FMO DATABASE

FMODB ID: 49KMN

Calculation Name: 5U64-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U64

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1114537.520794
FMO2-HF: Nuclear repulsion	1063331.295518
FMO2-HF: Total energy	-51206.225275
FMO2-MP2: Total energy	-51353.936383

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(B:1:ASP)

Summations of interaction energy for fragment #1(B:1:ASP)

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.
35.681	42.748	3.943	-4.64	-6.368	0.024

Interaction energy analysis for fragmet #1(B:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.941 / q_NPA : -0.977

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	B	3	GLN	0	-0.025	-0.012	2.670	6.048	9.183	0.754	-1.591	-2.297	-0.002
4	B	4	LEU	0	-0.021	-0.014	4.738	-3.802	-3.723	-0.001	-0.007	-0.071	0.000
5	B	5	GLN	0	-0.010	0.003	8.041	1.093	1.093	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.787	-0.914	11.173	21.485	21.485	0.000	0.000	0.000	0.000
7	B	7	SER	0	-0.046	-0.030	14.211	-0.710	-0.710	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.051	0.013	17.797	0.015	0.015	0.000	0.000	0.000	0.000
9	B	9	GLY	0	-0.005	0.018	20.537	-0.433	-0.433	0.000	0.000	0.000	0.000
10	B	10	GLY	0	0.010	-0.001	22.135	-0.249	-0.249	0.000	0.000	0.000	0.000
11	B	11	SER	0	-0.010	-0.005	25.554	0.115	0.115	0.000	0.000	0.000	0.000
12	B	12	VAL	0	-0.017	-0.001	28.873	-0.267	-0.267	0.000	0.000	0.000	0.000
13	B	13	GLN	0	0.019	0.006	31.334	0.004	0.004	0.000	0.000	0.000	0.000
14	B	14	ALA	0	-0.001	-0.007	33.687	0.157	0.157	0.000	0.000	0.000	0.000
15	B	15	GLY	0	-0.056	-0.033	34.360	-0.251	-0.251	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.019	-0.001	32.976	-0.074	-0.074	0.000	0.000	0.000	0.000
17	B	17	SER	0	-0.045	-0.040	29.792	0.163	0.163	0.000	0.000	0.000	0.000
18	B	18	LEU	0	0.019	0.011	24.738	-0.077	-0.077	0.000	0.000	0.000	0.000
19	B	19	ARG	1	0.905	0.958	22.938	-11.978	-11.978	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.005	0.011	18.846	0.103	0.103	0.000	0.000	0.000	0.000
21	B	21	SER	0	-0.019	-0.013	17.356	0.015	0.015	0.000	0.000	0.000	0.000
22	B	22	CYS	0	-0.047	-0.015	11.854	0.667	0.667	0.000	0.000	0.000	0.000
23	B	23	VAL	0	0.014	0.026	11.924	-0.535	-0.535	0.000	0.000	0.000	0.000
24	B	24	ALA	0	0.038	0.013	8.687	1.686	1.686	0.000	0.000	0.000	0.000
25	B	25	SER	0	-0.033	-0.017	7.600	-1.373	-1.373	0.000	0.000	0.000	0.000
26	B	26	GLY	0	0.047	0.011	4.413	2.889	2.872	-0.001	-0.016	0.034	0.000
27	B	27	VAL	0	-0.020	-0.001	5.021	4.584	4.637	-0.001	-0.005	-0.046	0.000
