FMO DATABASE

FMODB ID: RL148

Calculation Name: 1M4Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1M4Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYZ1

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1660485.630253
FMO2-HF: Nuclear repulsion	1596564.659073
FMO2-HF: Total energy	-63920.97118
FMO2-MP2: Total energy	-64108.787616

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:THR)

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

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.
-106.079	-97.819	32.615	-17.381	-23.494	-0.145

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.750 / q_NPA : 0.871

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	3	ILE	0	0.001	0.006	2.943	1.740	3.785	0.181	-0.574	-1.652	-0.004
4	A	4	LEU	0	0.000	0.006	4.936	0.565	0.557	-0.001	-0.003	0.012	0.000
17	A	17	ASP	-1	-0.728	-0.843	2.121	-81.593	-79.886	7.224	-4.817	-4.114	-0.053
18	A	18	GLY	0	0.052	0.035	4.738	-0.481	-0.383	-0.001	-0.005	-0.091	0.000
19	A	19	GLN	0	-0.069	-0.043	4.174	5.001	5.111	-0.001	-0.015	-0.095	0.000
20	A	20	VAL	0	-0.018	-0.008	4.043	-5.556	-5.240	0.002	-0.041	-0.277	0.000
21	A	21	THR	0	0.027	0.002	4.509	2.251	2.301	-0.001	0.000	-0.049	0.000
33	A	33	LYS	1	0.779	0.879	1.977	54.585	53.222	8.102	-2.619	-4.120	0.027
47	A	47	ALA	0	-0.013	-0.007	2.301	-7.480	-6.588	1.296	-0.717	-1.471	-0.002
48	A	48	GLY	0	0.045	0.009	3.187	4.325	3.806	0.024	0.662	-0.166	-0.001
122	A	122	ILE	0	-0.017	0.003	4.349	1.232	1.362	-0.001	-0.011	-0.118	0.000
123	A	123	GLY	0	0.026	0.003	2.801	-6.873	-6.356	0.161	-0.238	-0.441	0.000
124	A	124	SER	0	0.018	-0.004	2.158	-11.740	-10.046	2.486	-1.756	-2.424	-0.025
125	A	125	GLY	0	0.031	0.000	3.402	8.625	9.104	0.001	-0.175	-0.306	0.000
126	A	126	GLY	0	0.014	0.013	5.119	6.579	6.680	-0.001	-0.008	-0.093	0.000
159	A	159	CYS	0	-0.089	-0.026	4.236	-5.084	-4.795	0.017	-0.136	-0.169	-0.001
161	A	161	TYR	0	-0.034	-0.014	2.563	-0.168	0.817	0.572	-0.615	-0.942	-0.003
162	A	162	THR	0	-0.070	-0.031	2.046	-59.645	-59.214	12.508	-6.211	-6.727	-0.082
163	A	163	ASN	0	0.028	0.021	3.204	8.622	8.928	0.047	-0.102	-0.251	-0.001
5	A	5	VAL	0	-0.034	-0.016	8.589	0.864	0.864	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.022	0.006	11.815	0.087	0.087	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.908	0.968	15.281	14.785	14.785	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.845	0.889	18.808	13.197	13.197	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.024	-0.012	22.062	0.124	0.124	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.022	0.020	24.604	0.264	0.264	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.011	0.022	20.045	-0.267	-0.267	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.009	-0.004	16.313	-0.300	-0.300	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.014	0.003	14.046	0.075	0.075	0.000	0.000	0.000	0.000
14	A	14	MET	0	-0.007	0.005	9.509	-1.157	-1.157	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.032	0.015	9.427	1.189	1.189	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.023	-0.010	5.432	-2.252	-2.252	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.006	0.009	6.768	-0.631	-0.631	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.035	0.020	9.900	1.972	1.972	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.000	-0.005	9.351	-2.725	-2.725	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.024	-0.005	11.040	0.622	0.622	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.018	-0.001	7.677	-2.388	-2.388	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.016	0.011	9.790	2.219	2.219	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.891	0.934	9.703	24.249	24.249	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.067	0.039	8.904	-3.015	-3.015	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.052	0.042	9.638	-1.394	-1.394	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.045	-0.024	6.716	2.302	2.302	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.853	0.912	7.861	18.483	18.483	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.034	0.022	6.253	-0.554	-0.554	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.921	0.951	8.956	19.136	19.136	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.899	0.971	12.654	14.511	14.511	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.027	-0.013	14.354	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.040	0.012	17.873	0.230	0.230	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.927	-0.967	21.338	-10.397	-10.397	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.015	-0.002	20.100	0.279	0.279	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.854	0.919	20.632	10.721	10.721	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.009	0.009	16.298	-0.070	-0.070	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.010	0.006	13.409	-0.388	-0.388	