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: 7G86K

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973958.480621
FMO2-HF: Nuclear repulsion 1896613.941772
FMO2-HF: Total energy -77344.538849
FMO2-MP2: Total energy -77576.069262


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.
75.37877.801-0.028-1.272-1.1220.005
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 : 0.977 / q_NPA : 0.981
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].
3A362SER0-0.011-0.0123.806-4.445-2.022-0.028-1.272-1.1220.005
4A363PHE0-0.065-0.0336.2240.3150.3150.0000.0000.0000.000
5A364THR0-0.007-0.0249.2900.2190.2190.0000.0000.0000.000
6A365ASP-1-0.788-0.89712.408-16.061-16.0610.0000.0000.0000.000
7A366GLU-1-0.810-0.88415.759-16.559-16.5590.0000.0000.0000.000
8A367GLU-1-0.775-0.88110.310-24.579-24.5790.0000.0000.0000.000
9A368ASP-1-0.753-0.85713.020-21.644-21.6440.0000.0000.0000.000
10A369GLU-1-0.813-0.91715.351-13.799-13.7990.0000.0000.0000.000
11A370PHE0-0.0080.01115.8060.6440.6440.0000.0000.0000.000
12A371ILE0-0.032-0.03012.3280.3190.3190.0000.0000.0000.000
13A372LEU0-0.039-0.02416.9810.5770.5770.0000.0000.0000.000
14A373ASP-1-0.813-0.88020.000-11.544-11.5440.0000.0000.0000.000
15A374VAL00.0410.01919.3660.5920.5920.0000.0000.0000.000
16A375VAL0-0.035-0.01919.3980.5010.5010.0000.0000.0000.000
17A376ARG10.8070.91622.12813.41913.4190.0000.0000.0000.000
18A377LYS10.8570.91324.82212.04312.0430.0000.0000.0000.000
19A378ASN0-0.027-0.01023.6870.5590.5590.0000.0000.0000.000
20A379PRO00.0880.06325.066-0.447-0.4470.0000.0000.0000.000
21A380THR0-0.030-0.01325.937-0.387-0.3870.0000.0000.0000.000
22A381ARG10.7630.82922.23013.25513.2550.0000.0000.0000.000
23A382ARG10.9180.97621.49110.96810.9680.0000.0000.0000.000
24A383THR0-0.0130.00420.017-0.728-0.7280.0000.0000.0000.000
25A384THR0-0.060-0.02120.405-0.310-0.3100.0000.0000.0000.000
26A385HIS00.0280.01514.772-1.110-1.1100.0000.0000.0000.000
27A386THR00.0820.01517.215-0.630-0.6300.0000.0000.0000.000
28A387LEU00.0270.03919.089-0.042-0.0420.0000.0000.0000.000
29A388TYR0-0.005-0.04714.321-0.225-0.2250.0000.0000.0000.000
30A389ASP-1-0.852-0.93814.343-19.970-19.9700.0000.0000.0000.000
31A390GLU-1-0.770-0.82215.459-13.976-13.9760.0000.0000.0000.000
32A391ILE0-0.0080.00014.1220.0130.0130.0000.0000.0000.000
33A392SER0-0.074-0.06211.277-0.261-0.2610.0000.0000.0000.000
34A393HIS00.0020.00712.840-0.256-0.2560.0000.0000.0000.000
35A394TYR0-0.050-0.03015.4250.6780.6780.0000.0000.0000.000
36A395VAL0-0.0210.00211.3520.0840.0840.0000.0000.0000.000
37A396PRO00.0830.03110.370-1.950-1.9500.0000.0000.0000.000
38A397ASN0-0.0310.0096.762-1.249-1.2490.0000.0000.0000.000
39A398HIS10.7250.8515.44426.76726.7670.0000.0000.0000.000
40A399THR00.0960.0417.0251.7481.7480.0000.0000.0000.000
41A400GLY00.1320.0609.042-0.325-0.3250.0000.0000.0000.000
42A401ASN0-0.050-0.0258.7172.3982.3980.0000.0000.0000.000
43A402SER0-0.057-0.0236.440-0.671-0.6710.0000.0000.0000.000
