FMO DATABASE

FMODB ID: YZMK2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1113914.668761
FMO2-HF: Nuclear repulsion	1062707.499154
FMO2-HF: Total energy	-51207.169607
FMO2-MP2: Total energy	-51354.887418

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.
10.837	5.007	24.191	-10.758	-7.602	0.075

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 : -0.876 / q_NPA : -0.919

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	B	3	GLN	0	-0.020	-0.004	3.431	0.423	2.452	0.032	-0.938	-1.122	0.002
4	B	4	LEU	0	-0.009	-0.008	5.436	-2.717	-2.717	0.000	0.000	0.000	0.000
5	B	5	GLN	0	-0.026	-0.009	8.845	0.167	0.167	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.762	-0.879	12.023	19.440	19.440	0.000	0.000	0.000	0.000
7	B	7	SER	0	-0.036	-0.020	14.746	-0.645	-0.645	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.042	0.011	18.504	0.076	0.076	0.000	0.000	0.000	0.000
9	B	9	GLY	0	0.023	0.024	21.049	-0.408	-0.408	0.000	0.000	0.000	0.000
10	B	10	GLY	0	-0.025	-0.015	22.623	-0.210	-0.210	0.000	0.000	0.000	0.000
11	B	11	SER	0	-0.017	-0.010	26.084	0.106	0.106	0.000	0.000	0.000	0.000
12	B	12	VAL	0	-0.018	-0.007	29.425	-0.268	-0.268	0.000	0.000	0.000	0.000
13	B	13	GLN	0	0.024	0.008	32.033	-0.076	-0.076	0.000	0.000	0.000	0.000
14	B	14	ALA	0	0.011	-0.005	34.241	0.158	0.158	0.000	0.000	0.000	0.000
15	B	15	GLY	0	-0.060	-0.029	35.158	-0.249	-0.249	0.000	0.000	0.000	0.000
16	B	16	GLY	0	-0.010	0.002	33.904	-0.056	-0.056	0.000	0.000	0.000	0.000
17	B	17	SER	0	-0.043	-0.038	30.388	0.088	0.088	0.000	0.000	0.000	0.000
18	B	18	LEU	0	0.014	0.009	25.284	-0.046	-0.046	0.000	0.000	0.000	0.000
19	B	19	ARG	1	0.843	0.931	23.597	-12.012	-12.012	0.000	0.000	0.000	0.000
20	B	20	LEU	0	0.006	0.025	19.546	0.124	0.124	0.000	0.000	0.000	0.000
21	B	21	SER	0	-0.022	-0.016	18.552	-0.101	-0.101	0.000	0.000	0.000	0.000
22	B	22	CYS	0	-0.062	-0.032	12.434	0.642	0.642	0.000	0.000	0.000	0.000
23	B	23	VAL	0	0.017	0.026	12.970	-0.274	-0.274	0.000	0.000	0.000	0.000
24	B	24	ALA	0	0.023	0.011	9.654	1.543	1.543	0.000	0.000	0.000	0.000
25	B	25	SER	0	-0.030	-0.017	8.305	-1.213	-1.213	0.000	0.000	0.000	0.000
26	B	26	GLY	0	0.056	0.013	4.861	2.591	2.591	0.000	0.000	0.000	0.000
27	B	27	VAL	0	-0.025	-0.008	5.408	4.487	4.487	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.012	-0.003	6.143	-3.410	-3.410	0.000	0.000	0.000	0.000
29	B	29	SER	0	-0.021	-0.017	8.613	-2.695	-2.695	0.000	0.000	0.000	0.000
30	B	30	THR	0	-0.041	-0.009	10.431	-1.631	-1.631	0.000	0.000	0.000	0.000
