0.0660.0000.0000.0000.000
79R108LEU00.0730.07815.7110.0310.0310.0000.0000.0000.000
80R109ARG10.9911.07619.0950.0050.0050.0000.0000.0000.000
81R110MET0-0.015-0.04622.2040.0180.0180.0000.0000.0000.000
82R111PHE00.0470.00324.373-0.015-0.0150.0000.0000.0000.000
83R112GLY00.180-0.00428.0300.0080.0080.0000.0000.0000.000
84R113LEU0-0.069-0.08429.0710.0090.0090.0000.0000.0000.000
85R114ARG10.8340.93629.657-0.016-0.0160.0000.0000.0000.000
86R115VAL0-0.022-0.04729.158-0.002-0.0020.0000.0000.0000.000
87R116GLU-1-0.840-0.91225.5610.0300.0300.0000.0000.0000.000
88R117ASP-1-0.931-0.98125.042-0.033-0.0330.0000.0000.0000.000
89R118GLU-1-0.874-0.88620.552-0.065-0.0650.0000.0000.0000.000
90R119GLY0-0.005-0.03421.842-0.003-0.0030.0000.0000.0000.000
91R120SER0-0.014-0.14418.7090.0190.0190.0000.0000.0000.000
92R121TYR00.0340.04016.9370.0390.0390.0000.0000.0000.000
93R122THR00.0230.05411.5470.0110.0110.0000.0000.0000.000
94R124LEU00.0550.0439.9760.1030.1030.0000.0000.0000.000
95R125PHE00.003-0.0237.194-0.055-0.0550.0000.0000.0000.000
96R126VAL00.0130.0229.1180.1520.1520.0000.0000.0000.000
97R127THR0-0.026-0.0567.4800.1030.1030.0000.0000.0000.000
98R128PHE00.0320.0279.900-0.149-0.1490.0000.0000.0000.000
99R129PRO0-0.0010.0266.179-0.199-0.1990.0000.0000.0000.000
100R130GLN00.018-0.0016.2771.0111.0110.0000.0000.0000.000
101R131GLY00.0260.0116.0170.0690.0690.0000.0000.0000.000
102R132SER0-0.075-0.0126.648-0.254-0.2540.0000.0000.0000.000
103R133ARG10.8810.9412.018-6.194-6.1662.482-0.865-1.6450.002
104R134SER0-0.262-0.1706.2690.3600.3600.0000.0000.0000.000
105R135VAL00.0770.0446.9860.0050.0050.0000.0000.0000.000
106R136ASP-1-0.956-1.0338.846-0.038-0.0380.0000.0000.0000.000
107R137ILE0-0.0120.00211.184-0.074-0.0740.0000.0000.0000.000
108R138TRP0-0.0130.07314.2380.0370.0370.0000.0000.0000.000
109R139LEU0-0.1130.07215.841-0.029-0.0290.0000.0000.0000.000
110R140ARG10.9080.95819.7020.2460.2460.0000.0000.0000.000
111R141VAL00.1180.09123.0700.0040.0040.0000.0000.0000.000
112R142LEU0-0.027-0.00525.7060.0120.0120.0000.0000.0000.000
113R143ALA00.0410.01629.540-0.008-0.0080.0000.0000.0000.000
114R144LYS10.9470.99432.8740.0610.0610.0000.0000.0000.000
115R145PRO0-0.0270.06935.9100.0030.0030.0000.0000.0000.000
116R146GLN0-0.105-0.06339.657-0.002-0.0020.0000.0000.0000.000
117R147ASN00.0410.06742.4760.0030.0030.0000.0000.0000.000
118R148THR00.0150.02145.1820.0000.0000.0000.0000.0000.000
119R149ALA00.054-0.03348.725-0.001-0.0010.0000.0000.0000.000
120R150GLU-1-0.886-0.93151.366-0.030-0.0300.0000.0000.0000.000
121R151VAL00.0180.05255.0990.0000.0000.0000.0000.0000.000
122R152GLN0-0.103-0.08457.3260.0020.0020.0000.0000.0000.000