44A403ILE00.0720.0408.0890.6780.6780.0000.0000.0000.000
45A404ARG10.8430.92711.30819.92119.9210.0000.0000.0000.000
46A405HIS0-0.026-0.0148.0062.6632.6630.0000.0000.0000.000
47A406ARG10.8510.9069.96825.58125.5810.0000.0000.0000.000
48A407PHE00.0660.01811.2721.6081.6080.0000.0000.0000.000
49A408ARG10.9060.94313.89620.45420.4540.0000.0000.0000.000
50A409VAL0-0.0350.00112.2151.2681.2680.0000.0000.0000.000
51A410TYR0-0.034-0.0149.853-0.242-0.2420.0000.0000.0000.000
52A411LEU0-0.0060.00414.2671.1911.1910.0000.0000.0000.000
53A412SER0-0.013-0.00517.1631.1771.1770.0000.0000.0000.000
54A413LYS10.8630.92417.11017.84617.8460.0000.0000.0000.000
55A414ARG10.8130.89815.89916.98116.9810.0000.0000.0000.000
56A415LEU0-0.018-0.00321.9450.2700.2700.0000.0000.0000.000
57A416GLU-1-0.916-0.93323.590-10.862-10.8620.0000.0000.0000.000
58A417TYR0-0.062-0.03826.9420.5940.5940.0000.0000.0000.000
59A418VAL0-0.004-0.00725.994-0.549-0.5490.0000.0000.0000.000
60A419TYR00.0440.00826.9340.3640.3640.0000.0000.0000.000
61A420GLU-1-0.925-0.96930.763-8.706-8.7060.0000.0000.0000.000
62A421VAL0-0.005-0.01830.652-0.054-0.0540.0000.0000.0000.000
63A422ASP-1-0.764-0.89033.866-8.355-8.3550.0000.0000.0000.000
64A423LYS10.9250.94935.9407.2717.2710.0000.0000.0000.000
65A424PHE0-0.075-0.03337.0940.0220.0220.0000.0000.0000.000
66A425GLY0-0.036-0.02133.018-0.148-0.1480.0000.0000.0000.000
67A426LYS10.8920.95431.7518.5118.5110.0000.0000.0000.000
68A427LEU0-0.0030.01228.8640.0430.0430.0000.0000.0000.000
69A428VAL0-0.0120.00633.1640.1980.1980.0000.0000.0000.000
70A429ARG10.8290.92133.9698.3778.3770.0000.0000.0000.000
71A430ASP-1-0.796-0.87837.447-7.733-7.7330.0000.0000.0000.000
72A431ASP-1-0.918-0.95740.584-7.047-7.0470.0000.0000.0000.000
73A432ASP-1-0.901-0.93840.288-7.238-7.2380.0000.0000.0000.000
74A433GLY0-0.096-0.05437.483-0.170-0.1700.0000.0000.0000.000
75A434ASN0-0.051-0.04635.456-0.535-0.5350.0000.0000.0000.000
76A435LEU0-0.042-0.02630.286-0.012-0.0120.0000.0000.0000.000
77A436ILE00.0800.04234.3850.0460.0460.0000.0000.0000.000
78A437LYS10.8820.95230.4519.7939.7930.0000.0000.0000.000
79A438THR00.0690.03632.0450.2540.2540.0000.0000.0000.000
80A439LYS10.8960.93130.3939.8849.8840.0000.0000.0000.000
81A440VAL0-0.013-0.00131.548-0.142-0.1420.0000.0000.0000.000
82A441LEU0-0.023-0.01326.420-0.094-0.0940.0000.0000.0000.000
83A442PRO00.0730.04929.1070.2180.2180.0000.0000.0000.000
84A443PRO00.0340.01630.265-0.355-0.3550.0000.0000.0000.000
85A444SER0-0.023-0.01226.636-0.197-0.1970.0000.0000.0000.000
86A445ILE00.0240.00425.6010.2770.2770.0000.0000.0000.000
87A446LYS10.9150.96126.80611.43611.4360.0000.0000.0000.000
88A447ARG10.8910.92929.3288.4488.4480.0000.0000.0000.000
89A448LYS10.9500.96427.81710.91610.9160.0000.0000.0000.000
90A449PHE0-0.012-0.01432.0310.1170.1170.0000.0000.0000.000
91A450SER00.0240.02034.961-0.164-0.1640.0000.0000.0000.000
92A451ALA00.1050.04937.3200.0570.0570.0000.0000.0000.000
