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: 396LL

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1981683.968286
FMO2-HF: Nuclear repulsion 1907807.688752
FMO2-HF: Total energy -73876.279535
FMO2-MP2: Total energy -74092.352987


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.
-166.291-161.59911.2-7.353-8.5370.073
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 : -0.911 / q_NPA : -0.961
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].
3A351ILE0-0.022-0.0013.1485.6418.2680.101-1.185-1.542-0.003
4A352LYS10.8060.8971.765-110.482-111.8779.992-4.800-3.7970.072
5A353TRP0-0.015-0.0267.166-2.681-2.6810.0000.0000.0000.000
6A354GLN00.0110.01610.9321.1961.1960.0000.0000.0000.000
7A355PRO00.0390.00913.879-0.687-0.6870.0000.0000.0000.000
8A356HIS00.0090.01217.6980.6250.6250.0000.0000.0000.000
9A357GLN00.002-0.02019.389-0.486-0.4860.0000.0000.0000.000
10A358GLN00.0880.04421.646-0.141-0.1410.0000.0000.0000.000
11A359ASN0-0.009-0.00423.766-0.190-0.1900.0000.0000.0000.000
12A360LYS10.8860.93026.366-11.076-11.0760.0000.0000.0000.000
13A361TRP0-0.062-0.01320.479-0.062-0.0620.0000.0000.0000.000
14A362ALA00.0120.02127.791-0.250-0.2500.0000.0000.0000.000
15A363THR0-0.018-0.03229.4950.2950.2950.0000.0000.0000.000
16A364LEU00.0280.00330.120-0.189-0.1890.0000.0000.0000.000
17A365TYR0-0.056-0.05733.274-0.110-0.1100.0000.0000.0000.000
18A366ASP-1-0.710-0.85936.6367.9687.9680.0000.0000.0000.000
19A367ALA0-0.002-0.01738.303-0.151-0.1510.0000.0000.0000.000
20A368ASN0-0.110-0.06341.374-0.366-0.3660.0000.0000.0000.000
21A369TYR0-0.012-0.00841.236-0.072-0.0720.0000.0000.0000.000
22A370LYS10.9240.97738.791-7.576-7.5760.0000.0000.0000.000
23A371GLU-1-0.819-0.87233.3749.4769.4760.0000.0000.0000.000
24A372LEU0-0.022-0.01131.606-0.041-0.0410.0000.0000.0000.000
25A373PRO0-0.0070.00329.6700.1770.1770.0000.0000.0000.000
26A374MET0-0.026-0.00524.070-0.081-0.0810.0000.0000.0000.000
27A375LEU0-0.0090.00923.6130.2340.2340.0000.0000.0000.000
28A376THR00.0150.00221.2590.4930.4930.0000.0000.0000.000
29A377TYR00.007-0.01918.582-0.293-0.2930.0000.0000.0000.000
30A378ARG10.8370.91211.668-20.222-20.2220.0000.0000.0000.000
31A379VAL00.0160.00613.443-0.892-0.8920.0000.0000.0000.000
32A380ASP-1-0.831-0.90210.11726.01426.0140.0000.0000.0000.000
33A381ALA0-0.010-0.0029.820-1.862-1.8620.0000.0000.0000.000
34A382ASP-1-0.778-0.8709.09921.07721.0770.0000.0000.0000.000
35A383LYS10.8590.9278.311-15.411-15.4110.0000.0000.0000.000
36A384GLY00.039-0.0139.766-0.656-0.6560.0000.0000.0000.000
37A385PHE0-0.056-0.0197.745-0.835-0.8350.0000.0000.0000.000
38A386ASN00.0230.0075.415-0.262-0.2620.0000.0000.0000.000
39A387PHE00.0460.0342.834-1.4600.0620.324-0.430-1.4160.000
40A388SER0-0.055-0.0384.677-2.654-2.566-0.001-0.007-0.0800.000
41A389VAL00.0790.0166.0090.3560.3560.0000.0000.0000.000
42A390GLY0-0.019-0.0017.826-1.289-1.2890.0000.0000.0000.000
