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: 1641Z

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2056304.378868
FMO2-HF: Nuclear repulsion 1973890.709242
FMO2-HF: Total energy -82413.669626
FMO2-MP2: Total energy -82651.804525


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.
-8.88-3.9372.634-2.819-4.7580.001
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 : 0.016 / q_NPA : 0.005
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].
3R32GLN00.0020.0123.616-2.235-0.197-0.004-0.984-1.0490.003
4R33ALA00.0830.0286.2870.3500.3500.0000.0000.0000.000
5R34PRO0-0.0370.0019.9110.1260.1260.0000.0000.0000.000
6R35THR0-0.0050.00212.5130.0810.0810.0000.0000.0000.000
7R36GLN00.0790.02213.7680.1040.1040.0000.0000.0000.000
8R37VAL0-0.0100.00017.4570.0410.0410.0000.0000.0000.000
9R38PRO0-0.0150.01320.2000.0180.0180.0000.0000.0000.000
10R39GLY00.0420.02023.934-0.013-0.0130.0000.0000.0000.000
11R40PHE0-0.076-0.06925.8260.0100.0100.0000.0000.0000.000
12R41LEU0-0.050-0.01629.6600.0040.0040.0000.0000.0000.000
13R42GLY00.0200.02931.6860.0050.0050.0000.0000.0000.000
14R43ASP-1-0.764-0.86128.962-0.157-0.1570.0000.0000.0000.000
15R44SER0-0.012-0.06628.5780.0040.0040.0000.0000.0000.000
16R45VAL0-0.0440.00924.397-0.002-0.0020.0000.0000.0000.000
17R46THR0-0.039-0.03619.928-0.006-0.0060.0000.0000.0000.000
18R47LEU00.0200.01017.161-0.003-0.0030.0000.0000.0000.000
19R48PRO0-0.0100.00413.9160.0150.0150.0000.0000.0000.000
20R49CYS00.0080.00210.100-0.108-0.1080.0000.0000.0000.000
21R50TYR0-0.032-0.0018.4870.2860.2860.0000.0000.0000.000
22R51LEU0-0.006-0.0172.245-1.791-1.0770.787-0.389-1.111-0.004
23R52GLN0-0.033-0.0053.9191.0131.2750.000-0.049-0.2130.000
24R53VAL00.0250.0083.258-2.474-1.6420.069-0.413-0.489-0.003
25R54PRO0-0.041-0.0012.584-2.037-1.2601.783-0.941-1.6190.005
26R55ASN00.023-0.0244.8950.5070.603-0.001-0.002-0.0930.000
27R56MET0-0.074-0.0298.021-0.083-0.0830.0000.0000.0000.000
28R57GLU-1-0.859-0.9326.3341.6171.6170.0000.0000.0000.000
29R58VAL0-0.013-0.0147.533-0.105-0.1050.0000.0000.0000.000
30R59THR00.0010.0107.112-0.083-0.0830.0000.0000.0000.000
31R60HIS00.0500.0369.592-0.230-0.2300.0000.0000.0000.000
32R61VAL0-0.056-0.04111.0940.1820.1820.0000.0000.0000.000
33R62SER00.0490.0137.8590.0280.0280.0000.0000.0000.000
34R63GLN00.0050.00310.267-0.134-0.1340.0000.0000.0000.000
35R64LEU00.0120.01711.6000.0340.0340.0000.0000.0000.000
36R65THR0-0.040-0.03513.5120.0660.0660.0000.0000.0000.000
37R66TRP00.0040.01414.216-0.047-0.0470.0000.0000.0000.000
38R67ALA0-0.008-0.00816.7410.0400.0400.0000.0000.0000.000
