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: M3KNZ

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973101.712124
FMO2-HF: Nuclear repulsion 1895758.283025
FMO2-HF: Total energy -77343.429098
FMO2-MP2: Total energy -77574.895696


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.
77.40779.919-0.029-1.326-1.1560.005
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 : 0.988 / q_NPA : 0.987
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].
3A362SER0-0.013-0.0103.806-3.621-1.109-0.029-1.326-1.1560.005
4A363PHE0-0.068-0.0396.1520.1040.1040.0000.0000.0000.000
5A364THR00.0240.0229.2550.8890.8890.0000.0000.0000.000
6A365ASP-1-0.866-0.94512.345-16.088-16.0880.0000.0000.0000.000
7A366GLU-1-0.829-0.92015.710-16.555-16.5550.0000.0000.0000.000
8A367GLU-1-0.809-0.90110.257-25.102-25.1020.0000.0000.0000.000
9A368ASP-1-0.775-0.88113.054-22.413-22.4130.0000.0000.0000.000
10A369GLU-1-0.888-0.95515.330-14.031-14.0310.0000.0000.0000.000
11A370PHE0-0.0070.00916.0460.6420.6420.0000.0000.0000.000
12A371ILE0-0.037-0.03212.3110.2960.2960.0000.0000.0000.000
13A372LEU0-0.041-0.03116.9660.5880.5880.0000.0000.0000.000
14A373ASP-1-0.844-0.91019.981-11.794-11.7940.0000.0000.0000.000
15A374VAL00.0290.01419.1400.6160.6160.0000.0000.0000.000
16A375VAL0-0.038-0.02418.8600.5200.5200.0000.0000.0000.000
17A376ARG10.8410.92621.98413.45013.4500.0000.0000.0000.000
18A377LYS10.8920.94924.81412.14412.1440.0000.0000.0000.000
19A378ASN0-0.035-0.00623.6820.5900.5900.0000.0000.0000.000
20A379PRO00.0870.06424.579-0.473-0.4730.0000.0000.0000.000
21A380THR0-0.027-0.00925.351-0.404-0.4040.0000.0000.0000.000
22A381ARG10.7770.84422.30713.47013.4700.0000.0000.0000.000
23A382ARG10.9430.99020.89711.28211.2820.0000.0000.0000.000
24A383THR0-0.0380.00219.447-0.717-0.7170.0000.0000.0000.000
25A384THR0-0.059-0.02319.883-0.328-0.3280.0000.0000.0000.000
26A385HIS00.0220.00214.461-1.183-1.1830.0000.0000.0000.000
27A386THR00.0910.02116.632-0.636-0.6360.0000.0000.0000.000
28A387LEU00.0310.04219.090-0.036-0.0360.0000.0000.0000.000
29A388TYR0-0.006-0.05913.919-0.186-0.1860.0000.0000.0000.000
30A389ASP-1-0.876-0.94714.341-19.973-19.9730.0000.0000.0000.000
31A390GLU-1-0.768-0.83615.463-14.244-14.2440.0000.0000.0000.000
32A391ILE0-0.023-0.00214.168-0.002-0.0020.0000.0000.0000.000
33A392SER0-0.084-0.07011.292-0.251-0.2510.0000.0000.0000.000
34A393HIS00.0080.01012.846-0.274-0.2740.0000.0000.0000.000
35A394TYR0-0.050-0.02615.4290.7250.7250.0000.0000.0000.000
36A395VAL0-0.026-0.00211.3930.0640.0640.0000.0000.0000.000
37A396PRO00.0870.03410.371-2.051-2.0510.0000.0000.0000.000
38A397ASN0-0.0060.0136.772-0.973-0.9730.0000.0000.0000.000
39A398HIS10.7260.8545.44827.60127.6010.0000.0000.0000.000
40A399THR00.0890.0396.8831.8571.8570.0000.0000.0000.000
41A400GLY00.1280.0519.046-0.411-0.4110.0000.0000.0000.000
42A401ASN0-0.055-0.0198.1151.7401.7400.0000.0000.0000.000
43A402SER0-0.059-0.0215.699-0.982-0.9820.0000.0000.0000.000
