FMO DATABASE

FMODB ID: 6Y4ZZ

Calculation Name: 2NWU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NWU

Chain ID: A

ChEMBL ID:

UniProt ID: Q97Z89

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1226179.947493
FMO2-HF: Nuclear repulsion	1173075.692106
FMO2-HF: Total energy	-53104.255387
FMO2-MP2: Total energy	-53260.663634

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
-6.397	-42.117	77.911	-24.282	-17.909	0.076

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.845 / q_NPA : -0.899

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	4	VAL	0	-0.014	0.011	3.818	-4.149	-0.422	-0.041	-2.050	-1.636	0.010
4	A	5	MET	0	0.002	-0.002	7.100	-1.009	-1.009	0.000	0.000	0.000	0.000
5	A	6	VAL	0	0.013	-0.002	9.704	-0.642	-0.642	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.014	0.002	13.356	-0.487	-0.487	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.006	-0.006	16.034	-0.436	-0.436	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.870	-0.931	19.707	11.965	11.965	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.007	-0.005	23.017	-0.090	-0.090	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.815	0.896	25.721	-10.862	-10.862	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.047	0.012	29.113	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.001	0.005	32.186	-0.134	-0.134	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.897	-0.931	27.447	10.960	10.960	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.816	-0.915	29.669	9.939	9.939	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.065	0.018	23.874	0.259	0.259	0.000	0.000	0.000	0.000
16	A	17	ASN	0	0.021	0.008	24.775	0.767	0.767	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.931	0.967	26.059	-9.300	-9.300	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.010	0.001	21.743	0.206	0.206	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.017	0.002	20.079	0.564	0.564	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.036	-0.009	21.516	0.534	0.534	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.027	0.008	22.790	0.180	0.180	0.000	0.000	0.000	0.000
22	A	23	ILE	0	-0.044	-0.019	16.680	0.310	0.310	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.036	0.014	18.627	0.563	0.563	0.000	0.000	0.000	0.000
24	A	25	ASN	0	-0.062	-0.007	20.220	0.020	0.020	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.050	-0.049	17.542	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	27	PHE	0	-0.036	-0.036	10.579	0.872	0.872	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.859	-0.900	14.237	15.295	15.295	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.039	-0.026	13.062	1.262	1.262	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.829	-0.925	10.050	25.266	25.266	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.915	0.963	10.946	-23.947	-23.947	0.000	0.000	0.000	0.000
31	A	32	MET	0	-0.015	-0.005	14.274	0.556	0.556	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.034	-0.010	14.870	0.291	0.291	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.052	0.022	18.039	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.802	0.881	20.356	-13.148	-13.148	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.887	0.932	23.183	-10.794	-10.794	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.856	-0.914	22.877	13.215	13.215	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.045	0.049	26.630	-0.357	-0.357	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.002	-0.018	29.797	0.058	0.058	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.055	-0.037	25.847	-0.169	-0.169	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.823	-0.887	24.460	11.341	11.341	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.004	-0.003	18.675	0.072	0.072	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.026	-0.017	18.992	0.102	0.102	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.019	0.004	13.309	0.323	0.323	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.006	-0.009	14.120	-0.229	-0.229	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.896	-0.965	8.884	27.283	27.283	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.007	0.014	8.659	-1.847	-1.847	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.957	0.980	3.001	-52.901	-51.714	0.510	-0.436	-1.261	0.000
48	A	49	THR	0	-0.004	0.010	4.911	3.979	3.934	-0.001	-0.008	0.055	0.000
49	A	50	LEU	0	0.056	0.027	5.284	-2.507	-2.507	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.899	0.950	7.746	-28.688	-28.688	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.012	0.006	9.071	-1.897	-1.897	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.034	0.011	9.589	-1.279	-1.279	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.014	0.003	12.734	-0.862	-0.862	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.849	0.935	15.221	-15.751	-15.751	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.029	0.018	15.158	-0.826	-0.826	0.000	0.000	0.000	0.000
