FMO DATABASE

FMODB ID: 7272K

Calculation Name: 4NKJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NKJ

Chain ID: A

ChEMBL ID:

UniProt ID: S5DRP1

Base Structure: X-ray

Registration Date: 2023-09-19

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

DOI:

Apendix: None

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-919665.900211
FMO2-HF: Nuclear repulsion	865074.606666
FMO2-HF: Total energy	-54591.293545
FMO2-MP2: Total energy	-54750.010903

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:4:VAL)

Summations of interaction energy for fragment #1(A:4:VAL)

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.
-4.487	-1.35	2.382	-2.319	-3.2	-0.013

Interaction energy analysis for fragmet #1(A:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.031

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	6	ALA	0	0.032	0.008	2.555	-4.405	-1.391	0.980	-1.860	-2.134	-0.014
4	A	7	ASP	-1	-0.794	-0.904	5.281	-0.055	0.021	-0.001	-0.002	-0.073	0.000
5	A	8	LEU	0	-0.006	0.011	7.364	-0.011	-0.011	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.958	0.980	10.770	0.199	0.199	0.000	0.000	0.000	0.000
7	A	10	SER	0	0.053	0.028	9.429	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	11	THR	0	0.026	-0.007	9.373	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	12	GLN	0	-0.032	-0.007	11.804	0.070	0.070	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.896	-0.964	14.799	-0.262	-0.262	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.004	0.001	13.619	0.028	0.028	0.000	0.000	0.000	0.000
12	A	15	ILE	0	0.006	-0.002	15.230	0.036	0.036	0.000	0.000	0.000	0.000
13	A	16	ASN	0	-0.013	0.000	17.579	0.047	0.047	0.000	0.000	0.000	0.000
14	A	17	LYS	1	0.822	0.895	19.073	0.316	0.316	0.000	0.000	0.000	0.000
15	A	18	ILE	0	0.013	0.006	17.236	0.020	0.020	0.000	0.000	0.000	0.000
16	A	19	THR	0	0.005	-0.001	21.152	0.026	0.026	0.000	0.000	0.000	0.000
17	A	20	LYS	1	0.945	0.973	23.464	0.178	0.178	0.000	0.000	0.000	0.000
18	A	21	ASN	0	-0.027	-0.006	22.795	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.045	0.034	25.354	0.011	0.011	0.000	0.000	0.000	0.000
20	A	23	ASN	0	0.023	-0.004	27.162	0.014	0.014	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.057	-0.010	28.845	0.008	0.008	0.000	0.000	0.000	0.000
22	A	25	LEU	0	0.031	0.002	28.932	0.008	0.008	0.000	0.000	0.000	0.000
23	A	26	SER	0	0.005	0.012	31.267	0.010	0.010	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.845	-0.923	33.225	-0.087	-0.087	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.063	-0.041	32.735	0.006	0.006	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.803	-0.898	35.360	-0.087	-0.087	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.024	-0.009	37.107	0.006	0.006	0.000	0.000	0.000	0.000
28	A	31	LYS	1	0.842	0.915	37.575	0.090	0.090	0.000	0.000	0.000	0.000
29	A	32	ASN	0	-0.037	-0.024	37.908	0.007	0.007	0.000	0.000	0.000	0.000
30	A	33	LEU	0	0.014	0.003	40.209	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.012	-0.008	43.131	0.002	0.002	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.945	0.987	42.559	0.074	0.074	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.010	-0.009	43.859	0.003	0.003	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.000	0.000	47.280	0.003	0.003	0.000	0.000	0.000	0.000
35	A	38	GLY	0	0.009	0.012	49.241	0.002	0.002	0.000	0.000	0.000	0.000
36	A	39	ALA	0	-0.001	-0.003	50.536	0.002	0.002	0.000	0.000	0.000	0.000
37	A	40	MET	0	-0.021	-0.009	50.123	0.002	0.002	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.904	-0.959	53.235	-0.042	-0.042	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.924	-0.934	55.171	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.013	0.003	54.373	0.002	0.002	0.000	0.000	0.000	0.000
41	A	44	HIS	0	-0.014	-0.006	57.523	0.002	0.002	0.000	0.000	0.000	0.000
