FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 3K8ZL

Calculation Name: 1KNB-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KNB

Chain ID: A

ChEMBL ID:

UniProt ID: P11818

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1950584.81407
FMO2-HF: Nuclear repulsion 1879699.222842
FMO2-HF: Total energy -70885.591228
FMO2-MP2: Total energy -71093.915463


3D Structure Molmil
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:396:ASN)


Summations of interaction energy for fragment #1(A:396:ASN)
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.
-18.509-13.3798.468-5.108-8.49-0.039
Interaction energy analysis for fragmet #1(A:396:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.895
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].
3A398LYS10.8860.9213.88131.57632.450-0.010-0.303-0.5600.000
4A399LEU0-0.019-0.0032.1771.5873.6202.471-1.445-3.0590.002
5A400THR0-0.081-0.0602.242-28.008-27.0685.862-2.969-3.833-0.039
6A401LEU00.0120.0363.5923.0913.2070.008-0.058-0.066-0.001
31A426THR00.013-0.0083.316-11.470-11.1440.014-0.064-0.2760.000
86A481ARG10.8340.9422.90760.17561.0160.123-0.269-0.696-0.001
7A402TRP0-0.046-0.0407.199-1.381-1.3810.0000.0000.0000.000
8A403THR00.0210.0169.2830.9680.9680.0000.0000.0000.000
9A404THR0-0.0250.00910.3572.2472.2470.0000.0000.0000.000
10A405PRO00.0140.0049.9611.0091.0090.0000.0000.0000.000
11A406ALA0-0.011-0.01011.7331.3531.3530.0000.0000.0000.000
12A407PRO0-0.0040.02514.6170.8460.8460.0000.0000.0000.000
13A408SER00.0610.00916.7801.0461.0460.0000.0000.0000.000
14A409PRO0-0.049-0.03219.750-0.450-0.4500.0000.0000.0000.000
15A410ASN0-0.0010.00816.5340.9460.9460.0000.0000.0000.000
16A411CYS0-0.031-0.00420.264-0.348-0.3480.0000.0000.0000.000
17A412ARG10.8960.95122.16810.88410.8840.0000.0000.0000.000
18A413LEU0-0.037-0.01823.902-0.126-0.1260.0000.0000.0000.000
19A414ASN0-0.034-0.02127.2650.5150.5150.0000.0000.0000.000
20A415ALA0-0.044-0.02530.1890.2260.2260.0000.0000.0000.000
21A416GLU-1-0.868-0.95028.152-10.701-10.7010.0000.0000.0000.000
22A417LYS10.9060.94122.62213.82513.8250.0000.0000.0000.000
23A418ASP-1-0.744-0.85025.858-11.197-11.1970.0000.0000.0000.000
24A419ALA00.0550.01823.5280.1950.1950.0000.0000.0000.000
25A420LYS10.8910.96319.46614.40414.4040.0000.0000.0000.000
26A421LEU00.0380.01116.4500.2180.2180.0000.0000.0000.000
27A422THR0-0.021-0.00412.943-0.732-0.7320.0000.0000.0000.000
28A423LEU00.000-0.01412.3240.7070.7070.0000.0000.0000.000
29A424VAL0-0.005-0.0046.622-1.855-1.8550.0000.0000.0000.000
30A425LEU00.0300.0238.2551.9121.9120.0000.0000.0000.000
32A427LYS10.7930.8954.97331.73131.7310.0000.0000.0000.000
33A428CYS0-0.054-0.0205.992-2.597-2.5970.0000.0000.0000.000
34A429GLY00.0140.0018.0412.9632.9630.0000.0000.0000.000
35A430SER00.0250.01410.077-0.151-0.1510.0000.0000.0000.000
36A431GLN00.0230.02012.1401.2441.2440.0000.0000.0000.000
37A432ILE0-0.0200.0118.819-2.691-2.6910.0000.0000.0000.000
38A433LEU0-0.001-0.0038.3762.5702.5700.0000.0000.0000.000
