FMO DATABASE

FMODB ID: 2NJ4R

Calculation Name: 2P38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P38

Chain ID: A

ChEMBL ID:

UniProt ID: Q9V219

Base Structure: X-ray

Registration Date: 2023-09-21

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1559375.309053
FMO2-HF: Nuclear repulsion	1497517.462713
FMO2-HF: Total energy	-61857.846339
FMO2-MP2: Total energy	-62043.136867

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-7.037	-4.478	11.917	-4.07	-10.403	-0.028

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.030

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	7	VAL	0	-0.040	-0.028	3.265	-2.283	-0.043	0.079	-0.891	-1.428	0.001
4	A	8	ARG	1	0.721	0.808	5.207	0.945	0.993	-0.001	-0.003	-0.044	0.000
5	A	9	ARG	1	1.007	1.007	8.709	0.576	0.576	0.000	0.000	0.000	0.000
6	A	10	ALA	0	-0.052	-0.018	11.605	-0.042	-0.042	0.000	0.000	0.000	0.000
7	A	11	SER	0	0.003	-0.011	12.892	0.059	0.059	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.079	0.028	15.234	0.014	0.014	0.000	0.000	0.000	0.000
9	A	13	TRP	0	0.002	-0.015	16.191	0.012	0.012	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.750	-0.832	11.764	-0.454	-0.454	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.047	0.015	15.942	0.007	0.007	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.846	-0.905	17.921	-0.115	-0.115	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.114	-0.049	16.182	0.016	0.016	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.054	-0.029	14.294	0.012	0.012	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.068	0.022	18.426	0.014	0.014	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.943	0.990	21.989	0.087	0.087	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.879	-0.932	19.890	-0.068	-0.068	0.000	0.000	0.000	0.000
18	A	22	ALA	0	0.013	-0.004	21.939	0.011	0.011	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.857	-0.920	23.392	-0.081	-0.081	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.638	0.796	23.215	0.079	0.079	0.000	0.000	0.000	0.000
21	A	25	TYR	0	-0.098	-0.050	23.972	0.009	0.009	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.024	0.020	27.650	0.006	0.006	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.863	-0.908	27.625	-0.086	-0.086	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.054	-0.029	20.117	0.000	0.000	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.004	-0.005	24.048	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	30	HIS	0	-0.088	-0.040	17.018	0.018	0.018	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.904	-0.959	20.610	-0.168	-0.168	0.000	0.000	0.000	0.000
28	A	32	PHE	0	0.015	0.026	16.550	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	33	PHE	0	0.054	-0.003	13.331	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	34	CYS	0	-0.046	-0.014	8.765	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.025	-0.011	7.329	0.081	0.081	0.000	0.000	0.000	0.000
32	A	36	VAL	0	-0.010	-0.001	2.078	-0.310	-1.596	5.196	-1.104	-2.806	-0.008
33	A	37	GLU	-1	-0.862	-0.928	3.839	-0.620	-0.137	0.002	-0.116	-0.369	0.000
34	A	38	GLY	0	0.046	0.012	2.332	-3.826	-1.685	3.875	-2.919	-3.097	-0.020
35	A	39	LYS	1	0.900	0.955	3.081	1.474	-0.071	0.127	1.651	-0.232	-0.001
36	A	40	TYR	0	-0.007	-0.013	6.065	0.024	0.024	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.904	0.961	5.715	0.089	0.089	0.000	0.000	0.000	0.000
38	A	42	ASP	-1	-0.858	-0.918	5.601	-0.185	-0.185	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.019	-0.007	7.462	-0.170	-0.170	0.000	0.000	0.000	0.000
40	A	44	TYR	0	-0.007	-0.019	5.451	0.128	0.128	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.041	0.032	10.644	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.022	-0.011	11.408	0.007	0.007	0.000	0.000	0.000	0.000
43	A	47	ASN	0	0.076	0.034	14.367	0.010	0.010	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.838	-0.934	16.715	-0.194	-0.194	0.000	0.000	0.000	0.000
45	A	49	GLU	-1	-0.962	-0.977	18.122	-0.197	-0.197	0.000	0.000	0.000	0.000
46	A	50	VAL	0	0.002	-0.010	12.423	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	51	TRP	0	0.003	-0.003	13.838	-0.060	-0.060	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.911	0.946	14.959	0.152	0.152	0.000	0.000	0.000	0.000
