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: QV89Y

Calculation Name: 4URP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4URP

Chain ID: A

ChEMBL ID:

UniProt ID: P37261

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1715836.472904
FMO2-HF: Nuclear repulsion 1648061.871766
FMO2-HF: Total energy -67774.601138
FMO2-MP2: Total energy -67975.326993


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:3:PRO)


Summations of interaction energy for fragment #1(A:3:PRO)
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.
-3.956-0.9172.512-2.463-3.087-0.002
Interaction energy analysis for fragmet #1(A:3:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.020
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].
3A5GLY00.0690.0623.810-1.5520.333-0.030-0.891-0.9630.000
4A6ASN0-0.057-0.0442.149-1.636-0.6402.541-1.518-2.019-0.002
5A7TYR00.0470.0034.264-0.328-0.1700.001-0.054-0.1050.000
6A8LEU00.0390.0187.316-0.091-0.0910.0000.0000.0000.000
7A9ASN00.0080.0035.6080.2490.2490.0000.0000.0000.000
8A10ALA00.0180.0187.973-0.170-0.1700.0000.0000.0000.000
9A11ILE0-0.024-0.00910.044-0.090-0.0900.0000.0000.0000.000
10A12THR0-0.038-0.03310.8530.0040.0040.0000.0000.0000.000
11A13ASN0-0.081-0.0259.856-0.018-0.0180.0000.0000.0000.000
12A14ARG10.9691.00513.067-0.284-0.2840.0000.0000.0000.000
13A15ARG10.8530.92116.212-0.179-0.1790.0000.0000.0000.000
14A16THR0-0.052-0.00819.919-0.013-0.0130.0000.0000.0000.000
15A17ILE00.0210.01420.3480.0060.0060.0000.0000.0000.000
16A18TYR00.029-0.00224.183-0.008-0.0080.0000.0000.0000.000
17A19ASN00.0020.01624.507-0.015-0.0150.0000.0000.0000.000
18A20LEU00.0040.00725.4670.0000.0000.0000.0000.0000.000
19A21LYS10.9550.97427.361-0.029-0.0290.0000.0000.0000.000
20A22PRO0-0.0020.00928.333-0.003-0.0030.0000.0000.0000.000
21A23GLU-1-0.903-0.92024.222-0.011-0.0110.0000.0000.0000.000
22A24LEU0-0.091-0.02626.6850.0020.0020.0000.0000.0000.000
23A25PRO00.0410.02321.5300.0010.0010.0000.0000.0000.000
24A26GLN00.027-0.02322.012-0.016-0.0160.0000.0000.0000.000
25A27GLY0-0.0020.00921.468-0.010-0.0100.0000.0000.0000.000
26A28VAL0-0.038-0.01620.353-0.019-0.0190.0000.0000.0000.000
27A29GLY00.0560.03522.6500.0140.0140.0000.0000.0000.000
28A30LEU00.0430.01725.0160.0030.0030.0000.0000.0000.000
29A31ASP-1-0.821-0.93826.280-0.073-0.0730.0000.0000.0000.000
30A32ASP-1-0.803-0.87821.653-0.152-0.1520.0000.0000.0000.000
31A33VAL00.0450.02222.303-0.005-0.0050.0000.0000.0000.000
32A34LYS10.8310.90223.3520.0710.0710.0000.0000.0000.000
33A35ARG10.8500.91521.3380.1530.1530.0000.0000.0000.000
34A36THR0-0.0040.01018.200-0.006-0.0060.0000.0000.0000.000
35A37VAL00.0670.03820.6330.0080.0080.0000.0000.0000.000
36A38HIS00.0450.03023.1860.0100.0100.0000.0000.0000.000
37A39VAL0-0.058-0.04019.2850.0040.0040.0000.0000.0000.000