39A434ALA0-0.006-0.0058.806-3.566-3.5660.0000.0000.0000.000
40A435THR0-0.022-0.0149.8812.1032.1030.0000.0000.0000.000
41A436VAL00.0100.00512.273-0.956-0.9560.0000.0000.0000.000
42A437SER00.0180.00715.0731.0341.0340.0000.0000.0000.000
43A438VAL00.0120.01417.830-0.523-0.5230.0000.0000.0000.000
44A439LEU00.0180.01220.6450.3800.3800.0000.0000.0000.000
45A440ALA0-0.0060.00323.110-0.180-0.1800.0000.0000.0000.000
46A441VAL0-0.056-0.04124.7800.0410.0410.0000.0000.0000.000
47A442LYS10.8560.93827.59910.77710.7770.0000.0000.0000.000
48A443GLY00.0370.02130.598-0.161-0.1610.0000.0000.0000.000
49A444SER00.001-0.00433.342-0.097-0.0970.0000.0000.0000.000
50A445LEU00.0510.01728.4450.1070.1070.0000.0000.0000.000
51A446ALA0-0.0220.01329.493-0.272-0.2720.0000.0000.0000.000
52A447PRO00.0210.01031.4840.1110.1110.0000.0000.0000.000
53A448ILE0-0.018-0.01130.6710.0650.0650.0000.0000.0000.000
54A449SER00.0020.00534.1050.3530.3530.0000.0000.0000.000
55A450GLY00.021-0.01737.279-0.087-0.0870.0000.0000.0000.000
56A451THR0-0.065-0.02638.3320.0850.0850.0000.0000.0000.000
57A452VAL0-0.013-0.00233.674-0.038-0.0380.0000.0000.0000.000
58A453GLN00.0590.02034.7490.0680.0680.0000.0000.0000.000
59A454SER00.0240.01330.785-0.142-0.1420.0000.0000.0000.000
60A455ALA0-0.0190.00427.3830.1490.1490.0000.0000.0000.000
61A456HIS00.0290.01926.348-0.513-0.5130.0000.0000.0000.000
62A457LEU00.0150.01120.2270.0410.0410.0000.0000.0000.000
63A458ILE0-0.013-0.00722.740-0.425-0.4250.0000.0000.0000.000
64A459ILE00.0030.01016.7900.0980.0980.0000.0000.0000.000
65A460ARG10.8390.90820.55811.62311.6230.0000.0000.0000.000
66A461PHE00.012-0.00315.411-0.325-0.3250.0000.0000.0000.000
67A462ASP-1-0.709-0.86019.900-14.689-14.6890.0000.0000.0000.000
68A463GLU-1-0.910-0.98020.272-13.728-13.7280.0000.0000.0000.000
69A464ASN0-0.015-0.00818.376-0.651-0.6510.0000.0000.0000.000
70A465GLY00.035-0.00315.823-1.303-1.3030.0000.0000.0000.000
71A466VAL0-0.0120.00915.592-1.399-1.3990.0000.0000.0000.000
72A467LEU0-0.046-0.01617.0150.6800.6800.0000.0000.0000.000
73A468LEU00.011-0.00119.3080.4340.4340.0000.0000.0000.000
74A469ASN00.009-0.01223.104-0.216-0.2160.0000.0000.0000.000
75A470ASN0-0.043-0.00925.2310.1100.1100.0000.0000.0000.000
76A471SER00.0060.00521.4250.2220.2220.0000.0000.0000.000
77A472PHE0-0.035-0.02023.5610.1360.1360.0000.0000.0000.000
78A473LEU0-0.017-0.00815.746-0.026-0.0260.0000.0000.0000.000
79A474ASP-1-0.818-0.90620.037-14.371-14.3710.0000.0000.0000.000
80A475PRO00.016-0.00917.722-0.995-0.9950.0000.0000.0000.000
81A476GLU-1-0.963-0.96217.257-15.681-15.6810.0000.0000.0000.000
82A477TYR0-0.052-0.03214.820-0.482-0.4820.0000.0000.0000.000
83A478TRP0-0.013-0.00611.943-1.773-1.7730.0000.0000.0000.000
84A479ASN00.014-0.01311.5110.1150.1150.0000.0000.0000.000
85A480PHE00.014-0.0066.660-2.194-2.1940.0000.0000.0000.000
87A482ASN0-0.011-0.0196.334-3.682-3.6820.0000.0000.0000.000
88A483GLY00.0330.0227.4523.2393.2390.0000.0000.0000.000
