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: 22ZNR

Calculation Name: 1IGN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IGN

Chain ID: A

ChEMBL ID:

UniProt ID: P11938

Base Structure: X-ray

Registration Date: 2023-06-21

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973559.87835
FMO2-HF: Nuclear repulsion 1896214.615194
FMO2-HF: Total energy -77345.263155
FMO2-MP2: Total energy -77576.738927


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:360:LYS)


Summations of interaction energy for fragment #1(A:360:LYS)
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.
75.68677.591-0.018-1.006-0.8810.003
Interaction energy analysis for fragmet #1(A:360:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.973 / q_NPA : 0.977
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].
3A362SER0-0.015-0.0163.867-2.543-0.638-0.018-1.006-0.8810.003
4A363PHE0-0.034-0.0136.2470.4960.4960.0000.0000.0000.000
5A364THR0-0.006-0.0309.1200.1360.1360.0000.0000.0000.000
6A365ASP-1-0.785-0.88012.486-15.615-15.6150.0000.0000.0000.000
7A366GLU-1-0.813-0.88415.900-16.116-16.1160.0000.0000.0000.000
8A367GLU-1-0.766-0.86710.310-24.015-24.0150.0000.0000.0000.000
9A368ASP-1-0.767-0.85612.991-20.852-20.8520.0000.0000.0000.000
10A369GLU-1-0.753-0.88615.276-13.599-13.5990.0000.0000.0000.000
11A370PHE0-0.0030.02115.6100.6670.6670.0000.0000.0000.000
12A371ILE0-0.028-0.02512.1520.2420.2420.0000.0000.0000.000
13A372LEU0-0.044-0.01316.7690.4990.4990.0000.0000.0000.000
14A373ASP-1-0.786-0.87819.786-11.308-11.3080.0000.0000.0000.000
15A374VAL00.0470.02619.4200.5740.5740.0000.0000.0000.000
16A375VAL0-0.022-0.01519.0810.4800.4800.0000.0000.0000.000
17A376ARG10.7530.86821.86013.38813.3880.0000.0000.0000.000
18A377LYS10.8600.92524.53711.81311.8130.0000.0000.0000.000
19A378ASN0-0.024-0.01223.3170.4570.4570.0000.0000.0000.000
20A379PRO00.0770.05525.000-0.390-0.3900.0000.0000.0000.000
21A380THR0-0.010-0.00326.588-0.345-0.3450.0000.0000.0000.000
22A381ARG10.7770.84122.15813.08213.0820.0000.0000.0000.000
23A382ARG10.8910.96122.05510.85010.8500.0000.0000.0000.000
24A383THR00.0030.01220.598-0.673-0.6730.0000.0000.0000.000
25A384THR0-0.065-0.02820.516-0.498-0.4980.0000.0000.0000.000
26A385HIS00.0420.02014.525-1.039-1.0390.0000.0000.0000.000
27A386THR00.0480.02117.248-0.618-0.6180.0000.0000.0000.000
28A387LEU00.0280.03418.686-0.128-0.1280.0000.0000.0000.000
29A388TYR00.001-0.03514.187-0.188-0.1880.0000.0000.0000.000
30A389ASP-1-0.850-0.94613.989-20.205-20.2050.0000.0000.0000.000
31A390GLU-1-0.791-0.84215.023-14.005-14.0050.0000.0000.0000.000
32A391ILE0-0.010-0.00413.7710.1290.1290.0000.0000.0000.000
33A392SER0-0.039-0.04311.222-0.314-0.3140.0000.0000.0000.000
34A393HIS0-0.026-0.00712.768-0.167-0.1670.0000.0000.0000.000
35A394TYR0-0.044-0.02215.1080.7220.7220.0000.0000.0000.000
36A395VAL0-0.022-0.00111.1850.0850.0850.0000.0000.0000.000
37A396PRO00.0680.03210.068-1.939-1.9390.0000.0000.0000.000
38A397ASN0-0.054-0.0176.953-1.593-1.5930.0000.0000.0000.000
