FMO DATABASE

FMODB ID: 728MK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1497908.117074
FMO2-HF: Nuclear repulsion	1436044.69983
FMO2-HF: Total energy	-61863.417244
FMO2-MP2: Total energy	-62041.293864

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.
1.03	3.929	0.146	-0.981	-2.063	0

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 : -0.002 / q_NPA : -0.016

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].
3	A	3	LYS	1	0.984	0.982	2.869	1.231	4.130	0.146	-0.981	-2.063
4	A	4	PRO	0	-0.020	0.014	5.642	-0.016	-0.016	0.000	0.000	0.000
5	A	5	HIS	0	0.048	0.018	9.455	0.102	0.102	0.000	0.000	0.000
6	A	6	VAL	0	-0.014	-0.004	11.326	0.034	0.034	0.000	0.000	0.000
7	A	7	THR	0	0.019	0.011	13.850	0.008	0.008	0.000	0.000	0.000
8	A	8	VAL	0	-0.005	0.008	17.606	0.003	0.003	0.000	0.000	0.000
9	A	9	ALA	0	0.007	0.005	20.803	0.000	0.000	0.000	0.000	0.000
10	A	10	CYS	0	0.004	0.005	24.373	0.000	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.011	-0.011	27.808	0.001	0.001	0.000	0.000	0.000
12	A	12	VAL	0	0.009	0.006	30.865	0.001	0.001	0.000	0.000	0.000
13	A	13	HIS	0	-0.012	-0.013	33.617	0.001	0.001	0.000	0.000	0.000
14	A	14	ALA	0	0.049	0.011	36.833	0.000	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.919	-0.961	40.410	-0.018	-0.018	0.000	0.000	0.000
16	A	16	GLY	0	-0.034	-0.005	42.199	0.001	0.001	0.000	0.000	0.000
17	A	17	LYS	1	0.844	0.929	40.606	0.021	0.021	0.000	0.000	0.000
18	A	18	PHE	0	0.026	0.000	34.731	-0.001	-0.001	0.000	0.000	0.000
19	A	19	LEU	0	-0.011	0.013	33.641	0.001	0.001	0.000	0.000	0.000
20	A	20	VAL	0	-0.058	-0.024	32.769	-0.003	-0.003	0.000	0.000	0.000
21	A	21	VAL	0	0.047	0.029	29.264	0.003	0.003	0.000	0.000	0.000
22	A	22	GLU	-1	-0.931	-0.989	31.989	-0.024	-0.024	0.000	0.000	0.000
23	A	23	GLU	-1	-0.800	-0.910	26.817	-0.046	-0.046	0.000	0.000	0.000
24	A	24	THR	0	-0.053	-0.037	31.296	0.001	0.001	0.000	0.000	0.000
25	A	25	ILE	0	-0.013	0.004	25.727	-0.001	-0.001	0.000	0.000	0.000
26	A	26	ASN	0	-0.043	-0.043	27.470	-0.001	-0.001	0.000	0.000	0.000
27	A	27	GLY	0	-0.006	-0.001	29.869	0.002	0.002	0.000	0.000	0.000
28	A	28	LYS	1	0.897	0.944	32.257	0.017	0.017	0.000	0.000	0.000
29	A	29	ALA	0	0.060	0.060	32.330	-0.002	-0.002	0.000	0.000	0.000
30	A	30	LEU	0	-0.064	-0.044	28.726	0.001	0.001	0.000	0.000	0.000
31	A	31	TRP	0	0.004	0.003	32.036	-0.001	-0.001	0.000	0.000	0.000
32	A	32	ASN	0	0.034	0.005	24.861	-0.003	-0.003	0.000	0.000	0.000
33	A	33	GLN	0	-0.003	-0.016	27.326	0.000	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.000	0.002	27.509	-0.002	-0.002	0.000	0.000	0.000
35	A	35	ALA	0	-0.100	-0.049	23.185	-0.002	-0.002	0.000	0.000	0.000
36	A	36	GLY	0	0.155	0.102	21.572	0.002	0.002	0.000	0.000	0.000
