FMO DATABASE

FMODB ID: 1Y14Z

Calculation Name: 6EBD-C-Xray547

Preferred Name:

Target Type:

Ligand Name: (6s)-6,8-disulfanyloctanamide | chloride ion

Ligand 3-letter code: J3S | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6EBD

Chain ID: C

ChEMBL ID:

UniProt ID: A0A202

Base Structure: X-ray

Registration Date: 2025-10-04

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1037686.775014
FMO2-HF: Nuclear repulsion	985665.686288
FMO2-HF: Total energy	-52021.088726
FMO2-MP2: Total energy	-52173.146081

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:SER)

Summations of interaction energy for fragment #1(A:-1: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.
-48.854	-47.355	-0.016	-0.804	-0.679	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.912

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	1	MET	0	0.003	0.013	3.872	-6.086	-4.587	-0.016	-0.804	-0.679	-0.003
4	A	2	SER	0	0.016	0.000	6.711	0.833	0.833	0.000	0.000	0.000	0.000
5	A	3	ILE	0	0.009	0.009	9.892	2.085	2.085	0.000	0.000	0.000	0.000
6	A	4	GLU	-1	-0.938	-0.943	12.554	-18.901	-18.901	0.000	0.000	0.000	0.000
7	A	5	THR	0	-0.008	-0.014	15.200	0.648	0.648	0.000	0.000	0.000	0.000
8	A	6	ILE	0	-0.027	-0.012	14.341	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	7	LEU	0	0.006	-0.001	18.468	0.619	0.619	0.000	0.000	0.000	0.000
10	A	8	TYR	0	0.021	0.004	21.104	0.540	0.540	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.950	0.971	18.644	14.118	14.118	0.000	0.000	0.000	0.000
12	A	10	THR	0	0.026	0.024	21.259	0.556	0.556	0.000	0.000	0.000	0.000
13	A	11	GLN	0	-0.019	-0.014	21.007	-0.946	-0.946	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.009	0.011	22.277	0.626	0.626	0.000	0.000	0.000	0.000
15	A	13	THR	0	-0.034	-0.008	22.906	-0.727	-0.727	0.000	0.000	0.000	0.000
16	A	14	VAL	0	0.018	0.013	24.511	0.401	0.401	0.000	0.000	0.000	0.000
17	A	15	SER	0	-0.020	-0.019	26.462	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	16	GLY	0	0.043	0.022	29.413	0.068	0.068	0.000	0.000	0.000	0.000
19	A	17	GLY	0	-0.023	-0.009	31.558	0.287	0.287	0.000	0.000	0.000	0.000
20	A	18	ARG	1	0.948	0.961	32.393	8.189	8.189	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.899	-0.927	35.109	-8.091	-8.091	0.000	0.000	0.000	0.000
22	A	20	GLY	0	-0.031	-0.012	32.292	-0.100	-0.100	0.000	0.000	0.000	0.000
23	A	21	ASN	0	-0.037	-0.025	31.320	0.046	0.046	0.000	0.000	0.000	0.000
24	A	22	ALA	0	0.038	0.008	27.105	-0.409	-0.409	0.000	0.000	0.000	0.000
25	A	23	GLU	-1	-0.809	-0.891	28.286	-9.037	-9.037	0.000	0.000	0.000	0.000
26	A	24	SER	0	-0.028	-0.039	26.684	-0.374	-0.374	0.000	0.000	0.000	0.000
27	A	25	SER	0	-0.034	-0.027	25.664	0.319	0.319	0.000	0.000	0.000	0.000
28	A	26	ASP	-1	-0.851	-0.907	27.971	-10.615	-10.615	0.000	0.000	0.000	0.000
29	A	27	GLY	0	-0.005	-0.001	30.327	0.353	0.353	0.000	0.000	0.000	0.000
