FMO DATABASE

FMODB ID: J36L9

Calculation Name: 3NJC-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJC

Chain ID: A

ChEMBL ID:

UniProt ID: P42955

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1566430.37513
FMO2-HF: Nuclear repulsion	1502366.148862
FMO2-HF: Total energy	-64064.226268
FMO2-MP2: Total energy	-64248.794554

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:-8:ACE )

Summations of interaction energy for fragment #1(A:-8: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.
-0.557	0.532	0.002	-0.456	-0.634	-0.001

Interaction energy analysis for fragmet #1(A:-8:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.015

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	-6	HIS	0	-0.029	-0.010	3.807	0.775	1.714	-0.001	-0.416	-0.522	-0.001
4	A	-5	HIS	0	0.024	0.000	6.304	0.196	0.196	0.000	0.000	0.000	0.000
5	A	-4	HIS	0	0.010	0.015	9.706	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	-3	HIS	1	0.794	0.886	9.977	0.701	0.701	0.000	0.000	0.000	0.000
7	A	-2	HIS	0	-0.014	-0.003	14.417	0.051	0.051	0.000	0.000	0.000	0.000
8	A	-1	SER	0	0.052	0.036	18.160	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	0	HIS	0	-0.029	-0.029	21.427	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	1	MET	0	-0.019	-0.015	24.254	0.005	0.005	0.000	0.000	0.000	0.000
11	A	2	LYS	1	0.980	1.017	28.052	0.096	0.096	0.000	0.000	0.000	0.000
12	A	3	SER	0	-0.016	-0.007	30.138	0.009	0.009	0.000	0.000	0.000	0.000
13	A	4	LYS	1	0.973	0.958	33.029	0.063	0.063	0.000	0.000	0.000	0.000
14	A	5	PHE	0	0.052	0.030	34.956	0.002	0.002	0.000	0.000	0.000	0.000
15	A	6	GLU	-1	-0.784	-0.879	30.029	-0.113	-0.113	0.000	0.000	0.000	0.000
16	A	7	ALA	0	-0.016	-0.014	33.508	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	8	SER	0	-0.085	-0.046	34.786	0.003	0.003	0.000	0.000	0.000	0.000
18	A	9	ILE	0	0.057	-0.007	33.096	0.003	0.003	0.000	0.000	0.000	0.000
19	A	10	ASP	-1	-0.879	-0.929	34.450	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	11	ASN	0	-0.086	-0.051	37.140	0.003	0.003	0.000	0.000	0.000	0.000
21	A	12	LEU	0	-0.083	-0.031	39.249	0.003	0.003	0.000	0.000	0.000	0.000
22	A	13	LYS	1	0.857	0.949	34.542	0.072	0.072	0.000	0.000	0.000	0.000
23	A	14	GLU	-1	-0.921	-0.960	40.199	-0.050	-0.050	0.000	0.000	0.000	0.000
24	A	15	ILE	0	-0.062	-0.014	43.335	0.003	0.003	0.000	0.000	0.000	0.000
25	A	16	GLU	-1	-0.912	-0.945	43.540	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	17	MET	0	-0.045	-0.030	42.460	0.001	0.001	0.000	0.000	0.000	0.000
27	A	18	ASN	0	0.002	0.006	43.372	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	19	ALA	0	0.091	0.018	40.399	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	20	TYR	0	-0.022	-0.002	40.600	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	21	ALA	0	0.006	-0.006	41.978	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	22	TYR	0	0.014	0.013	32.743	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	23	GLU	-1	-0.728	-0.863	36.228	-0.083	-0.083	0.000	0.000	0.000	0.000
