FMO DATABASE

FMODB ID: 6616Z

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:

Apendix: None

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1613179.644056
FMO2-HF: Nuclear repulsion	1548695.633981
FMO2-HF: Total energy	-64484.010075
FMO2-MP2: Total energy	-64669.733711

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.
4.564	9.753	3.3	-2.998	-5.489	-0.004

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 : 0.023 / q_NPA : -0.007

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	0.029	0.029	2.335	-4.232	-1.799	1.645	-1.583	-2.494	0.005
4	A	9	PHE	0	-0.006	-0.006	2.438	-2.586	-0.974	1.646	-1.113	-2.145	-0.008
5	A	10	ASP	-1	-0.891	-0.955	5.047	-0.143	-0.025	-0.001	-0.006	-0.110	0.000
6	A	11	LYS	1	0.942	0.957	7.449	0.510	0.510	0.000	0.000	0.000	0.000
7	A	12	ASN	0	0.000	-0.007	10.881	0.009	0.009	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.032	0.030	7.590	0.090	0.090	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.002	0.008	8.515	0.083	0.083	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.896	-0.947	11.462	0.015	0.015	0.000	0.000	0.000	0.000
11	A	16	PHE	0	0.007	0.001	13.255	0.002	0.002	0.000	0.000	0.000	0.000
12	A	17	VAL	0	0.037	0.020	11.101	0.011	0.011	0.000	0.000	0.000	0.000
13	A	18	THR	0	-0.042	-0.015	14.320	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	19	VAL	0	-0.016	-0.009	17.130	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.022	0.015	16.784	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	21	ALA	0	0.035	0.013	18.011	0.000	0.000	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.966	-0.977	19.717	0.073	0.073	0.000	0.000	0.000	0.000
18	A	23	PHE	0	-0.044	-0.037	22.122	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.025	0.000	21.137	0.001	0.001	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.044	0.027	23.635	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	26	PHE	0	-0.072	-0.049	25.447	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.010	-0.012	26.727	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.770	-0.855	24.848	0.218	0.218	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.895	0.957	28.466	-0.107	-0.107	0.000	0.000	0.000	0.000
25	A	30	ALA	0	0.046	0.024	31.603	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.942	-0.971	33.824	0.109	0.109	0.000	0.000	0.000	0.000
27	A	32	SER	0	-0.095	-0.035	34.984	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	33	MET	0	-0.064	-0.015	32.291	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.943	0.970	37.899	-0.068	-0.068	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.952	0.975	38.683	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	36	SER	0	-0.027	-0.010	38.748	0.005	0.005	0.000	0.000	0.000	0.000
32	A	37	THR	0	0.042	0.016	35.379	0.000	0.000	0.000	0.000	0.000	0.000
33	A	38	PHE	0	0.078	0.032	32.204	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.016	0.008	33.937	0.007	0.007	0.000	0.000	0.000	0.000
35	A	40	ASP	-1	-0.862	-0.924	34.668	0.080	0.080	0.000	0.000	0.000	0.000
36	A	41	THR	0	-0.052	-0.029	29.906	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.050	0.023	29.677	0.007	0.007	0.000	0.000	0.000	0.000
