FMO DATABASE

FMODB ID: LNNV9

Calculation Name: 4XLT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XLT

Chain ID: A

ChEMBL ID:

UniProt ID: C6VVW9

Base Structure: X-ray

Registration Date: 2023-09-21

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1176086.116571
FMO2-HF: Nuclear repulsion	1124902.257444
FMO2-HF: Total energy	-51183.859127
FMO2-MP2: Total energy	-51333.944614

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:0:ALA)

Summations of interaction energy for fragment #1(A:0: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.
-2.867	-0.915	-0.024	-0.758	-1.169	0

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.032

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	2	ASP	-1	-0.817	-0.880	3.851	-1.625	-0.026	-0.022	-0.724	-0.853
4	A	3	PHE	0	-0.020	-0.025	6.936	0.218	0.218	0.000	0.000	0.000
5	A	4	ILE	0	-0.033	-0.013	9.864	0.013	0.013	0.000	0.000	0.000
6	A	5	ILE	0	-0.005	0.005	13.449	0.034	0.034	0.000	0.000	0.000
7	A	6	VAL	0	-0.007	-0.017	16.336	-0.018	-0.018	0.000	0.000	0.000
8	A	7	ASP	-1	-0.779	-0.887	19.841	0.034	0.034	0.000	0.000	0.000
9	A	8	ASP	-1	-0.836	-0.919	22.668	-0.011	-0.011	0.000	0.000	0.000
10	A	9	SER	0	-0.009	0.015	25.574	0.003	0.003	0.000	0.000	0.000
11	A	10	VAL	0	0.039	-0.002	24.346	0.005	0.005	0.000	0.000	0.000
12	A	11	PHE	0	-0.028	-0.014	24.003	0.008	0.008	0.000	0.000	0.000
13	A	12	ASP	-1	-0.821	-0.912	22.961	0.073	0.073	0.000	0.000	0.000
14	A	13	LEU	0	-0.033	-0.006	19.187	0.017	0.017	0.000	0.000	0.000
15	A	14	PHE	0	0.029	0.007	18.975	0.011	0.011	0.000	0.000	0.000
16	A	15	THR	0	-0.099	-0.052	19.306	0.028	0.028	0.000	0.000	0.000
17	A	16	GLN	0	0.019	-0.003	16.074	0.071	0.071	0.000	0.000	0.000
18	A	17	GLU	-1	-0.869	-0.944	14.603	0.092	0.092	0.000	0.000	0.000
19	A	18	LYS	1	0.923	0.964	14.550	-0.091	-0.091	0.000	0.000	0.000
20	A	19	LEU	0	-0.076	-0.046	15.797	0.049	0.049	0.000	0.000	0.000
21	A	20	LEU	0	0.028	0.008	11.137	0.078	0.078	0.000	0.000	0.000
22	A	21	LEU	0	0.025	0.024	10.515	0.137	0.137	0.000	0.000	0.000
23	A	22	LYS	1	0.879	0.964	12.226	-0.258	-0.258	0.000	0.000	0.000
24	A	23	SER	0	-0.103	-0.039	11.735	0.051	0.051	0.000	0.000	0.000
25	A	24	GLY	0	0.025	-0.002	9.200	-0.032	-0.032	0.000	0.000	0.000
26	A	25	LEU	0	-0.086	-0.043	7.226	0.525	0.525	0.000	0.000	0.000
27	A	26	THR	0	0.030	0.003	5.161	0.623	0.623	0.000	0.000	0.000
28	A	27	THR	0	-0.023	-0.010	5.748	-0.100	-0.100	0.000	0.000	0.000
29	A	28	SER	0	-0.054	-0.030	6.442	-0.016	-0.016	0.000	0.000	0.000
30	A	29	VAL	0	0.018	0.018	8.606	-0.090	-0.090	0.000	0.000	0.000
31	A	30	ARG	1	0.935	0.976	11.010	0.409	0.409	0.000	0.000	0.000
32	A	31	THR	0	0.023	0.015	14.041	0.011	0.011	0.000	0.000	0.000
33	A	32	PHE	0	-0.055	-0.037	16.067	-0.014	-0.014	0.000	0.000	0.000
34	A	33	ASN	0	0.054	0.017	20.349	0.014	0.014	0.000	0.000	0.000
35	A	34	SER	0	0.033	0.009	23.537	0.003	0.003	0.000	0.000	0.000
36	A	35	ALA	0	0.104	0.047	23.422	-0.014	-0.014	0.000	0.000	0.000
37	A	36	GLN	0	-0.045	-0.013	23.651	-0.011	-0.011	0.000	0.000	0.000
38	A	37	ALA	0	0.022	0.015	22.671	-0.013	-0.013	0.000	0.000	0.000
