Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZV98N

Calculation Name: 5I45-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I45

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NFJ9

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2262344.09194
FMO2-HF: Nuclear repulsion 2186491.807434
FMO2-HF: Total energy -75852.284506
FMO2-MP2: Total energy -76076.762844


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:141:GLY)


Summations of interaction energy for fragment #1(A:141:GLY)
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.
-2.9881.6483.475-3.863-4.246-0.017
Interaction energy analysis for fragmet #1(A:141:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.015
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].
3A143ASP-1-0.808-0.9053.755-1.1630.604-0.017-0.880-0.8690.004
4A144THR00.044-0.0016.7660.3310.3310.0000.0000.0000.000
5A145GLN0-0.051-0.0148.9380.4020.4020.0000.0000.0000.000
6A146VAL0-0.035-0.00710.3070.1330.1330.0000.0000.0000.000
7A147PHE0-0.020-0.0158.6180.1500.1500.0000.0000.0000.000
8A148TYR00.0340.01310.532-0.001-0.0010.0000.0000.0000.000
9A149PRO00.0150.00013.1420.0190.0190.0000.0000.0000.000
10A150ALA00.0040.00916.2460.0050.0050.0000.0000.0000.000
11A151GLU-1-0.931-0.95319.680-0.202-0.2020.0000.0000.0000.000
12A152ASN0-0.009-0.01722.5360.0190.0190.0000.0000.0000.000
13A153ARG10.8820.92817.5760.2930.2930.0000.0000.0000.000
14A154GLN00.0480.03023.0610.0020.0020.0000.0000.0000.000
15A155GLN0-0.069-0.03826.6170.0140.0140.0000.0000.0000.000
16A156GLN00.004-0.00521.816-0.034-0.0340.0000.0000.0000.000
17A157TRP0-0.013-0.01823.918-0.022-0.0220.0000.0000.0000.000
18A158GLN0-0.032-0.02025.5820.0050.0050.0000.0000.0000.000
19A159ASP-1-0.859-0.92026.412-0.226-0.2260.0000.0000.0000.000
20A160LYS10.8130.91222.0630.3800.3800.0000.0000.0000.000
21A161LYS10.8330.92727.4050.1780.1780.0000.0000.0000.000
22A162ILE00.0040.00826.1170.0060.0060.0000.0000.0000.000
23A163PRO0-0.0010.00630.7170.0040.0040.0000.0000.0000.000
24A164GLY00.0480.04330.599-0.009-0.0090.0000.0000.0000.000
25A165LYS10.7950.88530.0850.1100.1100.0000.0000.0000.000
26A166TYR0-0.027-0.01125.930-0.004-0.0040.0000.0000.0000.000
27A167GLY00.0640.03423.9430.0090.0090.0000.0000.0000.000
28A168ILE0-0.015-0.01521.590-0.011-0.0110.0000.0000.0000.000
29A169GLY00.0400.01319.8640.0090.0090.0000.0000.0000.000
30A170ILE0-0.052-0.01317.801-0.002-0.0020.0000.0000.0000.000
31A171PHE00.0630.03214.6010.0070.0070.0000.0000.0000.000
32A172GLY0-0.0090.00015.959-0.015-0.0150.0000.0000.0000.000
33A173ARG10.7960.88616.7860.2880.2880.0000.0000.0000.000
34A174ILE00.0120.02019.5150.0130.0130.0000.0000.0000.000
35A175ARG10.8610.89521.6550.1690.1690.0000.0000.0000.000
36A176LYS10.9120.95922.5960.0920.0920.0000.0000.0000.000
37A177THR0-0.036-0.03920.5340.0030.0030.0000.0000.0000.000
38A178LYS10.8500.92114.8090.3450.3450.0000.0000.0000.000
39A179GLY00.0510.03519.008-0.018-0.0180.0000.0000.0000.000
40A180THR00.021-0.00121.4690.0070.0070.0000.0000.0000.000
41A181GLN00.010-0.00223.0040.0000.0000.0000.0000.0000.000
