FMO DATABASE

FMODB ID: JM829

Calculation Name: 3NJ2-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJ2

Chain ID: A

ChEMBL ID:

UniProt ID: B1WPD5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1452864.146135
FMO2-HF: Nuclear repulsion	1393282.411372
FMO2-HF: Total energy	-59581.734764
FMO2-MP2: Total energy	-59758.566295

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:23:ACE )

Summations of interaction energy for fragment #1(A:23:ACE )

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.
-0.406	1.339	-0.005	-0.724	-1.017	-0.002

Interaction energy analysis for fragmet #1(A:23:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.012

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	25	GLU	-1	-0.817	-0.911	3.855	-1.209	0.168	-0.006	-0.652	-0.720	-0.002
4	A	26	THR	0	-0.005	-0.010	4.141	0.006	0.190	0.001	-0.047	-0.137	0.000
5	A	27	ASN	0	0.007	0.001	4.538	0.492	0.676	0.000	-0.025	-0.160	0.000
6	A	28	THR	0	0.030	0.005	6.185	0.243	0.243	0.000	0.000	0.000	0.000
7	A	29	LEU	0	-0.007	0.005	8.519	0.163	0.163	0.000	0.000	0.000	0.000
8	A	30	LEU	0	0.001	0.006	8.867	0.089	0.089	0.000	0.000	0.000	0.000
9	A	31	VAL	0	-0.044	-0.038	10.469	0.073	0.073	0.000	0.000	0.000	0.000
10	A	32	GLU	-1	-0.938	-0.940	12.506	-0.180	-0.180	0.000	0.000	0.000	0.000
11	A	33	GLN	0	0.002	-0.020	13.381	0.053	0.053	0.000	0.000	0.000	0.000
12	A	34	SER	0	-0.052	-0.017	13.886	0.038	0.038	0.000	0.000	0.000	0.000
13	A	35	PRO	0	0.045	0.012	15.615	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	36	PHE	0	0.035	0.019	16.500	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	37	LEU	0	-0.025	-0.028	12.102	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	38	GLN	0	-0.021	-0.022	16.471	0.005	0.005	0.000	0.000	0.000	0.000
17	A	39	SER	0	-0.032	-0.012	18.955	0.005	0.005	0.000	0.000	0.000	0.000
18	A	40	LEU	0	-0.029	-0.013	17.062	0.004	0.004	0.000	0.000	0.000	0.000
19	A	41	VAL	0	0.016	0.013	17.390	0.000	0.000	0.000	0.000	0.000	0.000
20	A	42	GLN	0	0.002	0.003	20.211	0.004	0.004	0.000	0.000	0.000	0.000
21	A	43	GLN	0	-0.001	-0.003	23.502	0.009	0.009	0.000	0.000	0.000	0.000
22	A	44	ILE	0	0.001	-0.008	19.673	0.005	0.005	0.000	0.000	0.000	0.000
23	A	45	ARG	1	0.804	0.873	19.927	0.197	0.197	0.000	0.000	0.000	0.000
24	A	46	ALA	0	-0.016	0.007	25.397	0.007	0.007	0.000	0.000	0.000	0.000
25	A	47	TYR	0	-0.044	-0.033	27.398	0.009	0.009	0.000	0.000	0.000	0.000
26	A	48	ASP	-1	-0.805	-0.870	26.632	-0.121	-0.121	0.000	0.000	0.000	0.000
27	A	49	HIS	0	0.016	0.008	28.705	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	50	TYR	0	-0.028	-0.020	31.602	0.004	0.004	0.000	0.000	0.000	0.000
29	A	51	GLY	0	-0.054	-0.031	28.682	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	52	VAL	0	-0.033	-0.011	26.973	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	53	TYR	0	-0.021	-0.041	22.743	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	54	ARG	1	0.936	0.966	23.381	0.088	0.088	0.000	0.000	0.000	0.000
