FMO DATABASE

FMODB ID: 3J8GL

Calculation Name: 3GKX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKX

Chain ID: A

ChEMBL ID:

UniProt ID: Q5L9Z8

Base Structure: X-ray

Registration Date: 2023-09-23

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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1010510.911689
FMO2-HF: Nuclear repulsion	963614.161887
FMO2-HF: Total energy	-46896.749803
FMO2-MP2: Total energy	-47034.336484

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-12.752	-6.043	4.494	-4.566	-6.639	-0.033

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.017

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	A	3	THR	0	0.043	0.027	3.630	-1.022	1.441	0.001	-1.258	-1.206	0.005
4	A	4	LEU	0	-0.046	-0.013	5.820	0.086	0.086	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.021	0.000	8.430	-0.177	-0.177	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.005	0.019	11.296	0.014	0.014	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.018	-0.039	14.271	-0.079	-0.079	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.066	0.009	17.770	0.026	0.026	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.068	0.034	21.167	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.033	0.029	23.219	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.060	-0.009	23.122	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.090	0.034	23.980	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.010	-0.020	21.677	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.008	0.018	19.831	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.004	-0.010	20.047	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.924	0.961	22.019	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.032	0.027	17.305	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.977	0.995	17.304	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.941	0.973	18.386	0.043	0.043	0.000	0.000	0.000	0.000
20	A	20	TRP	0	0.045	0.016	14.755	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.017	0.011	12.665	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.017	-0.002	15.789	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.972	-0.978	17.816	-0.143	-0.143	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.054	-0.036	17.051	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.071	-0.034	15.470	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.016	0.000	10.541	-0.077	-0.077	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.877	-0.939	8.110	-0.486	-0.486	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.068	-0.058	8.984	-0.050	-0.050	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.006	0.008	7.966	0.165	0.165	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.017	0.002	10.326	0.084	0.084	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.779	0.854	12.114	-0.700	-0.700	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.016	0.004	14.442	-0.058	-0.058	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.020	-0.014	16.760	0.015	0.015	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.081	-0.044	18.136	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.882	-0.954	20.986	0.207	0.207	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.826	-0.885	15.594	0.622	0.622	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.068	-0.017	16.851	0.018	0.018	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.020	-0.016	15.236	0.031	0.031	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.017	-0.005	14.664	-0.047	-0.047	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.043	0.011	16.190	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.850	-0.909	13.123	0.303	0.303	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.814	-0.892	10.783	0.943	0.943	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.012	-0.008	12.420	-0.053	-0.053	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.841	0.890	15.018	-0.158	-0.158	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.007	0.023	9.461	-0.066	-0.066	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.013	-0.041	9.517	-0.165	-0.165	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.004	0.000	12.041	-0.066	-0.066	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.053	0.029	13.291	-0.034	-0.034	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.006	0.014	7.451	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.065	-0.040	12.177	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.006	0.007	15.025	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.084	-0.033	17.955	0.009	0.009	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.038	0.023	19.703	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.082	0.037	20.275	0.010	0.010	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.972	0.988	21.893	0.009	0.009	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.879	0.936	21.390	0.026	0.026	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.047	0.025	15.271	0.002	0.002	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.043	0.032	20.848	0.021	0.021	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.044	-0.003	23.932	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	60	THR	0	0.003	-0.001	25.157	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.071	-0.049	26.875	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.011	0.001	28.490	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.039	0.012	29.433	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.091	0.043	30.031	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.020	0.014	28.388	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.884	0.944	31.207	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.900	-0.950	34.669	0.052	0.052	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.017	0.009	32.408	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.907	0.953	35.407	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.050	0.033	28.999	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.007	0.001	31.847	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.052	-0.027	32.810	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.911	0.958	33.234	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.027	0.016	27.305	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.090	-0.052	30.074	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.050	-0.026	32.202	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.002	0.017	28.526	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.016	-0.019	27.432	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.864	-0.956	22.558	0.005	0.005	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.789	-0.866	22.333	0.097	0.097	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.795	-0.871	24.025	0.058	0.058	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.080	-0.052	24.616	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.035	0.003	18.376	0.012	0.012	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.001	0.009	21.907	0.023	0.023	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.016	-0.004	23.885	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.057	-0.021	20.010	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.044	0.017	20.092	0.014	0.014	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.075	-0.034	21.324	0.013	0.013	0.000	0.000	0.000	0.000
89	A	89	ASN	0	0.038	0.001	24.004	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.122	0.058	21.096	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.911	0.954	21.920	-0.141	-0.141	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.025	-0.006	24.298	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.046	0.036	18.060	-0.018	-0.018	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.842	0.918	20.447	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.867	0.947	18.566	-0.102	-0.102	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.029	-0.040	16.270	-0.022	-0.022	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.034	-0.008	13.789	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.000	0.006	9.433	0.026	0.026	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.006	0.003	6.908	-0.079	-0.079	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.011	-0.010	4.205	-0.120	-0.008	-0.001	-0.021	-0.090	0.000
101	A	101	GLU	-1	-0.861	-0.945	2.252	-12.684	-8.745	4.494	-3.245	-5.189	-0.038
102	A	102	ARG	1	0.934	0.975	4.279	0.813	1.008	0.000	-0.042	-0.154	0.000
103	A	103	PHE	0	0.007	0.000	7.268	0.111	0.111	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.004	0.011	8.554	0.141	0.141	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.047	-0.012	11.195	-0.069	-0.069	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.024	0.003	13.940	0.059	0.059	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.031	-0.011	17.036	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.033	-0.022	18.116	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.770	0.859	18.989	0.108	0.108	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.003	0.012	19.231	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.732	-0.865	19.155	-0.136	-0.136	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.861	-0.917	17.602	-0.142	-0.142	0.000	0.000	0.000	0.000
113	A	113	TRP	0	-0.012	-0.024	14.932	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.810	-0.895	14.470	-0.307	-0.307	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.852	0.930	12.260	0.215	0.215	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.033	-0.010	9.298	-0.122	-0.122	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.864	0.941	8.136	0.806	0.806	0.000	0.000	0.000	0.000

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