FMO DATABASE

FMODB ID: Z67VN

Calculation Name: 5D90-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D90

Chain ID: B

ChEMBL ID:

UniProt ID: P44558

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	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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-942230.706389
FMO2-HF: Nuclear repulsion	891642.301133
FMO2-HF: Total energy	-50588.405256
FMO2-MP2: Total energy	-50735.054866

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:0:GLY)

Summations of interaction energy for fragment #1(B:0:GLY)

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.
-4.951	-1.588	0.132	-1.713	-1.783	-0.005

Interaction energy analysis for fragmet #1(B:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.009

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	2	THR	0	-0.050	-0.033	3.090	-1.321	0.496	0.006	-0.978	-0.845	0.001
4	B	3	TYR	0	0.003	0.029	3.077	-1.901	-0.355	0.126	-0.735	-0.938	-0.006
5	B	4	THR	0	0.032	-0.002	5.511	0.056	0.056	0.000	0.000	0.000	0.000
6	B	5	THR	0	0.079	0.018	9.005	-0.135	-0.135	0.000	0.000	0.000	0.000
7	B	6	ALA	0	-0.018	-0.011	11.539	-0.068	-0.068	0.000	0.000	0.000	0.000
8	B	7	LYS	1	1.004	0.996	5.658	-0.550	-0.550	0.000	0.000	0.000	0.000
9	B	8	ALA	0	0.020	0.017	7.863	-0.249	-0.249	0.000	0.000	0.000	0.000
10	B	9	ALA	0	-0.024	-0.017	8.704	-0.022	-0.022	0.000	0.000	0.000	0.000
11	B	10	GLU	-1	-0.914	-0.954	8.356	-0.301	-0.301	0.000	0.000	0.000	0.000
12	B	11	LYS	1	0.900	0.968	5.721	1.458	1.458	0.000	0.000	0.000	0.000
13	B	12	ILE	0	-0.040	-0.018	9.354	0.006	0.006	0.000	0.000	0.000	0.000
14	B	13	GLY	0	0.016	0.026	12.370	0.068	0.068	0.000	0.000	0.000	0.000
15	B	14	ILE	0	-0.049	-0.023	14.414	0.060	0.060	0.000	0.000	0.000	0.000
16	B	15	SER	0	0.044	0.023	15.295	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	16	ALA	0	0.074	0.003	15.486	-0.016	-0.016	0.000	0.000	0.000	0.000
18	B	17	TYR	0	-0.036	-0.015	16.541	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	18	THR	0	0.040	0.021	19.097	0.010	0.010	0.000	0.000	0.000	0.000
20	B	19	LEU	0	-0.012	0.012	12.675	0.007	0.007	0.000	0.000	0.000	0.000
21	B	20	ARG	1	0.966	0.962	16.185	0.063	0.063	0.000	0.000	0.000	0.000
22	B	21	PHE	0	-0.011	0.014	18.965	0.012	0.012	0.000	0.000	0.000	0.000
23	B	22	TYR	0	-0.014	-0.076	17.902	0.013	0.013	0.000	0.000	0.000	0.000
24	B	23	ASP	-1	-0.862	-0.926	18.074	-0.155	-0.155	0.000	0.000	0.000	0.000
25	B	24	LYS	1	0.927	0.969	19.968	0.083	0.083	0.000	0.000	0.000	0.000
26	B	25	GLU	-1	-0.901	-0.956	23.399	-0.100	-0.100	0.000	0.000	0.000	0.000
27	B	26	GLY	0	-0.024	0.001	23.328	0.003	0.003	0.000	0.000	0.000	0.000
28	B	27	LEU	0	-0.016	-0.005	21.422	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	28	LEU	0	-0.046	-0.022	15.635	-0.036	-0.036	0.000	0.000	0.000	0.000
30	B	29	PRO	0	-0.003	0.048	18.274	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	30	ASN	0	0.009	-0.030	17.637	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	31	VAL	0	-0.008	0.009	12.716	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	32	GLY	0	0.047	0.021	13.866	0.060	0.060	0.000	0.000	0.000	0.000
34	B	33	ARG	1	0.865	0.902	14.129	0.044	0.044	0.000	0.000	0.000	0.000
35	B	34	ASP	-1	-0.873	-0.933	12.377	0.179	0.179	0.000	0.000	0.000	0.000
36	B	35	GLU	-1	-0.913	-0.978	14.208	0.042	0.042	0.000	0.000	0.000	0.000