33	A	55	THR	0	-0.020	0.007	23.815	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	56	TRP	0	-0.026	0.001	19.244	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	57	THR	0	0.086	0.027	14.766	0.025	0.025	0.000	0.000	0.000	0.000
36	A	58	ASP	-1	-0.750	-0.877	16.067	-0.227	-0.227	0.000	0.000	0.000	0.000
37	A	59	GLU	-1	-0.867	-0.926	8.887	-1.086	-1.086	0.000	0.000	0.000	0.000
38	A	60	LEU	0	-0.023	-0.018	13.564	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	61	VAL	0	-0.028	-0.005	15.634	0.028	0.028	0.000	0.000	0.000	0.000
40	A	62	ILE	0	0.014	0.010	13.554	0.031	0.031	0.000	0.000	0.000	0.000
41	A	63	ALA	0	0.013	0.005	13.625	0.023	0.023	0.000	0.000	0.000	0.000
42	A	64	PRO	0	-0.015	-0.010	14.605	0.020	0.020	0.000	0.000	0.000	0.000
43	A	65	TYR	0	-0.070	-0.038	15.887	0.035	0.035	0.000	0.000	0.000	0.000
44	A	66	VAL	0	-0.053	-0.012	10.228	0.034	0.034	0.000	0.000	0.000	0.000
45	A	67	ILE	0	0.021	0.015	13.659	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	68	PRO	0	0.043	0.026	11.594	0.051	0.051	0.000	0.000	0.000	0.000
47	A	69	LYS	1	1.023	1.003	13.697	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	70	LYS	1	0.940	0.954	15.498	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	71	LYS	1	1.002	1.015	16.512	0.185	0.185	0.000	0.000	0.000	0.000
50	A	72	ARG	1	0.871	0.924	15.605	0.051	0.051	0.000	0.000	0.000	0.000
51	A	73	ARG	1	0.883	0.923	19.704	0.007	0.007	0.000	0.000	0.000	0.000
52	A	74	GLU	-1	-0.905	-0.947	21.902	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	75	ILE	0	-0.068	0.004	20.921	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	76	SER	0	0.037	0.017	24.717	0.008	0.008	0.000	0.000	0.000	0.000
55	A	77	LEU	0	-0.023	-0.032	27.346	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	78	GLU	-1	-0.959	-0.976	30.363	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	79	GLY	0	0.007	0.018	32.690	0.002	0.002	0.000	0.000	0.000	0.000
58	A	80	ASP	-1	-0.865	-0.929	33.311	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	81	ILE	0	-0.103	-0.049	28.017	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	82	ASP	-1	-0.849	-0.933	27.868	-0.084	-0.084	0.000	0.000	0.000	0.000
61	A	83	PRO	0	0.026	-0.013	29.350	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	84	THR	0	0.037	0.024	25.217	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	85	THR	0	-0.039	-0.030	24.317	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	86	LYS	1	0.956	0.983	25.886	0.048	0.048	0.000	0.000	0.000	0.000
65	A	87	LEU	0	0.049	0.045	26.790	0.002	0.002	0.000	0.000	0.000	0.000
66	A	88	ARG	1	0.971	0.999	20.542	0.123	0.123	0.000	0.000	0.000	0.000
67	A	89	ILE	0	-0.001	0.009	23.473	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	90	LEU	0	0.025	0.007	25.174	0.004	0.004	0.000	0.000	0.000	0.000
69	A	91	CYS	0	-0.009	-0.009	23.682	0.003	0.003	0.000	0.000	0.000	0.000
70	A	92	TYR	0	-0.023	-0.013	18.972	0.004	0.004	0.000	0.000	0.000	0.000
71	A	93	PHE	0	0.030	0.001	22.802	0.006	0.006	0.000	0.000	0.000	0.000
72	A	94	ARG	1	0.923	0.961	25.883	0.064	0.064	0.000	0.000	0.000	0.000
73	A	95	ALA	0	-0.005	0.010	21.763	0.003	0.003	0.000	0.000	0.000	0.000
