FMO DATABASE

FMODB ID: R98N8

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	OptAll
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	-831652.01294
FMO2-HF: Nuclear repulsion	777313.592238
FMO2-HF: Total energy	-54338.420701
FMO2-MP2: Total energy	-54496.725228

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.
-11.451	-8.302	4.514	-3.162	-4.501	-0.021

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 : -0.014 / q_NPA : -0.021

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	-0.048	-0.024	3.633	-2.288	-0.555	0.030	-0.653	-1.110	0.004
4	D	6	THR	0	0.071	0.039	2.084	-8.242	-7.433	4.483	-2.314	-2.978	-0.025
5	D	7	GLN	0	0.037	0.030	3.732	1.056	1.663	0.001	-0.195	-0.413	0.000
6	D	8	LEU	0	0.012	0.014	5.802	0.692	0.692	0.000	0.000	0.000	0.000
7	D	9	GLN	0	-0.026	-0.017	6.632	0.109	0.109	0.000	0.000	0.000	0.000
8	D	10	ASP	-1	-0.847	-0.927	6.726	-2.747	-2.747	0.000	0.000	0.000	0.000
9	D	11	THR	0	-0.042	-0.033	9.446	0.318	0.318	0.000	0.000	0.000	0.000
10	D	12	ILE	0	-0.020	-0.012	11.578	0.157	0.157	0.000	0.000	0.000	0.000
11	D	13	ASP	-1	-0.883	-0.937	12.336	-0.613	-0.613	0.000	0.000	0.000	0.000
12	D	14	GLU	-1	-0.860	-0.910	13.309	-0.528	-0.528	0.000	0.000	0.000	0.000
13	D	15	VAL	0	-0.001	0.004	15.510	0.072	0.072	0.000	0.000	0.000	0.000
14	D	16	ALA	0	-0.015	-0.006	17.163	0.045	0.045	0.000	0.000	0.000	0.000
15	D	17	THR	0	-0.029	-0.036	17.199	0.038	0.038	0.000	0.000	0.000	0.000
16	D	18	GLN	0	-0.031	-0.010	19.551	0.056	0.056	0.000	0.000	0.000	0.000
17	D	19	PHE	0	-0.004	0.016	21.039	0.033	0.033	0.000	0.000	0.000	0.000
18	D	20	TYR	0	0.016	0.011	21.041	0.029	0.029	0.000	0.000	0.000	0.000
19	D	21	SER	0	-0.027	-0.033	22.736	0.020	0.020	0.000	0.000	0.000	0.000
20	D	22	SER	0	-0.024	-0.030	25.189	0.022	0.022	0.000	0.000	0.000	0.000
21	D	23	ILE	0	0.006	-0.001	26.959	0.016	0.016	0.000	0.000	0.000	0.000
22	D	24	HIS	0	0.008	0.006	28.480	0.011	0.011	0.000	0.000	0.000	0.000
23	D	25	TYR	0	0.005	0.009	28.818	0.010	0.010	0.000	0.000	0.000	0.000
24	D	26	LEU	0	-0.023	-0.023	30.660	0.011	0.011	0.000	0.000	0.000	0.000
25	D	27	SER	0	-0.043	-0.012	32.930	0.010	0.010	0.000	0.000	0.000	0.000
26	D	28	SER	0	-0.076	-0.041	32.892	0.001	0.001	0.000	0.000	0.000	0.000
27	D	29	HIS	0	-0.079	-0.046	32.649	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	30	HIS	0	-0.057	-0.028	37.440	-0.001	-0.001	0.000	0.000	0.000	0.000
29	D	31	ASP	-1	-0.854	-0.925	39.925	-0.087	-0.087	0.000	0.000	0.000	0.000
30	D	32	PHE	0	-0.053	-0.020	41.664	0.006	0.006	0.000	0.000	0.000	0.000
31	D	33	VAL	0	0.035	0.012	45.509	0.002	0.002	0.000	0.000	0.000	0.000
