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: JL1N9

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 OptH
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 -1980706.584414
FMO2-HF: Nuclear repulsion 1906831.304042
FMO2-HF: Total energy -73875.280372
FMO2-MP2: Total energy -74091.374451


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.
-124.986-119.6821.444-2.359-4.3880.004
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 : -0.969 / q_NPA : -0.997
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].
3A351ILE0-0.0240.0003.5252.8015.0090.007-1.009-1.2060.000
4A352LYS10.9280.9603.909-61.738-61.369-0.001-0.149-0.2180.001
5A353TRP0-0.007-0.0207.437-2.369-2.3690.0000.0000.0000.000
6A354GLN0-0.0180.00411.2010.8840.8840.0000.0000.0000.000
7A355PRO00.0550.01914.268-0.599-0.5990.0000.0000.0000.000
8A356HIS00.0180.01818.0160.4170.4170.0000.0000.0000.000
9A357GLN0-0.011-0.02919.731-0.439-0.4390.0000.0000.0000.000
10A358GLN00.0880.04122.031-0.208-0.2080.0000.0000.0000.000
11A359ASN0-0.0070.00024.182-0.079-0.0790.0000.0000.0000.000
12A360LYS10.8730.92326.769-10.704-10.7040.0000.0000.0000.000
13A361TRP0-0.051-0.00520.909-0.069-0.0690.0000.0000.0000.000
14A362ALA00.0030.01328.061-0.234-0.2340.0000.0000.0000.000
15A363THR0-0.015-0.01429.8210.2620.2620.0000.0000.0000.000
16A364LEU00.0290.00030.481-0.177-0.1770.0000.0000.0000.000
17A365TYR0-0.0050.00133.651-0.083-0.0830.0000.0000.0000.000
18A366ASP-1-0.737-0.87737.0267.9227.9220.0000.0000.0000.000
19A367ALA0-0.026-0.03838.719-0.148-0.1480.0000.0000.0000.000
20A368ASN0-0.056-0.02141.883-0.319-0.3190.0000.0000.0000.000
21A369TYR0-0.036-0.01941.648-0.143-0.1430.0000.0000.0000.000
22A370LYS10.9200.97039.142-7.410-7.4100.0000.0000.0000.000
23A371GLU-1-0.878-0.94333.4289.3359.3350.0000.0000.0000.000
24A372LEU0-0.045-0.01932.093-0.027-0.0270.0000.0000.0000.000
25A373PRO00.0020.00829.9400.1650.1650.0000.0000.0000.000
26A374MET0-0.021-0.00424.214-0.064-0.0640.0000.0000.0000.000
27A375LEU0-0.0070.01124.0410.2180.2180.0000.0000.0000.000
28A376THR00.0050.00021.5750.4780.4780.0000.0000.0000.000
29A377TYR00.022-0.01218.792-0.239-0.2390.0000.0000.0000.000
30A378ARG10.9440.97412.496-18.501-18.5010.0000.0000.0000.000
31A379VAL0-0.007-0.00513.603-0.806-0.8060.0000.0000.0000.000
32A380ASP-1-0.921-0.96210.06924.81624.8160.0000.0000.0000.000
33A381ALA0-0.0020.00510.105-1.628-1.6280.0000.0000.0000.000
34A382ASP-1-0.761-0.8738.94020.70320.7030.0000.0000.0000.000
35A383LYS10.9070.9698.150-15.149-15.1490.0000.0000.0000.000
36A384GLY00.039-0.0159.687-0.726-0.7260.0000.0000.0000.000
37A385PHE0-0.051-0.0207.647-0.832-0.8320.0000.0000.0000.000
38A386ASN00.0410.0125.465-0.462-0.4620.0000.0000.0000.000
39A387PHE00.0410.0322.801-2.354-0.5960.471-0.623-1.6050.001
40A388SER0-0.080-0.0684.599-1.896-1.825-0.001-0.009-0.0610.000
41A389VAL00.0920.0216.2250.0440.0440.0000.0000.0000.000