74	A	96	ILE	0	-0.044	-0.019	22.594	0.005	0.005	0.000	0.000	0.000	0.000
75	A	97	ALA	0	0.002	0.005	24.511	0.005	0.005	0.000	0.000	0.000	0.000
76	A	98	ALA	0	0.016	0.011	25.463	0.003	0.003	0.000	0.000	0.000	0.000
77	A	99	LEU	0	-0.018	-0.013	21.110	0.001	0.001	0.000	0.000	0.000	0.000
78	A	100	ILE	0	0.014	0.000	25.139	0.005	0.005	0.000	0.000	0.000	0.000
79	A	101	GLU	-1	-0.919	-0.947	28.174	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	102	LYS	1	0.888	0.941	22.544	0.059	0.059	0.000	0.000	0.000	0.000
81	A	103	GLU	-1	-0.923	-0.960	25.954	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	104	THR	0	-0.069	-0.031	29.024	0.004	0.004	0.000	0.000	0.000	0.000
83	A	105	GLY	0	0.014	-0.001	32.152	0.002	0.002	0.000	0.000	0.000	0.000
84	A	106	LEU	0	-0.054	-0.013	33.701	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	107	LEU	0	-0.015	-0.005	30.682	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	108	CYS	0	-0.059	-0.018	31.869	0.003	0.003	0.000	0.000	0.000	0.000
87	A	109	GLN	0	-0.023	-0.002	32.843	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	110	VAL	0	0.018	-0.012	29.305	0.001	0.001	0.000	0.000	0.000	0.000
89	A	111	VAL	0	0.000	0.010	32.548	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	112	VAL	0	-0.042	-0.025	28.621	0.002	0.002	0.000	0.000	0.000	0.000
91	A	113	ASP	-1	-0.961	-0.966	31.897	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	114	LEU	0	-0.050	-0.030	29.310	0.002	0.002	0.000	0.000	0.000	0.000
93	A	115	ASN	0	0.051	0.031	33.897	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	116	HIS	0	0.038	0.027	34.308	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	117	GLU	-1	-0.824	-0.923	34.069	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	118	GLY	0	-0.062	-0.029	30.872	0.001	0.001	0.000	0.000	0.000	0.000
97	A	119	PHE	0	-0.049	-0.039	30.758	0.003	0.003	0.000	0.000	0.000	0.000
98	A	120	GLY	0	0.077	0.033	32.960	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	121	TRP	0	-0.027	-0.008	32.504	0.004	0.004	0.000	0.000	0.000	0.000
100	A	122	ALA	0	-0.015	0.008	28.717	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	123	LEU	0	-0.025	-0.025	30.628	0.005	0.005	0.000	0.000	0.000	0.000
102	A	124	VAL	0	0.028	0.009	28.729	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	125	TRP	0	-0.011	-0.014	32.252	0.003	0.003	0.000	0.000	0.000	0.000
104	A	126	GLY	0	0.076	0.024	35.383	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	127	GLY	0	0.076	0.069	37.056	0.002	0.002	0.000	0.000	0.000	0.000
106	A	128	LYS	1	0.845	0.902	40.777	0.010	0.010	0.000	0.000	0.000	0.000
107	A	129	LEU	0	0.019	0.020	35.762	0.002	0.002	0.000	0.000	0.000	0.000
108	A	130	MET	0	-0.024	-0.008	34.691	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	131	VAL	0	0.003	0.013	30.541	0.003	0.003	0.000	0.000	0.000	0.000
110	A	132	VAL	0	0.001	0.004	27.333	0.002	0.002	0.000	0.000	0.000	0.000
111	A	133	SER	0	0.047	0.008	30.645	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	134	ARG	1	0.870	0.944	24.393	0.006	0.006	0.000	0.000	0.000	0.000
