FMO DATABASE

FMODB ID: Y1M42

Calculation Name: 4X09-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4X09

Chain ID: A

ChEMBL ID:

UniProt ID: Q93091

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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1141615.810096
FMO2-HF: Nuclear repulsion	1087977.262808
FMO2-HF: Total energy	-53638.547288
FMO2-MP2: Total energy	-53788.525504

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:0:MET)

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

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.
99.025	102.593	0.5	-1.723	-2.347	-0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.919

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

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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	PRO	0	0.041	0.017	2.911	-6.820	-3.678	0.499	-1.683	-1.959	-0.010
4	A	3	LYS	1	0.994	0.979	3.876	32.041	32.417	0.002	-0.039	-0.340	0.000
5	A	4	ARG	1	0.963	0.991	5.362	22.000	22.050	-0.001	-0.001	-0.048	0.000
6	A	5	LEU	0	-0.008	0.026	8.226	-0.312	-0.312	0.000	0.000	0.000	0.000
7	A	6	THR	0	-0.044	-0.057	10.418	1.077	1.077	0.000	0.000	0.000	0.000
8	A	7	LYS	1	0.912	0.933	14.126	14.698	14.698	0.000	0.000	0.000	0.000
9	A	8	ALA	0	0.053	0.041	16.622	-0.287	-0.287	0.000	0.000	0.000	0.000
10	A	9	HIS	0	0.011	0.009	10.258	-2.845	-2.845	0.000	0.000	0.000	0.000
11	A	10	TRP	0	-0.004	-0.008	8.922	-2.044	-2.044	0.000	0.000	0.000	0.000
12	A	11	PHE	0	-0.011	0.000	12.835	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.901	-0.969	13.770	-21.530	-21.530	0.000	0.000	0.000	0.000
14	A	13	ILE	0	-0.047	-0.019	8.081	-0.178	-0.178	0.000	0.000	0.000	0.000
15	A	14	GLN	0	-0.022	-0.005	11.513	-0.513	-0.513	0.000	0.000	0.000	0.000
16	A	15	HIS	0	-0.027	-0.014	13.681	0.911	0.911	0.000	0.000	0.000	0.000
17	A	16	ILE	0	-0.016	0.015	15.574	1.183	1.183	0.000	0.000	0.000	0.000
18	A	17	GLN	0	0.015	0.004	15.117	-0.616	-0.616	0.000	0.000	0.000	0.000
19	A	18	PRO	0	0.029	0.014	16.872	0.824	0.824	0.000	0.000	0.000	0.000
20	A	19	SER	0	-0.017	0.000	18.835	0.988	0.988	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.011	0.020	18.835	-0.934	-0.934	0.000	0.000	0.000	0.000
22	A	21	LEU	0	0.010	0.005	14.278	-0.260	-0.260	0.000	0.000	0.000	0.000
23	A	22	GLN	0	0.003	-0.004	17.517	-0.308	-0.308	0.000	0.000	0.000	0.000
24	A	23	CYS	0	0.028	0.011	16.525	-0.936	-0.936	0.000	0.000	0.000	0.000
25	A	24	ASN	0	0.053	0.017	15.621	-0.821	-0.821	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.938	0.982	12.410	18.988	18.988	0.000	0.000	0.000	0.000
27	A	26	ALA	0	0.024	0.031	11.511	-2.352	-2.352	0.000	0.000	0.000	0.000
28	A	27	MET	0	0.013	0.013	11.402	-1.551	-1.551	0.000	0.000	0.000	0.000
29	A	28	SER	0	-0.067	-0.030	9.875	-1.827	-1.827	0.000	0.000	0.000	0.000
30	A	29	GLY	0	0.040	0.018	6.554	-1.211	-1.211	0.000	0.000	0.000	0.000
31	A	30	ILE	0	0.026	0.010	7.297	-1.446	-1.446	0.000	0.000	0.000	0.000
32	A	31	ASN	0	0.038	0.011	9.877	0.887	0.887	0.000	0.000	0.000	0.000
33	A	32	ASN	0	-0.045	-0.020	5.739	-3.873	-3.873	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.047	-0.033	5.264	1.485	1.485	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.040	-0.033	7.849	2.183	2.183	0.000	0.000	0.000	0.000
36	A	35	GLN	0	-0.026	0.003	8.458	3.540	3.540	0.000	0.000	0.000	0.000
37	A	36	HIS	0	0.020	0.004	12.131	2.772	2.772	0.000	0.000	0.000	0.000