37	B	36	TYR	0	-0.036	-0.014	16.139	0.020	0.020	0.000	0.000	0.000	0.000
38	B	37	GLY	0	0.020	0.026	17.567	-0.015	-0.015	0.000	0.000	0.000	0.000
39	B	38	ASN	0	-0.053	-0.012	14.559	-0.043	-0.043	0.000	0.000	0.000	0.000
40	B	39	ARG	1	0.809	0.904	13.496	0.189	0.189	0.000	0.000	0.000	0.000
41	B	40	ARG	1	0.943	0.976	8.412	-0.140	-0.140	0.000	0.000	0.000	0.000
42	B	41	PHE	0	-0.025	-0.006	8.214	0.005	0.005	0.000	0.000	0.000	0.000
43	B	42	THR	0	0.008	-0.014	6.918	-0.278	-0.278	0.000	0.000	0.000	0.000
44	B	43	ASP	-1	-0.819	-0.933	5.847	-3.153	-3.153	0.000	0.000	0.000	0.000
45	B	44	LYS	1	0.955	0.977	8.227	0.717	0.717	0.000	0.000	0.000	0.000
46	B	45	ASP	-1	-0.817	-0.914	10.693	-0.534	-0.534	0.000	0.000	0.000	0.000
47	B	46	LEU	0	0.007	0.004	7.006	0.139	0.139	0.000	0.000	0.000	0.000
48	B	47	GLN	0	-0.004	0.001	10.971	0.162	0.162	0.000	0.000	0.000	0.000
49	B	48	TRP	0	0.018	0.015	13.696	0.069	0.069	0.000	0.000	0.000	0.000
50	B	49	LEU	0	0.012	-0.004	11.860	0.060	0.060	0.000	0.000	0.000	0.000
51	B	50	SER	0	-0.025	-0.017	13.488	0.056	0.056	0.000	0.000	0.000	0.000
52	B	51	LEU	0	-0.040	-0.002	16.020	0.051	0.051	0.000	0.000	0.000	0.000
53	B	52	LEU	0	0.029	0.007	18.255	0.041	0.041	0.000	0.000	0.000	0.000
54	B	53	GLN	0	0.061	0.068	17.719	0.047	0.047	0.000	0.000	0.000	0.000
55	B	54	CYS	0	-0.041	-0.005	20.009	0.036	0.036	0.000	0.000	0.000	0.000
56	B	55	LEU	0	0.046	0.024	21.798	0.026	0.026	0.000	0.000	0.000	0.000
57	B	56	LYS	1	0.981	1.002	23.080	0.182	0.182	0.000	0.000	0.000	0.000
58	B	57	ASN	0	-0.080	-0.053	21.132	0.027	0.027	0.000	0.000	0.000	0.000
59	B	58	THR	0	-0.047	-0.012	25.031	0.014	0.014	0.000	0.000	0.000	0.000
60	B	59	GLY	0	0.013	0.007	27.629	0.010	0.010	0.000	0.000	0.000	0.000
61	B	60	MET	0	-0.018	0.018	27.023	0.009	0.009	0.000	0.000	0.000	0.000
62	B	61	SER	0	-0.011	-0.015	28.402	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	62	LEU	0	0.059	0.011	26.014	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	63	LYS	1	0.970	0.973	28.310	0.089	0.089	0.000	0.000	0.000	0.000
65	B	64	ASP	-1	-0.843	-0.918	30.643	-0.114	-0.114	0.000	0.000	0.000	0.000
66	B	65	ILE	0	-0.044	-0.014	23.814	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	66	LYS	1	0.877	0.929	26.046	0.104	0.104	0.000	0.000	0.000	0.000
68	B	67	ARG	1	0.842	0.933	27.383	0.107	0.107	0.000	0.000	0.000	0.000
69	B	68	PHE	0	0.043	0.013	22.851	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	69	ALA	0	0.001	-0.013	23.800	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	70	GLU	-1	-0.897	-0.940	25.131	-0.114	-0.114	0.000	0.000	0.000	0.000
72	B	71	CYS	0	-0.031	-0.013	28.061	0.005	0.005	0.000	0.000	0.000	0.000
73	B	72	THR	0	-0.121	-0.076	23.989	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	73	ILE	0	-0.042	-0.019	24.320	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	74	ILE	0	-0.039	-0.010	26.561	0.007	0.007	0.000	0.000	0.000	0.000
76	B	75	GLY	0	0.030	0.028	28.907	0.006	0.006	0.000	0.000	0.000	0.000
77	B	76	ASP	-1	-0.917	-0.982	29.897	-0.143	-0.143	0.000	0.000	0.000	0.000
78	B	77	ASP	-1	-0.899	-0.933	32.008	-0.093	-0.093	0.000	0.000	0.000	0.000
79	B	78	THR	0	-0.028	-0.028	31.218	0.000	0.000	0.000	0.000	0.000	0.000
80	B	79	ILE	0	-0.041	-0.020	30.367	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	80	GLU	-1	-0.893	-0.952	32.592	-0.096	-0.096	0.000	0.000	0.000	0.000