56	A	57	HIS	0	0.000	-0.004	15.204	-1.079	-1.079	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.928	0.964	17.146	-13.124	-13.124	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.042	0.016	20.434	-0.679	-0.679	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.014	0.000	17.785	-0.549	-0.549	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.813	0.907	18.038	-16.042	-16.042	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.027	-0.023	23.514	-0.366	-0.366	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.921	-0.958	25.397	10.167	10.167	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.822	0.915	26.232	-10.455	-10.455	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.042	0.032	23.015	-0.219	-0.219	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.002	-0.008	20.824	0.412	0.412	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.822	-0.884	21.996	12.389	12.389	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.050	-0.029	23.451	0.357	0.357	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.051	0.024	18.708	0.299	0.299	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.838	0.893	18.180	-15.627	-15.627	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.919	0.973	18.864	-11.492	-11.492	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.042	-0.043	18.870	0.079	0.079	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.015	0.015	13.658	0.510	0.510	0.000	0.000	0.000	0.000
73	A	74	MET	0	-0.011	-0.005	14.800	1.353	1.353	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.871	0.941	16.542	-13.692	-13.692	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.039	0.025	14.794	-0.223	-0.223	0.000	0.000	0.000	0.000
76	A	77	ILE	0	-0.075	-0.023	11.402	1.236	1.236	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.938	-0.939	11.894	17.673	17.673	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.022	0.001	11.108	-0.928	-0.928	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.035	-0.021	5.482	0.589	0.589	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.024	0.009	6.047	5.295	5.295	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.006	0.002	7.937	-2.665	-2.665	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.010	-0.011	10.017	0.635	0.635	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.004	0.001	12.008	-1.472	-1.472	0.000	0.000	0.000	0.000
84	A	85	MET	0	-0.014	-0.010	15.463	0.153	0.153	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.003	0.011	17.983	-0.284	-0.284	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.020	0.015	20.455	0.062	0.062	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.930	0.967	23.147	-11.822	-11.822	0.000	0.000	0.000	0.000
88	A	89	GLN	0	0.033	0.000	24.358	-0.109	-0.109	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.018	0.004	25.838	-0.191	-0.191	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.053	0.026	22.454	-0.113	-0.113	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.041	-0.031	24.384	0.063	0.063	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.078	-0.029	26.613	-0.212	-0.212	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.009	0.009	25.664	-0.210	-0.210	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.016	0.000	26.057	0.145	0.145	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.023	-0.001	19.091	0.236	0.236	0.000	0.000	0.000	0.000
96	A	97	SER	0	-0.006	-0.006	23.278	-0.169	-0.169	0.000	0.000	0.000	0.000
97	A	98	PHE	0	0.027	0.007	17.221	0.225	0.225	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.040	-0.011	21.058	-0.668	-0.668	0.000	0.000	0.000	0.000
99	A	109	ALA	0	-0.003	-0.019	21.642	-0.137	-0.137	0.000	0.000	0.000	0.000
100	A	110	ILE	0	0.000	0.013	17.302	0.145	0.145	0.000	0.000	0.000	0.000
101	A	111	LYS	1	0.931	0.956	15.382	-15.080	-15.080	0.000	0.000	0.000	0.000
102	A	112	PHE	0	0.029	0.021	11.972	0.249	0.249	0.000	0.000	0.000	0.000
103	A	113	TYR	0	0.006	-0.007	9.098	-1.069	-1.069	0.000	0.000	0.000	0.000
104	A	114	ILE	0	-0.039	-0.022	5.568	0.624	0.624	0.000	0.000	0.000	0.000
105	A	115	GLU	-1	-0.956	-0.975	2.755	44.603	45.948	0.285	-0.564	-1.066	0.000
106	A	116	TYR	0	-0.035	-0.047	2.155	-0.622	2.156	8.202	-6.016	-4.964	-0.004
107	A	117	GLN	0	0.043	0.001	1.485	-2.123	-47.185	68.956	-15.168	-8.726	0.070
108	A	118	ASN	0	-0.019	0.019	5.019	-7.768	-7.790	-0.001	-0.009	0.032	0.000
109	A	119	PRO	0	0.044	0.019	7.600	-1.775	-1.775	0.000	0.000	0.000	0.000
110	A	120	LYS	1	0.958	0.951	9.160	-20.792	-20.792	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.844	-0.918	9.926	28.616	28.616	0.000	0.000	0.000	0.000
112	A	122	ILE	0	0.017	0.016	6.598	-1.936	-1.936	0.000	0.000	0.000	0.000
113	A	123	VAL	0	-0.013	-0.013	10.628	-2.239	-2.239	0.000	0.000	0.000	0.000
114	A	124	ASP	-1	-0.809	-0.891	14.160	17.029	17.029	0.000	0.000	0.000	0.000
115	A	125	TRP	0	-0.008	0.024	10.472	-0.491	-0.491	0.000	0.000	0.000	0.000
116	A	126	LEU	0	-0.016	-0.021	12.121	-1.531	-1.531	0.000	0.000	0.000	0.000
117	A	127	ALA	0	-0.029	-0.017	15.488	-1.237	-1.237	0.000	0.000	0.000	0.000
118	A	128	PRO	0	0.014	0.029	18.397	-0.140	-0.140	0.000	0.000	0.000	0.000
119	A	129	LYS	1	0.940	0.984	20.229	-12.830	-12.830	0.000	0.000	0.000	0.000
120	A	130	THR	0	-0.068	-0.060	23.160	-0.259	-0.259	0.000	0.000	0.000	0.000
121	A	131	ALA	0	0.030	0.012	26.310	-0.186	-0.186	0.000	0.000	0.000	0.000
122	A	132	HIS	0	-0.002	-0.010	29.883	-0.258	-0.258	0.000	0.000	0.000	0.000
123	A	133	GLY	0	0.018	0.020	29.598	-0.179	-0.179	0.000	0.000	0.000	0.000
124	A	134	VAL	0	0.013	0.017	28.162	0.126	0.126	0.000	0.000	0.000	0.000
125	A	135	PRO	0	0.013	-0.010	22.938	0.038	0.038	0.000	0.000	0.000	0.000
126	A	136	LEU	0	-0.022	-0.010	24.391	-0.276	-0.276	0.000	0.000	0.000	0.000
127	A	137	TRP	0	-0.070	-0.046	18.083	-0.508	-0.508	0.000	0.000	0.000	0.000
128	A	138	ASP	-1	-0.957	-0.980	19.772	14.876	14.876	0.000	0.000	0.000	0.000
129	A	139	ASN	0	0.015	0.018	15.528	-0.763	-0.763	0.000	0.000	0.000	0.000
130	A	140	PRO	0	0.034	0.020	14.309	-0.133	-0.133	0.000	0.000	0.000	0.000
131	A	141	VAL	0	-0.020	-0.022	9.968	0.580	0.580	0.000	0.000	0.000	0.000
132	A	142	PRO	0	0.027	0.017	7.702	-0.189	-0.189	0.000	0.000	0.000	0.000
133	A	143	PRO	0	0.008	0.009	7.619	0.070	0.070	0.000	0.000	0.000	0.000
134	A	144	ASP	-1	-0.882	-0.946	4.099	55.859	56.231	0.001	-0.031	-0.343	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)