FMO DATABASE

FMODB ID: VY6M1

Calculation Name: 3HCI-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (2s)-2-(acetylamino)-n-methyl-4-[(r)-methylsulfinyl]butanamide | calcium ion | zinc ion

Ligand 3-letter code: RSM | CA | ZN

Ligand of Interest (LOI):

PDB ID: 3HCI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P4Q6

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1429116.968926
FMO2-HF: Nuclear repulsion	1370038.276188
FMO2-HF: Total energy	-59078.692738
FMO2-MP2: Total energy	-59249.593873

3D Structure

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:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-216.005	-216.116	40.368	-21.512	-18.745	-0.144

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.867

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	PHE	0	0.033	0.014	2.005	0.366	2.228	7.164	-4.133	-4.894	0.030
4	A	5	ASP	-1	-0.798	-0.875	3.553	-33.098	-32.684	0.052	0.007	-0.473	0.000
5	A	6	LEU	0	0.012	-0.004	2.998	1.456	2.279	0.180	-0.244	-0.759	-0.001
57	A	58	LEU	0	0.005	0.009	3.983	-0.514	-0.429	-0.001	-0.010	-0.073	0.000
79	A	80	TYR	0	-0.030	-0.024	4.751	0.463	0.512	-0.001	-0.005	-0.043	0.000
80	A	81	ASP	-1	-0.809	-0.928	2.180	-126.550	-119.284	7.826	-8.117	-6.975	-0.098
81	A	82	PRO	0	0.006	-0.007	4.500	1.999	2.050	-0.001	-0.008	-0.042	0.000
82	A	83	ALA	0	-0.011	0.006	2.911	4.342	4.721	0.078	-0.157	-0.300	0.000
83	A	84	HIS	0	-0.027	0.003	1.686	-30.652	-41.692	25.071	-8.845	-5.186	-0.075
6	A	7	THR	0	-0.033	-0.023	6.251	2.326	2.326	0.000	0.000	0.000	0.000
7	A	8	PRO	0	0.032	0.014	9.699	0.544	0.544	0.000	0.000	0.000	0.000
8	A	9	PRO	0	-0.031	0.004	12.386	0.527	0.527	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.006	-0.020	14.794	0.742	0.742	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.058	0.004	18.347	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.031	0.030	21.196	0.149	0.149	0.000	0.000	0.000	0.000
12	A	13	GLN	0	0.030	0.021	16.996	-0.094	-0.094	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.868	0.932	16.283	15.638	15.638	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.858	-0.943	18.856	-12.427	-12.427	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.043	-0.016	21.032	0.366	0.366	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.035	-0.019	15.568	0.126	0.126	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.026	-0.019	19.765	0.018	0.018	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.015	-0.005	21.984	0.366	0.366	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.027	0.004	22.656	0.398	0.398	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.052	-0.023	19.877	-0.358	-0.358	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.000	-0.023	23.506	0.569	0.569	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.908	-0.954	25.739	-9.962	-9.962	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.802	-0.865	25.843	-10.971	-10.971	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.765	-0.850	21.812	-12.900	-12.900	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.013	0.000	22.173	-0.652	-0.652	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.732	0.818	23.872	10.540	10.540	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.006	0.005	20.659	-0.093	-0.093	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.030	-0.011	16.678	-0.427	-0.427	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.054	-0.030	19.239	-0.730	-0.730	0.000	0.000	0.000	0.000
30	A	31	HIS	0	-0.036	-0.013	21.796	0.104	0.104	0.000	0.000	0.000	0.000
31	A	32	HIS	1	0.816	0.898	20.861	14.193	14.193	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.016	0.029	23.371	0.243	0.243	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.005	-0.010	23.732	-0.378	-0.378	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.739	-0.866	23.654	-12.227	-12.227	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.008	0.001	26.425	0.082	0.082	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.019	0.018	27.940	-0.191	-0.191	0.000	0.000	0.000	0.000
37	A	38	PHE	0	-0.010	-0.035	28.418	0.346	0.346	0.000	0.000	0.000	0.000
38	A	39	CYS	0	-0.076	-0.023	28.873	0.288	0.288	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.035	0.028	24.723	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.010	-0.011	22.842	0.013	0.013	0.000	0.000	0.000	0.000