37	A	37	HIS	0	-0.077	-0.054	15.538	0.001	0.001	0.000	0.000	0.000
38	A	38	LEU	0	-0.050	-0.009	13.506	0.009	0.009	0.000	0.000	0.000
39	A	39	GLU	-1	-0.934	-0.960	15.163	-0.073	-0.073	0.000	0.000	0.000
40	A	40	ALA	0	-0.075	-0.052	14.192	0.014	0.014	0.000	0.000	0.000
41	A	41	ASP	-1	-0.941	-0.975	15.048	0.014	0.014	0.000	0.000	0.000
42	A	42	GLU	-1	-0.725	-0.830	16.530	-0.048	-0.048	0.000	0.000	0.000
43	A	43	THR	0	-0.025	-0.008	17.013	0.006	0.006	0.000	0.000	0.000
44	A	44	LEU	0	0.028	0.000	16.168	-0.005	-0.005	0.000	0.000	0.000
45	A	45	VAL	0	0.014	-0.016	19.284	-0.004	-0.004	0.000	0.000	0.000
46	A	46	GLU	-1	-0.866	-0.944	21.823	-0.022	-0.022	0.000	0.000	0.000
47	A	47	ALA	0	0.043	0.040	19.501	-0.001	-0.001	0.000	0.000	0.000
48	A	48	ALA	0	-0.038	-0.027	21.618	-0.002	-0.002	0.000	0.000	0.000
49	A	49	ALA	0	-0.024	-0.024	24.084	0.001	0.001	0.000	0.000	0.000
50	A	50	ARG	1	0.770	0.853	20.125	0.053	0.053	0.000	0.000	0.000
51	A	51	GLU	-1	-0.792	-0.892	22.073	-0.057	-0.057	0.000	0.000	0.000
52	A	52	LEU	0	-0.060	-0.024	25.480	0.002	0.002	0.000	0.000	0.000
53	A	53	TRP	0	-0.010	0.017	28.832	0.003	0.003	0.000	0.000	0.000
54	A	54	GLU	-1	-0.848	-0.944	24.862	-0.040	-0.040	0.000	0.000	0.000
55	A	55	GLU	-1	-0.755	-0.885	26.360	-0.045	-0.045	0.000	0.000	0.000
56	A	56	THR	0	-0.035	-0.061	29.991	0.003	0.003	0.000	0.000	0.000
57	A	57	GLY	0	-0.024	0.007	32.688	0.002	0.002	0.000	0.000	0.000
58	A	58	ILE	0	-0.053	-0.034	33.864	0.002	0.002	0.000	0.000	0.000
59	A	59	SER	0	-0.009	-0.003	32.741	-0.002	-0.002	0.000	0.000	0.000
60	A	60	ALA	0	-0.026	-0.026	32.212	0.001	0.001	0.000	0.000	0.000
61	A	61	GLN	0	0.029	0.019	27.478	-0.002	-0.002	0.000	0.000	0.000
62	A	62	PRO	0	0.032	0.014	25.783	0.000	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.053	-0.025	28.914	0.001	0.001	0.000	0.000	0.000
64	A	64	HIS	0	-0.012	-0.015	29.005	0.000	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.036	0.018	20.887	-0.001	-0.001	0.000	0.000	0.000
66	A	66	ILE	0	-0.007	0.008	25.871	0.001	0.001	0.000	0.000	0.000
67	A	67	ARG	1	0.912	0.932	21.854	0.075	0.075	0.000	0.000	0.000
68	A	68	MET	0	0.035	0.044	15.956	0.000	0.000	0.000	0.000	0.000
69	A	69	HIS	0	-0.051	-0.025	20.226	-0.003	-0.003	0.000	0.000	0.000
70	A	70	GLN	0	-0.009	0.003	13.136	-0.038	-0.038	0.000	0.000	0.000
71	A	71	TRP	0	-0.013	-0.008	16.758	0.017	0.017	0.000	0.000	0.000
72	A	72	ILE	0	-0.006	0.002	14.802	-0.025	-0.025	0.000	0.000	0.000
73	A	73	ALA	0	0.057	0.040	17.284	0.023	0.023	0.000	0.000	0.000
74	A	74	PRO	0	-0.005	-0.018	18.901	0.000	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.877	-0.918	17.880	-0.093	-0.093	0.000	0.000	0.000