39R68ARG00.0650.02318.490-0.025-0.0250.0000.0000.0000.000
40R69HIS10.9060.95716.7550.0250.0250.0000.0000.0000.000
41R70GLY00.1130.04420.354-0.005-0.0050.0000.0000.0000.000
42R71GLU-1-0.906-0.93822.966-0.021-0.0210.0000.0000.0000.000
43R72SER0-0.068-0.04320.779-0.004-0.0040.0000.0000.0000.000
44R73GLY0-0.0320.00422.9370.0180.0180.0000.0000.0000.000
45R74SER0-0.040-0.04622.339-0.004-0.0040.0000.0000.0000.000
46R75MET00.001-0.00720.4810.0050.0050.0000.0000.0000.000
47R76ALA00.0180.03522.2250.0060.0060.0000.0000.0000.000
48R77VAL0-0.034-0.01519.974-0.020-0.0200.0000.0000.0000.000
49R78PHE00.0350.02016.259-0.003-0.0030.0000.0000.0000.000
50R79HIS0-0.014-0.01417.5460.0150.0150.0000.0000.0000.000
51R80GLN0-0.021-0.01117.1230.0010.0010.0000.0000.0000.000
52R81THR0-0.0050.00216.6160.0010.0010.0000.0000.0000.000
53R82GLN00.002-0.00218.7950.0100.0100.0000.0000.0000.000
54R83GLY00.0250.02121.4410.0010.0010.0000.0000.0000.000
55R84PRO00.013-0.00621.3390.0020.0020.0000.0000.0000.000
56R85SER0-0.044-0.01021.9880.0160.0160.0000.0000.0000.000
57R86TYR00.020-0.00422.521-0.024-0.0240.0000.0000.0000.000
58R87SER00.0310.02824.4900.0170.0170.0000.0000.0000.000
59R88GLU-1-0.871-0.92426.785-0.048-0.0480.0000.0000.0000.000
60R89SER0-0.062-0.05326.4830.0000.0000.0000.0000.0000.000
61R90LYN00.0020.01727.685-0.013-0.0130.0000.0000.0000.000
62R91ARG10.8420.92429.6400.0910.0910.0000.0000.0000.000
63R92LEU00.0530.02425.1490.0030.0030.0000.0000.0000.000
64R93GLU-1-0.946-0.98324.050-0.206-0.2060.0000.0000.0000.000
65R94PHE00.013-0.00619.493-0.012-0.0120.0000.0000.0000.000
66R95VAL0-0.011-0.00417.8980.0200.0200.0000.0000.0000.000
67R96ALA00.0290.04114.724-0.048-0.0480.0000.0000.0000.000
68R97ALA0-0.023-0.02916.7140.0380.0380.0000.0000.0000.000
69R98ARG10.9000.96016.9520.0400.0400.0000.0000.0000.000
70R99LEU0-0.045-0.04117.9440.0140.0140.0000.0000.0000.000
71R100GLY00.0310.02319.9040.0100.0100.0000.0000.0000.000
72R101ALA0-0.069-0.03315.0710.0350.0350.0000.0000.0000.000
73R102GLU-1-0.830-0.90213.389-0.360-0.3600.0000.0000.0000.000
74R103LEU0-0.040-0.0188.2860.0040.0040.0000.0000.0000.000
75R104ARG0-0.008-0.02210.566-0.169-0.1690.0000.0000.0000.000
76R105ASP-1-0.767-0.8887.900-1.802-1.8020.0000.0000.0000.000
77R106ALA0-0.023-0.00710.6460.0440.0440.0000.0000.0000.000
78R107SER0-0.0060.00613.435-0.084-0.0840.0000.0000.0000.000
79R108LEU00.0430.02015.6280.0610.0610.0000.0000.0000.000
80R109ARG10.8160.93318.8000.2070.2070.0000.0000.0000.000
81R110MET00.012-0.00721.9110.0380.0380.0000.0000.0000.000
82R111PHE0-0.015-0.00723.8630.0050.0050.0000.0000.0000.000