32	D	34	PRO	0	-0.013	-0.007	47.709	0.000	0.000	0.000	0.000	0.000	0.000
33	D	35	LEU	0	0.002	0.006	49.349	0.002	0.002	0.000	0.000	0.000	0.000
34	D	36	PRO	0	-0.040	-0.033	52.516	0.001	0.001	0.000	0.000	0.000	0.000
35	D	37	GLY	0	-0.018	0.016	55.098	0.002	0.002	0.000	0.000	0.000	0.000
36	D	38	GLN	0	-0.029	-0.027	55.237	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	39	GLU	-1	-0.860	-0.929	47.538	-0.064	-0.064	0.000	0.000	0.000	0.000
38	D	40	LYS	1	0.926	0.955	51.462	0.055	0.055	0.000	0.000	0.000	0.000
39	D	41	VAL	0	0.054	0.039	47.100	-0.001	-0.001	0.000	0.000	0.000	0.000
40	D	42	SER	0	-0.032	-0.019	47.407	0.002	0.002	0.000	0.000	0.000	0.000
41	D	43	ASP	-1	-0.818	-0.911	46.788	-0.083	-0.083	0.000	0.000	0.000	0.000
42	D	44	SER	0	-0.032	-0.027	45.101	-0.005	-0.005	0.000	0.000	0.000	0.000
43	D	45	LYS	1	0.859	0.919	43.158	0.082	0.082	0.000	0.000	0.000	0.000
44	D	46	VAL	0	-0.035	-0.004	42.157	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	47	ASN	0	-0.030	-0.003	37.600	0.000	0.000	0.000	0.000	0.000	0.000
46	D	48	PRO	0	0.020	0.010	40.009	-0.003	-0.003	0.000	0.000	0.000	0.000
47	D	49	ILE	0	0.017	0.008	36.404	-0.003	-0.003	0.000	0.000	0.000	0.000
48	D	50	SER	0	-0.040	-0.041	40.388	0.007	0.007	0.000	0.000	0.000	0.000
49	D	51	ALA	0	0.007	-0.009	40.173	-0.003	-0.003	0.000	0.000	0.000	0.000
50	D	52	GLU	-1	-0.953	-0.973	39.516	-0.060	-0.060	0.000	0.000	0.000	0.000
51	D	53	GLU	-1	-0.815	-0.891	36.824	-0.096	-0.096	0.000	0.000	0.000	0.000
52	D	54	LEU	0	0.010	0.019	35.557	-0.006	-0.006	0.000	0.000	0.000	0.000
53	D	55	GLN	0	-0.001	0.002	35.277	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	56	PHE	0	0.023	-0.009	32.253	0.002	0.002	0.000	0.000	0.000	0.000
55	D	57	ALA	0	0.042	0.021	31.375	-0.004	-0.004	0.000	0.000	0.000	0.000
56	D	58	GLN	0	0.007	-0.008	30.397	-0.004	-0.004	0.000	0.000	0.000	0.000
57	D	59	ARG	1	0.766	0.875	30.659	0.075	0.075	0.000	0.000	0.000	0.000
58	D	60	ASP	-1	-0.776	-0.862	28.101	-0.087	-0.087	0.000	0.000	0.000	0.000
59	D	61	LEU	0	0.013	0.018	25.261	-0.011	-0.011	0.000	0.000	0.000	0.000
60	D	62	ALA	0	0.012	0.008	25.568	-0.010	-0.010	0.000	0.000	0.000	0.000
61	D	63	LYS	1	0.799	0.890	25.807	0.080	0.080	0.000	0.000	0.000	0.000
62	D	64	ASP	-1	-0.841	-0.897	20.502	-0.250	-0.250	0.000	0.000	0.000	0.000
63	D	65	LEU	0	0.092	0.060	21.187	0.001	0.001	0.000	0.000	0.000	0.000
64	D	66	VAL	0	-0.025	-0.017	21.350	0.004	0.004	0.000	0.000	0.000	0.000
65	D	67	THR	0	-0.049	-0.039	20.061	0.016	0.016	0.000	0.000	0.000	0.000
66	D	68	LYS	1	0.841	0.906	15.268	0.449	0.449	0.000	0.000	0.000	0.000
