FMO DATABASE

FMODB ID: MZMJZ

Calculation Name: 5XMF-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XMF

Chain ID: B

ChEMBL ID:

UniProt ID: Q5MGS7

Base Structure: X-ray

Registration Date: 2025-10-06

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-757323.797325
FMO2-HF: Nuclear repulsion	715789.218203
FMO2-HF: Total energy	-41534.579122
FMO2-MP2: Total energy	-41652.847178

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1: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.
-43.676	-41.206	0.498	-0.731	-2.237	-0.002

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.916

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	B	3	GLN	0	0.008	0.008	2.498	0.459	2.901	0.499	-0.727	-2.214	-0.002
4	B	4	HIS	0	0.010	0.010	5.100	0.600	0.628	-0.001	-0.004	-0.023	0.000
5	B	5	SER	0	0.056	0.023	8.783	0.132	0.132	0.000	0.000	0.000	0.000
6	B	6	PRO	0	-0.016	0.012	11.323	0.624	0.624	0.000	0.000	0.000	0.000
7	B	7	LYS	1	0.941	0.969	14.686	16.402	16.402	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.006	-0.007	17.813	-0.013	-0.013	0.000	0.000	0.000	0.000
9	B	9	GLN	0	-0.022	-0.003	20.762	-0.022	-0.022	0.000	0.000	0.000	0.000
10	B	10	VAL	0	0.004	-0.009	24.499	-0.100	-0.100	0.000	0.000	0.000	0.000
11	B	11	TYR	0	0.045	0.022	26.602	0.026	0.026	0.000	0.000	0.000	0.000
12	B	12	SER	0	0.035	0.008	30.649	-0.080	-0.080	0.000	0.000	0.000	0.000
13	B	13	ARG	1	0.874	0.947	33.666	8.768	8.768	0.000	0.000	0.000	0.000
14	B	14	HIS	0	0.023	0.017	34.918	-0.009	-0.009	0.000	0.000	0.000	0.000
15	B	15	PRO	0	0.066	0.030	37.719	-0.122	-0.122	0.000	0.000	0.000	0.000
16	B	16	ALA	0	0.024	0.019	38.049	0.107	0.107	0.000	0.000	0.000	0.000
17	B	17	GLU	-1	-0.847	-0.907	40.010	-6.602	-6.602	0.000	0.000	0.000	0.000
18	B	18	ASN	0	0.019	0.008	42.616	-0.216	-0.216	0.000	0.000	0.000	0.000
19	B	19	GLY	0	-0.009	-0.004	44.103	0.160	0.160	0.000	0.000	0.000	0.000
20	B	20	LYS	1	0.823	0.902	44.236	6.711	6.711	0.000	0.000	0.000	0.000
21	B	21	PRO	0	-0.003	-0.002	41.841	-0.161	-0.161	0.000	0.000	0.000	0.000
22	B	22	ASN	0	-0.019	-0.006	37.620	-0.127	-0.127	0.000	0.000	0.000	0.000
23	B	23	PHE	0	0.002	-0.017	34.301	0.003	0.003	0.000	0.000	0.000	0.000
24	B	24	LEU	0	0.006	0.020	30.537	-0.036	-0.036	0.000	0.000	0.000	0.000
25	B	25	ASN	0	-0.016	-0.013	28.340	-0.135	-0.135	0.000	0.000	0.000	0.000
26	B	26	CYS	0	-0.015	-0.011	23.608	-0.161	-0.161	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.013	0.018	21.987	-0.414	-0.414	0.000	0.000	0.000	0.000
28	B	28	VAL	0	0.020	0.004	17.115	-0.193	-0.193	0.000	0.000	0.000	0.000
