FMO DATABASE

FMODB ID: 6NYLZ

Calculation Name: 5N9J-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: D

ChEMBL ID:

UniProt ID: P87310

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptH
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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-832859.381788
FMO2-HF: Nuclear repulsion	778523.487925
FMO2-HF: Total energy	-54335.893863
FMO2-MP2: Total energy	-54494.674424

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(D:3:CYS)

Summations of interaction energy for fragment #1(D:3:CYS)

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.
-1.692	-1.451	5.394	-1.946	-3.689	-0.007

Interaction energy analysis for fragmet #1(D:3:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.024

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	D	5	CYS	0	-0.035	-0.024	3.815	-1.751	-0.027	0.008	-0.651	-1.081	0.002
4	D	6	THR	0	0.025	0.029	1.912	-0.685	-2.570	5.387	-1.184	-2.318	-0.009
5	D	7	GLN	0	0.066	0.043	4.279	0.883	1.285	-0.001	-0.111	-0.290	0.000
6	D	8	LEU	0	0.072	0.028	6.013	0.472	0.472	0.000	0.000	0.000	0.000
7	D	9	GLN	0	-0.018	0.032	7.475	-0.044	-0.044	0.000	0.000	0.000	0.000
8	D	10	ASP	-1	-0.852	-0.915	8.127	-0.976	-0.976	0.000	0.000	0.000	0.000
9	D	11	THR	0	-0.122	-0.103	10.237	0.177	0.177	0.000	0.000	0.000	0.000
10	D	12	ILE	0	0.002	-0.019	12.078	0.076	0.076	0.000	0.000	0.000	0.000
11	D	13	ASP	-1	-0.905	-0.944	13.319	-0.322	-0.322	0.000	0.000	0.000	0.000
12	D	14	GLU	-1	-0.870	-0.942	13.961	-0.146	-0.146	0.000	0.000	0.000	0.000
13	D	15	VAL	0	-0.039	-0.013	16.011	0.036	0.036	0.000	0.000	0.000	0.000
14	D	16	ALA	0	0.005	0.002	18.242	0.018	0.018	0.000	0.000	0.000	0.000
15	D	17	THR	0	-0.005	-0.035	18.384	0.016	0.016	0.000	0.000	0.000	0.000
16	D	18	GLN	0	-0.024	-0.021	20.189	0.026	0.026	0.000	0.000	0.000	0.000
17	D	19	PHE	0	0.002	0.009	21.926	0.012	0.012	0.000	0.000	0.000	0.000
18	D	20	TYR	0	0.000	0.034	22.053	0.005	0.005	0.000	0.000	0.000	0.000
19	D	21	SER	0	-0.038	-0.004	23.900	0.008	0.008	0.000	0.000	0.000	0.000
20	D	22	SER	0	-0.014	-0.030	25.820	0.009	0.009	0.000	0.000	0.000	0.000
21	D	23	ILE	0	-0.012	-0.013	27.629	0.005	0.005	0.000	0.000	0.000	0.000
22	D	24	HIS	0	0.004	0.010	29.385	0.003	0.003	0.000	0.000	0.000	0.000
23	D	25	TYR	0	0.004	0.043	29.433	0.004	0.004	0.000	0.000	0.000	0.000
24	D	26	LEU	0	-0.047	-0.041	31.163	0.004	0.004	0.000	0.000	0.000	0.000
25	D	27	SER	0	-0.036	-0.010	33.786	0.003	0.003	0.000	0.000	0.000	0.000
26	D	28	SER	0	-0.066	-0.072	33.532	0.000	0.000	0.000	0.000	0.000	0.000
27	D	29	HIS	0	-0.071	-0.038	32.837	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	30	HIS	0	-0.014	0.030	37.580	0.000	0.000	0.000	0.000	0.000	0.000
