FMO DATABASE

FMODB ID: 1N68Z

Calculation Name: 5D50-D-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5D50

Chain ID: D

ChEMBL ID:
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UniProt ID: T1S9Z0

Base Structure: X-ray

Registration Date: 2023-09-22

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-639200.131941
FMO2-HF: Nuclear repulsion	599421.638191
FMO2-HF: Total energy	-39778.493749
FMO2-MP2: Total energy	-39893.586815

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(D:67:LEU)

Summations of interaction energy for fragment #1(D:67:LEU)

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.
-6.781	-3.408	2.047	-1.884	-3.536	-0.01

Interaction energy analysis for fragmet #1(D:67:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.069 / q_NPA : -0.055

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	D	69	VAL	0	0.032	0.014	3.874	-1.741	-0.150	-0.014	-0.704	-0.873	-0.001
4	D	70	ASP	-1	-0.888	-0.937	4.527	-2.508	-2.387	-0.001	-0.013	-0.106	0.000
5	D	71	HIS	0	-0.101	-0.068	2.385	-1.538	0.123	2.062	-1.167	-2.557	-0.009
6	D	72	GLU	-1	-0.894	-0.941	6.183	-0.406	-0.406	0.000	0.000	0.000	0.000
7	D	73	LEU	0	-0.047	-0.031	9.694	0.129	0.129	0.000	0.000	0.000	0.000
8	D	74	ASP	-1	-0.960	-0.965	7.640	-0.488	-0.488	0.000	0.000	0.000	0.000
9	D	75	ALA	0	-0.030	-0.015	9.736	0.056	0.056	0.000	0.000	0.000	0.000
10	D	76	VAL	0	-0.091	-0.036	7.891	-0.122	-0.122	0.000	0.000	0.000	0.000
11	D	90	TRP	0	0.025	0.003	22.987	0.010	0.010	0.000	0.000	0.000	0.000
12	D	91	THR	0	-0.028	-0.038	24.573	0.008	0.008	0.000	0.000	0.000	0.000
13	D	92	VAL	0	0.074	0.038	27.462	-0.009	-0.009	0.000	0.000	0.000	0.000
14	D	93	GLU	-1	-0.789	-0.861	29.535	-0.113	-0.113	0.000	0.000	0.000	0.000
15	D	94	LYS	1	0.876	0.928	23.917	0.142	0.142	0.000	0.000	0.000	0.000
16	D	95	GLN	0	0.029	0.040	23.922	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	96	ALA	0	0.032	0.028	26.355	-0.006	-0.006	0.000	0.000	0.000	0.000
18	D	97	ALA	0	-0.009	-0.001	25.945	-0.002	-0.002	0.000	0.000	0.000	0.000
19	D	98	ALA	0	-0.006	-0.001	22.303	-0.003	-0.003	0.000	0.000	0.000	0.000
20	D	99	THR	0	-0.006	-0.021	23.991	-0.013	-0.013	0.000	0.000	0.000	0.000
21	D	100	LEU	0	0.002	-0.002	26.202	0.004	0.004	0.000	0.000	0.000	0.000
22	D	101	ASN	0	-0.079	-0.053	24.046	0.006	0.006	0.000	0.000	0.000	0.000
23	D	102	ALA	0	-0.005	0.006	23.291	-0.005	-0.005	0.000	0.000	0.000	0.000
24	D	103	TRP	0	-0.043	-0.023	24.684	0.007	0.007	0.000	0.000	0.000	0.000
25	D	104	MET	0	-0.038	-0.005	25.308	0.013	0.013	0.000	0.000	0.000	0.000
26	D	120	ALA	0	-0.008	-0.002	41.775	0.000	0.000	0.000	0.000	0.000	0.000
27	D	121	GLY	0	0.063	0.023	39.034	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	122	ILE	0	-0.045	-0.032	40.049	0.003	0.003	0.000	0.000	0.000	0.000
