FMO DATABASE

FMODB ID: JQ7K9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1008338.714663
FMO2-HF: Nuclear repulsion	961442.351662
FMO2-HF: Total energy	-46896.363001
FMO2-MP2: Total energy	-47033.975624

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.
-11.125	-4.172	3.129	-4.202	-5.879	-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 : 0.022 / 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

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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	A	3	THR	0	0.047	0.023	2.889	-2.407	0.855	0.282	-1.822	-1.722	0.001
4	A	4	LEU	0	-0.057	-0.020	5.530	0.038	0.038	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.033	0.013	8.193	-0.093	-0.093	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.005	0.016	11.105	0.007	0.007	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.044	-0.052	14.114	-0.059	-0.059	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.050	-0.002	17.653	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.098	0.048	20.832	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.006	0.014	22.861	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.057	-0.006	22.887	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.083	0.025	24.020	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.009	-0.012	21.528	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.004	0.025	19.611	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.002	-0.009	19.793	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.911	0.951	22.022	0.034	0.034	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.042	0.029	17.128	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.974	0.997	17.070	0.048	0.048	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.933	0.961	18.143	0.065	0.065	0.000	0.000	0.000	0.000
20	A	20	TRP	0	0.051	0.023	14.748	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.046	0.023	12.551	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.050	-0.028	15.867	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.972	-0.979	17.899	-0.190	-0.190	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.053	-0.033	16.976	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.071	-0.021	15.289	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.011	0.017	10.137	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.899	-0.944	8.078	-0.694	-0.694	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.062	-0.048	8.666	-0.113	-0.113	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.006	-0.006	7.685	0.142	0.142	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.016	0.002	10.276	0.092	0.092	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.790	0.863	11.501	-0.665	-0.665	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.013	0.005	14.152	-0.051	-0.051	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.012	-0.002	16.672	0.025	0.025	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.086	-0.051	17.832	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.874	-0.944	20.436	0.183	0.183	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.862	-0.920	15.042	0.593	0.593	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.096	-0.022	16.426	0.025	0.025	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.006	-0.007	15.396	0.030	0.030	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.019	0.003	15.127	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.050	0.012	16.281	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.861	-0.925	13.071	0.358	0.358	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.806	-0.875	11.215	0.955	0.955	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.016	-0.017	12.636	-0.040	-0.040	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.837	0.895	15.274	-0.196	-0.196	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.014	0.022	9.648	-0.061	-0.061	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.008	-0.034	9.503	-0.176	-0.176	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.039	-0.020	12.129	-0.078	-0.078	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.046	0.022	13.285	-0.036	-0.036	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.024	0.017	7.512	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.076	-0.027	12.243	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.001	0.004	15.010	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.067	-0.023	17.733	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.026	0.007	19.945	0.011	0.011	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.136	0.068	20.511	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.991	0.998	21.873	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.873	0.926	21.446	0.016	0.016	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.031	0.022	15.157	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.036	0.030	20.635	0.018	0.018	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.085	-0.041	23.520	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.006	-0.004	24.723	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.072	-0.050	27.114	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.024	0.009	28.253	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.046	0.016	29.053	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.084	0.048	29.627	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.044	0.021	28.073	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.888	0.957	30.782	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.897	-0.949	34.067	0.047	0.047	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.015	-0.017	32.108	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.933	0.972	35.275	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.026	0.006	29.040	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.018	-0.003	31.832	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.007	-0.001	33.019	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.906	0.957	33.216	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.017	0.017	27.504	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.059	-0.032	30.273	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.062	-0.035	32.031	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.027	0.005	28.673	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.016	-0.021	27.806	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.895	-0.969	22.711	0.036	0.036	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.791	-0.879	22.704	0.130	0.130	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.809	-0.877	24.352	0.074	0.074	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.104	-0.060	24.659	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.031	-0.001	18.860	0.011	0.011	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.035	0.029	21.879	0.024	0.024	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.026	-0.011	23.956	0.007	0.007	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.060	-0.024	19.786	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.049	0.024	20.307	0.012	0.012	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.091	-0.032	21.480	0.008	0.008	0.000	0.000	0.000	0.000
89	A	89	ASN	0	0.028	-0.008	24.080	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.154	0.071	20.920	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.899	0.944	21.752	-0.120	-0.120	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.004	-0.001	23.907	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.058	0.048	17.828	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.863	0.929	19.925	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.894	0.966	18.192	-0.074	-0.074	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.046	-0.042	15.816	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.013	0.006	13.382	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.006	0.007	9.151	0.023	0.023	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.013	-0.006	6.727	-0.049	-0.049	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.010	-0.013	4.213	-0.140	-0.030	-0.001	-0.020	-0.089	0.000
101	A	101	GLU	-1	-0.876	-0.952	2.272	-9.543	-6.142	2.848	-2.324	-3.924	-0.025
102	A	102	ARG	1	0.919	0.974	4.302	0.735	0.915	0.000	-0.036	-0.144	0.000
103	A	103	PHE	0	0.026	-0.005	7.252	0.096	0.096	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.023	0.022	8.665	0.116	0.116	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.040	-0.003	11.187	-0.052	-0.052	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.035	0.007	13.746	0.052	0.052	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.060	-0.031	16.654	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.019	-0.023	17.749	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.767	0.872	19.162	0.114	0.114	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.006	-0.001	19.614	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.741	-0.866	19.396	-0.141	-0.141	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.845	-0.916	17.548	-0.145	-0.145	0.000	0.000	0.000	0.000
113	A	113	TRP	0	-0.076	-0.058	14.760	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.819	-0.901	14.689	-0.319	-0.319	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.932	0.977	12.366	0.216	0.216	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.098	-0.032	9.433	-0.109	-0.109	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.908	0.962	8.140	0.837	0.837	0.000	0.000	0.000	0.000

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