FMO DATABASE

FMODB ID: KGQN3

Calculation Name: 5X07-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X07

Chain ID: F

ChEMBL ID:

UniProt ID: Q9Y261

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-608399.529126
FMO2-HF: Nuclear repulsion	573138.943245
FMO2-HF: Total energy	-35260.585881
FMO2-MP2: Total energy	-35362.863669

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(F:155:GLY)

Summations of interaction energy for fragment #1(F:155:GLY)

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.
-2.116	0.324	0.014	-1.283	-1.171	0.005

Interaction energy analysis for fragmet #1(F:155:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.016

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	F	157	HIS	0	0.033	0.018	3.203	0.197	2.541	0.016	-1.265	-1.095	0.005
4	F	158	ALA	0	0.037	0.019	4.476	-0.627	-0.627	-0.001	-0.014	0.015	0.000
5	F	159	LYS	1	0.931	0.966	7.211	0.405	0.405	0.000	0.000	0.000	0.000
6	F	160	PRO	0	0.005	0.010	8.781	-0.009	-0.009	0.000	0.000	0.000	0.000
7	F	161	PRO	0	0.011	0.006	11.932	0.080	0.080	0.000	0.000	0.000	0.000
8	F	162	TYR	0	0.000	0.008	14.825	0.032	0.032	0.000	0.000	0.000	0.000
9	F	163	SER	0	0.007	0.000	15.540	0.032	0.032	0.000	0.000	0.000	0.000
10	F	164	TYR	0	0.049	-0.011	13.664	0.014	0.014	0.000	0.000	0.000	0.000
11	F	165	ILE	0	0.081	0.052	18.072	0.005	0.005	0.000	0.000	0.000	0.000
12	F	166	SER	0	0.024	0.025	19.496	-0.004	-0.004	0.000	0.000	0.000	0.000
13	F	167	LEU	0	-0.033	-0.017	14.462	-0.005	-0.005	0.000	0.000	0.000	0.000
14	F	168	ILE	0	0.004	0.004	18.940	0.004	0.004	0.000	0.000	0.000	0.000
15	F	169	THR	0	0.011	-0.005	21.589	-0.001	-0.001	0.000	0.000	0.000	0.000
16	F	170	MET	0	-0.053	-0.025	18.728	-0.010	-0.010	0.000	0.000	0.000	0.000
17	F	171	ALA	0	0.003	0.011	20.901	-0.002	-0.002	0.000	0.000	0.000	0.000
18	F	172	ILE	0	0.033	0.022	22.856	0.001	0.001	0.000	0.000	0.000	0.000
19	F	173	GLN	0	0.006	0.025	26.313	-0.009	-0.009	0.000	0.000	0.000	0.000
20	F	174	GLN	0	-0.002	-0.009	22.983	0.000	0.000	0.000	0.000	0.000	0.000
21	F	175	SER	0	-0.029	-0.002	26.834	0.001	0.001	0.000	0.000	0.000	0.000
22	F	176	PRO	0	0.016	-0.013	28.083	-0.005	-0.005	0.000	0.000	0.000	0.000
23	F	177	ASN	0	-0.004	-0.008	31.259	-0.007	-0.007	0.000	0.000	0.000	0.000
24	F	178	LYS	1	0.861	0.944	30.547	0.005	0.005	0.000	0.000	0.000	0.000
25	F	179	MET	0	-0.017	0.008	29.510	0.005	0.005	0.000	0.000	0.000	0.000
26	F	180	LEU	0	-0.007	0.014	23.706	-0.001	-0.001	0.000	0.000	0.000	0.000
27	F	181	THR	0	0.017	-0.015	26.214	0.011	0.011	0.000	0.000	0.000	0.000
28	F	182	LEU	0	-0.017	-0.016	21.596	0.003	0.003	0.000	0.000	0.000	0.000
29	F	183	SER	0	0.039	0.013	21.402	0.014	0.014	0.000	0.000	0.000	0.000
30	F	184	GLU	-1	-0.799	-0.867	20.958	0.108	0.108	0.000	0.000	0.000	0.000
31	F	185	ILE	0	0.006	0.007	19.564	-0.009	-0.009	0.000	0.000	0.000	0.000
32	F	186	TYR	0	-0.038	-0.050	17.356	0.011	0.011	0.000	0.000	0.000	0.000
33	F	187	GLN	0	-0.021	-0.030	16.426	0.044	0.044	0.000	0.000	0.000	0.000
34	F	188	TRP	0	0.067	0.038	17.287	-0.012	-0.012	0.000	0.000	0.000	0.000
35	F	189	ILE	0	-0.008	-0.010	13.211	-0.031	-0.031	0.000	0.000	0.000	0.000
36	F	190	MET	0	-0.050	-0.016	12.451	0.008	0.008	0.000	0.000	0.000	0.000
37	F	191	ASP	-1	-0.818	-0.888	12.944	0.096	0.096	0.000	0.000	0.000	0.000
38	F	192	LEU	0	-0.059	-0.014	14.991	-0.050	-0.050	0.000	0.000	0.000	0.000
39	F	193	PHE	0	0.002	-0.013	10.734	-0.110	-0.110	0.000	0.000	0.000	0.000