93A452ASP-1-0.770-0.85939.861-7.356-7.3560.0000.0000.0000.000
94A453GLU-1-0.841-0.87137.876-8.295-8.2950.0000.0000.0000.000
95A454ASP-1-0.767-0.85838.483-8.249-8.2490.0000.0000.0000.000
96A455TYR0-0.003-0.01941.5280.0890.0890.0000.0000.0000.000
97A456THR0-0.013-0.03044.7860.2010.2010.0000.0000.0000.000
98A457LEU0-0.085-0.04541.6540.1210.1210.0000.0000.0000.000
99A458ALA00.013-0.00445.1650.1260.1260.0000.0000.0000.000
100A459ILE00.0640.04046.7240.1540.1540.0000.0000.0000.000
101A460ALA0-0.0180.00348.4640.1520.1520.0000.0000.0000.000
102A461VAL0-0.037-0.02746.8750.1170.1170.0000.0000.0000.000
103A462LYS10.8750.95250.0716.1636.1630.0000.0000.0000.000
104A463LYS10.8690.91452.4475.8705.8700.0000.0000.0000.000
105A464GLN0-0.065-0.02752.6870.0900.0900.0000.0000.0000.000
106A465PHE00.009-0.01449.9110.0900.0900.0000.0000.0000.000
107A466TYR00.0250.01955.3640.0580.0580.0000.0000.0000.000
108A467ARG10.8930.94855.0895.7885.7880.0000.0000.0000.000
109A468ASP-1-0.851-0.91455.903-5.660-5.6600.0000.0000.0000.000
110A469LEU0-0.064-0.04757.2850.0680.0680.0000.0000.0000.000
111A470PHE0-0.008-0.01360.9030.0580.0580.0000.0000.0000.000
112A471GLN0-0.0160.01562.3970.1080.1080.0000.0000.0000.000
113A472ILE00.0080.01163.3490.0830.0830.0000.0000.0000.000
114A473ASP-1-0.839-0.91561.736-5.282-5.2820.0000.0000.0000.000
115A474PRO0-0.063-0.04957.9800.0330.0330.0000.0000.0000.000
116A475ASP-1-0.830-0.89058.509-5.562-5.5620.0000.0000.0000.000
117A476THR0-0.043-0.03561.3990.0790.0790.0000.0000.0000.000
118A477GLY00.0560.02965.0690.0490.0490.0000.0000.0000.000
119A478ARG10.9120.96665.3764.8984.8980.0000.0000.0000.000
120A479SER00.0450.01866.742-0.082-0.0820.0000.0000.0000.000
121A480LEU0-0.100-0.05862.2480.0120.0120.0000.0000.0000.000
122A481ILE0-0.0100.00766.5800.0130.0130.0000.0000.0000.000
123A513ARG10.8270.91154.2525.7785.7780.0000.0000.0000.000
124A514THR00.0350.02153.209-0.059-0.0590.0000.0000.0000.000
125A515GLN0-0.032-0.03951.3530.1540.1540.0000.0000.0000.000
126A516SER00.0340.00850.380-0.088-0.0880.0000.0000.0000.000
127A517ARG10.8880.97051.3095.8825.8820.0000.0000.0000.000
128A518ARG10.9630.97042.5557.0977.0970.0000.0000.0000.000
129A519GLY00.0280.02548.801-0.101-0.1010.0000.0000.0000.000
130A520PRO0-0.001-0.00151.0790.0630.0630.0000.0000.0000.000
131A521ILE0-0.005-0.00847.4800.0270.0270.0000.0000.0000.000
132A522ALA00.0340.02550.8600.0370.0370.0000.0000.0000.000
133A523ARG10.9600.95251.5295.7055.7050.0000.0000.0000.000
134A524GLU-1-0.825-0.89149.911-6.068-6.0680.0000.0000.0000.000
135A525PHE00.0430.03747.095-0.039-0.0390.0000.0000.0000.000
136A526PHE00.028-0.00644.259-0.063-0.0630.0000.0000.0000.000
137A527LYS10.8720.96245.5296.3356.3350.0000.0000.0000.000
138A528HIS10.8560.86847.1056.1936.1930.0000.0000.0000.000
139A529PHE00.0240.02543.534-0.020-0.0200.0000.0000.0000.000
140A530ALA0-0.034-0.04543.029-0.066-0.0660.0000.0000.0000.000
141A531GLU-1-0.890-0.91744.436-6.516-6.5160.0000.0000.0000.000
