FMO DATABASE

FMODB ID: 1NK5Z

Calculation Name: 3LFJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LFJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RD54

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1761105.819718
FMO2-HF: Nuclear repulsion	1694288.243333
FMO2-HF: Total energy	-66817.576385
FMO2-MP2: Total energy	-67010.821219

3D Structure

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:SER)

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

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.
-15.672	-10.387	4.253	-4.232	-5.307	-0.033

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.014

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	1	MET	0	0.024	0.026	3.312	-4.061	-2.093	0.052	-0.934	-1.086	0.000
4	A	2	TRP	0	-0.040	-0.019	5.945	0.187	0.187	0.000	0.000	0.000	0.000
5	A	3	LYS	1	0.850	0.913	5.317	2.027	2.027	0.000	0.000	0.000	0.000
6	A	4	ILE	0	0.006	-0.002	6.663	0.101	0.101	0.000	0.000	0.000	0.000
7	A	5	VAL	0	-0.058	-0.027	10.188	0.106	0.106	0.000	0.000	0.000	0.000
8	A	6	PHE	0	-0.009	-0.007	12.504	0.117	0.117	0.000	0.000	0.000	0.000
9	A	7	ALA	0	0.022	0.024	15.225	-0.061	-0.061	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.803	0.910	17.549	0.265	0.265	0.000	0.000	0.000	0.000
11	A	9	ILE	0	-0.001	0.010	21.203	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.792	-0.893	24.012	-0.183	-0.183	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.833	-0.904	26.731	-0.144	-0.144	0.000	0.000	0.000	0.000
14	A	12	ARG	1	0.844	0.916	29.128	0.160	0.160	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.030	-0.014	23.839	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	14	ILE	0	-0.021	0.008	22.749	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	15	HIS	0	0.015	-0.004	26.723	0.024	0.024	0.000	0.000	0.000	0.000
18	A	16	GLY	0	0.018	0.000	30.035	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	17	GLN	0	0.044	0.007	30.067	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	18	VAL	0	-0.008	0.011	26.678	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	19	MET	0	0.079	0.029	20.692	0.003	0.003	0.000	0.000	0.000	0.000
22	A	20	THR	0	0.000	0.000	23.803	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	21	ARG	1	0.891	0.939	25.259	0.181	0.181	0.000	0.000	0.000	0.000
24	A	22	TRP	0	0.007	-0.008	21.896	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	23	MET	0	0.006	0.011	16.992	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	24	LYS	1	0.923	0.973	20.454	0.246	0.246	0.000	0.000	0.000	0.000
27	A	25	GLY	0	-0.005	0.013	20.873	0.002	0.002	0.000	0.000	0.000	0.000
28	A	26	PHE	0	-0.058	-0.043	15.469	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	27	PRO	0	0.004	0.000	17.183	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	28	GLU	-1	-0.914	-0.954	13.423	-0.836	-0.836	0.000	0.000	0.000	0.000
31	A	29	ALA	0	-0.096	-0.034	13.349	-0.144	-0.144	0.000	0.000	0.000	0.000
32	A	30	SER	0	-0.052	-0.039	13.601	0.122	0.122	0.000	0.000	0.000	0.000
33	A	31	ILE	0	0.027	0.000	15.263	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	32	VAL	0	-0.019	-0.009	13.398	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	33	ILE	0	-0.006	-0.003	16.643	0.039	0.039	0.000	0.000	0.000	0.000
36	A	34	ILE	0	-0.023	-0.010	15.117	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	35	ASP	-1	-0.834	-0.945	19.646	-0.157	-0.157	0.000	0.000	0.000	0.000