30	A	28	ALA	0	-0.051	-0.015	30.276	0.259	0.259	0.000	0.000	0.000	0.000
31	A	29	LEU	0	-0.023	-0.009	26.983	0.129	0.129	0.000	0.000	0.000	0.000
32	A	30	LYS	1	0.858	0.915	30.361	8.766	8.766	0.000	0.000	0.000	0.000
33	A	31	VAL	0	-0.012	-0.002	30.359	0.284	0.284	0.000	0.000	0.000	0.000
34	A	32	GLN	0	0.040	0.016	32.333	-0.230	-0.230	0.000	0.000	0.000	0.000
35	A	33	LEU	0	-0.020	-0.005	28.341	-0.099	-0.099	0.000	0.000	0.000	0.000
36	A	34	SER	0	-0.047	-0.032	32.452	0.422	0.422	0.000	0.000	0.000	0.000
37	A	35	THR	0	0.019	0.026	30.802	-0.296	-0.296	0.000	0.000	0.000	0.000
38	A	36	PRO	0	0.014	0.005	31.417	0.333	0.333	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.919	0.965	34.331	7.797	7.797	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.896	-0.957	34.136	-8.682	-8.682	0.000	0.000	0.000	0.000
41	A	39	LEU	0	-0.033	-0.018	28.506	-0.204	-0.204	0.000	0.000	0.000	0.000
42	A	40	GLY	0	-0.007	0.004	31.869	-0.183	-0.183	0.000	0.000	0.000	0.000
43	A	41	GLY	0	-0.014	-0.002	34.368	0.078	0.078	0.000	0.000	0.000	0.000
44	A	42	ALA	0	0.008	-0.009	35.247	0.201	0.201	0.000	0.000	0.000	0.000
45	A	43	GLY	0	-0.003	0.007	36.818	0.246	0.246	0.000	0.000	0.000	0.000
46	A	44	GLY	0	-0.018	-0.020	37.807	0.033	0.033	0.000	0.000	0.000	0.000
47	A	45	PRO	0	-0.022	-0.024	38.507	-0.054	-0.054	0.000	0.000	0.000	0.000
48	A	46	GLY	0	-0.012	0.017	35.094	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	47	THR	0	0.016	-0.011	30.311	-0.139	-0.139	0.000	0.000	0.000	0.000
50	A	48	ASN	0	0.006	-0.012	29.154	-0.193	-0.193	0.000	0.000	0.000	0.000
51	A	49	PRO	0	0.044	0.012	23.673	0.030	0.030	0.000	0.000	0.000	0.000
52	A	50	GLU	-1	-0.812	-0.909	25.288	-12.241	-12.241	0.000	0.000	0.000	0.000
53	A	51	GLN	0	0.027	0.025	26.978	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	52	LEU	0	-0.029	-0.007	25.913	0.028	0.028	0.000	0.000	0.000	0.000
55	A	53	PHE	0	0.007	0.003	19.868	-0.161	-0.161	0.000	0.000	0.000	0.000
56	A	54	ALA	0	0.023	0.005	24.670	-0.105	-0.105	0.000	0.000	0.000	0.000
57	A	55	ALA	0	-0.010	-0.006	27.761	0.104	0.104	0.000	0.000	0.000	0.000
58	A	56	GLY	0	0.012	0.006	24.968	0.112	0.112	0.000	0.000	0.000	0.000
59	A	57	TYR	0	0.001	-0.031	22.511	-0.125	-0.125	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.002	-0.001	25.220	0.070	0.070	0.000	0.000	0.000	0.000
61	A	59	ALA	0	0.002	0.004	27.987	0.198	0.198	0.000	0.000	0.000	0.000
62	A	60	ALA	0	0.018	0.009	23.711	0.103	0.103	0.000	0.000	0.000	0.000
63	A	61	PHE	0	0.032	0.021	25.294	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	62	LEU	0	0.025	0.011	27.200	0.232	0.232	0.000	0.000	0.000	0.000
65	A	63	GLY	0	-0.024	-0.014	28.551	0.284	0.284	0.000	0.000	0.000	0.000
66	A	64	SER	0	-0.025	-0.030	25.230	-0.088	-0.088	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.007	0.003	27.449	0.146	0.146	0.000	0.000	0.000	0.000
