FMO DATABASE

FMODB ID: GNK51

Calculation Name: 4QYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QYB

Chain ID: A

ChEMBL ID:

UniProt ID: B4EGA9

Base Structure: X-ray

Registration Date: 2023-06-20

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-876069.310566
FMO2-HF: Nuclear repulsion	831494.876586
FMO2-HF: Total energy	-44574.43398
FMO2-MP2: Total energy	-44703.877908

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:HIS)

Summations of interaction energy for fragment #1(A:-1:HIS)

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.
-2.536	-0.413	0.005	-0.973	-1.157	0.001

Interaction energy analysis for fragmet #1(A:-1:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.025

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	1	MET	0	-0.005	-0.003	3.405	-0.429	1.319	0.006	-0.933	-0.822	0.001
4	A	2	GLN	0	0.052	0.029	6.034	0.047	0.047	0.000	0.000	0.000	0.000
5	A	3	VAL	0	0.041	-0.003	8.945	-0.069	-0.069	0.000	0.000	0.000	0.000
6	A	4	GLN	0	-0.079	-0.040	12.176	-0.044	-0.044	0.000	0.000	0.000	0.000
7	A	5	ASP	-1	-0.901	-0.953	9.996	0.262	0.262	0.000	0.000	0.000	0.000
8	A	6	LEU	0	-0.063	-0.012	10.891	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	7	THR	0	-0.011	-0.020	12.904	0.066	0.066	0.000	0.000	0.000	0.000
10	A	8	GLY	0	0.016	0.013	14.989	-0.043	-0.043	0.000	0.000	0.000	0.000
11	A	9	ALA	0	0.089	0.042	16.791	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	10	ALA	0	0.047	0.029	12.238	-0.037	-0.037	0.000	0.000	0.000	0.000
13	A	11	LEU	0	-0.034	-0.012	14.337	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	12	ASP	-1	-0.826	-0.899	15.964	-0.249	-0.249	0.000	0.000	0.000	0.000
15	A	13	TYR	0	0.042	0.012	13.251	0.031	0.031	0.000	0.000	0.000	0.000
16	A	14	TRP	0	0.025	0.012	10.301	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	15	VAL	0	-0.004	0.002	16.376	0.008	0.008	0.000	0.000	0.000	0.000
18	A	16	ALA	0	0.013	0.008	20.020	0.012	0.012	0.000	0.000	0.000	0.000
19	A	17	THR	0	-0.023	-0.019	15.577	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	18	ALA	0	-0.068	-0.032	18.669	0.002	0.002	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.907	-0.943	19.765	-0.232	-0.232	0.000	0.000	0.000	0.000
22	A	20	GLY	0	-0.031	-0.003	21.744	0.024	0.024	0.000	0.000	0.000	0.000
23	A	21	HIS	0	-0.013	0.010	22.390	0.011	0.011	0.000	0.000	0.000	0.000
24	A	22	GLU	-1	-0.869	-0.949	21.906	-0.375	-0.375	0.000	0.000	0.000	0.000
25	A	23	VAL	0	-0.099	-0.064	19.786	0.010	0.010	0.000	0.000	0.000	0.000
26	A	24	PRO	0	0.052	0.045	17.544	0.035	0.035	0.000	0.000	0.000	0.000
27	A	25	ARG	1	0.901	0.945	17.360	0.314	0.314	0.000	0.000	0.000	0.000
28	A	26	ALA	0	0.018	-0.013	14.973	0.039	0.039	0.000	0.000	0.000	0.000
29	A	27	ASP	-1	-0.891	-0.919	15.976	-0.322	-0.322	0.000	0.000	0.000	0.000
30	A	28	ALA	0	-0.006	-0.020	17.951	0.007	0.007	0.000	0.000	0.000	0.000
31	A	29	SER	0	-0.064	-0.036	18.751	0.011	0.011	0.000	0.000	0.000	0.000
32	A	30	GLY	0	0.033	0.013	20.580	0.019	0.019	0.000	0.000	0.000	0.000
33	A	31	CYS	0	-0.061	-0.003	19.379	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	32	THR	0	-0.056	-0.026	20.833	0.029	0.029	0.000	0.000	0.000	0.000
35	A	33	SER	0	0.019	-0.014	21.996	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	34	ILE	0	-0.010	0.010	23.998	0.032	0.032	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.854	0.927	26.145	0.194	0.194	0.000	0.000	0.000	0.000