29	D	31	ASP	-1	-0.856	-0.913	39.444	-0.026	-0.026	0.000	0.000	0.000	0.000
30	D	32	PHE	0	-0.115	-0.049	42.369	0.002	0.002	0.000	0.000	0.000	0.000
31	D	33	VAL	0	0.030	0.010	46.173	0.001	0.001	0.000	0.000	0.000	0.000
32	D	34	PRO	0	-0.028	-0.022	47.991	0.000	0.000	0.000	0.000	0.000	0.000
33	D	35	LEU	0	-0.041	-0.018	50.566	0.000	0.000	0.000	0.000	0.000	0.000
34	D	36	PRO	0	-0.027	-0.032	53.226	0.000	0.000	0.000	0.000	0.000	0.000
35	D	37	GLY	0	-0.006	0.019	56.472	0.000	0.000	0.000	0.000	0.000	0.000
36	D	38	GLN	0	0.015	0.004	55.622	0.000	0.000	0.000	0.000	0.000	0.000
37	D	39	GLU	-1	-0.857	-0.942	48.249	-0.017	-0.017	0.000	0.000	0.000	0.000
38	D	40	LYS	1	0.924	0.961	51.766	0.016	0.016	0.000	0.000	0.000	0.000
39	D	41	VAL	0	0.037	0.034	48.004	0.000	0.000	0.000	0.000	0.000	0.000
40	D	42	SER	0	-0.058	-0.038	47.999	0.000	0.000	0.000	0.000	0.000	0.000
41	D	43	ASP	-1	-0.815	-0.928	47.464	-0.025	-0.025	0.000	0.000	0.000	0.000
42	D	44	SER	0	-0.050	-0.012	45.824	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	45	LYS	1	0.924	0.942	43.853	0.028	0.028	0.000	0.000	0.000	0.000
44	D	46	VAL	0	-0.066	-0.012	42.596	-0.001	-0.001	0.000	0.000	0.000	0.000
45	D	47	ASN	0	-0.012	0.007	39.422	0.000	0.000	0.000	0.000	0.000	0.000
46	D	48	PRO	0	0.013	-0.010	40.555	-0.001	-0.001	0.000	0.000	0.000	0.000
47	D	49	ILE	0	0.068	0.021	36.688	-0.001	-0.001	0.000	0.000	0.000	0.000
48	D	50	SER	0	-0.049	-0.068	40.545	0.002	0.002	0.000	0.000	0.000	0.000
49	D	51	ALA	0	0.032	0.017	40.503	0.000	0.000	0.000	0.000	0.000	0.000
50	D	52	GLU	-1	-0.959	-0.984	39.800	-0.008	-0.008	0.000	0.000	0.000	0.000
51	D	53	GLU	-1	-0.815	-0.878	36.904	-0.023	-0.023	0.000	0.000	0.000	0.000
52	D	54	LEU	0	-0.002	0.015	36.290	-0.001	-0.001	0.000	0.000	0.000	0.000
53	D	55	GLN	0	-0.006	-0.007	35.839	0.002	0.002	0.000	0.000	0.000	0.000
54	D	56	PHE	0	-0.075	-0.044	32.066	0.002	0.002	0.000	0.000	0.000	0.000
55	D	57	ALA	0	0.072	0.047	32.176	0.000	0.000	0.000	0.000	0.000	0.000
56	D	58	GLN	0	-0.001	-0.005	31.019	0.000	0.000	0.000	0.000	0.000	0.000
57	D	59	ARG	1	0.935	0.963	31.060	0.001	0.001	0.000	0.000	0.000	0.000
58	D	60	ASP	-1	-0.935	-0.973	28.535	-0.010	-0.010	0.000	0.000	0.000	0.000
59	D	61	LEU	0	0.016	0.015	25.820	-0.001	-0.001	0.000	0.000	0.000	0.000
60	D	62	ALA	0	-0.014	0.000	26.166	-0.001	-0.001	0.000	0.000	0.000	0.000
61	D	63	LYS	1	0.879	0.930	25.983	-0.007	-0.007	0.000	0.000	0.000	0.000
62	D	64	ASP	-1	-0.815	-0.884	21.392	-0.040	-0.040	0.000	0.000	0.000	0.000
63	D	65	LEU	0	0.114	0.080	21.544	0.002	0.002	0.000	0.000	0.000	0.000
