FMO DATABASE

FMODB ID: YMYM2

Calculation Name: 5CZ3-A-Xray549

Preferred Name:

Target Type:

Ligand Name: beta-mercaptoethanol

Ligand 3-letter code: BME

Ligand of Interest (LOI):

PDB ID: 5CZ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Q8N4

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1581458.136914
FMO2-HF: Nuclear repulsion	1519809.865859
FMO2-HF: Total energy	-61648.271055
FMO2-MP2: Total energy	-61830.03807

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-180.57	-173.406	20.228	-10.693	-16.694	-0.091

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.766 / q_NPA : 0.860

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	2	GLU	-1	-0.963	-0.976	2.522	-51.413	-48.297	3.543	-2.277	-4.380	-0.014
4	A	3	GLU	-1	-0.833	-0.925	2.929	-39.229	-37.727	0.029	-0.423	-1.109	-0.003
5	A	4	GLY	0	0.001	0.013	4.792	5.964	6.040	-0.001	-0.003	-0.071	0.000
27	A	26	PHE	0	-0.031	-0.019	3.188	0.422	0.790	0.017	-0.067	-0.317	0.000
28	A	27	ASP	-1	-0.719	-0.847	1.739	-91.241	-92.732	12.225	-6.096	-4.637	-0.082
29	A	28	GLY	0	-0.009	0.009	3.597	-6.626	-6.088	0.017	-0.192	-0.363	-0.001
30	A	29	ASP	-1	-0.808	-0.898	4.914	-18.688	-18.656	-0.001	-0.003	-0.027	0.000
133	A	132	ARG	1	0.802	0.899	2.643	48.006	51.029	4.399	-1.632	-5.790	0.009
6	A	5	ILE	0	-0.019	0.002	5.877	3.903	3.903	0.000	0.000	0.000	0.000
7	A	6	VAL	0	-0.041	-0.032	6.660	-3.304	-3.304	0.000	0.000	0.000	0.000
8	A	7	HIS	0	-0.024	0.004	9.062	3.633	3.633	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.882	0.929	11.394	15.323	15.323	0.000	0.000	0.000	0.000
10	A	9	LEU	0	-0.037	-0.019	14.145	0.761	0.761	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.778	-0.849	16.132	-15.312	-15.312	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.014	-0.016	18.916	0.374	0.374	0.000	0.000	0.000	0.000
13	A	12	PHE	0	0.001	-0.007	21.558	0.092	0.092	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.003	0.006	24.597	0.077	0.077	0.000	0.000	0.000	0.000
15	A	14	ILE	0	0.007	-0.020	27.843	0.195	0.195	0.000	0.000	0.000	0.000
16	A	15	ASP	-1	-0.855	-0.913	30.943	-8.736	-8.736	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.890	-0.968	30.076	-9.573	-9.573	0.000	0.000	0.000	0.000
18	A	17	ASN	0	-0.050	-0.029	31.132	0.003	0.003	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.003	0.008	25.213	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	19	SER	0	-0.002	-0.028	23.810	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	20	ILE	0	-0.023	-0.002	18.936	-0.078	-0.078	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.874	0.932	18.959	12.704	12.704	0.000	0.000	0.000	0.000
23	A	22	HIS	0	-0.023	-0.023	14.029	-0.400	-0.400	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.010	-0.010	13.533	-0.986	-0.986	0.000	0.000	0.000	0.000
25	A	24	ASN	0	-0.014	-0.007	10.123	1.178	1.178	0.000	0.000	0.000	0.000
26	A	25	LEU	0	0.021	0.006	6.101	-0.107	-0.107	0.000	0.000	0.000	0.000
31	A	30	SER	0	-0.075	-0.057	8.555	2.270	2.270	0.000	0.000	0.000	0.000
