FMO DATABASE

FMODB ID: Z6ZZN

Calculation Name: 5D5X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D5X

Chain ID: B

ChEMBL ID:

UniProt ID: G0SB31

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSide
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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-892052.891523
FMO2-HF: Nuclear repulsion	848879.047781
FMO2-HF: Total energy	-43173.843742
FMO2-MP2: Total energy	-43302.808961

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:41:SER)

Summations of interaction energy for fragment #1(B:41:SER)

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.
-13.22	-8.273	4.042	-4.325	-4.663	0.004

Interaction energy analysis for fragmet #1(B:41:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.027

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	43	PHE	0	-0.038	-0.011	3.114	-3.948	-0.439	-0.005	-1.843	-1.661	0.004
4	B	44	VAL	0	0.102	0.048	3.891	-0.189	0.101	0.000	-0.039	-0.251	0.000
5	B	45	ARG	1	0.930	0.975	3.487	4.187	4.712	0.003	-0.167	-0.361	0.000
6	B	46	LYS	1	0.871	0.934	7.194	0.401	0.401	0.000	0.000	0.000	0.000
7	B	47	LEU	0	-0.013	0.001	8.436	0.127	0.127	0.000	0.000	0.000	0.000
8	B	48	TYR	0	-0.025	-0.033	9.614	0.027	0.027	0.000	0.000	0.000	0.000
9	B	49	LYS	1	0.848	0.921	11.210	0.441	0.441	0.000	0.000	0.000	0.000
10	B	50	MET	0	-0.057	-0.022	12.872	0.080	0.080	0.000	0.000	0.000	0.000
11	B	51	LEU	0	0.007	0.001	13.954	0.035	0.035	0.000	0.000	0.000	0.000
12	B	52	GLU	-1	-0.831	-0.894	15.058	-0.465	-0.465	0.000	0.000	0.000	0.000
13	B	53	ASP	-1	-0.901	-0.916	17.885	-0.116	-0.116	0.000	0.000	0.000	0.000
14	B	54	PRO	0	0.037	0.006	20.310	0.023	0.023	0.000	0.000	0.000	0.000
15	B	55	SER	0	-0.052	-0.045	23.275	0.023	0.023	0.000	0.000	0.000	0.000
16	B	56	TYR	0	-0.014	-0.038	17.996	0.022	0.022	0.000	0.000	0.000	0.000
17	B	57	HIS	0	0.050	0.037	23.130	0.021	0.021	0.000	0.000	0.000	0.000
18	B	58	SER	0	-0.015	-0.020	24.721	0.006	0.006	0.000	0.000	0.000	0.000
19	B	59	VAL	0	-0.057	-0.009	22.144	0.012	0.012	0.000	0.000	0.000	0.000
20	B	60	VAL	0	-0.042	-0.033	17.596	0.024	0.024	0.000	0.000	0.000	0.000
21	B	61	ARG	1	0.906	0.967	19.896	-0.021	-0.021	0.000	0.000	0.000	0.000
22	B	62	TRP	0	0.022	-0.005	13.829	0.024	0.024	0.000	0.000	0.000	0.000
23	B	63	SER	0	0.001	-0.003	19.899	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	64	ASP	-1	-0.830	-0.882	22.306	-0.014	-0.014	0.000	0.000	0.000	0.000
25	B	65	ASP	-1	-0.876	-0.930	23.480	-0.010	-0.010	0.000	0.000	0.000	0.000
26	B	66	GLY	0	-0.075	-0.040	20.405	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	67	ASP	-1	-0.816	-0.899	18.328	0.004	0.004	0.000	0.000	0.000	0.000
28	B	68	SER	0	-0.058	-0.061	16.926	0.020	0.020	0.000	0.000	0.000	0.000
