FMO DATABASE

FMODB ID: 49K2N

Calculation Name: 5GXB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GXB

Chain ID: B

ChEMBL ID:

UniProt ID: P02920

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	-1148179.453522
FMO2-HF: Nuclear repulsion	1096182.861392
FMO2-HF: Total energy	-51996.592129
FMO2-MP2: Total energy	-52147.564839

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:MET)

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

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.
1.933	-108.36	205.668	-56.222	-39.152	-0.023

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.070

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	2	VAL	0	-0.002	0.006	3.669	-2.411	0.124	-0.009	-1.114	-1.412	0.002
4	B	3	GLN	0	0.053	0.015	5.559	0.175	0.175	0.000	0.000	0.000	0.000
5	B	4	LEU	0	-0.070	-0.042	8.192	-0.059	-0.059	0.000	0.000	0.000	0.000
6	B	5	VAL	0	0.022	0.011	10.935	0.120	0.120	0.000	0.000	0.000	0.000
7	B	6	GLU	-1	-0.827	-0.920	14.543	-0.117	-0.117	0.000	0.000	0.000	0.000
8	B	7	SER	0	0.015	0.007	17.320	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	8	GLY	0	0.003	-0.005	20.917	0.005	0.005	0.000	0.000	0.000	0.000
10	B	9	GLY	0	-0.006	0.005	23.950	0.006	0.006	0.000	0.000	0.000	0.000
11	B	10	ARG	1	0.891	0.931	25.650	0.039	0.039	0.000	0.000	0.000	0.000
12	B	11	LEU	0	-0.001	0.016	28.936	0.010	0.010	0.000	0.000	0.000	0.000
13	B	12	VAL	0	-0.026	0.003	30.856	-0.011	-0.011	0.000	0.000	0.000	0.000
14	B	13	GLN	0	0.034	-0.001	33.419	0.008	0.008	0.000	0.000	0.000	0.000
15	B	14	ALA	0	0.021	0.011	35.998	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	15	GLY	0	-0.014	-0.004	35.909	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	16	ASP	-1	-0.828	-0.899	34.885	-0.048	-0.048	0.000	0.000	0.000	0.000
18	B	17	SER	0	-0.064	-0.056	31.894	0.005	0.005	0.000	0.000	0.000	0.000
19	B	18	LEU	0	-0.045	-0.029	27.147	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	19	ARG	1	0.903	0.969	25.531	0.149	0.149	0.000	0.000	0.000	0.000
21	B	20	LEU	0	-0.005	0.022	21.079	-0.010	-0.010	0.000	0.000	0.000	0.000
22	B	21	SER	0	-0.013	-0.008	20.126	-0.011	-0.011	0.000	0.000	0.000	0.000
23	B	22	CYS	0	-0.032	-0.006	13.617	0.000	0.000	0.000	0.000	0.000	0.000
24	B	23	ALA	0	0.048	0.024	15.266	-0.043	-0.043	0.000	0.000	0.000	0.000
25	B	24	ALA	0	-0.036	-0.022	10.256	-0.017	-0.017	0.000	0.000	0.000	0.000
26	B	25	SER	0	0.009	-0.002	10.865	-0.094	-0.094	0.000	0.000	0.000	0.000
27	B	26	GLY	0	0.004	0.009	7.942	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	27	ARG	1	0.959	0.982	7.933	1.262	1.262	0.000	0.000	0.000	0.000