49	A	53	ILE	0	0.039	0.026	12.957	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.056	-0.037	8.456	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.961	-0.975	11.664	-0.475	-0.475	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.941	-0.949	14.297	-0.289	-0.289	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.079	-0.035	11.422	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	58	ASN	0	0.007	0.000	4.472	0.123	0.210	-0.001	-0.017	-0.068	0.000
55	A	59	MET	0	0.028	0.015	7.008	0.197	0.197	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.915	0.953	3.167	-1.195	-0.481	0.081	-0.202	-0.592	0.000
57	A	61	PRO	0	0.114	0.029	2.238	-0.221	-0.589	2.560	-0.466	-1.726	0.000
58	A	62	TYR	0	-0.058	-0.034	5.345	-0.128	-0.083	-0.001	-0.003	-0.041	0.000
59	A	63	SER	0	-0.019	0.000	7.989	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.037	0.003	6.380	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.066	0.032	10.128	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.020	-0.006	11.329	0.024	0.024	0.000	0.000	0.000	0.000
63	A	67	PHE	0	-0.011	0.014	8.705	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	68	VAL	0	0.025	0.012	10.734	0.042	0.042	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.046	0.021	11.627	0.035	0.035	0.000	0.000	0.000	0.000
66	A	70	THR	0	-0.045	-0.010	9.004	-0.039	-0.039	0.000	0.000	0.000	0.000
67	A	71	ILE	0	-0.002	0.006	10.600	0.050	0.050	0.000	0.000	0.000	0.000
68	A	72	ARG	1	0.825	0.914	11.284	0.035	0.035	0.000	0.000	0.000	0.000
69	A	73	VAL	0	0.004	0.028	13.693	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	74	ASP	-1	-0.850	-0.906	16.874	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.911	-0.971	19.548	0.032	0.032	0.000	0.000	0.000	0.000
72	A	76	ASN	0	-0.144	-0.083	22.659	0.009	0.009	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.015	-0.014	21.050	0.000	0.000	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.008	-0.001	21.488	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	79	GLU	-1	-0.875	-0.921	16.572	-0.097	-0.097	0.000	0.000	0.000	0.000
76	A	80	LYN	0	0.052	0.031	16.978	0.000	0.000	0.000	0.000	0.000	0.000
77	A	81	PHE	0	0.066	0.023	13.408	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	82	TYR	0	-0.060	-0.043	14.687	0.034	0.034	0.000	0.000	0.000	0.000
79	A	83	PRO	0	0.050	0.057	14.860	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.038	-0.041	13.457	0.022	0.022	0.000	0.000	0.000	0.000
81	A	85	LEU	0	0.015	-0.016	16.730	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.873	-0.930	15.906	-0.091	-0.091	0.000	0.000	0.000	0.000
83	A	87	PHE	0	0.034	0.015	16.893	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	88	PHE	0	-0.027	-0.030	18.116	0.001	0.001	0.000	0.000	0.000	0.000
85	A	89	SER	0	-0.039	-0.009	19.800	0.004	0.004	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.006	-0.009	17.136	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.032	0.002	21.779	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.995	1.010	24.781	0.067	0.067	0.000	0.000	0.000	0.000
89	A	93	LEU	0	-0.051	-0.028	27.929	0.001	0.001	0.000	0.000	0.000	0.000
90	A	94	GLU	-1	-0.922	-0.973	29.529	-0.058	-0.058	0.000	0.000	0.000	0.000
91	A	95	LYS	1	0.871	0.904	30.598	0.061	0.061	0.000	0.000	0.000	0.000
92	A	96	ASN	0	-0.092	-0.058	29.930	0.002	0.002	0.000	0.000	0.000	0.000
93	A	97	TYR	0	0.029	0.018	30.070	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	98	VAL	0	-0.045	-0.033	31.951	0.003	0.003	0.000	0.000	0.000	0.000
95	A	99	ILE	0	0.047	0.041	33.224	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.018	-0.002	33.381	0.003	0.003	0.000	0.000	0.000	0.000
97	A	101	GLY	0	0.024	0.000	36.618	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.085	0.058	37.301	0.000	0.000	0.000	0.000	0.000	0.000
99	A	103	LYS	1	0.929	0.961	37.126	0.011	0.011	0.000	0.000	0.000	0.000
100	A	104	ALA	0	0.032	0.006	36.967	0.001	0.001	0.000	0.000	0.000	0.000
101	A	105	SER	0	0.013	0.010	33.619	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	106	PHE	0	0.043	0.017	32.608	0.000	0.000	0.000	0.000	0.000	0.000