41	A	42	PHE	0	-0.030	-0.028	19.033	-0.073	-0.073	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.027	0.007	21.875	-0.504	-0.504	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.886	-0.933	24.232	-11.253	-11.253	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.012	-0.012	20.606	0.403	0.403	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.913	0.971	22.776	12.462	12.462	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.068	-0.027	21.291	-0.104	-0.104	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.854	-0.926	18.872	-15.161	-15.161	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.098	0.055	15.189	0.355	0.355	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.071	-0.042	9.859	-1.178	-1.178	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.001	0.006	12.417	1.384	1.384	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.012	-0.020	10.296	-2.131	-2.131	0.000	0.000	0.000	0.000
52	A	53	CYS	0	-0.025	-0.015	10.668	1.973	1.973	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.801	0.898	12.462	13.950	13.950	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.011	0.009	15.096	0.475	0.475	0.000	0.000	0.000	0.000
55	A	56	CYS	0	-0.009	-0.031	10.803	-0.515	-0.515	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.059	0.025	11.203	-0.976	-0.976	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.007	0.010	5.749	1.361	1.361	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.033	-0.002	6.523	-3.809	-3.809	0.000	0.000	0.000	0.000
60	A	61	PHE	0	0.034	0.016	8.910	-1.524	-1.524	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.982	0.997	7.291	30.621	30.621	0.000	0.000	0.000	0.000
62	A	63	SER	0	0.042	0.023	13.048	0.147	0.147	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.027	-0.020	13.897	-0.181	-0.181	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.017	0.015	14.071	0.147	0.147	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.850	0.931	16.173	13.943	13.943	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.030	-0.032	18.767	0.538	0.538	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.852	-0.928	22.247	-12.501	-12.501	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.062	-0.045	24.025	0.559	0.559	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.002	0.003	25.942	0.272	0.272	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.056	-0.049	25.692	0.297	0.297	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.038	0.027	27.904	0.201	0.201	0.000	0.000	0.000	0.000
72	A	73	TRP	0	-0.009	0.000	22.886	0.182	0.182	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.015	0.019	19.775	-0.065	-0.065	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.033	0.001	19.732	-0.255	-0.255	0.000	0.000	0.000	0.000
75	A	76	PHE	0	0.027	0.008	15.428	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	77	PHE	0	0.020	0.021	16.145	-0.173	-0.173	0.000	0.000	0.000	0.000
77	A	78	ALA	0	0.027	0.017	12.221	-0.275	-0.275	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.005	0.007	8.450	0.552	0.552	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.007	0.004	5.618	4.446	4.446	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.823	0.894	9.206	20.573	20.573	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.865	-0.931	11.306	-18.468	-18.468	0.000	0.000	0.000	0.000
87	A	88	ILE	0	-0.028	-0.018	14.762	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.840	0.916	17.989	14.472	14.472	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.693	-0.813	21.590	-12.170	-12.170	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.015	-0.016	23.810	0.061	0.061	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.026	-0.039	26.398	0.564	0.564	0.000	0.000	0.000	0.000
92	A	93	TYR	0	-0.026	-0.037	28.925	-0.070	-0.070	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.003	0.017	31.639	0.269	0.269	0.000	0.000	0.000	0.000
94	A	95	MET	0	-0.045	-0.006	28.821	0.071	0.071	0.000	0.000	0.000	0.000
95	A	96	VAL	0	-0.008	-0.010	25.923	-0.117	-0.117	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.902	0.945	23.438	12.103	12.103	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.022	0.023	17.615	0.447	0.447	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.803	-0.858	17.835	-15.019	-15.019	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.009	0.002	14.067	-0.921	-0.921	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.031	0.006	12.992	0.858	0.858	0.000	0.000	0.000	0.000
