FMO DATABASE

FMODB ID: LZ1G9

Calculation Name: 4NVS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NVS

Chain ID: A

ChEMBL ID:

UniProt ID: Q18CP6

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1506486.671941
FMO2-HF: Nuclear repulsion	1442281.824541
FMO2-HF: Total energy	-64204.8474
FMO2-MP2: Total energy	-64391.480273

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.
0.787	2.846	0.029	-0.72	-1.368	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 : 0.008 / q_NPA : -0.008

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	PHE	0	0.009	0.022	3.854	0.959	2.980	0.030	-0.714	-1.337
4	A	4	LEU	0	-0.039	-0.028	5.597	-0.596	-0.558	-0.001	-0.006	-0.031
5	A	5	ASN	0	0.048	0.016	8.498	-0.357	-0.357	0.000	0.000	0.000
6	A	6	VAL	0	0.010	0.040	10.009	0.102	0.102	0.000	0.000	0.000
7	A	7	LEU	0	-0.019	0.001	12.472	-0.018	-0.018	0.000	0.000	0.000
8	A	8	ILE	0	-0.015	-0.015	14.556	-0.038	-0.038	0.000	0.000	0.000
9	A	9	VAL	0	0.000	-0.005	17.728	0.006	0.006	0.000	0.000	0.000
10	A	10	VAL	0	0.000	0.013	19.984	-0.018	-0.018	0.000	0.000	0.000
11	A	11	GLU	-1	-0.917	-0.969	23.558	0.099	0.099	0.000	0.000	0.000
12	A	12	ASP	-1	-0.918	-0.975	26.755	0.117	0.117	0.000	0.000	0.000
13	A	13	ILE	0	0.053	0.023	22.523	-0.002	-0.002	0.000	0.000	0.000
14	A	14	GLU	-1	-0.837	-0.904	26.167	0.159	0.159	0.000	0.000	0.000
15	A	15	LYS	1	0.907	0.955	29.366	-0.096	-0.096	0.000	0.000	0.000
16	A	16	SER	0	0.079	0.038	25.064	-0.007	-0.007	0.000	0.000	0.000
17	A	17	LYS	1	0.849	0.919	25.365	-0.180	-0.180	0.000	0.000	0.000
18	A	18	LYS	1	0.834	0.916	26.926	-0.096	-0.096	0.000	0.000	0.000
19	A	19	PHE	0	0.001	0.026	26.997	-0.005	-0.005	0.000	0.000	0.000
20	A	20	TYR	0	-0.005	-0.057	22.940	-0.004	-0.004	0.000	0.000	0.000
21	A	21	TYR	0	-0.028	0.001	26.807	-0.003	-0.003	0.000	0.000	0.000
22	A	22	ASP	-1	-0.852	-0.921	29.070	0.088	0.088	0.000	0.000	0.000
23	A	23	VAL	0	-0.037	-0.016	29.438	-0.009	-0.009	0.000	0.000	0.000
24	A	24	LEU	0	-0.010	-0.012	24.296	-0.006	-0.006	0.000	0.000	0.000
25	A	25	GLY	0	0.009	0.035	27.874	0.000	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.010	-0.010	21.824	0.007	0.007	0.000	0.000	0.000
27	A	27	LYS	1	0.911	0.968	25.348	-0.173	-0.173	0.000	0.000	0.000
28	A	28	VAL	0	-0.020	-0.019	22.825	0.016	0.016	0.000	0.000	0.000
29	A	29	ILE	0	-0.065	-0.033	18.012	-0.016	-0.016	0.000	0.000	0.000
30	A	30	CYS	0	-0.046	-0.028	19.077	0.028	0.028	0.000	0.000	0.000
31	A	31	ASP	-1	-0.898	-0.927	21.175	0.240	0.240	0.000	0.000	0.000
32	A	32	PHE	0	-0.008	-0.003	17.343	0.017	0.017	0.000	0.000	0.000
33	A	33	GLY	0	-0.037	-0.009	22.105	-0.013	-0.013	0.000	0.000	0.000
34	A	34	GLU	-1	-0.920	-0.983	20.983	0.276	0.276	0.000	0.000	0.000
35	A	35	ASN	0	-0.036	-0.018	15.835	0.016	0.016	0.000	0.000	0.000