38A40ILE00.0480.04018.616-0.002-0.0020.0000.0000.0000.000
39A41LEU0-0.0210.00621.9090.0090.0090.0000.0000.0000.000
40A42LYS10.8450.92824.6060.0870.0870.0000.0000.0000.000
41A43ASN0-0.059-0.04021.015-0.007-0.0070.0000.0000.0000.000
42A44THR0-0.041-0.03222.1620.0100.0100.0000.0000.0000.000
43A45PRO0-0.003-0.00222.765-0.002-0.0020.0000.0000.0000.000
44A46THR0-0.0410.02325.8920.0090.0090.0000.0000.0000.000
45A47ALA00.0360.00029.248-0.005-0.0050.0000.0000.0000.000
46A48PHE0-0.001-0.02030.971-0.002-0.0020.0000.0000.0000.000
47A49ASN0-0.014-0.00331.023-0.003-0.0030.0000.0000.0000.000
48A50SER00.0190.02232.733-0.004-0.0040.0000.0000.0000.000
49A51GLN0-0.028-0.02631.072-0.006-0.0060.0000.0000.0000.000
50A52VAL00.0610.01932.497-0.003-0.0030.0000.0000.0000.000
51A53ASN00.0120.02428.1690.0070.0070.0000.0000.0000.000
52A54ARG10.8670.92630.6260.0010.0010.0000.0000.0000.000
53A55ALA0-0.009-0.01528.8770.0070.0070.0000.0000.0000.000
54A56VAL00.0160.01730.909-0.006-0.0060.0000.0000.0000.000
55A57ILE0-0.0230.00427.0080.0050.0050.0000.0000.0000.000
56A58ILE0-0.0080.01031.005-0.005-0.0050.0000.0000.0000.000
57A59VAL00.0840.01831.0310.0020.0020.0000.0000.0000.000
58A60GLY00.0680.04033.8470.0000.0000.0000.0000.0000.000
59A61ASP-1-0.842-0.92836.399-0.005-0.0050.0000.0000.0000.000
60A62THR0-0.012-0.01737.5310.0010.0010.0000.0000.0000.000
61A63HIS0-0.0210.01132.4670.0000.0000.0000.0000.0000.000
62A64LYS10.9040.92236.3930.0090.0090.0000.0000.0000.000
63A65ARG10.9130.95738.6860.0070.0070.0000.0000.0000.000
64A66ILE00.0200.03038.1260.0020.0020.0000.0000.0000.000
65A67TRP00.009-0.00532.8370.0060.0060.0000.0000.0000.000
66A68ASP-1-0.840-0.90238.9430.0160.0160.0000.0000.0000.000
67A69ALA00.0220.02242.2400.0010.0010.0000.0000.0000.000
68A70VAL00.004-0.00339.2360.0020.0020.0000.0000.0000.000
69A71ALA0-0.016-0.01241.0640.0020.0020.0000.0000.0000.000
70A72SER0-0.026-0.01142.823-0.001-0.0010.0000.0000.0000.000
71A73ALA0-0.030-0.00244.7460.0000.0000.0000.0000.0000.000
72A74MET0-0.063-0.01040.8270.0020.0020.0000.0000.0000.000
73A75PRO0-0.014-0.01745.129-0.001-0.0010.0000.0000.0000.000
74A76THR00.0630.01145.030-0.001-0.0010.0000.0000.0000.000
75A77ALA0-0.0060.01545.0580.0020.0020.0000.0000.0000.000
76A78GLU-1-0.910-0.97042.1580.0470.0470.0000.0000.0000.000
77A79ALA0-0.051-0.02640.7510.0040.0040.0000.0000.0000.000
78A80LYS10.8860.92740.651-0.028-0.0280.0000.0000.0000.000
79A81LYS10.9090.95637.462-0.034-0.0340.0000.0000.0000.000
80A82ARG10.8930.97031.025-0.070-0.0700.0000.0000.0000.000
81A83PRO00.0160.01035.178-0.001-0.0010.0000.0000.0000.000
82A84GLU-1-0.796-0.89837.0510.0260.0260.0000.0000.0000.000
83A85SER0-0.032-0.02634.155-0.002-0.0020.0000.0000.0000.000
84A86CYS0-0.058-0.02532.6780.0030.0030.0000.0000.0000.000
85A87ARG10.7210.85133.744-0.020-0.0200.0000.0000.0000.000