44A403ILE00.0770.0437.4640.6800.6800.0000.0000.0000.000
45A404ARG10.8790.96110.99520.79220.7920.0000.0000.0000.000
46A405HIS0-0.029-0.0148.1871.9771.9770.0000.0000.0000.000
47A406ARG10.8300.9019.46526.64526.6450.0000.0000.0000.000
48A407PHE00.0680.01610.7351.7401.7400.0000.0000.0000.000
49A408ARG10.9010.93913.46520.66220.6620.0000.0000.0000.000
50A409VAL0-0.044-0.00111.8401.4041.4040.0000.0000.0000.000
51A410TYR0-0.035-0.0099.161-0.499-0.4990.0000.0000.0000.000
52A411LEU0-0.036-0.00214.2701.2161.2160.0000.0000.0000.000
53A412SER0-0.012-0.01416.6691.2731.2730.0000.0000.0000.000
54A413LYS10.9060.94617.42117.47317.4730.0000.0000.0000.000
55A414ARG10.9640.99216.05817.36417.3640.0000.0000.0000.000
56A415LEU0-0.0020.01021.6740.2830.2830.0000.0000.0000.000
57A416GLU-1-0.931-0.94823.064-11.248-11.2480.0000.0000.0000.000
58A417TYR0-0.084-0.05126.4310.5320.5320.0000.0000.0000.000
59A418VAL00.008-0.00625.411-0.571-0.5710.0000.0000.0000.000
60A419TYR00.0460.00427.0490.3810.3810.0000.0000.0000.000
61A420GLU-1-0.920-0.96830.513-8.825-8.8250.0000.0000.0000.000
62A421VAL0-0.003-0.01230.460-0.062-0.0620.0000.0000.0000.000
63A422ASP-1-0.760-0.88933.603-8.450-8.4500.0000.0000.0000.000
64A423LYS10.9180.94035.4537.3417.3410.0000.0000.0000.000
65A424PHE0-0.082-0.03436.8460.0360.0360.0000.0000.0000.000
66A425GLY0-0.058-0.02932.730-0.154-0.1540.0000.0000.0000.000
67A426LYS10.9310.97331.6998.6498.6490.0000.0000.0000.000
68A427LEU0-0.0020.00929.0410.0260.0260.0000.0000.0000.000
69A428VAL0-0.0130.01033.1540.1990.1990.0000.0000.0000.000
70A429ARG10.8500.92034.2268.4188.4180.0000.0000.0000.000
71A430ASP-1-0.793-0.88837.436-7.832-7.8320.0000.0000.0000.000
72A431ASP-1-0.922-0.96240.573-7.135-7.1350.0000.0000.0000.000
73A432ASP-1-0.900-0.94640.128-7.337-7.3370.0000.0000.0000.000
74A433GLY0-0.119-0.04937.463-0.169-0.1690.0000.0000.0000.000
75A434ASN0-0.046-0.02535.440-0.559-0.5590.0000.0000.0000.000
76A435LEU0-0.037-0.02730.308-0.016-0.0160.0000.0000.0000.000
77A436ILE00.0710.04134.3710.0510.0510.0000.0000.0000.000
78A437LYS10.9000.95530.9469.8139.8130.0000.0000.0000.000
79A438THR00.0550.02831.5030.2810.2810.0000.0000.0000.000
80A439LYS10.9210.95529.9929.9599.9590.0000.0000.0000.000
81A440VAL0-0.0110.00431.031-0.147-0.1470.0000.0000.0000.000
82A441LEU0-0.030-0.01725.692-0.101-0.1010.0000.0000.0000.000
83A442PRO00.0600.04728.4850.2350.2350.0000.0000.0000.000
84A443PRO00.0300.00129.713-0.350-0.3500.0000.0000.0000.000
85A444SER0-0.035-0.02225.944-0.064-0.0640.0000.0000.0000.000
86A445ILE00.0490.01524.7230.2760.2760.0000.0000.0000.000
87A446LYS10.9110.96026.35011.51211.5120.0000.0000.0000.000
88A447ARG10.9761.00928.8418.6248.6240.0000.0000.0000.000
89A448LYS10.9350.95127.57311.00111.0010.0000.0000.0000.000
90A449PHE0-0.010-0.01531.6130.0860.0860.0000.0000.0000.000
91A450SER00.0020.00834.593-0.167-0.1670.0000.0000.0000.000
92A451ALA00.1220.05236.9450.0520.0520.0000.0000.0000.000