83R112GLY00.0570.00927.5770.0040.0040.0000.0000.0000.000
84R113LEU0-0.055-0.03129.2070.0070.0070.0000.0000.0000.000
85R114ARG10.8300.91929.9760.1040.1040.0000.0000.0000.000
86R115VAL0-0.026-0.01629.302-0.010-0.0100.0000.0000.0000.000
87R116GLU-1-0.824-0.90326.216-0.092-0.0920.0000.0000.0000.000
88R117ASP-1-0.927-0.98725.318-0.147-0.1470.0000.0000.0000.000
89R118GLU-1-0.805-0.87919.877-0.283-0.2830.0000.0000.0000.000
90R119GLY0-0.0170.00422.6730.0140.0140.0000.0000.0000.000
91R120SER0-0.025-0.06019.1300.0160.0160.0000.0000.0000.000
92R121TYR0-0.032-0.00517.3000.0180.0180.0000.0000.0000.000
93R122THR0-0.015-0.01912.3910.0010.0010.0000.0000.0000.000
94R124LEU0-0.044-0.00410.3730.0160.0160.0000.0000.0000.000
95R125PHE00.0750.0327.533-0.085-0.0850.0000.0000.0000.000
96R126VAL0-0.009-0.0119.4180.1960.1960.0000.0000.0000.000
97R127THR0-0.062-0.0357.2980.0560.0560.0000.0000.0000.000
98R128PHE00.0460.02810.213-0.058-0.0580.0000.0000.0000.000
99R129PRO00.0180.0167.011-0.081-0.0810.0000.0000.0000.000
100R130GLN00.009-0.0096.6310.8470.8470.0000.0000.0000.000
101R131GLY00.0120.0055.820-0.173-0.1730.0000.0000.0000.000
102R132SER0-0.029-0.0066.671-0.415-0.4150.0000.0000.0000.000
103R133ARG10.8700.9273.729-2.418-2.1940.000-0.041-0.1840.000
104R134SER0-0.028-0.0546.3760.1730.1730.0000.0000.0000.000
105R135VAL0-0.0110.0097.2960.1540.1540.0000.0000.0000.000
106R136ASP-1-0.932-0.9509.300-0.210-0.2100.0000.0000.0000.000
107R137ILE0-0.050-0.03111.672-0.058-0.0580.0000.0000.0000.000
108R138TRP00.0020.03113.8270.0080.0080.0000.0000.0000.000
109R139LEU0-0.087-0.05116.8210.0000.0000.0000.0000.0000.000
110R140ARG10.8490.92319.6650.3380.3380.0000.0000.0000.000
111R141VAL00.0870.05823.007-0.004-0.0040.0000.0000.0000.000
112R142LEU0-0.035-0.02625.7470.0090.0090.0000.0000.0000.000
113R143ALA00.0220.02429.541-0.003-0.0030.0000.0000.0000.000
114R144LYS10.8900.93432.5990.1240.1240.0000.0000.0000.000
115R145PRO00.0400.03735.2310.0020.0020.0000.0000.0000.000
116R146GLN0-0.039-0.00139.011-0.004-0.0040.0000.0000.0000.000
117R147ASN00.011-0.00741.634-0.002-0.0020.0000.0000.0000.000
118R148THR0-0.0030.00544.6370.0010.0010.0000.0000.0000.000
119R149ALA00.041-0.01448.4160.0000.0000.0000.0000.0000.000
120R150GLU-1-0.807-0.86051.004-0.056-0.0560.0000.0000.0000.000
121R151VAL00.0110.02754.7880.0000.0000.0000.0000.0000.000
122R152GLN0-0.031-0.02956.5690.0030.0030.0000.0000.0000.000
123R153LYS10.9850.96660.1220.0410.0410.0000.0000.0000.000
124R154VAL0-0.0390.00263.2860.0010.0010.0000.0000.0000.000
125R155GLN00.0290.02663.7900.0000.0000.0000.0000.0000.000