29	B	28	THR	0	-0.016	-0.024	8.807	0.414	0.414	0.000	0.000	0.000	0.000
30	B	29	PHE	0	-0.013	-0.002	7.268	0.013	0.013	0.000	0.000	0.000	0.000
31	B	30	THR	0	0.017	0.029	4.840	0.085	0.085	0.000	0.000	0.000	0.000
32	B	31	THR	0	0.113	0.056	6.828	0.516	0.516	0.000	0.000	0.000	0.000
33	B	32	TYR	0	-0.055	-0.011	7.584	0.012	0.012	0.000	0.000	0.000	0.000
34	B	33	LEU	0	-0.094	-0.062	10.441	0.112	0.112	0.000	0.000	0.000	0.000
35	B	34	MET	0	0.022	0.025	11.193	-0.081	-0.081	0.000	0.000	0.000	0.000
36	B	35	GLY	0	0.030	0.014	13.504	0.058	0.058	0.000	0.000	0.000	0.000
37	B	36	TRP	0	-0.015	-0.002	14.964	-0.024	-0.024	0.000	0.000	0.000	0.000
38	B	37	PHE	0	0.020	-0.001	15.394	0.057	0.057	0.000	0.000	0.000	0.000
39	B	38	ARG	1	0.845	0.918	18.263	-0.156	-0.156	0.000	0.000	0.000	0.000
40	B	39	GLN	0	0.030	0.016	19.798	0.058	0.058	0.000	0.000	0.000	0.000
41	B	40	ALA	0	0.025	0.008	22.312	-0.026	-0.026	0.000	0.000	0.000	0.000
42	B	41	PRO	0	-0.008	0.009	25.068	0.019	0.019	0.000	0.000	0.000	0.000
43	B	42	GLY	0	0.034	0.006	27.602	0.002	0.002	0.000	0.000	0.000	0.000
44	B	43	LYS	1	0.870	0.954	27.035	-0.179	-0.179	0.000	0.000	0.000	0.000
45	B	44	GLU	-1	-0.880	-0.947	22.266	0.288	0.288	0.000	0.000	0.000	0.000
46	B	45	ARG	1	0.925	0.981	17.017	-0.559	-0.559	0.000	0.000	0.000	0.000
47	B	46	GLU	-1	-0.814	-0.892	20.628	0.183	0.183	0.000	0.000	0.000	0.000
48	B	47	PHE	0	-0.011	-0.020	17.702	-0.013	-0.013	0.000	0.000	0.000	0.000
49	B	48	VAL	0	0.010	0.010	19.901	-0.022	-0.022	0.000	0.000	0.000	0.000
50	B	49	ALA	0	-0.017	-0.020	19.937	-0.016	-0.016	0.000	0.000	0.000	0.000
51	B	50	ALA	0	0.031	0.014	16.760	0.007	0.007	0.000	0.000	0.000	0.000
52	B	51	ILE	0	-0.026	-0.016	16.571	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	52	ARG	1	0.962	0.998	14.131	0.091	0.091	0.000	0.000	0.000	0.000
54	B	53	TRP	0	-0.006	-0.024	11.745	0.087	0.087	0.000	0.000	0.000	0.000
55	B	54	SER	0	0.025	0.011	16.501	0.035	0.035	0.000	0.000	0.000	0.000
56	B	55	GLY	0	0.031	0.025	18.528	0.036	0.036	0.000	0.000	0.000	0.000
57	B	56	GLY	0	-0.021	-0.009	20.092	0.019	0.019	0.000	0.000	0.000	0.000
58	B	57	SER	0	0.000	0.000	19.878	0.023	0.023	0.000	0.000	0.000	0.000
59	B	58	THR	0	0.015	0.003	20.231	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	59	TYR	0	-0.001	-0.023	18.045	0.030	0.030	0.000	0.000	0.000	0.000
61	B	60	TYR	0	0.009	-0.014	21.748	-0.013	-0.013	0.000	0.000	0.000	0.000
62	B	61	ALA	0	0.013	0.037	23.475	0.003	0.003	0.000	0.000	0.000	0.000
63	B	62	ASP	-1	-0.889	-0.964	24.899	0.106	0.106	0.000	0.000	0.000	0.000