29	B	69	PHE	0	-0.011	-0.005	13.137	-0.016	-0.016	0.000	0.000	0.000	0.000
30	B	70	VAL	0	0.061	0.029	17.941	0.040	0.040	0.000	0.000	0.000	0.000
31	B	71	VAL	0	-0.082	-0.041	18.402	-0.013	-0.013	0.000	0.000	0.000	0.000
32	B	72	LEU	0	0.011	-0.008	21.054	0.010	0.010	0.000	0.000	0.000	0.000
33	B	73	GLU	-1	-0.693	-0.817	24.367	0.034	0.034	0.000	0.000	0.000	0.000
34	B	74	ASN	0	0.048	0.000	22.102	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	75	GLU	-1	-0.775	-0.859	22.845	0.128	0.128	0.000	0.000	0.000	0.000
36	B	76	LYS	1	0.871	0.916	24.498	-0.024	-0.024	0.000	0.000	0.000	0.000
37	B	77	PHE	0	0.032	0.025	15.828	0.001	0.001	0.000	0.000	0.000	0.000
38	B	78	THR	0	-0.061	-0.055	19.849	0.017	0.017	0.000	0.000	0.000	0.000
39	B	79	LYS	1	0.838	0.899	20.525	-0.100	-0.100	0.000	0.000	0.000	0.000
40	B	80	THR	0	-0.053	-0.025	22.471	-0.013	-0.013	0.000	0.000	0.000	0.000
41	B	81	ILE	0	0.016	0.019	17.427	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	82	LEU	0	-0.051	-0.021	14.661	0.000	0.000	0.000	0.000	0.000	0.000
43	B	83	PRO	0	-0.016	-0.006	15.425	0.022	0.022	0.000	0.000	0.000	0.000
44	B	84	LYS	1	0.920	0.971	16.507	0.096	0.096	0.000	0.000	0.000	0.000
45	B	85	HIS	0	0.030	0.037	12.859	-0.018	-0.018	0.000	0.000	0.000	0.000
46	B	86	PHE	0	-0.049	-0.042	8.752	0.045	0.045	0.000	0.000	0.000	0.000
47	B	87	LYS	1	0.924	0.978	12.156	0.019	0.019	0.000	0.000	0.000	0.000
48	B	88	HIS	0	-0.017	-0.006	12.478	-0.030	-0.030	0.000	0.000	0.000	0.000
49	B	89	SER	0	0.062	0.023	16.326	-0.023	-0.023	0.000	0.000	0.000	0.000
50	B	90	ASN	0	0.018	0.011	17.597	-0.034	-0.034	0.000	0.000	0.000	0.000
51	B	91	PHE	0	0.100	0.035	16.947	0.058	0.058	0.000	0.000	0.000	0.000
52	B	92	ALA	0	0.062	0.029	17.077	0.037	0.037	0.000	0.000	0.000	0.000
53	B	93	SER	0	-0.012	-0.009	13.966	0.044	0.044	0.000	0.000	0.000	0.000
54	B	94	PHE	0	0.003	0.014	12.116	0.148	0.148	0.000	0.000	0.000	0.000
55	B	95	VAL	0	0.031	0.020	12.736	0.067	0.067	0.000	0.000	0.000	0.000
56	B	96	ARG	1	0.907	0.958	13.169	-0.737	-0.737	0.000	0.000	0.000	0.000
57	B	97	GLN	0	-0.010	-0.027	5.914	0.192	0.192	0.000	0.000	0.000	0.000
58	B	98	LEU	0	0.036	0.028	9.434	0.183	0.183	0.000	0.000	0.000	0.000
59	B	99	ASN	0	0.048	0.020	10.835	0.030	0.030	0.000	0.000	0.000	0.000
60	B	100	LYS	1	0.850	0.933	8.884	-1.452	-1.452	0.000	0.000	0.000	0.000
61	B	101	TYR	0	-0.011	-0.021	1.966	-2.854	-2.693	4.043	-2.183	-2.021	0.000
62	B	102	ASP	-1	-0.800	-0.877	8.273	0.502	0.502	0.000	0.000	0.000	0.000
63	B	103	PHE	0	-0.041	-0.003	8.254	-0.109	-0.109	0.000	0.000	0.000	0.000
64	B	104	HIS	0	-0.013	-0.010	12.933	0.024	0.024	0.000	0.000	0.000	0.000
65	B	105	LYS	1	0.863	0.940	16.641	-0.236	-0.236	0.000	0.000	0.000	0.000
66	B	106	VAL	0	0.040	0.009	19.226	0.007	0.007	0.000	0.000	0.000	0.000