32	A	31	TYR	0	-0.034	-0.051	9.826	-0.955	-0.955	0.000	0.000	0.000	0.000
33	A	32	GLY	0	0.002	-0.005	12.470	1.084	1.084	0.000	0.000	0.000	0.000
34	A	33	CYS	0	-0.036	-0.009	14.380	-0.378	-0.378	0.000	0.000	0.000	0.000
35	A	34	ASN	0	-0.007	0.003	15.397	1.434	1.434	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.048	0.012	18.981	-0.082	-0.082	0.000	0.000	0.000	0.000
37	A	36	HIS	0	-0.012	-0.011	21.471	0.870	0.870	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.007	0.010	25.050	0.101	0.101	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.850	0.913	28.118	10.503	10.503	0.000	0.000	0.000	0.000
40	A	39	THR	0	-0.016	-0.015	31.144	0.035	0.035	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.006	0.012	34.788	0.033	0.033	0.000	0.000	0.000	0.000
42	A	41	THR	0	-0.040	-0.021	37.997	0.225	0.225	0.000	0.000	0.000	0.000
43	A	42	CYS	0	-0.007	0.021	38.011	-0.227	-0.227	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.814	0.909	34.737	8.849	8.849	0.000	0.000	0.000	0.000
45	A	44	TYR	0	0.001	-0.010	35.421	-0.141	-0.141	0.000	0.000	0.000	0.000
46	A	45	ILE	0	0.014	0.019	29.523	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.059	-0.041	30.505	-0.120	-0.120	0.000	0.000	0.000	0.000
48	A	47	PHE	0	0.014	-0.001	24.392	-0.179	-0.179	0.000	0.000	0.000	0.000
49	A	48	ILE	0	-0.008	-0.012	25.455	0.252	0.252	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.035	-0.010	19.823	-0.299	-0.299	0.000	0.000	0.000	0.000
51	A	50	VAL	0	-0.009	-0.001	21.282	0.291	0.291	0.000	0.000	0.000	0.000
52	A	51	LEU	0	0.033	0.019	15.031	-0.461	-0.461	0.000	0.000	0.000	0.000
53	A	52	GLU	-1	-0.857	-0.929	16.850	-13.658	-13.658	0.000	0.000	0.000	0.000
54	A	53	PRO	0	0.017	0.001	14.725	-0.937	-0.937	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.784	-0.870	10.960	-21.531	-21.531	0.000	0.000	0.000	0.000
56	A	55	TRP	0	-0.055	-0.072	13.753	-0.254	-0.254	0.000	0.000	0.000	0.000
57	A	56	GLU	-1	-0.967	-0.967	15.859	-14.778	-14.778	0.000	0.000	0.000	0.000
58	A	57	ASN	0	-0.058	-0.031	11.139	0.574	0.574	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.038	-0.011	11.890	-1.226	-1.226	0.000	0.000	0.000	0.000
60	A	59	VAL	0	-0.020	-0.014	14.244	0.981	0.981	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.977	-0.989	16.653	-13.405	-13.405	0.000	0.000	0.000	0.000
62	A	61	ALA	0	0.011	0.013	16.054	-0.986	-0.986	0.000	0.000	0.000	0.000
63	A	62	LYS	1	0.832	0.912	10.941	23.951	23.951	0.000	0.000	0.000	0.000
64	A	63	PRO	0	-0.011	-0.006	17.016	0.141	0.141	0.000	0.000	0.000	0.000
65	A	64	ILE	0	0.005	0.020	17.629	-0.715	-0.715	0.000	0.000	0.000	0.000
66	A	65	HIS	0	-0.053	-0.019	18.581	1.484	1.484	0.000	0.000	0.000	0.000
67	A	66	MET	0	0.050	0.020	20.457	-0.294	-0.294	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.819	0.900	22.417	12.794	12.794	0.000	0.000	0.000	0.000
69	A	68	LEU	0	0.052	0.040	24.307	-0.324	-0.324	0.000	0.000	0.000	0.000