38	A	37	CYS	0	-0.064	-0.011	14.133	-0.179	-0.179	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.912	0.957	15.344	18.936	18.936	0.000	0.000	0.000	0.000
40	A	39	HIS	0	-0.011	-0.024	17.145	0.621	0.621	0.000	0.000	0.000	0.000
41	A	40	GLN	0	-0.068	-0.054	19.848	0.360	0.360	0.000	0.000	0.000	0.000
42	A	41	ASN	0	0.007	0.000	16.121	-0.545	-0.545	0.000	0.000	0.000	0.000
43	A	42	THR	0	0.072	0.057	19.016	0.105	0.105	0.000	0.000	0.000	0.000
44	A	43	PHE	0	-0.011	-0.005	13.836	-0.626	-0.626	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.052	0.015	19.209	0.853	0.853	0.000	0.000	0.000	0.000
46	A	45	HIS	0	-0.087	-0.032	20.095	-0.273	-0.273	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.765	-0.874	21.337	-12.236	-12.236	0.000	0.000	0.000	0.000
48	A	47	SER	0	-0.019	-0.014	19.940	-0.951	-0.951	0.000	0.000	0.000	0.000
49	A	48	PHE	0	0.051	0.009	17.559	0.514	0.514	0.000	0.000	0.000	0.000
50	A	49	GLN	0	0.004	0.009	19.698	0.061	0.061	0.000	0.000	0.000	0.000
51	A	50	ASN	0	-0.034	-0.027	22.657	0.649	0.649	0.000	0.000	0.000	0.000
52	A	51	VAL	0	-0.012	-0.014	21.827	0.387	0.387	0.000	0.000	0.000	0.000
53	A	52	ALA	0	-0.005	-0.009	22.315	0.252	0.252	0.000	0.000	0.000	0.000
54	A	53	ALA	0	0.006	0.011	24.223	0.390	0.390	0.000	0.000	0.000	0.000
55	A	54	VAL	0	-0.032	-0.014	27.036	0.502	0.502	0.000	0.000	0.000	0.000
56	A	55	CYS	0	-0.068	-0.039	24.125	-0.585	-0.585	0.000	0.000	0.000	0.000
57	A	56	ASP	-1	-0.930	-0.955	28.511	-10.682	-10.682	0.000	0.000	0.000	0.000
58	A	57	LEU	0	-0.068	-0.023	31.601	0.469	0.469	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.006	-0.006	33.568	-0.081	-0.081	0.000	0.000	0.000	0.000
60	A	59	SER	0	-0.018	0.013	33.470	-0.142	-0.142	0.000	0.000	0.000	0.000
61	A	60	ILE	0	-0.023	-0.026	32.660	0.360	0.360	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.046	-0.018	33.457	-0.254	-0.254	0.000	0.000	0.000	0.000
63	A	62	CYS	0	-0.007	0.028	28.822	-0.746	-0.746	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.892	0.910	27.955	11.416	11.416	0.000	0.000	0.000	0.000
65	A	64	ASN	0	-0.030	-0.024	27.552	0.475	0.475	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.913	0.953	31.068	9.019	9.019	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.884	0.960	26.271	11.519	11.519	0.000	0.000	0.000	0.000
68	A	67	HIS	0	0.014	-0.005	32.586	-0.146	-0.146	0.000	0.000	0.000	0.000
69	A	68	ASN	0	0.011	-0.007	27.076	0.356	0.356	0.000	0.000	0.000	0.000
70	A	70	HIS	0	0.032	0.012	28.766	0.214	0.214	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.024	-0.018	29.263	-0.250	-0.250	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.022	0.005	28.787	0.102	0.102	0.000	0.000	0.000	0.000
73	A	73	SER	0	0.023	0.004	30.677	0.218	0.218	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.951	0.971	32.249	9.594	9.594	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.008	0.032	31.358	-0.332	-0.332	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.013	-0.003	25.966	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.013	0.003	26.107	0.323	0.323	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.029	-0.007	23.477	-0.549	-0.549	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.001	-0.025	21.482	0.624	0.624	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.891	-0.920	21.642	-13.670	-13.670	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.966	0.970	20.623	11.884	11.884	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.034	-0.016	18.871	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.061	-0.037	21.768	0.630	0.630	0.000	0.000	0.000	0.000
