FMO DATABASE

FMODB ID: 82YJY

Calculation Name: 3NJC-A-Xray372

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: 2023-06-20

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	OptAll
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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1562833.799417
FMO2-HF: Nuclear repulsion	1498939.480597
FMO2-HF: Total energy	-63894.31882
FMO2-MP2: Total energy	-64078.383805

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:-7:HIS)

Summations of interaction energy for fragment #1(A:-7:HIS)

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.
-73.356	-72.017	37.94	-17.248	-22.027	-0.031

Interaction energy analysis for fragmet #1(A:-7:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / 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	-5	HIS	0	0.010	0.014	2.508	-7.756	-3.306	2.553	-2.699	-4.303	0.027
4	A	-4	HIS	0	0.022	0.018	3.466	1.267	2.152	0.044	-0.294	-0.635	-0.001
5	A	-3	HIS	1	0.840	0.906	1.867	-23.682	-28.900	14.957	-4.562	-5.176	0.053
6	A	-2	HIS	0	-0.055	-0.024	6.564	-1.382	-1.382	0.000	0.000	0.000	0.000
7	A	-1	SER	0	0.063	0.030	10.326	0.064	0.064	0.000	0.000	0.000	0.000
8	A	0	HIS	0	-0.057	-0.047	13.295	0.025	0.025	0.000	0.000	0.000	0.000
9	A	1	MET	0	-0.018	-0.011	16.238	-0.097	-0.097	0.000	0.000	0.000	0.000
10	A	2	LYS	1	0.865	0.954	20.027	-0.322	-0.322	0.000	0.000	0.000	0.000
11	A	3	SER	0	-0.043	-0.050	21.687	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	4	LYS	1	0.963	0.949	24.343	-0.317	-0.317	0.000	0.000	0.000	0.000
13	A	5	PHE	0	0.048	0.039	25.932	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	6	GLU	-1	-0.702	-0.807	20.854	0.351	0.351	0.000	0.000	0.000	0.000
15	A	7	ALA	0	0.000	0.014	24.563	0.005	0.005	0.000	0.000	0.000	0.000
16	A	8	SER	0	-0.072	-0.048	26.373	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	9	ILE	0	0.064	0.020	24.361	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	10	ASP	-1	-0.818	-0.905	25.722	0.218	0.218	0.000	0.000	0.000	0.000
19	A	11	ASN	0	-0.100	-0.060	28.574	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	12	LEU	0	-0.054	-0.034	31.232	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	13	LYS	1	0.799	0.903	26.550	-0.163	-0.163	0.000	0.000	0.000	0.000
22	A	14	GLU	-1	-0.937	-0.960	32.165	0.064	0.064	0.000	0.000	0.000	0.000
23	A	15	ILE	0	-0.055	-0.017	35.061	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	16	GLU	-1	-0.899	-0.941	35.377	0.019	0.019	0.000	0.000	0.000	0.000
25	A	17	MET	0	-0.047	-0.029	33.939	0.002	0.002	0.000	0.000	0.000	0.000
26	A	18	ASN	0	-0.025	-0.011	35.322	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	19	ALA	0	0.098	0.029	32.876	0.000	0.000	0.000	0.000	0.000	0.000
28	A	20	TYR	0	-0.026	-0.005	32.901	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	21	ALA	0	0.026	0.003	34.049	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	22	TYR	0	-0.014	-0.007	25.152	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	23	GLU	-1	-0.759	-0.869	29.135	-0.144	-0.144	0.000	0.000	0.000	0.000