67	B	107	ARG	1	0.783	0.881	21.758	-0.145	-0.145	0.000	0.000	0.000	0.000
68	B	108	HIS	0	0.089	0.058	25.159	0.001	0.001	0.000	0.000	0.000	0.000
69	B	109	ASN	0	0.008	-0.001	27.705	0.013	0.013	0.000	0.000	0.000	0.000
70	B	110	ASP	-1	-1.023	-1.013	31.311	0.066	0.066	0.000	0.000	0.000	0.000
71	B	111	GLU	-1	-0.759	-0.883	33.371	0.048	0.048	0.000	0.000	0.000	0.000
72	B	112	ASN	0	-0.130	-0.071	33.840	-0.007	-0.007	0.000	0.000	0.000	0.000
73	B	113	GLY	0	0.055	0.038	33.518	0.001	0.001	0.000	0.000	0.000	0.000
74	B	114	GLU	-1	-0.868	-0.929	28.466	0.052	0.052	0.000	0.000	0.000	0.000
75	B	115	SER	0	-0.109	-0.041	30.253	0.007	0.007	0.000	0.000	0.000	0.000
76	B	116	PRO	0	-0.060	-0.027	27.931	0.002	0.002	0.000	0.000	0.000	0.000
77	B	117	TYR	0	-0.044	-0.078	24.719	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	118	GLY	0	0.049	0.030	28.307	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	119	ARG	1	0.918	0.939	28.601	-0.071	-0.071	0.000	0.000	0.000	0.000
80	B	120	ASP	-1	-0.937	-0.960	27.866	0.093	0.093	0.000	0.000	0.000	0.000
81	B	121	ALA	0	0.017	0.023	24.787	0.008	0.008	0.000	0.000	0.000	0.000
82	B	122	TRP	0	-0.105	-0.065	20.128	0.038	0.038	0.000	0.000	0.000	0.000
83	B	123	GLU	-1	-0.772	-0.855	20.050	0.081	0.081	0.000	0.000	0.000	0.000
84	B	124	PHE	0	-0.052	-0.032	15.004	0.046	0.046	0.000	0.000	0.000	0.000
85	B	125	LYS	1	0.878	0.929	16.010	-0.104	-0.104	0.000	0.000	0.000	0.000
86	B	126	HIS	0	0.034	0.009	10.379	-0.055	-0.055	0.000	0.000	0.000	0.000
87	B	127	PRO	0	0.054	0.036	13.831	-0.057	-0.057	0.000	0.000	0.000	0.000
88	B	128	GLU	-1	-0.839	-0.903	11.668	-0.049	-0.049	0.000	0.000	0.000	0.000
89	B	129	PHE	0	-0.058	-0.032	9.713	-0.102	-0.102	0.000	0.000	0.000	0.000
90	B	130	ARG	1	0.929	0.953	12.541	0.103	0.103	0.000	0.000	0.000	0.000
91	B	131	ALA	0	0.037	0.020	15.186	-0.066	-0.066	0.000	0.000	0.000	0.000
92	B	132	ASP	-1	-0.880	-0.930	17.351	-0.198	-0.198	0.000	0.000	0.000	0.000
93	B	133	ARG	1	0.788	0.878	14.654	0.250	0.250	0.000	0.000	0.000	0.000
94	B	134	LYS	1	0.870	0.927	12.773	0.581	0.581	0.000	0.000	0.000	0.000
95	B	135	ASP	-1	-0.855	-0.922	11.817	-0.513	-0.513	0.000	0.000	0.000	0.000
96	B	136	ASN	0	-0.033	-0.015	11.903	-0.031	-0.031	0.000	0.000	0.000	0.000
97	B	137	LEU	0	-0.034	-0.028	7.304	0.036	0.036	0.000	0.000	0.000	0.000
98	B	138	ASP	-1	-0.885	-0.936	5.772	-2.192	-2.192	0.000	0.000	0.000	0.000
99	B	139	ASN	0	-0.072	-0.037	6.851	0.520	0.520	0.000	0.000	0.000	0.000
100	B	140	ILE	0	-0.030	0.007	6.548	0.236	0.236	0.000	0.000	0.000	0.000
101	B	141	ARG	1	0.911	0.950	4.918	-0.452	-0.376	-0.001	-0.004	-0.071	0.000
102	B	142	ARG	1	0.888	0.933	3.594	-7.076	-6.690	0.002	-0.089	-0.298	0.000
103	B	143	LYS	1	0.852	0.935	6.969	-1.003	-1.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:41:SER)