142A532GLU-1-0.855-0.90547.001-6.350-6.3500.0000.0000.0000.000
143A533HIS10.8100.90143.8526.7626.7620.0000.0000.0000.000
144A534ALA00.0790.04142.306-0.183-0.1830.0000.0000.0000.000
145A535ALA0-0.0230.00338.348-0.176-0.1760.0000.0000.0000.000
146A536HIS10.7420.84934.8138.3958.3950.0000.0000.0000.000
147A537THR00.0880.04337.0310.1810.1810.0000.0000.0000.000
148A538GLU-1-0.789-0.91539.482-7.120-7.1200.0000.0000.0000.000
149A539ASN0-0.014-0.02537.5270.1470.1470.0000.0000.0000.000
150A540ALA0-0.045-0.01135.871-0.095-0.0950.0000.0000.0000.000
151A541TRP00.0600.02837.190-0.137-0.1370.0000.0000.0000.000
152A542ARG10.9821.00640.3077.5117.5110.0000.0000.0000.000
153A543ASP-1-0.822-0.89635.268-8.770-8.7700.0000.0000.0000.000
154A544ARG10.7610.87434.3618.7278.7270.0000.0000.0000.000
155A545PHE00.0520.01638.1350.0070.0070.0000.0000.0000.000
156A546ARG10.8310.90938.2928.1098.1090.0000.0000.0000.000
157A547LYS10.8180.87834.4309.0209.0200.0000.0000.0000.000
158A548PHE0-0.0090.00432.079-0.202-0.2020.0000.0000.0000.000
159A549LEU00.0700.03938.1260.0900.0900.0000.0000.0000.000
160A550LEU0-0.098-0.04741.7950.1310.1310.0000.0000.0000.000
161A551ALA0-0.057-0.01138.7200.0970.0970.0000.0000.0000.000
162A552TYR00.0000.00138.991-0.095-0.0950.0000.0000.0000.000
163A553GLY00.0580.04641.4430.1190.1190.0000.0000.0000.000
164A554ILE0-0.037-0.05245.089-0.032-0.0320.0000.0000.0000.000
165A555ASP-1-0.764-0.87447.001-6.181-6.1810.0000.0000.0000.000
166A556ASP-1-0.843-0.90445.277-6.729-6.7290.0000.0000.0000.000
167A557TYR0-0.046-0.06640.102-0.016-0.0160.0000.0000.0000.000
168A558ILE0-0.061-0.03144.836-0.013-0.0130.0000.0000.0000.000
169A559SER0-0.032-0.01148.0360.0330.0330.0000.0000.0000.000
170A560TYR0-0.053-0.07440.683-0.031-0.0310.0000.0000.0000.000
171A561TYR0-0.018-0.03843.1060.0210.0210.0000.0000.0000.000
172A562GLU-1-0.829-0.90845.487-6.177-6.1770.0000.0000.0000.000
173A563ALA0-0.117-0.03647.8290.1040.1040.0000.0000.0000.000
174A564GLU-1-0.988-0.97543.915-7.196-7.1960.0000.0000.0000.000
175A572GLU-1-0.785-0.87336.729-7.852-7.8520.0000.0000.0000.000
176A573PRO0-0.095-0.01734.4330.0880.0880.0000.0000.0000.000
177A574MET00.0270.03435.979-0.159-0.1590.0000.0000.0000.000
178A575LYS10.9230.93327.38110.64910.6490.0000.0000.0000.000
179A576ASN0-0.061-0.04228.871-0.195-0.1950.0000.0000.0000.000
180A577LEU00.1090.06231.3670.0770.0770.0000.0000.0000.000
181A578THR0-0.045-0.00129.6170.0980.0980.0000.0000.0000.000
182A587PRO00.0530.00618.6460.0770.0770.0000.0000.0000.000
183A588THR0-0.029-0.00516.4780.6860.6860.0000.0000.0000.000
184A589PRO00.0140.00117.353-0.750-0.7500.0000.0000.0000.000
185A590GLY0-0.041-0.02416.862-0.344-0.3440.0000.0000.0000.000
186A591ASN00.0110.00911.824-2.745-2.7450.0000.0000.0000.000
187A592TYR00.0120.01613.2690.8450.8450.0000.0000.0000.000
188A593ASN0-0.065-0.0479.453-1.576-1.5760.0000.0000.0000.000
189A594SER00.0710.0447.9840.5510.5510.0000.0000.0000.000