FMO DATABASE

FMODB ID: ZY4YN

Calculation Name: 3NRH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRH

Chain ID: A

ChEMBL ID:

UniProt ID: Q64XJ4

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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1613356.145289
FMO2-HF: Nuclear repulsion	1548871.27378
FMO2-HF: Total energy	-64484.871509
FMO2-MP2: Total energy	-64670.545097

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:6:GLN)

Summations of interaction energy for fragment #1(A:6:GLN)

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.
4.342	8.427	5.36	-3.404	-6.043	-0.005

Interaction energy analysis for fragmet #1(A:6:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.008

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	8	ILE	0	0.025	0.028	2.496	-4.507	-1.793	1.094	-1.509	-2.300	0.007
4	A	9	PHE	0	-0.003	-0.005	2.263	-2.411	-1.924	4.262	-1.727	-3.023	-0.011
5	A	10	ASP	-1	-0.801	-0.886	5.075	-0.588	-0.461	-0.001	-0.007	-0.119	0.000
6	A	11	LYS	1	0.800	0.864	7.449	0.785	0.785	0.000	0.000	0.000	0.000
7	A	12	ASN	0	-0.023	-0.025	10.909	0.021	0.021	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.042	0.034	7.800	0.089	0.089	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.012	0.012	8.501	0.104	0.104	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.837	-0.907	11.499	-0.022	-0.022	0.000	0.000	0.000	0.000
11	A	16	PHE	0	0.016	0.003	13.090	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	17	VAL	0	0.036	0.021	11.166	0.012	0.012	0.000	0.000	0.000	0.000
13	A	18	THR	0	-0.054	-0.026	14.360	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	19	VAL	0	-0.013	-0.010	17.166	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.024	0.019	16.808	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	21	ALA	0	0.043	0.014	18.003	0.002	0.002	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.961	-0.975	19.752	0.091	0.091	0.000	0.000	0.000	0.000
18	A	23	PHE	0	-0.040	-0.035	22.162	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.020	0.001	21.168	0.001	0.001	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.031	0.017	23.679	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	26	PHE	0	-0.068	-0.048	25.481	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.002	-0.005	26.720	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.767	-0.835	25.268	0.254	0.254	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.898	0.960	28.150	-0.123	-0.123	0.000	0.000	0.000	0.000
25	A	30	ALA	0	0.042	0.023	31.637	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.915	-0.954	33.861	0.120	0.120	0.000	0.000	0.000	0.000
27	A	32	SER	0	-0.092	-0.035	35.013	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	33	MET	0	-0.055	-0.012	32.323	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.939	0.968	37.963	-0.069	-0.069	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.898	0.933	38.722	-0.084	-0.084	0.000	0.000	0.000	0.000
31	A	36	SER	0	-0.004	-0.001	38.790	0.003	0.003	0.000	0.000	0.000	0.000
32	A	37	THR	0	0.021	0.005	35.525	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	38	PHE	0	0.079	0.042	32.460	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.029	0.016	33.979	0.005	0.005	0.000	0.000	0.000	0.000
