FMO DATABASE

FMODB ID: 6NJGZ

Calculation Name: 4NFX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NFX

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptAll
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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1501574.647249
FMO2-HF: Nuclear repulsion	1439710.185081
FMO2-HF: Total energy	-61864.462167
FMO2-MP2: Total energy	-62042.34664

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:MET)

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

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.
-1.851	1.979	1.507	-1.785	-3.553	0.005

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.010

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	3	LYS	1	0.962	0.975	2.199	-2.362	1.468	1.507	-1.785	-3.553	0.005
4	A	4	PRO	0	-0.016	0.010	5.530	-0.182	-0.182	0.000	0.000	0.000	0.000
5	A	5	HIS	0	0.072	0.036	9.386	0.250	0.250	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.016	-0.006	11.060	-0.001	-0.001	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.017	0.011	13.582	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.025	-0.008	17.301	0.009	0.009	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.007	0.006	20.629	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.015	-0.006	24.234	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.007	-0.011	27.770	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.007	0.008	30.805	0.004	0.004	0.000	0.000	0.000	0.000
13	A	13	HIS	0	-0.048	-0.047	33.407	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.078	0.039	36.824	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.863	-0.923	40.483	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.013	0.006	41.999	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.799	0.892	40.303	0.016	0.016	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.024	0.000	34.782	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.013	0.009	33.816	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.058	-0.020	32.594	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.019	0.011	28.960	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.852	-0.922	31.900	-0.049	-0.049	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.679	-0.806	26.192	-0.082	-0.082	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.048	-0.048	31.097	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.018	0.000	26.116	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.064	-0.040	27.696	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.010	0.011	30.402	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.878	0.930	32.742	0.088	0.088	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.071	0.052	32.500	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.067	-0.034	28.841	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	TRP	0	-0.015	-0.009	31.769	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.049	-0.001	25.044	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.015	0.008	27.340	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.040	0.015	27.405	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.090	-0.048	23.275	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.099	0.073	21.229	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.067	-0.054	14.597	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.064	-0.020	13.352	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.931	-0.961	14.680	0.074	0.074	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.062	-0.048	13.797	0.057	0.057	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.941	-0.978	14.565	0.296	0.296	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.750	-0.839	16.182	0.058	0.058	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.041	-0.045	16.537	0.030	0.030	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.007	-0.015	15.877	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.014	-0.014	19.021	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.824	-0.895	21.114	0.116	0.116	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.050	0.040	19.316	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.025	-0.021	21.457	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.005	-0.005	23.871	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.734	0.836	19.943	-0.048	-0.048	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.783	-0.901	21.204	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.050	-0.012	25.162	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	53	TRP	0	-0.007	0.005	28.610	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.843	-0.925	24.718	0.020	0.020	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.758	-0.889	26.736	-0.046	-0.046	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.056	-0.064	29.557	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.003	0.008	32.341	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.028	-0.027	33.684	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.018	-0.002	32.475	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.031	-0.021	31.900	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.045	0.025	27.562	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.020	0.013	25.377	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.043	-0.025	28.550	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.019	0.013	29.118	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.040	0.027	21.375	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.019	-0.010	25.856	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.886	0.918	21.946	0.073	0.073	0.000	0.000	0.000	0.000
68	A	68	MET	0	0.028	0.038	15.474	0.010	0.010	0.000	0.000	0.000	0.000
