FMO DATABASE

FMODB ID: 97ML2

Calculation Name: 3N1F-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3N1F

Chain ID: A

ChEMBL ID:

UniProt ID: Q4KMG0

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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1550311.425776
FMO2-HF: Nuclear repulsion	1489752.048607
FMO2-HF: Total energy	-60559.377169
FMO2-MP2: Total energy	-60736.93091

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:43:LYS)

Summations of interaction energy for fragment #1(A:43:LYS)

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.
-44.247	-42.545	-0.002	-0.67	-1.029	-0.001

Interaction energy analysis for fragmet #1(A:43:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.835 / q_NPA : 1.903

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	45	VAL	0	0.030	0.026	3.705	-3.251	-1.707	-0.001	-0.667	-0.875	-0.001
130	A	172	GLU	-1	-0.922	-0.962	5.022	-83.981	-83.823	-0.001	-0.003	-0.154	0.000
4	A	46	PRO	0	-0.006	0.003	5.764	3.301	3.301	0.000	0.000	0.000	0.000
5	A	47	LEU	0	-0.012	0.000	9.220	0.592	0.592	0.000	0.000	0.000	0.000
6	A	48	ALA	0	0.044	0.012	12.435	1.320	1.320	0.000	0.000	0.000	0.000
7	A	49	TYR	0	0.005	-0.020	15.035	0.825	0.825	0.000	0.000	0.000	0.000
8	A	50	LYS	1	0.817	0.895	18.574	24.954	24.954	0.000	0.000	0.000	0.000
9	A	51	GLN	0	0.035	0.041	12.226	0.137	0.137	0.000	0.000	0.000	0.000
10	A	52	PHE	0	-0.011	-0.006	16.313	-0.084	-0.084	0.000	0.000	0.000	0.000
11	A	53	SER	0	-0.038	-0.009	11.597	-2.141	-2.141	0.000	0.000	0.000	0.000
12	A	54	PRO	0	0.076	0.026	13.800	-0.185	-0.185	0.000	0.000	0.000	0.000
13	A	55	ASN	0	-0.017	-0.003	14.737	1.987	1.987	0.000	0.000	0.000	0.000
14	A	56	VAL	0	-0.008	-0.008	16.865	1.194	1.194	0.000	0.000	0.000	0.000
15	A	57	PRO	0	0.044	0.011	20.112	-0.506	-0.506	0.000	0.000	0.000	0.000
16	A	58	GLU	-1	-0.748	-0.822	21.347	-25.602	-25.602	0.000	0.000	0.000	0.000
17	A	59	LYS	1	0.913	0.948	22.401	20.652	20.652	0.000	0.000	0.000	0.000
18	A	60	THR	0	-0.074	-0.041	22.261	0.480	0.480	0.000	0.000	0.000	0.000
19	A	61	LEU	0	0.042	0.003	22.900	-0.580	-0.580	0.000	0.000	0.000	0.000
20	A	62	GLY	0	-0.016	0.002	19.460	-0.553	-0.553	0.000	0.000	0.000	0.000
21	A	63	ALA	0	-0.013	0.014	18.174	-1.670	-1.670	0.000	0.000	0.000	0.000
22	A	64	SER	0	0.015	-0.005	19.555	-0.292	-0.292	0.000	0.000	0.000	0.000
23	A	65	GLY	0	0.002	0.027	21.660	0.853	0.853	0.000	0.000	0.000	0.000