35	A	40	ASP	-1	-0.852	-0.913	34.712	0.061	0.061	0.000	0.000	0.000	0.000
36	A	41	THR	0	-0.047	-0.037	29.956	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.055	0.023	29.781	0.006	0.006	0.000	0.000	0.000	0.000
38	A	43	LEU	0	-0.046	-0.023	29.794	0.006	0.006	0.000	0.000	0.000	0.000
39	A	44	LYS	1	0.872	0.947	29.565	-0.063	-0.063	0.000	0.000	0.000	0.000
40	A	45	ILE	0	0.022	0.006	24.459	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	46	LEU	0	0.029	0.022	24.962	0.009	0.009	0.000	0.000	0.000	0.000
42	A	47	PRO	0	0.017	0.004	25.260	0.012	0.012	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.019	-0.001	21.775	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.040	0.016	19.584	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	50	TYR	0	0.021	0.009	20.417	0.029	0.029	0.000	0.000	0.000	0.000
46	A	51	LEU	0	-0.028	-0.005	20.826	0.010	0.010	0.000	0.000	0.000	0.000
47	A	52	LYS	1	0.825	0.880	16.904	0.001	0.001	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.037	0.033	16.240	0.016	0.016	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.060	-0.045	16.193	0.035	0.035	0.000	0.000	0.000	0.000
50	A	55	MET	0	-0.098	-0.035	15.790	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	56	LEU	0	-0.009	0.030	11.394	-0.088	-0.088	0.000	0.000	0.000	0.000
52	A	57	PRO	0	-0.028	-0.002	8.051	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.936	0.960	9.590	0.111	0.111	0.000	0.000	0.000	0.000
54	A	59	CYS	0	-0.004	0.012	7.119	0.070	0.070	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.953	-0.971	5.819	1.387	1.387	0.000	0.000	0.000	0.000
56	A	61	MET	0	-0.045	-0.016	7.280	0.878	0.878	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.041	-0.021	4.120	-0.239	-0.038	0.000	-0.017	-0.184	0.000
58	A	63	GLY	0	-0.051	-0.029	8.173	-0.539	-0.539	0.000	0.000	0.000	0.000
59	A	64	ASP	-1	-0.978	-0.991	11.272	1.411	1.411	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.971	-0.990	13.264	0.864	0.864	0.000	0.000	0.000	0.000
61	A	66	SER	0	-0.039	-0.022	13.771	0.128	0.128	0.000	0.000	0.000	0.000
62	A	67	PRO	0	0.019	-0.002	13.142	-0.056	-0.056	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.938	-0.956	15.677	0.482	0.482	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.061	-0.034	18.257	0.030	0.030	0.000	0.000	0.000	0.000
65	A	70	TYR	0	-0.060	-0.031	20.958	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	71	VAL	0	-0.034	-0.030	22.660	-0.047	-0.047	0.000	0.000	0.000	0.000
67	A	72	THR	0	0.002	0.010	25.316	0.005	0.005	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.878	-0.955	28.558	0.245	0.245	0.000	0.000	0.000	0.000
69	A	74	GLU	-1	-0.948	-0.974	31.624	0.176	0.176	0.000	0.000	0.000	0.000
70	A	75	ILE	0	-0.037	-0.015	26.954	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	76	TYR	0	-0.010	-0.032	28.562	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.771	-0.864	30.600	0.174	0.174	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.014	0.002	33.450	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	79	LEU	0	-0.017	0.004	28.468	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.834	0.879	32.569	-0.192	-0.192	0.000	0.000	0.000	0.000
