FMO DATABASE

FMODB ID: GN3Q1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1558751.734904
FMO2-HF: Nuclear repulsion	1494857.613424
FMO2-HF: Total energy	-63894.12148
FMO2-MP2: Total energy	-64078.197716

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.
-81.988	-79.661	39.101	-17.953	-23.475	-0.035

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 : -0.018 / q_NPA : -0.009

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	0.025	0.012	2.548	-7.095	-2.805	1.938	-2.339	-3.889	0.023
4	A	-4	HIS	0	0.009	0.014	3.653	1.694	2.337	0.019	-0.195	-0.468	-0.001
5	A	-3	HIS	1	0.812	0.887	1.867	-29.150	-33.758	14.153	-4.679	-4.866	0.062
6	A	-2	HIS	0	-0.048	-0.017	6.851	-1.188	-1.188	0.000	0.000	0.000	0.000
7	A	-1	SER	0	0.055	0.030	10.636	0.018	0.018	0.000	0.000	0.000	0.000
8	A	0	HIS	0	-0.046	-0.040	13.521	0.006	0.006	0.000	0.000	0.000	0.000
9	A	1	MET	0	-0.018	-0.014	16.281	-0.101	-0.101	0.000	0.000	0.000	0.000
10	A	2	LYS	1	0.937	1.010	20.044	-0.381	-0.381	0.000	0.000	0.000	0.000
11	A	3	SER	0	-0.041	-0.051	21.808	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	4	LYS	1	0.963	0.952	24.605	-0.336	-0.336	0.000	0.000	0.000	0.000
13	A	5	PHE	0	0.052	0.032	26.190	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	6	GLU	-1	-0.718	-0.811	20.979	0.394	0.394	0.000	0.000	0.000	0.000
15	A	7	ALA	0	-0.023	-0.023	24.816	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	8	SER	0	-0.072	-0.037	26.366	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	9	ILE	0	0.072	0.024	24.397	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	10	ASP	-1	-0.836	-0.920	26.116	0.256	0.256	0.000	0.000	0.000	0.000
19	A	11	ASN	0	-0.107	-0.059	28.897	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	12	LEU	0	-0.057	-0.037	30.948	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	13	LYS	1	0.805	0.916	26.695	-0.206	-0.206	0.000	0.000	0.000	0.000
22	A	14	GLU	-1	-0.918	-0.958	32.088	0.089	0.089	0.000	0.000	0.000	0.000
23	A	15	ILE	0	-0.080	-0.025	35.057	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	16	GLU	-1	-0.899	-0.937	35.207	0.037	0.037	0.000	0.000	0.000	0.000
25	A	17	MET	0	-0.046	-0.030	34.085	0.000	0.000	0.000	0.000	0.000	0.000
26	A	18	ASN	0	-0.008	-0.002	35.336	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	19	ALA	0	0.093	0.023	32.668	0.001	0.001	0.000	0.000	0.000	0.000
28	A	20	TYR	0	-0.019	-0.003	32.761	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	21	ALA	0	0.013	-0.002	33.994	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	22	TYR	0	-0.004	0.004	25.027	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	23	GLU	-1	-0.733	-0.857	28.744	-0.136	-0.136	0.000	0.000	0.000	0.000
32	A	24	LEU	0	-0.026	0.004	30.148	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	25	ILE	0	0.009	-0.003	26.966	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	26	ARG	1	0.792	0.874	20.969	0.181	0.181	0.000	0.000	0.000	0.000
35	A	27	GLU	-1	-0.813	-0.905	25.252	-0.239	-0.239	0.000	0.000	0.000	0.000