39A398HIS10.7220.8495.22626.21026.2100.0000.0000.0000.000
40A399THR00.0880.0456.9071.9401.9400.0000.0000.0000.000
41A400GLY00.1250.0608.946-0.893-0.8930.0000.0000.0000.000
42A401ASN0-0.054-0.0368.9642.5082.5080.0000.0000.0000.000
43A402SER0-0.058-0.0356.504-0.141-0.1410.0000.0000.0000.000
44A403ILE00.0600.0378.3830.5730.5730.0000.0000.0000.000
45A404ARG10.8590.92411.07519.66519.6650.0000.0000.0000.000
46A405HIS0-0.039-0.0268.4032.6362.6360.0000.0000.0000.000
47A406ARG10.8480.9069.78924.87224.8720.0000.0000.0000.000
48A407PHE00.0760.02011.7541.4231.4230.0000.0000.0000.000
49A408ARG10.9020.94913.25120.88520.8850.0000.0000.0000.000
50A409VAL0-0.0120.01912.5601.1751.1750.0000.0000.0000.000
51A410TYR0-0.024-0.00810.146-0.081-0.0810.0000.0000.0000.000
52A411LEU00.0110.01514.2731.1151.1150.0000.0000.0000.000
53A412SER0-0.020-0.01317.3661.0751.0750.0000.0000.0000.000
54A413LYS10.8510.90716.91617.66217.6620.0000.0000.0000.000
55A414ARG10.7930.87415.82416.56016.5600.0000.0000.0000.000
56A415LEU0-0.038-0.01221.8380.3410.3410.0000.0000.0000.000
57A416GLU-1-0.821-0.89123.343-10.371-10.3710.0000.0000.0000.000
58A417TYR0-0.061-0.03126.8330.5480.5480.0000.0000.0000.000
59A418VAL0-0.023-0.01926.273-0.526-0.5260.0000.0000.0000.000
60A419TYR00.028-0.00126.5020.4230.4230.0000.0000.0000.000
61A420GLU-1-0.911-0.95830.502-8.692-8.6920.0000.0000.0000.000
62A421VAL0-0.016-0.02430.453-0.051-0.0510.0000.0000.0000.000
63A422ASP-1-0.746-0.88633.697-8.136-8.1360.0000.0000.0000.000
64A423LYS10.8610.93835.6687.4227.4220.0000.0000.0000.000
65A424PHE0-0.014-0.01137.041-0.019-0.0190.0000.0000.0000.000
66A425GLY0-0.033-0.01032.873-0.134-0.1340.0000.0000.0000.000
67A426LYS10.8670.92831.7378.4718.4710.0000.0000.0000.000
68A427LEU0-0.0010.00628.6140.1270.1270.0000.0000.0000.000
69A428VAL0-0.0060.00632.9950.1830.1830.0000.0000.0000.000
70A429ARG10.8030.89834.3298.3188.3180.0000.0000.0000.000
71A430ASP-1-0.810-0.88137.536-7.697-7.6970.0000.0000.0000.000
72A431ASP-1-0.918-0.96540.722-6.959-6.9590.0000.0000.0000.000
73A432ASP-1-0.908-0.93640.474-7.167-7.1670.0000.0000.0000.000
74A433GLY0-0.049-0.02437.817-0.140-0.1400.0000.0000.0000.000
75A434ASN0-0.058-0.04635.413-0.501-0.5010.0000.0000.0000.000
76A435LEU0-0.039-0.03330.103-0.119-0.1190.0000.0000.0000.000
77A436ILE00.0490.04134.199-0.054-0.0540.0000.0000.0000.000
78A437LYS10.8910.95630.3019.6239.6230.0000.0000.0000.000
79A438THR00.0530.02632.2960.2530.2530.0000.0000.0000.000
80A439LYS10.8550.89830.1639.8369.8360.0000.0000.0000.000
81A440VAL0-0.0210.00531.963-0.176-0.1760.0000.0000.0000.000
82A441LEU0-0.010-0.00926.922-0.108-0.1080.0000.0000.0000.000
83A442PRO00.0690.04929.8370.2090.2090.0000.0000.0000.000
84A443PRO00.0250.00830.369-0.400-0.4000.0000.0000.0000.000
85A444SER0-0.007-0.00926.949-0.225-0.2250.0000.0000.0000.000
86A445ILE0-0.005-0.01125.9490.2920.2920.0000.0000.0000.000
87A446LYS10.9120.95627.07811.22411.2240.0000.0000.0000.000
88A447ARG10.8750.92129.4958.3658.3650.0000.0000.0000.000
89A448LYS10.9630.97428.21910.80510.8050.0000.0000.0000.000