42A182GLU-1-0.774-0.87923.660-0.105-0.1050.0000.0000.0000.000
43A183PHE00.0330.01421.4890.0080.0080.0000.0000.0000.000
44A184ILE00.0210.00624.0950.0060.0060.0000.0000.0000.000
45A185GLU-1-0.834-0.91127.311-0.076-0.0760.0000.0000.0000.000
46A186ALA00.0050.00225.7680.0080.0080.0000.0000.0000.000
47A187ALA00.0160.02126.5630.0060.0060.0000.0000.0000.000
48A188ILE0-0.024-0.02028.3100.0060.0060.0000.0000.0000.000
49A189VAL0-0.028-0.01431.1520.0060.0060.0000.0000.0000.000
50A190THR0-0.018-0.02927.8970.0060.0060.0000.0000.0000.000
51A191LEU0-0.024-0.02628.1850.0030.0030.0000.0000.0000.000
52A192LYS10.8570.94731.8520.0820.0820.0000.0000.0000.000
53A193LYS10.8090.90432.9690.0610.0610.0000.0000.0000.000
54A194TYR0-0.028-0.03530.7340.0040.0040.0000.0000.0000.000
55A195PRO00.0300.00032.401-0.010-0.0100.0000.0000.0000.000
56A196ASP-1-0.803-0.88131.829-0.116-0.1160.0000.0000.0000.000
57A197TRP0-0.0200.00223.846-0.015-0.0150.0000.0000.0000.000
58A198THR0-0.020-0.03527.6320.0140.0140.0000.0000.0000.000
59A199ALA0-0.034-0.00725.064-0.014-0.0140.0000.0000.0000.000
60A200VAL00.000-0.00321.8870.0100.0100.0000.0000.0000.000
61A201VAL0-0.029-0.01722.023-0.019-0.0190.0000.0000.0000.000
62A202ILE00.0060.01018.7070.0150.0150.0000.0000.0000.000
63A203GLY00.0530.01318.980-0.053-0.0530.0000.0000.0000.000
64A204GLU-1-0.850-0.93420.712-0.232-0.2320.0000.0000.0000.000
65A205ALA0-0.0210.00422.588-0.011-0.0110.0000.0000.0000.000
66A206THR0-0.021-0.03023.2020.0070.0070.0000.0000.0000.000
67A207PRO00.0940.01525.8840.0100.0100.0000.0000.0000.000
68A208ARG10.9040.95426.1740.1360.1360.0000.0000.0000.000
69A209ASP-1-0.727-0.82925.211-0.174-0.1740.0000.0000.0000.000
70A210LEU00.0440.02828.302-0.003-0.0030.0000.0000.0000.000
71A211ASP-1-0.909-0.95530.516-0.112-0.1120.0000.0000.0000.000
72A212PHE00.0030.00024.9070.0050.0050.0000.0000.0000.000
73A213LYS10.8470.91227.3140.1840.1840.0000.0000.0000.000
74A214LYS10.9770.98529.3380.1120.1120.0000.0000.0000.000
75A215GLU-1-0.838-0.88932.366-0.086-0.0860.0000.0000.0000.000
76A216LEU0-0.025-0.01826.6330.0040.0040.0000.0000.0000.000
77A217GLU-1-0.798-0.88930.753-0.161-0.1610.0000.0000.0000.000
78A218GLN0-0.037-0.02932.7210.0070.0070.0000.0000.0000.000
79A219LYS10.8700.93431.7230.0960.0960.0000.0000.0000.000
80A220VAL00.0060.00930.7600.0050.0050.0000.0000.0000.000
81A221LYS10.9030.95433.9510.1060.1060.0000.0000.0000.000
82A222GLN0-0.025-0.01637.2960.0030.0030.0000.0000.0000.000
83A223ALA0-0.0390.00235.6880.0060.0060.0000.0000.0000.000
84A224GLY00.0160.00037.8240.0020.0020.0000.0000.0000.000
85A225LEU0-0.021-0.00933.2280.0000.0000.0000.0000.0000.000
86A226ASP-1-0.852-0.93233.599-0.117-0.1170.0000.0000.0000.000
87A227LYS10.8820.93634.0950.0980.0980.0000.0000.0000.000
88A228GLN0-0.014-0.00631.5660.0030.0030.0000.0000.0000.000
89A229ILE0-0.0080.00927.828-0.009-0.0090.0000.0000.0000.000
90A230ILE0-0.0070.00327.8970.0080.0080.0000.0000.0000.000
91A231PHE0-0.006-0.01425.963-0.019-0.0190.0000.0000.0000.000
92A232ILE0-0.019-0.01023.7450.0150.0150.0000.0000.0000.000
93A233GLY00.0080.01525.242-0.003-0.0030.0000.0000.0000.000