76	A	81	ILE	0	0.023	0.009	34.301	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	82	ASN	0	0.001	0.008	34.607	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	83	LEU	0	-0.044	-0.027	31.063	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	84	ALA	0	0.026	0.013	35.768	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	85	SER	0	-0.065	-0.036	38.813	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	86	ILE	0	-0.078	-0.020	36.918	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	87	LEU	0	-0.014	-0.013	36.011	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	88	ALA	0	0.012	0.008	40.306	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	89	GLU	-1	-0.760	-0.873	43.123	0.082	0.082	0.000	0.000	0.000	0.000
85	A	90	LYS	1	0.713	0.840	41.245	-0.080	-0.080	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.711	-0.817	37.839	0.141	0.141	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.906	-0.927	39.090	0.119	0.119	0.000	0.000	0.000	0.000
88	A	93	TYR	0	-0.108	-0.079	34.194	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	94	LEU	0	-0.064	-0.033	40.496	0.005	0.005	0.000	0.000	0.000	0.000
90	A	95	GLU	-1	-0.896	-0.943	36.640	0.116	0.116	0.000	0.000	0.000	0.000
91	A	108	ILE	0	-0.006	-0.012	36.726	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	109	LYS	1	0.932	0.958	40.439	-0.106	-0.106	0.000	0.000	0.000	0.000
93	A	110	LYS	1	0.890	0.948	34.382	-0.176	-0.176	0.000	0.000	0.000	0.000
94	A	111	ASN	0	0.016	0.005	36.583	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	112	ILE	0	-0.001	-0.012	33.869	0.010	0.010	0.000	0.000	0.000	0.000
96	A	113	SER	0	-0.074	-0.076	33.244	0.015	0.015	0.000	0.000	0.000	0.000
97	A	114	GLU	-1	-0.814	-0.898	32.769	0.196	0.196	0.000	0.000	0.000	0.000
98	A	115	ASP	-1	-0.811	-0.876	30.484	0.208	0.208	0.000	0.000	0.000	0.000
99	A	116	LEU	0	-0.043	-0.031	28.729	0.017	0.017	0.000	0.000	0.000	0.000
100	A	117	ALA	0	0.013	0.014	27.859	0.018	0.018	0.000	0.000	0.000	0.000
101	A	118	ASP	-1	-0.764	-0.863	27.312	0.283	0.283	0.000	0.000	0.000	0.000
102	A	119	ILE	0	-0.066	-0.028	23.363	0.030	0.030	0.000	0.000	0.000	0.000
103	A	120	TYR	0	-0.068	-0.076	23.033	0.040	0.040	0.000	0.000	0.000	0.000
104	A	121	GLN	0	0.021	0.021	23.028	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.818	-0.897	19.278	0.615	0.615	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.082	-0.049	18.635	0.059	0.059	0.000	0.000	0.000	0.000
107	A	124	LYS	1	0.857	0.898	18.348	-0.275	-0.275	0.000	0.000	0.000	0.000
108	A	125	ASP	-1	-0.771	-0.884	18.921	0.540	0.540	0.000	0.000	0.000	0.000
109	A	126	PHE	0	0.001	-0.003	10.924	0.025	0.025	0.000	0.000	0.000	0.000
110	A	127	ILE	0	-0.031	-0.028	14.317	0.064	0.064	0.000	0.000	0.000	0.000
111	A	128	PHE	0	-0.020	-0.001	15.454	-0.031	-0.031	0.000	0.000	0.000	0.000
112	A	129	VAL	0	0.059	0.027	12.436	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	130	PHE	0	-0.052	-0.026	7.568	0.017	0.017	0.000	0.000	0.000	0.000
114	A	131	GLN	0	-0.047	-0.031	11.247	-0.038	-0.038	0.000	0.000	0.000	0.000
115	A	132	LEU	0	-0.037	-0.013	13.898	-0.091	-0.091	0.000	0.000	0.000	0.000
116	A	133	GLY	0	-0.048	-0.019	10.624	-0.061	-0.061	0.000	0.000	0.000	0.000