70	A	69	ASN	0	0.052	0.023	26.801	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.011	0.016	25.550	0.281	0.281	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.967	0.985	26.601	8.918	8.918	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.937	0.972	23.553	11.888	11.888	0.000	0.000	0.000	0.000
74	A	73	ILE	0	-0.004	0.000	26.087	0.469	0.469	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.950	0.969	26.056	8.957	8.957	0.000	0.000	0.000	0.000
76	A	75	VAL	0	0.065	0.026	22.920	0.229	0.229	0.000	0.000	0.000	0.000
77	A	76	PRO	0	-0.017	-0.009	25.760	-0.164	-0.164	0.000	0.000	0.000	0.000
78	A	77	LEU	0	0.018	0.020	23.624	-0.114	-0.114	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.051	-0.029	26.496	0.262	0.262	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.027	0.019	27.667	0.367	0.367	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.951	0.975	25.147	10.747	10.747	0.000	0.000	0.000	0.000
82	A	81	THR	0	0.045	0.030	24.650	0.339	0.339	0.000	0.000	0.000	0.000
83	A	82	HIS	0	-0.006	-0.014	25.692	-0.251	-0.251	0.000	0.000	0.000	0.000
84	A	83	THR	0	0.014	0.014	20.850	-0.245	-0.245	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.008	0.017	20.480	-0.471	-0.471	0.000	0.000	0.000	0.000
86	A	85	LEU	0	-0.037	-0.018	19.523	0.663	0.663	0.000	0.000	0.000	0.000
87	A	86	ILE	0	0.013	0.008	21.795	-0.387	-0.387	0.000	0.000	0.000	0.000
88	A	87	TYR	0	0.023	-0.003	20.016	0.579	0.579	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.946	0.978	24.909	9.290	9.290	0.000	0.000	0.000	0.000
90	A	89	VAL	0	-0.026	-0.012	25.874	0.167	0.167	0.000	0.000	0.000	0.000
91	A	90	VAL	0	-0.008	0.002	28.676	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	91	ILE	0	-0.044	-0.012	28.662	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	92	TYR	0	-0.053	-0.049	32.124	0.101	0.101	0.000	0.000	0.000	0.000
94	A	93	VAL	0	-0.046	-0.025	31.641	-0.216	-0.216	0.000	0.000	0.000	0.000
95	A	94	GLU	-1	-0.826	-0.918	35.023	-7.583	-7.583	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.938	-0.958	34.154	-8.502	-8.502	0.000	0.000	0.000	0.000
97	A	96	ASP	-1	-0.825	-0.916	30.649	-9.827	-9.827	0.000	0.000	0.000	0.000
98	A	97	ALA	0	-0.028	-0.020	29.236	0.024	0.024	0.000	0.000	0.000	0.000
99	A	98	LEU	0	-0.047	-0.011	21.500	-0.283	-0.283	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.000	-0.002	24.419	0.136	0.136	0.000	0.000	0.000	0.000
101	A	100	ARG	1	0.896	0.941	18.760	14.284	14.284	0.000	0.000	0.000	0.000
102	A	101	PHE	0	0.022	-0.001	18.721	0.626	0.626	0.000	0.000	0.000	0.000
103	A	102	TYR	0	-0.015	-0.015	15.630	-0.299	-0.299	0.000	0.000	0.000	0.000
104	A	103	SER	0	0.062	0.015	12.748	0.956	0.956	0.000	0.000	0.000	0.000
105	A	104	ASP	-1	-0.779	-0.801	11.840	-22.010	-22.010	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.053	-0.046	13.873	0.788	0.788	0.000	0.000	0.000	0.000
107	A	106	GLU	-1	-0.856	-0.923	10.847	-19.665	-19.665	0.000	0.000	0.000	0.000
108	A	107	ARG	1	0.852	0.910	11.070	17.833	17.833	0.000	0.000	0.000	0.000
109	A	108	SER	0	-0.011	-0.005	6.061	0.384	0.384	0.000	0.000	0.000	0.000
110	A	109	TYR	0	-0.054	-0.038	5.548	-2.189	-2.189	0.000	0.000	0.000	0.000