42A390GLY0-0.030-0.0077.880-1.474-1.4740.0000.0000.0000.000
43A391ASP-1-0.870-0.90810.29121.48321.4830.0000.0000.0000.000
44A392ASP-1-0.940-0.9467.00437.11537.1150.0000.0000.0000.000
45A393ALA00.006-0.0097.268-1.432-1.4320.0000.0000.0000.000
46A394PHE00.0390.0362.231-2.055-1.1570.968-0.569-1.2980.002
47A395VAL0-0.033-0.0177.493-4.113-4.1130.0000.0000.0000.000
48A396CYS0-0.0030.0229.5650.0960.0960.0000.0000.0000.000
49A397GLN00.004-0.00712.2430.1060.1060.0000.0000.0000.000
50A398LYS10.9650.98615.697-13.016-13.0160.0000.0000.0000.000
51A399LYS10.9000.94218.560-12.914-12.9140.0000.0000.0000.000
52A400ASN0-0.033-0.02214.967-0.045-0.0450.0000.0000.0000.000
53A401HIS0-0.041-0.01716.727-0.258-0.2580.0000.0000.0000.000
54A402PHE00.0240.02212.8680.8510.8510.0000.0000.0000.000
55A403GLN0-0.122-0.07313.277-1.934-1.9340.0000.0000.0000.000
56A404VAL00.0130.00713.4011.1561.1560.0000.0000.0000.000
57A405THR0-0.044-0.02314.677-1.666-1.6660.0000.0000.0000.000
58A406VAL0-0.008-0.00615.9200.8550.8550.0000.0000.0000.000
59A407TYR0-0.028-0.01815.155-0.879-0.8790.0000.0000.0000.000
60A408ILE00.021-0.00519.7460.3710.3710.0000.0000.0000.000
61A409GLY00.0200.01322.968-0.373-0.3730.0000.0000.0000.000
62A410MET0-0.032-0.00524.8170.0270.0270.0000.0000.0000.000
63A411LEU0-0.017-0.00926.754-0.194-0.1940.0000.0000.0000.000
64A412GLY00.1290.06130.244-0.166-0.1660.0000.0000.0000.000
65A413GLU-1-0.987-1.00633.3288.0988.0980.0000.0000.0000.000
66A414PRO0-0.049-0.01532.662-0.176-0.1760.0000.0000.0000.000
67A415LYS10.9480.97135.452-7.287-7.2870.0000.0000.0000.000
68A416TYR0-0.024-0.01737.722-0.196-0.1960.0000.0000.0000.000
69A417VAL00.0510.03433.3770.2700.2700.0000.0000.0000.000
70A418LYS10.9350.97435.229-8.470-8.4700.0000.0000.0000.000
71A419THR0-0.054-0.06935.4000.2120.2120.0000.0000.0000.000
72A420PRO0-0.016-0.02536.288-0.111-0.1110.0000.0000.0000.000
73A421GLU-1-0.917-0.94439.3436.8806.8800.0000.0000.0000.000
74A422GLY00.0370.03140.605-0.186-0.1860.0000.0000.0000.000
75A423LEU0-0.0360.01539.0450.1920.1920.0000.0000.0000.000
76A424LYS10.8670.94539.522-7.444-7.4440.0000.0000.0000.000
77A425PRO0-0.008-0.00439.1980.1980.1980.0000.0000.0000.000
78A426LEU0-0.025-0.02333.5840.0930.0930.0000.0000.0000.000
79A427ASP-1-0.876-0.92337.0487.6817.6810.0000.0000.0000.000
80A428CYS0-0.081-0.04733.9540.0070.0070.0000.0000.0000.000
81A429PHE00.0240.01028.9980.1490.1490.0000.0000.0000.000
82A430TYR00.0140.00228.501-0.049-0.0490.0000.0000.0000.000
83A431LEU00.0050.00921.1170.3130.3130.0000.0000.0000.000
84A432LYS10.9550.97423.722-11.786-11.7860.0000.0000.0000.000
85A433LEU0-0.008-0.01518.5590.5430.5430.0000.0000.0000.000
86A434HIS0-0.015-0.00720.088-0.681-0.6810.0000.0000.0000.000
87A435GLY00.0400.02918.1310.7650.7650.0000.0000.0000.000
88A436VAL0-0.0140.00218.317-0.942-0.9420.0000.0000.0000.000
89A437LYS10.9620.98518.559-11.815-11.8150.0000.0000.0000.000