123R153LYS11.0180.98960.4410.0210.0210.0000.0000.0000.000
124R154VAL00.012-0.03163.6930.0000.0000.0000.0000.0000.000
125R155GLN00.0210.11664.3990.0000.0000.0000.0000.0000.000
126R156LEU0-0.0090.01667.8860.0010.0010.0000.0000.0000.000
127R157THR0-0.011-0.00368.657-0.001-0.0010.0000.0000.0000.000
128R158GLY00.061-0.01267.5480.0010.0010.0000.0000.0000.000
129R159GLU-1-0.952-0.98663.361-0.022-0.0220.0000.0000.0000.000
130R160PRO0-0.066-0.01959.770-0.001-0.0010.0000.0000.0000.000
131R161VAL0-0.016-0.02456.6230.0000.0000.0000.0000.0000.000
132R162PRO0-0.0180.05458.5040.0010.0010.0000.0000.0000.000
133R163MET00.0550.05756.8940.0010.0010.0000.0000.0000.000
134R164ALA0-0.031-0.03953.404-0.001-0.0010.0000.0000.0000.000
135R165ARG10.8890.98251.5400.0290.0290.0000.0000.0000.000
136R166CYS00.0040.04748.064-0.001-0.0010.0000.0000.0000.000
137R167VAL0-0.057-0.05046.7410.0010.0010.0000.0000.0000.000
138R168SER0-0.064-0.05242.158-0.003-0.0030.0000.0000.0000.000
139R169THR00.0840.00643.2550.0030.0030.0000.0000.0000.000
140R170GLY00.0930.01441.404-0.001-0.0010.0000.0000.0000.000
141R171GLY00.000-0.04437.8090.0000.0000.0000.0000.0000.000
142R172ARG10.9711.01531.4020.0580.0580.0000.0000.0000.000
143R173PRO0-0.052-0.08831.4120.0020.0020.0000.0000.0000.000
144R174PRO0-0.012-0.00334.199-0.001-0.0010.0000.0000.0000.000
145R175ALA00.0120.01336.721-0.005-0.0050.0000.0000.0000.000
146R176GLN0-0.065-0.04238.814-0.001-0.0010.0000.0000.0000.000
147R177ILE00.0520.01641.901-0.004-0.0040.0000.0000.0000.000
148R178THR0-0.0120.00443.7740.0010.0010.0000.0000.0000.000
149R179TRP00.0590.02446.2220.0010.0010.0000.0000.0000.000
150R180HIS0-0.021-0.00146.0710.0010.0010.0000.0000.0000.000
151R181SER0-0.046-0.00651.3460.0000.0000.0000.0000.0000.000
152R182ASP-1-0.837-0.93154.645-0.044-0.0440.0000.0000.0000.000
153R183LEU00.0120.06456.7390.0000.0000.0000.0000.0000.000
154R184GLY00.014-0.03254.7300.0000.0000.0000.0000.0000.000
155R185GLY0-0.013-0.04355.2050.0000.0000.0000.0000.0000.000
156R186MET00.0000.01654.6350.0020.0020.0000.0000.0000.000
157R187PRO0-0.0320.01353.059-0.002-0.0020.0000.0000.0000.000
158R188GLN0-0.009-0.02052.8660.0000.0000.0000.0000.0000.000
159R189THR00.068-0.03249.7210.0000.0000.0000.0000.0000.000
160R190SER0-0.0400.02149.957-0.001-0.0010.0000.0000.0000.000
161R191GLN00.0540.00546.029-0.003-0.0030.0000.0000.0000.000
162R192VAL00.0960.03046.9110.0020.0020.0000.0000.0000.000
163R193PRO00.1000.10943.778-0.002-0.0020.0000.0000.0000.000
164R194GLY0-0.004-0.03344.3530.0020.0020.0000.0000.0000.000
165R195PHE00.0170.01443.6250.0020.0020.0000.0000.0000.000
166R196LEU0-0.082-0.07040.2300.0010.0010.0000.0000.0000.000
167R197SER00.0340.02242.4160.0010.0010.0000.0000.0000.000