67	D	69	PHE	0	0.012	-0.001	16.730	-0.007	-0.007	0.000	0.000	0.000	0.000
68	D	70	MET	0	-0.026	-0.006	17.929	0.033	0.033	0.000	0.000	0.000	0.000
69	D	71	GLN	0	-0.033	0.004	13.728	0.034	0.034	0.000	0.000	0.000	0.000
70	D	72	ILE	0	0.029	0.019	13.261	0.065	0.065	0.000	0.000	0.000	0.000
71	D	73	ASP	-1	-0.908	-0.949	13.919	0.266	0.266	0.000	0.000	0.000	0.000
72	D	74	THR	0	-0.032	-0.046	14.377	0.087	0.087	0.000	0.000	0.000	0.000
73	D	75	LEU	0	-0.022	-0.016	8.571	0.144	0.144	0.000	0.000	0.000	0.000
74	D	76	ILE	0	-0.037	-0.023	10.837	0.202	0.202	0.000	0.000	0.000	0.000
75	D	77	ASN	0	-0.064	-0.035	13.205	0.134	0.134	0.000	0.000	0.000	0.000
76	D	78	GLN	0	-0.050	-0.011	8.751	0.284	0.284	0.000	0.000	0.000	0.000
77	D	79	LEU	0	-0.038	-0.004	8.164	0.433	0.433	0.000	0.000	0.000	0.000
78	D	80	PRO	0	-0.058	-0.015	8.245	-0.141	-0.141	0.000	0.000	0.000	0.000
79	D	81	GLY	0	0.044	0.013	10.958	0.040	0.040	0.000	0.000	0.000	0.000
80	D	82	ILE	0	-0.034	-0.036	9.992	0.047	0.047	0.000	0.000	0.000	0.000
81	D	83	SER	0	-0.019	-0.010	13.917	-0.075	-0.075	0.000	0.000	0.000	0.000
82	D	84	THR	0	0.042	0.020	15.977	0.028	0.028	0.000	0.000	0.000	0.000
83	D	85	ALA	0	-0.003	0.015	17.005	-0.039	-0.039	0.000	0.000	0.000	0.000
84	D	86	PRO	0	0.068	0.029	16.464	0.028	0.028	0.000	0.000	0.000	0.000
85	D	87	LYS	1	0.960	0.977	17.765	-0.219	-0.219	0.000	0.000	0.000	0.000
86	D	88	HIS	0	0.035	0.016	16.328	-0.058	-0.058	0.000	0.000	0.000	0.000
87	D	89	GLN	0	0.028	0.008	11.783	-0.068	-0.068	0.000	0.000	0.000	0.000
88	D	90	LEU	0	0.007	0.011	16.599	-0.018	-0.018	0.000	0.000	0.000	0.000
89	D	91	GLU	-1	-0.796	-0.887	19.438	0.196	0.196	0.000	0.000	0.000	0.000
90	D	92	LYS	1	0.971	0.990	14.635	-0.660	-0.660	0.000	0.000	0.000	0.000
91	D	93	ILE	0	0.009	-0.003	14.914	-0.012	-0.012	0.000	0.000	0.000	0.000
92	D	94	LYS	1	0.858	0.920	18.860	-0.221	-0.221	0.000	0.000	0.000	0.000
93	D	95	LYS	1	0.909	0.951	22.098	-0.264	-0.264	0.000	0.000	0.000	0.000
94	D	96	LEU	0	-0.063	-0.045	17.013	-0.005	-0.005	0.000	0.000	0.000	0.000
95	D	97	GLN	0	0.003	-0.003	21.346	-0.028	-0.028	0.000	0.000	0.000	0.000
96	D	98	ASN	0	-0.013	-0.014	23.078	-0.019	-0.019	0.000	0.000	0.000	0.000
97	D	99	SER	0	-0.011	-0.035	24.251	-0.002	-0.002	0.000	0.000	0.000	0.000
98	D	100	ILE	0	-0.042	-0.013	20.802	-0.008	-0.008	0.000	0.000	0.000	0.000
99	D	101	GLU	-1	-0.917	-0.941	24.652	0.065	0.065	0.000	0.000	0.000	0.000
100	D	102	GLU	-1	-0.760	-0.846	27.887	0.150	0.150	0.000	0.000	0.000	0.000
101	D	103	LYS	1	0.804	0.876	27.016	-0.129	-0.129	0.000	0.000	0.000	0.000
