FMO DATABASE

FMODB ID: KK473

Calculation Name: 1VND-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VND

Chain ID: A

ChEMBL ID:

UniProt ID: P22808

Base Structure: SolutionNMR

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-533089.730159
FMO2-HF: Nuclear repulsion	501188.579378
FMO2-HF: Total energy	-31901.150781
FMO2-MP2: Total energy	-31997.210017

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:ALA)

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

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.
162.163	162.595	10.179	-5.894	-4.716	-0.061

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.888

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	ASP	-1	-0.863	-0.927	3.299	-41.595	-39.862	0.007	-0.716	-1.024	-0.002
4	A	4	GLY	0	-0.020	-0.024	3.160	7.480	8.300	0.043	-0.332	-0.530	-0.002
5	A	5	LEU	0	-0.018	-0.009	1.802	-37.513	-39.937	10.131	-4.754	-2.953	-0.057
6	A	6	PRO	0	0.042	0.039	4.326	4.694	4.814	-0.001	-0.040	-0.079	0.000
15	A	15	LEU	0	-0.035	-0.005	3.935	1.615	1.798	-0.001	-0.052	-0.130	0.000
7	A	7	ASN	0	0.032	0.010	7.498	6.000	6.000	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.952	0.972	9.807	20.804	20.804	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.956	0.972	11.785	21.753	21.753	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.899	0.975	11.720	20.944	20.944	0.000	0.000	0.000	0.000
11	A	11	LYS	0	-0.052	-0.001	8.922	-1.401	-1.401	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.971	0.964	10.779	25.122	25.122	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.960	0.976	6.146	42.141	42.141	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.062	0.038	9.015	-0.391	-0.391	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.018	0.004	6.648	-3.133	-3.133	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.089	0.033	6.151	0.830	0.830	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.977	0.993	8.640	22.052	22.052	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.001	0.016	11.938	1.367	1.367	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.052	0.003	11.212	1.546	1.546	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.036	-0.038	11.847	1.379	1.379	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.017	0.017	14.014	0.998	0.998	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.816	-0.938	16.963	-13.331	-13.331	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.031	-0.006	15.332	0.823	0.823	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.795	-0.881	16.898	-15.797	-15.797	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.881	0.963	19.601	13.924	13.924	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.883	0.924	22.241	12.636	12.636	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.055	-0.033	21.837	0.524	0.524	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.770	0.868	20.004	14.701	14.701	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.013	0.023	25.925	0.411	0.411	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.052	-0.025	26.972	0.582	0.582	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.951	0.977	27.437	9.551	9.551	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.004	-0.008	27.293	-0.438	-0.438	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.008	0.000	23.904	0.161	0.161	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.007	0.002	27.848	-0.135	-0.135	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.017	0.000	28.801	-0.204	-0.204	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.058	0.020	29.006	-0.324	-0.324	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.717	-0.840	28.232	-11.317	-11.317	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.811	0.900	23.826	12.277	12.277	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.767	-0.887	23.921	-13.540	-13.540	0.000	0.000	0.000	0.000
41	A	41	HIS	0	0.034	0.037	24.586	-0.360	-0.360	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.013	0.008	20.383	-0.362	-0.362	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.016	-0.014	19.918	-0.688	-0.688	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.021	-0.024	19.911	-0.686	-0.686	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.017	0.003	21.426	-0.107	-0.107	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.028	-0.015	15.841	-0.285	-0.285	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.879	0.955	15.912	14.244	14.244	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.033	-0.008	12.830	-1.556	-1.556	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.023	-0.010	16.555	1.369	1.369	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.055	0.009	18.690	-0.484	-0.484	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.003	-0.005	19.792	0.099	0.099	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.085	0.060	13.133	0.856	0.856	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.027	0.022	17.640	-0.254	-0.254	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.912	0.963	19.488	13.365	13.365	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.003	-0.017	17.736	0.536	0.536	0.000	0.000	0.000	0.000
56	A	56	TRP	0	0.023	0.027	14.309	0.350	0.350	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.028	-0.007	18.377	0.117	0.117	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.060	-0.008	21.913	1.013	1.013	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.001	-0.020	16.987	1.470	1.470	0.000	0.000	0.000	0.000
60	A	60	HIS	1	0.864	0.947	16.049	18.173	18.173	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.905	0.980	20.755	12.552	12.552	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.020	-0.020	22.566	0.774	0.774	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.811	0.879	23.577	11.773	11.773	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.050	0.035	20.193	0.445	0.445	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.914	0.969	19.137	15.126	15.126	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.990	0.990	21.656	12.290	12.290	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.012	0.000	19.536	-0.393	-0.393	0.000	0.000	0.000	0.000
68	A	68	GLN	0	0.023	0.026	20.506	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.076	0.041	19.583	0.422	0.422	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.791	-0.889	20.810	-13.031	-13.031	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.924	0.961	22.320	11.837	11.837	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.027	0.035	19.496	0.129	0.129	0.000	0.000	0.000	0.000
73	A	73	TYR	0	0.001	-0.012	16.005	-0.593	-0.593	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.901	-0.952	12.326	-21.847	-21.847	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.044	0.018	11.025	-2.236	-2.236	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.081	-0.073	11.833	1.031	1.031	0.000	0.000	0.000	0.000
77	A	77	PRO	-1	-0.819	-0.893	14.537	-18.097	-18.097	0.000	0.000	0.000	0.000

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