89A484ASP-1-0.921-0.9747.603-34.584-34.5840.0000.0000.0000.000
90A485LEU00.007-0.01210.0932.2192.2190.0000.0000.0000.000
91A486THR00.0270.0089.383-3.906-3.9060.0000.0000.0000.000
92A487GLU-1-0.837-0.9039.265-27.867-27.8670.0000.0000.0000.000
93A488GLY00.0040.00411.7611.3501.3500.0000.0000.0000.000
94A489THR0-0.026-0.00914.9271.6941.6940.0000.0000.0000.000
95A490ALA00.0370.02914.878-1.589-1.5890.0000.0000.0000.000
96A491TYR0-0.060-0.03812.3470.0210.0210.0000.0000.0000.000
97A492THR00.012-0.00314.4230.5530.5530.0000.0000.0000.000
98A493ASN0-0.005-0.01014.8320.0340.0340.0000.0000.0000.000
99A494ALA00.0030.00511.187-1.965-1.9650.0000.0000.0000.000
100A495VAL00.0500.03912.739-0.429-0.4290.0000.0000.0000.000
101A496GLY00.0440.02412.1290.2400.2400.0000.0000.0000.000
102A497PHE0-0.022-0.0305.573-2.383-2.3830.0000.0000.0000.000
103A498MET0-0.0410.03211.2450.8870.8870.0000.0000.0000.000
104A499PRO0-0.011-0.01714.967-0.003-0.0030.0000.0000.0000.000
105A500ASN00.0260.01417.1681.6211.6210.0000.0000.0000.000
106A501LEU00.0210.00519.2040.6040.6040.0000.0000.0000.000
107A502SER0-0.026-0.00722.5610.8200.8200.0000.0000.0000.000
108A503ALA0-0.096-0.03920.8780.4780.4780.0000.0000.0000.000
109A504TYR0-0.006-0.01318.2520.1720.1720.0000.0000.0000.000
110A505PRO00.0440.03023.408-0.239-0.2390.0000.0000.0000.000
111A506LYS10.9170.97323.47312.70012.7000.0000.0000.0000.000
112A507SER00.0280.03726.7610.3910.3910.0000.0000.0000.000
113A508HIS0-0.095-0.04728.1440.5490.5490.0000.0000.0000.000
114A509GLY00.0800.02227.043-0.173-0.1730.0000.0000.0000.000
115A510LYS10.9420.99228.0379.1339.1330.0000.0000.0000.000
116A511THR0-0.055-0.03128.5330.4260.4260.0000.0000.0000.000
117A512ALA00.0400.01927.985-0.366-0.3660.0000.0000.0000.000
118A513LYS10.9550.97624.31611.78911.7890.0000.0000.0000.000
119A514SER0-0.026-0.00923.705-0.585-0.5850.0000.0000.0000.000
120A515ASN0-0.043-0.02023.663-0.367-0.3670.0000.0000.0000.000
121A516ILE0-0.0010.01218.702-0.023-0.0230.0000.0000.0000.000
122A517VAL0-0.0010.00222.826-0.095-0.0950.0000.0000.0000.000
123A518SER0-0.0030.00123.1370.1690.1690.0000.0000.0000.000
124A519GLN0-0.022-0.01425.1510.6140.6140.0000.0000.0000.000
125A520VAL0-0.0220.00521.467-0.527-0.5270.0000.0000.0000.000
126A521TYR00.011-0.01024.4400.4390.4390.0000.0000.0000.000
127A522LEU00.0350.01825.480-0.444-0.4440.0000.0000.0000.000
128A523ASN0-0.065-0.04426.323-0.016-0.0160.0000.0000.0000.000
129A524GLY0-0.0060.00425.019-0.043-0.0430.0000.0000.0000.000
130A525ASP-1-0.822-0.88625.731-9.553-9.5530.0000.0000.0000.000
131A526LYS10.9720.97129.3859.4759.4750.0000.0000.0000.000
132A527THR0-0.115-0.08430.1840.2350.2350.0000.0000.0000.000
133A528LYS10.8270.92830.8569.6859.6850.0000.0000.0000.000
134A529PRO0-0.0210.00829.156-0.368-0.3680.0000.0000.0000.000
135A530VAL0-0.0070.00927.0630.3850.3850.0000.0000.0000.000
136A531THR00.0170.01227.182-0.388-0.3880.0000.0000.0000.000
137A532LEU0-0.032-0.01420.302-0.066-0.0660.0000.0000.0000.000