82	B	81	GLU	-1	-0.801	-0.884	33.201	-0.112	-0.112	0.000	0.000	0.000	0.000
83	B	82	ARG	1	0.901	0.944	25.742	0.169	0.169	0.000	0.000	0.000	0.000
84	B	83	LEU	0	0.006	0.013	30.365	-0.009	-0.009	0.000	0.000	0.000	0.000
85	B	84	SER	0	0.024	0.009	32.195	0.000	0.000	0.000	0.000	0.000	0.000
86	B	85	LEU	0	-0.012	-0.002	28.501	0.001	0.001	0.000	0.000	0.000	0.000
87	B	86	PHE	0	-0.007	-0.013	24.657	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	87	GLU	-1	-0.922	-0.943	30.084	-0.106	-0.106	0.000	0.000	0.000	0.000
89	B	88	ASN	0	-0.066	-0.032	33.396	0.005	0.005	0.000	0.000	0.000	0.000
90	B	89	GLN	0	0.040	0.012	28.095	0.009	0.009	0.000	0.000	0.000	0.000
91	B	90	THR	0	-0.029	-0.037	29.222	0.002	0.002	0.000	0.000	0.000	0.000
92	B	91	LYS	1	0.972	0.986	31.154	0.095	0.095	0.000	0.000	0.000	0.000
93	B	92	ASN	0	0.000	0.002	32.610	0.002	0.002	0.000	0.000	0.000	0.000
94	B	93	VAL	0	0.071	0.029	28.314	0.004	0.004	0.000	0.000	0.000	0.000
95	B	94	LYS	1	0.912	0.954	31.500	0.129	0.129	0.000	0.000	0.000	0.000
96	B	95	CYS	0	-0.020	-0.007	33.735	0.007	0.007	0.000	0.000	0.000	0.000
97	B	96	GLN	0	-0.010	0.002	30.904	0.003	0.003	0.000	0.000	0.000	0.000
98	B	97	ILE	0	-0.025	-0.010	29.555	0.004	0.004	0.000	0.000	0.000	0.000
99	B	98	ALA	0	-0.035	-0.016	33.448	0.005	0.005	0.000	0.000	0.000	0.000
100	B	99	GLU	-1	-0.913	-0.966	37.156	-0.073	-0.073	0.000	0.000	0.000	0.000
101	B	100	LEU	0	-0.002	0.001	31.910	0.004	0.004	0.000	0.000	0.000	0.000
102	B	101	LYS	1	0.957	0.974	33.842	0.103	0.103	0.000	0.000	0.000	0.000
103	B	102	ARG	1	0.962	0.998	37.134	0.070	0.070	0.000	0.000	0.000	0.000
104	B	103	TYR	0	-0.033	-0.029	38.018	0.006	0.006	0.000	0.000	0.000	0.000
105	B	104	LEU	0	-0.018	-0.007	34.921	0.003	0.003	0.000	0.000	0.000	0.000
106	B	105	ASP	-1	-0.830	-0.901	38.322	-0.062	-0.062	0.000	0.000	0.000	0.000
107	B	106	LEU	0	-0.076	-0.031	41.596	0.004	0.004	0.000	0.000	0.000	0.000
108	B	107	LEU	0	-0.026	-0.024	37.511	0.004	0.004	0.000	0.000	0.000	0.000
109	B	108	GLU	-1	-0.872	-0.943	37.479	-0.065	-0.065	0.000	0.000	0.000	0.000
110	B	109	TYR	0	-0.002	0.011	41.241	0.004	0.004	0.000	0.000	0.000	0.000
111	B	110	LYS	1	0.937	0.958	43.998	0.042	0.042	0.000	0.000	0.000	0.000
112	B	111	LEU	0	0.006	0.010	38.907	0.003	0.003	0.000	0.000	0.000	0.000
113	B	112	ALA	0	0.043	0.019	43.003	0.003	0.003	0.000	0.000	0.000	0.000
114	B	113	PHE	0	-0.091	-0.042	45.186	0.003	0.003	0.000	0.000	0.000	0.000
115	B	114	TYR	0	0.015	-0.018	45.273	0.002	0.002	0.000	0.000	0.000	0.000
116	B	115	GLN	0	-0.005	0.006	40.783	0.002	0.002	0.000	0.000	0.000	0.000
117	B	116	LYS	1	0.967	0.992	45.990	0.032	0.032	0.000	0.000	0.000	0.000
118	B	117	ALA	0	-0.019	-0.008	49.538	0.002	0.002	0.000	0.000	0.000	0.000
119	B	118	LYS	1	0.973	0.994	43.664	0.030	0.030	0.000	0.000	0.000	0.000
120	B	119	ALA	0	-0.041	-0.018	49.244	0.002	0.002	0.000	0.000	0.000	0.000
121	B	120	LEU	0	-0.048	-0.037	50.651	0.001	0.001	0.000	0.000	0.000	0.000
122	B	121	GLY	0	0.041	0.030	52.777	0.001	0.001	0.000	0.000	0.000	0.000
123	B	122	SER	0	-0.039	-0.020	53.940	0.001	0.001	0.000	0.000	0.000	0.000
124	B	123	VAL	0	-0.002	0.003	52.175	-0.001	-0.001	0.000	0.000	0.000	0.000
125	B	124	LYS	1	0.949	0.987	54.797	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:GLY)