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.018	-0.005	11.793	0.072	0.072	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.049	0.014	7.776	-0.153	-0.153	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.050	-0.020	5.623	1.120	1.120	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.031	-0.029	5.821	-0.902	-0.902	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.059	0.013	8.486	0.235	0.235	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.031	0.022	10.073	1.086	1.086	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.780	-0.867	10.431	-20.479	-20.479	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.035	0.015	8.636	0.928	0.928	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.062	-0.028	10.765	0.738	0.738	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.020	0.008	13.979	1.034	1.034	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.009	-0.005	12.062	0.931	0.931	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.012	-0.016	9.433	0.491	0.491	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.897	-0.941	15.178	-13.982	-13.982	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.762	0.856	18.260	13.224	13.224	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.022	-0.003	15.931	0.537	0.537	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.794	-0.912	18.415	-13.176	-13.176	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.094	-0.043	20.616	0.641	0.641	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.852	0.934	21.498	12.058	12.058	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.004	-0.004	19.042	0.401	0.401	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.914	0.967	22.656	12.126	12.126	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.928	-0.961	26.270	-10.142	-10.142	0.000	0.000	0.000	0.000
67	A	67	TRP	0	-0.005	-0.023	25.659	0.462	0.462	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.018	0.012	27.427	-0.090	-0.090	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.010	-0.004	24.478	0.079	0.079	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.023	-0.009	23.988	-0.716	-0.716	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.048	0.035	17.265	-0.112	-0.112	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.049	0.019	20.518	-0.526	-0.526	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.800	0.902	22.044	10.363	10.363	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.038	0.014	21.437	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.006	0.007	17.953	-0.287	-0.287	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.021	0.006	19.373	-0.245	-0.245	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.805	-0.881	21.989	-10.830	-10.830	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.015	0.002	15.377	0.111	0.111	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.028	0.019	18.328	-0.228	-0.228	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.837	0.905	19.253	11.152	11.152	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.764	-0.850	21.393	-11.697	-11.697	0.000	0.000	0.000	0.000
82	A	82	TRP	0	-0.029	-0.019	11.466	0.319	0.319	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.863	0.962	19.149	14.628	14.628	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.045	-0.043	20.940	0.357	0.357	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.765	-0.865	22.011	-11.881	-11.881	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.927	0.943	22.410	11.440	11.440	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.051	-0.019	20.338	-0.130	-0.130	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.048	0.014	17.665	-0.534	-0.534	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.875	0.944	17.413	12.612	12.612	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.875	0.941	18.087	12.676	12.676	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.026	0.019	13.560	-0.395	-0.395	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.911	-0.964	11.427	-20.248	-20.248	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.098	-0.035	7.645	-1.948	-1.948	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.009	0.004	6.568	2.033	2.033	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.020	-0.013	6.727	-2.677	-2.677	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.004	-0.003	7.975	0.383	0.383	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.018	-0.011	9.658	-0.092	-0.092	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.015	0.000	12.954	0.117	0.117	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.785	-0.884	15.629	-13.180	-13.180	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.903	0.924	19.056	11.104	11.104	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.900	-0.934	21.556	-10.949	-10.949	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.059	-0.031	19.922	0.052	0.052	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.016	-0.024	13.613	-0.638	-0.638	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.000	-0.008	14.644	0.586	0.586	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.009	0.011	10.175	-1.343	-1.343	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.022	-0.009	11.527	1.498	1.498	0.000	0.000	0.000	0.000