138A533THR00.007-0.00324.9200.1220.1220.0000.0000.0000.000
139A534ILE0-0.0120.00118.217-0.139-0.1390.0000.0000.0000.000
140A535THR0-0.029-0.02922.0690.2640.2640.0000.0000.0000.000
141A536LEU0-0.014-0.00718.032-0.461-0.4610.0000.0000.0000.000
142A537ASN0-0.038-0.04820.4330.3870.3870.0000.0000.0000.000
143A538GLY00.0270.00023.0760.5180.5180.0000.0000.0000.000
144A539THR0-0.079-0.06125.1980.4250.4250.0000.0000.0000.000
145A540GLN00.009-0.01226.5630.1620.1620.0000.0000.0000.000
146A541GLU-1-0.689-0.79527.459-11.473-11.4730.0000.0000.0000.000
147A542THR0-0.034-0.00330.8430.1980.1980.0000.0000.0000.000
148A543GLY00.004-0.00233.1530.1840.1840.0000.0000.0000.000
149A544ASP-1-0.944-0.96335.036-8.524-8.5240.0000.0000.0000.000
150A545THR0-0.049-0.03031.490-0.195-0.1950.0000.0000.0000.000
151A546THR0-0.008-0.00328.1060.0820.0820.0000.0000.0000.000
152A547PRO0-0.001-0.01828.721-0.291-0.2910.0000.0000.0000.000
153A548SER0-0.038-0.01223.278-0.364-0.3640.0000.0000.0000.000
154A549ALA0-0.0060.01022.1670.3920.3920.0000.0000.0000.000
155A550TYR0-0.013-0.01218.8590.1090.1090.0000.0000.0000.000
156A551SER0-0.008-0.02120.4590.3930.3930.0000.0000.0000.000
157A552MET0-0.030-0.00314.638-0.279-0.2790.0000.0000.0000.000
158A553SER00.0080.01219.7330.1070.1070.0000.0000.0000.000
159A554PHE00.0020.00616.253-0.144-0.1440.0000.0000.0000.000
160A555SER0-0.018-0.02122.4670.4990.4990.0000.0000.0000.000
161A556TRP00.0320.01020.380-0.114-0.1140.0000.0000.0000.000
162A557ASP-1-0.801-0.89126.800-9.142-9.1420.0000.0000.0000.000
163A558TRP0-0.019-0.00229.020-0.287-0.2870.0000.0000.0000.000
164A559SER0-0.016-0.03332.7640.3830.3830.0000.0000.0000.000
165A560GLY0-0.049-0.02436.0630.0060.0060.0000.0000.0000.000
166A561HIS10.8350.93135.0139.1279.1270.0000.0000.0000.000
167A562ASN00.0280.00837.007-0.211-0.2110.0000.0000.0000.000
168A563TYR00.015-0.02631.9130.0770.0770.0000.0000.0000.000
169A564ILE00.0110.01035.122-0.169-0.1690.0000.0000.0000.000
170A565ASN0-0.055-0.03636.8510.1100.1100.0000.0000.0000.000
171A566GLU-1-0.841-0.90432.087-9.539-9.5390.0000.0000.0000.000
172A567ILE00.002-0.00227.7280.0400.0400.0000.0000.0000.000
173A568PHE00.0380.01425.024-0.117-0.1170.0000.0000.0000.000
174A569ALA00.0330.01723.976-0.395-0.3950.0000.0000.0000.000
175A570THR0-0.0050.01120.7750.3970.3970.0000.0000.0000.000
176A571SER00.0020.00321.397-0.230-0.2300.0000.0000.0000.000
177A572SER0-0.018-0.01915.8450.3630.3630.0000.0000.0000.000
178A573TYR00.0020.01117.0660.5730.5730.0000.0000.0000.000
179A574THR0-0.010-0.00713.107-1.510-1.5100.0000.0000.0000.000
180A575PHE0-0.021-0.01714.3041.2091.2090.0000.0000.0000.000
181A576SER00.002-0.01013.661-1.458-1.4580.0000.0000.0000.000
182A577TYR0-0.035-0.02912.6551.3411.3410.0000.0000.0000.000
183A578ILE0-0.010-0.00814.277-1.268-1.2680.0000.0000.0000.000
184A579ALA00.0520.02412.5850.4500.4500.0000.0000.0000.000
185A580GLN00.0270.00814.6561.1631.1630.0000.0000.0000.000
186A581GLU-2-1.764-1.85613.513-40.011-40.0110.0000.0000.0000.000