43A391ASP-1-0.820-0.87410.62421.27621.2760.0000.0000.0000.000
44A392ASP-1-0.895-0.9307.54337.23337.2330.0000.0000.0000.000
45A393ALA00.0220.0117.324-0.742-0.7420.0000.0000.0000.000
46A394PHE00.0440.0322.303-4.384-2.6770.785-0.930-1.5620.004
47A395VAL0-0.036-0.0197.554-4.205-4.2050.0000.0000.0000.000
48A396CYS0-0.0060.0199.6930.1190.1190.0000.0000.0000.000
49A397GLN00.005-0.00512.374-0.150-0.1500.0000.0000.0000.000
50A398LYS10.9130.95815.763-13.385-13.3850.0000.0000.0000.000
51A399LYS10.9100.94618.695-13.189-13.1890.0000.0000.0000.000
52A400ASN0-0.028-0.01914.939-0.702-0.7020.0000.0000.0000.000
53A401HIS0-0.044-0.01716.783-0.143-0.1430.0000.0000.0000.000
54A402PHE00.0220.02213.0380.8940.8940.0000.0000.0000.000
55A403GLN0-0.086-0.05613.405-2.139-2.1390.0000.0000.0000.000
56A404VAL00.0100.00313.5511.3301.3300.0000.0000.0000.000
57A405THR0-0.029-0.00914.826-1.723-1.7230.0000.0000.0000.000
58A406VAL00.0020.00015.6790.9800.9800.0000.0000.0000.000
59A407TYR0-0.011-0.01015.163-0.966-0.9660.0000.0000.0000.000
60A408ILE00.021-0.00419.7190.4200.4200.0000.0000.0000.000
61A409GLY00.0230.01922.720-0.414-0.4140.0000.0000.0000.000
62A410MET0-0.030-0.00624.7680.0490.0490.0000.0000.0000.000
63A411LEU0-0.022-0.00526.501-0.227-0.2270.0000.0000.0000.000
64A412GLY00.1100.05730.109-0.179-0.1790.0000.0000.0000.000
65A413GLU-1-0.979-1.00433.1388.2508.2500.0000.0000.0000.000
66A414PRO0-0.052-0.01732.210-0.180-0.1800.0000.0000.0000.000
67A415LYS10.9200.95635.034-7.438-7.4380.0000.0000.0000.000
68A416TYR0-0.001-0.00637.331-0.202-0.2020.0000.0000.0000.000
69A417VAL00.0430.03133.1020.2900.2900.0000.0000.0000.000
70A418LYS10.8940.95634.898-8.902-8.9020.0000.0000.0000.000
71A419THR0-0.043-0.04335.0980.2460.2460.0000.0000.0000.000
72A420PRO0-0.010-0.01936.143-0.109-0.1090.0000.0000.0000.000
73A421GLU-1-0.897-0.93139.0946.9996.9990.0000.0000.0000.000
74A422GLY00.0410.03740.326-0.189-0.1890.0000.0000.0000.000
75A423LEU0-0.045-0.01438.8170.2000.2000.0000.0000.0000.000
76A424LYS10.8410.92939.084-7.603-7.6030.0000.0000.0000.000
77A425PRO0-0.010-0.00738.8530.2090.2090.0000.0000.0000.000
78A426LEU0-0.018-0.01433.2990.1060.1060.0000.0000.0000.000
79A427ASP-1-0.870-0.93136.7177.9087.9080.0000.0000.0000.000
80A428CYS0-0.088-0.04533.6330.0340.0340.0000.0000.0000.000
81A429PHE00.0400.01328.6700.1590.1590.0000.0000.0000.000
82A430TYR00.0210.00228.261-0.049-0.0490.0000.0000.0000.000
83A431LEU0-0.0050.00920.6580.3490.3490.0000.0000.0000.000
84A432LYS10.9490.97223.436-12.254-12.2540.0000.0000.0000.000
85A433LEU0-0.024-0.02118.3960.6030.6030.0000.0000.0000.000
86A434HIS00.0210.01219.923-0.833-0.8330.0000.0000.0000.000
87A435GLY00.0370.02618.0870.8560.8560.0000.0000.0000.000
88A436VAL0-0.0110.00118.303-1.021-1.0210.0000.0000.0000.000
89A437LYS10.9220.96218.383-11.783-11.7830.0000.0000.0000.000
90A438LEU0-0.0020.00214.154-0.215-0.2150.0000.0000.0000.000
