FMO DATABASE

FMODB ID: Z6VRN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-831977.844835
FMO2-HF: Nuclear repulsion	777640.155747
FMO2-HF: Total energy	-54337.689088
FMO2-MP2: Total energy	-54496.264848

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.
-6.554	-2.674	0.26	-1.446	-2.692	-0.004

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 : -0.021

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	-0.030	-0.023	3.718	-2.232	-0.640	0.005	-0.554	-1.042	0.003
4	D	6	THR	0	0.057	0.025	2.637	-3.784	-1.915	0.256	-0.809	-1.315	-0.007
5	D	7	GLN	0	0.040	0.043	4.261	1.074	1.493	-0.001	-0.083	-0.335	0.000
6	D	8	LEU	0	0.043	0.021	5.987	0.613	0.613	0.000	0.000	0.000	0.000
7	D	9	GLN	0	-0.035	-0.008	7.160	-0.015	-0.015	0.000	0.000	0.000	0.000
8	D	10	ASP	-1	-0.851	-0.926	7.601	-2.208	-2.208	0.000	0.000	0.000	0.000
9	D	11	THR	0	-0.075	-0.051	10.255	0.288	0.288	0.000	0.000	0.000	0.000
10	D	12	ILE	0	-0.009	-0.016	12.178	0.134	0.134	0.000	0.000	0.000	0.000
11	D	13	ASP	-1	-0.899	-0.945	13.190	-0.620	-0.620	0.000	0.000	0.000	0.000
12	D	14	GLU	-1	-0.843	-0.921	13.995	-0.475	-0.475	0.000	0.000	0.000	0.000
13	D	15	VAL	0	-0.026	-0.005	15.982	0.072	0.072	0.000	0.000	0.000	0.000
14	D	16	ALA	0	-0.002	0.004	18.214	0.042	0.042	0.000	0.000	0.000	0.000
15	D	17	THR	0	-0.033	-0.029	18.181	0.035	0.035	0.000	0.000	0.000	0.000
16	D	18	GLN	0	-0.014	-0.005	20.220	0.054	0.054	0.000	0.000	0.000	0.000
17	D	19	PHE	0	-0.004	0.007	22.042	0.030	0.030	0.000	0.000	0.000	0.000
18	D	20	TYR	0	0.007	0.012	22.122	0.026	0.026	0.000	0.000	0.000	0.000
19	D	21	SER	0	-0.035	-0.031	23.355	0.019	0.019	0.000	0.000	0.000	0.000
20	D	22	SER	0	-0.017	-0.020	25.795	0.023	0.023	0.000	0.000	0.000	0.000
21	D	23	ILE	0	0.006	-0.007	27.606	0.014	0.014	0.000	0.000	0.000	0.000
22	D	24	HIS	0	0.010	0.011	29.324	0.010	0.010	0.000	0.000	0.000	0.000
23	D	25	TYR	0	0.013	0.009	29.404	0.011	0.011	0.000	0.000	0.000	0.000
24	D	26	LEU	0	-0.034	-0.031	31.321	0.010	0.010	0.000	0.000	0.000	0.000
25	D	27	SER	0	-0.029	-0.010	33.765	0.007	0.007	0.000	0.000	0.000	0.000
26	D	28	SER	0	-0.079	-0.046	33.607	0.002	0.002	0.000	0.000	0.000	0.000
27	D	29	HIS	0	-0.073	-0.030	32.711	0.001	0.001	0.000	0.000	0.000	0.000
28	D	30	HIS	0	-0.049	-0.002	37.534	-0.001	-0.001	0.000	0.000	0.000	0.000
29	D	31	ASP	-1	-0.870	-0.934	40.344	-0.081	-0.081	0.000	0.000	0.000	0.000
30	D	32	PHE	0	-0.083	-0.029	42.349	0.005	0.005	0.000	0.000	0.000	0.000
31	D	33	VAL	0	0.030	0.012	46.153	0.002	0.002	0.000	0.000	0.000	0.000
32	D	34	PRO	0	-0.018	-0.012	47.971	0.000	0.000	0.000	0.000	0.000	0.000