36	A	28	ILE	0	-0.047	-0.017	27.763	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	29	VAL	0	0.036	0.019	28.595	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	30	LEU	0	-0.019	-0.007	22.634	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	31	PRO	0	-0.006	-0.003	25.044	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	32	ASP	-1	-0.914	-0.947	26.024	-0.153	-0.153	0.000	0.000	0.000	0.000
41	A	33	MET	0	-0.121	-0.057	26.266	0.007	0.007	0.000	0.000	0.000	0.000
42	A	34	LEU	0	-0.055	-0.023	20.649	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	35	GLY	0	0.032	0.026	23.569	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	36	GLN	0	-0.066	-0.040	22.669	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	37	ASP	-1	-0.893	-0.951	19.322	-0.511	-0.511	0.000	0.000	0.000	0.000
46	A	38	TYR	0	-0.002	-0.002	18.620	-0.053	-0.053	0.000	0.000	0.000	0.000
47	A	39	SER	0	0.006	-0.007	17.921	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	40	SER	0	0.034	0.006	14.221	-0.064	-0.064	0.000	0.000	0.000	0.000
49	A	41	MET	0	-0.013	-0.004	13.783	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	42	MET	0	0.019	0.010	15.300	0.091	0.091	0.000	0.000	0.000	0.000
51	A	43	TYR	0	-0.072	-0.045	7.940	0.056	0.056	0.000	0.000	0.000	0.000
52	A	44	TRP	0	0.012	-0.015	8.075	0.228	0.228	0.000	0.000	0.000	0.000
53	A	45	ALA	0	0.006	0.017	11.422	0.235	0.235	0.000	0.000	0.000	0.000
54	A	46	GLY	0	0.041	0.024	13.617	0.136	0.136	0.000	0.000	0.000	0.000
55	A	47	LYS	1	0.838	0.924	4.737	0.776	0.822	-0.001	0.000	-0.046	0.000
56	A	48	HIS	0	-0.033	-0.035	10.412	0.312	0.312	0.000	0.000	0.000	0.000
57	A	49	LEU	0	-0.010	0.004	12.466	0.125	0.125	0.000	0.000	0.000	0.000
58	A	50	ALA	0	0.036	0.015	11.498	0.039	0.039	0.000	0.000	0.000	0.000
59	A	51	ARG	1	0.793	0.887	6.439	-3.831	-3.831	0.000	0.000	0.000	0.000
60	A	52	LYS	1	0.832	0.913	13.067	-0.467	-0.467	0.000	0.000	0.000	0.000
61	A	53	PHE	0	-0.052	-0.030	16.346	-0.067	-0.067	0.000	0.000	0.000	0.000
62	A	54	PRO	0	-0.020	0.013	14.611	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	55	LEU	0	-0.018	-0.013	15.678	-0.100	-0.100	0.000	0.000	0.000	0.000
64	A	56	GLU	-1	-0.930	-0.954	16.089	0.563	0.563	0.000	0.000	0.000	0.000
65	A	57	SER	0	-0.039	-0.042	17.411	0.013	0.013	0.000	0.000	0.000	0.000
66	A	58	TRP	0	-0.007	-0.030	13.986	-0.093	-0.093	0.000	0.000	0.000	0.000
67	A	59	GLU	-1	-0.983	-0.979	18.243	0.070	0.070	0.000	0.000	0.000	0.000
68	A	60	GLU	-1	-0.796	-0.901	20.065	0.365	0.365	0.000	0.000	0.000	0.000
69	A	61	PHE	0	-0.059	-0.037	14.495	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	62	PRO	0	0.009	0.003	20.175	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	63	ALA	0	0.035	0.020	23.532	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	64	PHE	0	0.022	0.017	19.398	0.011	0.011	0.000	0.000	0.000	0.000
73	A	65	PHE	0	-0.004	-0.022	17.521	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	66	GLU	-1	-0.841	-0.898	22.687	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	67	GLU	-1	-0.861	-0.918	25.665	0.157	0.157	0.000	0.000	0.000	0.000