68	A	66	LYS	1	0.954	0.979	30.849	9.426	9.426	0.000	0.000	0.000	0.000
69	A	67	PHE	0	-0.004	0.007	25.836	0.176	0.176	0.000	0.000	0.000	0.000
70	A	68	VAL	0	-0.023	-0.017	27.799	0.122	0.122	0.000	0.000	0.000	0.000
71	A	69	ALA	0	0.017	0.008	30.598	0.227	0.227	0.000	0.000	0.000	0.000
72	A	70	ALA	0	0.012	0.004	33.256	0.215	0.215	0.000	0.000	0.000	0.000
73	A	71	LYS	1	0.909	0.962	26.722	11.748	11.748	0.000	0.000	0.000	0.000
74	A	72	ARG	1	0.840	0.907	33.107	9.010	9.010	0.000	0.000	0.000	0.000
75	A	73	LYS	1	0.930	0.974	35.789	7.803	7.803	0.000	0.000	0.000	0.000
76	A	74	THR	0	-0.028	-0.006	37.120	0.225	0.225	0.000	0.000	0.000	0.000
77	A	75	THR	0	-0.027	-0.021	37.758	-0.110	-0.110	0.000	0.000	0.000	0.000
78	A	76	LEU	0	-0.005	0.000	34.556	0.048	0.048	0.000	0.000	0.000	0.000
79	A	77	SER	0	0.008	-0.007	39.222	0.070	0.070	0.000	0.000	0.000	0.000
80	A	78	ALA	0	-0.003	-0.017	40.407	-0.188	-0.188	0.000	0.000	0.000	0.000
81	A	79	ASP	-1	-0.903	-0.946	41.145	-7.269	-7.269	0.000	0.000	0.000	0.000
82	A	80	ALA	0	-0.079	-0.022	37.358	-0.103	-0.103	0.000	0.000	0.000	0.000
83	A	81	SER	0	-0.027	-0.019	35.873	-0.107	-0.107	0.000	0.000	0.000	0.000
84	A	82	VAL	0	-0.001	-0.001	29.908	-0.046	-0.046	0.000	0.000	0.000	0.000
85	A	83	SER	0	-0.029	-0.006	33.182	0.149	0.149	0.000	0.000	0.000	0.000
86	A	84	CYS	0	-0.056	-0.009	27.595	-0.213	-0.213	0.000	0.000	0.000	0.000
87	A	85	GLY	0	0.003	0.012	30.278	0.263	0.263	0.000	0.000	0.000	0.000
88	A	86	VAL	0	0.000	-0.014	25.274	-0.360	-0.360	0.000	0.000	0.000	0.000
89	A	87	GLY	0	0.018	0.023	27.339	0.415	0.415	0.000	0.000	0.000	0.000
90	A	88	ILE	0	-0.009	-0.015	24.857	-0.529	-0.529	0.000	0.000	0.000	0.000
91	A	89	GLY	0	0.034	0.020	25.462	0.552	0.552	0.000	0.000	0.000	0.000
92	A	90	THR	0	-0.025	-0.016	24.946	-0.374	-0.374	0.000	0.000	0.000	0.000
93	A	91	LEU	0	-0.008	0.000	19.583	0.017	0.017	0.000	0.000	0.000	0.000
94	A	92	PRO	0	0.005	-0.002	21.249	0.186	0.186	0.000	0.000	0.000	0.000
95	A	93	SER	0	-0.022	-0.016	17.862	0.297	0.297	0.000	0.000	0.000	0.000
96	A	94	GLY	0	0.015	0.009	19.672	-0.420	-0.420	0.000	0.000	0.000	0.000
97	A	95	PHE	0	-0.025	-0.015	21.046	0.742	0.742	0.000	0.000	0.000	0.000
98	A	96	GLY	0	0.011	0.011	20.380	-0.979	-0.979	0.000	0.000	0.000	0.000
99	A	97	LEU	0	-0.028	-0.016	21.008	0.662	0.662	0.000	0.000	0.000	0.000
100	A	98	GLU	-1	-0.937	-0.953	22.443	-11.574	-11.574	0.000	0.000	0.000	0.000
101	A	99	VAL	0	-0.015	-0.023	23.397	0.267	0.267	0.000	0.000	0.000	0.000
102	A	100	GLU	-1	-0.826	-0.885	26.098	-9.436	-9.436	0.000	0.000	0.000	0.000
103	A	101	LEU	0	-0.007	-0.004	25.892	0.119	0.119	0.000	0.000	0.000	0.000
104	A	102	GLN	0	0.009	0.008	29.893	0.385	0.385	0.000	0.000	0.000	0.000
105	A	103	ILE	0	-0.008	-0.008	30.131	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.898	0.944	34.273	8.096	8.096	0.000	0.000	0.000	0.000