64	D	66	VAL	0	-0.035	-0.029	21.675	0.005	0.005	0.000	0.000	0.000	0.000
65	D	67	THR	0	-0.087	-0.068	19.891	0.013	0.013	0.000	0.000	0.000	0.000
66	D	68	LYS	1	0.880	0.926	14.742	0.110	0.110	0.000	0.000	0.000	0.000
67	D	69	PHE	0	-0.001	-0.004	17.108	0.006	0.006	0.000	0.000	0.000	0.000
68	D	70	MET	0	-0.031	-0.013	18.203	0.018	0.018	0.000	0.000	0.000	0.000
69	D	71	GLN	0	-0.028	-0.010	13.795	0.030	0.030	0.000	0.000	0.000	0.000
70	D	72	ILE	0	0.027	0.018	13.554	0.044	0.044	0.000	0.000	0.000	0.000
71	D	73	ASP	-1	-0.930	-0.952	14.213	0.204	0.204	0.000	0.000	0.000	0.000
72	D	74	THR	0	-0.052	-0.036	14.392	0.054	0.054	0.000	0.000	0.000	0.000
73	D	75	LEU	0	-0.011	-0.015	9.211	0.081	0.081	0.000	0.000	0.000	0.000
74	D	76	ILE	0	-0.013	-0.007	10.924	0.136	0.136	0.000	0.000	0.000	0.000
75	D	77	ASN	0	-0.044	-0.025	13.320	0.056	0.056	0.000	0.000	0.000	0.000
76	D	78	GLN	0	-0.067	-0.029	8.175	0.225	0.225	0.000	0.000	0.000	0.000
77	D	79	LEU	0	-0.036	0.003	8.904	0.256	0.256	0.000	0.000	0.000	0.000
78	D	80	PRO	0	-0.063	-0.016	8.532	-0.086	-0.086	0.000	0.000	0.000	0.000
79	D	81	GLY	0	0.041	0.014	11.362	0.061	0.061	0.000	0.000	0.000	0.000
80	D	82	ILE	0	-0.024	-0.032	10.587	0.004	0.004	0.000	0.000	0.000	0.000
81	D	83	SER	0	-0.037	-0.020	14.133	-0.043	-0.043	0.000	0.000	0.000	0.000
82	D	84	THR	0	0.039	0.028	15.297	0.034	0.034	0.000	0.000	0.000	0.000
83	D	85	ALA	0	-0.007	0.006	16.375	-0.020	-0.020	0.000	0.000	0.000	0.000
84	D	86	PRO	0	0.088	0.035	16.321	0.032	0.032	0.000	0.000	0.000	0.000
85	D	87	LYS	1	0.968	0.990	17.520	-0.132	-0.132	0.000	0.000	0.000	0.000
86	D	88	HIS	0	0.055	0.021	15.686	-0.043	-0.043	0.000	0.000	0.000	0.000
87	D	89	GLN	0	0.018	0.006	11.176	-0.039	-0.039	0.000	0.000	0.000	0.000
88	D	90	LEU	0	0.002	0.003	16.568	-0.024	-0.024	0.000	0.000	0.000	0.000
89	D	91	GLU	-1	-0.917	-0.966	18.838	0.087	0.087	0.000	0.000	0.000	0.000
90	D	92	LYS	1	0.975	0.995	15.081	-0.264	-0.264	0.000	0.000	0.000	0.000
91	D	93	ILE	0	-0.009	-0.013	14.728	-0.021	-0.021	0.000	0.000	0.000	0.000
92	D	94	LYS	1	0.978	0.992	18.496	-0.076	-0.076	0.000	0.000	0.000	0.000
93	D	95	LYS	1	0.987	1.008	21.876	-0.092	-0.092	0.000	0.000	0.000	0.000
94	D	96	LEU	0	-0.082	-0.061	16.949	-0.008	-0.008	0.000	0.000	0.000	0.000
95	D	97	GLN	0	0.003	0.006	21.088	-0.012	-0.012	0.000	0.000	0.000	0.000
96	D	98	ASN	0	0.051	0.021	22.515	-0.011	-0.011	0.000	0.000	0.000	0.000
97	D	99	SER	0	-0.017	0.004	23.562	-0.003	-0.003	0.000	0.000	0.000	0.000
98	D	100	ILE	0	-0.014	-0.025	21.076	-0.006	-0.006	0.000	0.000	0.000	0.000
99	D	101	GLU	-1	-0.981	-0.976	24.590	0.000	0.000	0.000	0.000	0.000	0.000
100	D	102	GLU	-1	-0.835	-0.920	27.379	0.031	0.031	0.000	0.000	0.000	0.000