38	A	36	GLU	-1	-0.918	-0.971	28.226	-0.175	-0.175	0.000	0.000	0.000	0.000
39	A	37	PRO	0	0.009	0.023	30.010	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	38	GLY	0	0.005	0.003	31.073	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	39	GLY	0	-0.007	-0.009	31.118	0.015	0.015	0.000	0.000	0.000	0.000
42	A	40	VAL	0	-0.028	-0.017	30.504	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	41	PRO	0	0.002	-0.002	25.868	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	42	THR	0	-0.063	-0.031	27.335	0.024	0.024	0.000	0.000	0.000	0.000
45	A	43	PRO	0	0.023	-0.003	25.708	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	44	PHE	0	0.027	0.031	22.789	0.015	0.015	0.000	0.000	0.000	0.000
47	A	45	ALA	0	0.016	0.016	22.959	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	46	PRO	0	0.053	0.027	22.142	0.029	0.029	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.038	-0.058	20.374	0.028	0.028	0.000	0.000	0.000	0.000
50	A	48	SER	0	-0.052	-0.040	22.368	0.025	0.025	0.000	0.000	0.000	0.000
51	A	49	SER	0	-0.004	0.004	24.703	0.021	0.021	0.000	0.000	0.000	0.000
52	A	50	TRP	0	0.055	0.005	27.806	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	51	ALA	0	-0.034	-0.008	30.245	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	52	ASP	-1	-0.799	-0.900	27.152	-0.176	-0.176	0.000	0.000	0.000	0.000
55	A	53	GLY	0	0.026	-0.001	26.824	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	54	GLY	0	-0.031	-0.024	27.509	0.001	0.001	0.000	0.000	0.000	0.000
57	A	55	PRO	0	-0.005	-0.010	30.527	0.004	0.004	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.003	0.013	25.601	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	57	VAL	0	-0.061	-0.037	27.702	0.000	0.000	0.000	0.000	0.000	0.000
60	A	58	GLU	-1	-0.964	-0.975	29.552	-0.081	-0.081	0.000	0.000	0.000	0.000
61	A	59	ARG	1	0.831	0.911	27.906	0.202	0.202	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.012	-0.003	25.775	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	61	PRO	0	0.029	0.028	28.552	0.012	0.012	0.000	0.000	0.000	0.000
64	A	62	PHE	0	-0.022	-0.033	24.722	0.008	0.008	0.000	0.000	0.000	0.000
65	A	63	ALA	0	-0.030	-0.015	29.794	0.005	0.005	0.000	0.000	0.000	0.000
66	A	64	GLY	0	-0.029	-0.017	30.114	0.009	0.009	0.000	0.000	0.000	0.000
67	A	65	PHE	0	0.022	0.009	26.431	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	66	GLU	-1	-0.900	-0.949	28.646	0.009	0.009	0.000	0.000	0.000	0.000
69	A	67	ARG	1	0.945	0.970	28.540	0.003	0.003	0.000	0.000	0.000	0.000
70	A	68	ASP	-1	-0.808	-0.894	30.052	0.043	0.043	0.000	0.000	0.000	0.000
71	A	69	GLY	0	-0.006	-0.006	31.977	0.002	0.002	0.000	0.000	0.000	0.000
72	A	70	GLY	0	-0.063	-0.034	33.769	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	71	ARG	1	0.914	0.945	31.862	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	72	GLY	0	0.006	0.011	27.779	0.004	0.004	0.000	0.000	0.000	0.000
75	A	73	ALA	0	-0.010	-0.009	23.541	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	74	TRP	0	-0.008	0.002	24.692	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	75	ARG	1	0.866	0.948	23.855	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	76	ALA	0	-0.008	-0.008	23.661	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	77	VAL	0	0.013	0.001	24.775	0.002	0.002	0.000	0.000	0.000	0.000