29	D	123	GLY	0	0.073	0.029	40.745	0.004	0.004	0.000	0.000	0.000	0.000
30	D	124	PRO	0	0.009	0.015	38.181	-0.004	-0.004	0.000	0.000	0.000	0.000
31	D	125	ALA	0	0.021	-0.001	36.929	-0.004	-0.004	0.000	0.000	0.000	0.000
32	D	126	THR	0	0.003	-0.007	36.867	-0.001	-0.001	0.000	0.000	0.000	0.000
33	D	127	VAL	0	0.037	0.015	33.494	-0.003	-0.003	0.000	0.000	0.000	0.000
34	D	128	ASN	0	-0.001	-0.003	32.611	-0.010	-0.010	0.000	0.000	0.000	0.000
35	D	129	ARG	1	0.817	0.921	31.874	0.076	0.076	0.000	0.000	0.000	0.000
36	D	130	ILE	0	0.048	0.024	31.080	-0.005	-0.005	0.000	0.000	0.000	0.000
37	D	131	MET	0	-0.010	0.001	28.038	-0.003	-0.003	0.000	0.000	0.000	0.000
38	D	132	LYS	1	0.875	0.922	26.525	0.088	0.088	0.000	0.000	0.000	0.000
39	D	133	ALA	0	0.037	0.024	27.608	0.002	0.002	0.000	0.000	0.000	0.000
40	D	134	GLU	-1	-0.861	-0.908	29.397	-0.081	-0.081	0.000	0.000	0.000	0.000
41	D	135	VAL	0	-0.069	-0.035	31.717	0.009	0.009	0.000	0.000	0.000	0.000
42	D	136	SER	0	0.009	-0.019	33.091	-0.006	-0.006	0.000	0.000	0.000	0.000
43	D	137	THR	0	-0.006	0.000	34.907	0.003	0.003	0.000	0.000	0.000	0.000
44	D	138	THR	0	0.027	0.005	37.217	-0.002	-0.002	0.000	0.000	0.000	0.000
45	D	139	ILE	0	0.081	0.025	38.620	-0.001	-0.001	0.000	0.000	0.000	0.000
46	D	140	GLY	0	0.020	0.021	40.246	-0.001	-0.001	0.000	0.000	0.000	0.000
47	D	141	VAL	0	0.003	0.005	38.741	0.000	0.000	0.000	0.000	0.000	0.000
48	D	142	LEU	0	0.011	0.011	33.815	-0.001	-0.001	0.000	0.000	0.000	0.000
49	D	143	SER	0	0.009	-0.001	37.341	-0.002	-0.002	0.000	0.000	0.000	0.000
50	D	144	SER	0	-0.063	-0.042	39.705	0.000	0.000	0.000	0.000	0.000	0.000
51	D	145	LEU	0	-0.014	-0.007	34.547	0.000	0.000	0.000	0.000	0.000	0.000
52	D	146	ALA	0	0.038	0.015	35.185	-0.003	-0.003	0.000	0.000	0.000	0.000
53	D	147	ARG	1	0.853	0.910	36.178	0.080	0.080	0.000	0.000	0.000	0.000
54	D	148	ALA	0	-0.035	-0.001	37.222	0.002	0.002	0.000	0.000	0.000	0.000
55	D	149	PHE	0	-0.028	-0.010	31.595	0.000	0.000	0.000	0.000	0.000	0.000
56	D	150	GLY	0	-0.029	-0.011	34.637	-0.005	-0.005	0.000	0.000	0.000	0.000
57	D	151	HIS	1	0.790	0.884	30.940	0.138	0.138	0.000	0.000	0.000	0.000
58	D	152	GLU	-1	-0.773	-0.890	35.159	-0.083	-0.083	0.000	0.000	0.000	0.000
59	D	153	ALA	0	-0.044	-0.030	34.852	-0.006	-0.006	0.000	0.000	0.000	0.000
60	D	154	TYR	0	-0.024	-0.036	32.623	0.001	0.001	0.000	0.000	0.000	0.000
61	D	155	GLU	-1	-0.742	-0.850	31.020	-0.139	-0.139	0.000	0.000	0.000	0.000
62	D	156	MET	0	-0.031	0.002	29.565	-0.007	-0.007	0.000	0.000	0.000	0.000
63	D	157	ILE	0	-0.057	-0.039	29.418	-0.003	-0.003	0.000	0.000	0.000	0.000
64	D	158	ILE	0	0.007	0.014	27.643	0.004	0.004	0.000	0.000	0.000	0.000
65	D	159	PRO	0	-0.031	-0.008	25.877	-0.010	-0.010	0.000	0.000	0.000	0.000