29	B	29	SER	0	0.001	-0.011	17.634	-0.210	-0.210	0.000	0.000	0.000	0.000
30	B	30	GLY	0	0.016	0.008	14.849	-0.038	-0.038	0.000	0.000	0.000	0.000
31	B	31	PHE	0	-0.011	0.002	11.468	-1.300	-1.300	0.000	0.000	0.000	0.000
32	B	32	HIS	0	0.027	0.013	7.416	-2.199	-2.199	0.000	0.000	0.000	0.000
33	B	33	PRO	0	0.012	0.007	5.558	-2.061	-2.061	0.000	0.000	0.000	0.000
34	B	34	PRO	0	0.016	0.002	8.290	1.402	1.402	0.000	0.000	0.000	0.000
35	B	35	GLN	0	-0.010	0.002	9.948	0.253	0.253	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.016	-0.016	12.054	-1.064	-1.064	0.000	0.000	0.000	0.000
37	B	37	ASP	-1	-0.879	-0.925	14.728	-13.329	-13.329	0.000	0.000	0.000	0.000
38	B	38	ILE	0	0.012	-0.004	18.021	-0.280	-0.280	0.000	0.000	0.000	0.000
39	B	39	THR	0	0.016	0.014	20.665	0.596	0.596	0.000	0.000	0.000	0.000
40	B	40	LEU	0	0.046	0.017	24.047	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	41	MET	0	-0.050	-0.034	25.152	0.192	0.192	0.000	0.000	0.000	0.000
42	B	42	LYS	1	0.898	0.951	29.600	7.957	7.957	0.000	0.000	0.000	0.000
43	B	43	ASN	0	-0.055	-0.043	33.344	-0.025	-0.025	0.000	0.000	0.000	0.000
44	B	44	GLY	0	0.008	0.009	30.631	0.104	0.104	0.000	0.000	0.000	0.000
45	B	45	LYS	1	0.922	0.959	30.645	8.126	8.126	0.000	0.000	0.000	0.000
46	B	46	LYS	1	0.864	0.924	26.384	10.653	10.653	0.000	0.000	0.000	0.000
47	B	47	MET	0	-0.033	-0.003	29.734	0.331	0.331	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.851	-0.912	29.514	-10.363	-10.363	0.000	0.000	0.000	0.000
49	B	49	ALA	0	-0.022	-0.020	27.972	0.224	0.224	0.000	0.000	0.000	0.000
50	B	50	GLU	-1	-0.914	-0.941	28.388	-9.743	-9.743	0.000	0.000	0.000	0.000
51	B	51	GLN	0	-0.015	-0.026	20.176	-0.324	-0.324	0.000	0.000	0.000	0.000
52	B	52	THR	0	-0.031	-0.005	23.004	0.182	0.182	0.000	0.000	0.000	0.000
53	B	53	ASP	-1	-0.878	-0.941	22.988	-12.524	-12.524	0.000	0.000	0.000	0.000
54	B	54	LEU	0	-0.060	-0.033	15.255	-0.248	-0.248	0.000	0.000	0.000	0.000
55	B	55	SER	0	0.008	0.006	19.278	-0.053	-0.053	0.000	0.000	0.000	0.000
56	B	56	PHE	0	-0.010	-0.014	15.118	-0.882	-0.882	0.000	0.000	0.000	0.000
57	B	57	ASN	0	-0.007	0.009	16.431	1.775	1.775	0.000	0.000	0.000	0.000
58	B	58	ARG	1	0.943	0.947	16.407	13.681	13.681	0.000	0.000	0.000	0.000
59	B	59	ASP	-1	-0.833	-0.883	13.704	-20.709	-20.709	0.000	0.000	0.000	0.000
60	B	60	TRP	0	-0.042	-0.028	11.037	-2.108	-2.108	0.000	0.000	0.000	0.000
61	B	61	THR	0	-0.084	-0.044	11.603	-0.296	-0.296	0.000	0.000	0.000	0.000
62	B	62	PHE	0	0.030	-0.007	10.757	1.489	1.489	0.000	0.000	0.000	0.000
63	B	63	TYR	0	-0.047	-0.029	15.024	0.099	0.099	0.000	0.000	0.000	0.000
64	B	64	LEU	0	-0.026	0.000	17.896	0.061	0.061	0.000	0.000	0.000	0.000