76	A	76	LYS	1	0.879	0.919	15.067	0.029	0.029	0.000	0.000	0.000
77	A	77	THR	0	0.023	0.019	13.472	-0.042	-0.042	0.000	0.000	0.000
78	A	78	PRO	0	-0.068	-0.023	10.527	0.028	0.028	0.000	0.000	0.000
79	A	79	PHE	0	0.039	0.003	12.880	-0.047	-0.047	0.000	0.000	0.000
80	A	80	LEU	0	-0.033	-0.033	11.584	0.005	0.005	0.000	0.000	0.000
81	A	81	ARG	1	0.926	0.979	15.341	0.083	0.083	0.000	0.000	0.000
82	A	82	PHE	0	0.012	-0.008	14.942	0.005	0.005	0.000	0.000	0.000
83	A	83	LEU	0	-0.031	0.008	20.251	0.003	0.003	0.000	0.000	0.000
84	A	84	PHE	0	0.041	0.000	21.381	0.001	0.001	0.000	0.000	0.000
85	A	85	ALA	0	0.014	-0.001	26.471	0.000	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.016	-0.009	29.676	0.001	0.001	0.000	0.000	0.000
87	A	87	GLU	-1	-0.813	-0.858	32.793	-0.030	-0.030	0.000	0.000	0.000
88	A	88	LEU	0	-0.006	-0.012	36.080	0.000	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.954	-0.985	39.005	-0.020	-0.020	0.000	0.000	0.000
90	A	90	GLN	0	-0.043	-0.020	42.267	0.001	0.001	0.000	0.000	0.000
91	A	91	ILE	0	-0.013	0.007	41.383	-0.001	-0.001	0.000	0.000	0.000
92	A	92	CYS	0	-0.020	-0.002	38.974	0.001	0.001	0.000	0.000	0.000
93	A	93	PRO	0	-0.036	-0.036	40.701	-0.001	-0.001	0.000	0.000	0.000
94	A	94	THR	0	-0.020	-0.005	36.662	-0.001	-0.001	0.000	0.000	0.000
95	A	95	GLN	0	-0.068	-0.053	36.720	0.001	0.001	0.000	0.000	0.000
96	A	96	PRO	0	0.048	0.036	32.772	0.000	0.000	0.000	0.000	0.000
97	A	97	HIS	1	0.723	0.866	31.455	0.026	0.026	0.000	0.000	0.000
98	A	98	ASP	-1	-0.731	-0.881	27.346	-0.040	-0.040	0.000	0.000	0.000
99	A	99	SER	0	-0.098	-0.054	30.357	0.001	0.001	0.000	0.000	0.000
100	A	100	ASP	-1	-0.928	-0.925	26.127	-0.039	-0.039	0.000	0.000	0.000
101	A	101	ILE	0	-0.080	-0.034	28.425	0.001	0.001	0.000	0.000	0.000
102	A	102	ASP	-1	-0.867	-0.912	31.762	-0.021	-0.021	0.000	0.000	0.000
103	A	103	CYS	0	-0.105	-0.066	35.292	0.002	0.002	0.000	0.000	0.000
104	A	104	CYS	0	0.018	0.024	35.048	-0.003	-0.003	0.000	0.000	0.000
105	A	105	ARG	1	0.866	0.931	36.593	0.024	0.024	0.000	0.000	0.000
106	A	106	TRP	0	0.030	0.016	37.512	-0.002	-0.002	0.000	0.000	0.000
107	A	107	VAL	0	0.002	0.000	37.129	0.002	0.002	0.000	0.000	0.000
108	A	108	SER	0	0.037	0.014	39.038	-0.001	-0.001	0.000	0.000	0.000
109	A	109	ALA	0	0.069	0.021	37.923	-0.001	-0.001	0.000	0.000	0.000
110	A	110	GLU	-1	-0.930	-0.975	38.247	-0.023	-0.023	0.000	0.000	0.000
111	A	111	GLU	-1	-0.956	-0.975	40.224	-0.020	-0.020	0.000	0.000	0.000
112	A	112	ILE	0	0.007	0.012	33.571	-0.001	-0.001	0.000	0.000	0.000
113	A	113	LEU	0	-0.069	-0.045	34.569	-0.001	-0.001	0.000	0.000	0.000
114	A	114	GLN	0	-0.055	-0.026	36.767	0.000	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.013	0.033	36.039	0.002	0.002	0.000	0.000	0.000