36	A	36	VAL	0	0.013	0.005	20.060	0.017	0.017	0.000	0.000	0.000
37	A	37	VAL	0	0.028	0.014	16.171	0.007	0.007	0.000	0.000	0.000
38	A	38	LEU	0	0.023	-0.009	18.899	-0.029	-0.029	0.000	0.000	0.000
39	A	39	GLU	-1	-0.867	-0.958	18.786	0.223	0.223	0.000	0.000	0.000
40	A	40	GLY	0	0.013	0.011	17.389	-0.023	-0.023	0.000	0.000	0.000
41	A	41	ASN	0	-0.095	-0.045	12.411	-0.042	-0.042	0.000	0.000	0.000
42	A	42	ILE	0	0.043	0.030	14.082	0.062	0.062	0.000	0.000	0.000
43	A	43	SER	0	-0.019	-0.013	14.713	-0.004	-0.004	0.000	0.000	0.000
44	A	44	LEU	0	-0.034	-0.010	16.799	-0.022	-0.022	0.000	0.000	0.000
45	A	45	GLN	0	0.018	0.018	17.437	0.058	0.058	0.000	0.000	0.000
46	A	46	GLU	-1	-0.777	-0.878	19.573	0.121	0.121	0.000	0.000	0.000
47	A	47	LYS	1	0.888	0.920	21.735	-0.079	-0.079	0.000	0.000	0.000
48	A	48	LYS	1	0.919	0.939	22.669	-0.112	-0.112	0.000	0.000	0.000
49	A	49	LEU	0	-0.006	0.002	20.041	-0.005	-0.005	0.000	0.000	0.000
50	A	50	TRP	0	0.017	0.003	13.329	0.013	0.013	0.000	0.000	0.000
51	A	51	LEU	0	-0.063	-0.029	19.100	-0.007	-0.007	0.000	0.000	0.000
52	A	52	GLU	-1	-0.966	-0.975	21.123	0.128	0.128	0.000	0.000	0.000
53	A	53	PHE	0	-0.032	-0.018	15.999	-0.002	-0.002	0.000	0.000	0.000
54	A	54	ILE	0	-0.046	-0.016	14.655	-0.010	-0.010	0.000	0.000	0.000
55	A	55	ASN	0	-0.077	-0.027	16.900	-0.023	-0.023	0.000	0.000	0.000
56	A	56	LYS	1	0.924	0.968	18.179	-0.012	-0.012	0.000	0.000	0.000
57	A	57	SER	0	-0.012	-0.015	22.069	0.010	0.010	0.000	0.000	0.000
58	A	58	ASP	-1	-0.820	-0.914	24.840	0.066	0.066	0.000	0.000	0.000
59	A	59	SER	0	-0.027	-0.003	26.473	0.001	0.001	0.000	0.000	0.000
60	A	60	GLU	-1	-0.958	-0.982	22.540	0.004	0.004	0.000	0.000	0.000
61	A	61	VAL	0	-0.003	0.013	20.695	-0.001	-0.001	0.000	0.000	0.000
62	A	62	LYS	1	0.909	0.957	22.778	-0.023	-0.023	0.000	0.000	0.000
63	A	63	PHE	0	0.041	0.021	22.525	0.005	0.005	0.000	0.000	0.000
64	A	64	ASN	0	0.020	-0.008	24.854	-0.004	-0.004	0.000	0.000	0.000
65	A	65	GLY	0	-0.035	0.001	23.616	-0.009	-0.009	0.000	0.000	0.000
66	A	66	ASN	0	-0.015	0.008	24.220	-0.004	-0.004	0.000	0.000	0.000
67	A	67	ASP	-1	-0.918	-0.951	19.037	0.021	0.021	0.000	0.000	0.000
68	A	68	ALA	0	-0.025	-0.010	17.283	-0.003	-0.003	0.000	0.000	0.000
69	A	69	GLH	0	-0.025	-0.046	18.297	-0.006	-0.006	0.000	0.000	0.000
70	A	70	LEU	0	-0.047	-0.006	16.947	0.013	0.013	0.000	0.000	0.000
71	A	71	TYR	0	-0.082	-0.077	18.393	-0.016	-0.016	0.000	0.000	0.000
72	A	72	PHE	0	0.011	-0.004	19.418	0.017	0.017	0.000	0.000	0.000
73	A	73	GLU	-1	-0.817	-0.879	22.145	-0.015	-0.015	0.000	0.000	0.000
74	A	74	GLU	-1	-0.868	-0.933	24.430	0.078	0.078	0.000	0.000	0.000
75	A	75	ASP	-1	-0.898	-0.956	27.711	0.036	0.036	0.000	0.000	0.000
76	A	76	ASN	0	-0.115	-0.053	30.094	-0.011	-0.011	0.000	0.000	0.000