66	D	160	VAL	0	0.030	0.015	21.154	0.004	0.004	0.000	0.000	0.000	0.000
67	D	161	GLY	0	0.025	0.013	21.151	-0.020	-0.020	0.000	0.000	0.000	0.000
68	D	162	ALA	0	0.021	-0.008	20.716	0.004	0.004	0.000	0.000	0.000	0.000
69	D	163	PRO	0	-0.015	-0.007	21.869	-0.003	-0.003	0.000	0.000	0.000	0.000
70	D	164	GLY	0	0.010	0.001	24.762	0.009	0.009	0.000	0.000	0.000	0.000
71	D	165	ILE	0	-0.044	-0.007	18.031	0.004	0.004	0.000	0.000	0.000	0.000
72	D	166	ILE	0	-0.022	-0.004	22.005	-0.017	-0.017	0.000	0.000	0.000	0.000
73	D	167	ASP	-1	-0.932	-0.966	21.067	-0.259	-0.259	0.000	0.000	0.000	0.000
74	D	168	TYR	0	-0.010	-0.012	23.684	0.002	0.002	0.000	0.000	0.000	0.000
75	D	169	ASP	-1	-0.742	-0.858	26.338	-0.143	-0.143	0.000	0.000	0.000	0.000
76	D	170	HIS	0	0.064	0.032	28.719	0.019	0.019	0.000	0.000	0.000	0.000
77	D	171	ARG	1	0.851	0.924	31.141	0.140	0.140	0.000	0.000	0.000	0.000
78	D	172	MET	0	-0.064	-0.033	28.830	0.006	0.006	0.000	0.000	0.000	0.000
79	D	173	TYR	0	0.041	0.014	31.933	0.008	0.008	0.000	0.000	0.000	0.000
80	D	174	ALA	0	-0.015	-0.018	33.823	0.007	0.007	0.000	0.000	0.000	0.000
81	D	175	ALA	0	-0.006	0.003	36.798	0.006	0.006	0.000	0.000	0.000	0.000
82	D	176	LEU	0	-0.031	0.012	33.284	0.004	0.004	0.000	0.000	0.000	0.000
83	D	177	PRO	0	0.040	0.018	37.789	0.003	0.003	0.000	0.000	0.000	0.000
84	D	178	GLN	0	0.003	-0.001	39.381	-0.005	-0.005	0.000	0.000	0.000	0.000
85	D	179	GLU	-1	-0.847	-0.941	40.276	-0.081	-0.081	0.000	0.000	0.000	0.000
86	D	180	GLU	-1	-0.825	-0.898	36.186	-0.100	-0.100	0.000	0.000	0.000	0.000
87	D	181	LYS	1	0.840	0.922	35.772	0.092	0.092	0.000	0.000	0.000	0.000
88	D	182	ASN	0	-0.007	0.005	35.982	-0.003	-0.003	0.000	0.000	0.000	0.000
89	D	183	LYS	1	0.818	0.903	34.889	0.095	0.095	0.000	0.000	0.000	0.000
90	D	184	ILE	0	0.018	0.012	30.411	-0.004	-0.004	0.000	0.000	0.000	0.000
91	D	185	THR	0	-0.014	-0.025	31.835	-0.004	-0.004	0.000	0.000	0.000	0.000
92	D	186	SER	0	-0.001	0.001	33.710	0.001	0.001	0.000	0.000	0.000	0.000
93	D	187	PHE	0	-0.028	-0.009	26.404	0.002	0.002	0.000	0.000	0.000	0.000
94	D	188	ILE	0	0.012	0.003	28.204	-0.004	-0.004	0.000	0.000	0.000	0.000
95	D	189	ASN	0	0.001	-0.012	29.906	-0.005	-0.005	0.000	0.000	0.000	0.000
96	D	190	PHE	0	-0.018	-0.001	29.858	0.002	0.002	0.000	0.000	0.000	0.000
97	D	191	VAL	0	0.013	0.005	25.306	0.000	0.000	0.000	0.000	0.000	0.000
98	D	192	PHE	0	-0.020	-0.003	27.454	-0.005	-0.005	0.000	0.000	0.000	0.000
99	D	193	GLU	-1	-0.803	-0.870	29.640	-0.095	-0.095	0.000	0.000	0.000	0.000
100	D	194	GLN	0	-0.090	-0.034	27.921	0.010	0.010	0.000	0.000	0.000	0.000
101	D	195	ASN	0	-0.088	-0.022	24.875	-0.011	-0.011	0.000	0.000	0.000	0.000
102	D	196	LYS	1	0.838	0.878	28.054	0.124	0.124	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:67:LEU)