FMO DATABASE

FMODB ID: YVNJ2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-634947.975858
FMO2-HF: Nuclear repulsion	595170.358659
FMO2-HF: Total energy	-39777.617199
FMO2-MP2: Total energy	-39892.662029

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.
-7.647	-4.819	3.604	-2.068	-4.364	-0.016

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 : -0.053

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	0.023	-0.004	3.826	-1.549	0.282	-0.022	-0.800	-1.010	-0.001
4	D	70	ASP	-1	-0.882	-0.934	4.438	-2.712	-2.590	-0.001	-0.011	-0.110	0.000
5	D	71	HIS	0	-0.079	-0.061	2.488	-2.063	-1.188	3.627	-1.257	-3.244	-0.015
6	D	72	GLU	-1	-0.882	-0.923	6.268	-0.606	-0.606	0.000	0.000	0.000	0.000
7	D	73	LEU	0	-0.073	-0.052	9.791	0.141	0.141	0.000	0.000	0.000	0.000
8	D	74	ASP	-1	-0.967	-0.972	7.683	-0.539	-0.539	0.000	0.000	0.000	0.000
9	D	75	ALA	0	-0.037	-0.010	9.756	0.064	0.064	0.000	0.000	0.000	0.000
10	D	76	VAL	0	-0.061	-0.024	7.943	-0.139	-0.139	0.000	0.000	0.000	0.000
11	D	90	TRP	0	-0.009	-0.022	22.974	0.008	0.008	0.000	0.000	0.000	0.000
12	D	91	THR	0	-0.005	-0.006	24.565	0.009	0.009	0.000	0.000	0.000	0.000
13	D	92	VAL	0	0.090	0.036	27.195	-0.010	-0.010	0.000	0.000	0.000	0.000
14	D	93	GLU	-1	-0.866	-0.935	29.426	-0.119	-0.119	0.000	0.000	0.000	0.000
15	D	94	LYS	1	0.918	0.957	23.763	0.156	0.156	0.000	0.000	0.000	0.000
16	D	95	GLN	0	0.027	0.037	23.528	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	96	ALA	0	0.020	0.017	26.171	-0.006	-0.006	0.000	0.000	0.000	0.000
18	D	97	ALA	0	-0.014	0.003	25.467	0.001	0.001	0.000	0.000	0.000	0.000
19	D	98	ALA	0	0.013	0.016	22.254	-0.004	-0.004	0.000	0.000	0.000	0.000
20	D	99	THR	0	0.023	-0.005	23.935	-0.012	-0.012	0.000	0.000	0.000	0.000
21	D	100	LEU	0	0.008	0.003	26.257	0.005	0.005	0.000	0.000	0.000	0.000
22	D	101	ASN	0	-0.066	-0.055	23.711	0.006	0.006	0.000	0.000	0.000	0.000
23	D	102	ALA	0	-0.031	-0.001	23.296	-0.009	-0.009	0.000	0.000	0.000	0.000
24	D	103	TRP	0	-0.090	-0.036	24.556	0.006	0.006	0.000	0.000	0.000	0.000
25	D	104	MET	0	-0.005	0.004	25.368	0.016	0.016	0.000	0.000	0.000	0.000
26	D	120	ALA	0	-0.030	-0.001	42.061	-0.001	-0.001	0.000	0.000	0.000	0.000
27	D	121	GLY	0	0.078	0.007	39.265	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	122	ILE	0	-0.055	-0.014	40.208	0.003	0.003	0.000	0.000	0.000	0.000
29	D	123	GLY	0	0.067	0.025	41.270	0.004	0.004	0.000	0.000	0.000	0.000
30	D	124	PRO	0	0.037	0.020	38.598	-0.004	-0.004	0.000	0.000	0.000	0.000
31	D	125	ALA	0	0.026	0.005	37.205	-0.005	-0.005	0.000	0.000	0.000	0.000
32	D	126	THR	0	-0.015	-0.017	37.063	-0.002	-0.002	0.000	0.000	0.000	0.000
