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

tag_button

FMODB ID: LZ1Y9

Calculation Name: 5H5P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H5P

Chain ID: A

ChEMBL ID:

UniProt ID: Q3UR85

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1982459.668542
FMO2-HF: Nuclear repulsion 1908583.017092
FMO2-HF: Total energy -73876.651451
FMO2-MP2: Total energy -74092.799248


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:349:GLU)


Summations of interaction energy for fragment #1(A:349:GLU)
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.
-179.208-177.78217.265-9.336-9.3540.084
Interaction energy analysis for fragmet #1(A:349:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.899 / q_NPA : -0.947
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].
3A351ILE0-0.038-0.0093.0125.6298.2350.185-1.310-1.481-0.005
4A352LYS10.8210.8921.665-115.989-121.56115.837-6.026-4.2390.079
5A353TRP0-0.005-0.0186.651-3.264-3.2640.0000.0000.0000.000
6A354GLN00.0060.01710.4481.5141.5140.0000.0000.0000.000
7A355PRO00.0370.00813.649-0.706-0.7060.0000.0000.0000.000
8A356HIS00.0110.00717.4140.7650.7650.0000.0000.0000.000
9A357GLN00.012-0.01019.256-0.442-0.4420.0000.0000.0000.000
10A358GLN00.0830.04521.467-0.139-0.1390.0000.0000.0000.000
11A359ASN00.0010.00923.606-0.433-0.4330.0000.0000.0000.000
12A360LYS10.8510.90426.442-11.455-11.4550.0000.0000.0000.000
13A361TRP0-0.050-0.00420.358-0.008-0.0080.0000.0000.0000.000
14A362ALA00.0100.01927.493-0.276-0.2760.0000.0000.0000.000
15A363THR0-0.022-0.02929.4110.2670.2670.0000.0000.0000.000
16A364LEU00.0360.01130.022-0.231-0.2310.0000.0000.0000.000
17A365TYR0-0.057-0.06032.944-0.087-0.0870.0000.0000.0000.000
18A366ASP-1-0.655-0.81736.3437.9137.9130.0000.0000.0000.000
19A367ALA0-0.008-0.01637.961-0.150-0.1500.0000.0000.0000.000
20A368ASN0-0.128-0.06741.116-0.355-0.3550.0000.0000.0000.000
21A369TYR0-0.014-0.00140.833-0.069-0.0690.0000.0000.0000.000
22A370LYS10.8800.93738.397-7.793-7.7930.0000.0000.0000.000
23A371GLU-1-0.754-0.84033.0609.3899.3890.0000.0000.0000.000
24A372LEU0-0.010-0.00731.267-0.063-0.0630.0000.0000.0000.000
25A373PRO0-0.016-0.00429.7890.2010.2010.0000.0000.0000.000
26A374MET0-0.050-0.01524.024-0.069-0.0690.0000.0000.0000.000
27A375LEU00.0280.02123.5390.2720.2720.0000.0000.0000.000
28A376THR00.0010.00020.7830.4720.4720.0000.0000.0000.000
29A377TYR00.004-0.02818.311-0.308-0.3080.0000.0000.0000.000
30A378ARG10.8210.90011.358-20.743-20.7430.0000.0000.0000.000
31A379VAL00.0160.01113.160-0.715-0.7150.0000.0000.0000.000
32A380ASP-1-0.809-0.89310.09526.27326.2730.0000.0000.0000.000
33A381ALA0-0.017-0.0169.105-1.632-1.6320.0000.0000.0000.000
34A382ASP-1-0.797-0.8809.42320.57720.5770.0000.0000.0000.000
35A383LYS10.8810.9469.570-17.149-17.1490.0000.0000.0000.000
36A384GLY00.0450.00710.112-0.816-0.8160.0000.0000.0000.000
37A385PHE0-0.044-0.0187.789-0.886-0.8860.0000.0000.0000.000
38A386ASN00.0060.0005.289-0.715-0.7150.0000.0000.0000.000