126R156LEU00.0200.01466.9850.0010.0010.0000.0000.0000.000
127R157THR0-0.017-0.01068.621-0.001-0.0010.0000.0000.0000.000
128R158GLY00.0220.00567.2950.0010.0010.0000.0000.0000.000
129R159GLU-1-0.925-0.96662.945-0.034-0.0340.0000.0000.0000.000
130R160PRO0-0.055-0.00359.319-0.001-0.0010.0000.0000.0000.000
131R161VAL0-0.012-0.01856.2760.0000.0000.0000.0000.0000.000
132R162PRO0-0.0040.03958.6130.0000.0000.0000.0000.0000.000
133R163MET0-0.044-0.02754.8490.0000.0000.0000.0000.0000.000
134R164ALA00.0420.00352.930-0.001-0.0010.0000.0000.0000.000
135R165ARG10.8240.91550.9110.0570.0570.0000.0000.0000.000
136R166CYS0-0.0350.01547.288-0.002-0.0020.0000.0000.0000.000
137R167VAL0-0.002-0.00246.0870.0000.0000.0000.0000.0000.000
138R168SER0-0.013-0.02340.791-0.005-0.0050.0000.0000.0000.000
139R169THR00.023-0.01342.2380.0000.0000.0000.0000.0000.000
140R170GLY00.0550.01941.108-0.004-0.0040.0000.0000.0000.000
141R171GLY00.0210.01737.272-0.004-0.0040.0000.0000.0000.000
142R172ARG10.9500.98030.5950.1220.1220.0000.0000.0000.000
143R173PRO0-0.026-0.01431.1130.0060.0060.0000.0000.0000.000
144R174PRO0-0.0060.00433.8160.0010.0010.0000.0000.0000.000
145R175ALA00.0090.02036.445-0.005-0.0050.0000.0000.0000.000
146R176GLN0-0.037-0.01837.1270.0030.0030.0000.0000.0000.000
147R177ILE00.007-0.00341.044-0.004-0.0040.0000.0000.0000.000
148R178THR0-0.0110.01042.7490.0030.0030.0000.0000.0000.000
149R179TRP00.0390.00245.354-0.001-0.0010.0000.0000.0000.000
150R180HIS00.0320.01645.4740.0020.0020.0000.0000.0000.000
151R181SER00.0100.01950.8060.0000.0000.0000.0000.0000.000
152R182ASP-1-0.848-0.92154.231-0.053-0.0530.0000.0000.0000.000
153R183LEU0-0.0150.00456.2760.0010.0010.0000.0000.0000.000
154R184GLY00.015-0.00554.2040.0010.0010.0000.0000.0000.000
155R185GLY0-0.0180.00254.8120.0000.0000.0000.0000.0000.000
156R186MET0-0.019-0.01454.4080.0010.0010.0000.0000.0000.000
157R187PRO0-0.0170.01652.418-0.002-0.0020.0000.0000.0000.000
158R188GLN0-0.015-0.01752.6490.0000.0000.0000.0000.0000.000
159R189THR00.0370.00048.8480.0000.0000.0000.0000.0000.000
160R190SER0-0.0090.01749.011-0.002-0.0020.0000.0000.0000.000
161R191GLN00.0460.01845.342-0.001-0.0010.0000.0000.0000.000
162R192VAL00.0540.03047.0860.0030.0030.0000.0000.0000.000
163R193PRO0-0.0090.00043.729-0.004-0.0040.0000.0000.0000.000
164R194GLY0-0.005-0.00443.528-0.002-0.0020.0000.0000.0000.000
165R195PHE0-0.034-0.01944.0420.0020.0020.0000.0000.0000.000
166R196LEU0-0.033-0.00839.2760.0000.0000.0000.0000.0000.000
167R197SER00.0170.00242.3520.0000.0000.0000.0000.0000.000
168R198GLY00.0360.02540.4200.0020.0020.0000.0000.0000.000