24	A	66	ARG	1	0.965	0.962	24.759	19.965	19.965	0.000	0.000	0.000	0.000
25	A	67	TYR	0	0.056	0.038	28.420	-0.318	-0.318	0.000	0.000	0.000	0.000
26	A	68	GLU	-1	-0.900	-0.927	29.628	-20.015	-20.015	0.000	0.000	0.000	0.000
27	A	69	GLY	0	-0.024	-0.004	32.915	0.579	0.579	0.000	0.000	0.000	0.000
28	A	70	LYS	1	0.862	0.934	34.343	16.839	16.839	0.000	0.000	0.000	0.000
29	A	71	ILE	0	-0.006	0.024	32.382	0.478	0.478	0.000	0.000	0.000	0.000
30	A	72	ALA	0	0.028	0.007	36.054	-0.126	-0.126	0.000	0.000	0.000	0.000
31	A	73	ARG	1	0.847	0.898	37.090	16.517	16.517	0.000	0.000	0.000	0.000
32	A	74	SER	0	-0.030	-0.008	39.700	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	75	SER	0	-0.046	-0.029	38.970	0.165	0.165	0.000	0.000	0.000	0.000
34	A	76	GLU	-1	-0.890	-0.959	40.027	-14.705	-14.705	0.000	0.000	0.000	0.000
35	A	77	ARG	1	0.881	0.921	32.134	18.293	18.293	0.000	0.000	0.000	0.000
36	A	78	PHE	0	-0.020	-0.002	35.240	-0.547	-0.547	0.000	0.000	0.000	0.000
37	A	79	LYS	1	0.932	0.968	35.487	15.637	15.637	0.000	0.000	0.000	0.000
38	A	80	GLU	-1	-0.851	-0.914	31.486	-18.766	-18.766	0.000	0.000	0.000	0.000
39	A	81	LEU	0	-0.043	-0.002	29.854	-0.890	-0.890	0.000	0.000	0.000	0.000
40	A	82	THR	0	0.008	-0.004	29.027	0.334	0.334	0.000	0.000	0.000	0.000
41	A	83	PRO	0	0.021	0.010	29.304	-0.648	-0.648	0.000	0.000	0.000	0.000
42	A	84	ASN	0	-0.031	-0.014	23.044	0.225	0.225	0.000	0.000	0.000	0.000
43	A	85	TYR	0	0.019	-0.007	27.509	0.318	0.318	0.000	0.000	0.000	0.000
44	A	86	ASN	0	-0.002	0.012	21.161	0.946	0.946	0.000	0.000	0.000	0.000
45	A	87	PRO	0	0.035	0.016	25.488	-0.134	-0.134	0.000	0.000	0.000	0.000
46	A	88	ASP	-1	-0.852	-0.918	20.563	-28.630	-28.630	0.000	0.000	0.000	0.000
47	A	89	ILE	0	-0.091	-0.051	21.111	-0.996	-0.996	0.000	0.000	0.000	0.000
48	A	90	ILE	0	-0.075	-0.032	23.537	1.138	1.138	0.000	0.000	0.000	0.000
49	A	91	PHE	0	0.014	-0.010	25.199	-0.809	-0.809	0.000	0.000	0.000	0.000
50	A	92	LYS	1	0.743	0.873	28.039	20.065	20.065	0.000	0.000	0.000	0.000
51	A	93	ASP	-1	-0.810	-0.914	30.130	-17.573	-17.573	0.000	0.000	0.000	0.000
52	A	94	GLU	-1	-0.796	-0.881	32.536	-19.104	-19.104	0.000	0.000	0.000	0.000
53	A	95	GLU	0	0.003	0.001	32.316	0.580	0.580	0.000	0.000	0.000	0.000
54	A	96	ASN	0	-0.104	-0.042	36.610	0.566	0.566	0.000	0.000	0.000	0.000
55	A	97	THR	0	-0.022	-0.009	36.746	0.265	0.265	0.000	0.000	0.000	0.000