33	D	35	LEU	0	-0.046	-0.027	49.992	0.001	0.001	0.000	0.000	0.000	0.000
34	D	36	PRO	0	-0.017	-0.020	53.205	0.001	0.001	0.000	0.000	0.000	0.000
35	D	37	GLY	0	-0.016	0.011	56.458	0.001	0.001	0.000	0.000	0.000	0.000
36	D	38	GLN	0	0.006	-0.003	55.572	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	39	GLU	-1	-0.850	-0.924	47.957	-0.057	-0.057	0.000	0.000	0.000	0.000
38	D	40	LYS	1	0.924	0.956	51.759	0.050	0.050	0.000	0.000	0.000	0.000
39	D	41	VAL	0	0.050	0.036	47.663	-0.001	-0.001	0.000	0.000	0.000	0.000
40	D	42	SER	0	-0.060	-0.037	48.100	0.002	0.002	0.000	0.000	0.000	0.000
41	D	43	ASP	-1	-0.850	-0.937	47.404	-0.074	-0.074	0.000	0.000	0.000	0.000
42	D	44	SER	0	-0.018	-0.004	45.728	-0.004	-0.004	0.000	0.000	0.000	0.000
43	D	45	LYS	1	0.898	0.936	43.822	0.078	0.078	0.000	0.000	0.000	0.000
44	D	46	VAL	0	-0.056	-0.008	42.574	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	47	ASN	0	0.002	0.012	38.266	0.000	0.000	0.000	0.000	0.000	0.000
46	D	48	PRO	0	0.014	-0.005	40.381	-0.003	-0.003	0.000	0.000	0.000	0.000
47	D	49	ILE	0	0.049	0.009	36.180	-0.003	-0.003	0.000	0.000	0.000	0.000
48	D	50	SER	0	-0.043	-0.047	40.150	0.006	0.006	0.000	0.000	0.000	0.000
49	D	51	ALA	0	0.028	0.012	40.024	-0.002	-0.002	0.000	0.000	0.000	0.000
50	D	52	GLU	-1	-0.955	-0.981	39.223	-0.048	-0.048	0.000	0.000	0.000	0.000
51	D	53	GLU	-1	-0.811	-0.891	36.971	-0.084	-0.084	0.000	0.000	0.000	0.000
52	D	54	LEU	0	-0.013	0.011	35.737	-0.005	-0.005	0.000	0.000	0.000	0.000
53	D	55	GLN	0	-0.005	-0.004	35.437	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	56	PHE	0	0.021	-0.001	31.876	0.002	0.002	0.000	0.000	0.000	0.000
55	D	57	ALA	0	0.053	0.033	31.604	-0.003	-0.003	0.000	0.000	0.000	0.000
56	D	58	GLN	0	0.005	-0.007	30.599	-0.004	-0.004	0.000	0.000	0.000	0.000
57	D	59	ARG	1	0.762	0.870	30.748	0.058	0.058	0.000	0.000	0.000	0.000
58	D	60	ASP	-1	-0.777	-0.875	27.947	-0.072	-0.072	0.000	0.000	0.000	0.000
59	D	61	LEU	0	0.037	0.031	25.664	-0.007	-0.007	0.000	0.000	0.000	0.000
60	D	62	ALA	0	-0.007	0.001	25.921	-0.008	-0.008	0.000	0.000	0.000	0.000
61	D	63	LYS	1	0.800	0.895	25.600	0.058	0.058	0.000	0.000	0.000	0.000
62	D	64	ASP	-1	-0.848	-0.907	20.763	-0.204	-0.204	0.000	0.000	0.000	0.000
63	D	65	LEU	0	0.089	0.054	21.268	-0.006	-0.006	0.000	0.000	0.000	0.000
64	D	66	VAL	0	-0.034	-0.027	21.597	0.003	0.003	0.000	0.000	0.000	0.000
65	D	67	THR	0	-0.056	-0.037	19.680	0.016	0.016	0.000	0.000	0.000	0.000
66	D	68	LYS	1	0.860	0.917	14.936	0.411	0.411	0.000	0.000	0.000	0.000
