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: VKR31

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 OptHSide
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 -2070291.394434
FMO2-HF: Nuclear repulsion 1987883.892587
FMO2-HF: Total energy -82407.501847
FMO2-MP2: Total energy -82646.759816


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.
-8.809-3.9372.756-2.84-4.787-0.005
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 : 0.003 / 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].
3R32GLN0-0.089-0.0853.871-2.2100.352-0.013-1.283-1.2670.002
4R33ALA0-0.076-0.1066.6660.1250.1250.0000.0000.0000.000
5R34PRO0-0.047-0.01110.2710.1060.1060.0000.0000.0000.000
6R35THR0-0.0220.00012.4710.0620.0620.0000.0000.0000.000
7R36GLN00.087-0.01113.9120.0800.0800.0000.0000.0000.000
8R37VAL00.002-0.00117.7970.0290.0290.0000.0000.0000.000
9R38PRO0-0.0100.06020.5710.0180.0180.0000.0000.0000.000
10R39GLY00.059-0.00224.397-0.012-0.0120.0000.0000.0000.000
11R40PHE0-0.090-0.06526.0820.0110.0110.0000.0000.0000.000
12R41LEU00.0400.00529.894-0.001-0.0010.0000.0000.0000.000
13R42GLY0-0.0290.03732.080-0.003-0.0030.0000.0000.0000.000
14R43ASP-1-0.780-0.81928.741-0.133-0.1330.0000.0000.0000.000
15R44SER0-0.061-0.09328.7320.0060.0060.0000.0000.0000.000
16R45VAL0-0.121-0.06124.776-0.003-0.0030.0000.0000.0000.000
17R46THR0-0.0350.01820.1780.0030.0030.0000.0000.0000.000
18R47LEU00.015-0.00317.545-0.013-0.0130.0000.0000.0000.000
19R48PRO00.0160.00613.8650.0210.0210.0000.0000.0000.000
20R49CYS00.002-0.00910.101-0.061-0.0610.0000.0000.0000.000
21R50TYR0-0.057-0.0188.7370.2450.2450.0000.0000.0000.000
22R51LEU00.2400.2372.298-1.889-1.1520.752-0.329-1.160-0.005
23R52GLN0-0.0300.0184.3700.8191.003-0.001-0.021-0.1620.000
24R53VAL00.0210.0033.448-2.246-1.7560.016-0.229-0.277-0.002
25R54PRO0-0.081-0.0142.044-0.234-0.0661.960-0.774-1.353-0.001
26R55ASN00.070-0.0155.3180.6990.789-0.0010.000-0.0880.000
27R56MET0-0.109-0.0438.055-0.052-0.0520.0000.0000.0000.000
28R57GLU-1-0.835-0.9246.1061.6371.6370.0000.0000.0000.000
29R58VAL0-0.022-0.0207.518-0.283-0.2830.0000.0000.0000.000
30R59THR0-0.0070.0086.774-0.082-0.0820.0000.0000.0000.000
31R60HIS00.0320.0669.273-0.244-0.2440.0000.0000.0000.000
32R61VAL0-0.018-0.05010.2380.2500.2500.0000.0000.0000.000
33R62SER00.004-0.0297.9360.0170.0170.0000.0000.0000.000
34R63GLN0-0.032-0.01610.313-0.156-0.1560.0000.0000.0000.000
35R64LEU00.0260.01311.8260.0420.0420.0000.0000.0000.000
36R65THR00.032-0.00913.2700.0440.0440.0000.0000.0000.000
37R66TRP0-0.0200.00214.120-0.040-0.0400.0000.0000.0000.000