102	D	104	GLN	0	-0.027	-0.022	25.902	-0.020	-0.020	0.000	0.000	0.000	0.000
103	D	105	LEU	0	-0.004	0.015	29.474	-0.011	-0.011	0.000	0.000	0.000	0.000
104	D	106	GLU	-1	-0.814	-0.892	32.033	0.101	0.101	0.000	0.000	0.000	0.000
105	D	107	ARG	1	0.803	0.880	28.464	-0.048	-0.048	0.000	0.000	0.000	0.000
106	D	108	LYS	1	0.979	0.984	32.372	-0.036	-0.036	0.000	0.000	0.000	0.000
107	D	109	SER	0	-0.009	-0.003	34.544	-0.006	-0.006	0.000	0.000	0.000	0.000
108	D	110	LEU	0	-0.003	0.002	34.182	-0.004	-0.004	0.000	0.000	0.000	0.000
109	D	111	GLU	-1	-0.865	-0.920	32.666	0.026	0.026	0.000	0.000	0.000	0.000
110	D	112	SER	0	-0.023	-0.022	36.380	-0.005	-0.005	0.000	0.000	0.000	0.000
111	D	113	GLU	-1	-0.958	-0.965	39.618	0.038	0.038	0.000	0.000	0.000	0.000
112	D	114	ASN	0	0.052	0.024	38.103	-0.007	-0.007	0.000	0.000	0.000	0.000
113	D	115	GLU	-1	-0.826	-0.909	37.558	0.009	0.009	0.000	0.000	0.000	0.000
114	D	116	ASP	-1	-0.944	-0.953	41.289	0.016	0.016	0.000	0.000	0.000	0.000
115	D	117	LEU	0	0.015	0.005	42.320	-0.003	-0.003	0.000	0.000	0.000	0.000
116	D	118	LYS	1	0.806	0.883	37.227	-0.018	-0.018	0.000	0.000	0.000	0.000
117	D	119	LEU	0	-0.012	0.003	43.670	-0.003	-0.003	0.000	0.000	0.000	0.000
118	D	120	GLN	0	0.012	0.000	46.401	-0.002	-0.002	0.000	0.000	0.000	0.000
119	D	121	LEU	0	-0.004	-0.002	45.190	-0.001	-0.001	0.000	0.000	0.000	0.000
120	D	122	ALA	0	0.021	0.004	46.260	-0.001	-0.001	0.000	0.000	0.000	0.000
121	D	123	LYS	1	1.008	0.999	48.145	-0.005	-0.005	0.000	0.000	0.000	0.000
122	D	124	ARG	1	0.843	0.938	51.293	-0.016	-0.016	0.000	0.000	0.000	0.000
123	D	125	ILE	0	0.020	0.011	47.980	-0.001	-0.001	0.000	0.000	0.000	0.000
124	D	126	GLU	-1	-0.816	-0.894	51.310	-0.001	-0.001	0.000	0.000	0.000	0.000
125	D	127	THR	0	-0.034	-0.027	52.790	-0.001	-0.001	0.000	0.000	0.000	0.000
126	D	128	PHE	0	0.002	-0.002	53.617	0.000	0.000	0.000	0.000	0.000	0.000
127	D	129	GLY	0	0.021	0.029	54.188	-0.001	-0.001	0.000	0.000	0.000	0.000
128	D	130	ARG	1	0.829	0.896	55.008	0.000	0.000	0.000	0.000	0.000	0.000
129	D	131	LEU	0	-0.012	0.003	58.092	0.000	0.000	0.000	0.000	0.000	0.000
130	D	132	SER	0	-0.021	-0.033	56.847	-0.001	-0.001	0.000	0.000	0.000	0.000
131	D	133	CYS	0	-0.024	-0.002	57.873	-0.001	-0.001	0.000	0.000	0.000	0.000
132	D	134	VAL	0	0.012	-0.008	59.793	0.000	0.000	0.000	0.000	0.000	0.000
133	D	135	LEU	0	-0.048	-0.028	62.899	0.000	0.000	0.000	0.000	0.000	0.000
134	D	136	PHE	0	-0.051	-0.011	61.717	0.001	0.001	0.000	0.000	0.000	0.000
135	D	137	GLN	0	-0.036	-0.003	60.208	-0.001	-0.001	0.000	0.000	0.000	0.000

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