FMO DATABASE

FMODB ID: V5KK1

Calculation Name: 3NJE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJE

Chain ID: A

ChEMBL ID:

UniProt ID: Q00517

Base Structure: X-ray

Registration Date: 2023-06-22

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1646549.60304
FMO2-HF: Nuclear repulsion	1582241.126413
FMO2-HF: Total energy	-64308.476627
FMO2-MP2: Total energy	-64498.490599

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:35:ARG)

Summations of interaction energy for fragment #1(A:35:ARG)

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.
-19.389	-14.742	0.2	-1.805	-3.043	-0.002

Interaction energy analysis for fragmet #1(A:35:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.040 / q_NPA : 1.008

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	37	GLN	0	0.019	0.002	2.976	-2.502	-0.115	0.042	-0.991	-1.438	0.002
4	A	38	GLU	-1	-0.847	-0.912	2.917	-51.074	-49.215	0.159	-0.708	-1.310	-0.004
5	A	39	GLN	0	-0.100	-0.066	4.152	-0.891	-0.490	-0.001	-0.106	-0.295	0.000
6	A	40	ARG	1	0.990	0.997	5.825	27.578	27.578	0.000	0.000	0.000	0.000
7	A	41	MET	0	0.040	0.039	7.903	2.247	2.247	0.000	0.000	0.000	0.000
8	A	42	ARG	1	0.877	0.923	5.954	42.783	42.783	0.000	0.000	0.000	0.000
9	A	43	GLU	-1	-0.886	-0.924	9.587	-25.065	-25.065	0.000	0.000	0.000	0.000
10	A	44	LEU	0	0.046	0.027	11.991	1.641	1.641	0.000	0.000	0.000	0.000
11	A	45	VAL	0	-0.006	-0.007	13.141	1.399	1.399	0.000	0.000	0.000	0.000
12	A	46	ARG	1	0.912	0.951	12.565	23.024	23.024	0.000	0.000	0.000	0.000
13	A	47	ALA	0	-0.009	0.008	16.034	1.092	1.092	0.000	0.000	0.000	0.000
14	A	48	MET	0	0.018	0.002	17.797	1.161	1.161	0.000	0.000	0.000	0.000
15	A	49	GLY	0	0.023	0.014	18.865	0.711	0.711	0.000	0.000	0.000	0.000
16	A	50	ALA	0	-0.074	-0.051	20.293	0.680	0.680	0.000	0.000	0.000	0.000
17	A	51	LEU	0	0.058	0.038	22.226	0.547	0.547	0.000	0.000	0.000	0.000
18	A	52	GLU	-1	-0.811	-0.875	23.382	-12.669	-12.669	0.000	0.000	0.000	0.000
19	A	53	ARG	1	0.928	0.962	20.067	15.006	15.006	0.000	0.000	0.000	0.000
20	A	54	ASP	-1	-0.740	-0.841	26.433	-11.244	-11.244	0.000	0.000	0.000	0.000
21	A	55	LEU	0	0.025	0.017	27.244	0.425	0.425	0.000	0.000	0.000	0.000
22	A	56	THR	0	-0.059	-0.040	28.612	0.391	0.391	0.000	0.000	0.000	0.000
23	A	57	GLN	0	-0.080	-0.039	30.420	0.397	0.397	0.000	0.000	0.000	0.000
24	A	58	ALA	0	0.036	0.032	32.769	0.208	0.208	0.000	0.000	0.000	0.000
25	A	59	VAL	0	-0.029	-0.024	34.591	0.134	0.134	0.000	0.000	0.000	0.000