101	A	102	CYS	0	-0.021	0.002	8.999	-2.120	-2.120	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.015	-0.014	7.378	1.362	1.362	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.739	0.829	7.129	28.176	28.176	0.000	0.000	0.000	0.000
104	A	105	CYS	0	0.006	-0.013	9.422	1.280	1.280	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.818	-0.879	12.788	-17.165	-17.165	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.001	0.017	14.291	0.791	0.791	0.000	0.000	0.000	0.000
107	A	108	HIS	0	-0.036	-0.024	15.135	-0.945	-0.945	0.000	0.000	0.000	0.000
108	A	109	LEU	0	0.017	0.011	11.795	0.056	0.056	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.046	0.027	16.519	0.649	0.649	0.000	0.000	0.000	0.000
110	A	111	HIS	0	-0.072	-0.044	19.057	-0.206	-0.206	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.013	0.014	16.168	-0.033	-0.033	0.000	0.000	0.000	0.000
112	A	113	PHE	0	-0.039	-0.021	18.680	0.825	0.825	0.000	0.000	0.000	0.000
113	A	114	PRO	0	-0.018	-0.003	20.824	-0.505	-0.505	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.793	-0.872	22.566	-12.391	-12.391	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.001	0.017	21.756	0.314	0.314	0.000	0.000	0.000	0.000
116	A	117	PRO	0	-0.015	0.002	21.504	0.452	0.452	0.000	0.000	0.000	0.000
117	A	118	PRO	0	-0.001	-0.003	21.445	-0.661	-0.661	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.025	-0.018	17.469	0.167	0.167	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.023	-0.037	15.260	0.473	0.473	0.000	0.000	0.000	0.000
120	A	121	GLY	0	0.004	0.015	18.480	0.181	0.181	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.913	-0.938	15.309	-20.361	-20.361	0.000	0.000	0.000	0.000
122	A	123	ARG	1	0.819	0.859	19.313	13.024	13.024	0.000	0.000	0.000	0.000
123	A	124	HIS	0	-0.007	-0.014	13.419	0.080	0.080	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.002	-0.009	17.333	0.578	0.578	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.042	-0.024	14.740	-0.183	-0.183	0.000	0.000	0.000	0.000
126	A	127	ASN	0	0.011	0.008	18.942	1.453	1.453	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.001	-0.015	19.037	-0.666	-0.666	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.019	-0.015	19.779	-0.449	-0.449	0.000	0.000	0.000	0.000
129	A	130	SER	0	-0.020	-0.032	16.589	0.258	0.258	0.000	0.000	0.000	0.000
130	A	131	LEU	0	-0.056	-0.023	14.010	-1.218	-1.218	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.016	0.010	15.070	1.115	1.115	0.000	0.000	0.000	0.000
132	A	133	PHE	0	-0.008	0.001	14.851	-1.082	-1.082	0.000	0.000	0.000	0.000
133	A	134	THR	0	-0.048	-0.030	13.980	0.262	0.262	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.897	-0.948	15.568	-14.017	-14.017	0.000	0.000	0.000	0.000
135	A	136	ASP	-1	-0.886	-0.969	16.149	-18.457	-18.457	0.000	0.000	0.000	0.000
136	A	137	GLY	0	-0.038	-0.010	16.049	0.990	0.990	0.000	0.000	0.000	0.000
137	A	138	GLN	0	-0.045	-0.023	17.204	0.634	0.634	0.000	0.000	0.000	0.000
138	A	139	PRO	0	-0.034	-0.010	15.290	-1.150	-1.150	0.000	0.000	0.000	0.000
139	A	140	LEU	0	0.040	0.016	8.896	-0.044	-0.044	0.000	0.000	0.000	0.000
140	A	141	PRO	0	-0.019	-0.008	12.304	0.486	0.486	0.000	0.000	0.000	0.000
141	A	142	ASN	0	-0.039	-0.013	11.785	0.614	0.614	0.000	0.000	0.000	0.000
142	A	143	PRO	0	0.037	0.018	12.610	0.718	0.718	0.000	0.000	0.000	0.000
143	A	144	LEU	0	-0.050	-0.021	11.015	0.729	0.729	0.000	0.000	0.000	0.000
144	A	145	GLN	0	-0.055	-0.019	13.981	0.313	0.313	0.000	0.000	0.000	0.000
145	A	146	ARG	1	0.821	0.912	8.907	24.551	24.551	0.000	0.000	0.000	0.000
146	A	147	ALA	0	0.043	0.016	11.275	0.160	0.160	0.000	0.000	0.000	0.000
147	A	148	GLY	0	0.012	0.007	7.975	-1.955	-1.955	0.000	0.000	0.000	0.000
148	A	149	ALA	0	0.032	0.005	5.848	2.316	2.316	0.000	0.000	0.000	0.000
149	A	150	GLU	-1	-0.779	-0.864	7.710	-26.111	-26.111	0.000	0.000	0.000	0.000
150	A	151	THR	0	-0.077	-0.036	9.046	2.135	2.135	0.000	0.000	0.000	0.000
151	A	152	GLN	0	-0.071	-0.028	10.961	1.934	1.934	0.000	0.000	0.000	0.000
152	A	153	PRO	0	-0.032	-0.017	12.611	-0.097	-0.097	0.000	0.000	0.000	0.000
153	A	154	ALA	-1	-0.885	-0.933	11.575	-23.378	-23.378	0.000	0.000	0.000	0.000

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