64	B	63	SER	0	0.007	0.010	27.884	-0.016	-0.016	0.000	0.000	0.000	0.000
65	B	64	VAL	0	-0.033	-0.009	26.302	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	65	LYS	1	1.060	1.023	28.260	-0.087	-0.087	0.000	0.000	0.000	0.000
67	B	66	GLY	0	-0.034	0.010	29.543	0.000	0.000	0.000	0.000	0.000	0.000
68	B	67	ARG	1	0.788	0.876	30.611	-0.046	-0.046	0.000	0.000	0.000	0.000
69	B	68	PHE	0	-0.009	-0.004	24.894	-0.010	-0.010	0.000	0.000	0.000	0.000
70	B	69	THR	0	-0.023	-0.010	26.172	0.001	0.001	0.000	0.000	0.000	0.000
71	B	70	ILE	0	-0.012	0.023	18.171	-0.012	-0.012	0.000	0.000	0.000	0.000
72	B	71	SER	0	-0.021	-0.015	21.825	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	72	ARG	1	0.813	0.894	18.355	0.290	0.290	0.000	0.000	0.000	0.000
74	B	73	ASP	-1	-0.851	-0.926	19.294	-0.358	-0.358	0.000	0.000	0.000	0.000
75	B	74	ASN	0	-0.006	-0.020	17.056	-0.025	-0.025	0.000	0.000	0.000	0.000
76	B	75	ALA	0	0.033	0.012	17.758	-0.059	-0.059	0.000	0.000	0.000	0.000
77	B	76	LYS	1	0.943	0.976	18.353	0.564	0.564	0.000	0.000	0.000	0.000
78	B	77	ASN	0	0.000	0.068	13.689	-0.042	-0.042	0.000	0.000	0.000	0.000
79	B	78	THR	0	0.023	-0.040	15.558	-0.026	-0.026	0.000	0.000	0.000	0.000
80	B	79	VAL	0	-0.019	0.002	15.116	0.024	0.024	0.000	0.000	0.000	0.000
81	B	80	TYR	0	-0.028	-0.023	17.942	0.012	0.012	0.000	0.000	0.000	0.000
82	B	81	LEU	0	0.010	-0.001	21.079	0.016	0.016	0.000	0.000	0.000	0.000
83	B	82	GLN	0	-0.010	-0.029	22.899	-0.017	-0.017	0.000	0.000	0.000	0.000
84	B	83	MET	0	0.002	0.008	25.551	0.018	0.018	0.000	0.000	0.000	0.000
85	B	84	ASN	0	0.076	0.035	28.217	-0.010	-0.010	0.000	0.000	0.000	0.000
86	B	85	SER	0	-0.017	-0.007	31.985	0.010	0.010	0.000	0.000	0.000	0.000
87	B	86	LEU	0	0.014	0.015	29.000	0.010	0.010	0.000	0.000	0.000	0.000
88	B	87	LYS	1	0.953	0.970	32.568	-0.040	-0.040	0.000	0.000	0.000	0.000
89	B	88	LEU	0	0.078	0.060	33.723	-0.005	-0.005	0.000	0.000	0.000	0.000
90	B	89	GLU	-1	-0.864	-0.945	31.526	0.073	0.073	0.000	0.000	0.000	0.000
91	B	90	ASP	-1	-0.929	-0.942	28.927	0.062	0.062	0.000	0.000	0.000	0.000
92	B	91	THR	0	0.025	0.020	27.847	-0.013	-0.013	0.000	0.000	0.000	0.000
93	B	92	ALA	0	-0.017	-0.022	24.210	0.018	0.018	0.000	0.000	0.000	0.000
94	B	93	VAL	0	-0.021	0.012	19.568	-0.031	-0.031	0.000	0.000	0.000	0.000
95	B	94	TYR	0	-0.045	-0.029	20.175	0.032	0.032	0.000	0.000	0.000	0.000
96	B	95	TYR	0	0.002	0.004	14.669	-0.018	-0.018	0.000	0.000	0.000	0.000
97	B	97	ALA	0	0.031	0.005	10.445	0.039	0.039	0.000	0.000	0.000	0.000
98	B	98	ALA	0	-0.004	-0.018	7.911	-0.105	-0.105	0.000	0.000	0.000	0.000
