FMO DATABASE

FMODB ID: 3KMRL

Calculation Name: 1C6V-X-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1C6V

Chain ID: X

ChEMBL ID:

UniProt ID: P05896

Base Structure: X-ray

Registration Date: 2025-09-02

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-290957.849619
FMO2-HF: Nuclear repulsion	269222.997636
FMO2-HF: Total energy	-21734.851984
FMO2-MP2: Total energy	-21800.614823

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:216:LYS)

Summations of interaction energy for fragment #1(A:216: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.
221.765	224.377	-0.016	-0.978	-1.618	-0.004

Interaction energy analysis for fragmet #1(A:216:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.852 / q_NPA : 1.901

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	218	SER	0	0.111	0.052	3.413	12.359	14.640	-0.014	-0.951	-1.316	-0.004
4	A	219	LYS	1	0.874	0.952	4.432	44.560	44.753	-0.001	-0.022	-0.170	0.000
5	A	220	PHE	0	0.055	0.015	4.736	4.278	4.416	-0.001	-0.005	-0.132	0.000
6	A	221	LYS	1	0.901	0.943	8.233	41.889	41.889	0.000	0.000	0.000	0.000
7	A	222	ASN	0	0.048	0.058	11.634	3.838	3.838	0.000	0.000	0.000	0.000
8	A	223	PHE	0	-0.014	-0.019	10.198	0.338	0.338	0.000	0.000	0.000	0.000
9	A	224	ARG	1	0.897	0.954	15.275	30.818	30.818	0.000	0.000	0.000	0.000
10	A	225	VAL	0	-0.009	-0.009	18.348	0.416	0.416	0.000	0.000	0.000	0.000
11	A	226	TYR	0	0.039	0.027	20.272	1.215	1.215	0.000	0.000	0.000	0.000
12	A	227	TYR	0	0.039	0.013	24.092	0.354	0.354	0.000	0.000	0.000	0.000
13	A	228	ARG	1	0.863	0.908	25.876	20.070	20.070	0.000	0.000	0.000	0.000
14	A	229	GLU	-1	-0.806	-0.893	28.507	-19.039	-19.039	0.000	0.000	0.000	0.000
15	A	230	GLY	0	-0.011	-0.017	30.687	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	231	ARG	1	0.852	0.922	34.297	17.510	17.510	0.000	0.000	0.000	0.000
17	A	232	ASP	-1	-0.698	-0.839	35.727	-15.921	-15.921	0.000	0.000	0.000	0.000
18	A	233	GLN	0	-0.058	-0.019	33.969	-0.564	-0.564	0.000	0.000	0.000	0.000
19	A	234	LEU	0	0.017	0.019	33.072	-0.567	-0.567	0.000	0.000	0.000	0.000
20	A	235	TRP	0	-0.014	-0.008	28.983	-0.737	-0.737	0.000	0.000	0.000	0.000
21	A	236	LYS	1	0.927	0.962	28.343	19.287	19.287	0.000	0.000	0.000	0.000
22	A	237	GLY	0	0.025	0.005	26.551	-0.732	-0.732	0.000	0.000	0.000	0.000
23	A	238	PRO	0	-0.023	-0.014	22.036	-0.371	-0.371	0.000	0.000	0.000	0.000
24	A	239	GLY	0	0.058	0.044	21.178	-0.129	-0.129	0.000	0.000	0.000	0.000
25	A	240	GLU	-1	-0.820	-0.907	15.261	-35.580	-35.580	0.000	0.000	0.000	0.000
26	A	241	LEU	0	-0.004	-0.004	13.690	0.692	0.692	0.000	0.000	0.000	0.000
27	A	242	LEU	0	-0.011	-0.017	13.028	-2.713	-2.713	0.000	0.000	0.000	0.000
28	A	243	TRP	0	-0.065	-0.022	13.775	-1.648	-1.648	0.000	0.000	0.000	0.000
29	A	244	LYS	1	0.975	0.970	13.022	30.930	30.930	0.000	0.000	0.000	0.000
30	A	245	GLY	0	-0.003	0.010	14.743	1.801	1.801	0.000	0.000	0.000	0.000
31	A	246	GLU	-1	-0.789	-0.879	16.738	-28.417	-28.417	0.000	0.000	0.000	0.000
32	A	247	GLY	0	0.072	0.042	19.431	0.308	0.308	0.000	0.000	0.000	0.000
33	A	248	ALA	0	-0.094	-0.052	21.458	1.224	1.224	0.000	0.000	0.000	0.000
34	A	249	VAL	0	-0.022	-0.005	18.673	-1.387	-1.387	0.000	0.000	0.000	0.000
35	A	250	LEU	0	0.025	0.016	17.494	1.042	1.042	0.000	0.000	0.000	0.000
36	A	251	LEU	0	0.001	-0.012	17.419	-1.885	-1.885	0.000	0.000	0.000	0.000
37	A	252	LYS	1	0.887	0.958	16.997	32.444	32.444	0.000	0.000	0.000	0.000
38	A	253	VAL	0	-0.012	-0.021	20.373	-0.641	-0.641	0.000	0.000	0.000	0.000
39	A	254	GLY	0	0.047	0.029	22.276	0.939	0.939	0.000	0.000	0.000	0.000
40	A	255	THR	0	0.013	-0.004	22.101	-1.140	-1.140	0.000	0.000	0.000	0.000
41	A	256	ASP	-1	-0.879	-0.930	23.471	-21.726	-21.726	0.000	0.000	0.000	0.000
42	A	257	ILE	0	-0.034	-0.016	19.574	-0.831	-0.831	0.000	0.000	0.000	0.000
43	A	258	LYS	1	0.935	0.966	22.415	22.457	22.457	0.000	0.000	0.000	0.000
44	A	259	VAL	0	0.023	0.011	22.345	-1.234	-1.234	0.000	0.000	0.000	0.000
45	A	260	VAL	0	-0.006	-0.004	22.912	1.246	1.246	0.000	0.000	0.000	0.000
46	A	261	PRO	0	0.033	-0.004	23.483	-0.904	-0.904	0.000	0.000	0.000	0.000
47	A	262	ARG	1	0.880	0.920	20.099	29.029	29.029	0.000	0.000	0.000	0.000
48	A	263	ARG	1	0.973	0.986	23.688	21.181	21.181	0.000	0.000	0.000	0.000
49	A	264	LYS	1	0.850	0.942	26.296	20.889	20.889	0.000	0.000	0.000	0.000
50	A	265	ALA	0	-0.007	-0.010	22.423	0.009	0.009	0.000	0.000	0.000	0.000
51	A	266	LYS	1	0.943	0.983	22.861	22.609	22.609	0.000	0.000	0.000	0.000
52	A	267	ILE	0	-0.019	-0.011	16.088	-0.051	-0.051	0.000	0.000	0.000	0.000
53	A	268	ILE	0	0.040	0.027	18.953	0.363	0.363	0.000	0.000	0.000	0.000
54	A	269	LYS	1	0.866	0.926	13.122	34.217	34.217	0.000	0.000	0.000	0.000
55	A	270	ASP	-2	-1.815	-1.889	16.264	-60.314	-60.314	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:216:LYS)