90A449PHE00.007-0.00232.1400.0990.0990.0000.0000.0000.000
91A450SER0-0.036-0.03635.088-0.230-0.2300.0000.0000.0000.000
92A451ALA00.1070.05137.7290.0370.0370.0000.0000.0000.000
93A452ASP-1-0.687-0.80040.210-7.474-7.4740.0000.0000.0000.000
94A453GLU-1-0.833-0.85738.191-8.201-8.2010.0000.0000.0000.000
95A454ASP-1-0.782-0.86338.372-8.260-8.2600.0000.0000.0000.000
96A455TYR0-0.007-0.02641.5670.0890.0890.0000.0000.0000.000
97A456THR0-0.013-0.02344.8940.2080.2080.0000.0000.0000.000
98A457LEU0-0.071-0.03841.8640.1250.1250.0000.0000.0000.000
99A458ALA0-0.001-0.00345.2480.1230.1230.0000.0000.0000.000
100A459ILE00.0660.03746.8560.1530.1530.0000.0000.0000.000
101A460ALA0-0.0090.00648.5700.1550.1550.0000.0000.0000.000
102A461VAL0-0.043-0.02347.0170.1200.1200.0000.0000.0000.000
103A462LYS10.8600.93950.1856.1166.1160.0000.0000.0000.000
104A463LYS10.8530.89352.5385.8885.8880.0000.0000.0000.000
105A464GLN0-0.067-0.03752.7550.0840.0840.0000.0000.0000.000
106A465PHE0-0.005-0.02949.9930.0810.0810.0000.0000.0000.000
107A466TYR00.0220.01755.3590.0510.0510.0000.0000.0000.000
108A467ARG10.9020.95155.0615.7765.7760.0000.0000.0000.000
109A468ASP-1-0.846-0.90055.989-5.650-5.6500.0000.0000.0000.000
110A469LEU0-0.052-0.02957.0710.0710.0710.0000.0000.0000.000
111A470PHE00.006-0.00160.8270.0540.0540.0000.0000.0000.000
112A471GLN0-0.0220.00262.2020.1160.1160.0000.0000.0000.000
113A472ILE00.0000.00863.4860.0820.0820.0000.0000.0000.000
114A473ASP-1-0.807-0.90261.655-5.289-5.2890.0000.0000.0000.000
115A474PRO0-0.064-0.04357.9090.0400.0400.0000.0000.0000.000
116A475ASP-1-0.809-0.86858.244-5.589-5.5890.0000.0000.0000.000
117A476THR0-0.059-0.05261.1180.0760.0760.0000.0000.0000.000
118A477GLY00.0400.02564.5630.0710.0710.0000.0000.0000.000
119A478ARG10.9250.97465.3854.8884.8880.0000.0000.0000.000
120A479SER00.0340.01166.520-0.094-0.0940.0000.0000.0000.000
121A480LEU0-0.067-0.04662.2370.0160.0160.0000.0000.0000.000
122A481ILE0-0.0360.00366.5950.0460.0460.0000.0000.0000.000
123A513ARG10.8160.89654.3365.7575.7570.0000.0000.0000.000
124A514THR00.0460.02653.225-0.051-0.0510.0000.0000.0000.000
125A515GLN0-0.037-0.03951.4220.1670.1670.0000.0000.0000.000
126A516SER00.0670.02950.623-0.059-0.0590.0000.0000.0000.000
127A517ARG10.8120.92650.8495.8545.8540.0000.0000.0000.000
128A518ARG11.0040.98042.3967.1447.1440.0000.0000.0000.000
129A519GLY0-0.015-0.00148.436-0.125-0.1250.0000.0000.0000.000
130A520PRO00.0260.01851.0590.0560.0560.0000.0000.0000.000
131A521ILE00.0170.00347.8830.0100.0100.0000.0000.0000.000
132A522ALA00.0280.02551.2100.0350.0350.0000.0000.0000.000
133A523ARG10.9420.94251.5325.7055.7050.0000.0000.0000.000
134A524GLU-1-0.800-0.86449.851-6.038-6.0380.0000.0000.0000.000
135A525PHE00.0170.02147.321-0.042-0.0420.0000.0000.0000.000
136A526PHE00.020-0.00444.233-0.053-0.0530.0000.0000.0000.000
137A527LYS10.8660.94745.5906.3346.3340.0000.0000.0000.000
138A528HIS10.8480.87347.0286.1566.1560.0000.0000.0000.000
139A529PHE00.0500.03243.715-0.001-0.0010.0000.0000.0000.000