38R67ALA0-0.0090.00116.5170.0260.0260.0000.0000.0000.000
39R68ARG00.061-0.00218.597-0.019-0.0190.0000.0000.0000.000
40R69HIS10.9700.99916.871-0.027-0.0270.0000.0000.0000.000
41R70GLY00.163-0.02820.621-0.006-0.0060.0000.0000.0000.000
42R71GLU-1-0.937-0.87922.9640.0110.0110.0000.0000.0000.000
43R72SER0-0.097-0.06319.600-0.002-0.0020.0000.0000.0000.000
44R73GLY0-0.0640.04622.2340.0190.0190.0000.0000.0000.000
45R74SER00.000-0.04922.367-0.009-0.0090.0000.0000.0000.000
46R75MET0-0.069-0.03920.3060.0160.0160.0000.0000.0000.000
47R76ALA00.0080.03721.9670.0020.0020.0000.0000.0000.000
48R77VAL0-0.031-0.00519.398-0.019-0.0190.0000.0000.0000.000
49R78PHE0-0.014-0.02316.450-0.009-0.0090.0000.0000.0000.000
50R79HIS00.0530.04816.3780.0330.0330.0000.0000.0000.000
51R80GLN00.015-0.00216.854-0.016-0.0160.0000.0000.0000.000
52R81THR0-0.027-0.03416.4300.0250.0250.0000.0000.0000.000
53R82GLN00.0180.01018.2020.0190.0190.0000.0000.0000.000
54R83GLY0-0.026-0.00720.839-0.004-0.0040.0000.0000.0000.000
55R84PRO00.0200.02420.7700.0040.0040.0000.0000.0000.000
56R85SER0-0.023-0.01021.7530.0060.0060.0000.0000.0000.000
57R86TYR00.013-0.01022.295-0.017-0.0170.0000.0000.0000.000
58R87SER00.0560.04524.0820.0140.0140.0000.0000.0000.000
59R88GLU-1-0.897-0.93026.497-0.020-0.0200.0000.0000.0000.000
60R89SER0-0.103-0.08426.495-0.002-0.0020.0000.0000.0000.000
61R90LYN00.0780.05427.278-0.009-0.0090.0000.0000.0000.000
62R91ARG10.8290.91228.7760.0620.0620.0000.0000.0000.000
63R92LEU00.0490.03325.2570.0030.0030.0000.0000.0000.000
64R93GLU-1-0.920-0.99124.493-0.166-0.1660.0000.0000.0000.000
65R94PHE00.0280.01819.554-0.014-0.0140.0000.0000.0000.000
66R95VAL0-0.021-0.02317.9380.0090.0090.0000.0000.0000.000
67R96ALA0-0.0200.02414.924-0.020-0.0200.0000.0000.0000.000
68R97ALA0-0.034-0.03317.0450.0290.0290.0000.0000.0000.000
69R98ARG10.9770.99116.887-0.035-0.0350.0000.0000.0000.000
70R99LEU0-0.070-0.03418.2010.0040.0040.0000.0000.0000.000
71R100GLY00.0120.00019.610-0.001-0.0010.0000.0000.0000.000
72R101ALA0-0.070-0.03514.9120.0390.0390.0000.0000.0000.000
73R102GLU-1-0.858-0.92512.505-0.353-0.3530.0000.0000.0000.000
74R103LEU0-0.071-0.0288.001-0.003-0.0030.0000.0000.0000.000
75R104ARG0-0.018-0.0419.667-0.190-0.1900.0000.0000.0000.000
76R105ASP-1-0.704-0.8538.073-1.757-1.7570.0000.0000.0000.000
77R106ALA0-0.0320.01110.6280.0850.0850.0000.0000.0000.000
78R107SER0-0.0160.00313.044-0.090-0.0900.0000.0000.0000.000
79R108LEU00.0230.00615.4650.0400.0400.0000.0000.0000.000
80R109ARG10.9200.99818.8200.1770.1770.0000.0000.0000.000
81R110MET0-0.028-0.06021.8760.0310.0310.0000.0000.0000.000
