FMO DATABASE

FMODB ID: 559NZ

Calculation Name: 1KVV-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KVV

Chain ID: A

ChEMBL ID:

UniProt ID: O29010

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-815333.722085
FMO2-HF: Nuclear repulsion	772750.910611
FMO2-HF: Total energy	-42582.811473
FMO2-MP2: Total energy	-42709.055176

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
123.236	127.671	5.63	-5.583	-4.48	-0.064

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.898

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	3	GLU	-1	-0.790	-0.898	3.811	-49.762	-48.176	-0.013	-0.839	-0.733	0.001
69	A	69	GLU	-1	-0.871	-0.936	2.929	-56.192	-54.923	0.051	-0.540	-0.779	-0.004
70	A	70	LYS	1	0.863	0.927	1.967	3.791	5.312	5.593	-4.155	-2.959	-0.061
71	A	71	ARG	1	1.003	1.010	3.977	30.602	30.661	-0.001	-0.049	-0.009	0.000
4	A	4	SER	0	-0.063	-0.039	6.549	4.081	4.081	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.048	0.028	8.646	0.191	0.191	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.062	-0.020	11.466	1.039	1.039	0.000	0.000	0.000	0.000
7	A	7	TRP	0	0.031	-0.001	14.113	0.518	0.518	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.047	0.018	17.615	-0.327	-0.327	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.037	0.014	19.632	-0.136	-0.136	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.064	-0.036	17.228	-0.707	-0.707	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.044	0.002	16.467	0.045	0.045	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.722	-0.861	19.571	-11.661	-11.661	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.042	-0.034	23.336	0.107	0.107	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.943	0.972	25.909	10.407	10.407	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.828	0.939	24.807	11.696	11.696	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.066	0.024	26.373	-0.112	-0.112	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.938	0.945	25.616	10.852	10.852	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.031	0.014	26.008	-0.375	-0.375	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.845	-0.909	26.753	-10.770	-10.770	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.019	0.026	23.074	-0.414	-0.414	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.861	0.951	21.864	11.856	11.856	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.894	0.935	16.732	17.409	17.409	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.022	0.039	17.044	-0.729	-0.729	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.005	-0.005	19.167	0.915	0.915	0.000	0.000	0.000	0.000
25	A	25	ARG	1	1.009	0.976	22.284	10.224	10.224	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.941	0.974	23.310	12.383	12.383	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.033	0.013	19.830	0.004	0.004	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.020	0.010	20.666	-0.590	-0.590	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.017	0.002	20.730	0.528	0.528	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.074	-0.035	23.353	0.016	0.016	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.051	-0.031	26.548	0.188	0.188	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.012	0.021	22.007	-0.199	-0.199	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.850	0.921	22.225	13.526	13.526	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.074	0.035	20.633	-0.677	-0.677	0.000	0.000	0.000	0.000
35	A	35	HIS	0	0.027	0.001	20.465	-0.838	-0.838	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.774	-0.907	19.301	-14.624	-14.624	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.012	-0.002	16.080	-1.061	-1.061	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.036	0.000	15.812	-1.240	-1.240	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.860	-0.931	16.419	-15.078	-15.078	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.006	-0.007	14.428	-0.671	-0.671	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.119	-0.058	11.818	-1.787	-1.787	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.985	0.984	12.849	14.780	14.780	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.903	-0.952	15.132	-17.234	-17.234	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.054	-0.029	8.955	-0.599	-0.599	0.000	0.000	0.000	0.000
45	A	45	GLY	0	-0.005	0.028	10.776	-1.340	-1.340	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.014	-0.010	5.076	0.228	0.228	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.895	0.960	6.461	24.258	24.258	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.058	-0.041	6.558	-3.971	-3.971	0.000	0.000	0.000	0.000
49	A	49	ARG	1	1.019	1.035	8.909	28.567	28.567	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.008	-0.002	11.713	0.040	0.040	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.912	-0.968	13.979	-21.456	-21.456	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.887	-0.946	16.942	-13.689	-13.689	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.922	0.970	20.744	11.750	11.750	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.934	0.961	23.205	12.693	12.693	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.025	0.003	24.252	0.156	0.156	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.075	0.044	25.610	0.259	0.259	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.915	0.969	27.435	9.709	9.709	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.012	0.005	29.474	0.334	0.334	0.000	0.000	0.000	0.000
59	A	59	TRP	0	0.015	0.006	31.337	-0.122	-0.122	0.000	0.000	0.000	0.000
60	A	60	TRP	0	-0.019	-0.011	31.759	-0.105	-0.105	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.864	-0.943	24.860	-12.546	-12.546	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.866	-0.936	23.980	-11.694	-11.694	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.028	-0.009	23.483	-0.603	-0.603	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.047	0.023	20.655	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.833	0.927	15.451	17.327	17.327	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.010	-0.003	13.172	-0.120	-0.120	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.016	0.021	8.826	-0.611	-0.611	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.019	-0.029	6.721	-1.039	-1.039	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.021	0.032	6.892	-0.744	-0.744	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.033	-0.032	8.051	4.622	4.622	0.000	0.000	0.000	0.000
74	A	74	LYS	1	1.026	0.995	10.184	18.257	18.257	0.000	0.000	0.000	0.000
75	A	75	THR	0	0.051	0.019	12.494	-1.086	-1.086	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.984	0.989	12.711	19.506	19.506	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.009	0.019	7.628	-0.557	-0.557	0.000	0.000	0.000	0.000
78	A	78	MET	0	0.000	0.008	10.605	0.580	0.580	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.008	0.005	13.577	0.872	0.872	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.849	-0.932	10.834	-22.334	-22.334	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.069	-0.025	10.778	-0.299	-0.299	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.036	0.006	12.708	0.802	0.802	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.868	0.935	14.783	19.997	19.997	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.979	0.993	12.397	21.837	21.837	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.028	0.025	15.046	0.772	0.772	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.032	-0.025	17.961	0.966	0.966	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.890	-0.931	18.484	-15.554	-15.554	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.041	0.039	18.084	0.752	0.752	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.828	0.906	21.875	12.717	12.717	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.872	-0.940	23.882	-10.756	-10.756	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.007	-0.009	22.571	0.374	0.374	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.934	0.977	26.239	11.228	11.228	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.884	0.957	28.196	10.747	10.747	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.846	-0.910	29.234	-9.374	-9.374	0.000	0.000	0.000	0.000
95	A	95	GLN	0	0.003	-0.021	29.733	0.612	0.612	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.895	0.940	31.131	9.161	9.161	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.941	0.971	33.134	9.084	9.084	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.829	-0.911	34.703	-8.119	-8.119	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.878	0.925	34.263	9.252	9.252	0.000	0.000	0.000	0.000
100	A	100	LYS	1	1.033	1.033	31.787	9.811	9.811	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.794	0.906	36.904	7.905	7.905	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.935	0.952	39.069	7.105	7.105	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.924	0.966	38.006	8.087	8.087	0.000	0.000	0.000	0.000
104	A	104	LYS	0	0.118	0.080	42.443	-0.373	-0.373	0.000	0.000	0.000	0.000

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