33	A	24	LEU	0	-0.020	0.007	37.923	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	25	ILE	0	0.011	0.003	35.218	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	26	ARG	1	0.838	0.911	28.728	0.108	0.108	0.000	0.000	0.000	0.000
36	A	27	GLU	-1	-0.835	-0.931	32.243	-0.103	-0.103	0.000	0.000	0.000	0.000
37	A	28	ILE	0	-0.044	-0.009	35.204	0.003	0.003	0.000	0.000	0.000	0.000
38	A	29	VAL	0	0.028	0.018	36.632	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	30	LEU	0	-0.024	-0.015	30.734	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	31	PRO	0	0.006	0.005	32.132	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	32	ASP	-1	-0.913	-0.945	33.169	-0.069	-0.069	0.000	0.000	0.000	0.000
42	A	33	MET	0	-0.125	-0.060	34.183	0.002	0.002	0.000	0.000	0.000	0.000
43	A	34	LEU	0	-0.052	-0.023	28.368	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	35	GLY	0	0.037	0.029	30.114	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	36	GLN	0	-0.054	-0.038	27.754	0.001	0.001	0.000	0.000	0.000	0.000
46	A	37	ASP	-1	-0.904	-0.950	25.604	-0.143	-0.143	0.000	0.000	0.000	0.000
47	A	38	TYR	0	0.003	-0.007	25.275	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	39	SER	0	0.015	0.000	23.404	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	40	SER	0	0.033	0.001	20.463	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	41	MET	0	-0.016	-0.004	21.055	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	42	MET	0	0.008	0.008	23.376	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	43	TYR	0	-0.056	-0.049	14.652	-0.026	-0.026	0.000	0.000	0.000	0.000
53	A	44	TRP	0	0.010	-0.015	15.212	0.000	0.000	0.000	0.000	0.000	0.000
54	A	45	ALA	0	0.014	0.020	19.729	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	46	GLY	0	0.034	0.018	21.910	0.010	0.010	0.000	0.000	0.000	0.000
56	A	47	LYS	1	0.890	0.953	13.025	0.567	0.567	0.000	0.000	0.000	0.000
57	A	48	HIS	0	-0.030	-0.032	19.116	0.022	0.022	0.000	0.000	0.000	0.000
58	A	49	LEU	0	-0.009	0.004	21.357	0.012	0.012	0.000	0.000	0.000	0.000
59	A	50	ALA	0	0.039	0.016	19.925	0.014	0.014	0.000	0.000	0.000	0.000
60	A	51	ARG	1	0.839	0.929	14.570	0.364	0.364	0.000	0.000	0.000	0.000
61	A	52	LYS	1	0.868	0.935	21.447	0.152	0.152	0.000	0.000	0.000	0.000
62	A	53	PHE	0	-0.073	-0.042	24.729	0.018	0.018	0.000	0.000	0.000	0.000
63	A	54	PRO	0	-0.018	0.014	22.298	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	55	LEU	0	-0.026	-0.018	22.749	0.013	0.013	0.000	0.000	0.000	0.000
65	A	56	GLU	-1	-0.969	-0.992	22.644	-0.089	-0.089	0.000	0.000	0.000	0.000
66	A	57	SER	0	-0.026	-0.010	22.559	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	58	TRP	0	0.018	-0.022	16.996	0.005	0.005	0.000	0.000	0.000	0.000
68	A	59	GLU	-1	-0.978	-0.973	23.001	-0.063	-0.063	0.000	0.000	0.000	0.000
69	A	60	GLU	-1	-0.802	-0.907	25.997	-0.093	-0.093	0.000	0.000	0.000	0.000
70	A	61	PHE	0	-0.047	-0.029	20.193	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	62	PRO	0	-0.003	-0.003	26.139	0.000	0.000	0.000	0.000	0.000	0.000
72	A	63	ALA	0	0.050	0.026	29.377	0.002	0.002	0.000	0.000	0.000	0.000
73	A	64	PHE	0	0.012	0.014	27.597	0.000	0.000	0.000	0.000	0.000	0.000