39A387PHE00.0500.0362.905-1.650-0.4650.154-0.308-1.0310.000
40A388SER0-0.045-0.0384.795-2.825-2.745-0.001-0.005-0.0740.000
41A389VAL00.0710.0116.2060.0330.0330.0000.0000.0000.000
42A390GLY0-0.0130.0088.335-1.914-1.9140.0000.0000.0000.000
43A391ASP-1-0.815-0.86610.80420.18020.1800.0000.0000.0000.000
44A392ASP-1-0.869-0.9288.03135.21735.2170.0000.0000.0000.000
45A393ALA00.0420.0277.0880.1520.1520.0000.0000.0000.000
46A394PHE00.0460.0342.437-7.127-4.1731.091-1.682-2.3630.010
47A395VAL0-0.041-0.0207.370-4.305-4.3050.0000.0000.0000.000
48A396CYS0-0.0070.0199.7100.1790.1790.0000.0000.0000.000
49A397GLN00.006-0.01112.476-0.200-0.2000.0000.0000.0000.000
50A398LYS10.9120.96216.052-13.379-13.3790.0000.0000.0000.000
51A399LYS10.9210.95519.012-13.312-13.3120.0000.0000.0000.000
52A400ASN0-0.021-0.00914.893-0.960-0.9600.0000.0000.0000.000
53A401HIS0-0.051-0.02317.125-0.189-0.1890.0000.0000.0000.000
54A402PHE00.0110.00713.3810.8780.8780.0000.0000.0000.000
55A403GLN0-0.089-0.06113.648-2.087-2.0870.0000.0000.0000.000
56A404VAL00.0200.01713.6141.4281.4280.0000.0000.0000.000
57A405THR0-0.038-0.02714.564-1.728-1.7280.0000.0000.0000.000
58A406VAL0-0.007-0.00515.2301.0011.0010.0000.0000.0000.000
59A407TYR00.0080.00214.996-0.928-0.9280.0000.0000.0000.000
60A408ILE00.0300.00319.3440.4560.4560.0000.0000.0000.000
61A409GLY00.0060.01422.378-0.447-0.4470.0000.0000.0000.000
62A410MET0-0.0230.00424.6180.0730.0730.0000.0000.0000.000
63A411LEU0-0.025-0.00126.106-0.256-0.2560.0000.0000.0000.000
64A412GLY00.0810.03329.603-0.172-0.1720.0000.0000.0000.000
65A413GLU-1-0.954-0.98232.8978.1888.1880.0000.0000.0000.000
66A414PRO0-0.060-0.02732.065-0.184-0.1840.0000.0000.0000.000
67A415LYS10.9110.95435.030-7.370-7.3700.0000.0000.0000.000
68A416TYR00.000-0.01037.225-0.185-0.1850.0000.0000.0000.000
69A417VAL00.0100.00532.9920.3070.3070.0000.0000.0000.000
70A418LYS10.8580.93734.673-9.147-9.1470.0000.0000.0000.000
71A419THR0-0.036-0.02834.6670.2670.2670.0000.0000.0000.000
72A420PRO0-0.013-0.02835.977-0.119-0.1190.0000.0000.0000.000
73A421GLU-1-0.903-0.93039.0497.0287.0280.0000.0000.0000.000
74A422GLY00.0490.03140.694-0.152-0.1520.0000.0000.0000.000
75A423LEU0-0.031-0.01238.4370.2360.2360.0000.0000.0000.000
76A424LYS10.8370.93538.750-7.666-7.6660.0000.0000.0000.000
77A425PRO00.0120.00738.7630.1930.1930.0000.0000.0000.000
78A426LEU0-0.018-0.01233.1660.1450.1450.0000.0000.0000.000
79A427ASP-1-0.868-0.92836.7967.9027.9020.0000.0000.0000.000
80A428CYS0-0.080-0.04333.6160.0220.0220.0000.0000.0000.000
81A429PHE00.0370.01728.6520.1620.1620.0000.0000.0000.000
82A430TYR00.0380.01428.007-0.089-0.0890.0000.0000.0000.000
83A431LEU0-0.0110.00420.3870.3260.3260.0000.0000.0000.000
84A432LYS10.9160.95223.532-12.679-12.6790.0000.0000.0000.000
85A433LEU0-0.008-0.00918.0920.6060.6060.0000.0000.0000.000
86A434HIS00.0280.02019.724-0.960-0.9600.0000.0000.0000.000
87A435GLY00.0470.02818.1490.9050.9050.0000.0000.0000.000