31	B	31	ARG	1	0.877	0.929	10.162	-16.938	-16.938	0.000	0.000	0.000	0.000
32	B	32	PRO	0	-0.025	0.001	9.061	-0.788	-0.788	0.000	0.000	0.000	0.000
33	B	33	CYS	0	0.036	0.049	11.248	-2.264	-2.264	0.000	0.000	0.000	0.000
34	B	34	ILE	0	-0.008	-0.001	11.365	1.946	1.946	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.027	0.001	13.561	-1.498	-1.498	0.000	0.000	0.000	0.000
36	B	36	TRP	0	-0.008	-0.009	14.717	0.867	0.867	0.000	0.000	0.000	0.000
37	B	37	PHE	0	0.014	0.011	15.062	-0.744	-0.744	0.000	0.000	0.000	0.000
38	B	38	ARG	1	0.749	0.848	18.203	-11.990	-11.990	0.000	0.000	0.000	0.000
39	B	39	GLN	0	0.018	0.005	19.392	0.776	0.776	0.000	0.000	0.000	0.000
40	B	40	ALA	0	0.029	0.022	21.545	-0.072	-0.072	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.008	-0.017	25.007	0.158	0.158	0.000	0.000	0.000	0.000
42	B	42	GLY	0	-0.021	-0.005	26.509	-0.367	-0.367	0.000	0.000	0.000	0.000
43	B	43	LYS	1	0.909	0.963	25.557	-11.053	-11.053	0.000	0.000	0.000	0.000
44	B	44	GLU	-1	-0.880	-0.929	22.936	13.193	13.193	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.818	0.903	13.180	-20.799	-20.799	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.826	-0.891	20.428	11.914	11.914	0.000	0.000	0.000	0.000
47	B	47	GLY	0	0.051	0.011	19.897	0.630	0.630	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.043	-0.027	20.471	-0.740	-0.740	0.000	0.000	0.000	0.000
49	B	49	ALA	0	-0.014	-0.019	20.399	-0.739	-0.739	0.000	0.000	0.000	0.000
50	B	50	VAL	0	-0.008	0.005	17.399	0.825	0.825	0.000	0.000	0.000	0.000
51	B	51	VAL	0	-0.008	-0.008	17.745	-0.978	-0.978	0.000	0.000	0.000	0.000
52	B	52	ASN	0	0.014	-0.007	17.133	1.097	1.097	0.000	0.000	0.000	0.000
53	B	52	PHE	0	-0.028	-0.034	15.847	-0.307	-0.307	0.000	0.000	0.000	0.000
54	B	53	ARG	1	0.786	0.889	17.232	-12.814	-12.814	0.000	0.000	0.000	0.000
55	B	54	GLY	0	0.086	0.055	20.431	-0.613	-0.613	0.000	0.000	0.000	0.000
56	B	55	ASP	-1	-0.827	-0.880	22.282	12.393	12.393	0.000	0.000	0.000	0.000
57	B	56	SER	0	-0.011	0.001	21.839	0.500	0.500	0.000	0.000	0.000	0.000
58	B	57	THR	0	-0.043	-0.036	22.507	-0.514	-0.514	0.000	0.000	0.000	0.000
59	B	58	TYR	0	0.027	0.007	22.855	0.486	0.486	0.000	0.000	0.000	0.000
60	B	59	ILE	0	0.005	0.018	23.151	-0.257	-0.257	0.000	0.000	0.000	0.000
61	B	60	THR	0	0.023	0.003	25.346	-0.467	-0.467	0.000	0.000	0.000	0.000
62	B	61	ASP	-1	-0.800	-0.903	29.139	9.855	9.855	0.000	0.000	0.000	0.000
63	B	62	SER	0	-0.038	-0.014	31.767	-0.151	-0.151	0.000	0.000	0.000	0.000
64	B	63	VAL	0	-0.004	0.011	25.475	-0.078	-0.078	0.000	0.000	0.000	0.000