74	A	65	PHE	0	-0.006	-0.024	24.294	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	66	GLU	-1	-0.867	-0.916	29.743	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	67	GLU	-1	-0.861	-0.926	33.232	-0.069	-0.069	0.000	0.000	0.000	0.000
77	A	68	ALA	0	-0.070	-0.021	30.668	0.002	0.002	0.000	0.000	0.000	0.000
78	A	69	GLY	0	-0.025	-0.013	32.626	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	70	TRP	0	-0.090	-0.059	25.503	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	71	GLY	0	-0.026	-0.014	31.338	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	72	THR	0	-0.016	-0.019	32.286	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	73	LEU	0	-0.029	-0.003	25.456	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	74	THR	0	0.030	0.014	29.871	0.002	0.002	0.000	0.000	0.000	0.000
84	A	75	ASN	0	-0.074	-0.054	24.223	0.003	0.003	0.000	0.000	0.000	0.000
85	A	76	VAL	0	0.029	0.033	26.010	0.007	0.007	0.000	0.000	0.000	0.000
86	A	77	SER	0	-0.027	-0.022	22.875	0.011	0.011	0.000	0.000	0.000	0.000
87	A	78	ALA	0	0.073	0.040	22.171	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	79	LYS	1	0.904	0.958	19.740	0.056	0.056	0.000	0.000	0.000	0.000
89	A	80	LYS	1	0.958	0.972	14.958	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	81	GLN	0	-0.064	-0.053	11.564	0.035	0.035	0.000	0.000	0.000	0.000
91	A	82	GLU	-1	-0.922	-0.965	14.730	-0.130	-0.130	0.000	0.000	0.000	0.000
92	A	83	LEU	0	-0.059	-0.012	17.348	0.020	0.020	0.000	0.000	0.000	0.000
93	A	84	GLU	-1	-0.925	-0.965	20.132	-0.098	-0.098	0.000	0.000	0.000	0.000
94	A	85	PHE	0	0.039	-0.003	21.852	0.010	0.010	0.000	0.000	0.000	0.000
95	A	86	GLU	-1	-0.911	-0.951	25.751	-0.069	-0.069	0.000	0.000	0.000	0.000
96	A	87	LEU	0	-0.013	-0.002	27.700	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	88	GLU	-1	-0.886	-0.971	30.153	-0.066	-0.066	0.000	0.000	0.000	0.000
98	A	89	GLY	0	0.115	0.062	33.779	0.000	0.000	0.000	0.000	0.000	0.000
99	A	90	PRO	0	-0.011	-0.014	37.033	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	91	ILE	0	0.022	0.007	36.359	0.001	0.001	0.000	0.000	0.000	0.000
101	A	92	ILE	0	0.027	0.029	32.024	0.000	0.000	0.000	0.000	0.000	0.000
102	A	93	SER	0	0.023	0.003	35.201	0.001	0.001	0.000	0.000	0.000	0.000
103	A	94	ASN	0	-0.036	-0.016	37.800	0.005	0.005	0.000	0.000	0.000	0.000
104	A	95	ARG	1	0.808	0.878	31.865	0.090	0.090	0.000	0.000	0.000	0.000
105	A	96	LEU	0	-0.015	-0.013	32.223	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	97	LYS	1	0.900	0.979	35.601	0.046	0.046	0.000	0.000	0.000	0.000
107	A	98	HIS	0	-0.053	-0.040	38.801	0.005	0.005	0.000	0.000	0.000	0.000
108	A	99	GLN	0	-0.010	0.001	33.652	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	100	LYS	1	0.936	0.970	32.132	0.073	0.073	0.000	0.000	0.000	0.000
110	A	101	GLU	-1	-0.972	-1.001	28.559	-0.096	-0.096	0.000	0.000	0.000	0.000
111	A	102	PRO	0	0.020	0.035	30.304	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	103	CYS	0	-0.043	-0.013	26.129	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	104	PHE	0	0.053	0.013	25.600	0.007	0.007	0.000	0.000	0.000	0.000
114	A	105	GLN	0	0.027	0.005	19.379	0.006	0.006	0.000	0.000	0.000	0.000
115	A	106	LEU	0	0.004	0.024	21.762	-0.021	-0.021	0.000	0.000	0.000	0.000