93A452ASP-1-0.791-0.87839.525-7.329-7.3290.0000.0000.0000.000
94A453GLU-1-0.890-0.93637.347-8.372-8.3720.0000.0000.0000.000
95A454ASP-1-0.753-0.85938.087-8.301-8.3010.0000.0000.0000.000
96A455TYR00.0170.01741.1760.1040.1040.0000.0000.0000.000
97A456THR0-0.017-0.02144.3190.2170.2170.0000.0000.0000.000
98A457LEU0-0.079-0.04741.3700.1310.1310.0000.0000.0000.000
99A458ALA00.009-0.00544.8620.1310.1310.0000.0000.0000.000
100A459ILE00.0810.04646.3840.1620.1620.0000.0000.0000.000
101A460ALA0-0.044-0.01148.0610.1590.1590.0000.0000.0000.000
102A461VAL0-0.021-0.01846.3910.1200.1200.0000.0000.0000.000
103A462LYS10.9470.99849.7116.1246.1240.0000.0000.0000.000
104A463LYS10.9820.98252.1096.1126.1120.0000.0000.0000.000
105A464GLN0-0.064-0.02252.3140.0750.0750.0000.0000.0000.000
106A465PHE0-0.023-0.02749.7400.0920.0920.0000.0000.0000.000
107A466TYR0-0.0050.01255.0460.0610.0610.0000.0000.0000.000
108A467ARG10.9380.97054.4405.8265.8260.0000.0000.0000.000
109A468ASP-1-0.931-0.96355.664-5.660-5.6600.0000.0000.0000.000
110A469LEU0-0.081-0.06157.3970.0610.0610.0000.0000.0000.000
111A470PHE00.003-0.00959.9570.0480.0480.0000.0000.0000.000
112A471GLN00.0060.02162.5320.1290.1290.0000.0000.0000.000
113A472ILE00.0000.01262.9910.0780.0780.0000.0000.0000.000
114A473ASP-1-0.846-0.92261.185-5.331-5.3310.0000.0000.0000.000
115A474PRO0-0.097-0.06557.7020.0330.0330.0000.0000.0000.000
116A475ASP-1-0.914-0.93358.406-5.540-5.5400.0000.0000.0000.000
117A476THR0-0.066-0.05261.0220.0840.0840.0000.0000.0000.000
118A477GLY00.0430.02164.6690.0520.0520.0000.0000.0000.000
119A478ARG10.9150.96564.8414.9314.9310.0000.0000.0000.000
120A479SER00.0320.01366.362-0.086-0.0860.0000.0000.0000.000
121A480LEU0-0.097-0.05561.8980.0040.0040.0000.0000.0000.000
122A481ILE00.0010.01166.184-0.005-0.0050.0000.0000.0000.000
123A513ARG10.9180.97554.6795.7605.7600.0000.0000.0000.000
124A514THR00.0260.01552.801-0.046-0.0460.0000.0000.0000.000
125A515GLN0-0.144-0.10250.9440.1210.1210.0000.0000.0000.000
126A516SER00.0640.02050.140-0.083-0.0830.0000.0000.0000.000
127A517ARG10.9471.00151.0145.8945.8940.0000.0000.0000.000
128A518ARG10.9730.97742.6457.0857.0850.0000.0000.0000.000
129A519GLY00.0270.02448.527-0.104-0.1040.0000.0000.0000.000
130A520PRO0-0.017-0.01150.8090.0660.0660.0000.0000.0000.000
131A521ILE00.0100.00047.1970.0270.0270.0000.0000.0000.000
132A522ALA00.0370.02550.5540.0380.0380.0000.0000.0000.000
133A523ARG11.0250.99451.1185.6915.6910.0000.0000.0000.000
134A524GLU-1-0.952-0.98349.463-6.107-6.1070.0000.0000.0000.000
135A525PHE00.0380.03246.673-0.047-0.0470.0000.0000.0000.000
136A526PHE00.044-0.00243.852-0.064-0.0640.0000.0000.0000.000
137A527LYS10.9671.00645.0706.4546.4540.0000.0000.0000.000
138A528HIS10.9330.94946.6326.2146.2140.0000.0000.0000.000
139A529PHE0-0.0010.01743.366-0.008-0.0080.0000.0000.0000.000
140A530ALA0-0.026-0.04242.555-0.063-0.0630.0000.0000.0000.000
141A531GLU-1-0.963-0.97643.940-6.590-6.5900.0000.0000.0000.000