65	B	64	LYS	1	0.915	0.947	28.597	-9.956	-9.956	0.000	0.000	0.000	0.000
66	B	65	GLY	0	-0.030	-0.004	29.479	-0.097	-0.097	0.000	0.000	0.000	0.000
67	B	66	ARG	1	0.714	0.835	29.882	-10.237	-10.237	0.000	0.000	0.000	0.000
68	B	67	PHE	0	-0.014	-0.013	25.051	0.020	0.020	0.000	0.000	0.000	0.000
69	B	68	THR	0	-0.040	-0.027	26.271	-0.248	-0.248	0.000	0.000	0.000	0.000
70	B	69	ILE	0	-0.023	0.004	18.390	0.082	0.082	0.000	0.000	0.000	0.000
71	B	70	SER	0	-0.030	-0.020	21.612	-0.554	-0.554	0.000	0.000	0.000	0.000
72	B	71	ARG	1	0.759	0.854	13.761	-18.031	-18.031	0.000	0.000	0.000	0.000
73	B	72	ASP	-1	-0.782	-0.872	19.642	13.159	13.159	0.000	0.000	0.000	0.000
74	B	73	GLU	-1	-0.905	-0.960	18.582	13.018	13.018	0.000	0.000	0.000	0.000
75	B	74	ASP	-1	-0.831	-0.872	16.764	16.248	16.248	0.000	0.000	0.000	0.000
76	B	75	SER	0	-0.074	-0.049	15.402	1.005	1.005	0.000	0.000	0.000	0.000
77	B	76	ASP	-1	-0.811	-0.917	12.625	20.946	20.946	0.000	0.000	0.000	0.000
78	B	77	THR	0	0.025	0.033	13.899	1.161	1.161	0.000	0.000	0.000	0.000
79	B	78	VAL	0	-0.010	-0.011	15.836	-0.748	-0.748	0.000	0.000	0.000	0.000
80	B	79	TYR	0	-0.074	-0.073	17.694	-0.056	-0.056	0.000	0.000	0.000	0.000
81	B	80	LEU	0	-0.027	-0.010	20.346	-0.069	-0.069	0.000	0.000	0.000	0.000
82	B	81	GLN	0	0.014	0.015	22.039	0.048	0.048	0.000	0.000	0.000	0.000
83	B	82	MET	0	-0.023	-0.005	24.068	0.134	0.134	0.000	0.000	0.000	0.000
84	B	82	ASN	0	0.056	0.011	27.307	-0.178	-0.178	0.000	0.000	0.000	0.000
85	B	82	SER	0	0.011	0.001	31.135	0.046	0.046	0.000	0.000	0.000	0.000
86	B	82	LEU	0	-0.009	0.022	27.770	0.002	0.002	0.000	0.000	0.000	0.000
87	B	83	LYS	1	0.897	0.936	31.593	-9.210	-9.210	0.000	0.000	0.000	0.000
88	B	84	PRO	0	0.033	0.012	31.522	0.264	0.264	0.000	0.000	0.000	0.000
89	B	85	GLU	-1	-0.847	-0.930	31.237	9.199	9.199	0.000	0.000	0.000	0.000
90	B	86	ASP	-1	-0.766	-0.833	27.702	10.656	10.656	0.000	0.000	0.000	0.000
91	B	87	THR	0	-0.026	-0.002	26.560	0.462	0.462	0.000	0.000	0.000	0.000
92	B	88	ALA	0	-0.035	-0.020	23.069	-0.039	-0.039	0.000	0.000	0.000	0.000
93	B	89	THR	0	-0.027	-0.001	18.233	-0.389	-0.389	0.000	0.000	0.000	0.000
94	B	90	TYR	0	0.004	-0.019	19.153	0.152	0.152	0.000	0.000	0.000	0.000
95	B	91	TYR	0	0.015	0.009	13.725	-0.212	-0.212	0.000	0.000	0.000	0.000
96	B	93	ALA	0	0.022	0.005	10.256	1.444	1.444	0.000	0.000	0.000	0.000
97	B	94	ALA	0	0.019	-0.006	7.839	-1.601	-1.601	0.000	0.000	0.000	0.000
98	B	95	ASP	-1	-0.764	-0.865	9.036	28.608	28.608	0.000	0.000	0.000	0.000