38	A	43	LEU	0	-0.039	-0.019	29.749	0.010	0.010	0.000	0.000	0.000	0.000
39	A	44	LYS	1	0.886	0.950	29.414	-0.071	-0.071	0.000	0.000	0.000	0.000
40	A	45	ILE	0	0.023	0.005	24.430	0.000	0.000	0.000	0.000	0.000	0.000
41	A	46	LEU	0	0.024	0.019	24.917	0.014	0.014	0.000	0.000	0.000	0.000
42	A	47	PRO	0	0.010	0.004	25.095	0.020	0.020	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.011	0.000	21.699	0.004	0.004	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.048	0.018	19.597	0.005	0.005	0.000	0.000	0.000	0.000
45	A	50	TYR	0	0.016	0.006	20.179	0.042	0.042	0.000	0.000	0.000	0.000
46	A	51	LEU	0	-0.037	-0.011	20.567	0.025	0.025	0.000	0.000	0.000	0.000
47	A	52	LYS	1	0.866	0.904	16.918	-0.068	-0.068	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.044	0.033	16.067	0.032	0.032	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.067	-0.042	15.930	0.065	0.065	0.000	0.000	0.000	0.000
50	A	55	MET	0	-0.114	-0.042	15.867	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	56	LEU	0	-0.011	0.015	11.227	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	57	PRO	0	-0.041	-0.003	7.999	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.933	0.959	9.674	-0.547	-0.547	0.000	0.000	0.000	0.000
54	A	59	CYS	0	-0.003	0.013	6.898	0.322	0.322	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.945	-0.965	5.310	3.832	3.832	0.000	0.000	0.000	0.000
56	A	61	MET	0	-0.061	-0.023	6.917	0.927	0.927	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.044	-0.008	4.144	-0.170	0.016	-0.001	-0.016	-0.169	0.000
58	A	63	GLY	0	-0.055	-0.029	8.122	-0.569	-0.569	0.000	0.000	0.000	0.000
59	A	64	ASP	-1	-0.956	-0.973	11.551	1.141	1.141	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.973	-0.994	13.424	0.627	0.627	0.000	0.000	0.000	0.000
61	A	66	SER	0	-0.063	-0.034	13.914	0.127	0.127	0.000	0.000	0.000	0.000
62	A	67	PRO	0	0.019	-0.002	13.235	-0.075	-0.075	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.929	-0.957	15.712	0.369	0.369	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.039	-0.022	18.257	0.043	0.043	0.000	0.000	0.000	0.000
65	A	70	TYR	0	-0.066	-0.031	20.950	-0.054	-0.054	0.000	0.000	0.000	0.000
66	A	71	VAL	0	-0.036	-0.023	22.634	-0.047	-0.047	0.000	0.000	0.000	0.000
67	A	72	THR	0	0.002	0.014	25.285	0.009	0.009	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.864	-0.956	28.526	0.245	0.245	0.000	0.000	0.000	0.000
69	A	74	GLU	-1	-0.926	-0.965	31.564	0.165	0.165	0.000	0.000	0.000	0.000
70	A	75	ILE	0	-0.047	-0.016	26.974	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	76	TYR	0	-0.018	-0.041	28.444	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.780	-0.875	30.565	0.184	0.184	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.019	0.000	33.313	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	79	LEU	0	-0.018	0.000	28.445	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.866	0.904	32.532	-0.195	-0.195	0.000	0.000	0.000	0.000
