FMO DATABASE

FMODB ID: 1NM1Z

Calculation Name: 1NWA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NWA

Chain ID: A

ChEMBL ID:

UniProt ID: P9WJM5

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	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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1797657.635858
FMO2-HF: Nuclear repulsion	1730886.36832
FMO2-HF: Total energy	-66771.267538
FMO2-MP2: Total energy	-66968.900744

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:-1:ARG)

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

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.
-39.956	-33.713	0.774	-3.905	-3.111	-0.018

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.974 / q_NPA : 0.991

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	1	MET	0	0.023	0.019	3.737	-1.100	2.275	-0.025	-2.025	-1.324	0.001
4	A	2	THR	0	0.023	0.009	6.359	1.410	1.410	0.000	0.000	0.000	0.000
5	A	3	SER	0	-0.032	-0.014	2.228	-6.221	-3.408	0.800	-1.873	-1.740	-0.019
6	A	4	ASN	0	0.031	0.013	4.941	2.726	2.781	-0.001	-0.007	-0.047	0.000
7	A	5	GLN	0	-0.014	0.000	6.892	0.347	0.347	0.000	0.000	0.000	0.000
8	A	6	LYS	1	0.853	0.923	9.289	19.144	19.144	0.000	0.000	0.000	0.000
9	A	7	ALA	0	0.015	0.009	12.114	0.369	0.369	0.000	0.000	0.000	0.000
10	A	8	ILE	0	0.027	0.018	15.654	-0.195	-0.195	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.027	0.003	18.777	0.336	0.336	0.000	0.000	0.000	0.000
12	A	10	ALA	0	0.053	0.027	22.026	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.077	0.026	25.614	0.143	0.143	0.000	0.000	0.000	0.000
14	A	12	GLY	0	0.023	0.020	28.611	0.262	0.262	0.000	0.000	0.000	0.000
15	A	13	CYS	0	-0.034	0.012	30.002	-0.288	-0.288	0.000	0.000	0.000	0.000
16	A	14	PHE	0	0.019	-0.006	26.853	-0.113	-0.113	0.000	0.000	0.000	0.000
17	A	15	TRP	0	0.001	-0.017	27.759	-0.189	-0.189	0.000	0.000	0.000	0.000
18	A	16	GLY	0	0.077	0.040	29.402	-0.163	-0.163	0.000	0.000	0.000	0.000
19	A	17	LEU	0	-0.033	-0.014	24.817	-0.183	-0.183	0.000	0.000	0.000	0.000
20	A	18	GLN	0	0.005	-0.015	22.799	0.141	0.141	0.000	0.000	0.000	0.000
21	A	19	ASP	-1	-0.867	-0.929	25.108	-10.886	-10.886	0.000	0.000	0.000	0.000
22	A	20	LEU	0	-0.003	0.001	27.353	-0.057	-0.057	0.000	0.000	0.000	0.000
23	A	21	ILE	0	-0.008	-0.015	20.920	-0.240	-0.240	0.000	0.000	0.000	0.000
24	A	22	ARG	1	0.786	0.893	21.733	12.026	12.026	0.000	0.000	0.000	0.000
25	A	23	ASN	0	-0.038	-0.012	22.242	-0.605	-0.605	0.000	0.000	0.000	0.000
26	A	24	GLN	0	-0.026	0.003	21.317	-0.063	-0.063	0.000	0.000	0.000	0.000
27	A	25	PRO	0	0.022	-0.003	20.814	-0.628	-0.628	0.000	0.000	0.000	0.000
28	A	26	GLY	0	0.033	0.004	16.789	-0.060	-0.060	0.000	0.000	0.000	0.000
29	A	27	VAL	0	-0.032	-0.008	15.493	-1.268	-1.268	0.000	0.000	0.000	0.000
30	A	28	VAL	0	-0.038	-0.015	12.618	0.077	0.077	0.000	0.000	0.000	0.000
31	A	29	SER	0	-0.012	-0.015	15.526	0.606	0.606	0.000	0.000	0.000	0.000
32	A	30	THR	0	-0.005	-0.006	16.980	0.242	0.242	0.000	0.000	0.000	0.000
33	A	31	ARG	1	0.813	0.888	16.741	16.069	16.069	0.000	0.000	0.000	0.000
34	A	32	VAL	0	-0.006	-0.004	21.291	-0.068	-0.068	0.000	0.000	0.000	0.000
35	A	33	GLY	0	0.058	0.017	23.791	-0.215	-0.215	0.000	0.000	0.000	0.000
36	A	34	TYR	0	-0.067	-0.048	24.719	0.435	0.435	0.000	0.000	0.000	0.000
37	A	35	SER	0	-0.019	-0.035	21.847	-0.413	-0.413	0.000	0.000	0.000	0.000
38	A	36	GLY	0	0.084	0.043	24.020	0.331	0.331	0.000	0.000	0.000	0.000
39	A	37	GLY	0	-0.043	-0.030	25.351	0.360	0.360	0.000	0.000	0.000	0.000
40	A	38	ASN	0	-0.010	-0.004	27.379	-0.289	-0.289	0.000	0.000	0.000	0.000
41	A	39	ILE	0	-0.031	-0.004	28.874	-0.148	-0.148	0.000	0.000	0.000	0.000
42	A	40	PRO	0	0.060	0.029	27.260	-0.233	-0.233	0.000	0.000	0.000	0.000
43	A	41	ASN	0	-0.057	-0.035	26.948	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	42	ALA	0	-0.026	0.013	27.700	0.311	0.311	0.000	0.000	0.000	0.000
45	A	43	THR	0	0.019	-0.005	28.696	-0.134	-0.134	0.000	0.000	0.000	0.000
46	A	44	TYR	0	0.008	-0.008	31.190	0.289	0.289	0.000	0.000	0.000	0.000
47	A	45	ARG	1	0.908	0.948	33.092	8.220	8.220	0.000	0.000	0.000	0.000
48	A	46	ASN	0	-0.015	-0.012	34.308	0.327	0.327	0.000	0.000	0.000	0.000
49	A	47	HIS	1	0.909	0.959	30.270	8.948	8.948	0.000	0.000	0.000	0.000
50	A	48	GLY	0	0.027	0.019	31.358	-0.160	-0.160	0.000	0.000	0.000	0.000
51	A	49	THR	0	-0.025	-0.020	31.569	0.042	0.042	0.000	0.000	0.000	0.000
52	A	50	HIS	0	-0.025	-0.002	25.686	-0.187	-0.187	0.000	0.000	0.000	0.000
53	A	51	ALA	0	-0.012	0.000	26.820	0.330	0.330	0.000	0.000	0.000	0.000
54	A	52	GLU	-1	-0.839	-0.932	26.955	-9.682	-9.682	0.000	0.000	0.000	0.000
55	A	53	ALA	0	-0.031	-0.023	22.947	0.059	0.059	0.000	0.000	0.000	0.000
56	A	54	VAL	0	0.017	-0.010	20.808	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	55	GLU	-1	-0.801	-0.857	15.829	-17.605	-17.605	0.000	0.000	0.000	0.000
58	A	56	ILE	0	-0.007	-0.014	16.320	-0.058	-0.058	0.000	0.000	0.000	0.000
59	A	57	ILE	0	-0.019	-0.012	11.026	-0.818	-0.818	0.000	0.000	0.000	0.000
60	A	58	PHE	0	0.005	-0.010	12.172	0.643	0.643	0.000	0.000	0.000	0.000
61	A	59	ASP	-1	-0.761	-0.857	11.013	-24.681	-24.681	0.000	0.000	0.000	0.000
62	A	60	PRO	0	-0.059	-0.039	8.707	1.455	1.455	0.000	0.000	0.000	0.000
63	A	61	THR	0	-0.086	-0.058	11.268	0.778	0.778	0.000	0.000	0.000	0.000
64	A	62	VAL	0	-0.059	-0.011	13.793	1.012	1.012	0.000	0.000	0.000	0.000
65	A	63	THR	0	0.001	0.001	15.444	1.210	1.210	0.000	0.000	0.000	0.000
66	A	64	ASP	-1	-0.802	-0.879	14.844	-14.963	-14.963	0.000	0.000	0.000	0.000
67	A	65	TYR	0	0.045	0.003	14.679	0.745	0.745	0.000	0.000	0.000	0.000
68	A	66	ARG	1	0.792	0.879	16.449	11.530	11.530	0.000	0.000	0.000	0.000
69	A	67	THR	0	-0.024	-0.038	19.425	0.861	0.861	0.000	0.000	0.000	0.000
70	A	68	LEU	0	-0.012	0.009	16.288	0.501	0.501	0.000	0.000	0.000	0.000
71	A	69	LEU	0	-0.001	0.001	19.842	0.520	0.520	0.000	0.000	0.000	0.000
72	A	70	GLU	-1	-0.778	-0.860	22.184	-10.491	-10.491	0.000	0.000	0.000	0.000
73	A	71	PHE	0	0.024	0.003	23.632	0.448	0.448	0.000	0.000	0.000	0.000
74	A	72	PHE	0	0.031	0.011	23.459	0.339	0.339	0.000	0.000	0.000	0.000
75	A	73	PHE	0	0.007	-0.002	25.034	0.330	0.330	0.000	0.000	0.000	0.000
76	A	74	GLN	0	-0.007	0.012	28.009	0.153	0.153	0.000	0.000	0.000	0.000
77	A	75	ILE	0	-0.008	-0.012	26.194	0.338	0.338	0.000	0.000	0.000	0.000
78	A	76	HIS	0	-0.019	0.015	27.872	0.254	0.254	0.000	0.000	0.000	0.000
79	A	77	ASP	-1	-0.819	-0.900	31.378	-8.012	-8.012	0.000	0.000	0.000	0.000
80	A	78	PRO	0	0.004	0.017	30.245	0.021	0.021	0.000	0.000	0.000	0.000
81	A	79	THR	0	-0.034	-0.035	32.142	0.067	0.067	0.000	0.000	0.000	0.000
82	A	80	THR	0	-0.048	-0.016	35.340	0.250	0.250	0.000	0.000	0.000	0.000
83	A	81	LYS	1	0.950	0.970	35.086	7.202	7.202	0.000	0.000	0.000	0.000
84	A	82	ASP	-1	-0.883	-0.955	34.353	-8.108	-8.108	0.000	0.000	0.000	0.000
85	A	83	ARG	1	0.934	0.957	35.387	7.411	7.411	0.000	0.000	0.000	0.000
86	A	84	GLN	0	0.031	0.040	32.913	-0.086	-0.086	0.000	0.000	0.000	0.000
87	A	85	GLY	0	0.076	0.045	35.640	0.038	0.038	0.000	0.000	0.000	0.000
88	A	86	ASN	0	-0.023	-0.037	38.610	0.227	0.227	0.000	0.000	0.000	0.000
89	A	87	ASP	-1	-0.802	-0.854	35.822	-8.069	-8.069	0.000	0.000	0.000	0.000
90	A	88	ARG	1	0.861	0.923	37.505	6.795	6.795	0.000	0.000	0.000	0.000
91	A	89	GLY	0	0.037	0.006	37.367	0.056	0.056	0.000	0.000	0.000	0.000
92	A	90	THR	0	0.014	-0.001	33.247	-0.121	-0.121	0.000	0.000	0.000	0.000
93	A	91	SER	0	0.009	0.017	31.845	-0.293	-0.293	0.000	0.000	0.000	0.000
94	A	92	TYR	0	-0.062	-0.025	31.020	-0.152	-0.152	0.000	0.000	0.000	0.000
95	A	93	ARG	1	0.787	0.894	28.165	9.671	9.671	0.000	0.000	0.000	0.000
96	A	94	SER	0	-0.020	-0.018	28.737	-0.313	-0.313	0.000	0.000	0.000	0.000
97	A	95	ALA	0	-0.010	-0.012	25.510	0.188	0.188	0.000	0.000	0.000	0.000
98	A	96	ILE	0	-0.010	0.004	20.448	-0.256	-0.256	0.000	0.000	0.000	0.000
99	A	97	PHE	0	0.012	-0.005	20.076	0.223	0.223	0.000	0.000	0.000	0.000
100	A	98	TYR	0	-0.013	0.002	17.117	-0.441	-0.441	0.000	0.000	0.000	0.000
101	A	99	PHE	0	0.036	0.000	12.339	0.029	0.029	0.000	0.000	0.000	0.000
102	A	100	ASP	-1	-0.854	-0.919	11.729	-17.683	-17.683	0.000	0.000	0.000	0.000
103	A	101	GLU	-1	-0.743	-0.877	13.890	-11.474	-11.474	0.000	0.000	0.000	0.000
104	A	102	GLN	0	-0.004	0.004	12.036	0.996	0.996	0.000	0.000	0.000	0.000
105	A	103	GLN	0	0.012	-0.001	12.292	1.344	1.344	0.000	0.000	0.000	0.000
106	A	104	LYS	1	0.877	0.950	16.487	12.116	12.116	0.000	0.000	0.000	0.000
107	A	105	ARG	1	0.853	0.905	18.906	12.535	12.535	0.000	0.000	0.000	0.000
108	A	106	ILE	0	0.057	0.042	16.402	0.380	0.380	0.000	0.000	0.000	0.000
109	A	107	ALA	0	-0.001	0.006	20.357	0.421	0.421	0.000	0.000	0.000	0.000
110	A	108	LEU	0	-0.019	-0.009	22.090	0.422	0.422	0.000	0.000	0.000	0.000
111	A	109	ASP	-1	-0.885	-0.941	22.940	-10.601	-10.601	0.000	0.000	0.000	0.000
112	A	110	THR	0	-0.105	-0.085	22.885	0.216	0.216	0.000	0.000	0.000	0.000
113	A	111	ILE	0	0.002	0.002	25.503	0.305	0.305	0.000	0.000	0.000	0.000
114	A	112	ALA	0	-0.001	0.005	28.085	0.339	0.339	0.000	0.000	0.000	0.000
115	A	113	ASP	-1	-0.754	-0.856	27.956	-9.425	-9.425	0.000	0.000	0.000	0.000
116	A	114	VAL	0	-0.042	-0.017	28.728	0.245	0.245	0.000	0.000	0.000	0.000
117	A	115	GLU	-1	-0.802	-0.876	31.265	-7.958	-7.958	0.000	0.000	0.000	0.000
118	A	116	ALA	0	-0.043	-0.013	33.378	0.261	0.261	0.000	0.000	0.000	0.000
119	A	117	SER	0	-0.081	-0.052	33.683	0.216	0.216	0.000	0.000	0.000	0.000
120	A	118	GLY	0	0.004	0.001	35.661	0.170	0.170	0.000	0.000	0.000	0.000
121	A	119	LEU	0	-0.069	-0.026	34.790	0.145	0.145	0.000	0.000	0.000	0.000
122	A	120	TRP	0	-0.015	-0.017	30.421	0.017	0.017	0.000	0.000	0.000	0.000
123	A	121	PRO	0	-0.028	-0.017	36.374	0.131	0.131	0.000	0.000	0.000	0.000
124	A	122	GLY	0	-0.001	0.001	37.823	0.235	0.235	0.000	0.000	0.000	0.000
125	A	123	LYS	1	0.790	0.886	33.841	7.977	7.977	0.000	0.000	0.000	0.000
126	A	124	VAL	0	0.039	0.019	29.837	0.009	0.009	0.000	0.000	0.000	0.000
127	A	125	VAL	0	-0.110	-0.072	32.972	0.062	0.062	0.000	0.000	0.000	0.000
128	A	126	THR	0	-0.037	-0.025	26.443	0.009	0.009	0.000	0.000	0.000	0.000
129	A	127	GLU	-1	-0.791	-0.853	26.238	-10.011	-10.011	0.000	0.000	0.000	0.000
130	A	128	VAL	0	-0.008	-0.011	22.439	-0.338	-0.338	0.000	0.000	0.000	0.000
131	A	129	SER	0	-0.040	-0.048	23.084	0.275	0.275	0.000	0.000	0.000	0.000
132	A	130	PRO	0	-0.045	-0.009	19.478	-0.370	-0.370	0.000	0.000	0.000	0.000
133	A	131	ALA	0	-0.005	-0.006	16.696	0.377	0.377	0.000	0.000	0.000	0.000
134	A	132	GLY	0	0.016	0.004	18.472	-0.121	-0.121	0.000	0.000	0.000	0.000
135	A	133	ASP	-1	-0.929	-0.957	19.035	-13.121	-13.121	0.000	0.000	0.000	0.000
136	A	134	PHE	0	-0.018	-0.006	18.958	0.356	0.356	0.000	0.000	0.000	0.000
137	A	135	TRP	0	-0.035	-0.011	20.904	-0.419	-0.419	0.000	0.000	0.000	0.000
138	A	136	GLU	-1	-0.886	-0.915	20.193	-14.367	-14.367	0.000	0.000	0.000	0.000
139	A	137	ALA	0	-0.006	-0.003	23.603	0.418	0.418	0.000	0.000	0.000	0.000
140	A	138	GLU	-1	-0.711	-0.841	26.021	-10.315	-10.315	0.000	0.000	0.000	0.000
141	A	139	PRO	0	0.056	0.008	26.555	-0.012	-0.012	0.000	0.000	0.000	0.000
142	A	140	GLU	-1	-0.988	-0.983	27.942	-9.077	-9.077	0.000	0.000	0.000	0.000
143	A	141	HIS	0	0.046	0.024	29.431	0.123	0.123	0.000	0.000	0.000	0.000
144	A	142	GLN	0	-0.008	0.009	24.371	-0.294	-0.294	0.000	0.000	0.000	0.000
145	A	143	ASP	-1	-0.785	-0.869	24.343	-12.487	-12.487	0.000	0.000	0.000	0.000
146	A	144	TYR	0	-0.023	-0.002	27.249	0.344	0.344	0.000	0.000	0.000	0.000
147	A	145	LEU	0	-0.010	-0.010	30.838	0.227	0.227	0.000	0.000	0.000	0.000
148	A	146	GLN	0	-0.039	-0.021	26.852	-0.067	-0.067	0.000	0.000	0.000	0.000
149	A	147	ARG	1	0.782	0.888	28.603	10.471	10.471	0.000	0.000	0.000	0.000
150	A	148	TYR	0	-0.051	-0.033	31.887	0.219	0.219	0.000	0.000	0.000	0.000
151	A	149	PRO	0	0.054	0.026	34.447	0.082	0.082	0.000	0.000	0.000	0.000
152	A	150	ASN	0	-0.065	-0.021	35.702	-0.009	-0.009	0.000	0.000	0.000	0.000
153	A	151	GLY	0	-0.007	0.002	37.094	0.210	0.210	0.000	0.000	0.000	0.000
154	A	152	TYR	0	-0.084	-0.074	36.592	0.060	0.060	0.000	0.000	0.000	0.000
155	A	153	THR	0	0.071	0.018	33.525	-0.296	-0.296	0.000	0.000	0.000	0.000
156	A	154	CYS	0	-0.049	-0.014	35.051	0.197	0.197	0.000	0.000	0.000	0.000
157	A	155	HIS	0	-0.063	-0.027	30.850	0.087	0.087	0.000	0.000	0.000	0.000
158	A	156	PHE	0	-0.004	-0.013	33.223	0.055	0.055	0.000	0.000	0.000	0.000
159	A	157	VAL	0	0.031	0.030	30.276	-0.019	-0.019	0.000	0.000	0.000	0.000
160	A	158	ARG	1	0.872	0.963	32.700	8.844	8.844	0.000	0.000	0.000	0.000
161	A	159	PRO	0	-0.011	-0.026	33.715	-0.140	-0.140	0.000	0.000	0.000	0.000
162	A	160	GLY	0	-0.006	-0.007	34.602	-0.059	-0.059	0.000	0.000	0.000	0.000
163	A	161	TRP	0	-0.052	-0.007	32.545	0.058	0.058	0.000	0.000	0.000	0.000
164	A	162	ARG	1	0.987	0.990	30.681	8.703	8.703	0.000	0.000	0.000	0.000
165	A	163	LEU	0	0.053	0.033	27.794	0.291	0.291	0.000	0.000	0.000	0.000
166	A	164	PRO	0	-0.072	-0.041	30.105	-0.209	-0.209	0.000	0.000	0.000	0.000
167	A	165	ARG	1	0.918	0.949	29.621	8.413	8.413	0.000	0.000	0.000	0.000
168	A	166	ARG	1	0.830	0.898	21.349	12.067	12.067	0.000	0.000	0.000	0.000

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