33	D	127	VAL	0	0.030	0.010	33.996	-0.003	-0.003	0.000	0.000	0.000	0.000
34	D	128	ASN	0	-0.035	-0.021	32.560	-0.012	-0.012	0.000	0.000	0.000	0.000
35	D	129	ARG	1	0.898	0.954	32.265	0.079	0.079	0.000	0.000	0.000	0.000
36	D	130	ILE	0	0.017	0.016	31.116	-0.004	-0.004	0.000	0.000	0.000	0.000
37	D	131	MET	0	0.004	0.010	27.622	-0.003	-0.003	0.000	0.000	0.000	0.000
38	D	132	LYS	1	0.947	0.980	26.420	0.095	0.095	0.000	0.000	0.000	0.000
39	D	133	ALA	0	0.045	0.028	27.685	0.003	0.003	0.000	0.000	0.000	0.000
40	D	134	GLU	-1	-0.985	-0.994	29.432	-0.090	-0.090	0.000	0.000	0.000	0.000
41	D	135	VAL	0	-0.047	-0.032	31.901	0.009	0.009	0.000	0.000	0.000	0.000
42	D	136	SER	0	0.000	0.002	33.474	-0.006	-0.006	0.000	0.000	0.000	0.000
43	D	137	THR	0	-0.004	0.002	34.745	0.005	0.005	0.000	0.000	0.000	0.000
44	D	138	THR	0	0.043	0.019	37.197	-0.002	-0.002	0.000	0.000	0.000	0.000
45	D	139	ILE	0	0.094	0.031	38.569	-0.002	-0.002	0.000	0.000	0.000	0.000
46	D	140	GLY	0	-0.008	0.001	40.118	-0.001	-0.001	0.000	0.000	0.000	0.000
47	D	141	VAL	0	-0.013	-0.016	38.955	0.001	0.001	0.000	0.000	0.000	0.000
48	D	142	LEU	0	-0.024	-0.011	33.944	-0.002	-0.002	0.000	0.000	0.000	0.000
49	D	143	SER	0	0.000	-0.002	37.371	-0.003	-0.003	0.000	0.000	0.000	0.000
50	D	144	SER	0	-0.048	-0.030	39.581	-0.003	-0.003	0.000	0.000	0.000	0.000
51	D	145	LEU	0	0.021	0.018	34.516	0.001	0.001	0.000	0.000	0.000	0.000
52	D	146	ALA	0	0.030	0.022	35.419	-0.004	-0.004	0.000	0.000	0.000	0.000
53	D	147	ARG	1	0.980	0.977	36.328	0.085	0.085	0.000	0.000	0.000	0.000
54	D	148	ALA	0	-0.038	0.005	36.797	0.001	0.001	0.000	0.000	0.000	0.000
55	D	149	PHE	0	0.014	0.012	31.944	0.001	0.001	0.000	0.000	0.000	0.000
56	D	150	GLY	0	-0.065	-0.029	35.191	-0.004	-0.004	0.000	0.000	0.000	0.000
57	D	151	HIS	1	0.802	0.911	30.535	0.153	0.153	0.000	0.000	0.000	0.000
58	D	152	GLU	-1	-0.923	-0.975	35.226	-0.095	-0.095	0.000	0.000	0.000	0.000
59	D	153	ALA	0	-0.026	-0.035	34.955	-0.005	-0.005	0.000	0.000	0.000	0.000
60	D	154	TYR	0	-0.006	-0.018	33.291	-0.001	-0.001	0.000	0.000	0.000	0.000
61	D	155	GLU	-1	-0.739	-0.858	31.079	-0.152	-0.152	0.000	0.000	0.000	0.000
62	D	156	MET	0	0.021	0.007	29.627	-0.009	-0.009	0.000	0.000	0.000	0.000
63	D	157	ILE	0	-0.058	-0.030	29.172	-0.005	-0.005	0.000	0.000	0.000	0.000
64	D	158	ILE	0	-0.027	0.006	27.926	0.004	0.004	0.000	0.000	0.000	0.000
65	D	159	PRO	0	-0.029	-0.012	25.912	-0.009	-0.009	0.000	0.000	0.000	0.000
66	D	160	VAL	0	0.031	0.021	21.174	0.004	0.004	0.000	0.000	0.000	0.000
67	D	161	GLY	0	-0.001	0.002	21.431	-0.016	-0.016	0.000	0.000	0.000	0.000