94A234PHE0-0.022-0.02021.163-0.025-0.0250.0000.0000.0000.000
95A235ILE0-0.019-0.00922.7650.0250.0250.0000.0000.0000.000
96A236ALA0-0.019-0.01421.765-0.032-0.0320.0000.0000.0000.000
97A237ASP-1-0.863-0.93820.635-0.499-0.4990.0000.0000.0000.000
98A238SER00.0110.00516.283-0.032-0.0320.0000.0000.0000.000
99A239ASN0-0.028-0.03016.476-0.163-0.1630.0000.0000.0000.000
100A240GLU-1-0.793-0.87818.013-0.393-0.3930.0000.0000.0000.000
101A241ILE00.0320.02714.0670.0090.0090.0000.0000.0000.000
102A242PRO00.0210.01413.2170.0180.0180.0000.0000.0000.000
103A243SER0-0.064-0.04015.0370.0600.0600.0000.0000.0000.000
104A244TRP00.023-0.01118.2300.0610.0610.0000.0000.0000.000
105A245TYR0-0.042-0.04711.4750.1190.1190.0000.0000.0000.000
106A246ARG10.8340.92314.3500.7360.7360.0000.0000.0000.000
107A247ALA0-0.0140.00417.9600.0530.0530.0000.0000.0000.000
108A248LEU0-0.0350.00018.1230.0420.0420.0000.0000.0000.000
109A249ASP-1-0.792-0.88918.906-0.216-0.2160.0000.0000.0000.000
110A250ILE0-0.034-0.00218.7060.0060.0060.0000.0000.0000.000
111A251VAL0-0.001-0.00514.458-0.021-0.0210.0000.0000.0000.000
112A252VAL0-0.0020.00016.8710.0360.0360.0000.0000.0000.000
113A253CYS0-0.041-0.00512.075-0.056-0.0560.0000.0000.0000.000
114A254ALA00.0530.01315.4870.0510.0510.0000.0000.0000.000
115A255SER0-0.049-0.03815.2950.0330.0330.0000.0000.0000.000
116A256HIS0-0.041-0.03617.3070.0460.0460.0000.0000.0000.000
117A257LYS10.9260.94817.2670.0030.0030.0000.0000.0000.000
118A258GLU-1-0.847-0.88315.005-0.207-0.2070.0000.0000.0000.000
119A259GLY00.0460.02511.202-0.038-0.0380.0000.0000.0000.000
120A260PHE00.003-0.0066.6450.1270.1270.0000.0000.0000.000
121A261GLY00.0660.0526.1100.0300.0300.0000.0000.0000.000
122A262LEU0-0.012-0.0044.000-0.0750.081-0.001-0.043-0.1120.000
123A263PRO00.0670.0346.209-0.095-0.0950.0000.0000.0000.000
124A264ALA00.0130.0079.2030.1180.1180.0000.0000.0000.000
125A265LEU00.0350.0132.630-0.444-0.0420.413-0.265-0.550-0.001
126A266GLU-1-0.854-0.9126.665-1.865-1.8650.0000.0000.0000.000
127A267ALA00.0110.0098.5790.2330.2330.0000.0000.0000.000
128A268MET0-0.035-0.0038.7610.0970.0970.0000.0000.0000.000
129A269ALA00.002-0.0027.4730.1540.1540.0000.0000.0000.000
130A270SER0-0.031-0.0319.5320.1010.1010.0000.0000.0000.000
131A271LYS10.8250.91512.6690.3020.3020.0000.0000.0000.000
132A272CYS0-0.0400.01014.0020.0410.0410.0000.0000.0000.000
133A273ALA00.0020.00414.6550.0070.0070.0000.0000.0000.000
134A274VAL00.010-0.00212.214-0.029-0.0290.0000.0000.0000.000
135A275ILE0-0.0020.01515.5090.0660.0660.0000.0000.0000.000
136A276ALA00.000-0.00914.197-0.055-0.0550.0000.0000.0000.000
137A277THR00.0020.00516.1920.0380.0380.0000.0000.0000.000
138A278LYS10.9350.94414.947-0.254-0.2540.0000.0000.0000.000
139A279ALA0-0.052-0.02513.4150.0410.0410.0000.0000.0000.000
140A280GLY0-0.042-0.02211.947-0.045-0.0450.0000.0000.0000.000
141A281ALA00.0360.01410.153-0.155-0.1550.0000.0000.0000.000
142A282TRP0-0.0290.0166.9810.1920.1920.0000.0000.0000.000
143A283PRO0-0.030-0.0227.121-0.098-0.0980.0000.0000.0000.000
144A284GLU-1-0.864-0.95910.2060.5790.5790.0000.0000.0000.000