56	A	98	GLY	0	-0.021	-0.018	33.844	0.065	0.065	0.000	0.000	0.000	0.000
57	A	99	ALA	0	0.005	0.008	32.641	-0.525	-0.525	0.000	0.000	0.000	0.000
58	A	100	ASP	-1	-0.737	-0.880	28.486	-21.568	-21.568	0.000	0.000	0.000	0.000
59	A	101	ARG	1	0.836	0.914	27.731	19.883	19.883	0.000	0.000	0.000	0.000
60	A	102	LEU	0	-0.024	0.000	28.644	-0.318	-0.318	0.000	0.000	0.000	0.000
61	A	103	MET	0	-0.011	-0.005	24.490	-0.935	-0.935	0.000	0.000	0.000	0.000
62	A	104	THR	0	0.023	0.002	25.300	0.332	0.332	0.000	0.000	0.000	0.000
63	A	105	GLN	0	-0.048	-0.030	23.420	0.176	0.176	0.000	0.000	0.000	0.000
64	A	106	ARG	1	0.862	0.893	18.357	28.109	28.109	0.000	0.000	0.000	0.000
65	A	107	CYS	0	0.003	-0.001	20.297	-1.863	-1.863	0.000	0.000	0.000	0.000
66	A	108	LYS	1	0.867	0.922	20.590	21.258	21.258	0.000	0.000	0.000	0.000
67	A	109	ASP	-1	-0.858	-0.922	19.025	-28.421	-28.421	0.000	0.000	0.000	0.000
68	A	110	ARG	1	0.841	0.949	15.387	31.748	31.748	0.000	0.000	0.000	0.000
69	A	111	LEU	0	0.029	0.015	16.168	-1.855	-1.855	0.000	0.000	0.000	0.000
70	A	112	ASN	0	0.030	0.006	18.182	-0.167	-0.167	0.000	0.000	0.000	0.000
71	A	113	SER	0	-0.011	-0.009	13.525	-0.882	-0.882	0.000	0.000	0.000	0.000
72	A	114	LEU	0	-0.033	-0.005	13.170	-2.398	-2.398	0.000	0.000	0.000	0.000
73	A	115	ALA	0	0.001	0.007	14.572	-1.421	-1.421	0.000	0.000	0.000	0.000
74	A	116	ILE	0	0.058	0.032	14.101	-0.583	-0.583	0.000	0.000	0.000	0.000
75	A	117	SER	0	-0.073	-0.043	10.444	-2.115	-2.115	0.000	0.000	0.000	0.000
76	A	118	VAL	0	-0.011	-0.022	12.130	-1.825	-1.825	0.000	0.000	0.000	0.000
77	A	119	MET	0	-0.005	-0.001	14.331	0.264	0.264	0.000	0.000	0.000	0.000
78	A	120	ASN	0	-0.035	-0.008	12.196	2.155	2.155	0.000	0.000	0.000	0.000
79	A	121	GLN	0	-0.078	-0.026	8.039	-6.946	-6.946	0.000	0.000	0.000	0.000
80	A	122	TRP	0	-0.017	-0.029	11.597	-0.318	-0.318	0.000	0.000	0.000	0.000
81	A	123	PRO	0	0.084	0.037	14.714	1.708	1.708	0.000	0.000	0.000	0.000
82	A	124	GLY	0	0.000	0.010	17.751	1.013	1.013	0.000	0.000	0.000	0.000
83	A	125	VAL	0	-0.087	-0.031	17.582	1.335	1.335	0.000	0.000	0.000	0.000
84	A	126	LYS	1	0.906	0.934	18.798	24.441	24.441	0.000	0.000	0.000	0.000
85	A	127	LEU	0	0.027	0.012	17.641	-0.297	-0.297	0.000	0.000	0.000	0.000
86	A	128	ARG	1	0.884	0.937	19.801	25.245	25.245	0.000	0.000	0.000	0.000
87	A	129	VAL	0	0.027	0.019	22.606	-0.843	-0.843	0.000	0.000	0.000	0.000