77	A	77	PHE	0	0.020	0.015	29.516	0.002	0.002	0.000	0.000	0.000
78	A	78	ASP	-1	-0.793	-0.879	32.353	0.018	0.018	0.000	0.000	0.000
79	A	79	THR	0	-0.002	0.000	35.108	0.003	0.003	0.000	0.000	0.000
80	A	80	PHE	0	0.016	0.010	29.579	0.002	0.002	0.000	0.000	0.000
81	A	81	VAL	0	0.013	-0.002	33.044	0.002	0.002	0.000	0.000	0.000
82	A	82	GLU	-1	-0.934	-0.981	34.865	0.025	0.025	0.000	0.000	0.000
83	A	83	ARG	1	0.848	0.928	33.535	-0.071	-0.071	0.000	0.000	0.000
84	A	84	LEU	0	0.011	0.000	31.859	0.002	0.002	0.000	0.000	0.000
85	A	85	SER	0	-0.084	-0.023	35.686	-0.001	-0.001	0.000	0.000	0.000
86	A	86	THR	0	-0.094	-0.054	38.789	-0.001	-0.001	0.000	0.000	0.000
87	A	87	MET	0	-0.074	-0.028	34.091	0.002	0.002	0.000	0.000	0.000
88	A	88	LYS	1	0.921	0.948	38.502	-0.050	-0.050	0.000	0.000	0.000
89	A	89	ASP	-1	-0.946	-0.985	36.463	0.053	0.053	0.000	0.000	0.000
90	A	90	ILE	0	-0.013	0.021	32.484	0.005	0.005	0.000	0.000	0.000
91	A	91	ASP	-1	-0.912	-0.951	31.400	0.034	0.034	0.000	0.000	0.000
92	A	92	TYR	0	-0.013	-0.020	31.238	0.004	0.004	0.000	0.000	0.000
93	A	93	VAL	0	-0.002	0.009	27.460	-0.003	-0.003	0.000	0.000	0.000
94	A	94	HIS	0	-0.060	-0.053	29.673	-0.008	-0.008	0.000	0.000	0.000
95	A	95	LEU	0	0.012	0.008	33.345	0.004	0.004	0.000	0.000	0.000
96	A	96	ALA	0	0.033	0.032	32.994	-0.002	-0.002	0.000	0.000	0.000
97	A	97	ILE	0	-0.032	-0.002	28.411	-0.004	-0.004	0.000	0.000	0.000
98	A	98	GLU	-1	-0.903	-0.963	32.114	-0.019	-0.019	0.000	0.000	0.000
99	A	99	HIS	1	0.779	0.885	25.423	0.019	0.019	0.000	0.000	0.000
100	A	100	ARG	1	0.911	0.955	29.018	0.079	0.079	0.000	0.000	0.000
101	A	101	TRP	0	0.013	-0.016	24.388	-0.004	-0.004	0.000	0.000	0.000
102	A	102	GLY	0	0.049	0.014	29.661	0.000	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.027	-0.004	24.587	-0.005	-0.005	0.000	0.000	0.000
104	A	104	ARG	1	0.769	0.858	29.841	-0.007	-0.007	0.000	0.000	0.000
105	A	105	ALA	0	0.023	0.004	27.380	0.003	0.003	0.000	0.000	0.000
106	A	106	ILE	0	-0.037	-0.006	28.922	-0.005	-0.005	0.000	0.000	0.000
107	A	107	ARG	1	0.832	0.888	24.455	0.000	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.001	0.008	27.633	-0.006	-0.006	0.000	0.000	0.000
109	A	109	TYR	0	-0.048	-0.046	26.548	0.004	0.004	0.000	0.000	0.000
110	A	110	ASP	-1	-0.778	-0.871	23.909	0.125	0.125	0.000	0.000	0.000
111	A	111	LEU	0	-0.021	-0.034	26.948	-0.008	-0.008	0.000	0.000	0.000
112	A	112	ASP	-1	-0.844	-0.911	24.476	0.113	0.113	0.000	0.000	0.000
113	A	113	GLY	0	0.029	0.014	24.980	0.000	0.000	0.000	0.000	0.000
114	A	114	HIS	1	0.765	0.861	20.073	-0.142	-0.142	0.000	0.000	0.000
115	A	115	ILE	0	0.024	0.021	22.658	-0.002	-0.002	0.000	0.000	0.000
116	A	116	ILE	0	0.017	0.018	22.084	0.014	0.014	0.000	0.000	0.000
117	A	117	GLU	-1	-0.766	-0.858	23.116	-0.012	-0.012	0.000	0.000	0.000