26	A	60	GLU	-1	-0.763	-0.870	38.276	-7.633	-7.633	0.000	0.000	0.000	0.000
27	A	61	ARG	1	0.918	0.966	40.496	7.514	7.514	0.000	0.000	0.000	0.000
28	A	62	PRO	0	0.066	0.057	40.745	-0.246	-0.246	0.000	0.000	0.000	0.000
29	A	63	VAL	0	-0.063	-0.040	39.337	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	64	ARG	1	0.892	0.953	42.562	6.561	6.561	0.000	0.000	0.000	0.000
31	A	65	ASP	-1	-0.842	-0.931	41.561	-7.363	-7.363	0.000	0.000	0.000	0.000
32	A	66	GLU	-1	-0.953	-0.996	42.377	-7.256	-7.256	0.000	0.000	0.000	0.000
33	A	67	LEU	0	-0.036	-0.014	44.379	0.148	0.148	0.000	0.000	0.000	0.000
34	A	68	GLY	0	-0.040	-0.013	46.388	0.175	0.175	0.000	0.000	0.000	0.000
35	A	69	ASP	-1	-0.880	-0.932	44.804	-6.787	-6.787	0.000	0.000	0.000	0.000
36	A	70	ASN	0	-0.059	-0.031	45.039	-0.164	-0.164	0.000	0.000	0.000	0.000
37	A	71	ARG	1	0.860	0.914	37.177	8.001	8.001	0.000	0.000	0.000	0.000
38	A	72	GLY	0	0.091	0.035	41.626	0.003	0.003	0.000	0.000	0.000	0.000
39	A	73	ALA	0	-0.032	-0.006	39.679	-0.231	-0.231	0.000	0.000	0.000	0.000
40	A	74	PHE	0	-0.015	-0.029	32.586	-0.352	-0.352	0.000	0.000	0.000	0.000
41	A	75	LEU	0	-0.031	0.002	36.196	0.214	0.214	0.000	0.000	0.000	0.000
42	A	76	SER	0	-0.019	-0.038	34.588	-0.305	-0.305	0.000	0.000	0.000	0.000
43	A	77	GLU	-1	-0.735	-0.842	34.664	-8.192	-8.192	0.000	0.000	0.000	0.000
44	A	78	GLY	0	-0.018	-0.010	33.993	-0.297	-0.297	0.000	0.000	0.000	0.000
45	A	79	GLU	-1	-0.916	-0.965	32.534	-8.781	-8.781	0.000	0.000	0.000	0.000
46	A	80	ASN	0	-0.072	-0.055	32.311	-0.081	-0.081	0.000	0.000	0.000	0.000
47	A	81	ASP	-1	-0.796	-0.859	33.066	-8.386	-8.386	0.000	0.000	0.000	0.000
48	A	82	GLN	0	-0.021	-0.015	27.498	-0.304	-0.304	0.000	0.000	0.000	0.000
49	A	83	ILE	0	-0.069	-0.031	29.199	-0.488	-0.488	0.000	0.000	0.000	0.000
50	A	84	VAL	0	0.036	0.033	30.062	0.284	0.284	0.000	0.000	0.000	0.000
51	A	85	GLU	-1	-0.803	-0.885	30.987	-9.007	-9.007	0.000	0.000	0.000	0.000
52	A	86	PHE	0	0.010	0.006	29.467	0.146	0.146	0.000	0.000	0.000	0.000
53	A	87	THR	0	-0.024	-0.017	33.941	-0.268	-0.268	0.000	0.000	0.000	0.000
54	A	88	ARG	1	0.840	0.905	28.295	10.537	10.537	0.000	0.000	0.000	0.000
55	A	89	GLY	0	0.104	0.051	34.438	0.138	0.138	0.000	0.000	0.000	0.000
56	A	90	GLY	0	-0.048	-0.013	32.760	-0.310	-0.310	0.000	0.000	0.000	0.000
57	A	91	TRP	0	-0.031	-0.006	26.465	-0.042	-0.042	0.000	0.000	0.000	0.000
58	A	102	LEU	0	0.006	0.012	36.364	0.044	0.044	0.000	0.000	0.000	0.000