28	B	28	THR	0	-0.009	-0.009	6.208	-2.943	-2.943	0.000	0.000	0.000	0.000
29	B	29	SER	0	-0.004	-0.003	8.789	-2.505	-2.505	0.000	0.000	0.000	0.000
30	B	30	THR	0	-0.059	-0.024	10.661	-1.480	-1.480	0.000	0.000	0.000	0.000
31	B	31	ARG	1	0.908	0.953	10.005	-15.826	-15.826	0.000	0.000	0.000	0.000
32	B	32	PRO	0	0.006	0.012	9.036	-0.748	-0.748	0.000	0.000	0.000	0.000
33	B	33	CYS	0	-0.059	0.010	11.069	-2.446	-2.446	0.000	0.000	0.000	0.000
34	B	34	ILE	0	0.026	0.006	10.660	2.050	2.050	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.037	0.008	13.260	-1.700	-1.700	0.000	0.000	0.000	0.000
36	B	36	TRP	0	-0.024	-0.013	14.262	1.174	1.174	0.000	0.000	0.000	0.000
37	B	37	PHE	0	0.024	0.006	14.753	-0.720	-0.720	0.000	0.000	0.000	0.000
38	B	38	ARG	1	0.780	0.874	17.790	-12.313	-12.313	0.000	0.000	0.000	0.000
39	B	39	GLN	0	-0.012	-0.009	18.584	0.620	0.620	0.000	0.000	0.000	0.000
40	B	40	ALA	0	0.048	0.037	21.076	-0.016	-0.016	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.014	-0.017	24.146	0.169	0.169	0.000	0.000	0.000	0.000
42	B	42	GLY	0	-0.009	0.001	25.043	-0.433	-0.433	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.911	0.963	24.671	-11.289	-11.289	0.000	0.000	0.000	0.000
44	B	44	GLU	-1	-0.882	-0.934	22.058	13.641	13.641	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.805	0.912	12.838	-21.550	-21.550	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.809	-0.892	19.950	12.297	12.297	0.000	0.000	0.000	0.000
47	B	47	GLY	0	0.036	0.009	19.821	0.655	0.655	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.046	-0.025	20.224	-0.770	-0.770	0.000	0.000	0.000	0.000
49	B	49	ALA	0	-0.009	-0.021	20.035	-0.790	-0.790	0.000	0.000	0.000	0.000
50	B	50	VAL	0	0.012	0.017	16.992	0.861	0.861	0.000	0.000	0.000	0.000
51	B	51	VAL	0	-0.003	0.003	17.443	-1.043	-1.043	0.000	0.000	0.000	0.000
52	B	52	ASN	0	0.008	-0.031	16.819	1.194	1.194	0.000	0.000	0.000	0.000
53	B	52	PHE	0	-0.012	-0.031	15.658	-0.319	-0.319	0.000	0.000	0.000	0.000
54	B	53	ARG	1	0.853	0.935	17.067	-13.030	-13.030	0.000	0.000	0.000	0.000
55	B	54	GLY	0	0.052	0.038	20.045	-0.570	-0.570	0.000	0.000	0.000	0.000
56	B	55	ASP	-1	-0.845	-0.900	21.799	12.205	12.205	0.000	0.000	0.000	0.000
57	B	56	SER	0	-0.035	-0.023	21.563	0.544	0.544	0.000	0.000	0.000	0.000
58	B	57	THR	0	-0.045	-0.029	22.184	-0.614	-0.614	0.000	0.000	0.000	0.000
59	B	58	TYR	0	0.035	0.016	22.592	0.547	0.547	0.000	0.000	0.000	0.000
60	B	59	ILE	0	0.017	0.020	23.317	-0.269	-0.269	0.000	0.000	0.000	0.000
61	B	60	THR	0	0.013	-0.001	25.317	-0.489	-0.489	0.000	0.000	0.000	0.000
62	B	61	ASP	-1	-0.844	-0.926	29.042	9.797	9.797	0.000	0.000	0.000	0.000