116	A	107	GLU	-1	-0.798	-0.921	22.941	-0.149	-0.149	0.000	0.000	0.000	0.000
117	A	108	ALA	0	-0.005	-0.003	19.472	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	109	GLY	0	0.011	-0.004	17.957	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	110	PHE	0	0.006	0.007	18.329	-0.028	-0.028	0.000	0.000	0.000	0.000
120	A	111	ILE	0	0.018	0.007	18.481	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	112	ALA	0	0.009	0.005	14.488	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	113	GLU	-1	-0.857	-0.926	14.801	-0.479	-0.479	0.000	0.000	0.000	0.000
123	A	114	GLN	0	0.009	-0.006	16.286	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	115	ILE	0	-0.014	0.003	13.927	0.012	0.012	0.000	0.000	0.000	0.000
125	A	116	GLN	0	-0.058	-0.036	8.880	0.036	0.036	0.000	0.000	0.000	0.000
126	A	117	LEU	0	-0.103	-0.042	13.523	0.014	0.014	0.000	0.000	0.000	0.000
127	A	118	MET	0	-0.023	0.015	16.427	0.024	0.024	0.000	0.000	0.000	0.000
128	A	119	ASN	0	-0.008	-0.005	13.723	0.041	0.041	0.000	0.000	0.000	0.000
129	A	120	ASP	-1	-0.858	-0.918	11.981	-0.193	-0.193	0.000	0.000	0.000	0.000
130	A	121	GLN	0	-0.047	-0.043	9.783	0.020	0.020	0.000	0.000	0.000	0.000
131	A	122	ILE	0	-0.033	-0.008	8.788	0.048	0.048	0.000	0.000	0.000	0.000
132	A	123	ALA	0	-0.071	-0.043	3.744	-0.201	-0.122	0.003	-0.031	-0.051	0.000
133	A	124	GLU	-1	-0.857	-0.913	5.590	-2.123	-2.123	0.000	0.000	0.000	0.000
134	A	125	SER	0	-0.023	-0.038	7.169	0.308	0.308	0.000	0.000	0.000	0.000
135	A	126	TYR	0	-0.066	-0.030	7.132	-0.074	-0.074	0.000	0.000	0.000	0.000
136	A	127	GLU	-1	-0.789	-0.864	12.982	-0.403	-0.403	0.000	0.000	0.000	0.000
137	A	128	GLN	0	-0.057	-0.030	16.659	0.020	0.020	0.000	0.000	0.000	0.000
138	A	129	VAL	0	0.056	0.032	19.798	0.007	0.007	0.000	0.000	0.000	0.000
139	A	130	LYS	1	0.903	0.959	23.300	0.085	0.085	0.000	0.000	0.000	0.000
140	A	131	LYS	1	0.919	0.969	25.954	0.113	0.113	0.000	0.000	0.000	0.000
141	A	132	ARG	1	0.868	0.941	28.446	0.071	0.071	0.000	0.000	0.000	0.000
142	A	133	ALA	0	-0.028	-0.020	32.313	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	134	ASP	-1	-0.903	-0.950	35.754	-0.053	-0.053	0.000	0.000	0.000	0.000
144	A	135	LYN	0	0.054	0.037	31.668	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	136	VAL	0	-0.060	-0.032	27.797	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	137	VAL	0	-0.002	0.000	24.724	0.002	0.002	0.000	0.000	0.000	0.000
147	A	138	LEU	0	-0.023	-0.009	22.557	-0.010	-0.010	0.000	0.000	0.000	0.000
148	A	139	THR	0	0.039	0.013	18.625	0.009	0.009	0.000	0.000	0.000	0.000
149	A	140	VAL	0	-0.002	0.016	15.137	-0.026	-0.026	0.000	0.000	0.000	0.000
150	A	141	LYS	1	0.973	0.993	12.775	0.259	0.259	0.000	0.000	0.000	0.000
151	A	142	TRP	0	0.010	-0.001	9.976	-0.076	-0.076	0.000	0.000	0.000	0.000
152	A	143	ASP	-1	-0.875	-0.920	6.478	-0.079	-0.079	0.000	0.000	0.000	0.000
153	A	144	MET	0	-0.053	-0.025	7.786	-0.180	-0.180	0.000	0.000	0.000	0.000
154	A	145	LYS	1	0.878	0.949	4.674	0.549	0.620	0.000	-0.009	-0.061	0.000
155	A	146	NME	0	-0.006	0.000	5.731	0.091	0.091	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-8:ACE )