59	A	103	GLN	0	-0.069	-0.056	29.464	-0.160	-0.160	0.000	0.000	0.000	0.000
60	A	104	ARG	1	0.798	0.889	34.188	8.558	8.558	0.000	0.000	0.000	0.000
61	A	105	VAL	0	-0.035	-0.027	28.863	-0.309	-0.309	0.000	0.000	0.000	0.000
62	A	106	ARG	1	0.807	0.875	29.261	9.456	9.456	0.000	0.000	0.000	0.000
63	A	107	TRP	0	-0.030	-0.013	21.582	-0.737	-0.737	0.000	0.000	0.000	0.000
64	A	108	SER	0	0.048	0.018	25.958	0.462	0.462	0.000	0.000	0.000	0.000
65	A	109	LEU	0	0.006	0.003	22.591	-0.613	-0.613	0.000	0.000	0.000	0.000
66	A	110	SER	0	-0.027	0.003	24.003	0.590	0.590	0.000	0.000	0.000	0.000
67	A	111	GLY	0	0.035	0.017	23.301	-0.482	-0.482	0.000	0.000	0.000	0.000
68	A	112	GLU	-1	-0.781	-0.863	18.166	-14.083	-14.083	0.000	0.000	0.000	0.000
69	A	113	THR	0	-0.050	-0.029	18.254	-0.664	-0.664	0.000	0.000	0.000	0.000
70	A	114	LEU	0	-0.013	0.001	19.471	0.669	0.669	0.000	0.000	0.000	0.000
71	A	115	GLU	-1	-0.818	-0.901	20.534	-12.742	-12.742	0.000	0.000	0.000	0.000
72	A	116	ARG	1	0.800	0.890	23.093	12.458	12.458	0.000	0.000	0.000	0.000
73	A	117	ARG	1	0.839	0.887	24.729	10.896	10.896	0.000	0.000	0.000	0.000
74	A	118	TYR	0	0.040	0.012	25.441	0.135	0.135	0.000	0.000	0.000	0.000
75	A	119	TRP	0	0.021	0.011	29.962	-0.256	-0.256	0.000	0.000	0.000	0.000
76	A	120	LEU	0	-0.018	-0.009	33.060	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	121	VAL	0	0.021	0.018	35.524	0.095	0.095	0.000	0.000	0.000	0.000
78	A	122	LEU	0	-0.047	-0.033	38.882	0.024	0.024	0.000	0.000	0.000	0.000
79	A	123	ASP	-1	-0.892	-0.935	41.851	-6.874	-6.874	0.000	0.000	0.000	0.000
80	A	124	ARG	1	0.828	0.899	42.839	7.382	7.382	0.000	0.000	0.000	0.000
81	A	125	ALA	0	0.085	0.049	41.624	-0.160	-0.160	0.000	0.000	0.000	0.000
82	A	126	GLN	0	0.053	0.049	41.036	-0.177	-0.177	0.000	0.000	0.000	0.000
83	A	127	ASP	-1	-0.852	-0.894	40.153	-7.980	-7.980	0.000	0.000	0.000	0.000
84	A	128	SER	0	-0.025	-0.020	36.847	-0.189	-0.189	0.000	0.000	0.000	0.000
85	A	129	LYS	1	0.806	0.874	33.704	8.313	8.313	0.000	0.000	0.000	0.000
86	A	130	PRO	0	-0.011	0.002	31.662	-0.285	-0.285	0.000	0.000	0.000	0.000
87	A	131	ARG	1	0.886	0.953	26.758	10.774	10.774	0.000	0.000	0.000	0.000
88	A	132	VAL	0	0.042	0.011	24.274	0.061	0.061	0.000	0.000	0.000	0.000
89	A	133	GLN	0	-0.046	-0.019	21.087	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	134	GLN	0	0.011	-0.006	19.010	-0.291	-0.291	0.000	0.000	0.000	0.000
91	A	135	VAL	0	-0.068	-0.039	17.370	-0.855	-0.855	0.000	0.000	0.000	0.000