90A438LEU00.0000.00214.582-0.194-0.1940.0000.0000.0000.000
91A439GLU-1-0.894-0.96218.50814.26614.2660.0000.0000.0000.000
92A440ALA0-0.040-0.02521.496-0.758-0.7580.0000.0000.0000.000
93A441LEU00.0570.02519.130-0.093-0.0930.0000.0000.0000.000
94A442ASN0-0.038-0.00922.8180.2230.2230.0000.0000.0000.000
95A443GLN0-0.009-0.00724.645-0.430-0.4300.0000.0000.0000.000
96A444SER0-0.015-0.01223.1500.4630.4630.0000.0000.0000.000
97A445ILE0-0.030-0.00320.516-0.238-0.2380.0000.0000.0000.000
98A446ASN00.0290.00622.1910.1930.1930.0000.0000.0000.000
99A447ILE00.0060.01318.6030.4880.4880.0000.0000.0000.000
100A448GLU-1-0.919-0.96922.16410.99110.9910.0000.0000.0000.000
101A449GLN0-0.011-0.02122.1150.2500.2500.0000.0000.0000.000
102A450SER0-0.051-0.02222.361-0.528-0.5280.0000.0000.0000.000
103A451GLN00.007-0.00424.7080.3010.3010.0000.0000.0000.000
104A452SER0-0.012-0.01726.8060.2290.2290.0000.0000.0000.000
105A453ASP-1-0.820-0.89328.1309.2059.2050.0000.0000.0000.000
106A454ARG10.8920.93825.373-10.441-10.4410.0000.0000.0000.000
107A455SER0-0.0240.00227.7770.1380.1380.0000.0000.0000.000
108A456LYS10.9160.93723.260-11.370-11.3700.0000.0000.0000.000
109A457ARG10.9600.99827.259-9.497-9.4970.0000.0000.0000.000
110A458PRO00.0540.03426.8120.4400.4400.0000.0000.0000.000
111A459PHE0-0.012-0.02223.309-0.198-0.1980.0000.0000.0000.000
112A460ASN0-0.007-0.00426.0610.1770.1770.0000.0000.0000.000
113A461PRO0-0.010-0.02326.7460.2230.2230.0000.0000.0000.000
114A462VAL00.0100.02825.412-0.330-0.3300.0000.0000.0000.000
115A463THR00.0330.00428.0680.2300.2300.0000.0000.0000.000
116A464VAL0-0.059-0.01925.7210.1670.1670.0000.0000.0000.000
117A465ASN00.0240.00329.173-0.314-0.3140.0000.0000.0000.000
118A466LEU0-0.047-0.03126.6370.3560.3560.0000.0000.0000.000
119A467PRO0-0.0020.01329.563-0.214-0.2140.0000.0000.0000.000
120A468PRO00.0740.02130.6700.3260.3260.0000.0000.0000.000
121A469GLU-1-0.917-0.95230.8219.2459.2450.0000.0000.0000.000
122A470GLN0-0.032-0.00128.3460.3480.3480.0000.0000.0000.000
123A471VAL0-0.019-0.01921.5460.2630.2630.0000.0000.0000.000
124A472THR00.0020.00724.751-0.279-0.2790.0000.0000.0000.000
125A473LYS10.9190.96717.135-14.380-14.3800.0000.0000.0000.000
126A474VAL00.0170.00521.029-0.489-0.4890.0000.0000.0000.000
127A475THR0-0.012-0.00217.5830.5700.5700.0000.0000.0000.000
128A476VAL00.0010.00618.756-0.711-0.7110.0000.0000.0000.000
129A477GLY00.0680.03017.9430.8490.8490.0000.0000.0000.000
130A478ARG10.8870.94018.448-11.968-11.9680.0000.0000.0000.000
131A479LEU00.0370.04317.604-0.657-0.6570.0000.0000.0000.000
132A480HIS0-0.002-0.00918.1030.1240.1240.0000.0000.0000.000
133A481PHE00.0650.03214.423-0.496-0.4960.0000.0000.0000.000
134A482SER0-0.0120.00319.921-0.227-0.2270.0000.0000.0000.000
135A483GLU-1-0.909-0.96621.63911.59611.5960.0000.0000.0000.000
136A484THR0-0.046-0.02819.5810.4960.4960.0000.0000.0000.000
137A485THR0-0.040-0.00516.506-0.144-0.1440.0000.0000.0000.000