39	A	38	ALA	0	0.004	0.009	19.564	-0.020	-0.020	0.000	0.000	0.000
40	A	39	ILE	0	-0.021	-0.019	19.467	-0.036	-0.036	0.000	0.000	0.000
41	A	40	ASP	-1	-0.890	-0.954	21.329	-0.157	-0.157	0.000	0.000	0.000
42	A	41	HIS	0	-0.003	-0.004	13.556	0.026	0.026	0.000	0.000	0.000
43	A	42	LEU	0	0.017	0.007	15.510	-0.044	-0.044	0.000	0.000	0.000
44	A	43	ARG	1	0.918	0.965	17.887	0.135	0.135	0.000	0.000	0.000
45	A	44	SER	0	-0.110	-0.043	18.332	0.003	0.003	0.000	0.000	0.000
46	A	45	GLN	0	-0.054	-0.018	13.471	-0.086	-0.086	0.000	0.000	0.000
47	A	46	GLY	0	0.057	0.032	14.912	0.049	0.049	0.000	0.000	0.000
48	A	47	ALA	0	-0.057	-0.046	14.054	-0.051	-0.051	0.000	0.000	0.000
49	A	48	ASP	-1	-0.936	-0.974	11.642	-0.658	-0.658	0.000	0.000	0.000
50	A	49	ILE	0	-0.040	0.002	9.743	-0.098	-0.098	0.000	0.000	0.000
51	A	50	PRO	0	0.046	0.014	4.391	-0.168	-0.084	-0.001	-0.010	-0.072
52	A	51	ASP	-1	-0.828	-0.872	4.523	-1.950	-1.681	-0.001	-0.024	-0.244
53	A	52	THR	0	-0.024	-0.014	6.228	-0.262	-0.262	0.000	0.000	0.000
54	A	53	VAL	0	0.000	-0.007	8.510	0.198	0.198	0.000	0.000	0.000
55	A	54	ILE	0	-0.013	-0.007	10.804	0.000	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.051	-0.025	13.971	0.047	0.047	0.000	0.000	0.000
57	A	56	LEU	0	0.012	0.008	16.502	-0.011	-0.011	0.000	0.000	0.000
58	A	57	ASP	-1	-0.867	-0.948	20.064	0.028	0.028	0.000	0.000	0.000
59	A	58	LEU	0	-0.026	-0.012	23.083	-0.012	-0.012	0.000	0.000	0.000
60	A	59	GLN	0	-0.050	-0.035	26.126	-0.010	-0.010	0.000	0.000	0.000
61	A	60	MET	0	0.044	0.048	24.189	-0.004	-0.004	0.000	0.000	0.000
62	A	61	PRO	0	-0.036	-0.034	28.402	-0.005	-0.005	0.000	0.000	0.000
63	A	62	GLY	0	0.005	0.019	30.397	0.001	0.001	0.000	0.000	0.000
64	A	63	ILE	0	-0.122	-0.058	26.615	-0.002	-0.002	0.000	0.000	0.000
65	A	64	ASN	0	0.024	0.018	28.136	0.000	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.083	0.018	25.219	-0.011	-0.011	0.000	0.000	0.000
67	A	66	PHE	0	-0.007	-0.031	25.577	-0.013	-0.013	0.000	0.000	0.000
68	A	67	GLU	-1	-0.809	-0.901	28.119	-0.050	-0.050	0.000	0.000	0.000
69	A	68	PHE	0	-0.020	-0.021	19.661	-0.013	-0.013	0.000	0.000	0.000
70	A	69	THR	0	0.041	0.001	22.726	-0.015	-0.015	0.000	0.000	0.000
71	A	70	GLU	-1	-0.967	-0.962	24.547	-0.086	-0.086	0.000	0.000	0.000
72	A	71	HIS	0	-0.010	-0.018	25.570	-0.015	-0.015	0.000	0.000	0.000
73	A	72	TYR	0	-0.023	-0.008	16.146	-0.009	-0.009	0.000	0.000	0.000
74	A	73	GLY	0	0.006	0.000	22.126	-0.023	-0.023	0.000	0.000	0.000
75	A	74	MET	0	-0.075	-0.036	24.187	0.001	0.001	0.000	0.000	0.000
76	A	75	LEU	0	-0.042	-0.003	18.779	-0.006	-0.006	0.000	0.000	0.000
77	A	76	PRO	0	0.032	0.013	20.101	0.009	0.009	0.000	0.000	0.000
78	A	77	GLU	-1	-0.877	-0.953	19.578	-0.227	-0.227	0.000	0.000	0.000
79	A	78	ALA	0	-0.036	-0.020	17.436	-0.026	-0.026	0.000	0.000	0.000
80	A	79	VAL	0	0.023	0.011	14.536	-0.063	-0.063	0.000	0.000	0.000
81	A	80	ARG	1	0.915	0.953	14.597	0.166	0.166	0.000	0.000	0.000
82	A	81	ALA	0	-0.006	0.011	14.927	-0.004	-0.004	0.000	0.000	0.000
83	A	82	ARG	1	0.759	0.867	7.353	1.505	1.505	0.000	0.000	0.000
84	A	83	ILE	0	-0.006	0.004	10.217	-0.170	-0.170	0.000	0.000	0.000
85	A	84	ARG	1	0.787	0.898	10.911	0.494	0.494	0.000	0.000	0.000