63	B	62	SER	0	-0.066	-0.036	31.746	-0.086	-0.086	0.000	0.000	0.000	0.000
64	B	63	VAL	0	-0.009	-0.007	25.339	-0.081	-0.081	0.000	0.000	0.000	0.000
65	B	64	LYS	1	0.982	0.999	28.148	-10.373	-10.373	0.000	0.000	0.000	0.000
66	B	65	GLY	0	-0.030	-0.001	29.072	-0.105	-0.105	0.000	0.000	0.000	0.000
67	B	66	ARG	1	0.734	0.855	29.477	-10.560	-10.560	0.000	0.000	0.000	0.000
68	B	67	PHE	0	-0.004	-0.012	24.590	0.106	0.106	0.000	0.000	0.000	0.000
69	B	68	THR	0	-0.041	-0.024	25.889	-0.279	-0.279	0.000	0.000	0.000	0.000
70	B	69	ILE	0	-0.033	-0.002	18.086	0.135	0.135	0.000	0.000	0.000	0.000
71	B	70	SER	0	-0.049	-0.027	21.322	-0.493	-0.493	0.000	0.000	0.000	0.000
72	B	71	ARG	1	0.797	0.866	13.558	-18.189	-18.189	0.000	0.000	0.000	0.000
73	B	72	ASP	-1	-0.811	-0.897	19.269	13.165	13.165	0.000	0.000	0.000	0.000
74	B	73	GLU	-1	-0.966	-0.991	18.556	13.006	13.006	0.000	0.000	0.000	0.000
75	B	74	ASP	-1	-0.855	-0.893	17.107	16.002	16.002	0.000	0.000	0.000	0.000
76	B	75	SER	0	-0.037	-0.022	15.434	0.983	0.983	0.000	0.000	0.000	0.000
77	B	76	ASP	-1	-0.862	-0.939	12.290	21.417	21.417	0.000	0.000	0.000	0.000
78	B	77	THR	0	0.024	0.020	13.239	1.268	1.268	0.000	0.000	0.000	0.000
79	B	78	VAL	0	-0.036	-0.018	15.369	-0.953	-0.953	0.000	0.000	0.000	0.000
80	B	79	TYR	0	-0.044	-0.019	17.228	0.129	0.129	0.000	0.000	0.000	0.000
81	B	80	LEU	0	-0.013	-0.006	19.930	-0.195	-0.195	0.000	0.000	0.000	0.000
82	B	81	GLN	0	0.003	0.011	21.568	0.021	0.021	0.000	0.000	0.000	0.000
83	B	82	MET	0	-0.023	0.006	23.712	-0.085	-0.085	0.000	0.000	0.000	0.000
84	B	82	ASN	0	0.074	0.012	26.811	-0.119	-0.119	0.000	0.000	0.000	0.000
85	B	82	SER	0	0.007	-0.006	30.612	0.053	0.053	0.000	0.000	0.000	0.000
86	B	82	LEU	0	-0.024	0.004	27.227	-0.032	-0.032	0.000	0.000	0.000	0.000
87	B	83	LYS	1	0.989	0.993	31.070	-9.448	-9.448	0.000	0.000	0.000	0.000
88	B	84	PRO	0	0.035	0.010	31.057	0.290	0.290	0.000	0.000	0.000	0.000
89	B	85	GLU	-1	-0.901	-0.962	30.785	9.499	9.499	0.000	0.000	0.000	0.000
90	B	86	ASP	-1	-0.802	-0.862	27.200	11.047	11.047	0.000	0.000	0.000	0.000
91	B	87	THR	0	0.003	0.017	26.007	0.477	0.477	0.000	0.000	0.000	0.000
92	B	88	ALA	0	-0.049	-0.021	22.570	-0.034	-0.034	0.000	0.000	0.000	0.000
93	B	89	THR	0	-0.026	-0.003	17.582	-0.423	-0.423	0.000	0.000	0.000	0.000
94	B	90	TYR	0	-0.017	-0.028	18.462	0.072	0.072	0.000	0.000	0.000	0.000
95	B	91	TYR	0	0.019	0.003	13.153	0.151	0.151	0.000	0.000	0.000	0.000
96	B	93	ALA	0	0.041	0.015	9.791	1.906	1.906	0.000	0.000	0.000	0.000
97	B	94	ALA	0	0.024	0.000	7.546	-2.180	-2.180	0.000	0.000	0.000	0.000