67	D	69	PHE	0	0.005	-0.004	17.095	-0.001	-0.001	0.000	0.000	0.000	0.000
68	D	70	MET	0	-0.038	-0.015	18.203	0.032	0.032	0.000	0.000	0.000	0.000
69	D	71	GLN	0	-0.028	-0.011	13.700	0.021	0.021	0.000	0.000	0.000	0.000
70	D	72	ILE	0	0.028	0.018	13.553	0.062	0.062	0.000	0.000	0.000	0.000
71	D	73	ASP	-1	-0.916	-0.943	14.213	0.252	0.252	0.000	0.000	0.000	0.000
72	D	74	THR	0	-0.028	-0.033	14.524	0.085	0.085	0.000	0.000	0.000	0.000
73	D	75	LEU	0	-0.014	-0.011	9.089	0.135	0.135	0.000	0.000	0.000	0.000
74	D	76	ILE	0	-0.018	-0.012	11.146	0.187	0.187	0.000	0.000	0.000	0.000
75	D	77	ASN	0	-0.071	-0.035	13.429	0.089	0.089	0.000	0.000	0.000	0.000
76	D	78	GLN	0	-0.068	-0.030	8.418	0.282	0.282	0.000	0.000	0.000	0.000
77	D	79	LEU	0	-0.036	0.003	8.614	0.379	0.379	0.000	0.000	0.000	0.000
78	D	80	PRO	0	-0.048	-0.013	8.751	-0.102	-0.102	0.000	0.000	0.000	0.000
79	D	81	GLY	0	0.038	0.010	11.508	0.029	0.029	0.000	0.000	0.000	0.000
80	D	82	ILE	0	-0.023	-0.031	10.326	0.037	0.037	0.000	0.000	0.000	0.000
81	D	83	SER	0	-0.036	-0.014	14.228	-0.080	-0.080	0.000	0.000	0.000	0.000
82	D	84	THR	0	0.064	0.031	15.264	0.028	0.028	0.000	0.000	0.000	0.000
83	D	85	ALA	0	-0.039	-0.008	16.345	-0.029	-0.029	0.000	0.000	0.000	0.000
84	D	86	PRO	0	0.087	0.038	16.331	0.051	0.051	0.000	0.000	0.000	0.000
85	D	87	LYS	1	0.968	0.989	17.540	-0.195	-0.195	0.000	0.000	0.000	0.000
86	D	88	HIS	0	0.050	0.021	16.057	-0.059	-0.059	0.000	0.000	0.000	0.000
87	D	89	GLN	0	0.026	0.008	11.325	-0.078	-0.078	0.000	0.000	0.000	0.000
88	D	90	LEU	0	-0.002	0.000	16.600	-0.019	-0.019	0.000	0.000	0.000	0.000
89	D	91	GLU	-1	-0.915	-0.960	18.862	0.183	0.183	0.000	0.000	0.000	0.000
90	D	92	LYS	1	0.959	0.981	14.773	-0.591	-0.591	0.000	0.000	0.000	0.000
91	D	93	ILE	0	-0.007	-0.013	14.451	-0.020	-0.020	0.000	0.000	0.000	0.000
92	D	94	LYS	1	0.995	1.001	18.524	-0.151	-0.151	0.000	0.000	0.000	0.000
93	D	95	LYS	1	0.946	0.978	22.094	-0.244	-0.244	0.000	0.000	0.000	0.000
94	D	96	LEU	0	-0.047	-0.039	16.909	-0.006	-0.006	0.000	0.000	0.000	0.000
95	D	97	GLN	0	-0.006	0.002	21.121	-0.023	-0.023	0.000	0.000	0.000	0.000
96	D	98	ASN	0	0.044	0.021	22.540	-0.021	-0.021	0.000	0.000	0.000	0.000
97	D	99	SER	0	-0.049	-0.022	24.084	0.001	0.001	0.000	0.000	0.000	0.000
98	D	100	ILE	0	-0.036	-0.020	20.825	-0.008	-0.008	0.000	0.000	0.000	0.000
99	D	101	GLU	-1	-0.972	-0.971	24.619	0.049	0.049	0.000	0.000	0.000	0.000
100	D	102	GLU	-1	-0.793	-0.904	27.403	0.124	0.124	0.000	0.000	0.000	0.000
101	D	103	LYS	1	0.793	0.869	26.699	-0.118	-0.118	0.000	0.000	0.000	0.000