99	B	96	VAL	0	0.024	0.010	6.599	-2.348	-2.348	0.000	0.000	0.000	0.000
100	B	97	ASN	0	-0.072	-0.043	8.596	-0.937	-0.937	0.000	0.000	0.000	0.000
101	B	98	ARG	1	0.857	0.915	11.687	-24.415	-24.415	0.000	0.000	0.000	0.000
102	B	99	GLY	0	-0.008	-0.002	13.783	-1.314	-1.314	0.000	0.000	0.000	0.000
103	B	100	GLY	0	0.061	0.032	13.914	-0.755	-0.755	0.000	0.000	0.000	0.000
104	B	100	PHE	0	-0.068	-0.038	14.803	-0.953	-0.953	0.000	0.000	0.000	0.000
105	B	100	CYS	0	-0.045	-0.039	16.273	1.034	1.034	0.000	0.000	0.000	0.000
106	B	100	TYR	0	-0.020	0.010	17.897	-0.590	-0.590	0.000	0.000	0.000	0.000
107	B	100	ILE	0	-0.004	-0.013	18.527	0.496	0.496	0.000	0.000	0.000	0.000
108	B	100	GLU	-1	-0.813	-0.914	19.720	14.976	14.976	0.000	0.000	0.000	0.000
109	B	100	ASP	-1	-0.789	-0.896	15.727	18.948	18.948	0.000	0.000	0.000	0.000
110	B	100	TRP	0	-0.001	-0.002	14.480	1.503	1.503	0.000	0.000	0.000	0.000
111	B	100	TYR	0	-0.095	-0.040	14.108	0.932	0.932	0.000	0.000	0.000	0.000
112	B	100	PHE	0	-0.020	-0.017	11.112	1.460	1.460	0.000	0.000	0.000	0.000
113	B	101	SER	0	0.007	0.009	6.532	-1.091	-1.091	0.000	0.000	0.000	0.000
114	B	102	TYR	0	-0.064	-0.050	1.595	-30.681	-38.540	24.159	-9.820	-6.480	0.073
115	B	103	TRP	0	-0.021	-0.035	6.470	-6.031	-6.031	0.000	0.000	0.000	0.000
116	B	104	GLY	0	0.045	0.041	7.722	2.270	2.270	0.000	0.000	0.000	0.000
117	B	105	GLN	0	-0.038	-0.028	10.301	1.679	1.679	0.000	0.000	0.000	0.000
118	B	106	GLY	0	-0.009	-0.011	12.534	-0.934	-0.934	0.000	0.000	0.000	0.000
119	B	107	THR	0	-0.062	-0.036	15.592	-0.682	-0.682	0.000	0.000	0.000	0.000
120	B	108	GLN	0	0.016	0.010	18.616	-0.672	-0.672	0.000	0.000	0.000	0.000
121	B	109	VAL	0	0.011	0.012	22.100	-0.206	-0.206	0.000	0.000	0.000	0.000
122	B	110	THR	0	-0.002	-0.014	24.863	-0.122	-0.122	0.000	0.000	0.000	0.000
123	B	111	VAL	0	-0.011	0.005	28.417	-0.141	-0.141	0.000	0.000	0.000	0.000
124	B	112	SER	0	0.025	0.026	31.442	-0.038	-0.038	0.000	0.000	0.000	0.000
125	B	113	SER	0	0.008	-0.007	34.839	-0.104	-0.104	0.000	0.000	0.000	0.000
126	B	114	ALA	0	0.031	-0.002	38.065	-0.011	-0.011	0.000	0.000	0.000	0.000
127	B	115	ALA	0	-0.021	-0.006	41.014	-0.065	-0.065	0.000	0.000	0.000	0.000
128	B	116	ALA	0	-0.007	-0.006	37.946	-0.074	-0.074	0.000	0.000	0.000	0.000
129	B	117	HIS	0	-0.020	-0.020	34.127	0.294	0.294	0.000	0.000	0.000	0.000
130	B	118	HIS	0	-0.017	-0.004	36.738	-0.272	-0.272	0.000	0.000	0.000	0.000
131	B	119	HIS	0	0.023	0.036	34.770	0.349	0.349	0.000	0.000	0.000	0.000

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