76	A	81	ILE	0	0.010	0.003	34.262	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	82	ASN	0	0.022	0.017	34.302	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	83	LEU	0	-0.042	-0.024	31.074	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	84	ALA	0	0.025	0.011	35.728	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	85	SER	0	-0.058	-0.027	38.772	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	86	ILE	0	-0.080	-0.020	36.661	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	87	LEU	0	-0.021	-0.019	36.193	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	88	ALA	0	-0.008	-0.003	40.264	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	89	GLU	-1	-0.865	-0.958	43.018	0.093	0.093	0.000	0.000	0.000	0.000
85	A	90	LYS	1	0.795	0.899	41.005	-0.091	-0.091	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.722	-0.821	37.677	0.159	0.159	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.881	-0.920	38.899	0.141	0.141	0.000	0.000	0.000	0.000
88	A	93	TYR	0	-0.128	-0.082	34.082	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	94	LEU	0	-0.069	-0.038	40.290	0.005	0.005	0.000	0.000	0.000	0.000
90	A	95	GLU	-1	-0.917	-0.960	36.334	0.165	0.165	0.000	0.000	0.000	0.000
91	A	108	ILE	0	0.000	-0.012	36.520	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	109	LYS	1	0.925	0.956	40.234	-0.128	-0.128	0.000	0.000	0.000	0.000
93	A	110	LYS	1	0.971	0.998	33.648	-0.211	-0.211	0.000	0.000	0.000	0.000
94	A	111	ASN	0	0.064	0.031	36.378	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	112	ILE	0	-0.004	-0.008	33.563	0.011	0.011	0.000	0.000	0.000	0.000
96	A	113	SER	0	-0.087	-0.090	33.063	0.016	0.016	0.000	0.000	0.000	0.000
97	A	114	GLU	-1	-0.932	-0.963	32.491	0.225	0.225	0.000	0.000	0.000	0.000
98	A	115	ASP	-1	-0.855	-0.900	30.311	0.241	0.241	0.000	0.000	0.000	0.000
99	A	116	LEU	0	-0.066	-0.051	28.551	0.020	0.020	0.000	0.000	0.000	0.000
100	A	117	ALA	0	0.012	0.016	27.696	0.017	0.017	0.000	0.000	0.000	0.000
101	A	118	ASP	-1	-0.801	-0.887	27.123	0.315	0.315	0.000	0.000	0.000	0.000
102	A	119	ILE	0	-0.082	-0.037	23.140	0.033	0.033	0.000	0.000	0.000	0.000
103	A	120	TYR	0	-0.086	-0.083	22.872	0.041	0.041	0.000	0.000	0.000	0.000
104	A	121	GLN	0	0.030	0.018	22.989	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.841	-0.917	19.530	0.657	0.657	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.089	-0.051	18.624	0.057	0.057	0.000	0.000	0.000	0.000
107	A	124	LYS	1	0.885	0.930	18.310	-0.260	-0.260	0.000	0.000	0.000	0.000
108	A	125	ASP	-1	-0.772	-0.896	18.767	0.513	0.513	0.000	0.000	0.000	0.000
109	A	126	PHE	0	-0.011	-0.007	10.925	0.004	0.004	0.000	0.000	0.000	0.000
110	A	127	ILE	0	-0.032	-0.028	14.284	0.037	0.037	0.000	0.000	0.000	0.000
111	A	128	PHE	0	-0.036	-0.006	15.426	-0.049	-0.049	0.000	0.000	0.000	0.000
112	A	129	VAL	0	0.062	0.029	12.494	-0.035	-0.035	0.000	0.000	0.000	0.000
113	A	130	PHE	0	-0.051	-0.025	7.557	-0.034	-0.034	0.000	0.000	0.000	0.000
114	A	131	GLN	0	-0.048	-0.030	11.229	-0.073	-0.073	0.000	0.000	0.000	0.000
115	A	132	LEU	0	-0.034	-0.015	13.880	-0.097	-0.097	0.000	0.000	0.000	0.000
116	A	133	GLY	0	-0.048	-0.018	10.623	-0.065	-0.065	0.000	0.000	0.000	0.000
117	A	134	LEU	0	0.006	0.022	10.285	-0.162	-0.162	0.000	0.000	0.000	0.000