142A532GLU-1-0.936-0.95046.497-6.340-6.3400.0000.0000.0000.000
143A533HIS10.8840.94643.2886.8836.8830.0000.0000.0000.000
144A534ALA00.0740.04041.790-0.183-0.1830.0000.0000.0000.000
145A535ALA0-0.0220.00437.816-0.181-0.1810.0000.0000.0000.000
146A536HIS10.7430.85534.2968.4868.4860.0000.0000.0000.000
147A537THR00.0870.04136.5420.1850.1850.0000.0000.0000.000
148A538GLU-1-0.826-0.93138.993-7.235-7.2350.0000.0000.0000.000
149A539ASN0-0.016-0.01936.8640.1840.1840.0000.0000.0000.000
150A540ALA0-0.044-0.01035.371-0.098-0.0980.0000.0000.0000.000
151A541TRP00.0500.02036.753-0.122-0.1220.0000.0000.0000.000
152A542ARG10.9801.00639.8887.5657.5650.0000.0000.0000.000
153A543ASP-1-0.889-0.95134.743-8.878-8.8780.0000.0000.0000.000
154A544ARG10.7660.87033.6988.8258.8250.0000.0000.0000.000
155A545PHE00.0420.00937.7740.0060.0060.0000.0000.0000.000
156A546ARG10.8860.93639.1888.0688.0680.0000.0000.0000.000
157A547LYS10.8350.90134.9618.8998.8990.0000.0000.0000.000
158A548PHE0-0.0060.01231.804-0.191-0.1910.0000.0000.0000.000
159A549LEU00.0840.03737.8330.0860.0860.0000.0000.0000.000
160A550LEU0-0.115-0.05641.4910.1330.1330.0000.0000.0000.000
161A551ALA0-0.056-0.01138.4900.1000.1000.0000.0000.0000.000
162A552TYR00.0020.00738.9280.0170.0170.0000.0000.0000.000
163A553GLY00.0650.04941.1830.1190.1190.0000.0000.0000.000
164A554ILE0-0.043-0.04944.822-0.039-0.0390.0000.0000.0000.000
165A555ASP-1-0.734-0.87046.699-6.245-6.2450.0000.0000.0000.000
166A556ASP-1-0.855-0.91245.034-6.779-6.7790.0000.0000.0000.000
167A557TYR0-0.042-0.06139.749-0.032-0.0320.0000.0000.0000.000
168A558ILE0-0.069-0.03544.518-0.010-0.0100.0000.0000.0000.000
169A559SER0-0.024-0.01047.7010.0240.0240.0000.0000.0000.000
170A560TYR00.008-0.00440.025-0.067-0.0670.0000.0000.0000.000
171A561TYR0-0.001-0.01842.9380.0100.0100.0000.0000.0000.000
172A562GLU-1-0.884-0.95745.216-6.180-6.1800.0000.0000.0000.000
173A563ALA0-0.116-0.03347.4610.1070.1070.0000.0000.0000.000
174A564GLU-1-0.999-0.98043.797-7.279-7.2790.0000.0000.0000.000
175A572GLU-1-0.829-0.93236.435-7.840-7.8400.0000.0000.0000.000
176A573PRO0-0.114-0.03334.2570.0790.0790.0000.0000.0000.000
177A574MET00.0280.04435.669-0.165-0.1650.0000.0000.0000.000
178A575LYS10.9130.92927.35210.61810.6180.0000.0000.0000.000
179A576ASN0-0.064-0.04429.346-0.035-0.0350.0000.0000.0000.000
180A577LEU00.1250.07231.1020.0910.0910.0000.0000.0000.000
181A578THR0-0.051-0.00229.5070.1120.1120.0000.0000.0000.000
182A587PRO00.0550.01318.5000.0610.0610.0000.0000.0000.000
183A588THR0-0.030-0.00815.9750.7520.7520.0000.0000.0000.000
184A589PRO00.004-0.00417.180-0.780-0.7800.0000.0000.0000.000
185A590GLY0-0.039-0.02016.449-0.342-0.3420.0000.0000.0000.000
186A591ASN00.0080.00111.563-2.943-2.9430.0000.0000.0000.000
187A592TYR00.0250.01813.0120.8280.8280.0000.0000.0000.000
188A593ASN0-0.045-0.0339.397-1.019-1.0190.0000.0000.0000.000
189A594SER00.0710.0417.9590.6590.6590.0000.0000.0000.000