111	A	110	THR	0	0.005	-0.019	8.666	0.578	0.578	0.000	0.000	0.000	0.000
112	A	111	ASP	-1	-0.881	-0.925	9.141	-20.779	-20.779	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.034	-0.007	5.277	-1.083	-1.083	0.000	0.000	0.000	0.000
114	A	113	TYR	0	0.043	0.019	8.720	0.891	0.891	0.000	0.000	0.000	0.000
115	A	114	PRO	0	-0.023	0.024	12.160	0.629	0.629	0.000	0.000	0.000	0.000
116	A	115	THR	0	-0.029	-0.027	14.290	1.187	1.187	0.000	0.000	0.000	0.000
117	A	116	PHE	0	0.051	0.015	16.594	0.302	0.302	0.000	0.000	0.000	0.000
118	A	117	LEU	0	-0.046	-0.017	20.948	0.305	0.305	0.000	0.000	0.000	0.000
119	A	118	VAL	0	0.039	0.011	24.645	-0.035	-0.035	0.000	0.000	0.000	0.000
120	A	119	ASN	0	0.014	0.020	27.245	0.397	0.397	0.000	0.000	0.000	0.000
121	A	120	THR	0	0.026	-0.005	30.744	0.221	0.221	0.000	0.000	0.000	0.000
122	A	121	ASP	-1	-0.798	-0.867	32.763	-8.259	-8.259	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.074	-0.068	33.643	0.060	0.060	0.000	0.000	0.000	0.000
124	A	123	ARG	1	0.945	0.977	31.649	8.749	8.749	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.943	0.989	30.015	8.801	8.801	0.000	0.000	0.000	0.000
126	A	125	TYR	0	0.014	-0.002	24.145	0.169	0.169	0.000	0.000	0.000	0.000
127	A	126	TYR	0	-0.035	-0.016	22.111	0.328	0.328	0.000	0.000	0.000	0.000
128	A	127	ILE	0	0.030	0.019	17.020	0.003	0.003	0.000	0.000	0.000	0.000
129	A	128	LEU	0	-0.073	-0.034	18.970	0.137	0.137	0.000	0.000	0.000	0.000
130	A	129	ASP	-1	-0.818	-0.914	13.006	-22.035	-22.035	0.000	0.000	0.000	0.000
131	A	130	SER	0	0.006	0.003	12.685	0.900	0.900	0.000	0.000	0.000	0.000
132	A	131	GLY	0	0.011	0.027	10.297	-0.562	-0.562	0.000	0.000	0.000	0.000
134	A	133	THR	0	-0.008	-0.016	6.924	-0.966	-0.966	0.000	0.000	0.000	0.000
135	A	134	TYR	0	-0.018	-0.018	7.680	-0.197	-0.197	0.000	0.000	0.000	0.000
136	A	135	THR	0	-0.050	-0.014	11.867	1.593	1.593	0.000	0.000	0.000	0.000
137	A	136	TYR	0	-0.025	-0.019	14.810	0.109	0.109	0.000	0.000	0.000	0.000
138	A	137	ILE	0	-0.020	-0.016	18.417	0.101	0.101	0.000	0.000	0.000	0.000
139	A	138	ASP	-1	-0.839	-0.908	21.953	-11.998	-11.998	0.000	0.000	0.000	0.000
140	A	139	PRO	0	-0.062	-0.038	25.052	0.107	0.107	0.000	0.000	0.000	0.000
141	A	140	PHE	0	-0.015	-0.018	27.083	0.506	0.506	0.000	0.000	0.000	0.000
142	A	141	ILE	0	-0.015	0.039	27.715	-0.414	-0.414	0.000	0.000	0.000	0.000
143	A	142	SER	0	-0.003	-0.010	27.216	0.481	0.481	0.000	0.000	0.000	0.000
144	A	143	ASP	-1	-0.813	-0.929	29.842	-8.845	-8.845	0.000	0.000	0.000	0.000
145	A	144	GLY	0	-0.056	-0.027	29.358	0.112	0.112	0.000	0.000	0.000	0.000
146	A	145	ASP	-1	-0.750	-0.868	24.455	-12.130	-12.130	0.000	0.000	0.000	0.000
147	A	146	LYS	1	0.879	0.941	27.222	9.022	9.022	0.000	0.000	0.000	0.000
148	A	147	ARG	1	0.939	0.975	30.137	9.110	9.110	0.000	0.000	0.000	0.000
149	A	148	ARG	1	0.732	0.854	20.255	13.147	13.147	0.000	0.000	0.000	0.000
150	A	149	TRP	0	-0.055	-0.044	26.079	-0.280	-0.280	0.000	0.000	0.000	0.000
151	A	150	LEU	-1	-0.951	-0.952	29.125	-8.779	-8.779	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:0:HIS)