92	A	136	LEU	0	-0.029	-0.014	13.822	-1.169	-1.169	0.000	0.000	0.000	0.000
93	A	137	ASP	-1	-0.808	-0.882	14.250	-15.919	-15.919	0.000	0.000	0.000	0.000
94	A	138	GLY	0	0.005	0.012	15.046	-0.841	-0.841	0.000	0.000	0.000	0.000
95	A	139	VAL	0	-0.058	-0.037	16.197	0.096	0.096	0.000	0.000	0.000	0.000
96	A	140	THR	0	0.018	-0.002	18.871	0.222	0.222	0.000	0.000	0.000	0.000
97	A	141	ALA	0	-0.017	0.001	21.194	0.564	0.564	0.000	0.000	0.000	0.000
98	A	142	LEU	0	0.005	0.000	22.612	-0.596	-0.596	0.000	0.000	0.000	0.000
99	A	143	SER	0	0.026	0.017	25.068	0.337	0.337	0.000	0.000	0.000	0.000
100	A	144	TRP	0	-0.032	-0.036	26.367	-0.568	-0.568	0.000	0.000	0.000	0.000
101	A	145	ARG	1	0.844	0.905	29.966	9.313	9.313	0.000	0.000	0.000	0.000
102	A	146	PHE	0	-0.002	-0.004	32.221	-0.347	-0.347	0.000	0.000	0.000	0.000
103	A	147	LEU	0	-0.039	0.007	34.979	0.178	0.178	0.000	0.000	0.000	0.000
104	A	148	ASP	-1	-0.684	-0.851	36.992	-7.281	-7.281	0.000	0.000	0.000	0.000
105	A	149	LYS	1	0.948	0.955	40.704	6.740	6.740	0.000	0.000	0.000	0.000
106	A	150	GLU	-1	-0.979	-0.980	43.307	-6.398	-6.398	0.000	0.000	0.000	0.000
107	A	151	HIS	0	-0.086	-0.049	40.250	-0.117	-0.117	0.000	0.000	0.000	0.000
108	A	152	ASN	0	-0.007	0.008	40.056	-0.089	-0.089	0.000	0.000	0.000	0.000
109	A	153	TRP	0	-0.066	-0.047	32.129	-0.158	-0.158	0.000	0.000	0.000	0.000
110	A	154	GLN	0	0.010	0.001	37.151	0.108	0.108	0.000	0.000	0.000	0.000
111	A	155	GLY	0	-0.014	-0.024	35.228	-0.273	-0.273	0.000	0.000	0.000	0.000
112	A	156	HIS	0	-0.019	0.002	35.347	-0.119	-0.119	0.000	0.000	0.000	0.000
113	A	157	TRP	0	-0.050	-0.018	37.158	0.061	0.061	0.000	0.000	0.000	0.000
114	A	158	PRO	0	0.046	0.014	38.800	-0.136	-0.136	0.000	0.000	0.000	0.000
115	A	159	THR	0	0.010	-0.009	41.521	0.001	0.001	0.000	0.000	0.000	0.000
116	A	160	ASP	-1	-0.883	-0.947	43.596	-6.481	-6.481	0.000	0.000	0.000	0.000
117	A	161	GLU	-1	-0.961	-0.968	46.736	-6.175	-6.175	0.000	0.000	0.000	0.000
118	A	162	GLY	0	-0.015	-0.009	48.164	-0.097	-0.097	0.000	0.000	0.000	0.000
119	A	163	SER	0	-0.062	-0.071	50.663	0.006	0.006	0.000	0.000	0.000	0.000
120	A	164	GLU	-1	-0.869	-0.960	49.659	-6.533	-6.533	0.000	0.000	0.000	0.000
121	A	165	GLU	-1	-0.967	-0.976	48.660	-6.247	-6.247	0.000	0.000	0.000	0.000
122	A	166	GLU	-1	-0.819	-0.884	47.929	-6.358	-6.358	0.000	0.000	0.000	0.000
123	A	167	ARG	1	0.844	0.925	45.379	6.385	6.385	0.000	0.000	0.000	0.000
124	A	168	LEU	0	-0.039	-0.020	43.979	-0.233	-0.233	0.000	0.000	0.000	0.000