101	D	103	LYS	1	0.891	0.939	26.561	-0.020	-0.020	0.000	0.000	0.000	0.000
102	D	104	GLN	0	-0.048	-0.027	26.241	-0.011	-0.011	0.000	0.000	0.000	0.000
103	D	105	LEU	0	0.013	0.022	29.121	-0.004	-0.004	0.000	0.000	0.000	0.000
104	D	106	GLU	-1	-0.908	-0.963	31.905	0.009	0.009	0.000	0.000	0.000	0.000
105	D	107	ARG	1	0.838	0.899	28.164	0.022	0.022	0.000	0.000	0.000	0.000
106	D	108	LYS	1	0.992	0.994	32.232	0.010	0.010	0.000	0.000	0.000	0.000
107	D	109	SER	0	-0.058	-0.025	34.374	-0.001	-0.001	0.000	0.000	0.000	0.000
108	D	110	LEU	0	0.045	0.015	33.542	-0.001	-0.001	0.000	0.000	0.000	0.000
109	D	111	GLU	-1	-0.873	-0.911	33.674	-0.024	-0.024	0.000	0.000	0.000	0.000
110	D	112	SER	0	-0.006	-0.005	36.351	-0.001	-0.001	0.000	0.000	0.000	0.000
111	D	113	GLU	-1	-0.962	-0.973	39.577	-0.005	-0.005	0.000	0.000	0.000	0.000
112	D	114	ASN	0	0.039	0.009	37.857	-0.003	-0.003	0.000	0.000	0.000	0.000
113	D	115	GLU	-1	-0.957	-0.981	37.574	-0.023	-0.023	0.000	0.000	0.000	0.000
114	D	116	ASP	-1	-0.954	-0.959	40.945	-0.010	-0.010	0.000	0.000	0.000	0.000
115	D	117	LEU	0	0.047	0.007	42.513	0.000	0.000	0.000	0.000	0.000	0.000
116	D	118	LYS	1	0.858	0.920	36.572	0.021	0.021	0.000	0.000	0.000	0.000
117	D	119	LEU	0	0.023	0.029	43.586	0.000	0.000	0.000	0.000	0.000	0.000
118	D	120	GLN	0	-0.018	-0.016	46.341	0.001	0.001	0.000	0.000	0.000	0.000
119	D	121	LEU	0	-0.010	-0.017	45.120	0.000	0.000	0.000	0.000	0.000	0.000
120	D	122	ALA	0	0.034	0.020	46.098	0.000	0.000	0.000	0.000	0.000	0.000
121	D	123	LYS	1	1.004	1.004	48.002	0.012	0.012	0.000	0.000	0.000	0.000
122	D	124	ARG	1	0.907	0.964	50.995	0.008	0.008	0.000	0.000	0.000	0.000
123	D	125	ILE	0	-0.020	-0.003	47.750	0.000	0.000	0.000	0.000	0.000	0.000
124	D	126	GLU	-1	-0.889	-0.942	51.189	-0.014	-0.014	0.000	0.000	0.000	0.000
125	D	127	THR	0	-0.098	-0.066	52.932	0.000	0.000	0.000	0.000	0.000	0.000
126	D	128	PHE	0	0.035	0.023	53.656	0.000	0.000	0.000	0.000	0.000	0.000
127	D	129	GLY	0	0.016	0.028	54.115	0.000	0.000	0.000	0.000	0.000	0.000
128	D	130	ARG	1	0.953	0.975	54.939	0.012	0.012	0.000	0.000	0.000	0.000
129	D	131	LEU	0	0.001	0.004	57.871	0.000	0.000	0.000	0.000	0.000	0.000
130	D	132	SER	0	-0.019	-0.034	56.734	0.000	0.000	0.000	0.000	0.000	0.000
131	D	133	CYS	0	-0.006	0.001	58.168	0.000	0.000	0.000	0.000	0.000	0.000
132	D	134	VAL	0	0.003	-0.007	59.523	0.000	0.000	0.000	0.000	0.000	0.000
133	D	135	LEU	0	-0.075	-0.038	62.646	0.000	0.000	0.000	0.000	0.000	0.000
134	D	136	PHE	0	-0.053	-0.024	61.286	0.000	0.000	0.000	0.000	0.000	0.000
135	D	137	GLN	0	-0.050	-0.001	59.864	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:3:CYS)