69	A	69	HIS	0	-0.054	-0.048	20.051	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.007	0.014	12.869	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	71	TRP	0	-0.021	-0.019	16.385	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.020	-0.010	14.618	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.056	0.055	17.142	0.043	0.043	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.005	-0.012	18.975	-0.029	-0.029	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.841	-0.917	17.939	-0.325	-0.325	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.864	0.924	15.245	0.285	0.285	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.014	-0.004	13.409	-0.115	-0.115	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.043	-0.014	10.188	0.076	0.076	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.037	0.009	12.528	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.029	-0.032	12.001	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.899	0.960	15.280	0.109	0.109	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.014	-0.010	15.055	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.032	0.003	20.306	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	PHE	0	0.048	0.007	21.487	0.005	0.005	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.000	0.002	26.693	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.015	-0.010	29.405	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.788	-0.845	32.898	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.004	-0.006	36.436	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.963	-0.986	39.181	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.067	-0.031	42.471	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.021	-0.011	41.431	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	CYS	0	-0.039	-0.014	38.964	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.025	-0.026	40.564	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.020	0.016	36.402	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.068	-0.047	36.456	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.065	0.041	32.541	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	HIS	1	0.718	0.867	31.055	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.778	-0.881	26.449	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.088	-0.051	29.919	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.914	-0.940	25.980	-0.069	-0.069	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.085	-0.037	27.921	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.835	-0.888	31.469	-0.046	-0.046	0.000	0.000	0.000	0.000
103	A	103	CYS	0	-0.128	-0.072	34.695	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	CYS	0	0.024	0.019	33.725	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.853	0.911	36.056	0.039	0.039	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.034	0.015	37.195	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.022	-0.008	37.136	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.015	-0.018	38.956	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.024	0.008	37.503	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.842	-0.925	37.899	-0.034	-0.034	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.924	-0.943	39.799	-0.039	-0.039	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.011	0.003	33.237	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.080	-0.054	34.444	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.091	-0.044	36.340	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.013	0.030	35.708	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.053	-0.034	35.595	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.046	-0.028	33.723	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.020	0.024	30.121	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.814	0.875	23.579	0.099	0.099	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.001	-0.014	23.642	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	121	PRO	0	0.044	0.008	25.513	0.010	0.010	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.002	-0.002	21.177	0.009	0.009	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.003	0.044	25.848	0.010	0.010	0.000	0.000	0.000	0.000
124	A	124	ALA	0	0.070	0.036	28.631	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.844	-0.893	26.056	-0.075	-0.075	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.005	-0.010	27.160	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	ILE	0	0.019	0.026	28.773	0.006	0.006	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.882	0.927	29.555	0.075	0.075	0.000	0.000	0.000	0.000
129	A	129	CYS	0	-0.064	-0.035	28.006	0.001	0.001	0.000	0.000	0.000	0.000
130	A	130	TYR	0	-0.033	-0.026	30.495	0.002	0.002	0.000	0.000	0.000	0.000
131	A	131	GLN	0	0.000	-0.015	32.832	0.001	0.001	0.000	0.000	0.000	0.000
132	A	132	SER	0	-0.076	-0.038	32.309	0.002	0.002	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.003	-0.001	34.895	0.002	0.002	0.000	0.000	0.000	0.000
134	A	134	GLN	0	-0.072	-0.030	30.974	0.003	0.003	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.913	0.942	30.207	0.002	0.002	0.000	0.000	0.000	0.000
136	A	136	TYR	0	-0.040	-0.016	27.095	0.002	0.002	0.000	0.000	0.000	0.000
137	A	137	PRO	0	0.007	0.002	27.300	0.002	0.002	0.000	0.000	0.000	0.000
138	A	138	LEU	0	0.035	0.008	25.109	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.887	-0.952	23.371	0.069	0.069	0.000	0.000	0.000	0.000
140	A	140	MET	0	-0.115	-0.039	22.344	0.003	0.003	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.074	-0.036	19.173	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.012	0.016	18.931	0.015	0.015	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.808	-0.881	17.383	0.135	0.135	0.000	0.000	0.000	0.000
144	A	144	PHE	0	-0.004	-0.025	16.526	-0.024	-0.024	0.000	0.000	0.000	0.000
145	A	145	ASN	0	-0.081	-0.049	17.319	0.014	0.014	0.000	0.000	0.000	0.000
146	A	146	TRP	0	0.040	0.035	15.243	0.025	0.025	0.000	0.000	0.000	0.000
147	A	147	PRO	0	-0.033	-0.007	17.496	-0.020	-0.020	0.000	0.000	0.000	0.000
148	A	148	PHE	0	-0.010	0.006	16.886	-0.015	-0.015	0.000	0.000	0.000	0.000
149	A	149	THR	0	-0.035	-0.037	22.451	-0.007	-0.007	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.900	0.945	22.646	-0.108	-0.108	0.000	0.000	0.000	0.000
151	A	151	GLY	0	-0.001	0.013	25.458	-0.007	-0.007	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.017	-0.009	29.226	0.002	0.002	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.045	-0.013	32.825	-0.004	-0.004	0.000	0.000	0.000	0.000

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