145A285ILE0-0.0330.0006.4250.0450.0450.0000.0000.0000.000
146A286ILE0-0.015-0.00710.055-0.029-0.0290.0000.0000.0000.000
147A287VAL00.0030.01413.1600.0350.0350.0000.0000.0000.000
148A288ASP-1-0.791-0.90816.3280.0010.0010.0000.0000.0000.000
149A289ASP-1-0.844-0.91319.0690.0420.0420.0000.0000.0000.000
150A290GLU-1-0.945-0.94216.2040.2460.2460.0000.0000.0000.000
151A291ASN0-0.032-0.05613.452-0.041-0.0410.0000.0000.0000.000
152A292GLY00.0330.01814.150-0.054-0.0540.0000.0000.0000.000
153A293TYR0-0.089-0.07316.1590.0240.0240.0000.0000.0000.000
154A294LEU0-0.026-0.01615.232-0.025-0.0250.0000.0000.0000.000
155A295VAL0-0.049-0.02918.856-0.002-0.0020.0000.0000.0000.000
156A296GLU-1-0.883-0.95320.2050.0660.0660.0000.0000.0000.000
157A297PRO0-0.060-0.03920.401-0.027-0.0270.0000.0000.0000.000
158A298LYS10.8720.93022.0460.0510.0510.0000.0000.0000.000
159A299SER00.0200.01624.5520.0040.0040.0000.0000.0000.000
160A300SER00.0260.01125.7570.0010.0010.0000.0000.0000.000
161A301GLN0-0.014-0.02127.158-0.010-0.0100.0000.0000.0000.000
162A302GLN00.0910.05724.7840.0020.0020.0000.0000.0000.000
163A303ILE0-0.021-0.01521.934-0.004-0.0040.0000.0000.0000.000
164A304ALA00.0080.00124.339-0.007-0.0070.0000.0000.0000.000
165A305ASP-1-0.846-0.90527.401-0.036-0.0360.0000.0000.0000.000
166A306LYS10.8110.90622.2060.0000.0000.0000.0000.0000.000
167A307LEU0-0.008-0.00322.602-0.009-0.0090.0000.0000.0000.000
168A308ASP-1-0.780-0.86025.068-0.062-0.0620.0000.0000.0000.000
169A309MET00.0160.01625.8800.0010.0010.0000.0000.0000.000
170A310LEU0-0.018-0.00520.435-0.002-0.0020.0000.0000.0000.000
171A311ILE0-0.030-0.01024.734-0.008-0.0080.0000.0000.0000.000
172A312SER0-0.045-0.02327.2100.0020.0020.0000.0000.0000.000
173A313ASP-1-0.836-0.88527.661-0.030-0.0300.0000.0000.0000.000
174A314SER00.0540.01625.9920.0000.0000.0000.0000.0000.000
175A315LYS10.8410.90525.0520.0270.0270.0000.0000.0000.000
176A316LEU00.0110.01623.4060.0010.0010.0000.0000.0000.000
177A317ARG10.8200.88921.1950.1440.1440.0000.0000.0000.000
178A318TYR0-0.045-0.03720.270-0.008-0.0080.0000.0000.0000.000
179A319LYS10.9290.96919.836-0.057-0.0570.0000.0000.0000.000
180A320ILE0-0.0210.00817.3980.0060.0060.0000.0000.0000.000
181A321ALA00.010-0.00115.8660.0040.0040.0000.0000.0000.000
182A322GLN0-0.045-0.02014.833-0.067-0.0670.0000.0000.0000.000
183A323ASN00.0240.02114.9870.0110.0110.0000.0000.0000.000
184A324GLY00.0500.01512.0920.0650.0650.0000.0000.0000.000
185A325TYR0-0.006-0.01110.429-0.010-0.0100.0000.0000.0000.000
186A326ASP-1-0.805-0.89010.6220.0120.0120.0000.0000.0000.000
187A327LEU0-0.0130.0158.9040.1250.1250.0000.0000.0000.000
188A328VAL0-0.024-0.0155.6980.2880.2880.0000.0000.0000.000
189A329THR0-0.073-0.0496.1520.1530.1530.0000.0000.0000.000
190A330THR0-0.051-0.0238.6050.0370.0370.0000.0000.0000.000
191A331LYS10.8960.9477.386-1.290-1.2900.0000.0000.0000.000
192A332TYR00.006-0.0072.378-0.0580.4200.709-0.532-0.655-0.001
193A333LYS10.9931.0212.661-3.107-1.8141.954-1.909-1.338-0.018
194A334ILE0-0.030-0.0162.7530.4950.9620.417-0.215-0.668-0.001
195A335GLN0-0.053-0.0224.2900.4470.5200.000-0.019-0.0540.000