91A439GLU-1-0.880-0.95618.00014.99914.9990.0000.0000.0000.000
92A440ALA0-0.046-0.03121.092-0.833-0.8330.0000.0000.0000.000
93A441LEU00.0600.02718.400-0.105-0.1050.0000.0000.0000.000
94A442ASN0-0.037-0.01122.2440.2570.2570.0000.0000.0000.000
95A443GLN00.0230.01724.267-0.398-0.3980.0000.0000.0000.000
96A444SER0-0.006-0.00923.1460.4900.4900.0000.0000.0000.000
97A445ILE0-0.047-0.01220.527-0.284-0.2840.0000.0000.0000.000
98A446ASN00.0240.00622.1530.1810.1810.0000.0000.0000.000
99A447ILE00.0060.01318.5070.4910.4910.0000.0000.0000.000
100A448GLU-1-0.899-0.96522.08211.42811.4280.0000.0000.0000.000
101A449GLN00.0260.01822.2020.1780.1780.0000.0000.0000.000
102A450SER0-0.040-0.01923.072-0.358-0.3580.0000.0000.0000.000
103A451GLN00.000-0.00424.8190.3780.3780.0000.0000.0000.000
104A452SER0-0.008-0.01526.9100.2280.2280.0000.0000.0000.000
105A453ASP-1-0.799-0.87628.2469.4539.4530.0000.0000.0000.000
106A454ARG10.8930.94025.227-10.537-10.5370.0000.0000.0000.000
107A455SER0-0.025-0.01027.8550.1290.1290.0000.0000.0000.000
108A456LYS10.8800.92722.633-11.977-11.9770.0000.0000.0000.000
109A457ARG10.9480.99627.353-9.625-9.6250.0000.0000.0000.000
110A458PRO00.0490.02726.9020.4690.4690.0000.0000.0000.000
111A459PHE0-0.013-0.02623.214-0.239-0.2390.0000.0000.0000.000
112A460ASN0-0.011-0.00425.8960.0860.0860.0000.0000.0000.000
113A461PRO00.003-0.01326.4910.2530.2530.0000.0000.0000.000
114A462VAL00.0060.02125.150-0.357-0.3570.0000.0000.0000.000
115A463THR00.0210.00627.7490.1970.1970.0000.0000.0000.000
116A464VAL0-0.062-0.02525.3560.1720.1720.0000.0000.0000.000
117A465ASN00.0210.00228.804-0.249-0.2490.0000.0000.0000.000
118A466LEU0-0.036-0.02326.1280.3710.3710.0000.0000.0000.000
119A467PRO00.0080.01629.601-0.206-0.2060.0000.0000.0000.000
120A468PRO00.0620.02130.6420.3360.3360.0000.0000.0000.000
121A469GLU-1-0.915-0.96330.7479.4069.4060.0000.0000.0000.000
122A470GLN0-0.036-0.00328.2960.2460.2460.0000.0000.0000.000
123A471VAL0-0.016-0.01821.4640.2850.2850.0000.0000.0000.000
124A472THR00.0020.00824.727-0.313-0.3130.0000.0000.0000.000
125A473LYS10.9110.96417.655-14.546-14.5460.0000.0000.0000.000
126A474VAL00.0170.00620.999-0.513-0.5130.0000.0000.0000.000
127A475THR0-0.026-0.02017.7440.6500.6500.0000.0000.0000.000
128A476VAL00.0090.01318.934-0.748-0.7480.0000.0000.0000.000
129A477GLY00.0500.02018.0900.9270.9270.0000.0000.0000.000
130A478ARG10.8510.90918.584-12.155-12.1550.0000.0000.0000.000
131A479LEU00.0380.03917.687-0.719-0.7190.0000.0000.0000.000
132A480HIS00.0180.00718.1820.0530.0530.0000.0000.0000.000
133A481PHE00.0830.04514.565-0.489-0.4890.0000.0000.0000.000
134A482SER00.000-0.01520.035-0.122-0.1220.0000.0000.0000.000
135A483GLU-1-0.881-0.93321.74411.87611.8760.0000.0000.0000.000
136A484THR0-0.037-0.01919.6810.4940.4940.0000.0000.0000.000
137A485THR0-0.041-0.01016.341-0.144-0.1440.0000.0000.0000.000