118	A	118	VAL	0	0.029	0.020	23.613	0.009	0.009	0.000	0.000	0.000
119	A	119	GLY	0	0.029	-0.009	25.502	-0.008	-0.008	0.000	0.000	0.000
120	A	120	GLU	-1	-0.698	-0.810	27.106	0.003	0.003	0.000	0.000	0.000
121	A	121	THR	0	0.092	0.066	25.873	-0.007	-0.007	0.000	0.000	0.000
122	A	122	MET	0	0.020	0.008	23.417	-0.005	-0.005	0.000	0.000	0.000
123	A	123	SER	0	0.017	0.001	26.288	-0.005	-0.005	0.000	0.000	0.000
124	A	124	SER	0	-0.032	-0.017	28.243	-0.001	-0.001	0.000	0.000	0.000
125	A	125	VAL	0	-0.021	0.004	28.991	-0.001	-0.001	0.000	0.000	0.000
126	A	126	CYS	0	-0.027	-0.018	28.805	-0.003	-0.003	0.000	0.000	0.000
127	A	127	ARG	1	0.950	0.968	31.395	0.009	0.009	0.000	0.000	0.000
128	A	128	ARG	1	0.845	0.922	32.857	0.012	0.012	0.000	0.000	0.000
129	A	129	PHE	0	-0.049	-0.040	32.364	0.000	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.025	-0.020	33.667	-0.002	-0.002	0.000	0.000	0.000
131	A	131	ASP	-1	-0.906	-0.928	37.195	-0.012	-0.012	0.000	0.000	0.000
132	A	132	SER	0	-0.173	-0.082	39.539	0.001	0.001	0.000	0.000	0.000
133	A	133	GLY	0	-0.001	-0.016	41.123	0.000	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.081	-0.013	36.770	-0.002	-0.002	0.000	0.000	0.000
135	A	135	SER	0	0.024	0.014	37.871	0.000	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.098	0.034	31.621	-0.001	-0.001	0.000	0.000	0.000
137	A	137	ASP	-1	-0.896	-0.965	33.420	-0.069	-0.069	0.000	0.000	0.000
138	A	138	GLU	-1	-0.956	-0.976	34.222	-0.049	-0.049	0.000	0.000	0.000
139	A	139	VAL	0	0.036	0.018	31.486	-0.003	-0.003	0.000	0.000	0.000
140	A	140	ALA	0	0.014	-0.004	29.681	-0.002	-0.002	0.000	0.000	0.000
141	A	141	LYS	1	0.899	0.955	29.996	0.066	0.066	0.000	0.000	0.000
142	A	142	ARG	1	0.828	0.918	32.295	0.046	0.046	0.000	0.000	0.000
143	A	143	MET	0	-0.045	-0.019	27.635	0.004	0.004	0.000	0.000	0.000
144	A	144	ASP	-1	-0.899	-0.931	26.961	-0.093	-0.093	0.000	0.000	0.000
145	A	145	VAL	0	-0.028	-0.013	24.140	-0.014	-0.014	0.000	0.000	0.000
146	A	146	THR	0	0.015	0.002	24.149	0.011	0.011	0.000	0.000	0.000
147	A	147	VAL	0	0.056	0.004	26.930	0.003	0.003	0.000	0.000	0.000
148	A	148	GLU	-1	-0.921	-0.958	24.060	-0.158	-0.158	0.000	0.000	0.000
149	A	149	TYR	0	-0.009	0.001	21.343	0.006	0.006	0.000	0.000	0.000
150	A	150	ILE	0	0.043	0.035	24.293	0.010	0.010	0.000	0.000	0.000
151	A	151	GLU	-1	-0.927	-0.972	27.347	-0.056	-0.056	0.000	0.000	0.000
152	A	152	SER	0	-0.082	-0.043	22.825	0.006	0.006	0.000	0.000	0.000
153	A	153	VAL	0	0.008	-0.002	23.077	0.014	0.014	0.000	0.000	0.000
154	A	154	LEU	0	-0.041	-0.029	25.259	0.013	0.013	0.000	0.000	0.000
155	A	155	GLU	-1	-1.008	-0.988	27.193	-0.019	-0.019	0.000	0.000	0.000
156	A	156	LEU	0	-0.066	-0.021	22.907	0.010	0.010	0.000	0.000	0.000

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