116	A	116	SER	0	-0.051	-0.039	35.906	0.000	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.057	-0.024	33.973	0.000	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.033	0.039	30.624	-0.001	-0.001	0.000	0.000	0.000
119	A	119	ARG	1	0.948	0.977	22.784	0.060	0.060	0.000	0.000	0.000
120	A	120	SER	0	-0.020	-0.022	24.520	-0.005	-0.005	0.000	0.000	0.000
121	A	121	PRO	0	0.040	0.000	25.306	0.002	0.002	0.000	0.000	0.000
122	A	122	LEU	0	0.011	-0.004	21.786	0.002	0.002	0.000	0.000	0.000
123	A	123	VAL	0	-0.003	0.051	26.317	0.001	0.001	0.000	0.000	0.000
124	A	124	ALA	0	0.065	0.027	28.960	0.002	0.002	0.000	0.000	0.000
125	A	125	GLU	-1	-0.886	-0.952	27.039	-0.052	-0.052	0.000	0.000	0.000
126	A	126	SER	0	0.004	-0.016	27.296	-0.001	-0.001	0.000	0.000	0.000
127	A	127	ILE	0	0.008	0.021	29.099	0.001	0.001	0.000	0.000	0.000
128	A	128	ARG	1	0.908	0.953	30.437	0.042	0.042	0.000	0.000	0.000
129	A	129	CYS	0	-0.058	-0.036	28.346	-0.001	-0.001	0.000	0.000	0.000
130	A	130	TYR	0	-0.038	-0.030	30.806	0.000	0.000	0.000	0.000	0.000
131	A	131	GLN	0	0.008	-0.015	32.689	0.001	0.001	0.000	0.000	0.000
132	A	132	SER	0	-0.092	-0.050	32.509	0.001	0.001	0.000	0.000	0.000
133	A	133	GLY	0	0.020	0.015	34.687	0.001	0.001	0.000	0.000	0.000
134	A	134	GLN	0	-0.081	-0.035	31.062	-0.002	-0.002	0.000	0.000	0.000
135	A	135	ARG	1	0.934	0.973	30.004	0.033	0.033	0.000	0.000	0.000
136	A	136	TYR	0	-0.032	-0.015	26.676	0.001	0.001	0.000	0.000	0.000
137	A	137	PRO	0	0.023	0.009	27.098	0.001	0.001	0.000	0.000	0.000
138	A	138	LEU	0	0.013	-0.010	25.141	-0.003	-0.003	0.000	0.000	0.000
139	A	139	GLU	-1	-0.886	-0.953	23.516	-0.042	-0.042	0.000	0.000	0.000
140	A	140	MET	0	-0.093	-0.017	21.944	-0.002	-0.002	0.000	0.000	0.000
141	A	141	ILE	0	-0.088	-0.039	18.899	-0.007	-0.007	0.000	0.000	0.000
142	A	142	GLY	0	0.016	0.020	19.101	0.005	0.005	0.000	0.000	0.000
143	A	143	ASP	-1	-0.832	-0.893	18.022	-0.028	-0.028	0.000	0.000	0.000
144	A	144	PHE	0	-0.001	-0.025	16.821	-0.008	-0.008	0.000	0.000	0.000
145	A	145	ASN	0	-0.085	-0.045	17.767	0.006	0.006	0.000	0.000	0.000
146	A	146	TRP	0	0.024	0.018	15.562	0.006	0.006	0.000	0.000	0.000
147	A	147	PRO	0	-0.019	0.000	17.987	-0.003	-0.003	0.000	0.000	0.000
148	A	148	PHE	0	-0.001	0.009	17.327	-0.003	-0.003	0.000	0.000	0.000
149	A	149	THR	0	-0.029	-0.030	22.652	-0.002	-0.002	0.000	0.000	0.000
150	A	150	LYS	1	0.895	0.943	22.689	0.027	0.027	0.000	0.000	0.000
151	A	151	GLY	0	0.018	0.018	25.997	-0.001	-0.001	0.000	0.000	0.000
152	A	152	VAL	0	-0.049	-0.030	29.610	0.000	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.007	0.013	33.123	0.000	0.000	0.000	0.000	0.000

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