140A530ALA0-0.040-0.03643.073-0.096-0.0960.0000.0000.0000.000
141A531GLU-1-0.881-0.92344.620-6.481-6.4810.0000.0000.0000.000
142A532GLU-1-0.866-0.91147.272-6.350-6.3500.0000.0000.0000.000
143A533HIS10.8030.89043.9396.7486.7480.0000.0000.0000.000
144A534ALA00.0890.04042.639-0.201-0.2010.0000.0000.0000.000
145A535ALA0-0.029-0.00138.943-0.194-0.1940.0000.0000.0000.000
146A536HIS10.7510.86235.1168.3278.3270.0000.0000.0000.000
147A537THR00.0810.04237.3240.1860.1860.0000.0000.0000.000
148A538GLU-1-0.799-0.91439.794-7.114-7.1140.0000.0000.0000.000
149A539ASN0-0.003-0.02137.7860.1070.1070.0000.0000.0000.000
150A540ALA0-0.0200.00535.993-0.111-0.1110.0000.0000.0000.000
151A541TRP00.0600.03137.338-0.135-0.1350.0000.0000.0000.000
152A542ARG10.9660.99440.4917.4807.4800.0000.0000.0000.000
153A543ASP-1-0.815-0.89535.304-8.781-8.7810.0000.0000.0000.000
154A544ARG10.7520.86834.3948.6968.6960.0000.0000.0000.000
155A545PHE00.0620.01538.155-0.006-0.0060.0000.0000.0000.000
156A546ARG10.8330.90638.1278.1168.1160.0000.0000.0000.000
157A547LYS10.8060.88534.0539.1019.1010.0000.0000.0000.000
158A548PHE0-0.0010.00032.066-0.240-0.2400.0000.0000.0000.000
159A549LEU00.0660.03038.0660.0950.0950.0000.0000.0000.000
160A550LEU0-0.093-0.04541.7600.1460.1460.0000.0000.0000.000
161A551ALA0-0.057-0.01738.8720.0590.0590.0000.0000.0000.000
162A552TYR0-0.014-0.00138.964-0.131-0.1310.0000.0000.0000.000
163A553GLY00.0520.04141.4380.1060.1060.0000.0000.0000.000
164A554ILE0-0.041-0.04345.162-0.041-0.0410.0000.0000.0000.000
165A555ASP-1-0.734-0.86547.251-6.159-6.1590.0000.0000.0000.000
166A556ASP-1-0.848-0.89345.507-6.694-6.6940.0000.0000.0000.000
167A557TYR0-0.040-0.05839.912-0.048-0.0480.0000.0000.0000.000
168A558ILE0-0.088-0.03944.754-0.012-0.0120.0000.0000.0000.000
169A559SER0-0.009-0.02347.929-0.003-0.0030.0000.0000.0000.000
170A560TYR0-0.063-0.06440.741-0.012-0.0120.0000.0000.0000.000
171A561TYR0-0.005-0.03743.2300.0580.0580.0000.0000.0000.000
172A562GLU-1-0.861-0.92245.691-6.154-6.1540.0000.0000.0000.000
173A563ALA0-0.0370.00447.6680.1190.1190.0000.0000.0000.000
174A564GLU-1-1.050-1.01043.557-7.104-7.1040.0000.0000.0000.000
175A572GLU-1-0.784-0.86736.748-7.908-7.9080.0000.0000.0000.000
176A573PRO0-0.076-0.00534.2920.1150.1150.0000.0000.0000.000
177A574MET00.0130.02035.719-0.167-0.1670.0000.0000.0000.000
178A575LYS10.9140.93927.23610.71110.7110.0000.0000.0000.000
179A576ASN0-0.029-0.04228.597-0.170-0.1700.0000.0000.0000.000
180A577LEU00.0830.06831.670-0.049-0.0490.0000.0000.0000.000
181A578THR0-0.046-0.00429.8840.0200.0200.0000.0000.0000.000
182A587PRO00.0580.00718.3360.0170.0170.0000.0000.0000.000
183A588THR0-0.029-0.00916.1910.6700.6700.0000.0000.0000.000
184A589PRO00.0090.00317.237-0.796-0.7960.0000.0000.0000.000
185A590GLY0-0.029-0.02216.750-0.161-0.1610.0000.0000.0000.000
186A591ASN00.0170.01111.491-2.828-2.8280.0000.0000.0000.000
187A592TYR00.0110.02513.3370.4960.4960.0000.0000.0000.000
188A593ASN0-0.063-0.0399.259-2.422-2.4220.0000.0000.0000.000
189A594SER00.0690.0467.7750.6350.6350.0000.0000.0000.000