80	A	78	LEU	0	0.016	0.022	24.080	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	79	HIS	0	-0.014	-0.010	26.975	0.012	0.012	0.000	0.000	0.000	0.000
82	A	80	ARG	1	0.972	0.986	24.597	0.100	0.100	0.000	0.000	0.000	0.000
83	A	81	ALA	0	-0.012	-0.008	28.531	0.012	0.012	0.000	0.000	0.000	0.000
84	A	82	VAL	0	-0.023	-0.020	30.026	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	83	PRO	0	0.034	0.045	32.351	0.001	0.001	0.000	0.000	0.000	0.000
86	A	84	ALA	0	0.034	0.010	33.505	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	85	ALA	0	-0.001	-0.018	36.751	0.001	0.001	0.000	0.000	0.000	0.000
88	A	86	GLY	0	-0.023	-0.016	39.395	0.004	0.004	0.000	0.000	0.000	0.000
89	A	87	GLU	-1	-0.936	-0.953	32.957	-0.040	-0.040	0.000	0.000	0.000	0.000
90	A	88	ARG	1	0.911	0.936	33.262	0.038	0.038	0.000	0.000	0.000	0.000
91	A	89	CYS	0	-0.006	0.018	28.002	0.008	0.008	0.000	0.000	0.000	0.000
92	A	90	THR	0	-0.058	-0.047	26.581	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	91	PHE	0	0.013	0.030	20.782	0.004	0.004	0.000	0.000	0.000	0.000
94	A	92	ASN	0	0.036	0.006	22.160	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	93	GLN	0	0.063	0.048	16.999	0.042	0.042	0.000	0.000	0.000	0.000
96	A	94	SER	0	0.024	0.001	19.456	0.000	0.000	0.000	0.000	0.000	0.000
97	A	95	GLY	0	0.030	0.008	19.232	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	96	PRO	0	-0.017	0.001	19.833	0.005	0.005	0.000	0.000	0.000	0.000
99	A	97	THR	0	-0.007	0.000	22.817	0.001	0.001	0.000	0.000	0.000	0.000
100	A	98	LEU	0	0.027	0.021	24.073	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	99	LEU	0	0.032	0.015	24.574	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	100	ILE	0	-0.002	0.013	18.742	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	101	ALA	0	-0.013	0.001	20.217	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	102	ALA	0	0.022	0.009	21.543	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	103	MET	0	0.009	0.020	20.265	-0.019	-0.019	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.863	0.922	15.521	0.032	0.032	0.000	0.000	0.000	0.000
107	A	105	THR	0	-0.022	-0.028	17.999	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	106	LEU	0	-0.007	0.013	20.587	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	107	VAL	0	0.025	0.023	14.856	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	108	ALA	0	0.022	0.013	16.452	-0.043	-0.043	0.000	0.000	0.000	0.000
111	A	109	SER	0	-0.134	-0.084	17.419	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	110	THR	0	-0.044	-0.015	17.199	0.003	0.003	0.000	0.000	0.000	0.000
113	A	111	PHE	0	-0.045	-0.045	12.760	-0.046	-0.046	0.000	0.000	0.000	0.000
114	A	112	GLY	0	-0.018	0.016	13.201	-0.055	-0.055	0.000	0.000	0.000	0.000
115	A	113	ASP	-1	-0.881	-0.948	12.165	0.018	0.018	0.000	0.000	0.000	0.000
116	A	114	ASP	-1	-0.972	-0.982	7.446	-0.488	-0.488	0.000	0.000	0.000	0.000
117	A	115	VAL	0	0.016	0.005	8.591	-0.101	-0.101	0.000	0.000	0.000	0.000
118	A	116	PRO	0	-0.033	-0.008	5.515	-0.160	-0.160	0.000	0.000	0.000	0.000
119	A	117	ASP	-1	-0.903	-0.952	4.611	-0.851	-0.476	-0.001	-0.040	-0.335	0.000
120	A	118	LEU	0	-0.059	-0.025	6.480	0.077	0.077	0.000	0.000	0.000	0.000

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