107	A	107	SER	0	0.030	-0.001	11.609	-1.610	-1.610	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.088	0.052	13.402	1.232	1.232	0.000	0.000	0.000	0.000
109	A	109	ASN	0	-0.039	-0.055	15.314	1.763	1.763	0.000	0.000	0.000	0.000
110	A	110	GLY	0	-0.030	-0.016	17.478	0.826	0.826	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.949	-0.956	15.158	-15.924	-15.924	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.001	-0.021	16.256	-0.527	-0.527	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.002	0.006	14.827	0.720	0.720	0.000	0.000	0.000	0.000
114	A	114	GLN	0	0.062	0.039	15.394	-1.180	-1.180	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.070	-0.044	14.322	0.465	0.465	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.904	-0.942	17.598	-14.060	-14.060	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.811	-0.887	18.178	-15.315	-15.315	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.914	-0.933	18.314	-14.292	-14.292	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.022	-0.024	14.366	-0.606	-0.606	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.013	-0.005	12.246	0.334	0.334	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.002	0.002	7.660	-0.808	-0.808	0.000	0.000	0.000	0.000
127	A	127	PRO	0	0.018	-0.004	7.189	3.908	3.908	0.000	0.000	0.000	0.000
128	A	128	TYR	0	0.034	0.017	7.133	3.943	3.943	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.041	0.036	8.744	2.451	2.451	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.013	-0.005	10.593	2.818	2.818	0.000	0.000	0.000	0.000
131	A	131	ALA	0	-0.004	0.000	12.436	2.050	2.050	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.024	0.015	13.565	1.627	1.627	0.000	0.000	0.000	0.000
133	A	133	ALA	0	0.029	0.004	13.746	1.405	1.405	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.835	0.909	15.702	19.373	19.373	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.007	0.002	18.210	1.108	1.108	0.000	0.000	0.000	0.000
136	A	136	LEU	0	0.039	0.008	17.758	0.975	0.975	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.000	0.011	18.111	0.797	0.797	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.837	0.907	20.742	15.199	15.199	0.000	0.000	0.000	0.000
139	A	139	ASN	0	-0.071	-0.030	23.351	0.986	0.986	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.033	-0.022	22.996	0.140	0.140	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.883	-0.931	25.362	-11.579	-11.579	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.003	0.003	20.883	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	143	SER	0	0.062	0.033	21.660	-0.258	-0.258	0.000	0.000	0.000	0.000
144	A	144	ALA	0	0.051	0.015	17.862	-0.535	-0.535	0.000	0.000	0.000	0.000
145	A	145	ARG	1	0.782	0.877	16.294	15.722	15.722	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.848	-0.926	16.638	-16.047	-16.047	0.000	0.000	0.000	0.000
147	A	147	ILE	0	-0.035	-0.011	15.939	-0.744	-0.744	0.000	0.000	0.000	0.000
148	A	148	VAL	0	-0.005	-0.003	11.435	-1.470	-1.470	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-0.792	-0.886	12.542	-19.982	-19.982	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.868	0.945	13.175	14.632	14.632	0.000	0.000	0.000	0.000
151	A	151	ALA	0	0.017	0.007	12.905	-0.783	-0.783	0.000	0.000	0.000	0.000
152	A	152	MET	0	-0.057	-0.028	5.672	-3.224	-3.224	0.000	0.000	0.000	0.000
153	A	153	THR	0	-0.018	-0.018	8.866	-3.023	-3.023	0.000	0.000	0.000	0.000
154	A	154	ILE	0	0.045	0.026	10.698	-0.725	-0.725	0.000	0.000	0.000	0.000
155	A	155	ALA	0	-0.027	-0.017	6.560	-0.623	-0.623	0.000	0.000	0.000	0.000
156	A	156	GLY	0	-0.041	-0.032	6.072	-5.807	-5.807	0.000	0.000	0.000	0.000
157	A	157	GLU	-1	-0.998	-0.980	7.069	-20.371	-20.371	0.000	0.000	0.000	0.000
158	A	158	ILE	0	-0.027	-0.003	9.211	1.044	1.044	0.000	0.000	0.000	0.000
160	A	160	ILE	0	0.076	0.031	5.202	-5.435	-5.435	0.000	0.000	0.000	0.000
164	A	164	GLN	0	0.099	0.028	6.867	-3.628	-3.628	0.000	0.000	0.000	0.000
165	A	165	ASN	0	-0.110	-0.049	8.612	3.223	3.223	0.000	0.000	0.000	0.000
166	A	166	ILE	0	-0.026	-0.013	8.549	-2.248	-2.248	0.000	0.000	0.000	0.000
167	A	167	VAL	0	-0.033	-0.012	8.547	2.858	2.858	0.000	0.000	0.000	0.000
168	A	168	ILE	0	0.005	-0.015	9.564	-1.798	-1.798	0.000	0.000	0.000	0.000
169	A	169	GLU	-1	-0.866	-0.911	12.239	-16.590	-16.590	0.000	0.000	0.000	0.000
170	A	170	GLU	-1	-0.831	-0.923	14.415	-15.809	-15.809	0.000	0.000	0.000	0.000
171	A	171	VAL	-1	-0.877	-0.935	17.408	-13.320	-13.320	0.000	0.000	0.000	0.000

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