169R199THR0-0.007-0.00637.370-0.002-0.0020.0000.0000.0000.000
170R200VAL0-0.043-0.02335.809-0.004-0.0040.0000.0000.0000.000
171R201THR0-0.015-0.00338.2840.0060.0060.0000.0000.0000.000
172R202VAL0-0.0110.01540.1980.0040.0040.0000.0000.0000.000
173R203THR0-0.018-0.00741.6310.0030.0030.0000.0000.0000.000
174R204SER00.005-0.01544.262-0.002-0.0020.0000.0000.0000.000
175R205LEU00.0080.00544.3070.0010.0010.0000.0000.0000.000
176R206TRP00.007-0.00948.291-0.001-0.0010.0000.0000.0000.000
177R207ILE00.0100.02051.5370.0010.0010.0000.0000.0000.000
178R208LEU0-0.034-0.03853.6030.0010.0010.0000.0000.0000.000
179R209VAL0-0.010-0.01956.4910.0010.0010.0000.0000.0000.000
180R210PRO00.0430.02658.5570.0010.0010.0000.0000.0000.000
181R211SER00.015-0.02162.177-0.001-0.0010.0000.0000.0000.000
182R212SER0-0.023-0.00965.0680.0000.0000.0000.0000.0000.000
183R213GLN0-0.042-0.04667.0580.0010.0010.0000.0000.0000.000
184R214VAL0-0.018-0.00462.856-0.001-0.0010.0000.0000.0000.000
185R215ASP-1-0.819-0.91963.700-0.041-0.0410.0000.0000.0000.000
186R216GLY00.0120.01462.1930.0000.0000.0000.0000.0000.000
187R217LYS10.7790.87057.5490.0500.0500.0000.0000.0000.000
188R218GLN00.0200.00353.0660.0010.0010.0000.0000.0000.000
189R219VAL0-0.0070.00652.3230.0010.0010.0000.0000.0000.000
190R220THR0-0.002-0.01748.7180.0000.0000.0000.0000.0000.000
191R222LYS10.8230.88839.3290.0970.0970.0000.0000.0000.000
192R223VAL00.005-0.01539.9060.0010.0010.0000.0000.0000.000
193R224GLU-1-0.754-0.85736.299-0.112-0.1120.0000.0000.0000.000
194R225HIS10.8190.86533.6550.1310.1310.0000.0000.0000.000
195R226GLH00.0550.04229.438-0.002-0.0020.0000.0000.0000.000
196R227SER0-0.064-0.04330.253-0.007-0.0070.0000.0000.0000.000
197R228PHE0-0.010-0.01332.2230.0050.0050.0000.0000.0000.000
198R229GLU-1-0.894-0.93132.344-0.143-0.1430.0000.0000.0000.000
199R230LYS10.9690.99533.3740.1110.1110.0000.0000.0000.000
200R231PRO00.001-0.00836.3100.0030.0030.0000.0000.0000.000
201R232GLN0-0.044-0.01138.4610.0020.0020.0000.0000.0000.000
202R233LEU0-0.006-0.00741.6310.0010.0010.0000.0000.0000.000
203R234LEU0-0.0190.00745.1380.0000.0000.0000.0000.0000.000
204R235THR00.012-0.00948.5320.0000.0000.0000.0000.0000.000
205R236VAL0-0.032-0.00551.9950.0000.0000.0000.0000.0000.000
206R237SER00.0650.03955.671-0.001-0.0010.0000.0000.0000.000
207R238LEU0-0.061-0.04857.404-0.001-0.0010.0000.0000.0000.000
208R239THR00.0020.00060.8920.0000.0000.0000.0000.0000.000
209R240VAL00.0200.03264.4150.0000.0000.0000.0000.0000.000
210R241TYR0-0.003-0.01567.6030.0000.0000.0000.0000.0000.000
211R242TYR00.0090.03370.2150.0000.0000.0000.0000.0000.000