FMO DATABASE

FMODB ID: 3ML6L

Calculation Name: 3ULP-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ULP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8I415

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-944411.246991
FMO2-HF: Nuclear repulsion	895936.081226
FMO2-HF: Total energy	-48475.165765
FMO2-MP2: Total energy	-48616.560129

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:77:MET)

Summations of interaction energy for fragment #1(A:77: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.
61.221	66.174	-0.042	-2.422	-2.49	-0.012

Interaction energy analysis for fragmet #1(A:77:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.888

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	79	GLU	-1	-0.849	-0.892	3.746	-32.417	-27.464	-0.042	-2.422	-2.490	-0.012
4	A	80	LYS	1	0.929	0.968	5.799	23.831	23.831	0.000	0.000	0.000	0.000
5	A	81	SER	0	0.041	0.030	7.309	3.207	3.207	0.000	0.000	0.000	0.000
6	A	82	LEU	0	-0.009	-0.020	9.657	1.352	1.352	0.000	0.000	0.000	0.000
7	A	83	ASN	0	-0.010	-0.013	10.813	1.232	1.232	0.000	0.000	0.000	0.000
8	A	84	LYS	1	0.919	0.963	13.749	15.922	15.922	0.000	0.000	0.000	0.000
9	A	85	ILE	0	-0.002	0.010	17.439	0.192	0.192	0.000	0.000	0.000	0.000
10	A	86	MET	0	0.004	-0.008	19.613	0.123	0.123	0.000	0.000	0.000	0.000
11	A	87	LEU	0	-0.016	-0.006	22.591	0.109	0.109	0.000	0.000	0.000	0.000
12	A	88	ILE	0	0.039	0.016	25.798	0.100	0.100	0.000	0.000	0.000	0.000
13	A	89	GLY	0	0.010	0.008	29.494	0.051	0.051	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.816	0.900	30.604	8.264	8.264	0.000	0.000	0.000	0.000
15	A	91	VAL	0	0.019	0.017	29.513	-0.254	-0.254	0.000	0.000	0.000	0.000
16	A	92	GLY	0	0.024	0.010	30.554	0.323	0.323	0.000	0.000	0.000	0.000
17	A	93	CYS	0	-0.156	-0.072	29.460	0.119	0.119	0.000	0.000	0.000	0.000
18	A	94	GLU	-1	-0.729	-0.875	32.096	-8.251	-8.251	0.000	0.000	0.000	0.000
19	A	95	PRO	0	-0.036	-0.016	28.287	-0.232	-0.232	0.000	0.000	0.000	0.000
20	A	96	ASP	-1	-0.891	-0.936	26.543	-9.842	-9.842	0.000	0.000	0.000	0.000
21	A	97	ILE	0	-0.011	-0.006	26.373	-0.487	-0.487	0.000	0.000	0.000	0.000
22	A	98	LYS	1	0.911	0.957	24.113	10.686	10.686	0.000	0.000	0.000	0.000
23	A	99	ILE	0	0.020	0.007	25.583	-0.190	-0.190	0.000	0.000	0.000	0.000
24	A	100	LEU	0	-0.031	-0.009	19.560	-0.070	-0.070	0.000	0.000	0.000	0.000
25	A	101	ASN	0	0.015	-0.011	22.630	0.606	0.606	0.000	0.000	0.000	0.000
26	A	102	GLY	0	-0.001	0.003	22.949	-0.396	-0.396	0.000	0.000	0.000	0.000
27	A	103	GLY	0	-0.011	-0.005	25.241	0.178	0.178	0.000	0.000	0.000	0.000
28	A	104	ASP	-1	-0.903	-0.931	21.103	-12.169	-12.169	0.000	0.000	0.000	0.000
29	A	105	LYS	1	0.876	0.921	23.939	9.559	9.559	0.000	0.000	0.000	0.000
30	A	106	VAL	0	-0.033	-0.009	19.815	-0.557	-0.557	0.000	0.000	0.000	0.000
31	A	107	ALA	0	0.025	0.034	22.670	0.459	0.459	0.000	0.000	0.000	0.000
32	A	108	THR	0	-0.085	-0.041	21.396	-0.607	-0.607	0.000	0.000	0.000	0.000
33	A	109	PHE	0	0.068	0.023	23.857	0.450	0.450	0.000	0.000	0.000	0.000
34	A	110	SER	0	0.004	-0.006	24.665	-0.334	-0.334	0.000	0.000	0.000	0.000
35	A	111	LEU	0	0.026	0.009	25.594	0.321	0.321	0.000	0.000	0.000	0.000