88	A	130	THR	0	-0.100	-0.081	24.507	0.515	0.515	0.000	0.000	0.000	0.000
89	A	131	GLU	-1	-0.714	-0.821	26.129	-19.415	-19.415	0.000	0.000	0.000	0.000
90	A	132	GLY	0	0.005	0.005	26.085	-1.171	-1.171	0.000	0.000	0.000	0.000
91	A	133	TRP	0	-0.051	-0.024	27.685	-0.070	-0.070	0.000	0.000	0.000	0.000
92	A	134	ASP	-1	-0.814	-0.914	30.235	-18.325	-18.325	0.000	0.000	0.000	0.000
93	A	135	GLU	-1	-0.822	-0.896	32.771	-16.277	-16.277	0.000	0.000	0.000	0.000
94	A	136	ASP	-1	-0.920	-0.957	35.634	-16.649	-16.649	0.000	0.000	0.000	0.000
95	A	137	GLY	0	-0.075	-0.037	35.481	0.375	0.375	0.000	0.000	0.000	0.000
96	A	138	HIS	0	-0.042	-0.025	30.841	0.141	0.141	0.000	0.000	0.000	0.000
97	A	139	HIS	1	0.796	0.893	27.949	20.725	20.725	0.000	0.000	0.000	0.000
98	A	140	SER	0	0.014	-0.001	28.678	0.543	0.543	0.000	0.000	0.000	0.000
99	A	141	GLU	-1	-0.871	-0.950	31.640	-16.623	-16.623	0.000	0.000	0.000	0.000
100	A	142	GLU	-1	-0.953	-0.993	31.872	-19.002	-19.002	0.000	0.000	0.000	0.000
101	A	143	SER	0	0.014	0.031	28.886	-1.047	-1.047	0.000	0.000	0.000	0.000
102	A	144	LEU	0	0.039	0.009	24.179	0.406	0.406	0.000	0.000	0.000	0.000
103	A	145	HIS	0	-0.025	-0.022	25.505	-0.616	-0.616	0.000	0.000	0.000	0.000
104	A	146	TYR	0	-0.035	-0.019	28.700	0.385	0.385	0.000	0.000	0.000	0.000
105	A	147	GLU	-1	-0.741	-0.875	29.078	-19.857	-19.857	0.000	0.000	0.000	0.000
106	A	148	GLY	0	0.019	0.011	28.393	-0.257	-0.257	0.000	0.000	0.000	0.000
107	A	149	ARG	1	0.806	0.901	24.977	22.230	22.230	0.000	0.000	0.000	0.000
108	A	150	ALA	0	-0.034	-0.036	23.012	-1.262	-1.262	0.000	0.000	0.000	0.000
109	A	151	VAL	0	0.004	0.014	20.760	0.685	0.685	0.000	0.000	0.000	0.000
110	A	152	ASP	-1	-0.828	-0.893	22.014	-25.796	-25.796	0.000	0.000	0.000	0.000
111	A	153	ILE	0	0.000	-0.007	17.022	0.363	0.363	0.000	0.000	0.000	0.000
112	A	154	THR	0	-0.039	-0.026	20.169	0.171	0.171	0.000	0.000	0.000	0.000
113	A	155	THR	0	0.037	0.003	16.543	-0.522	-0.522	0.000	0.000	0.000	0.000
114	A	156	SER	0	0.024	0.024	19.495	0.988	0.988	0.000	0.000	0.000	0.000
115	A	157	ASP	-1	-0.771	-0.863	19.728	-28.704	-28.704	0.000	0.000	0.000	0.000
116	A	158	ARG	1	0.864	0.929	22.053	23.884	23.884	0.000	0.000	0.000	0.000
117	A	159	ASP	-1	-0.790	-0.874	18.180	-30.482	-30.482	0.000	0.000	0.000	0.000
118	A	160	ARG	1	0.981	0.982	18.607	22.580	22.580	0.000	0.000	0.000	0.000
119	A	161	ASN	0	-0.055	-0.026	16.126	-1.283	-1.283	0.000	0.000	0.000	0.000