103	A	107	LEU	0	-0.007	0.012	32.708	0.001	0.001	0.000	0.000	0.000	0.000
104	A	108	PHE	0	0.012	0.016	27.634	0.002	0.002	0.000	0.000	0.000	0.000
105	A	109	THR	0	-0.036	-0.035	28.388	0.000	0.000	0.000	0.000	0.000	0.000
106	A	110	THR	0	-0.072	-0.039	28.211	0.002	0.002	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.076	0.046	28.360	0.004	0.004	0.000	0.000	0.000	0.000
108	A	112	LYS	1	0.744	0.880	29.170	0.004	0.004	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.790	-0.899	31.912	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.009	-0.002	33.464	0.000	0.000	0.000	0.000	0.000	0.000
111	A	115	PRO	0	-0.059	-0.024	35.770	0.000	0.000	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.997	0.972	39.260	0.010	0.010	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.900	-0.944	40.687	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	118	ALA	0	-0.044	-0.021	38.835	0.000	0.000	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.044	-0.029	37.023	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	120	ARG	1	0.933	0.964	39.045	0.021	0.021	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.851	-0.915	38.237	-0.032	-0.032	0.000	0.000	0.000	0.000
118	A	122	ILE	0	-0.025	-0.013	36.031	0.000	0.000	0.000	0.000	0.000	0.000
119	A	123	LYS	1	0.945	1.017	35.548	0.040	0.040	0.000	0.000	0.000	0.000
120	A	124	TRP	0	-0.070	-0.030	32.533	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	125	GLN	0	0.016	-0.014	33.697	0.001	0.001	0.000	0.000	0.000	0.000
122	A	126	GLY	0	0.069	0.002	33.351	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	127	SER	0	-0.068	-0.036	27.861	0.002	0.002	0.000	0.000	0.000	0.000
124	A	128	LYS	1	0.914	0.959	27.735	0.023	0.023	0.000	0.000	0.000	0.000
125	A	129	ARG	1	0.965	0.986	22.355	0.038	0.038	0.000	0.000	0.000	0.000
126	A	130	VAL	0	0.012	0.037	27.228	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	131	VAL	0	0.083	0.040	25.717	0.001	0.001	0.000	0.000	0.000	0.000
128	A	132	VAL	0	-0.046	-0.023	27.920	0.003	0.003	0.000	0.000	0.000	0.000
129	A	133	LEU	0	0.020	0.017	29.081	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	134	ASN	0	0.077	0.024	31.484	0.002	0.002	0.000	0.000	0.000	0.000
131	A	135	ASP	-1	-0.949	-0.993	33.584	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	136	LEU	0	-0.037	-0.029	34.269	0.001	0.001	0.000	0.000	0.000	0.000
133	A	137	GLY	0	-0.001	0.015	33.634	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	138	ASP	-1	-0.887	-0.932	29.223	-0.045	-0.045	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.020	-0.023	24.605	0.004	0.004	0.000	0.000	0.000	0.000
136	A	140	ILE	0	-0.046	-0.021	26.702	0.001	0.001	0.000	0.000	0.000	0.000
137	A	141	GLY	0	0.045	0.000	24.667	0.003	0.003	0.000	0.000	0.000	0.000
138	A	142	ILE	0	-0.086	-0.021	22.723	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	143	GLY	0	0.068	0.024	25.759	0.005	0.005	0.000	0.000	0.000	0.000
140	A	144	LEU	0	-0.064	-0.039	26.604	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	145	ILE	0	0.054	0.058	29.507	0.004	0.004	0.000	0.000	0.000	0.000
142	A	146	ASN	0	-0.110	-0.070	32.912	0.002	0.002	0.000	0.000	0.000	0.000
143	A	147	PRO	0	-0.014	-0.014	34.930	0.001	0.001	0.000	0.000	0.000	0.000
144	A	148	LYS	1	1.023	1.013	38.028	0.004	0.004	0.000	0.000	0.000	0.000
145	A	149	SER	0	-0.050	-0.018	38.035	0.001	0.001	0.000	0.000	0.000	0.000
146	A	150	ASP	-1	-0.782	-0.896	40.114	-0.010	-0.010	0.000	0.000	0.000	0.000
147	A	151	ARG	1	0.872	0.929	40.479	0.006	0.006	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.949	0.977	35.464	0.000	0.000	0.000	0.000	0.000	0.000
149	A	153	PHE	0	0.012	0.021	35.628	0.000	0.000	0.000	0.000	0.000	0.000
150	A	154	ILE	0	0.004	0.009	31.540	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	155	LYS	1	0.858	0.931	30.575	0.014	0.014	0.000	0.000	0.000	0.000
152	A	156	ASN	0	0.016	-0.004	27.136	-0.005	-0.005	0.000	0.000	0.000	0.000
153	A	157	LEU	0	-0.100	-0.042	23.793	0.003	0.003	0.000	0.000	0.000	0.000
154	A	158	LYS	1	0.870	0.928	19.148	0.064	0.064	0.000	0.000	0.000	0.000
155	A	159	ASP	-1	-0.774	-0.878	23.156	-0.019	-0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)