FMO DATABASE

FMODB ID: GV7M1

Calculation Name: 3C1V-A-Xray547

Preferred Name: Protein S100-A4

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C1V

Chain ID: A

ChEMBL ID: CHEMBL2362976

UniProt ID: P26447

Base Structure: X-ray

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-659662.578406
FMO2-HF: Nuclear repulsion	620640.677742
FMO2-HF: Total energy	-39021.900664
FMO2-MP2: Total energy	-39130.48837

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:2:ALA)

Summations of interaction energy for fragment #1(A:2: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.
-36.699	-35.057	-0.014	-0.627	-1.001	-0.001

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.905

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 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	4	PRO	0	-0.002	-0.006	3.875	1.850	3.291	-0.014	-0.592	-0.835	-0.001
6	A	7	LYS	1	0.988	0.987	3.553	56.454	56.655	0.000	-0.035	-0.166	0.000
4	A	5	LEU	0	0.059	0.029	5.947	3.668	3.668	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.851	-0.916	5.904	-37.208	-37.208	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.003	0.010	7.967	2.972	2.972	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.036	0.018	11.008	2.409	2.409	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.875	-0.937	9.406	-27.396	-27.396	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.037	0.000	11.428	1.881	1.881	0.000	0.000	0.000	0.000
11	A	12	MET	0	-0.001	0.023	13.731	1.366	1.366	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.055	0.028	15.722	1.391	1.391	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.056	-0.043	14.903	1.237	1.237	0.000	0.000	0.000	0.000
14	A	15	THR	0	-0.031	-0.042	16.865	1.027	1.027	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.013	0.021	19.245	0.730	0.730	0.000	0.000	0.000	0.000
16	A	17	HIS	0	0.009	-0.004	20.415	1.051	1.051	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.749	0.877	19.703	15.613	15.613	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.137	-0.123	22.682	0.643	0.643	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.029	0.008	25.534	0.164	0.164	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.017	0.004	26.638	0.288	0.288	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.755	0.874	27.179	11.440	11.440	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.894	-0.950	30.816	-8.748	-8.748	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.012	0.002	33.205	-0.075	-0.075	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.858	-0.941	31.725	-10.071	-10.071	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.944	0.966	28.518	10.050	10.050	0.000	0.000	0.000	0.000
26	A	27	PHE	0	-0.044	-0.014	25.969	-0.499	-0.499	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.843	0.923	27.992	9.236	9.236	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.026	0.004	25.394	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.108	0.037	29.640	0.112	0.112	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.870	0.910	32.434	8.271	8.271	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.035	-0.023	34.014	0.006	0.006	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.749	-0.873	29.002	-10.609	-10.609	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.008	0.009	28.234	-0.429	-0.429	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.841	0.912	29.220	8.495	8.495	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.763	-0.850	28.387	-11.235	-11.235	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.032	0.023	22.942	-0.277	-0.277	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.024	-0.026	25.103	-0.414	-0.414	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.063	-0.045	26.920	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.786	0.885	24.751	12.089	12.089	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.807	-0.849	20.215	-15.396	-15.396	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.021	0.004	20.978	-0.554	-0.554	0.000	0.000	0.000	0.000
42	A	43	PRO	0	0.051	0.038	23.589	0.451	0.451	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.042	-0.048	23.751	0.550	0.550	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.006	0.019	25.843	0.216	0.216	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.014	0.015	27.539	0.359	0.359	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.016	0.007	29.862	0.410	0.410	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.922	0.949	31.367	8.593	8.593	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.784	0.871	34.380	8.644	8.644	0.000	0.000	0.000	0.000
49	A	50	THR	0	0.055	0.024	32.665	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	51	ASP	-1	-0.751	-0.840	35.283	-8.184	-8.184	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.787	-0.910	37.844	-8.493	-8.493	0.000	0.000	0.000	0.000
52	A	53	ALA	0	-0.024	-0.001	39.598	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.013	-0.006	35.894	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	55	PHE	0	0.063	0.020	31.213	-0.160	-0.160	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.020	0.036	35.764	-0.160	-0.160	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.883	0.943	37.303	8.522	8.522	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.006	-0.003	29.874	-0.036	-0.036	0.000	0.000	0.000	0.000
58	A	59	MET	0	0.040	0.027	33.172	-0.195	-0.195	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.051	-0.044	34.664	0.024	0.024	0.000	0.000	0.000	0.000
60	A	61	ASN	0	-0.068	-0.022	33.301	0.388	0.388	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.043	-0.016	28.675	-0.203	-0.203	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.763	-0.873	31.893	-8.978	-8.978	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.146	-0.090	32.802	0.277	0.277	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.052	-0.047	34.197	0.365	0.365	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.880	0.945	36.437	8.182	8.182	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.833	-0.896	35.373	-8.956	-8.956	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.102	-0.060	37.573	0.229	0.229	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.951	-0.981	32.936	-9.310	-9.310	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.011	-0.001	28.160	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.791	-0.886	28.455	-11.388	-11.388	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.040	-0.005	18.959	-0.396	-0.396	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.025	-0.007	23.874	-0.683	-0.683	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.738	-0.846	25.681	-10.387	-10.387	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.045	-0.039	19.390	0.029	0.029	0.000	0.000	0.000	0.000
75	A	76	CYS	0	-0.047	-0.020	21.172	-0.676	-0.676	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.011	0.013	22.672	-0.347	-0.347	0.000	0.000	0.000	0.000
77	A	78	PHE	0	0.009	-0.003	25.201	0.006	0.006	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.025	0.001	19.081	-0.100	-0.100	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.039	-0.026	21.701	-0.577	-0.577	0.000	0.000	0.000	0.000
80	A	81	CYS	0	-0.033	-0.011	22.683	0.173	0.173	0.000	0.000	0.000	0.000
81	A	82	ILE	0	0.011	0.005	22.006	0.154	0.154	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.003	0.002	19.871	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	84	MET	0	-0.029	-0.017	21.449	0.134	0.134	0.000	0.000	0.000	0.000
84	A	85	MET	0	-0.012	-0.016	24.568	0.250	0.250	0.000	0.000	0.000	0.000
85	A	86	CYS	0	-0.074	-0.039	21.109	0.080	0.080	0.000	0.000	0.000	0.000
86	A	87	ASN	0	-0.087	-0.038	22.485	-0.638	-0.638	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.896	-0.946	23.381	-11.465	-11.465	0.000	0.000	0.000	0.000
88	A	89	PHE	0	-0.026	-0.008	25.539	0.545	0.545	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.050	-0.013	17.887	-0.450	-0.450	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.935	-0.968	23.252	-13.190	-13.190	0.000	0.000	0.000	0.000
91	A	92	GLY	0	-0.069	-0.032	25.700	0.310	0.310	0.000	0.000	0.000	0.000
92	A	93	PHE	0	-0.145	-0.074	27.188	0.459	0.459	0.000	0.000	0.000	0.000
93	A	94	PRO	-1	-0.893	-0.936	28.994	-10.331	-10.331	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)