FMO DATABASE

FMODB ID: R96J8

Calculation Name: 4L1D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L1D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NY72

Base Structure: X-ray

Registration Date: 2023-09-19

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-990493.63237
FMO2-HF: Nuclear repulsion	942279.554348
FMO2-HF: Total energy	-48214.078021
FMO2-MP2: Total energy	-48352.412571

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:VAL)

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

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.
-2.126	0.836	0.097	-1.189	-1.871	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / 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

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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	VAL	0	0.032	0.013	3.084	-2.418	0.469	0.098	-1.186	-1.800	-0.001
4	A	4	GLU	-1	-0.791	-0.913	5.265	-0.470	-0.395	-0.001	-0.003	-0.071	0.000
5	A	5	VAL	0	-0.039	-0.012	8.441	0.094	0.094	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.012	0.003	11.348	0.065	0.065	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.033	-0.034	14.976	-0.041	-0.041	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.930	-0.952	17.548	-0.423	-0.423	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.011	-0.030	20.390	0.001	0.001	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.782	-0.846	23.498	-0.200	-0.200	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.032	0.005	24.867	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.014	0.001	26.926	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.020	-0.015	29.345	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.040	-0.020	31.787	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.024	-0.002	26.581	0.012	0.012	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.031	-0.016	23.789	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	MET	0	0.011	0.022	21.622	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.933	0.973	13.672	0.622	0.622	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.000	0.007	19.824	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.926	0.950	12.523	0.727	0.727	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.028	-0.008	14.974	0.039	0.039	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.008	0.004	8.286	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.043	-0.010	10.853	0.053	0.053	0.000	0.000	0.000	0.000
24	A	25	MET	0	0.015	0.005	7.080	0.080	0.080	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.852	0.911	7.559	0.336	0.336	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.875	0.928	6.037	-0.448	-0.448	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.894	-0.923	10.071	0.060	0.060	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.898	-0.944	13.610	0.248	0.248	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.081	-0.057	16.217	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.923	-0.962	18.031	0.071	0.071	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.008	0.000	14.751	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.021	0.008	16.651	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.024	-0.015	16.009	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.004	0.008	18.334	0.008	0.008	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.035	-0.024	17.856	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.927	-0.953	20.486	-0.109	-0.109	0.000	0.000	0.000	0.000
37	A	38	TRP	0	0.008	-0.003	18.496	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.008	-0.007	23.807	0.019	0.019	0.000	0.000	0.000	0.000
39	A	40	TYR	0	0.000	-0.025	26.132	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.873	0.929	28.803	0.154	0.154	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.013	0.028	31.367	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.903	-0.973	33.991	-0.126	-0.126	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.020	-0.001	35.505	0.006	0.006	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.022	-0.005	36.029	0.007	0.007	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.908	0.933	34.789	0.080	0.080	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.830	-0.894	28.871	-0.147	-0.147	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.037	-0.011	31.254	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.003	-0.004	26.620	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.045	-0.031	25.832	0.006	0.006	0.000	0.000	0.000	0.000
50	A	51	TYR	0	0.003	-0.050	21.936	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.820	-0.897	24.492	-0.101	-0.101	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.063	-0.020	20.551	0.008	0.008	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.935	0.937	22.581	0.085	0.085	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.009	0.008	23.654	0.012	0.012	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.052	0.025	23.267	0.006	0.006	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.012	0.012	19.405	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.015	0.011	24.506	0.012	0.012	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.935	-0.968	27.814	-0.084	-0.084	0.000	0.000	0.000	0.000
59	A	60	VAL	0	-0.061	-0.018	28.376	0.005	0.005	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.945	-0.967	31.252	-0.072	-0.072	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.020	0.009	31.520	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.014	0.000	34.292	0.002	0.002	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.002	-0.018	29.414	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.007	0.010	30.593	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.008	0.011	30.877	0.006	0.006	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.777	0.880	29.503	0.139	0.139	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.001	0.016	25.316	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	69	GLN	0	-0.006	-0.001	21.719	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.048	0.034	16.000	-0.032	-0.032	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.055	-0.039	16.813	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.066	0.040	13.894	-0.073	-0.073	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.230	-0.178	9.976	0.039	0.039	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.994	0.970	12.168	0.014	0.014	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.750	-0.819	7.921	-0.336	-0.336	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.044	0.039	11.524	0.008	0.008	0.000	0.000	0.000	0.000
76	A	77	GLN	0	0.092	0.041	5.396	0.022	0.022	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.871	-0.886	10.042	-0.902	-0.902	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.021	0.000	11.711	0.102	0.102	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.027	-0.052	14.029	0.038	0.038	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.037	0.000	16.643	0.032	0.032	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.022	-0.016	19.964	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	83	VAL	0	0.020	0.018	21.931	0.023	0.023	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.010	-0.026	25.197	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	85	ASN	0	-0.031	-0.022	27.388	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	VAL	0	0.023	0.026	27.045	0.009	0.009	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.039	0.021	30.306	0.008	0.008	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.042	0.002	32.857	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.030	-0.040	34.761	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.780	-0.844	30.010	-0.148	-0.148	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.044	0.053	30.177	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.008	0.028	29.943	0.013	0.013	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.058	-0.020	25.530	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.033	-0.060	23.800	0.010	0.010	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.015	-0.012	22.778	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	97	ASN	0	0.028	0.002	19.302	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	98	VAL	0	0.031	0.021	14.709	0.007	0.007	0.000	0.000	0.000	0.000
97	A	99	SER	0	-0.073	-0.040	17.640	0.005	0.005	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.839	0.893	11.590	0.241	0.241	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.927	-0.958	17.586	-0.036	-0.036	0.000	0.000	0.000	0.000
100	A	102	PHE	0	0.057	0.035	17.029	0.005	0.005	0.000	0.000	0.000	0.000
101	A	110	PHE	0	0.053	0.034	19.116	0.002	0.002	0.000	0.000	0.000	0.000
102	A	111	VAL	0	-0.067	-0.046	15.013	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.993	0.982	18.021	0.143	0.143	0.000	0.000	0.000	0.000
104	A	113	THR	0	-0.085	-0.020	14.141	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	114	THR	0	0.023	0.007	17.256	0.008	0.008	0.000	0.000	0.000	0.000
106	A	115	ARG	1	0.837	0.921	12.051	0.498	0.498	0.000	0.000	0.000	0.000
107	A	116	LEU	0	0.013	0.006	18.693	0.020	0.020	0.000	0.000	0.000	0.000
108	A	117	ILE	0	-0.003	-0.003	19.040	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	118	PRO	0	-0.004	0.003	22.593	0.020	0.020	0.000	0.000	0.000	0.000
110	A	119	LEU	0	-0.006	0.006	24.826	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	120	ARG	1	0.911	0.948	26.713	0.212	0.212	0.000	0.000	0.000	0.000
112	A	121	VAL	0	-0.034	-0.014	28.980	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	122	HIS	0	-0.070	-0.040	29.537	0.021	0.021	0.000	0.000	0.000	0.000
114	A	123	HIS	0	0.037	0.012	32.688	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	124	HIS	0	-0.014	0.003	32.262	-0.003	-0.003	0.000	0.000	0.000	0.000

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