107	A	105	LEU	0	0.023	-0.003	34.432	-0.075	-0.075	0.000	0.000	0.000	0.000
108	A	106	PRO	0	0.035	0.029	38.804	0.112	0.112	0.000	0.000	0.000	0.000
109	A	107	GLY	0	0.027	0.004	42.665	0.005	0.005	0.000	0.000	0.000	0.000
110	A	108	LEU	0	-0.038	-0.007	37.911	-0.022	-0.022	0.000	0.000	0.000	0.000
111	A	109	SER	0	0.041	0.023	41.710	0.068	0.068	0.000	0.000	0.000	0.000
112	A	110	ASP	-1	-0.828	-0.930	39.495	-7.939	-7.939	0.000	0.000	0.000	0.000
113	A	111	GLU	-1	-0.963	-0.977	37.757	-8.393	-8.393	0.000	0.000	0.000	0.000
114	A	112	GLU	-1	-0.859	-0.912	36.566	-8.385	-8.385	0.000	0.000	0.000	0.000
115	A	113	ALA	0	0.015	-0.005	35.740	-0.292	-0.292	0.000	0.000	0.000	0.000
116	A	114	ARG	1	0.815	0.904	30.878	9.581	9.581	0.000	0.000	0.000	0.000
117	A	115	GLN	0	0.000	-0.009	32.004	-0.444	-0.444	0.000	0.000	0.000	0.000
118	A	116	LEU	0	-0.037	-0.011	31.151	-0.360	-0.360	0.000	0.000	0.000	0.000
119	A	117	ILE	0	0.012	0.004	29.607	-0.415	-0.415	0.000	0.000	0.000	0.000
120	A	118	GLU	-1	-0.825	-0.913	27.405	-11.625	-11.625	0.000	0.000	0.000	0.000
121	A	119	GLN	0	-0.035	-0.019	26.045	-0.586	-0.586	0.000	0.000	0.000	0.000
122	A	120	ALA	0	-0.010	-0.009	25.611	-0.506	-0.506	0.000	0.000	0.000	0.000
123	A	121	HIS	0	0.074	0.055	22.662	-0.455	-0.455	0.000	0.000	0.000	0.000
124	A	122	ILE	0	-0.032	0.001	21.128	-0.788	-0.788	0.000	0.000	0.000	0.000
125	A	123	VAL	0	-0.020	-0.016	20.631	-0.695	-0.695	0.000	0.000	0.000	0.000
126	A	124	CYS	0	-0.046	0.015	21.357	-0.464	-0.464	0.000	0.000	0.000	0.000
127	A	125	PRO	0	0.041	0.007	18.234	-0.542	-0.542	0.000	0.000	0.000	0.000
128	A	126	TYR	0	0.019	0.002	17.517	-0.900	-0.900	0.000	0.000	0.000	0.000
129	A	127	SER	0	0.017	0.009	18.858	-0.290	-0.290	0.000	0.000	0.000	0.000
130	A	128	ASP	-1	-0.918	-0.931	14.594	-20.858	-20.858	0.000	0.000	0.000	0.000
131	A	129	ALA	0	0.000	-0.005	13.742	-1.175	-1.175	0.000	0.000	0.000	0.000
132	A	130	THR	0	-0.041	-0.048	14.371	-0.641	-0.641	0.000	0.000	0.000	0.000
133	A	131	ARG	1	0.800	0.886	14.548	17.850	17.850	0.000	0.000	0.000	0.000
134	A	132	GLY	0	-0.038	-0.021	14.648	-1.123	-1.123	0.000	0.000	0.000	0.000
135	A	133	ASN	0	-0.053	-0.015	12.478	-0.493	-0.493	0.000	0.000	0.000	0.000
136	A	134	ILE	0	-0.031	-0.015	16.398	0.361	0.361	0.000	0.000	0.000	0.000
137	A	135	ASP	-1	-0.902	-0.942	20.157	-11.899	-11.899	0.000	0.000	0.000	0.000
138	A	136	VAL	0	0.013	-0.005	21.566	0.011	0.011	0.000	0.000	0.000	0.000
139	A	137	ARG	1	0.886	0.947	24.550	10.348	10.348	0.000	0.000	0.000	0.000
140	A	138	LEU	0	0.031	0.018	26.020	0.188	0.188	0.000	0.000	0.000	0.000
141	A	139	ARG	1	0.862	0.916	29.569	9.087	9.087	0.000	0.000	0.000	0.000
142	A	140	LEU	0	-0.011	0.001	33.338	-0.131	-0.131	0.000	0.000	0.000	0.000
143	A	141	ALA	-1	-0.880	-0.924	36.002	-7.835	-7.835	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:-1:SER)