118	A	135	ASN	0	0.017	-0.011	3.597	-2.126	-1.434	0.012	-0.244	-0.460	-0.001
119	A	136	GLU	-1	-0.884	-0.959	6.787	2.053	2.053	0.000	0.000	0.000	0.000
120	A	137	THR	0	0.104	0.057	8.037	0.459	0.459	0.000	0.000	0.000	0.000
121	A	138	MET	0	-0.057	-0.001	7.051	-0.095	-0.095	0.000	0.000	0.000	0.000
122	A	139	ASN	0	-0.072	-0.037	4.241	1.950	2.098	-0.001	-0.036	-0.111	0.000
123	A	140	ASP	-1	-0.730	-0.883	6.831	2.807	2.807	0.000	0.000	0.000	0.000
124	A	141	SER	0	-0.021	-0.013	9.912	-0.350	-0.350	0.000	0.000	0.000	0.000
125	A	142	LEU	0	-0.021	-0.014	7.014	-0.301	-0.301	0.000	0.000	0.000	0.000
126	A	143	ALA	0	-0.001	-0.008	8.987	-0.285	-0.285	0.000	0.000	0.000	0.000
127	A	144	ILE	0	0.019	0.009	10.607	-0.274	-0.274	0.000	0.000	0.000	0.000
128	A	145	CYS	0	-0.013	0.010	13.751	-0.203	-0.203	0.000	0.000	0.000	0.000
129	A	146	GLN	0	-0.024	-0.045	11.377	0.037	0.037	0.000	0.000	0.000	0.000
130	A	147	GLU	-1	-0.920	-0.961	14.303	0.755	0.755	0.000	0.000	0.000	0.000
131	A	148	ASN	0	0.031	-0.011	16.062	-0.116	-0.116	0.000	0.000	0.000	0.000
132	A	149	PHE	0	-0.084	-0.018	17.628	-0.117	-0.117	0.000	0.000	0.000	0.000
133	A	150	GLY	0	-0.019	-0.014	18.801	-0.076	-0.076	0.000	0.000	0.000	0.000
134	A	151	LEU	0	-0.066	-0.008	20.088	-0.078	-0.078	0.000	0.000	0.000	0.000
135	A	152	LEU	0	-0.043	-0.034	22.223	-0.059	-0.059	0.000	0.000	0.000	0.000
136	A	153	TRP	0	0.076	0.029	17.043	-0.054	-0.054	0.000	0.000	0.000	0.000
137	A	154	GLY	0	0.043	0.023	22.387	-0.040	-0.040	0.000	0.000	0.000	0.000
138	A	155	GLN	0	-0.036	-0.028	23.393	-0.031	-0.031	0.000	0.000	0.000	0.000
139	A	156	LYS	1	0.946	0.972	26.533	-0.336	-0.336	0.000	0.000	0.000	0.000
140	A	157	LEU	0	0.007	0.030	23.518	-0.029	-0.029	0.000	0.000	0.000	0.000
141	A	158	VAL	0	-0.005	-0.007	26.654	-0.028	-0.028	0.000	0.000	0.000	0.000
142	A	159	ASN	0	0.002	-0.002	29.030	-0.027	-0.027	0.000	0.000	0.000	0.000
143	A	160	THR	0	0.046	0.012	30.163	-0.019	-0.019	0.000	0.000	0.000	0.000
144	A	161	MET	0	-0.032	-0.013	28.765	-0.013	-0.013	0.000	0.000	0.000	0.000
145	A	162	ARG	1	0.854	0.948	32.008	-0.181	-0.181	0.000	0.000	0.000	0.000
146	A	163	ALA	0	0.052	0.037	34.974	-0.011	-0.011	0.000	0.000	0.000	0.000
147	A	164	LEU	0	0.035	-0.002	32.498	-0.013	-0.013	0.000	0.000	0.000	0.000
148	A	165	HIS	0	-0.017	0.002	35.780	-0.009	-0.009	0.000	0.000	0.000	0.000
149	A	166	ASP	-1	-0.909	-0.959	37.337	0.104	0.104	0.000	0.000	0.000	0.000
150	A	167	VAL	0	-0.048	-0.025	39.262	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	168	LYS	1	0.797	0.895	38.244	-0.082	-0.082	0.000	0.000	0.000	0.000
152	A	169	TYR	0	-0.043	-0.036	37.619	-0.011	-0.011	0.000	0.000	0.000	0.000
153	A	170	SER	0	-0.002	0.024	42.958	-0.004	-0.004	0.000	0.000	0.000	0.000
154	A	171	PRO	0	-0.017	-0.003	44.878	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	172	LYS	1	0.854	0.913	44.536	-0.078	-0.078	0.000	0.000	0.000	0.000
156	A	173	ALA	0	0.003	0.002	49.901	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	174	ARG	1	0.962	0.993	46.325	-0.090	-0.090	0.000	0.000	0.000	0.000
158	A	175	DLE	0	0.025	0.016	52.370	0.001	0.001	0.000	0.000	0.000	0.000

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