36	A	112	ALA	0	0.015	0.009	26.984	-0.329	-0.329	0.000	0.000	0.000	0.000
37	A	113	THR	0	0.029	0.019	27.331	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	114	ASN	0	-0.045	-0.040	29.812	0.105	0.105	0.000	0.000	0.000	0.000
39	A	115	GLU	-1	-0.863	-0.902	29.423	-10.291	-10.291	0.000	0.000	0.000	0.000
40	A	116	PHE	0	0.011	-0.021	32.736	0.228	0.228	0.000	0.000	0.000	0.000
41	A	117	TRP	0	-0.040	-0.007	33.344	-0.124	-0.124	0.000	0.000	0.000	0.000
42	A	118	ARG	1	0.933	0.956	37.065	7.357	7.357	0.000	0.000	0.000	0.000
43	A	119	ASP	-1	-0.803	-0.881	38.110	-8.259	-8.259	0.000	0.000	0.000	0.000
44	A	120	ARG	1	0.938	0.970	36.188	8.783	8.783	0.000	0.000	0.000	0.000
45	A	121	ASN	0	0.007	-0.002	38.466	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	122	THR	0	0.012	-0.010	41.530	0.192	0.192	0.000	0.000	0.000	0.000
47	A	123	ASN	0	-0.027	-0.003	42.461	0.095	0.095	0.000	0.000	0.000	0.000
48	A	124	GLU	-1	-0.837	-0.896	41.599	-7.427	-7.427	0.000	0.000	0.000	0.000
49	A	125	LEU	0	-0.039	-0.026	40.707	-0.177	-0.177	0.000	0.000	0.000	0.000
50	A	126	LYS	1	0.819	0.895	36.617	8.120	8.120	0.000	0.000	0.000	0.000
51	A	127	SER	0	0.001	-0.001	35.799	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	128	LYS	1	0.842	0.902	27.106	10.685	10.685	0.000	0.000	0.000	0.000
53	A	129	THR	0	0.005	0.005	31.092	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	130	ASP	-1	-0.866	-0.913	26.009	-11.112	-11.112	0.000	0.000	0.000	0.000
55	A	131	TRP	0	0.013	0.011	26.910	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	132	HIS	1	0.868	0.921	22.519	11.343	11.343	0.000	0.000	0.000	0.000
57	A	133	ARG	1	0.891	0.930	19.202	13.092	13.092	0.000	0.000	0.000	0.000
58	A	134	ILE	0	-0.009	0.001	20.276	-0.745	-0.745	0.000	0.000	0.000	0.000
59	A	135	VAL	0	0.003	-0.008	17.501	0.467	0.467	0.000	0.000	0.000	0.000
60	A	136	VAL	0	-0.028	-0.008	18.993	-0.606	-0.606	0.000	0.000	0.000	0.000
61	A	137	TYR	0	0.078	0.014	15.785	0.065	0.065	0.000	0.000	0.000	0.000
62	A	138	ASP	-1	-0.823	-0.912	19.612	-12.398	-12.398	0.000	0.000	0.000	0.000
63	A	139	GLN	0	0.063	0.011	21.437	0.778	0.778	0.000	0.000	0.000	0.000
64	A	140	ASN	0	0.006	0.011	24.338	0.731	0.731	0.000	0.000	0.000	0.000
65	A	141	ILE	0	-0.012	-0.003	22.935	0.348	0.348	0.000	0.000	0.000	0.000
66	A	142	VAL	0	-0.019	-0.015	23.521	0.314	0.314	0.000	0.000	0.000	0.000
67	A	143	ASP	-1	-0.833	-0.905	26.290	-8.809	-8.809	0.000	0.000	0.000	0.000
68	A	144	LEU	0	0.006	-0.005	29.307	0.377	0.377	0.000	0.000	0.000	0.000
69	A	145	ILE	0	-0.045	-0.025	25.795	0.246	0.246	0.000	0.000	0.000	0.000
70	A	146	ASP	-1	-0.869	-0.928	29.901	-8.708	-8.708	0.000	0.000	0.000	0.000
71	A	147	LYS	1	0.879	0.934	31.657	8.888	8.888	0.000	0.000	0.000	0.000
72	A	148	TYR	0	-0.015	-0.009	33.542	0.211	0.211	0.000	0.000	0.000	0.000
73	A	149	LEU	0	-0.086	-0.012	28.812	0.104	0.104	0.000	0.000	0.000	0.000
74	A	150	ARG	1	0.863	0.925	32.805	8.309	8.309	0.000	0.000	0.000	0.000
75	A	151	LYS	1	0.932	0.964	34.127	7.907	7.907	0.000	0.000	0.000	0.000
76	A	152	GLY	0	-0.020	-0.004	34.816	0.216	0.216	0.000	0.000	0.000	0.000
77	A	153	ARG	1	0.879	0.938	34.246	8.235	8.235	0.000	0.000	0.000	0.000