82R111PHE00.0260.01824.240-0.001-0.0010.0000.0000.0000.000
83R112GLY00.1260.01427.8850.0030.0030.0000.0000.0000.000
84R113LEU0-0.099-0.07929.0890.0060.0060.0000.0000.0000.000
85R114ARG10.7970.90029.7190.0790.0790.0000.0000.0000.000
86R115VAL0-0.035-0.02329.225-0.008-0.0080.0000.0000.0000.000
87R116GLU-1-0.826-0.89025.815-0.067-0.0670.0000.0000.0000.000
88R117ASP-1-0.940-1.00225.163-0.117-0.1170.0000.0000.0000.000
89R118GLU-1-0.849-0.84620.168-0.236-0.2360.0000.0000.0000.000
90R119GLY00.015-0.01421.9280.0110.0110.0000.0000.0000.000
91R120SER0-0.025-0.07918.5880.0170.0170.0000.0000.0000.000
92R121TYR00.0000.00717.2290.0360.0360.0000.0000.0000.000
93R122THR00.0530.02711.9570.0090.0090.0000.0000.0000.000
94R124LEU0-0.011-0.0149.9710.0170.0170.0000.0000.0000.000
95R125PHE00.0190.0027.248-0.040-0.0400.0000.0000.0000.000
96R126VAL00.0030.0099.1260.2220.2220.0000.0000.0000.000
97R127THR0-0.046-0.0227.0950.0320.0320.0000.0000.0000.000
98R128PHE00.0400.0309.902-0.051-0.0510.0000.0000.0000.000
99R129PRO00.0030.0146.643-0.005-0.0050.0000.0000.0000.000
100R130GLN00.020-0.0036.2600.9640.9640.0000.0000.0000.000
101R131GLY00.0340.0235.915-0.058-0.0580.0000.0000.0000.000
102R132SER0-0.079-0.0326.548-0.472-0.4720.0000.0000.0000.000
103R133ARG10.9620.9622.991-4.086-3.4450.043-0.204-0.4800.001
104R134SER0-0.127-0.0806.1960.0660.0660.0000.0000.0000.000
105R135VAL00.0210.0157.1040.1350.1350.0000.0000.0000.000
106R136ASP-1-0.962-0.9929.091-0.195-0.1950.0000.0000.0000.000
107R137ILE0-0.0370.02011.673-0.083-0.0830.0000.0000.0000.000
108R138TRP00.0290.02714.2850.0300.0300.0000.0000.0000.000
109R139LEU0-0.179-0.05716.658-0.013-0.0130.0000.0000.0000.000
110R140ARG10.8650.90319.5980.3160.3160.0000.0000.0000.000
111R141VAL00.1530.09322.914-0.003-0.0030.0000.0000.0000.000
112R142LEU0-0.020-0.01625.6200.0150.0150.0000.0000.0000.000
113R143ALA00.0560.03229.442-0.007-0.0070.0000.0000.0000.000
114R144LYS10.8760.95332.7500.1120.1120.0000.0000.0000.000
115R145PRO00.0090.08535.7450.0020.0020.0000.0000.0000.000
116R146GLN0-0.030-0.02939.492-0.003-0.0030.0000.0000.0000.000
117R147ASN00.0360.03142.2800.0000.0000.0000.0000.0000.000
118R148THR00.0360.02044.9740.0010.0010.0000.0000.0000.000
119R149ALA00.056-0.03248.501-0.001-0.0010.0000.0000.0000.000
120R150GLU-1-0.852-0.89651.132-0.052-0.0520.0000.0000.0000.000
121R151VAL00.0480.04054.8560.0000.0000.0000.0000.0000.000
122R152GLN00.0060.00057.3430.0020.0020.0000.0000.0000.000
123R153LYS10.9810.96360.2080.0370.0370.0000.0000.0000.000
124R154VAL0-0.023-0.00163.4690.0000.0000.0000.0000.0000.000
125R155GLN00.0410.02564.4130.0000.0000.0000.0000.0000.000