42	A	45	ASN	0	-0.021	-0.013	59.378	0.001	0.001	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.859	-0.933	59.677	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	47	ILE	0	-0.041	-0.025	60.032	0.001	0.001	0.000	0.000	0.000	0.000
45	A	48	LEU	0	-0.027	-0.012	63.051	0.001	0.001	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.799	-0.893	65.341	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.023	-0.018	66.377	0.001	0.001	0.000	0.000	0.000	0.000
48	A	51	ASP	-1	-0.946	-0.975	67.950	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.786	-0.891	69.772	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.921	0.975	71.337	0.028	0.028	0.000	0.000	0.000	0.000
51	A	54	VAL	0	-0.052	-0.030	71.776	0.001	0.001	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.782	-0.900	74.104	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	56	ASP	-1	-0.782	-0.906	75.984	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.012	0.012	76.495	0.001	0.001	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.875	0.931	78.237	0.021	0.021	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.012	-0.013	80.305	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.834	-0.886	81.579	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.061	-0.032	82.522	0.001	0.001	0.000	0.000	0.000	0.000
59	A	62	ILE	0	-0.075	-0.036	83.733	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.022	-0.010	85.702	0.001	0.001	0.000	0.000	0.000	0.000
61	A	64	SER	0	0.029	0.014	87.142	0.001	0.001	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.043	-0.025	86.688	0.000	0.000	0.000	0.000	0.000	0.000
63	A	66	ILE	0	-0.045	-0.023	89.222	0.001	0.001	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.822	-0.909	92.002	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.039	-0.014	93.597	0.000	0.000	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.023	-0.020	94.889	0.000	0.000	0.000	0.000	0.000	0.000
67	A	70	VAL	0	-0.001	0.012	96.183	0.000	0.000	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.014	0.002	98.070	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.023	-0.018	98.078	0.000	0.000	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.034	-0.027	100.435	0.000	0.000	0.000	0.000	0.000	0.000
71	A	74	ASN	0	-0.066	-0.037	101.353	0.000	0.000	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.966	-0.965	104.109	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	76	GLY	0	0.003	0.014	105.968	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	ILE	0	-0.019	-0.019	104.338	0.000	0.000	0.000	0.000	0.000	0.000
75	A	78	ILE	0	-0.059	-0.021	102.237	0.000	0.000	0.000	0.000	0.000	0.000
76	A	79	ASN	0	-0.024	-0.017	105.585	0.000	0.000	0.000	0.000	0.000	0.000
77	A	80	SER	0	0.016	0.005	107.230	0.000	0.000	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.871	-0.918	101.753	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	82	ASP	-1	-0.799	-0.889	102.328	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	83	GLU	-1	-0.768	-0.877	101.264	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	84	HIS	1	0.750	0.848	99.041	0.012	0.012	0.000	0.000	0.000	0.000
82	A	85	LEU	0	0.040	0.039	97.569	0.000	0.000	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.066	0.035	97.452	0.000	0.000	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.036	-0.032	96.207	0.000	0.000	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.060	-0.027	91.913	0.000	0.000	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.764	-0.887	92.609	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	90	ARG	1	0.716	0.840	92.472	0.012	0.012	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.892	0.938	89.502	0.014	0.014	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.033	0.015	88.291	0.000	0.000	0.000	0.000	0.000	0.000
90	A	93	LYS	1	0.955	0.965	87.573	0.014	0.014	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.870	0.942	86.263	0.015	0.015	0.000	0.000	0.000	0.000