88A436VAL0-0.023-0.00518.114-1.038-1.0380.0000.0000.0000.000
89A437LYS10.9180.96318.085-11.752-11.7520.0000.0000.0000.000
90A438LEU00.000-0.00113.984-0.152-0.1520.0000.0000.0000.000
91A439GLU-1-0.859-0.95617.78015.14615.1460.0000.0000.0000.000
92A440ALA0-0.038-0.02221.003-0.791-0.7910.0000.0000.0000.000
93A441LEU00.0420.02517.983-0.187-0.1870.0000.0000.0000.000
94A442ASN0-0.0010.00121.8500.2780.2780.0000.0000.0000.000
95A443GLN00.0040.01324.353-0.374-0.3740.0000.0000.0000.000
96A444SER00.001-0.01322.9490.5140.5140.0000.0000.0000.000
97A445ILE0-0.050-0.00820.383-0.307-0.3070.0000.0000.0000.000
98A446ASN00.0170.00422.2300.1740.1740.0000.0000.0000.000
99A447ILE0-0.0080.01018.6350.5360.5360.0000.0000.0000.000
100A448GLU-1-0.866-0.95322.06711.67111.6710.0000.0000.0000.000
101A449GLN00.0260.01922.3290.2680.2680.0000.0000.0000.000
102A450SER0-0.024-0.00823.330-0.361-0.3610.0000.0000.0000.000
103A451GLN00.000-0.00725.1840.3890.3890.0000.0000.0000.000
104A452SER00.012-0.00426.9790.2620.2620.0000.0000.0000.000
105A453ASP-1-0.806-0.87828.2139.5779.5770.0000.0000.0000.000
106A454ARG10.8870.93825.359-10.480-10.4800.0000.0000.0000.000
107A455SER0-0.020-0.01428.0450.1310.1310.0000.0000.0000.000
108A456LYS10.8710.92422.810-12.065-12.0650.0000.0000.0000.000
109A457ARG10.9660.99727.638-9.708-9.7080.0000.0000.0000.000
110A458PRO00.0260.02126.8510.4900.4900.0000.0000.0000.000
111A459PHE0-0.002-0.02023.008-0.312-0.3120.0000.0000.0000.000
112A460ASN0-0.034-0.01825.6670.0020.0020.0000.0000.0000.000
113A461PRO0-0.009-0.01226.2370.2270.2270.0000.0000.0000.000
114A462VAL00.0150.02524.895-0.387-0.3870.0000.0000.0000.000
115A463THR00.0350.00927.4690.2110.2110.0000.0000.0000.000
116A464VAL0-0.070-0.03225.3890.1560.1560.0000.0000.0000.000
117A465ASN00.0130.00228.846-0.255-0.2550.0000.0000.0000.000
118A466LEU0-0.023-0.01925.7780.4200.4200.0000.0000.0000.000
119A467PRO00.0050.01529.369-0.198-0.1980.0000.0000.0000.000
120A468PRO00.0570.01930.6190.3130.3130.0000.0000.0000.000
121A469GLU-1-0.880-0.94230.5819.4849.4840.0000.0000.0000.000
122A470GLN0-0.055-0.02328.0850.1970.1970.0000.0000.0000.000
123A471VAL0-0.035-0.02721.2270.2670.2670.0000.0000.0000.000
124A472THR00.0240.01924.435-0.173-0.1730.0000.0000.0000.000
125A473LYS10.8950.95717.315-14.897-14.8970.0000.0000.0000.000
126A474VAL00.0120.00620.717-0.575-0.5750.0000.0000.0000.000
127A475THR0-0.021-0.03217.8750.6860.6860.0000.0000.0000.000
128A476VAL0-0.0050.00618.814-0.787-0.7870.0000.0000.0000.000
129A477GLY00.0540.02718.0810.9350.9350.0000.0000.0000.000
130A478ARG10.8620.91118.784-12.323-12.3230.0000.0000.0000.000
131A479LEU00.0150.02917.653-0.689-0.6890.0000.0000.0000.000
132A480HIS00.0150.00918.3640.0500.0500.0000.0000.0000.000
133A481PHE00.0540.03014.602-0.402-0.4020.0000.0000.0000.000
134A482SER0-0.004-0.04020.049-0.181-0.1810.0000.0000.0000.000
135A483GLU-1-0.858-0.89722.19312.05512.0550.0000.0000.0000.000
136A484THR0-0.035-0.02519.6580.4670.4670.0000.0000.0000.000