126R156LEU00.0170.02467.6390.0010.0010.0000.0000.0000.000
127R157THR0-0.0100.00268.428-0.001-0.0010.0000.0000.0000.000
128R158GLY00.052-0.00667.3140.0010.0010.0000.0000.0000.000
129R159GLU-1-0.997-1.00763.415-0.031-0.0310.0000.0000.0000.000
130R160PRO0-0.061-0.00559.410-0.001-0.0010.0000.0000.0000.000
131R161VAL00.008-0.02356.2590.0000.0000.0000.0000.0000.000
132R162PRO0-0.0420.04858.3550.0000.0000.0000.0000.0000.000
133R163MET00.0020.02155.5770.0010.0010.0000.0000.0000.000
134R164ALA0-0.035-0.03953.171-0.001-0.0010.0000.0000.0000.000
135R165ARG10.7900.91651.2030.0520.0520.0000.0000.0000.000
136R166CYS0-0.0090.05847.843-0.002-0.0020.0000.0000.0000.000
137R167VAL0-0.018-0.03746.5560.0010.0010.0000.0000.0000.000
138R168SER0-0.063-0.03641.536-0.005-0.0050.0000.0000.0000.000
139R169THR00.0770.00143.2970.0030.0030.0000.0000.0000.000
140R170GLY00.0560.00641.297-0.003-0.0030.0000.0000.0000.000
141R171GLY00.002-0.03237.689-0.003-0.0030.0000.0000.0000.000
142R172ARG10.9530.95531.2100.1070.1070.0000.0000.0000.000
143R173PRO0-0.073-0.03831.3450.0050.0050.0000.0000.0000.000
144R174PRO0-0.0080.00634.0420.0000.0000.0000.0000.0000.000
145R175ALA0-0.0220.00136.521-0.005-0.0050.0000.0000.0000.000
146R176GLN0-0.009-0.02137.8120.0010.0010.0000.0000.0000.000
147R177ILE00.0280.00441.644-0.005-0.0050.0000.0000.0000.000
148R178THR0-0.038-0.00443.6530.0020.0020.0000.0000.0000.000
149R179TRP00.0690.01445.9170.0000.0000.0000.0000.0000.000
150R180HIS0-0.0240.00845.6700.0020.0020.0000.0000.0000.000
151R181SER00.0240.00150.9940.0000.0000.0000.0000.0000.000
152R182ASP-1-0.857-0.90854.303-0.052-0.0520.0000.0000.0000.000
153R183LEU00.0070.01656.3680.0000.0000.0000.0000.0000.000
154R184GLY00.012-0.02854.5600.0000.0000.0000.0000.0000.000
155R185GLY00.014-0.00854.8890.0000.0000.0000.0000.0000.000
156R186MET0-0.0260.01054.4150.0010.0010.0000.0000.0000.000
157R187PRO0-0.0540.00752.779-0.002-0.0020.0000.0000.0000.000
158R188GLN0-0.022-0.01952.620-0.001-0.0010.0000.0000.0000.000
159R189THR00.0810.01649.409-0.001-0.0010.0000.0000.0000.000
160R190SER0-0.0310.00749.735-0.002-0.0020.0000.0000.0000.000
161R191GLN00.0400.00845.563-0.002-0.0020.0000.0000.0000.000
162R192VAL00.0600.01646.7570.0030.0030.0000.0000.0000.000
163R193PRO00.0220.04443.718-0.004-0.0040.0000.0000.0000.000
164R194GLY0-0.022-0.06044.2450.0010.0010.0000.0000.0000.000
165R195PHE00.0110.01843.5640.0030.0030.0000.0000.0000.000
166R196LEU0-0.100-0.05839.7830.0000.0000.0000.0000.0000.000
167R197SER00.0480.02742.4160.0010.0010.0000.0000.0000.000
168R198GLY0-0.0310.01440.6280.0030.0030.0000.0000.0000.000