117	A	134	LEU	0	-0.006	0.017	10.277	-0.105	-0.105	0.000	0.000	0.000	0.000
118	A	135	ASN	0	-0.044	-0.056	3.723	-0.294	0.139	0.006	-0.130	-0.309	-0.001
119	A	136	GLU	-1	-0.806	-0.900	6.723	3.248	3.248	0.000	0.000	0.000	0.000
120	A	137	THR	0	0.086	0.047	8.348	0.303	0.303	0.000	0.000	0.000	0.000
121	A	138	MET	0	-0.059	0.014	7.164	-0.179	-0.179	0.000	0.000	0.000	0.000
122	A	139	ASN	0	-0.082	-0.045	4.489	0.976	1.099	-0.001	-0.014	-0.108	0.000
123	A	140	ASP	-1	-0.714	-0.859	6.862	2.674	2.674	0.000	0.000	0.000	0.000
124	A	141	SER	0	-0.025	-0.027	9.942	-0.408	-0.408	0.000	0.000	0.000	0.000
125	A	142	LEU	0	-0.030	-0.014	7.243	-0.334	-0.334	0.000	0.000	0.000	0.000
126	A	143	ALA	0	-0.001	-0.007	9.049	-0.329	-0.329	0.000	0.000	0.000	0.000
127	A	144	ILE	0	0.019	0.006	10.760	-0.270	-0.270	0.000	0.000	0.000	0.000
128	A	145	CYS	0	-0.025	0.007	13.889	-0.197	-0.197	0.000	0.000	0.000	0.000
129	A	146	GLN	0	-0.023	-0.042	11.345	0.001	0.001	0.000	0.000	0.000	0.000
130	A	147	GLU	-1	-0.918	-0.960	14.515	0.516	0.516	0.000	0.000	0.000	0.000
131	A	148	ASN	0	-0.008	-0.036	16.251	-0.107	-0.107	0.000	0.000	0.000	0.000
132	A	149	PHE	0	-0.089	-0.015	17.906	-0.097	-0.097	0.000	0.000	0.000	0.000
133	A	150	GLY	0	-0.013	-0.013	19.017	-0.063	-0.063	0.000	0.000	0.000	0.000
134	A	151	LEU	0	-0.053	-0.009	20.273	-0.057	-0.057	0.000	0.000	0.000	0.000
135	A	152	LEU	0	-0.040	-0.026	22.424	-0.041	-0.041	0.000	0.000	0.000	0.000
136	A	153	TRP	0	0.067	0.022	17.083	-0.049	-0.049	0.000	0.000	0.000	0.000
137	A	154	GLY	0	0.044	0.015	22.608	-0.032	-0.032	0.000	0.000	0.000	0.000
138	A	155	GLN	0	-0.028	-0.020	23.623	-0.032	-0.032	0.000	0.000	0.000	0.000
139	A	156	LYS	1	0.844	0.903	26.759	-0.265	-0.265	0.000	0.000	0.000	0.000
140	A	157	LEU	0	-0.009	0.023	23.673	-0.023	-0.023	0.000	0.000	0.000	0.000
141	A	158	VAL	0	0.019	-0.002	26.886	-0.022	-0.022	0.000	0.000	0.000	0.000
142	A	159	ASN	0	0.000	-0.006	29.272	-0.027	-0.027	0.000	0.000	0.000	0.000
143	A	160	THR	0	0.039	0.007	30.340	-0.014	-0.014	0.000	0.000	0.000	0.000
144	A	161	MET	0	-0.034	-0.014	28.946	-0.010	-0.010	0.000	0.000	0.000	0.000
145	A	162	ARG	1	0.832	0.937	32.249	-0.133	-0.133	0.000	0.000	0.000	0.000
146	A	163	ALA	0	0.042	0.030	35.202	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	164	LEU	0	0.037	-0.002	32.639	-0.010	-0.010	0.000	0.000	0.000	0.000
148	A	165	HIS	0	-0.019	0.000	35.976	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	166	ASP	-1	-0.913	-0.960	37.574	0.072	0.072	0.000	0.000	0.000	0.000
150	A	167	VAL	0	-0.046	-0.022	39.330	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	168	LYS	1	0.792	0.890	38.229	-0.062	-0.062	0.000	0.000	0.000	0.000
152	A	169	TYR	0	-0.044	-0.040	37.546	-0.008	-0.008	0.000	0.000	0.000	0.000
153	A	170	SER	0	-0.014	0.021	43.034	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	171	PRO	0	0.011	0.005	45.117	0.000	0.000	0.000	0.000	0.000	0.000
155	A	172	LYS	1	0.846	0.908	44.296	-0.060	-0.060	0.000	0.000	0.000	0.000
156	A	173	ALA	0	-0.013	-0.004	50.083	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	174	ARG	1	0.956	0.991	46.196	-0.068	-0.068	0.000	0.000	0.000	0.000
158	A	175	DLE	0	0.025	0.017	52.597	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLN)