FMO DATABASE

FMODB ID: MV95Z

Calculation Name: 4NEE-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NEE

Chain ID: E

ChEMBL ID:

UniProt ID: P18484

Base Structure: X-ray

Registration Date: 2023-06-22

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1291102.867254
FMO2-HF: Nuclear repulsion	1235556.701672
FMO2-HF: Total energy	-55546.165582
FMO2-MP2: Total energy	-55710.397555

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(E:55:ALA)

Summations of interaction energy for fragment #1(E:55:ALA)

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.
-18.48	-15.295	12.542	-6.887	-8.842	-0.011

Interaction energy analysis for fragmet #1(E:55:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.021

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	E	57	ALA	0	0.075	0.030	3.880	1.036	2.238	-0.007	-0.537	-0.658	0.002
4	E	58	ALA	0	-0.029	-0.001	1.898	-0.185	-0.738	3.244	-0.982	-1.709	0.004
5	E	59	ALA	0	0.035	0.004	2.285	-5.459	-6.526	6.012	-2.234	-2.711	0.013
6	E	60	ALA	0	-0.044	-0.013	3.903	-2.283	-2.171	0.035	0.049	-0.197	0.002
7	E	61	ALA	0	-0.005	0.020	7.071	-0.638	-0.638	0.000	0.000	0.000	0.000
8	E	72	PRO	0	-0.034	-0.039	19.785	0.018	0.018	0.000	0.000	0.000	0.000
9	E	73	GLN	0	-0.018	-0.004	19.182	-0.048	-0.048	0.000	0.000	0.000	0.000
10	E	74	VAL	0	0.018	0.027	19.708	-0.033	-0.033	0.000	0.000	0.000	0.000
11	E	75	PRO	0	-0.051	-0.016	21.760	-0.005	-0.005	0.000	0.000	0.000	0.000
12	E	76	LEU	0	-0.006	-0.007	23.097	0.005	0.005	0.000	0.000	0.000	0.000
13	E	77	ARG	1	0.942	0.971	19.754	-0.186	-0.186	0.000	0.000	0.000	0.000
14	E	78	PRO	0	-0.013	0.007	23.338	0.003	0.003	0.000	0.000	0.000	0.000
15	E	79	MET	0	0.052	0.023	17.814	-0.002	-0.002	0.000	0.000	0.000	0.000
16	E	80	THR	0	-0.018	-0.020	22.060	-0.015	-0.015	0.000	0.000	0.000	0.000
17	E	81	TYR	0	-0.014	-0.058	21.673	0.004	0.004	0.000	0.000	0.000	0.000
18	E	82	LYS	1	0.954	0.969	21.100	-0.022	-0.022	0.000	0.000	0.000	0.000
19	E	83	ALA	0	0.007	0.028	19.210	-0.004	-0.004	0.000	0.000	0.000	0.000
20	E	84	ALA	0	0.099	0.045	17.007	0.007	0.007	0.000	0.000	0.000	0.000
21	E	85	VAL	0	0.023	0.064	16.071	-0.033	-0.033	0.000	0.000	0.000	0.000
22	E	86	ASP	-1	-0.906	-0.960	15.842	-0.024	-0.024	0.000	0.000	0.000	0.000
23	E	87	LEU	0	-0.069	-0.029	12.468	0.000	0.000	0.000	0.000	0.000	0.000
24	E	88	SER	0	-0.030	-0.057	11.712	-0.027	-0.027	0.000	0.000	0.000	0.000
25	E	89	HIS	0	0.018	-0.003	11.024	-0.142	-0.142	0.000	0.000	0.000	0.000
26	E	90	PHE	0	0.000	0.023	9.266	-0.038	-0.038	0.000	0.000	0.000	0.000
27	E	91	LEU	0	-0.003	-0.009	6.979	0.037	0.037	0.000	0.000	0.000	0.000
28	E	92	LYS	1	0.948	0.979	6.107	0.016	0.016	0.000	0.000	0.000	0.000
29	E	93	GLU	-1	-0.987	-1.002	7.712	-0.362	-0.362	0.000	0.000	0.000	0.000
30	E	94	LYS	1	0.744	0.893	3.610	-3.823	-3.431	0.008	-0.107	-0.292	0.000
31	E	95	GLY	0	0.012	0.019	3.544	-1.363	-0.499	0.013	-0.442	-0.435	-0.003
32	E	96	GLY	0	-0.004	-0.049	2.399	-6.016	-4.016	3.231	-2.660	-2.572	-0.029
33	E	97	LEU	0	-0.012	0.002	3.599	0.956	1.130	0.007	0.031	-0.212	0.000
34	E	98	GLU	-1	-0.792	-0.895	6.184	-0.370	-0.370	0.000	0.000	0.000	0.000
35	E	99	GLY	0	-0.032	-0.006	7.033	-0.167	-0.167	0.000	0.000	0.000	0.000
36	E	100	LEU	0	-0.105	-0.040	4.706	0.044	0.105	-0.001	-0.005	-0.056	0.000
37	E	101	ILE	0	0.040	0.011	8.048	0.099	0.099	0.000	0.000	0.000	0.000
38	E	102	HIS	0	-0.021	-0.016	10.422	0.007	0.007	0.000	0.000	0.000	0.000
39	E	103	SER	0	-0.009	-0.016	12.549	0.037	0.037	0.000	0.000	0.000	0.000
40	E	104	GLN	0	0.036	-0.028	13.772	-0.003	-0.003	0.000	0.000	0.000	0.000
41	E	105	ARG	1	0.957	0.989	11.087	-0.160	-0.160	0.000	0.000	0.000	0.000
42	E	106	ARG	1	0.788	0.900	8.144	0.239	0.239	0.000	0.000	0.000	0.000
43	E	107	GLN	0	0.073	0.045	11.128	0.077	0.077	0.000	0.000	0.000	0.000
44	E	108	ASP	-1	-0.805	-0.868	12.970	0.250	0.250	0.000	0.000	0.000	0.000
45	E	109	ILE	0	-0.038	-0.021	9.476	0.048	0.048	0.000	0.000	0.000	0.000
46	E	110	LEU	0	-0.031	-0.009	8.360	0.144	0.144	0.000	0.000	0.000	0.000
47	E	111	ASP	-1	-0.802	-0.906	10.833	0.215	0.215	0.000	0.000	0.000	0.000
48	E	112	LEU	0	-0.010	-0.018	14.158	-0.001	-0.001	0.000	0.000	0.000	0.000
49	E	113	TRP	0	-0.027	-0.002	10.143	0.091	0.091	0.000	0.000	0.000	0.000
50	E	114	ILE	0	0.010	-0.010	11.567	-0.037	-0.037	0.000	0.000	0.000	0.000
51	E	115	TYR	0	-0.024	0.017	13.892	-0.056	-0.056	0.000	0.000	0.000	0.000
52	E	116	HIS	0	0.025	-0.001	15.625	-0.046	-0.046	0.000	0.000	0.000	0.000
53	E	117	THR	0	-0.045	-0.025	13.057	-0.037	-0.037	0.000	0.000	0.000	0.000
54	E	118	GLN	0	-0.059	-0.051	13.181	-0.083	-0.083	0.000	0.000	0.000	0.000
55	E	119	GLY	0	0.006	0.035	17.168	-0.048	-0.048	0.000	0.000	0.000	0.000
56	E	120	TYR	0	-0.004	-0.012	17.046	-0.051	-0.051	0.000	0.000	0.000	0.000
57	E	121	PHE	0	0.016	-0.009	19.252	0.030	0.030	0.000	0.000	0.000	0.000
58	E	122	PRO	0	-0.014	0.001	18.126	-0.015	-0.015	0.000	0.000	0.000	0.000
59	E	123	ASP	-1	-0.864	-0.933	19.661	0.088	0.088	0.000	0.000	0.000	0.000
60	E	124	TRP	0	0.002	-0.003	14.197	-0.037	-0.037	0.000	0.000	0.000	0.000
61	E	125	GLN	0	-0.024	0.012	13.272	-0.115	-0.115	0.000	0.000	0.000	0.000
62	E	126	ASN	0	-0.002	0.004	18.328	0.004	0.004	0.000	0.000	0.000	0.000
63	E	127	TYR	0	-0.002	-0.048	14.729	-0.034	-0.034	0.000	0.000	0.000	0.000
64	E	128	THR	0	-0.026	-0.019	21.258	0.007	0.007	0.000	0.000	0.000	0.000
65	E	129	PRO	0	-0.002	-0.006	23.524	-0.006	-0.006	0.000	0.000	0.000	0.000
66	E	130	GLY	0	0.006	0.050	25.070	-0.009	-0.009	0.000	0.000	0.000	0.000
67	E	131	PRO	0	0.004	-0.012	25.487	0.008	0.008	0.000	0.000	0.000	0.000
68	E	132	GLY	0	0.003	-0.001	24.138	0.001	0.001	0.000	0.000	0.000	0.000
69	E	133	VAL	0	-0.050	-0.028	19.592	-0.004	-0.004	0.000	0.000	0.000	0.000
70	E	134	ARG	1	0.791	0.875	19.237	0.105	0.105	0.000	0.000	0.000	0.000
71	E	135	TYR	0	-0.018	-0.021	19.222	-0.028	-0.028	0.000	0.000	0.000	0.000
72	E	136	PRO	0	0.007	0.019	18.031	0.018	0.018	0.000	0.000	0.000	0.000
73	E	137	LEU	0	-0.008	-0.019	20.192	0.000	0.000	0.000	0.000	0.000	0.000
74	E	138	THR	0	-0.056	-0.032	20.030	0.008	0.008	0.000	0.000	0.000	0.000
75	E	139	PHE	0	-0.030	-0.010	20.930	-0.013	-0.013	0.000	0.000	0.000	0.000
76	E	140	GLY	0	0.045	-0.005	20.425	0.014	0.014	0.000	0.000	0.000	0.000
77	E	141	TRP	0	-0.005	-0.001	11.609	-0.004	-0.004	0.000	0.000	0.000	0.000
78	E	142	CYS	0	-0.068	-0.043	14.751	0.002	0.002	0.000	0.000	0.000	0.000
79	E	143	TYR	0	-0.010	-0.002	8.358	-0.038	-0.038	0.000	0.000	0.000	0.000
80	E	144	LYS	1	0.920	0.958	14.177	0.282	0.282	0.000	0.000	0.000	0.000
81	E	145	LEU	0	0.036	0.023	13.944	-0.054	-0.054	0.000	0.000	0.000	0.000
82	E	146	VAL	0	-0.035	-0.020	15.810	0.032	0.032	0.000	0.000	0.000	0.000
83	E	147	PRO	0	0.042	0.021	16.984	-0.022	-0.022	0.000	0.000	0.000	0.000
84	E	148	VAL	0	-0.043	-0.021	15.748	-0.013	-0.013	0.000	0.000	0.000	0.000
85	E	149	GLU	-1	-0.931	-0.960	18.638	-0.167	-0.167	0.000	0.000	0.000	0.000
86	E	150	PRO	0	0.077	0.014	21.056	-0.009	-0.009	0.000	0.000	0.000	0.000
87	E	151	ASP	-1	-0.866	-0.926	22.912	-0.131	-0.131	0.000	0.000	0.000	0.000
88	E	152	LYS	1	0.905	0.946	18.186	0.206	0.206	0.000	0.000	0.000	0.000
89	E	153	VAL	0	-0.008	-0.002	18.910	-0.008	-0.008	0.000	0.000	0.000	0.000
90	E	154	GLU	-1	-0.940	-0.982	19.974	-0.090	-0.090	0.000	0.000	0.000	0.000
91	E	155	GLU	-1	-0.981	-1.002	20.844	-0.142	-0.142	0.000	0.000	0.000	0.000
92	E	156	ALA	0	-0.054	-0.020	16.174	-0.004	-0.004	0.000	0.000	0.000	0.000
93	E	157	ASN	0	0.001	-0.006	18.003	0.003	0.003	0.000	0.000	0.000	0.000
94	E	158	LYS	1	0.892	0.978	20.074	0.133	0.133	0.000	0.000	0.000	0.000
95	E	159	GLY	0	-0.015	-0.009	20.946	-0.010	-0.010	0.000	0.000	0.000	0.000
96	E	160	GLU	-1	-0.955	-0.982	22.925	-0.046	-0.046	0.000	0.000	0.000	0.000
97	E	161	ASN	0	-0.050	-0.039	20.576	0.016	0.016	0.000	0.000	0.000	0.000
98	E	162	THR	0	0.015	0.032	17.564	0.002	0.002	0.000	0.000	0.000	0.000
99	E	163	SER	0	-0.015	-0.013	16.159	0.009	0.009	0.000	0.000	0.000	0.000
100	E	164	LEU	0	0.071	0.045	18.051	-0.010	-0.010	0.000	0.000	0.000	0.000
101	E	165	LEU	0	0.018	0.008	17.623	-0.002	-0.002	0.000	0.000	0.000	0.000
102	E	166	HIS	0	-0.026	0.003	10.276	0.050	0.050	0.000	0.000	0.000	0.000
103	E	167	PRO	0	0.008	-0.036	10.972	0.003	0.003	0.000	0.000	0.000	0.000
104	E	168	VAL	0	0.000	0.003	12.934	-0.008	-0.008	0.000	0.000	0.000	0.000
105	E	169	SER	0	0.015	-0.017	15.305	-0.002	-0.002	0.000	0.000	0.000	0.000
106	E	170	LEU	0	-0.074	-0.026	16.368	0.013	0.013	0.000	0.000	0.000	0.000
107	E	171	HIS	0	-0.049	-0.017	19.129	0.001	0.001	0.000	0.000	0.000	0.000
108	E	172	GLY	0	0.044	0.030	19.320	0.003	0.003	0.000	0.000	0.000	0.000
109	E	173	MET	0	-0.038	-0.013	19.824	0.007	0.007	0.000	0.000	0.000	0.000
110	E	174	ASP	-1	-0.826	-0.912	17.484	0.041	0.041	0.000	0.000	0.000	0.000
111	E	175	ASP	-1	-0.803	-0.889	20.400	-0.059	-0.059	0.000	0.000	0.000	0.000
112	E	176	PRO	0	-0.002	0.010	21.910	0.001	0.001	0.000	0.000	0.000	0.000
113	E	177	GLU	-1	-0.936	-0.972	24.943	-0.041	-0.041	0.000	0.000	0.000	0.000
114	E	178	ARG	1	0.858	0.925	23.788	0.031	0.031	0.000	0.000	0.000	0.000
115	E	179	GLU	-1	-0.807	-0.895	21.768	-0.114	-0.114	0.000	0.000	0.000	0.000
116	E	180	VAL	0	-0.001	-0.003	16.572	0.001	0.001	0.000	0.000	0.000	0.000
117	E	181	LEU	0	-0.001	0.012	16.357	-0.017	-0.017	0.000	0.000	0.000	0.000
118	E	182	GLU	-1	-0.879	-0.945	12.272	-0.468	-0.468	0.000	0.000	0.000	0.000
119	E	183	TRP	0	-0.003	0.012	9.469	0.023	0.023	0.000	0.000	0.000	0.000
120	E	184	ARG	1	0.816	0.898	10.943	0.442	0.442	0.000	0.000	0.000	0.000
121	E	185	PHE	0	-0.009	-0.008	11.228	0.072	0.072	0.000	0.000	0.000	0.000
122	E	186	ASP	-1	-0.856	-0.939	13.103	-0.190	-0.190	0.000	0.000	0.000	0.000
123	E	187	SER	0	0.037	-0.001	16.800	0.007	0.007	0.000	0.000	0.000	0.000
124	E	188	ARG	1	0.929	0.978	18.594	0.139	0.139	0.000	0.000	0.000	0.000
125	E	189	LEU	0	0.017	0.011	17.622	0.020	0.020	0.000	0.000	0.000	0.000
126	E	190	ALA	0	0.028	0.021	19.794	0.019	0.019	0.000	0.000	0.000	0.000
127	E	191	PHE	0	-0.036	0.017	21.535	0.016	0.016	0.000	0.000	0.000	0.000
128	E	192	HIS	0	-0.022	-0.005	24.578	0.012	0.012	0.000	0.000	0.000	0.000
129	E	193	HIS	0	0.004	0.017	24.679	-0.016	-0.016	0.000	0.000	0.000	0.000
130	E	194	VAL	0	0.044	0.005	23.800	0.007	0.007	0.000	0.000	0.000	0.000
131	E	195	ALA	0	0.039	0.024	24.253	0.004	0.004	0.000	0.000	0.000	0.000
132	E	196	ARG	1	0.926	0.963	26.013	0.025	0.025	0.000	0.000	0.000	0.000
133	E	197	GLU	-1	-0.910	-0.965	29.157	-0.062	-0.062	0.000	0.000	0.000	0.000
134	E	198	LEU	0	-0.016	-0.002	26.683	0.003	0.003	0.000	0.000	0.000	0.000
135	E	199	HIS	1	0.832	0.902	27.710	0.044	0.044	0.000	0.000	0.000	0.000
136	E	200	PRO	0	0.032	0.012	30.911	0.005	0.005	0.000	0.000	0.000	0.000
137	E	201	GLU	-1	-0.860	-0.919	33.030	-0.023	-0.023	0.000	0.000	0.000	0.000
138	E	202	TYR	0	-0.038	-0.014	28.223	0.002	0.002	0.000	0.000	0.000	0.000
139	E	203	PHE	0	-0.059	-0.009	26.711	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:55:ALA)