38	A	36	ASP	-1	-0.778	-0.868	23.248	-0.166	-0.166	0.000	0.000	0.000	0.000
39	A	37	GLU	-1	-0.883	-0.924	25.147	-0.126	-0.126	0.000	0.000	0.000	0.000
40	A	38	LEU	0	-0.012	-0.017	24.048	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	39	ALA	0	-0.020	-0.008	23.201	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	40	VAL	0	-0.007	-0.002	24.838	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	41	ASP	-1	-0.852	-0.906	28.224	-0.163	-0.163	0.000	0.000	0.000	0.000
44	A	42	GLU	-1	-0.811	-0.926	28.467	-0.251	-0.251	0.000	0.000	0.000	0.000
45	A	43	PHE	0	-0.038	-0.004	30.331	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	44	MET	0	0.016	-0.009	29.768	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	45	LYS	1	0.796	0.898	24.921	0.237	0.237	0.000	0.000	0.000	0.000
48	A	46	ASN	0	0.001	0.014	26.984	-0.033	-0.033	0.000	0.000	0.000	0.000
49	A	47	ILE	0	-0.013	-0.005	29.417	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	48	TYR	0	-0.001	-0.023	25.691	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	49	THR	0	-0.039	-0.032	24.361	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	50	MET	0	-0.064	-0.031	25.999	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	51	ALA	0	-0.052	-0.007	28.509	0.006	0.006	0.000	0.000	0.000	0.000
54	A	52	ALA	0	-0.024	0.003	23.572	0.000	0.000	0.000	0.000	0.000	0.000
55	A	53	PRO	0	-0.023	-0.008	23.046	0.018	0.018	0.000	0.000	0.000	0.000
56	A	54	PRO	0	0.027	-0.004	24.475	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	55	GLY	0	-0.018	-0.005	23.265	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	56	VAL	0	-0.005	0.012	18.920	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	57	LYS	1	0.848	0.921	13.626	1.073	1.073	0.000	0.000	0.000	0.000
60	A	58	VAL	0	0.059	0.018	18.675	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	59	LYS	1	0.803	0.915	12.255	1.141	1.141	0.000	0.000	0.000	0.000
62	A	60	VAL	0	0.016	0.005	18.783	0.000	0.000	0.000	0.000	0.000	0.000
63	A	61	PHE	0	-0.026	-0.011	14.793	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	62	GLY	0	0.085	0.040	19.285	0.023	0.023	0.000	0.000	0.000	0.000
65	A	63	VAL	0	0.013	-0.015	19.038	-0.042	-0.042	0.000	0.000	0.000	0.000
66	A	64	ASP	-1	-0.878	-0.935	18.013	-0.107	-0.107	0.000	0.000	0.000	0.000
67	A	65	ALA	0	-0.038	-0.023	17.316	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.014	0.009	14.874	-0.076	-0.076	0.000	0.000	0.000	0.000
69	A	67	LEU	0	0.005	0.017	13.234	-0.107	-0.107	0.000	0.000	0.000	0.000
70	A	68	LYS	1	0.859	0.921	12.170	0.113	0.113	0.000	0.000	0.000	0.000
71	A	69	GLU	-1	-0.810	-0.906	10.914	-1.074	-1.074	0.000	0.000	0.000	0.000
72	A	70	TRP	0	0.035	0.015	7.512	-0.217	-0.217	0.000	0.000	0.000	0.000
73	A	71	SER	0	-0.063	-0.036	7.583	-0.178	-0.178	0.000	0.000	0.000	0.000
74	A	72	GLN	0	0.031	0.039	7.974	0.735	0.735	0.000	0.000	0.000	0.000
75	A	73	LYS	1	0.831	0.898	3.656	-3.287	-2.668	0.018	-0.255	-0.382	0.001
76	A	74	THR	0	0.013	0.001	2.540	0.634	1.735	0.128	-0.391	-0.838	0.000
77	A	75	SER	0	0.001	-0.003	2.089	-8.684	-7.971	3.964	-2.427	-2.251	-0.033
78	A	76	VAL	0	-0.029	-0.017	4.489	-0.465	-0.289	-0.001	-0.012	-0.163	0.000
79	A	77	GLU	-1	-0.812	-0.880	3.031	-4.555	-3.905	0.093	-0.205	-0.538	-0.001
80	A	78	GLU	-1	-0.747	-0.843	4.605	-0.379	-0.321	-0.001	-0.008	-0.049	0.000