125	A	169	GLU	-1	-0.924	-0.962	43.438	-6.974	-6.974	0.000	0.000	0.000	0.000
126	A	170	SER	0	-0.067	-0.016	42.826	-0.182	-0.182	0.000	0.000	0.000	0.000
127	A	171	LEU	0	-0.030	-0.019	36.964	-0.172	-0.172	0.000	0.000	0.000	0.000
128	A	172	PRO	0	-0.001	0.017	35.052	0.141	0.141	0.000	0.000	0.000	0.000
129	A	173	LEU	0	0.026	0.007	36.902	-0.121	-0.121	0.000	0.000	0.000	0.000
130	A	174	ALA	0	-0.049	-0.033	32.606	-0.216	-0.216	0.000	0.000	0.000	0.000
131	A	175	VAL	0	0.025	0.025	29.293	0.177	0.177	0.000	0.000	0.000	0.000
132	A	176	GLU	-1	-0.857	-0.892	27.984	-10.018	-10.018	0.000	0.000	0.000	0.000
133	A	177	MET	0	-0.020	0.007	20.973	-0.063	-0.063	0.000	0.000	0.000	0.000
134	A	178	THR	0	0.008	-0.003	23.860	-0.265	-0.265	0.000	0.000	0.000	0.000
135	A	179	LEU	0	-0.021	-0.012	17.751	0.069	0.069	0.000	0.000	0.000	0.000
136	A	180	GLU	-1	-0.851	-0.925	19.358	-11.637	-11.637	0.000	0.000	0.000	0.000
137	A	181	HIS	0	0.008	-0.001	11.790	-0.159	-0.159	0.000	0.000	0.000	0.000
138	A	182	ARG	1	0.812	0.858	14.613	13.749	13.749	0.000	0.000	0.000	0.000
139	A	183	HIS	0	-0.066	-0.047	9.841	-0.589	-0.589	0.000	0.000	0.000	0.000
140	A	184	TYR	0	-0.027	-0.019	11.335	-0.751	-0.751	0.000	0.000	0.000	0.000
141	A	185	GLY	0	0.047	0.045	12.771	0.361	0.361	0.000	0.000	0.000	0.000
142	A	186	LYS	1	0.857	0.927	16.320	10.971	10.971	0.000	0.000	0.000	0.000
143	A	187	LEU	0	-0.038	-0.017	17.324	-0.286	-0.286	0.000	0.000	0.000	0.000
144	A	188	VAL	0	0.022	0.007	19.743	0.274	0.274	0.000	0.000	0.000	0.000
145	A	189	ARG	1	0.843	0.927	20.247	13.118	13.118	0.000	0.000	0.000	0.000
146	A	190	VAL	0	0.039	0.016	24.068	0.286	0.286	0.000	0.000	0.000	0.000
147	A	191	TRP	0	-0.091	-0.066	22.515	-0.246	-0.246	0.000	0.000	0.000	0.000
148	A	192	ARG	1	0.970	0.982	28.809	9.252	9.252	0.000	0.000	0.000	0.000
149	A	193	LEU	0	-0.015	-0.001	31.972	-0.289	-0.289	0.000	0.000	0.000	0.000
150	A	194	LEU	0	-0.054	-0.028	33.516	0.103	0.103	0.000	0.000	0.000	0.000
151	A	195	ASP	-1	-0.929	-0.932	35.804	-7.581	-7.581	0.000	0.000	0.000	0.000
152	A	196	PRO	0	-0.021	-0.023	39.203	0.076	0.076	0.000	0.000	0.000	0.000
153	A	197	PRO	0	0.037	0.008	37.884	-0.172	-0.172	0.000	0.000	0.000	0.000
154	A	198	LEU	0	-0.009	0.005	35.323	0.231	0.231	0.000	0.000	0.000	0.000
155	A	199	LYS	1	0.842	0.908	38.799	7.628	7.628	0.000	0.000	0.000	0.000
156	A	200	GLN	0	-0.024	-0.012	37.418	-0.185	-0.185	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:35:ARG)