78	A	154	ARG	1	0.853	0.915	33.450	8.248	8.248	0.000	0.000	0.000	0.000
79	A	155	VAL	0	-0.003	0.000	28.568	0.052	0.052	0.000	0.000	0.000	0.000
80	A	156	TYR	0	0.023	0.008	25.620	-0.146	-0.146	0.000	0.000	0.000	0.000
81	A	157	VAL	0	-0.008	-0.007	22.667	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	158	GLN	0	-0.006	0.004	19.549	-0.191	-0.191	0.000	0.000	0.000	0.000
83	A	159	GLY	0	0.020	0.002	18.496	0.132	0.132	0.000	0.000	0.000	0.000
84	A	160	SER	0	-0.030	-0.010	13.020	-0.164	-0.164	0.000	0.000	0.000	0.000
85	A	161	LEU	0	0.000	0.001	14.553	0.658	0.658	0.000	0.000	0.000	0.000
86	A	162	HIS	0	-0.003	0.000	8.789	-0.993	-0.993	0.000	0.000	0.000	0.000
87	A	163	THR	0	0.004	-0.002	10.679	1.658	1.658	0.000	0.000	0.000	0.000
88	A	164	ARG	1	0.906	0.937	10.170	14.143	14.143	0.000	0.000	0.000	0.000
89	A	165	LYS	1	0.961	0.968	11.018	20.868	20.868	0.000	0.000	0.000	0.000
90	A	166	TRP	0	-0.034	-0.031	13.911	0.095	0.095	0.000	0.000	0.000	0.000
91	A	167	HIS	0	0.078	0.040	16.125	0.467	0.467	0.000	0.000	0.000	0.000
92	A	168	THR	0	0.090	0.042	19.997	0.506	0.506	0.000	0.000	0.000	0.000
93	A	169	ASN	0	-0.065	-0.042	19.093	0.037	0.037	0.000	0.000	0.000	0.000
94	A	170	ASP	-1	-0.796	-0.882	22.336	-11.027	-11.027	0.000	0.000	0.000	0.000
95	A	171	MET	0	-0.039	-0.012	24.135	0.336	0.336	0.000	0.000	0.000	0.000
96	A	172	ASN	0	-0.030	-0.014	21.437	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	173	SER	0	0.029	-0.001	22.557	-0.333	-0.333	0.000	0.000	0.000	0.000
98	A	174	GLN	0	-0.001	0.008	19.745	-0.267	-0.267	0.000	0.000	0.000	0.000
99	A	175	PRO	0	-0.031	-0.022	16.792	0.074	0.074	0.000	0.000	0.000	0.000
100	A	176	LYS	1	0.862	0.941	18.544	11.486	11.486	0.000	0.000	0.000	0.000
101	A	177	GLN	0	0.014	0.001	13.756	-1.726	-1.726	0.000	0.000	0.000	0.000
102	A	178	ILE	0	-0.071	-0.002	15.557	0.792	0.792	0.000	0.000	0.000	0.000
103	A	179	THR	0	0.021	0.004	15.005	-1.066	-1.066	0.000	0.000	0.000	0.000
104	A	180	GLU	-1	-0.789	-0.867	15.274	-14.028	-14.028	0.000	0.000	0.000	0.000
105	A	181	ILE	0	-0.009	-0.002	15.545	-0.953	-0.953	0.000	0.000	0.000	0.000
106	A	182	ILE	0	-0.010	-0.003	13.157	0.618	0.618	0.000	0.000	0.000	0.000
107	A	183	LEU	0	0.026	0.009	16.311	-0.466	-0.466	0.000	0.000	0.000	0.000
108	A	184	SER	0	0.010	-0.002	14.696	0.098	0.098	0.000	0.000	0.000	0.000
109	A	185	TYR	0	0.055	0.017	17.023	0.211	0.211	0.000	0.000	0.000	0.000
110	A	186	ASN	0	-0.054	-0.023	17.711	-0.510	-0.510	0.000	0.000	0.000	0.000
111	A	187	LYS	1	0.912	0.963	11.925	20.417	20.417	0.000	0.000	0.000	0.000
112	A	188	GLY	0	-0.016	0.000	18.194	-0.210	-0.210	0.000	0.000	0.000	0.000
113	A	189	ASP	-1	-0.858	-0.932	20.294	-11.183	-11.183	0.000	0.000	0.000	0.000
114	A	190	LEU	0	-0.035	-0.027	24.043	-0.169	-0.169	0.000	0.000	0.000	0.000
115	A	191	ILE	0	0.017	0.024	26.903	0.274	0.274	0.000	0.000	0.000	0.000
116	A	192	PHE	0	-0.011	-0.017	30.445	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	193	LEU	0	-0.028	-0.010	32.330	0.074	0.074	0.000	0.000	0.000	0.000
118	A	194	ASP	-2	-1.634	-1.787	35.489	-15.910	-15.910	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:77:MET)