81	A	79	LYS	1	0.898	0.948	7.777	2.087	2.087	0.000	0.000	0.000	0.000
82	A	80	VAL	0	0.013	0.014	9.816	0.152	0.152	0.000	0.000	0.000	0.000
83	A	81	PHE	0	0.020	0.013	12.032	0.076	0.076	0.000	0.000	0.000	0.000
84	A	82	LEU	0	0.000	-0.008	12.805	0.012	0.012	0.000	0.000	0.000	0.000
85	A	83	LEU	0	-0.032	-0.016	16.271	0.051	0.051	0.000	0.000	0.000	0.000
86	A	84	PHE	0	0.062	0.016	16.834	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	85	LYS	1	0.929	0.964	22.093	0.167	0.167	0.000	0.000	0.000	0.000
88	A	86	ASN	0	0.023	0.008	25.015	0.023	0.023	0.000	0.000	0.000	0.000
89	A	87	ILE	0	0.066	0.015	24.563	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	88	ASP	-1	-0.877	-0.932	24.432	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	89	THR	0	-0.017	-0.023	21.379	0.005	0.005	0.000	0.000	0.000	0.000
92	A	90	CYS	0	-0.024	-0.003	20.005	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	91	LYS	1	0.811	0.886	19.965	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	92	ARG	1	0.874	0.932	21.291	0.114	0.114	0.000	0.000	0.000	0.000
95	A	93	VAL	0	-0.013	-0.003	16.269	0.013	0.013	0.000	0.000	0.000	0.000
96	A	94	MET	0	-0.033	-0.010	16.615	0.008	0.008	0.000	0.000	0.000	0.000
97	A	95	ASP	-1	-0.814	-0.882	17.419	0.100	0.100	0.000	0.000	0.000	0.000
98	A	96	GLY	0	-0.038	-0.003	17.375	0.038	0.038	0.000	0.000	0.000	0.000
99	A	97	GLY	0	-0.029	-0.016	13.990	0.029	0.029	0.000	0.000	0.000	0.000
100	A	98	LEU	0	-0.033	-0.014	11.582	0.029	0.029	0.000	0.000	0.000	0.000
101	A	99	PRO	0	-0.034	-0.009	9.381	0.018	0.018	0.000	0.000	0.000	0.000
102	A	100	ILE	0	0.033	-0.004	11.847	-0.130	-0.130	0.000	0.000	0.000	0.000
103	A	101	THR	0	0.029	0.012	12.870	0.039	0.039	0.000	0.000	0.000	0.000
104	A	102	THR	0	-0.027	-0.015	15.616	0.027	0.027	0.000	0.000	0.000	0.000
105	A	103	LEU	0	-0.013	-0.005	17.841	-0.041	-0.041	0.000	0.000	0.000	0.000
106	A	104	ASN	0	-0.024	-0.004	20.463	0.008	0.008	0.000	0.000	0.000	0.000
107	A	105	ILE	0	0.008	-0.019	23.027	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	106	GLY	0	0.011	-0.013	26.097	0.007	0.007	0.000	0.000	0.000	0.000
109	A	107	GLY	0	-0.015	-0.018	27.378	0.006	0.006	0.000	0.000	0.000	0.000
110	A	108	VAL	0	-0.015	-0.001	29.367	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	109	ALA	0	0.034	0.017	31.780	0.008	0.008	0.000	0.000	0.000	0.000
112	A	110	LYS	1	0.877	0.930	35.265	0.060	0.060	0.000	0.000	0.000	0.000
113	A	111	THR	0	0.045	0.013	37.177	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	112	PRO	0	-0.023	-0.025	39.931	0.002	0.002	0.000	0.000	0.000	0.000
115	A	113	GLN	0	0.054	0.029	38.989	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	114	ARG	1	0.759	0.865	32.502	0.084	0.084	0.000	0.000	0.000	0.000
117	A	115	LYS	1	0.855	0.932	38.058	0.030	0.030	0.000	0.000	0.000	0.000
118	A	116	GLY	0	-0.003	-0.004	37.733	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	117	ILE	0	-0.029	-0.008	34.031	0.005	0.005	0.000	0.000	0.000	0.000
120	A	118	SER	0	0.021	0.003	33.665	0.002	0.002	0.000	0.000	0.000	0.000
121	A	119	GLN	0	0.014	0.007	35.068	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	120	SER	0	-0.025	-0.022	32.074	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	121	VAL	0	0.032	0.028	30.322	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	122	SER	0	0.007	-0.001	33.443	0.010	0.010	0.000	0.000	0.000	0.000