120	A	162	LYS	1	0.791	0.888	14.086	30.088	30.088	0.000	0.000	0.000	0.000
121	A	163	TYR	0	-0.004	0.004	14.039	-2.278	-2.278	0.000	0.000	0.000	0.000
122	A	164	GLY	0	0.086	0.045	13.227	-0.724	-0.724	0.000	0.000	0.000	0.000
123	A	165	LEU	0	-0.034	-0.021	6.936	-3.168	-3.168	0.000	0.000	0.000	0.000
124	A	166	LEU	0	0.022	0.017	10.843	-2.970	-2.970	0.000	0.000	0.000	0.000
125	A	167	ALA	0	0.023	0.010	13.210	-0.319	-0.319	0.000	0.000	0.000	0.000
126	A	168	ARG	1	0.831	0.905	5.444	65.843	65.843	0.000	0.000	0.000	0.000
127	A	169	LEU	0	-0.001	-0.011	8.073	-2.727	-2.727	0.000	0.000	0.000	0.000
128	A	170	ALA	0	0.028	0.017	10.230	0.323	0.323	0.000	0.000	0.000	0.000
129	A	171	VAL	0	-0.019	-0.009	9.080	1.604	1.604	0.000	0.000	0.000	0.000
131	A	173	ALA	0	-0.044	-0.007	8.264	0.556	0.556	0.000	0.000	0.000	0.000
132	A	174	GLY	0	0.023	0.010	11.388	3.216	3.216	0.000	0.000	0.000	0.000
133	A	175	PHE	0	-0.022	-0.023	13.001	2.922	2.922	0.000	0.000	0.000	0.000
134	A	176	ASP	-1	-0.783	-0.845	14.670	-33.450	-33.450	0.000	0.000	0.000	0.000
135	A	177	TRP	0	-0.035	-0.030	16.543	0.246	0.246	0.000	0.000	0.000	0.000
136	A	178	VAL	0	0.004	0.012	13.721	0.565	0.565	0.000	0.000	0.000	0.000
137	A	179	TYR	0	0.044	0.022	16.165	-0.385	-0.385	0.000	0.000	0.000	0.000
138	A	180	TYR	0	-0.008	0.013	15.713	1.470	1.470	0.000	0.000	0.000	0.000
139	A	181	GLU	-1	-0.872	-0.932	18.444	-23.690	-23.690	0.000	0.000	0.000	0.000
140	A	182	SER	0	0.046	0.033	22.152	1.302	1.302	0.000	0.000	0.000	0.000
141	A	183	LYS	1	0.929	0.954	21.778	23.303	23.303	0.000	0.000	0.000	0.000
142	A	184	ALA	0	-0.055	-0.038	22.745	-0.202	-0.202	0.000	0.000	0.000	0.000
143	A	185	HIS	0	0.007	-0.008	22.263	0.270	0.270	0.000	0.000	0.000	0.000
144	A	186	VAL	0	-0.018	-0.005	16.198	-0.260	-0.260	0.000	0.000	0.000	0.000
145	A	187	HIS	1	0.817	0.902	19.541	26.675	26.675	0.000	0.000	0.000	0.000
146	A	188	CYS	0	-0.061	-0.030	17.415	-2.440	-2.440	0.000	0.000	0.000	0.000
147	A	189	SER	0	0.008	-0.020	18.905	1.107	1.107	0.000	0.000	0.000	0.000
148	A	190	VAL	0	-0.005	-0.009	18.900	-1.977	-1.977	0.000	0.000	0.000	0.000
149	A	191	LYS	1	0.797	0.883	18.704	30.774	30.774	0.000	0.000	0.000	0.000
150	A	192	SER	0	-0.030	-0.044	22.768	-0.477	-0.477	0.000	0.000	0.000	0.000
151	A	193	GLU	-2	-1.759	-1.854	24.645	-47.613	-47.613	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:43:LYS)