76	A	68	ALA	0	-0.045	-0.008	22.757	0.001	0.001	0.000	0.000	0.000	0.000
77	A	69	GLY	0	-0.016	-0.014	24.694	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	70	TRP	0	-0.086	-0.059	17.343	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	71	GLY	0	-0.019	-0.009	24.125	-0.038	-0.038	0.000	0.000	0.000	0.000
80	A	72	THR	0	-0.021	-0.030	25.724	0.016	0.016	0.000	0.000	0.000	0.000
81	A	73	LEU	0	-0.031	-0.011	19.940	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	74	THR	0	0.020	0.008	24.375	0.023	0.023	0.000	0.000	0.000	0.000
83	A	75	ASN	0	-0.060	-0.049	21.303	-0.026	-0.026	0.000	0.000	0.000	0.000
84	A	76	VAL	0	0.025	0.025	23.560	0.013	0.013	0.000	0.000	0.000	0.000
85	A	77	SER	0	-0.023	-0.006	20.972	0.015	0.015	0.000	0.000	0.000	0.000
86	A	78	ALA	0	0.083	0.042	19.923	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	79	LYS	1	0.867	0.941	18.005	0.440	0.440	0.000	0.000	0.000	0.000
88	A	80	LYS	1	0.936	0.965	13.854	0.237	0.237	0.000	0.000	0.000	0.000
89	A	81	GLN	0	-0.053	-0.049	10.993	0.242	0.242	0.000	0.000	0.000	0.000
90	A	82	GLU	-1	-0.905	-0.964	13.214	-0.943	-0.943	0.000	0.000	0.000	0.000
91	A	83	LEU	0	-0.049	-0.002	15.553	0.120	0.120	0.000	0.000	0.000	0.000
92	A	84	GLU	-1	-0.956	-0.978	17.322	-0.545	-0.545	0.000	0.000	0.000	0.000
93	A	85	PHE	0	0.047	0.003	17.500	0.071	0.071	0.000	0.000	0.000	0.000
94	A	86	GLU	-1	-0.803	-0.875	21.702	-0.315	-0.315	0.000	0.000	0.000	0.000
95	A	87	LEU	0	0.002	0.009	21.330	0.025	0.025	0.000	0.000	0.000	0.000
96	A	88	GLU	-1	-0.886	-0.965	24.700	-0.179	-0.179	0.000	0.000	0.000	0.000
97	A	89	GLY	0	0.112	0.052	28.067	0.023	0.023	0.000	0.000	0.000	0.000
98	A	90	PRO	0	-0.004	-0.006	30.834	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	91	ILE	0	0.014	0.005	29.306	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	92	ILE	0	0.024	0.027	25.580	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	93	SER	0	0.021	0.002	28.869	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	94	ASN	0	-0.051	-0.025	31.996	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	95	ARG	1	0.807	0.872	24.535	0.165	0.165	0.000	0.000	0.000	0.000
104	A	96	LEU	0	-0.024	-0.016	26.989	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	97	LYS	1	0.901	0.972	30.308	0.135	0.135	0.000	0.000	0.000	0.000
106	A	98	HIS	0	-0.031	-0.021	33.149	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	99	GLN	0	-0.023	-0.016	27.546	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	100	LYS	1	0.832	0.910	28.015	0.374	0.374	0.000	0.000	0.000	0.000
109	A	101	GLU	-1	-0.859	-0.935	24.449	-0.434	-0.434	0.000	0.000	0.000	0.000
110	A	102	PRO	0	0.029	0.041	25.004	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	103	CYS	0	-0.050	-0.014	19.706	-0.075	-0.075	0.000	0.000	0.000	0.000
112	A	104	PHE	0	0.052	0.013	19.420	0.043	0.043	0.000	0.000	0.000	0.000
113	A	105	GLN	0	0.034	0.006	13.821	0.046	0.046	0.000	0.000	0.000	0.000