125	A	123	LEU	0	0.033	0.012	30.415	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	124	SER	0	0.044	0.018	34.454	0.005	0.005	0.000	0.000	0.000	0.000
127	A	125	GLU	-1	-0.825	-0.907	34.737	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	126	ASP	-1	-0.879	-0.933	34.184	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	127	GLU	-1	-0.803	-0.869	31.011	-0.067	-0.067	0.000	0.000	0.000	0.000
130	A	128	VAL	0	0.007	-0.002	30.007	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	129	LYS	1	0.813	0.878	30.558	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	130	THR	0	-0.012	-0.008	26.487	0.010	0.010	0.000	0.000	0.000	0.000
133	A	131	LEU	0	-0.019	-0.014	25.423	0.004	0.004	0.000	0.000	0.000	0.000
134	A	132	LEU	0	0.009	0.005	25.845	0.007	0.007	0.000	0.000	0.000	0.000
135	A	133	GLU	-1	-0.781	-0.874	25.917	0.064	0.064	0.000	0.000	0.000	0.000
136	A	134	LEU	0	0.024	0.005	21.221	0.017	0.017	0.000	0.000	0.000	0.000
137	A	135	LYS	1	0.931	0.979	22.040	-0.037	-0.037	0.000	0.000	0.000	0.000
138	A	136	THR	0	-0.100	-0.076	23.277	0.018	0.018	0.000	0.000	0.000	0.000
139	A	137	LYS	1	0.811	0.927	21.679	-0.063	-0.063	0.000	0.000	0.000	0.000
140	A	138	TYR	0	-0.040	-0.061	17.915	0.037	0.037	0.000	0.000	0.000	0.000
141	A	139	ASN	0	-0.065	-0.012	18.229	0.009	0.009	0.000	0.000	0.000	0.000
142	A	140	VAL	0	-0.021	0.003	18.667	-0.011	-0.011	0.000	0.000	0.000	0.000
143	A	141	ASP	-1	-0.891	-0.955	19.735	-0.073	-0.073	0.000	0.000	0.000	0.000
144	A	142	VAL	0	0.008	0.002	21.492	-0.030	-0.030	0.000	0.000	0.000	0.000
145	A	143	TYR	0	-0.017	-0.019	21.426	0.004	0.004	0.000	0.000	0.000	0.000
146	A	144	LEU	0	0.009	0.027	25.811	-0.018	-0.018	0.000	0.000	0.000	0.000
147	A	145	GLN	0	-0.008	-0.030	26.242	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	146	MET	0	0.031	0.044	27.352	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	147	ILE	0	-0.023	-0.036	27.530	-0.018	-0.018	0.000	0.000	0.000	0.000
150	A	148	PRO	0	0.064	0.027	24.745	0.016	0.016	0.000	0.000	0.000	0.000
151	A	149	ASP	-1	-0.901	-0.940	26.925	-0.179	-0.179	0.000	0.000	0.000	0.000
152	A	150	SER	0	-0.098	-0.036	30.201	0.014	0.014	0.000	0.000	0.000	0.000
153	A	151	GLU	-1	-0.894	-0.959	30.967	-0.080	-0.080	0.000	0.000	0.000	0.000
154	A	152	LYS	1	0.882	0.965	24.286	0.142	0.142	0.000	0.000	0.000	0.000
155	A	153	ILE	0	-0.005	0.004	30.191	0.010	0.010	0.000	0.000	0.000	0.000
156	A	154	HIS	0	0.043	0.017	26.122	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	155	LEU	0	0.063	0.022	27.008	0.004	0.004	0.000	0.000	0.000	0.000
158	A	156	THR	0	0.022	0.000	29.537	0.001	0.001	0.000	0.000	0.000	0.000
159	A	157	THR	0	0.021	0.017	31.817	0.001	0.001	0.000	0.000	0.000	0.000
160	A	158	VAL	0	-0.018	-0.010	31.822	0.000	0.000	0.000	0.000	0.000	0.000
161	A	159	VAL	0	0.012	-0.003	32.791	0.001	0.001	0.000	0.000	0.000	0.000
162	A	160	GLU	-1	-0.930	-0.963	35.421	-0.006	-0.006	0.000	0.000	0.000	0.000
163	A	161	LYS	1	0.927	0.967	37.628	0.042	0.042	0.000	0.000	0.000	0.000
164	A	162	TYR	0	-0.048	-0.020	36.987	-0.001	-0.001	0.000	0.000	0.000	0.000
165	A	163	PHE	0	-0.067	-0.037	35.879	-0.002	-0.002	0.000	0.000	0.000	0.000
166	A	164	PRO	0	0.047	0.039	38.739	0.004	0.004	0.000	0.000	0.000	0.000
167	A	165	GLU	-1	-0.868	-0.904	37.805	0.011	0.011	0.000	0.000	0.000	0.000

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