86A88ASP-1-0.856-0.91235.8800.0110.0110.0000.0000.0000.000
87A89GLU-1-0.934-0.97931.9270.0350.0350.0000.0000.0000.000
88A90ALA0-0.0160.00429.8400.0000.0000.0000.0000.0000.000
89A91TYR0-0.020-0.00528.426-0.005-0.0050.0000.0000.0000.000
90A92GLY0-0.015-0.02529.737-0.006-0.0060.0000.0000.0000.000
91A93SER0-0.047-0.02729.1230.0080.0080.0000.0000.0000.000
92A94VAL0-0.020-0.00625.771-0.006-0.0060.0000.0000.0000.000
93A95ILE00.0000.00928.7930.0100.0100.0000.0000.0000.000
94A96PHE00.0190.00324.977-0.005-0.0050.0000.0000.0000.000
95A97PHE00.0460.00130.7400.0040.0040.0000.0000.0000.000
96A98THR00.016-0.00332.2340.0020.0020.0000.0000.0000.000
97A99ASP-1-0.830-0.91334.4730.0010.0010.0000.0000.0000.000
98A100LEU00.0120.00337.2430.0010.0010.0000.0000.0000.000
99A101GLY00.0760.04739.7200.0000.0000.0000.0000.0000.000
100A102PRO0-0.020-0.02037.2400.0010.0010.0000.0000.0000.000
101A103THR0-0.014-0.00837.3700.0010.0010.0000.0000.0000.000
102A104GLU-1-0.880-0.93239.2650.0160.0160.0000.0000.0000.000
103A105LYS10.7800.88241.139-0.003-0.0030.0000.0000.0000.000
104A106LEU0-0.031-0.01937.183-0.001-0.0010.0000.0000.0000.000
105A107GLN0-0.034-0.01541.5000.0000.0000.0000.0000.0000.000
106A108ARG10.9360.98643.564-0.008-0.0080.0000.0000.0000.000
107A109ASP-1-0.847-0.91943.9530.0060.0060.0000.0000.0000.000
108A110PHE0-0.046-0.01841.0420.0000.0000.0000.0000.0000.000
109A111PRO00.0510.02243.9880.0030.0030.0000.0000.0000.000
110A112ALA0-0.015-0.00445.0840.0020.0020.0000.0000.0000.000
111A113LEU00.0060.00039.1980.0030.0030.0000.0000.0000.000
112A114ALA00.0420.02240.5360.0020.0020.0000.0000.0000.000
113A115ALA0-0.030-0.02140.7920.0000.0000.0000.0000.0000.000
114A116ALA00.0270.01135.8040.0040.0040.0000.0000.0000.000
115A117PHE00.0410.02235.5120.0030.0030.0000.0000.0000.000
116A118PRO00.0560.02336.0090.0000.0000.0000.0000.0000.000
117A119THR00.0220.01133.1300.0030.0030.0000.0000.0000.000
118A120CYS0-0.065-0.03131.5730.0060.0060.0000.0000.0000.000
119A121ALA0-0.0070.00030.891-0.001-0.0010.0000.0000.0000.000
120A122ALA00.0230.00331.142-0.001-0.0010.0000.0000.0000.000
121A123HIS0-0.039-0.02827.1850.0130.0130.0000.0000.0000.000
122A124THR00.004-0.00626.3470.0050.0050.0000.0000.0000.000
123A125THR00.0180.01126.397-0.007-0.0070.0000.0000.0000.000
124A126GLY0-0.021-0.00326.065-0.002-0.0020.0000.0000.0000.000
125A127ALA00.0080.00322.5930.0150.0150.0000.0000.0000.000
126A128VAL00.0270.01821.682-0.001-0.0010.0000.0000.0000.000
127A129GLN0-0.0140.01622.981-0.011-0.0110.0000.0000.0000.000
128A130ILE00.0320.01518.620-0.003-0.0030.0000.0000.0000.000
129A131GLN0-0.0140.00417.4820.0080.0080.0000.0000.0000.000
130A132SER00.021-0.00818.079-0.018-0.0180.0000.0000.0000.000
131A133TRP0-0.043-0.02719.8700.0010.0010.0000.0000.0000.000
132A134THR0-0.039-0.05213.8950.0150.0150.0000.0000.0000.000
