FMO DATABASE

FMODB ID: NNJ6Q

Calculation Name: 3GKX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1006760.960748
FMO2-HF: Nuclear repulsion	959865.475563
FMO2-HF: Total energy	-46895.485185
FMO2-MP2: Total energy	-47033.12152

3D Structure Molmil

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.
-10.973	-3.491	2.618	-4.306	-5.794	-0.024

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 : 0.016 / q_NPA : 0.011

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	0.055	0.021	2.822	-2.211	1.436	0.372	-2.022	-1.997	0.000
4	A	4	LEU	0	-0.054	-0.020	5.437	-0.076	-0.076	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.035	0.014	8.188	-0.051	-0.051	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.016	0.017	11.165	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.040	-0.053	14.150	-0.046	-0.046	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.033	-0.016	17.659	0.012	0.012	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.096	0.045	20.739	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.038	0.025	22.808	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.088	-0.009	22.896	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.093	0.023	23.986	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.011	-0.007	21.407	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.004	0.024	19.599	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.004	-0.004	19.729	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.907	0.949	21.919	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.043	0.039	17.034	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.991	0.997	16.950	0.052	0.052	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.926	0.958	18.024	0.042	0.042	0.000	0.000	0.000	0.000
20	A	20	TRP	0	0.054	0.026	14.714	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.037	0.025	12.179	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.058	-0.027	15.659	-0.042	-0.042	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.973	-0.981	17.725	-0.179	-0.179	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.054	-0.036	16.696	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.035	-0.007	14.875	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.007	0.007	10.080	-0.074	-0.074	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.922	-0.960	7.952	-0.903	-0.903	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.046	-0.037	8.469	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.011	-0.016	7.318	0.112	0.112	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.012	0.014	10.110	0.136	0.136	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.774	0.842	11.629	-0.661	-0.661	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.017	0.003	14.123	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.012	0.000	16.748	0.024	0.024	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.080	-0.048	17.901	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.890	-0.950	20.384	0.169	0.169	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.903	-0.945	15.366	0.519	0.519	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.047	0.005	16.522	0.051	0.051	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.001	-0.012	15.625	0.031	0.031	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.068	0.045	14.720	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.043	0.006	16.504	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.923	-0.971	13.228	0.379	0.379	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.785	-0.845	11.272	0.934	0.934	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.017	-0.016	12.927	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.964	0.977	15.564	-0.260	-0.260	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.022	0.026	10.058	-0.051	-0.051	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.002	-0.029	9.441	-0.146	-0.146	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.029	-0.015	12.726	-0.069	-0.069	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.040	0.023	13.722	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.038	0.022	8.014	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.086	-0.034	12.660	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.000	0.004	15.204	-0.036	-0.036	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.058	-0.022	18.092	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.034	0.010	20.421	0.011	0.011	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.141	0.076	21.032	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.971	0.985	22.442	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.868	0.922	21.784	-0.054	-0.054	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.049	0.027	15.390	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.030	0.029	20.844	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.079	-0.046	23.620	-0.026	-0.026	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.020	-0.012	24.868	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.071	-0.041	27.386	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.008	0.002	28.381	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.047	0.012	29.173	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.086	0.049	29.806	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.036	0.017	28.426	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.916	0.967	30.954	-0.055	-0.055	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.932	-0.965	34.224	0.057	0.057	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.024	-0.015	32.596	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.954	0.973	35.469	-0.048	-0.048	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.017	0.003	29.292	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.058	-0.015	32.052	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.042	0.013	33.226	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.937	0.982	33.438	-0.076	-0.076	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.010	0.010	27.817	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.041	-0.026	30.881	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.058	-0.027	32.612	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.026	0.005	28.939	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.033	0.016	28.363	0.002	0.002	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.891	-0.969	22.991	0.109	0.109	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.931	-0.962	23.489	0.152	0.152	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.862	-0.933	24.661	0.103	0.103	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.088	-0.058	25.213	0.011	0.011	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.021	-0.001	19.282	0.011	0.011	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.028	0.027	22.075	0.022	0.022	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.029	-0.015	24.172	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.042	-0.046	20.843	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.035	0.021	20.480	0.011	0.011	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.091	-0.016	21.692	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ASN	0	0.036	0.005	24.248	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.137	0.054	21.063	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.856	0.921	21.884	-0.119	-0.119	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.027	-0.009	24.127	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.052	0.053	17.929	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.893	0.941	19.974	-0.088	-0.088	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.968	0.993	18.277	-0.083	-0.083	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.047	-0.044	15.856	-0.022	-0.022	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.018	0.005	13.375	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.016	0.012	9.063	0.006	0.006	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.010	-0.002	6.768	-0.028	-0.028	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.010	-0.013	4.378	-0.146	-0.044	-0.001	-0.016	-0.085	0.000
101	A	101	GLU	-1	-0.891	-0.962	2.294	-8.251	-4.661	2.248	-2.247	-3.590	-0.024
102	A	102	ARG	1	0.932	0.983	4.489	0.118	0.261	-0.001	-0.021	-0.122	0.000
103	A	103	PHE	0	0.016	-0.009	7.316	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.020	0.022	8.868	0.153	0.153	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.034	0.000	11.393	-0.076	-0.076	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.033	0.009	13.884	0.044	0.044	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.059	-0.038	16.796	-0.027	-0.027	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.035	-0.032	17.745	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.895	0.969	19.206	0.019	0.019	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.002	0.000	19.646	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.811	-0.912	19.410	-0.073	-0.073	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.878	-0.956	17.628	-0.049	-0.049	0.000	0.000	0.000	0.000
113	A	113	TRP	0	-0.085	-0.062	14.509	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.814	-0.896	14.686	-0.222	-0.222	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.937	0.977	12.336	0.076	0.076	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.107	-0.033	9.046	-0.059	-0.059	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.902	0.957	8.260	0.506	0.506	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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