65	B	65	LEU	0	-0.012	-0.002	20.785	0.056	0.056	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.010	0.013	22.693	0.123	0.123	0.000	0.000	0.000	0.000
67	B	67	HIS	0	-0.030	-0.019	25.336	0.318	0.318	0.000	0.000	0.000	0.000
68	B	68	THR	0	0.029	0.012	29.149	0.091	0.091	0.000	0.000	0.000	0.000
69	B	69	GLU	-1	-0.931	-0.956	32.413	-7.863	-7.863	0.000	0.000	0.000	0.000
70	B	70	PHE	0	-0.037	-0.027	35.458	-0.047	-0.047	0.000	0.000	0.000	0.000
71	B	71	THR	0	0.007	0.002	37.532	0.200	0.200	0.000	0.000	0.000	0.000
72	B	72	PRO	0	-0.028	0.011	38.492	-0.036	-0.036	0.000	0.000	0.000	0.000
73	B	73	THR	0	0.009	-0.008	40.075	0.188	0.188	0.000	0.000	0.000	0.000
74	B	74	VAL	0	-0.041	-0.029	41.425	-0.109	-0.109	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.876	-0.947	41.693	-6.953	-6.953	0.000	0.000	0.000	0.000
76	B	76	ASP	-1	-0.868	-0.916	37.740	-7.780	-7.780	0.000	0.000	0.000	0.000
77	B	77	GLU	-1	-0.843	-0.912	33.920	-8.890	-8.890	0.000	0.000	0.000	0.000
78	B	78	TYR	0	0.019	0.004	32.520	-0.115	-0.115	0.000	0.000	0.000	0.000
79	B	79	SER	0	-0.037	-0.017	27.863	-0.122	-0.122	0.000	0.000	0.000	0.000
80	B	81	GLN	0	0.001	0.005	21.350	-0.105	-0.105	0.000	0.000	0.000	0.000
81	B	82	VAL	0	0.022	0.010	16.448	-0.103	-0.103	0.000	0.000	0.000	0.000
82	B	83	ASN	0	-0.013	-0.009	16.022	-0.460	-0.460	0.000	0.000	0.000	0.000
83	B	84	HIS	0	0.063	0.015	8.740	0.169	0.169	0.000	0.000	0.000	0.000
84	B	85	THR	0	-0.004	0.004	6.563	0.685	0.685	0.000	0.000	0.000	0.000
85	B	86	THR	0	-0.060	-0.049	6.887	-0.458	-0.458	0.000	0.000	0.000	0.000
86	B	87	LEU	0	-0.064	-0.019	8.973	0.570	0.570	0.000	0.000	0.000	0.000
87	B	88	SER	0	-0.014	-0.014	11.977	-0.083	-0.083	0.000	0.000	0.000	0.000
88	B	89	GLU	-1	-0.951	-0.966	13.736	-12.958	-12.958	0.000	0.000	0.000	0.000
89	B	90	PRO	0	-0.003	-0.001	16.690	-0.544	-0.544	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.968	0.991	17.356	14.790	14.790	0.000	0.000	0.000	0.000
91	B	92	VAL	0	-0.021	-0.014	19.295	0.167	0.167	0.000	0.000	0.000	0.000
92	B	93	VAL	0	-0.050	-0.022	22.285	-0.043	-0.043	0.000	0.000	0.000	0.000
93	B	94	LYS	1	0.915	0.941	25.045	9.517	9.517	0.000	0.000	0.000	0.000
94	B	95	TRP	0	-0.005	-0.010	28.675	-0.068	-0.068	0.000	0.000	0.000	0.000
95	B	96	ASP	-1	-0.840	-0.928	30.870	-8.682	-8.682	0.000	0.000	0.000	0.000
96	B	97	ARG	1	0.833	0.903	32.999	7.631	7.631	0.000	0.000	0.000	0.000
97	B	98	ASP	-1	-0.974	-0.978	35.576	-7.804	-7.804	0.000	0.000	0.000	0.000
98	B	99	MET	-1	-1.039	-1.001	30.753	-9.925	-9.925	0.000	0.000	0.000	0.000

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