133A135ALA00.0040.01414.8940.0020.0020.0000.0000.0000.000
134A136LEU0-0.024-0.02716.383-0.027-0.0270.0000.0000.0000.000
135A137GLU-1-0.796-0.91316.5900.1280.1280.0000.0000.0000.000
136A138LEU0-0.064-0.02510.7070.0060.0060.0000.0000.0000.000
137A139LEU0-0.071-0.03114.165-0.038-0.0380.0000.0000.0000.000
138A140GLY00.0260.01916.839-0.020-0.0200.0000.0000.0000.000
139A141LEU0-0.066-0.01817.8820.0150.0150.0000.0000.0000.000
140A142GLY00.0370.02519.5620.0170.0170.0000.0000.0000.000
141A143ALA00.006-0.00921.877-0.013-0.0130.0000.0000.0000.000
142A144ASN0-0.027-0.01223.1770.0150.0150.0000.0000.0000.000
143A145LEU0-0.021-0.00825.570-0.008-0.0080.0000.0000.0000.000
144A146GLN00.0510.01827.4770.0030.0030.0000.0000.0000.000
145A147HIS00.0290.01828.965-0.001-0.0010.0000.0000.0000.000
146A148TYR00.0330.03033.7360.0000.0000.0000.0000.0000.000
147A149ASN00.039-0.00834.394-0.005-0.0050.0000.0000.0000.000
148A150ASP-1-0.841-0.92237.4910.0350.0350.0000.0000.0000.000
149A151TYR00.005-0.01240.170-0.004-0.0040.0000.0000.0000.000
150A152VAL00.006-0.00936.120-0.003-0.0030.0000.0000.0000.000
151A153LYS10.8640.95439.564-0.018-0.0180.0000.0000.0000.000
152A154SER0-0.021-0.01240.997-0.003-0.0030.0000.0000.0000.000
153A155ALA0-0.034-0.00741.462-0.002-0.0020.0000.0000.0000.000
154A156LEU0-0.068-0.02737.511-0.003-0.0030.0000.0000.0000.000
155A157PRO0-0.0090.00840.5320.0000.0000.0000.0000.0000.000
156A158GLN00.031-0.00143.6210.0000.0000.0000.0000.0000.000
157A159ASP-1-0.968-0.96341.374-0.011-0.0110.0000.0000.0000.000
158A160VAL0-0.004-0.01139.331-0.002-0.0020.0000.0000.0000.000
159A161PRO00.0140.00639.5570.0020.0020.0000.0000.0000.000
160A162ILE00.0350.01141.3580.0030.0030.0000.0000.0000.000
161A163ALA00.0410.01941.8090.0030.0030.0000.0000.0000.000
162A164TRP0-0.059-0.04336.1500.0020.0020.0000.0000.0000.000
163A165THR00.0130.01137.1210.0010.0010.0000.0000.0000.000
164A166VAL0-0.016-0.00235.0890.0000.0000.0000.0000.0000.000
165A167GLN0-0.0130.00131.5740.0080.0080.0000.0000.0000.000
166A168SER0-0.031-0.03229.0750.0110.0110.0000.0000.0000.000
167A169GLN0-0.001-0.01630.615-0.005-0.0050.0000.0000.0000.000
168A170LEU0-0.031-0.00222.8970.0060.0060.0000.0000.0000.000
169A171VAL00.0160.00827.263-0.012-0.0120.0000.0000.0000.000
170A172PHE00.0050.00624.2480.0070.0070.0000.0000.0000.000
171A173GLY00.033-0.01823.936-0.003-0.0030.0000.0000.0000.000
172A186ASN0-0.036-0.03621.114-0.007-0.0070.0000.0000.0000.000
173A187ASN0-0.032-0.01919.336-0.023-0.0230.0000.0000.0000.000
174A188VAL00.0570.03623.4790.0120.0120.0000.0000.0000.000
175A189ILE00.0070.00322.097-0.001-0.0010.0000.0000.0000.000
176A190ASN0-0.0170.00025.500-0.003-0.0030.0000.0000.0000.000
177A191VAL0-0.063-0.03826.095-0.002-0.0020.0000.0000.0000.000
178A192TYR00.0840.05228.9200.0050.0050.0000.0000.0000.000