68	D	162	ALA	0	0.021	-0.015	20.844	0.000	0.000	0.000	0.000	0.000	0.000
69	D	163	PRO	0	-0.028	-0.012	21.919	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	164	GLY	0	-0.003	-0.003	25.533	0.003	0.003	0.000	0.000	0.000	0.000
71	D	165	ILE	0	0.014	0.015	18.453	0.003	0.003	0.000	0.000	0.000	0.000
72	D	166	ILE	0	-0.017	-0.002	22.301	-0.018	-0.018	0.000	0.000	0.000	0.000
73	D	167	ASP	-1	-0.930	-0.959	20.928	-0.290	-0.290	0.000	0.000	0.000	0.000
74	D	168	TYR	0	-0.048	-0.033	23.627	-0.001	-0.001	0.000	0.000	0.000	0.000
75	D	169	ASP	-1	-0.819	-0.917	26.269	-0.166	-0.166	0.000	0.000	0.000	0.000
76	D	170	HIS	0	0.055	0.004	28.833	0.009	0.009	0.000	0.000	0.000	0.000
77	D	171	ARG	1	0.941	0.992	32.007	0.149	0.149	0.000	0.000	0.000	0.000
78	D	172	MET	0	-0.070	-0.040	28.983	0.007	0.007	0.000	0.000	0.000	0.000
79	D	173	TYR	0	0.056	0.024	32.132	0.007	0.007	0.000	0.000	0.000	0.000
80	D	174	ALA	0	-0.032	-0.025	33.978	0.007	0.007	0.000	0.000	0.000	0.000
81	D	175	ALA	0	-0.017	-0.012	36.952	0.007	0.007	0.000	0.000	0.000	0.000
82	D	176	LEU	0	-0.041	-0.002	33.673	0.004	0.004	0.000	0.000	0.000	0.000
83	D	177	PRO	0	0.055	0.028	38.174	0.003	0.003	0.000	0.000	0.000	0.000
84	D	178	GLN	0	-0.006	-0.005	39.749	-0.005	-0.005	0.000	0.000	0.000	0.000
85	D	179	GLU	-1	-0.841	-0.938	40.270	-0.092	-0.092	0.000	0.000	0.000	0.000
86	D	180	GLU	-1	-0.978	-1.001	36.910	-0.114	-0.114	0.000	0.000	0.000	0.000
87	D	181	LYS	1	0.895	0.970	35.846	0.102	0.102	0.000	0.000	0.000	0.000
88	D	182	ASN	0	-0.055	-0.034	35.866	-0.003	-0.003	0.000	0.000	0.000	0.000
89	D	183	LYS	1	0.966	0.988	34.760	0.109	0.109	0.000	0.000	0.000	0.000
90	D	184	ILE	0	0.032	0.027	30.440	-0.005	-0.005	0.000	0.000	0.000	0.000
91	D	185	THR	0	0.010	-0.005	31.788	-0.004	-0.004	0.000	0.000	0.000	0.000
92	D	186	SER	0	-0.040	-0.008	33.951	0.000	0.000	0.000	0.000	0.000	0.000
93	D	187	PHE	0	0.024	0.014	26.352	0.001	0.001	0.000	0.000	0.000	0.000
94	D	188	ILE	0	0.009	0.006	28.353	-0.004	-0.004	0.000	0.000	0.000	0.000
95	D	189	ASN	0	-0.005	-0.022	29.798	-0.008	-0.008	0.000	0.000	0.000	0.000
96	D	190	PHE	0	0.000	0.018	30.013	0.005	0.005	0.000	0.000	0.000	0.000
97	D	191	VAL	0	0.004	-0.005	25.167	0.000	0.000	0.000	0.000	0.000	0.000
98	D	192	PHE	0	-0.058	-0.033	27.155	-0.004	-0.004	0.000	0.000	0.000	0.000
99	D	193	GLU	-1	-0.861	-0.942	29.370	-0.110	-0.110	0.000	0.000	0.000	0.000
100	D	194	GLN	0	-0.068	-0.012	27.969	0.012	0.012	0.000	0.000	0.000	0.000
101	D	195	ASN	0	-0.111	-0.038	25.222	-0.015	-0.015	0.000	0.000	0.000	0.000
102	D	196	LYS	1	0.927	0.965	28.204	0.131	0.131	0.000	0.000	0.000	0.000

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