92	A	95	MET	0	-0.074	-0.029	83.895	0.000	0.000	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.035	0.037	83.154	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.046	0.000	80.235	0.000	0.000	0.000	0.000	0.000	0.000
95	A	98	PRO	0	-0.022	0.006	76.881	0.001	0.001	0.000	0.000	0.000	0.000
96	A	99	SER	0	-0.026	-0.046	78.426	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	100	ALA	0	-0.049	-0.015	80.860	0.000	0.000	0.000	0.000	0.000	0.000
98	A	101	VAL	0	-0.004	0.001	84.049	0.000	0.000	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.909	-0.934	86.851	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	103	ILE	0	-0.067	-0.047	90.539	0.000	0.000	0.000	0.000	0.000	0.000
101	A	104	GLY	0	0.010	0.012	93.497	0.000	0.000	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.047	-0.039	94.485	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.008	-0.005	97.436	0.000	0.000	0.000	0.000	0.000	0.000
104	A	107	SER	0	0.025	0.011	93.922	0.000	0.000	0.000	0.000	0.000	0.000
105	A	108	PHE	0	-0.083	-0.043	89.159	0.000	0.000	0.000	0.000	0.000	0.000
106	A	109	GLU	-1	-0.801	-0.877	84.760	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	110	THR	0	-0.025	-0.046	83.366	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	LYN	0	-0.096	-0.001	77.401	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	HIS	1	0.814	0.894	78.321	0.020	0.020	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.685	0.822	74.087	0.023	0.023	0.000	0.000	0.000	0.000
111	A	114	CYS	0	0.045	0.073	66.739	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	115	ASN	0	-0.056	-0.036	71.494	0.000	0.000	0.000	0.000	0.000	0.000
113	A	116	GLN	0	0.026	0.012	67.315	0.000	0.000	0.000	0.000	0.000	0.000
114	A	117	THR	0	0.032	-0.007	64.209	0.000	0.000	0.000	0.000	0.000	0.000
115	A	119	LEU	0	-0.097	-0.060	68.948	0.000	0.000	0.000	0.000	0.000	0.000
116	A	120	ASP	-1	-0.962	-0.987	65.136	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.811	0.897	58.034	0.038	0.038	0.000	0.000	0.000	0.000
118	A	122	ILE	0	-0.003	-0.004	62.792	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	123	ALA	0	-0.088	-0.047	64.572	0.000	0.000	0.000	0.000	0.000	0.000
120	A	124	ALA	0	-0.050	-0.020	64.266	0.000	0.000	0.000	0.000	0.000	0.000
121	A	125	GLY	0	0.122	0.066	61.656	0.000	0.000	0.000	0.000	0.000	0.000
122	A	126	THR	0	-0.102	-0.057	55.830	0.000	0.000	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.080	0.054	52.806	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	128	ASN	0	-0.079	-0.047	50.235	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	129	ALA	0	0.035	0.018	49.632	0.000	0.000	0.000	0.000	0.000	0.000
126	A	130	GLY	0	0.011	-0.008	46.527	0.000	0.000	0.000	0.000	0.000	0.000
127	A	131	GLU	-1	-0.998	-0.980	42.378	-0.079	-0.079	0.000	0.000	0.000	0.000
128	A	132	PHE	0	-0.027	-0.009	40.393	0.000	0.000	0.000	0.000	0.000	0.000
129	A	133	SER	0	-0.016	-0.012	36.420	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.006	-0.007	33.007	0.001	0.001	0.000	0.000	0.000	0.000
131	A	135	PRO	0	-0.031	0.000	29.624	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	136	THR	0	0.038	0.021	26.891	0.001	0.001	0.000	0.000	0.000	0.000
133	A	137	PHE	0	-0.040	-0.043	23.745	0.001	0.001	0.000	0.000	0.000	0.000
134	A	138	ASP	-1	-0.864	-0.914	20.557	-0.260	-0.260	0.000	0.000	0.000	0.000
135	A	139	SER	0	-0.010	-0.006	15.104	0.013	0.013	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.009	-0.009	14.652	0.007	0.007	0.000	0.000	0.000	0.000
137	A	141	ASN	0	-0.027	-0.014	11.392	-0.078	-0.078	0.000	0.000	0.000	0.000
138	A	142	ILE	0	-0.005	0.006	8.161	0.057	0.057	0.000	0.000	0.000	0.000
139	A	143	THR	0	0.004	0.006	7.219	-0.223	-0.223	0.000	0.000	0.000	0.000
140	A	144	ALA	0	-0.008	-0.015	2.447	-0.181	-0.275	1.403	-0.441	-0.868	0.001
141	A	145	ALA	0	-0.013	0.004	4.299	0.249	0.390	0.000	-0.016	-0.125	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:VAL)