113	A	135	SER	0	0.052	0.030	29.864	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	136	LEU	0	-0.086	-0.042	26.992	0.001	0.001	0.000	0.000	0.000	0.000
115	A	137	ARG	1	0.974	0.974	28.535	0.005	0.005	0.000	0.000	0.000	0.000
116	A	138	ASP	-1	-0.882	-0.932	27.286	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	139	ALA	0	0.012	-0.005	26.444	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	140	HIS	0	0.024	0.006	25.702	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	141	ARG	1	0.827	0.916	22.682	0.022	0.022	0.000	0.000	0.000	0.000
120	A	142	PHE	0	-0.034	-0.012	20.931	0.002	0.002	0.000	0.000	0.000	0.000
121	A	143	GLY	0	0.039	0.015	18.252	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	144	PHE	0	-0.075	-0.031	14.377	0.030	0.030	0.000	0.000	0.000	0.000
123	A	145	ASP	-1	-0.864	-0.938	12.008	0.002	0.002	0.000	0.000	0.000	0.000
124	A	146	THR	0	0.002	-0.006	8.014	-0.045	-0.045	0.000	0.000	0.000	0.000
125	A	147	LEU	0	0.070	0.040	7.820	0.067	0.067	0.000	0.000	0.000	0.000
126	A	148	GLU	-1	-0.867	-0.929	6.548	0.531	0.531	0.000	0.000	0.000	0.000
127	A	149	LYS	1	0.892	0.949	9.720	-0.131	-0.131	0.000	0.000	0.000	0.000
128	A	150	LEU	0	-0.022	0.006	12.632	0.006	0.006	0.000	0.000	0.000	0.000
129	A	151	ASN	0	0.097	0.053	12.435	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	152	ASP	-1	-0.882	-0.931	13.085	0.127	0.127	0.000	0.000	0.000	0.000
131	A	153	GLN	0	-0.059	-0.030	15.383	0.012	0.012	0.000	0.000	0.000	0.000
132	A	154	GLY	0	-0.010	-0.021	17.604	0.001	0.001	0.000	0.000	0.000	0.000
133	A	155	THR	0	0.027	0.002	16.902	0.000	0.000	0.000	0.000	0.000	0.000
134	A	156	LYS	1	0.927	0.976	19.410	-0.043	-0.043	0.000	0.000	0.000	0.000
135	A	157	LEU	0	-0.073	-0.036	21.287	0.002	0.002	0.000	0.000	0.000	0.000
136	A	158	ALA	0	0.044	0.029	22.809	0.000	0.000	0.000	0.000	0.000	0.000
137	A	159	ASN	0	0.028	0.002	21.471	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	160	ALA	0	-0.031	-0.012	24.957	0.002	0.002	0.000	0.000	0.000	0.000
139	A	161	GLY	0	0.010	-0.012	27.249	0.000	0.000	0.000	0.000	0.000	0.000
140	A	162	ILE	0	0.029	0.022	25.756	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	163	GLU	-1	-0.939	-0.977	28.569	0.018	0.018	0.000	0.000	0.000	0.000
142	A	164	LEU	0	-0.052	-0.012	31.128	0.000	0.000	0.000	0.000	0.000	0.000
143	A	165	VAL	0	-0.018	-0.025	32.807	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	166	ASN	0	0.004	-0.004	32.413	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	167	LYS	1	0.888	0.962	35.322	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	168	PHE	0	-0.048	-0.011	36.905	0.001	0.001	0.000	0.000	0.000	0.000
147	A	169	PRO	0	0.045	0.023	39.326	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	170	GLU	-1	-0.855	-0.952	40.620	0.001	0.001	0.000	0.000	0.000	0.000
149	A	171	VAL	0	-0.018	0.002	40.287	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	172	ALA	0	-0.050	-0.037	37.373	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	173	ARG	1	0.843	0.911	35.708	0.008	0.008	0.000	0.000	0.000	0.000
152	A	174	LEU	-1	-0.958	-0.945	41.398	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:ACE )