32	A	24	LEU	0	-0.032	-0.005	30.081	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	25	ILE	0	0.007	0.004	26.705	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	26	ARG	1	0.755	0.835	21.073	0.212	0.212	0.000	0.000	0.000	0.000
35	A	27	GLU	-1	-0.777	-0.876	25.407	-0.236	-0.236	0.000	0.000	0.000	0.000
36	A	28	ILE	0	-0.044	-0.010	27.918	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	29	VAL	0	0.033	0.015	28.899	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	30	LEU	0	-0.011	-0.003	22.746	0.002	0.002	0.000	0.000	0.000	0.000
39	A	31	PRO	0	-0.008	-0.006	24.952	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	32	ASP	-1	-0.915	-0.955	25.926	-0.142	-0.142	0.000	0.000	0.000	0.000
41	A	33	MET	0	-0.122	-0.058	26.282	0.010	0.010	0.000	0.000	0.000	0.000
42	A	34	LEU	0	-0.047	-0.018	20.784	0.001	0.001	0.000	0.000	0.000	0.000
43	A	35	GLY	0	0.018	0.016	23.225	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	36	GLN	0	-0.090	-0.059	22.314	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	37	ASP	-1	-0.861	-0.929	19.284	-0.479	-0.479	0.000	0.000	0.000	0.000
46	A	38	TYR	0	-0.002	-0.013	18.580	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	39	SER	0	0.007	-0.001	18.035	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	40	SER	0	0.022	-0.002	14.509	-0.076	-0.076	0.000	0.000	0.000	0.000
49	A	41	MET	0	-0.015	-0.010	13.947	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	42	MET	0	0.008	0.011	15.503	0.081	0.081	0.000	0.000	0.000	0.000
51	A	43	TYR	0	-0.054	-0.031	8.000	0.034	0.034	0.000	0.000	0.000	0.000
52	A	44	TRP	0	-0.010	-0.019	8.533	0.198	0.198	0.000	0.000	0.000	0.000
53	A	45	ALA	0	0.032	0.024	11.570	0.207	0.207	0.000	0.000	0.000	0.000
54	A	46	GLY	0	0.038	0.026	13.650	0.123	0.123	0.000	0.000	0.000	0.000
55	A	47	LYS	1	0.824	0.915	5.106	1.085	1.085	0.000	0.000	0.000	0.000
56	A	48	HIS	0	-0.046	-0.038	10.425	0.300	0.300	0.000	0.000	0.000	0.000
57	A	49	LEU	0	-0.003	0.006	12.750	0.116	0.116	0.000	0.000	0.000	0.000
58	A	50	ALA	0	0.031	0.017	11.552	0.041	0.041	0.000	0.000	0.000	0.000
59	A	51	ARG	1	0.775	0.878	6.312	-3.739	-3.739	0.000	0.000	0.000	0.000
60	A	52	LYS	1	0.826	0.907	13.225	-0.411	-0.411	0.000	0.000	0.000	0.000
61	A	53	PHE	0	-0.009	-0.011	16.575	-0.061	-0.061	0.000	0.000	0.000	0.000
62	A	54	PRO	0	-0.013	0.009	14.679	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	55	LEU	0	-0.023	-0.003	15.737	-0.086	-0.086	0.000	0.000	0.000	0.000
64	A	56	GLU	-1	-0.948	-0.963	16.027	0.423	0.423	0.000	0.000	0.000	0.000
65	A	57	SER	0	-0.028	-0.037	17.405	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	58	TRP	0	0.001	-0.035	14.237	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	59	GLU	-1	-0.975	-0.971	18.605	0.000	0.000	0.000	0.000	0.000	0.000
68	A	60	GLU	-1	-0.782	-0.899	20.284	0.285	0.285	0.000	0.000	0.000	0.000
69	A	61	PHE	0	-0.047	-0.023	14.719	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	62	PRO	0	0.009	-0.006	20.326	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	63	ALA	0	0.016	0.020	23.759	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	64	PHE	0	0.026	0.008	19.405	0.012	0.012	0.000	0.000	0.000	0.000