138A486ALA00.0160.00219.621-0.268-0.2680.0000.0000.0000.000
139A487ASN0-0.035-0.03520.3730.2090.2090.0000.0000.0000.000
140A488ASN00.0600.04818.0051.0911.0910.0000.0000.0000.000
141A489MET0-0.035-0.00319.0460.2450.2450.0000.0000.0000.000
142A490ARG10.9290.95715.256-19.006-19.0060.0000.0000.0000.000
143A491LYS10.9460.97021.315-12.915-12.9150.0000.0000.0000.000
144A492LYS11.0020.99423.143-11.097-11.0970.0000.0000.0000.000
145A493GLY00.0160.01822.2220.0700.0700.0000.0000.0000.000
146A494LYS10.9940.99719.011-14.584-14.5840.0000.0000.0000.000
147A495PRO00.0250.00215.228-0.801-0.8010.0000.0000.0000.000
148A496ASN0-0.003-0.00518.016-0.736-0.7360.0000.0000.0000.000
149A497PRO00.0210.01819.0960.7510.7510.0000.0000.0000.000
150A498ASP-1-0.792-0.88220.67613.45513.4550.0000.0000.0000.000
151A499GLN0-0.090-0.06115.264-0.211-0.2110.0000.0000.0000.000
152A500ARG10.8130.91918.009-14.363-14.3630.0000.0000.0000.000
153A501TYR00.041-0.00512.0390.4570.4570.0000.0000.0000.000
154A502PHE0-0.009-0.00215.004-1.325-1.3250.0000.0000.0000.000
155A503MET00.0080.01012.8441.5001.5000.0000.0000.0000.000
156A504LEU0-0.0010.00013.467-1.655-1.6550.0000.0000.0000.000
157A505VAL00.0250.00915.2090.5600.5600.0000.0000.0000.000
158A506VAL00.0030.00115.891-0.655-0.6550.0000.0000.0000.000
159A507ALA0-0.021-0.01118.4560.2570.2570.0000.0000.0000.000
160A508LEU00.0470.03121.668-0.262-0.2620.0000.0000.0000.000
161A509GLN0-0.075-0.06024.193-0.142-0.1420.0000.0000.0000.000
162A510ALA00.0680.04427.730-0.074-0.0740.0000.0000.0000.000
163A511HIS0-0.069-0.04231.231-0.201-0.2010.0000.0000.0000.000
164A512ALA00.0990.04034.242-0.081-0.0810.0000.0000.0000.000
165A513GLN00.0450.01637.374-0.169-0.1690.0000.0000.0000.000
166A514ASN0-0.032-0.01239.0540.0010.0010.0000.0000.0000.000
167A515GLN00.0110.03435.355-0.024-0.0240.0000.0000.0000.000
168A516ASN0-0.024-0.00531.0960.0470.0470.0000.0000.0000.000
169A517TYR00.024-0.00231.129-0.003-0.0030.0000.0000.0000.000
170A518THR0-0.012-0.00724.5310.0240.0240.0000.0000.0000.000
171A519LEU00.0250.02426.379-0.172-0.1720.0000.0000.0000.000
172A520ALA00.0320.01621.5990.1450.1450.0000.0000.0000.000
173A521ALA0-0.033-0.01020.221-0.148-0.1480.0000.0000.0000.000
174A522GLN0-0.010-0.00814.5241.1551.1550.0000.0000.0000.000
175A523ILE0-0.020-0.00614.722-0.512-0.5120.0000.0000.0000.000
176A524SER0-0.0120.00310.1580.2710.2710.0000.0000.0000.000
177A525GLU-1-0.745-0.8675.01957.86158.004-0.001-0.001-0.1400.000
178A526ARG10.8420.9209.405-30.844-30.8440.0000.0000.0000.000
179A527ILE00.000-0.0019.3162.7442.7440.0000.0000.0000.000
180A528ILE0-0.019-0.00711.632-2.304-2.3040.0000.0000.0000.000
181A529VAL00.0080.00013.2050.5080.5080.0000.0000.0000.000
182A530ARG10.8310.89513.064-22.547-22.5470.0000.0000.0000.000
183A531ALA00.0470.02717.381-0.179-0.1790.0000.0000.0000.000
184A532SER00.0120.00219.4670.2610.2610.0000.0000.0000.000