40	F	194	PRO	0	0.030	-0.001	7.765	0.151	0.151	0.000	0.000	0.000	0.000
41	F	195	PHE	0	-0.021	-0.003	4.747	0.446	0.542	-0.001	-0.004	-0.091	0.000
42	F	196	TYR	0	-0.015	-0.018	6.444	0.514	0.514	0.000	0.000	0.000	0.000
43	F	197	ARG	1	0.885	0.945	7.923	-0.163	-0.163	0.000	0.000	0.000	0.000
44	F	198	GLN	0	0.065	0.038	5.541	-0.055	-0.055	0.000	0.000	0.000	0.000
45	F	199	ASN	0	-0.019	-0.029	6.460	-0.544	-0.544	0.000	0.000	0.000	0.000
46	F	200	GLN	0	0.037	0.014	9.726	-0.153	-0.153	0.000	0.000	0.000	0.000
47	F	201	GLN	0	0.009	0.005	12.478	-0.071	-0.071	0.000	0.000	0.000	0.000
48	F	202	ARG	1	0.930	0.963	9.001	-1.518	-1.518	0.000	0.000	0.000	0.000
49	F	203	TRP	0	0.016	0.016	10.527	-0.182	-0.182	0.000	0.000	0.000	0.000
50	F	204	GLN	0	0.065	0.043	14.029	-0.093	-0.093	0.000	0.000	0.000	0.000
51	F	205	ASN	0	0.019	0.017	16.644	-0.090	-0.090	0.000	0.000	0.000	0.000
52	F	206	SER	0	-0.007	-0.008	16.576	-0.022	-0.022	0.000	0.000	0.000	0.000
53	F	207	ILE	0	-0.003	0.011	16.791	-0.044	-0.044	0.000	0.000	0.000	0.000
54	F	208	ARG	1	0.925	0.957	19.305	-0.344	-0.344	0.000	0.000	0.000	0.000
55	F	209	HIS	0	-0.009	0.008	21.475	-0.010	-0.010	0.000	0.000	0.000	0.000
56	F	210	SER	0	-0.024	-0.019	20.962	-0.028	-0.028	0.000	0.000	0.000	0.000
57	F	211	LEU	0	-0.022	-0.007	22.997	-0.017	-0.017	0.000	0.000	0.000	0.000
58	F	212	SER	0	-0.034	-0.016	25.419	-0.012	-0.012	0.000	0.000	0.000	0.000
59	F	213	PHE	0	-0.063	-0.019	25.758	-0.006	-0.006	0.000	0.000	0.000	0.000
60	F	214	ASN	0	-0.035	-0.028	24.319	-0.019	-0.019	0.000	0.000	0.000	0.000
61	F	215	ASP	-1	-0.813	-0.901	28.302	0.059	0.059	0.000	0.000	0.000	0.000
62	F	216	CYS	0	-0.082	-0.037	28.796	-0.004	-0.004	0.000	0.000	0.000	0.000
63	F	217	PHE	0	-0.052	-0.034	24.301	-0.002	-0.002	0.000	0.000	0.000	0.000
64	F	218	LEU	0	0.078	0.053	29.476	0.007	0.007	0.000	0.000	0.000	0.000
65	F	219	LYS	1	0.935	0.982	30.785	-0.103	-0.103	0.000	0.000	0.000	0.000
66	F	220	VAL	0	0.041	0.012	32.298	-0.006	-0.006	0.000	0.000	0.000	0.000
67	F	221	PRO	0	-0.019	-0.010	34.039	0.006	0.006	0.000	0.000	0.000	0.000
68	F	222	ARG	0	-0.007	0.015	30.209	-0.001	-0.001	0.000	0.000	0.000	0.000
69	F	223	SER	0	0.040	-0.016	36.358	-0.003	-0.003	0.000	0.000	0.000	0.000
70	F	224	PRO	0	-0.026	-0.007	38.694	0.000	0.000	0.000	0.000	0.000	0.000
71	F	225	ASP	-1	-0.879	-0.938	41.369	0.049	0.049	0.000	0.000	0.000	0.000
72	F	226	LYS	1	0.944	0.980	37.225	-0.044	-0.044	0.000	0.000	0.000	0.000
73	F	227	PRO	0	-0.071	0.015	36.534	0.004	0.004	0.000	0.000	0.000	0.000
74	F	228	GLY	0	0.128	-0.019	34.498	-0.003	-0.003	0.000	0.000	0.000	0.000
75	F	229	LYN	0	-0.088	-0.006	28.033	0.005	0.005	0.000	0.000	0.000	0.000
76	F	230	GLY	0	0.002	0.007	29.357	0.002	0.002	0.000	0.000	0.000	0.000
77	F	231	SER	0	-0.070	-0.054	29.810	-0.009	-0.009	0.000	0.000	0.000	0.000
78	F	232	PHE	0	0.034	0.021	29.455	0.009	0.009	0.000	0.000	0.000	0.000
79	F	233	TRP	0	-0.068	-0.046	26.865	0.002	0.002	0.000	0.000	0.000	0.000
80	F	234	THR	0	-0.045	-0.062	28.720	-0.005	-0.005	0.000	0.000	0.000	0.000
81	F	235	LEU	0	0.010	-0.009	27.241	0.004	0.004	0.000	0.000	0.000	0.000
82	F	236	HIS	0	0.017	0.018	31.095	-0.004	-0.004	0.000	0.000	0.000	0.000
83	F	237	PRO	0	0.002	-0.009	33.792	-0.004	-0.004	0.000	0.000	0.000	0.000
84	F	238	ASP	-1	-0.976	-0.964	34.623	0.001	0.001	0.000	0.000	0.000	0.000
85	F	239	SER	0	-0.039	-0.021	32.284	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:155:GLY)