86	A	85	LEU	0	0.004	0.010	13.102	0.012	0.012	0.000	0.000	0.000
87	A	86	PHE	0	-0.017	-0.018	12.732	0.040	0.040	0.000	0.000	0.000
88	A	87	MET	0	0.037	0.053	17.687	-0.012	-0.012	0.000	0.000	0.000
89	A	88	ILE	0	-0.037	-0.020	18.639	0.030	0.030	0.000	0.000	0.000
90	A	89	SER	0	0.080	0.029	21.769	-0.016	-0.016	0.000	0.000	0.000
91	A	90	SER	0	-0.011	-0.006	25.227	0.015	0.015	0.000	0.000	0.000
92	A	91	THR	0	-0.009	-0.001	27.493	0.004	0.004	0.000	0.000	0.000
93	A	92	VAL	0	-0.018	-0.016	26.774	-0.003	-0.003	0.000	0.000	0.000
94	A	93	ASP	-1	-0.825	-0.899	30.088	0.025	0.025	0.000	0.000	0.000
95	A	94	ILE	0	-0.044	-0.031	31.713	-0.001	-0.001	0.000	0.000	0.000
96	A	95	SER	0	0.005	0.003	32.598	-0.004	-0.004	0.000	0.000	0.000
97	A	96	ASP	-1	-0.849	-0.937	29.069	0.007	0.007	0.000	0.000	0.000
98	A	97	ILE	0	-0.074	-0.043	27.337	-0.003	-0.003	0.000	0.000	0.000
99	A	98	GLU	-1	-0.926	-0.946	27.944	-0.006	-0.006	0.000	0.000	0.000
100	A	99	GLN	0	0.020	0.015	28.980	-0.005	-0.005	0.000	0.000	0.000
101	A	100	ALA	0	-0.080	-0.057	24.244	-0.010	-0.010	0.000	0.000	0.000
102	A	101	GLU	-1	-0.969	-0.977	24.811	-0.006	-0.006	0.000	0.000	0.000
103	A	102	ALA	0	-0.022	-0.004	26.243	-0.008	-0.008	0.000	0.000	0.000
104	A	103	ASN	0	-0.058	-0.034	24.474	-0.022	-0.022	0.000	0.000	0.000
105	A	104	PRO	0	0.024	0.006	23.678	-0.001	-0.001	0.000	0.000	0.000
106	A	105	HIS	0	-0.037	-0.023	20.307	-0.024	-0.024	0.000	0.000	0.000
107	A	106	ILE	0	-0.059	-0.020	19.240	-0.013	-0.013	0.000	0.000	0.000
108	A	107	ILE	0	0.001	0.022	14.918	0.008	0.008	0.000	0.000	0.000
109	A	108	GLN	0	0.005	-0.022	18.780	0.021	0.021	0.000	0.000	0.000
110	A	109	LEU	0	0.014	0.012	20.042	-0.003	-0.003	0.000	0.000	0.000
111	A	110	LEU	0	-0.083	-0.049	16.739	0.024	0.024	0.000	0.000	0.000
112	A	111	PRO	0	0.031	0.018	21.368	-0.017	-0.017	0.000	0.000	0.000
113	A	112	LYS	1	0.768	0.901	22.025	-0.028	-0.028	0.000	0.000	0.000
114	A	113	PRO	0	-0.029	-0.041	21.984	-0.008	-0.008	0.000	0.000	0.000
115	A	114	LEU	0	0.055	0.029	14.977	0.005	0.005	0.000	0.000	0.000
116	A	115	GLU	-1	-0.876	-0.939	18.970	0.217	0.217	0.000	0.000	0.000
117	A	116	ILE	0	0.010	-0.005	13.123	0.029	0.029	0.000	0.000	0.000
118	A	117	PRO	0	-0.064	-0.036	14.471	0.085	0.085	0.000	0.000	0.000
119	A	118	LEU	0	0.043	0.025	15.822	0.032	0.032	0.000	0.000	0.000
120	A	119	LEU	0	0.067	0.030	11.646	0.010	0.010	0.000	0.000	0.000
121	A	120	ARG	1	0.959	0.971	9.929	-1.110	-1.110	0.000	0.000	0.000
122	A	121	GLU	-1	-0.870	-0.929	11.267	0.612	0.612	0.000	0.000	0.000
123	A	122	LEU	0	-0.013	0.000	13.477	-0.025	-0.025	0.000	0.000	0.000
124	A	123	LEU	0	0.014	-0.009	8.101	-0.064	-0.064	0.000	0.000	0.000
125	A	124	LYS	1	0.822	0.913	9.280	-0.795	-0.795	0.000	0.000	0.000
126	A	125	ARG	1	0.905	0.961	10.698	-0.223	-0.223	0.000	0.000	0.000
127	A	126	TRP	0	0.005	0.009	11.763	-0.082	-0.082	0.000	0.000	0.000
128	A	127	PHE	0	-0.003	-0.005	6.239	-0.247	-0.247	0.000	0.000	0.000
129	A	128	PRO	0	0.014	0.031	7.344	0.233	0.233	0.000	0.000	0.000
130	A	129	SER	0	-0.033	-0.019	7.214	-0.111	-0.111	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)