138A486ALA00.011-0.00119.586-0.223-0.2230.0000.0000.0000.000
139A487ASN0-0.040-0.04020.3140.1910.1910.0000.0000.0000.000
140A488ASN00.0610.04318.0440.9930.9930.0000.0000.0000.000
141A489MET0-0.048-0.01018.9700.3090.3090.0000.0000.0000.000
142A490ARG10.9350.97515.715-18.483-18.4830.0000.0000.0000.000
143A491LYS10.9660.97620.948-12.731-12.7310.0000.0000.0000.000
144A492LYS10.9930.98922.659-11.190-11.1900.0000.0000.0000.000
145A493GLY00.0100.01421.9920.0920.0920.0000.0000.0000.000
146A494LYS11.0070.99618.546-14.891-14.8910.0000.0000.0000.000
147A495PRO00.0240.00814.743-0.850-0.8500.0000.0000.0000.000
148A496ASN00.0120.01017.440-0.718-0.7180.0000.0000.0000.000
149A497PRO00.0050.01018.7710.7430.7430.0000.0000.0000.000
150A498ASP-1-0.865-0.92420.43613.09713.0970.0000.0000.0000.000
151A499GLN0-0.108-0.07215.043-0.138-0.1380.0000.0000.0000.000
152A500ARG10.9080.97817.994-14.062-14.0620.0000.0000.0000.000
153A501TYR00.0510.00012.3110.4160.4160.0000.0000.0000.000
154A502PHE0-0.012-0.00315.118-1.255-1.2550.0000.0000.0000.000
155A503MET0-0.0030.00613.5701.3591.3590.0000.0000.0000.000
156A504LEU00.0230.00013.245-1.454-1.4540.0000.0000.0000.000
157A505VAL00.0030.00515.3180.4340.4340.0000.0000.0000.000
158A506VAL00.0130.00616.177-0.567-0.5670.0000.0000.0000.000
159A507ALA0-0.025-0.01518.7130.2190.2190.0000.0000.0000.000
160A508LEU00.0410.02921.947-0.219-0.2190.0000.0000.0000.000
161A509GLN0-0.072-0.05324.522-0.126-0.1260.0000.0000.0000.000
162A510ALA00.0690.04428.037-0.059-0.0590.0000.0000.0000.000
163A511HIS0-0.060-0.02731.557-0.183-0.1830.0000.0000.0000.000
164A512ALA00.0930.03234.547-0.081-0.0810.0000.0000.0000.000
165A513GLN00.0460.01637.683-0.144-0.1440.0000.0000.0000.000
166A514ASN0-0.025-0.00639.3730.0450.0450.0000.0000.0000.000
167A515GLN00.0030.02035.686-0.092-0.0920.0000.0000.0000.000
168A516ASN0-0.034-0.02431.3590.1130.1130.0000.0000.0000.000
169A517TYR00.0400.02431.395-0.020-0.0200.0000.0000.0000.000
170A518THR0-0.032-0.02024.7810.0160.0160.0000.0000.0000.000
171A519LEU00.0280.02326.693-0.162-0.1620.0000.0000.0000.000
172A520ALA00.0350.02221.9320.1430.1430.0000.0000.0000.000
173A521ALA0-0.028-0.00720.508-0.135-0.1350.0000.0000.0000.000
174A522GLN0-0.010-0.00615.0720.6890.6890.0000.0000.0000.000
175A523ILE0-0.023-0.00815.079-0.444-0.4440.0000.0000.0000.000
176A524SER00.0120.02610.2430.2070.2070.0000.0000.0000.000
177A525GLU-1-0.790-0.8985.43947.09447.0940.0000.0000.0000.000
178A526ARG10.8830.9389.818-28.130-28.1300.0000.0000.0000.000
179A527ILE0-0.006-0.0019.6132.4222.4220.0000.0000.0000.000
180A528ILE00.0000.00311.610-2.121-2.1210.0000.0000.0000.000
181A529VAL0-0.001-0.00113.1130.4870.4870.0000.0000.0000.000
182A530ARG10.9190.95012.934-22.294-22.2940.0000.0000.0000.000
183A531ALA00.0280.01617.273-0.191-0.1910.0000.0000.0000.000
184A532SER0-0.006-0.00619.4470.2660.2660.0000.0000.0000.000