99	B	99	ALA	0	-0.067	-0.002	6.918	0.195	0.195	0.000	0.000	0.000	0.000
100	B	100	ALA	0	0.007	-0.044	3.802	-1.038	-0.871	0.003	-0.039	-0.131	0.000
101	B	101	ARG	1	0.915	0.998	1.795	12.544	-104.046	179.925	-42.232	-21.103	-0.015
102	B	102	PRO	0	0.007	0.014	4.854	-0.079	-0.039	-0.001	-0.012	-0.026	0.000
103	B	103	SER	0	0.025	-0.030	6.696	0.991	0.991	0.000	0.000	0.000	0.000
104	B	104	TYR	0	-0.024	0.009	9.130	-0.332	-0.332	0.000	0.000	0.000	0.000
105	B	105	SER	0	0.027	0.005	12.903	0.011	0.011	0.000	0.000	0.000	0.000
106	B	106	GLY	0	-0.017	0.003	15.961	-0.066	-0.066	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.952	-0.969	13.826	0.822	0.822	0.000	0.000	0.000	0.000
108	B	108	TYR	0	0.049	0.031	12.449	-0.023	-0.023	0.000	0.000	0.000	0.000
109	B	109	GLY	0	0.038	0.019	14.123	-0.005	-0.005	0.000	0.000	0.000	0.000
110	B	110	TYR	0	-0.040	-0.017	14.860	0.039	0.039	0.000	0.000	0.000	0.000
111	B	111	THR	0	0.041	0.005	16.442	-0.052	-0.052	0.000	0.000	0.000	0.000
112	B	112	GLU	-1	-0.925	-0.953	14.966	0.521	0.521	0.000	0.000	0.000	0.000
113	B	113	ALA	0	0.018	0.001	13.994	0.058	0.058	0.000	0.000	0.000	0.000
114	B	114	LEU	0	-0.039	-0.024	11.491	0.042	0.042	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.850	0.942	10.069	-0.503	-0.503	0.000	0.000	0.000	0.000
116	B	116	TYR	0	-0.057	-0.032	8.394	0.074	0.074	0.000	0.000	0.000	0.000
117	B	117	ASP	-1	-0.770	-0.883	3.184	1.407	2.200	0.054	-0.248	-0.598	-0.001
118	B	118	TYR	0	-0.107	0.018	1.846	-12.770	-10.008	25.696	-12.577	-15.882	-0.009
119	B	119	TRP	0	0.014	0.001	6.249	-0.209	-0.209	0.000	0.000	0.000	0.000
120	B	120	GLY	0	0.006	0.013	9.531	-0.122	-0.122	0.000	0.000	0.000	0.000
121	B	121	GLN	0	-0.036	-0.012	12.127	0.060	0.060	0.000	0.000	0.000	0.000
122	B	122	GLY	0	0.059	0.019	14.838	0.074	0.074	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.064	-0.033	17.897	-0.032	-0.032	0.000	0.000	0.000	0.000
124	B	124	GLN	0	0.035	0.017	21.317	0.017	0.017	0.000	0.000	0.000	0.000
125	B	125	VAL	0	-0.001	0.006	24.251	-0.021	-0.021	0.000	0.000	0.000	0.000
126	B	126	THR	0	-0.022	-0.019	26.730	0.021	0.021	0.000	0.000	0.000	0.000
127	B	127	VAL	0	-0.031	-0.028	30.265	-0.012	-0.012	0.000	0.000	0.000	0.000
128	B	128	SER	0	-0.146	-0.144	32.834	0.010	0.010	0.000	0.000	0.000	0.000
129	B	129	SER	0	0.056	-0.009	36.368	0.000	0.000	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.058	0.050	38.910	-0.003	-0.003	0.000	0.000	0.000	0.000
131	B	131	HIS	0	0.056	0.097	39.720	-0.004	-0.004	0.000	0.000	0.000	0.000

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