168R198GLY0-0.0280.01640.6460.0030.0030.0000.0000.0000.000
169R199THR0-0.016-0.03537.0000.0020.0020.0000.0000.0000.000
170R200VAL00.0350.02035.821-0.002-0.0020.0000.0000.0000.000
171R201THR0-0.027-0.01138.8470.0020.0020.0000.0000.0000.000
172R202VAL0-0.0680.04940.7160.0020.0020.0000.0000.0000.000
173R203THR0-0.150-0.12542.5460.0010.0010.0000.0000.0000.000
174R204SER00.0040.01045.008-0.001-0.0010.0000.0000.0000.000
175R205LEU00.0470.00144.9140.0000.0000.0000.0000.0000.000
176R206TRP0-0.105-0.01548.665-0.002-0.0020.0000.0000.0000.000
177R207ILE00.011-0.00151.7760.0010.0010.0000.0000.0000.000
178R208LEU0-0.020-0.02954.0390.0010.0010.0000.0000.0000.000
179R209VAL00.010-0.01257.0960.0010.0010.0000.0000.0000.000
180R210PRO00.0320.03159.3120.0010.0010.0000.0000.0000.000
181R211SER00.051-0.07162.8900.0010.0010.0000.0000.0000.000
182R212SER0-0.035-0.01265.411-0.001-0.0010.0000.0000.0000.000
183R213GLN0-0.023-0.03867.3680.0010.0010.0000.0000.0000.000
184R214VAL0-0.019-0.01262.746-0.001-0.0010.0000.0000.0000.000
185R215ASP-1-0.774-0.85364.109-0.030-0.0300.0000.0000.0000.000
186R216GLY0-0.083-0.06262.7590.0000.0000.0000.0000.0000.000
187R217LYS10.9240.93358.3210.0400.0400.0000.0000.0000.000
188R218GLN0-0.024-0.01553.8620.0010.0010.0000.0000.0000.000
189R219VAL00.0040.00053.4830.0000.0000.0000.0000.0000.000
190R220THR0-0.004-0.00949.5930.0000.0000.0000.0000.0000.000
191R222LYS10.9271.03141.3460.0760.0760.0000.0000.0000.000
192R223VAL0-0.046-0.06341.1290.0020.0020.0000.0000.0000.000
193R224GLU-1-0.888-0.91936.137-0.093-0.0930.0000.0000.0000.000
194R225HIS10.8450.87733.8080.0810.0810.0000.0000.0000.000
195R226GLH00.0900.07930.193-0.002-0.0020.0000.0000.0000.000
196R227SER0-0.090-0.06431.2180.0020.0020.0000.0000.0000.000
197R228PHE0-0.026-0.01833.1210.0010.0010.0000.0000.0000.000
198R229GLU-1-0.869-0.94333.196-0.114-0.1140.0000.0000.0000.000
199R230LYS10.9521.03734.1950.0770.0770.0000.0000.0000.000
200R231PRO00.049-0.01936.8380.0060.0060.0000.0000.0000.000
201R232GLN0-0.062-0.02539.4170.0040.0040.0000.0000.0000.000
202R233LEU00.062-0.01542.6390.0000.0000.0000.0000.0000.000
203R234LEU0-0.071-0.03345.8820.0000.0000.0000.0000.0000.000
204R235THR0-0.015-0.00649.3080.0000.0000.0000.0000.0000.000
205R236VAL00.0050.00552.7750.0010.0010.0000.0000.0000.000
206R237SER00.0760.04856.459-0.001-0.0010.0000.0000.0000.000
207R238LEU0-0.057-0.03658.6440.0000.0000.0000.0000.0000.000
208R239THR00.025-0.00561.6490.0000.0000.0000.0000.0000.000
209R240VAL00.0060.04764.9930.0000.0000.0000.0000.0000.000
210R241TYR0-0.024-0.00467.5760.0010.0010.0000.0000.0000.000
211R242TYR0-0.0040.04270.8130.0000.0000.0000.0000.0000.000