102	D	104	GLN	0	0.003	-0.002	26.228	-0.016	-0.016	0.000	0.000	0.000	0.000
103	D	105	LEU	0	0.006	0.019	29.157	-0.010	-0.010	0.000	0.000	0.000	0.000
104	D	106	GLU	-1	-0.818	-0.894	31.874	0.091	0.091	0.000	0.000	0.000	0.000
105	D	107	ARG	1	0.822	0.888	28.498	-0.033	-0.033	0.000	0.000	0.000	0.000
106	D	108	LYS	1	0.986	0.995	32.254	-0.025	-0.025	0.000	0.000	0.000	0.000
107	D	109	SER	0	-0.014	-0.009	34.388	-0.005	-0.005	0.000	0.000	0.000	0.000
108	D	110	LEU	0	-0.006	-0.007	33.710	-0.004	-0.004	0.000	0.000	0.000	0.000
109	D	111	GLU	-1	-0.855	-0.902	32.661	0.018	0.018	0.000	0.000	0.000	0.000
110	D	112	SER	0	-0.009	-0.012	36.345	-0.005	-0.005	0.000	0.000	0.000	0.000
111	D	113	GLU	-1	-0.975	-0.979	39.571	0.034	0.034	0.000	0.000	0.000	0.000
112	D	114	ASN	0	0.046	0.020	37.836	-0.006	-0.006	0.000	0.000	0.000	0.000
113	D	115	GLU	-1	-0.843	-0.917	37.372	0.005	0.005	0.000	0.000	0.000	0.000
114	D	116	ASP	-1	-0.963	-0.966	40.915	0.013	0.013	0.000	0.000	0.000	0.000
115	D	117	LEU	0	0.028	0.007	42.701	-0.002	-0.002	0.000	0.000	0.000	0.000
116	D	118	LYS	1	0.786	0.873	36.940	-0.013	-0.013	0.000	0.000	0.000	0.000
117	D	119	LEU	0	-0.002	0.010	43.545	-0.003	-0.003	0.000	0.000	0.000	0.000
118	D	120	GLN	0	0.039	0.019	46.295	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	121	LEU	0	0.002	-0.003	45.089	-0.001	-0.001	0.000	0.000	0.000	0.000
120	D	122	ALA	0	0.037	0.018	45.996	-0.001	-0.001	0.000	0.000	0.000	0.000
121	D	123	LYS	1	0.981	0.992	47.941	-0.003	-0.003	0.000	0.000	0.000	0.000
122	D	124	ARG	1	0.848	0.923	51.298	-0.015	-0.015	0.000	0.000	0.000	0.000
123	D	125	ILE	0	0.009	0.004	47.739	-0.001	-0.001	0.000	0.000	0.000	0.000
124	D	126	GLU	-1	-0.814	-0.890	51.122	-0.002	-0.002	0.000	0.000	0.000	0.000
125	D	127	THR	0	-0.044	-0.028	52.855	-0.001	-0.001	0.000	0.000	0.000	0.000
126	D	128	PHE	0	0.015	0.010	53.541	0.000	0.000	0.000	0.000	0.000	0.000
127	D	129	GLY	0	0.022	0.030	54.024	0.000	0.000	0.000	0.000	0.000	0.000
128	D	130	ARG	1	0.831	0.901	54.852	0.001	0.001	0.000	0.000	0.000	0.000
129	D	131	LEU	0	-0.009	0.004	57.780	0.000	0.000	0.000	0.000	0.000	0.000
130	D	132	SER	0	-0.009	-0.030	56.676	0.000	0.000	0.000	0.000	0.000	0.000
131	D	133	CYS	0	-0.024	-0.003	57.653	-0.001	-0.001	0.000	0.000	0.000	0.000
132	D	134	VAL	0	0.026	-0.003	59.514	0.000	0.000	0.000	0.000	0.000	0.000
133	D	135	LEU	0	-0.057	-0.027	62.625	0.000	0.000	0.000	0.000	0.000	0.000
134	D	136	PHE	0	-0.065	-0.029	61.421	0.000	0.000	0.000	0.000	0.000	0.000
135	D	137	GLN	0	-0.052	-0.004	60.360	-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)