73	A	65	PHE	0	-0.008	-0.018	17.860	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	66	GLU	-1	-0.815	-0.884	22.927	-0.080	-0.080	0.000	0.000	0.000	0.000
75	A	67	GLU	-1	-0.868	-0.918	25.520	0.125	0.125	0.000	0.000	0.000	0.000
76	A	68	ALA	0	-0.034	-0.005	22.670	0.006	0.006	0.000	0.000	0.000	0.000
77	A	69	GLY	0	-0.013	-0.004	24.660	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	70	TRP	0	-0.078	-0.049	17.371	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	71	GLY	0	-0.011	-0.004	24.334	-0.033	-0.033	0.000	0.000	0.000	0.000
80	A	72	THR	0	-0.024	-0.030	25.669	0.006	0.006	0.000	0.000	0.000	0.000
81	A	73	LEU	0	-0.021	-0.009	20.281	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	74	THR	0	-0.002	-0.010	24.759	0.014	0.014	0.000	0.000	0.000	0.000
83	A	75	ASN	0	-0.074	-0.050	21.549	-0.025	-0.025	0.000	0.000	0.000	0.000
84	A	76	VAL	0	0.000	0.006	23.917	0.018	0.018	0.000	0.000	0.000	0.000
85	A	77	SER	0	-0.008	-0.004	20.700	0.002	0.002	0.000	0.000	0.000	0.000
86	A	78	ALA	0	0.064	0.040	19.846	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	79	LYS	1	0.863	0.934	17.902	0.489	0.489	0.000	0.000	0.000	0.000
88	A	80	LYS	1	0.924	0.954	14.042	0.384	0.384	0.000	0.000	0.000	0.000
89	A	81	GLN	0	-0.039	-0.030	11.060	0.213	0.213	0.000	0.000	0.000	0.000
90	A	82	GLU	-1	-0.897	-0.957	13.213	-0.972	-0.972	0.000	0.000	0.000	0.000
91	A	83	LEU	0	-0.059	-0.006	15.710	0.119	0.119	0.000	0.000	0.000	0.000
92	A	84	GLU	-1	-0.939	-0.978	17.482	-0.570	-0.570	0.000	0.000	0.000	0.000
93	A	85	PHE	0	0.037	0.015	17.997	0.067	0.067	0.000	0.000	0.000	0.000
94	A	86	GLU	-1	-0.788	-0.861	22.090	-0.329	-0.329	0.000	0.000	0.000	0.000
95	A	87	LEU	0	0.014	0.006	21.654	0.017	0.017	0.000	0.000	0.000	0.000
96	A	88	GLU	-1	-0.825	-0.923	25.125	-0.202	-0.202	0.000	0.000	0.000	0.000
97	A	89	GLY	0	0.104	0.042	28.631	0.018	0.018	0.000	0.000	0.000	0.000
98	A	90	PRO	0	-0.031	-0.022	31.200	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	91	ILE	0	0.017	0.009	29.288	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	92	ILE	0	0.013	0.027	25.993	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	93	SER	0	0.011	-0.008	29.063	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	94	ASN	0	-0.047	-0.024	32.202	0.000	0.000	0.000	0.000	0.000	0.000
103	A	95	ARG	1	0.792	0.869	24.723	0.175	0.175	0.000	0.000	0.000	0.000
104	A	96	LEU	0	-0.018	-0.018	27.622	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	97	LYS	1	0.890	0.970	30.751	0.134	0.134	0.000	0.000	0.000	0.000
106	A	98	HIS	0	-0.045	-0.023	33.122	0.002	0.002	0.000	0.000	0.000	0.000
107	A	99	GLN	0	-0.031	-0.026	27.670	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	100	LYS	1	0.811	0.890	28.314	0.345	0.345	0.000	0.000	0.000	0.000
109	A	101	GLU	-1	-0.816	-0.907	24.596	-0.391	-0.391	0.000	0.000	0.000	0.000
110	A	102	PRO	0	0.001	0.025	25.086	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	103	CYS	0	-0.048	-0.013	20.204	-0.071	-0.071	0.000	0.000	0.000	0.000
112	A	104	PHE	0	0.065	0.020	19.765	0.044	0.044	0.000	0.000	0.000	0.000