114	A	106	LEU	0	0.000	0.022	14.373	-0.039	-0.039	0.000	0.000	0.000	0.000
115	A	107	GLU	-1	-0.746	-0.882	15.081	-0.173	-0.173	0.000	0.000	0.000	0.000
116	A	108	ALA	0	-0.008	-0.007	13.569	0.042	0.042	0.000	0.000	0.000	0.000
117	A	109	GLY	0	0.034	0.009	10.434	-0.075	-0.075	0.000	0.000	0.000	0.000
118	A	110	PHE	0	0.003	0.006	10.429	0.242	0.242	0.000	0.000	0.000	0.000
119	A	111	ILE	0	0.006	0.002	12.263	0.209	0.209	0.000	0.000	0.000	0.000
120	A	112	ALA	0	0.018	0.012	8.007	0.183	0.183	0.000	0.000	0.000	0.000
121	A	113	GLU	-1	-0.796	-0.882	6.063	4.318	4.318	0.000	0.000	0.000	0.000
122	A	114	GLN	0	0.012	-0.001	8.533	0.778	0.778	0.000	0.000	0.000	0.000
123	A	115	ILE	0	-0.007	0.005	9.365	0.197	0.197	0.000	0.000	0.000	0.000
124	A	116	GLN	0	-0.029	-0.028	3.053	0.123	1.314	0.495	-0.474	-1.212	0.002
125	A	117	LEU	0	-0.094	-0.035	7.358	0.544	0.544	0.000	0.000	0.000	0.000
126	A	118	MET	0	-0.026	0.015	9.507	-0.191	-0.191	0.000	0.000	0.000	0.000
127	A	119	ASN	0	-0.006	-0.006	9.468	-0.255	-0.255	0.000	0.000	0.000	0.000
128	A	120	ASP	-1	-0.840	-0.899	6.467	1.955	1.955	0.000	0.000	0.000	0.000
129	A	121	GLN	0	-0.048	-0.037	6.030	-0.351	-0.351	0.000	0.000	0.000	0.000
130	A	122	ILE	0	-0.037	-0.010	5.992	-0.954	-0.954	0.000	0.000	0.000	0.000
131	A	123	ALA	0	-0.055	-0.030	2.372	0.413	1.219	1.122	-0.685	-1.243	-0.001
132	A	124	GLU	-1	-0.858	-0.924	1.737	-46.603	-47.701	21.353	-9.379	-10.876	-0.120
133	A	125	SER	0	-0.035	-0.045	3.951	2.369	2.635	0.008	-0.044	-0.229	0.000
134	A	126	TYR	0	-0.072	-0.053	7.073	-0.992	-0.992	0.000	0.000	0.000	0.000
135	A	127	GLU	-1	-0.761	-0.851	9.237	-1.920	-1.920	0.000	0.000	0.000	0.000
136	A	128	GLN	0	-0.062	-0.035	12.756	0.046	0.046	0.000	0.000	0.000	0.000
137	A	129	VAL	0	0.039	0.027	16.365	0.097	0.097	0.000	0.000	0.000	0.000
138	A	130	LYS	1	0.912	0.961	19.087	0.509	0.509	0.000	0.000	0.000	0.000
139	A	131	LYS	1	0.915	0.962	22.178	0.516	0.516	0.000	0.000	0.000	0.000
140	A	132	ARG	1	0.780	0.863	25.707	0.305	0.305	0.000	0.000	0.000	0.000
141	A	133	ALA	0	-0.034	-0.024	28.733	0.006	0.006	0.000	0.000	0.000	0.000
142	A	134	ASP	-1	-0.892	-0.946	31.572	-0.197	-0.197	0.000	0.000	0.000	0.000
143	A	135	LYN	0	0.019	0.031	27.523	0.001	0.001	0.000	0.000	0.000	0.000
144	A	136	VAL	0	-0.062	-0.031	22.552	-0.031	-0.031	0.000	0.000	0.000	0.000
145	A	137	VAL	0	0.005	0.005	21.486	0.026	0.026	0.000	0.000	0.000	0.000
146	A	138	LEU	0	-0.025	-0.008	17.438	-0.073	-0.073	0.000	0.000	0.000	0.000
147	A	139	THR	0	0.022	-0.002	16.621	0.060	0.060	0.000	0.000	0.000	0.000
148	A	140	VAL	0	0.009	0.015	11.027	-0.150	-0.150	0.000	0.000	0.000	0.000
149	A	141	LYS	1	0.941	0.986	10.859	2.163	2.163	0.000	0.000	0.000	0.000
150	A	142	TRP	0	0.035	0.005	7.698	-0.344	-0.344	0.000	0.000	0.000	0.000
151	A	143	ASP	-1	-0.857	-0.896	6.553	-2.599	-2.599	0.000	0.000	0.000	0.000
152	A	144	MET	0	-0.048	-0.017	6.364	0.004	0.004	0.000	0.000	0.000	0.000
153	A	145	LYS	1	0.854	0.927	3.260	-2.693	-1.902	0.014	-0.158	-0.646	0.000

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