84	A	85	SER	0	0.006	0.001	22.683	0.411	0.411	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.029	0.020	20.996	-0.649	-0.649	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.971	0.981	19.627	14.079	14.079	0.000	0.000	0.000	0.000
87	A	88	TYR	0	0.024	0.011	10.745	-0.790	-0.790	0.000	0.000	0.000	0.000
88	A	89	PRO	0	0.019	-0.010	12.445	0.692	0.692	0.000	0.000	0.000	0.000
89	A	90	GLN	0	-0.041	-0.010	14.347	-0.294	-0.294	0.000	0.000	0.000	0.000
90	A	92	ARG	1	0.946	0.979	17.216	13.771	13.771	0.000	0.000	0.000	0.000
91	A	93	TYR	0	-0.010	-0.018	16.172	0.035	0.035	0.000	0.000	0.000	0.000
92	A	94	SER	0	-0.028	0.005	20.902	0.372	0.372	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.015	-0.017	22.586	-0.529	-0.529	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.018	0.015	24.017	0.510	0.510	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.012	0.015	25.892	-0.321	-0.321	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.022	-0.022	26.658	0.208	0.208	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.014	0.008	28.074	-0.182	-0.182	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.852	0.910	29.091	9.885	9.885	0.000	0.000	0.000	0.000
99	A	101	PHE	0	0.035	0.029	29.655	-0.222	-0.222	0.000	0.000	0.000	0.000
100	A	102	PHE	0	0.024	0.000	26.076	-0.235	-0.235	0.000	0.000	0.000	0.000
101	A	103	ILE	0	0.009	0.015	27.847	0.248	0.248	0.000	0.000	0.000	0.000
102	A	104	VAL	0	0.005	-0.001	23.310	-0.432	-0.432	0.000	0.000	0.000	0.000
103	A	105	ALA	0	0.039	0.015	24.805	0.475	0.475	0.000	0.000	0.000	0.000
104	A	107	ASP	-1	-0.818	-0.889	23.273	-12.075	-12.075	0.000	0.000	0.000	0.000
105	A	108	PRO	0	0.026	0.006	24.499	-0.233	-0.233	0.000	0.000	0.000	0.000
106	A	109	PRO	0	-0.017	0.016	21.309	-0.442	-0.442	0.000	0.000	0.000	0.000
107	A	110	GLN	0	-0.001	-0.021	17.101	-0.250	-0.250	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.938	0.945	18.699	12.827	12.827	0.000	0.000	0.000	0.000
109	A	112	SER	0	0.012	0.015	14.085	0.314	0.314	0.000	0.000	0.000	0.000
110	A	113	ASP	-1	-0.785	-0.849	15.491	-19.731	-19.731	0.000	0.000	0.000	0.000
111	A	114	PRO	0	0.019	0.011	17.183	0.611	0.611	0.000	0.000	0.000	0.000
112	A	115	PRO	0	-0.004	0.001	19.828	0.331	0.331	0.000	0.000	0.000	0.000
113	A	116	TYR	0	0.020	0.003	21.016	0.730	0.730	0.000	0.000	0.000	0.000
114	A	117	LYS	1	0.968	0.984	25.417	9.880	9.880	0.000	0.000	0.000	0.000
115	A	118	LEU	0	-0.041	-0.025	26.123	0.122	0.122	0.000	0.000	0.000	0.000
116	A	119	VAL	0	0.006	0.010	20.684	-0.282	-0.282	0.000	0.000	0.000	0.000
117	A	120	PRO	0	0.040	0.023	20.419	0.286	0.286	0.000	0.000	0.000	0.000
118	A	121	VAL	0	-0.060	-0.043	19.599	-0.993	-0.993	0.000	0.000	0.000	0.000
119	A	122	HIS	0	0.015	-0.001	19.637	-0.548	-0.548	0.000	0.000	0.000	0.000
120	A	123	LEU	0	0.053	0.041	21.240	0.424	0.424	0.000	0.000	0.000	0.000
121	A	124	ASP	-1	-0.820	-0.872	22.946	-10.916	-10.916	0.000	0.000	0.000	0.000
122	A	125	SER	0	-0.060	-0.070	26.289	0.252	0.252	0.000	0.000	0.000	0.000
123	A	126	ILE	0	0.004	0.005	25.788	-0.297	-0.297	0.000	0.000	0.000	0.000
124	A	127	LEU	-1	-0.808	-0.873	28.825	-9.452	-9.452	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)