113	A	105	GLN	0	0.027	0.005	14.620	0.014	0.014	0.000	0.000	0.000	0.000
114	A	106	LEU	0	-0.003	0.015	14.600	-0.056	-0.056	0.000	0.000	0.000	0.000
115	A	107	GLU	-1	-0.756	-0.867	15.323	-0.216	-0.216	0.000	0.000	0.000	0.000
116	A	108	ALA	0	0.011	-0.001	14.273	0.026	0.026	0.000	0.000	0.000	0.000
117	A	109	GLY	0	0.038	0.008	10.831	-0.082	-0.082	0.000	0.000	0.000	0.000
118	A	110	PHE	0	0.005	0.004	10.645	0.164	0.164	0.000	0.000	0.000	0.000
119	A	111	ILE	0	0.008	0.009	12.328	0.172	0.172	0.000	0.000	0.000	0.000
120	A	112	ALA	0	0.014	0.007	8.527	0.151	0.151	0.000	0.000	0.000	0.000
121	A	113	GLU	-1	-0.807	-0.879	6.060	3.707	3.707	0.000	0.000	0.000	0.000
122	A	114	GLN	0	0.016	-0.006	8.627	0.681	0.681	0.000	0.000	0.000	0.000
123	A	115	ILE	0	-0.011	0.002	9.454	0.163	0.163	0.000	0.000	0.000	0.000
124	A	116	GLN	0	-0.063	-0.053	3.258	0.964	2.052	0.208	-0.357	-0.939	0.001
125	A	117	LEU	0	-0.090	-0.037	7.323	0.842	0.842	0.000	0.000	0.000	0.000
126	A	118	MET	0	-0.028	0.018	9.520	-0.167	-0.167	0.000	0.000	0.000	0.000
127	A	119	ASN	0	-0.008	-0.011	9.685	-0.144	-0.144	0.000	0.000	0.000	0.000
128	A	120	ASP	-1	-0.757	-0.854	6.233	1.495	1.495	0.000	0.000	0.000	0.000
129	A	121	GLN	0	-0.091	-0.051	5.273	-0.396	-0.396	0.000	0.000	0.000	0.000
130	A	122	ILE	0	-0.010	0.002	5.664	-0.833	-0.833	0.000	0.000	0.000	0.000
131	A	123	ALA	0	-0.049	-0.024	2.253	-0.284	0.374	1.439	-0.884	-1.212	-0.002
132	A	124	GLU	-1	-0.835	-0.910	1.734	-43.317	-44.578	18.733	-8.332	-9.139	-0.109
133	A	125	SER	0	-0.030	-0.051	4.131	1.967	2.183	0.002	-0.036	-0.182	0.000
134	A	126	TYR	0	-0.060	-0.043	7.412	-0.854	-0.854	0.000	0.000	0.000	0.000
135	A	127	GLU	-1	-0.744	-0.837	9.953	-1.834	-1.834	0.000	0.000	0.000	0.000
136	A	128	GLN	0	-0.065	-0.038	13.075	0.062	0.062	0.000	0.000	0.000	0.000
137	A	129	VAL	0	0.057	0.036	16.719	0.074	0.074	0.000	0.000	0.000	0.000
138	A	130	LYS	1	0.950	0.986	19.476	0.549	0.549	0.000	0.000	0.000	0.000
139	A	131	LYS	1	0.903	0.959	22.325	0.512	0.512	0.000	0.000	0.000	0.000
140	A	132	ARG	1	0.775	0.845	26.050	0.300	0.300	0.000	0.000	0.000	0.000
141	A	133	ALA	0	-0.018	-0.013	29.382	0.004	0.004	0.000	0.000	0.000	0.000
142	A	134	ASP	-1	-0.863	-0.918	31.868	-0.207	-0.207	0.000	0.000	0.000	0.000
143	A	135	LYN	0	0.000	0.023	28.095	0.003	0.003	0.000	0.000	0.000	0.000
144	A	136	VAL	0	-0.057	-0.036	23.043	-0.024	-0.024	0.000	0.000	0.000	0.000
145	A	137	VAL	0	-0.003	-0.005	21.460	0.025	0.025	0.000	0.000	0.000	0.000
146	A	138	LEU	0	-0.027	-0.005	17.697	-0.065	-0.065	0.000	0.000	0.000	0.000
147	A	139	THR	0	0.028	0.008	17.090	0.052	0.052	0.000	0.000	0.000	0.000
148	A	140	VAL	0	-0.006	-0.007	11.592	-0.116	-0.116	0.000	0.000	0.000	0.000
149	A	141	LYS	1	0.872	0.956	10.113	2.289	2.289	0.000	0.000	0.000	0.000
150	A	142	TRP	0	0.025	-0.004	7.977	-0.298	-0.298	0.000	0.000	0.000	0.000
151	A	143	ASP	-1	-0.826	-0.885	6.647	-2.266	-2.266	0.000	0.000	0.000	0.000
152	A	144	MET	0	-0.051	-0.016	6.724	0.061	0.061	0.000	0.000	0.000	0.000
153	A	145	LYS	1	0.811	0.896	3.718	-1.412	-0.891	0.004	-0.084	-0.441	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-7:HIS)