169R199THR0-0.011-0.03337.775-0.001-0.0010.0000.0000.0000.000
170R200VAL00.0290.01136.051-0.003-0.0030.0000.0000.0000.000
171R201THR0-0.026-0.01238.7760.0040.0040.0000.0000.0000.000
172R202VAL0-0.0440.05840.6240.0030.0030.0000.0000.0000.000
173R203THR0-0.031-0.00542.1350.0020.0020.0000.0000.0000.000
174R204SER00.0290.01144.878-0.002-0.0020.0000.0000.0000.000
175R205LEU00.003-0.01044.3570.0000.0000.0000.0000.0000.000
176R206TRP0-0.039-0.00748.467-0.002-0.0020.0000.0000.0000.000
177R207ILE00.0320.01451.5500.0020.0020.0000.0000.0000.000
178R208LEU0-0.009-0.04653.9250.0010.0010.0000.0000.0000.000
179R209VAL00.0100.00056.9300.0010.0010.0000.0000.0000.000
180R210PRO00.0210.01659.0420.0010.0010.0000.0000.0000.000
181R211SER00.1070.04262.6280.0000.0000.0000.0000.0000.000
182R212SER0-0.094-0.03065.118-0.001-0.0010.0000.0000.0000.000
183R213GLN0-0.020-0.03667.2250.0010.0010.0000.0000.0000.000
184R214VAL0-0.0070.00862.640-0.001-0.0010.0000.0000.0000.000
185R215ASP-1-0.812-0.91463.779-0.039-0.0390.0000.0000.0000.000
186R216GLY00.0120.00662.4650.0000.0000.0000.0000.0000.000
187R217LYS10.8440.91258.3290.0490.0490.0000.0000.0000.000
188R218GLN0-0.014-0.01553.6480.0010.0010.0000.0000.0000.000
189R219VAL00.005-0.00152.7920.0010.0010.0000.0000.0000.000
190R220THR0-0.006-0.01749.003-0.001-0.0010.0000.0000.0000.000
191R222LYS10.8751.00339.5810.0940.0940.0000.0000.0000.000
192R223VAL0-0.011-0.03440.4760.0020.0020.0000.0000.0000.000
193R224GLU-1-0.842-0.90836.542-0.113-0.1130.0000.0000.0000.000
194R225HIS10.8970.91233.8020.1220.1220.0000.0000.0000.000
195R226GLH00.0530.04129.945-0.001-0.0010.0000.0000.0000.000
196R227SER0-0.089-0.06230.958-0.005-0.0050.0000.0000.0000.000
197R228PHE0-0.011-0.00932.8380.0030.0030.0000.0000.0000.000
198R229GLU-1-0.881-0.95232.851-0.140-0.1400.0000.0000.0000.000
199R230LYS10.9541.02833.8270.1060.1060.0000.0000.0000.000
200R231PRO00.028-0.01436.5310.0040.0040.0000.0000.0000.000
201R232GLN0-0.061-0.01738.9220.0040.0040.0000.0000.0000.000
202R233LEU00.019-0.02642.3070.0000.0000.0000.0000.0000.000
203R234LEU0-0.036-0.03045.5550.0000.0000.0000.0000.0000.000
204R235THR00.010-0.00848.9970.0000.0000.0000.0000.0000.000
205R236VAL0-0.024-0.01052.4510.0000.0000.0000.0000.0000.000
206R237SER00.0650.05056.1450.0000.0000.0000.0000.0000.000
207R238LEU0-0.048-0.05257.996-0.001-0.0010.0000.0000.0000.000
208R239THR0-0.015-0.03161.3530.0000.0000.0000.0000.0000.000
209R240VAL0-0.0050.03664.7130.0010.0010.0000.0000.0000.000
210R241TYR0-0.011-0.03067.8210.0000.0000.0000.0000.0000.000
211R242TYR00.0040.04470.5440.0000.0000.0000.0000.0000.000