137A485THR0-0.029-0.00716.088-0.194-0.1940.0000.0000.0000.000
138A486ALA00.0290.00719.380-0.283-0.2830.0000.0000.0000.000
139A487ASN0-0.039-0.03720.1980.2790.2790.0000.0000.0000.000
140A488ASN00.0360.03617.9271.0851.0850.0000.0000.0000.000
141A489MET0-0.0110.02219.4770.1260.1260.0000.0000.0000.000
142A490ARG10.9330.95215.121-19.402-19.4020.0000.0000.0000.000
143A491LYS10.9090.93921.273-13.122-13.1220.0000.0000.0000.000
144A492LYS10.9810.98323.059-11.052-11.0520.0000.0000.0000.000
145A493GLY00.0380.02722.5100.0720.0720.0000.0000.0000.000
146A494LYS10.9850.99919.056-14.201-14.2010.0000.0000.0000.000
147A495PRO00.0330.00515.071-0.902-0.9020.0000.0000.0000.000
148A496ASN0-0.021-0.00817.782-0.749-0.7490.0000.0000.0000.000
149A497PRO00.0290.01419.1110.7390.7390.0000.0000.0000.000
150A498ASP-1-0.785-0.87620.66813.50213.5020.0000.0000.0000.000
151A499GLN0-0.067-0.04315.505-0.200-0.2000.0000.0000.0000.000
152A500ARG10.7950.90817.718-13.979-13.9790.0000.0000.0000.000
153A501TYR00.0350.00211.7350.2780.2780.0000.0000.0000.000
154A502PHE0-0.012-0.00814.858-1.377-1.3770.0000.0000.0000.000
155A503MET00.0080.01112.6051.4461.4460.0000.0000.0000.000
156A504LEU0-0.004-0.00513.428-1.707-1.7070.0000.0000.0000.000
157A505VAL00.0180.00714.7250.8500.8500.0000.0000.0000.000
158A506VAL00.001-0.00915.668-0.616-0.6160.0000.0000.0000.000
159A507ALA0-0.019-0.00718.2750.3180.3180.0000.0000.0000.000
160A508LEU00.0510.04921.448-0.341-0.3410.0000.0000.0000.000
161A509GLN0-0.060-0.05823.980-0.055-0.0550.0000.0000.0000.000
162A510ALA00.0560.03827.449-0.094-0.0940.0000.0000.0000.000
163A511HIS0-0.052-0.04130.885-0.151-0.1510.0000.0000.0000.000
164A512ALA00.0810.02733.978-0.061-0.0610.0000.0000.0000.000
165A513GLN00.0370.01337.140-0.158-0.1580.0000.0000.0000.000
166A514ASN0-0.023-0.00439.038-0.097-0.0970.0000.0000.0000.000
167A515GLN0-0.0020.02835.2490.0200.0200.0000.0000.0000.000
168A516ASN0-0.0090.00830.8290.0490.0490.0000.0000.0000.000
169A517TYR00.022-0.01530.9760.0070.0070.0000.0000.0000.000
170A518THR0-0.028-0.01424.3360.0420.0420.0000.0000.0000.000
171A519LEU00.0220.02526.174-0.198-0.1980.0000.0000.0000.000
172A520ALA00.0310.01221.3850.1330.1330.0000.0000.0000.000
173A521ALA0-0.032-0.01719.983-0.066-0.0660.0000.0000.0000.000
174A522GLN0-0.010-0.01113.9641.3081.3080.0000.0000.0000.000
175A523ILE0-0.035-0.01214.403-0.750-0.7500.0000.0000.0000.000
176A524SER00.0100.00210.0240.1950.1950.0000.0000.0000.000
177A525GLU-1-0.745-0.8674.72861.75961.932-0.001-0.005-0.1660.000
178A526ARG10.8230.9249.166-31.810-31.8100.0000.0000.0000.000
179A527ILE0-0.0010.0009.0143.0963.0960.0000.0000.0000.000
180A528ILE0-0.028-0.01011.266-2.460-2.4600.0000.0000.0000.000
181A529VAL00.0090.00313.1130.5210.5210.0000.0000.0000.000
182A530ARG10.8050.87613.584-22.150-22.1500.0000.0000.0000.000
183A531ALA00.0480.02017.429-0.284-0.2840.0000.0000.0000.000
184A532SER00.0020.00919.3150.2810.2810.0000.0000.0000.000