98	B	95	ASP	-1	-0.763	-0.876	9.034	26.877	26.877	0.000	0.000	0.000	0.000
99	B	96	VAL	0	0.007	-0.005	6.357	-2.074	-2.074	0.000	0.000	0.000	0.000
100	B	97	ASN	0	-0.025	-0.011	9.002	-1.280	-1.280	0.000	0.000	0.000	0.000
101	B	98	ARG	1	0.835	0.903	11.600	-24.007	-24.007	0.000	0.000	0.000	0.000
102	B	99	GLY	0	0.015	0.011	13.920	-1.178	-1.178	0.000	0.000	0.000	0.000
103	B	100	GLY	0	0.059	0.038	13.905	-0.773	-0.773	0.000	0.000	0.000	0.000
104	B	100	PHE	0	-0.088	-0.045	14.843	-0.915	-0.915	0.000	0.000	0.000	0.000
105	B	100	CYS	0	-0.014	-0.017	15.893	1.147	1.147	0.000	0.000	0.000	0.000
106	B	100	TYR	0	-0.013	0.013	17.341	-0.740	-0.740	0.000	0.000	0.000	0.000
107	B	100	ILE	0	-0.006	-0.007	18.049	0.711	0.711	0.000	0.000	0.000	0.000
108	B	100	GLU	-1	-0.875	-0.951	19.271	14.976	14.976	0.000	0.000	0.000	0.000
109	B	100	ASP	-1	-0.803	-0.918	15.111	19.266	19.266	0.000	0.000	0.000	0.000
110	B	100	TRP	0	0.011	0.016	14.175	1.598	1.598	0.000	0.000	0.000	0.000
111	B	100	TYR	0	-0.082	-0.038	14.615	0.423	0.423	0.000	0.000	0.000	0.000
112	B	100	PHE	0	-0.025	-0.012	11.169	1.149	1.149	0.000	0.000	0.000	0.000
113	B	101	SER	0	-0.011	-0.005	7.087	-1.535	-1.535	0.000	0.000	0.000	0.000
114	B	102	TYR	0	-0.027	0.006	2.541	-11.623	-7.806	3.192	-3.021	-3.988	0.026
115	B	103	TRP	0	-0.024	-0.024	6.286	-7.305	-7.305	0.000	0.000	0.000	0.000
116	B	104	GLY	0	0.043	0.029	7.641	2.743	2.743	0.000	0.000	0.000	0.000
117	B	105	GLN	0	-0.016	-0.017	9.717	2.035	2.035	0.000	0.000	0.000	0.000
118	B	106	GLY	0	-0.009	0.003	12.009	-1.173	-1.173	0.000	0.000	0.000	0.000
119	B	107	THR	0	-0.065	-0.034	15.046	-0.751	-0.751	0.000	0.000	0.000	0.000
120	B	108	GLN	0	0.002	-0.007	18.032	-0.619	-0.619	0.000	0.000	0.000	0.000
121	B	109	VAL	0	0.016	0.012	21.572	-0.251	-0.251	0.000	0.000	0.000	0.000
122	B	110	THR	0	-0.027	-0.007	24.232	-0.058	-0.058	0.000	0.000	0.000	0.000
123	B	111	VAL	0	-0.007	0.003	27.774	-0.183	-0.183	0.000	0.000	0.000	0.000
124	B	112	SER	0	0.026	0.025	30.681	-0.097	-0.097	0.000	0.000	0.000	0.000
125	B	113	SER	0	0.018	-0.008	34.071	-0.136	-0.136	0.000	0.000	0.000	0.000
126	B	114	ALA	0	0.033	-0.001	37.453	0.002	0.002	0.000	0.000	0.000	0.000
127	B	115	ALA	0	-0.029	-0.013	40.182	-0.071	-0.071	0.000	0.000	0.000	0.000
128	B	116	ALA	0	-0.013	-0.007	37.192	-0.075	-0.075	0.000	0.000	0.000	0.000
129	B	117	HIS	0	0.008	0.010	34.236	0.267	0.267	0.000	0.000	0.000	0.000
130	B	118	HIS	0	0.007	0.009	36.115	-0.308	-0.308	0.000	0.000	0.000	0.000
131	B	119	HIS	0	-0.015	0.001	34.438	0.381	0.381	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ASP)