FMO DATABASE

FMODB ID: 221QR

Calculation Name: 5D6H-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D6H

Chain ID: B

ChEMBL ID:

UniProt ID: Q6XBY4

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:

Apendix: None

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-669515.245877
FMO2-HF: Nuclear repulsion	630035.099504
FMO2-HF: Total energy	-39480.146373
FMO2-MP2: Total energy	-39595.568638

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(B:7:HIS)

Summations of interaction energy for fragment #1(B:7: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.
-13.61	-9.173	1.711	-2.28	-3.867	-0.009

Interaction energy analysis for fragmet #1(B:7:HIS)

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 : 0.005

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	B	9	HIS	0	-0.027	-0.021	2.540	-10.953	-6.890	1.710	-2.276	-3.497	-0.009
4	B	10	SER	0	-0.060	-0.035	3.783	2.332	2.706	0.001	-0.004	-0.370	0.000
5	B	11	THR	0	-0.047	-0.034	5.554	-0.007	-0.007	0.000	0.000	0.000	0.000
6	B	12	GLY	0	0.006	0.014	8.108	0.389	0.389	0.000	0.000	0.000	0.000
7	B	13	CYS	0	-0.058	-0.030	10.408	0.008	0.008	0.000	0.000	0.000	0.000
8	B	14	THR	0	0.005	0.013	13.861	0.112	0.112	0.000	0.000	0.000	0.000
9	B	15	VAL	0	-0.002	-0.020	16.394	0.041	0.041	0.000	0.000	0.000	0.000
10	B	16	GLY	0	0.004	0.017	19.905	0.011	0.011	0.000	0.000	0.000	0.000
11	B	17	GLY	0	-0.002	0.023	22.681	0.040	0.040	0.000	0.000	0.000	0.000
12	B	18	SER	0	-0.028	-0.023	22.604	0.044	0.044	0.000	0.000	0.000	0.000
13	B	28	GLY	0	0.033	0.023	31.618	0.000	0.000	0.000	0.000	0.000	0.000
14	B	29	THR	0	-0.079	-0.051	32.540	-0.007	-0.007	0.000	0.000	0.000	0.000
15	B	30	LEU	0	0.021	0.017	34.731	0.003	0.003	0.000	0.000	0.000	0.000
16	B	31	ASN	0	-0.003	0.001	37.982	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	32	PHE	0	0.029	0.039	41.683	0.003	0.003	0.000	0.000	0.000	0.000
18	B	43	LEU	0	0.029	0.023	52.362	0.000	0.000	0.000	0.000	0.000	0.000
19	B	44	THR	0	-0.106	-0.074	55.778	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	45	ALA	0	0.025	0.005	54.973	0.004	0.004	0.000	0.000	0.000	0.000
21	B	46	GLU	-1	-0.903	-0.939	54.216	-0.141	-0.141	0.000	0.000	0.000	0.000
22	B	47	VAL	0	-0.063	-0.031	54.332	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	48	ALA	0	0.036	0.024	52.931	0.004	0.004	0.000	0.000	0.000	0.000
24	B	49	SER	0	-0.047	-0.030	47.625	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	50	ALA	0	0.000	0.019	46.715	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	51	ALA	0	-0.032	-0.039	42.265	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	52	THR	0	-0.005	-0.010	39.135	0.005	0.005	0.000	0.000	0.000	0.000
28	B	53	GLY	0	0.001	-0.008	36.001	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	54	GLY	0	0.015	0.020	32.893	0.010	0.010	0.000	0.000	0.000	0.000
30	B	55	ASN	0	-0.036	-0.020	28.654	0.012	0.012	0.000	0.000	0.000	0.000
31	B	56	ILE	0	0.044	0.031	25.267	-0.026	-0.026	0.000	0.000	0.000	0.000
32	B	57	SER	0	-0.035	-0.020	22.359	0.007	0.007	0.000	0.000	0.000	0.000
33	B	58	VAL	0	0.040	0.020	18.055	-0.024	-0.024	0.000	0.000	0.000	0.000
34	B	59	THR	0	-0.013	-0.023	15.494	0.089	0.089	0.000	0.000	0.000	0.000
35	B	61	ASP	-1	-0.753	-0.859	8.065	-3.875	-3.875	0.000	0.000	0.000	0.000
36	B	62	GLY	0	0.043	0.038	9.413	-0.259	-0.259	0.000	0.000	0.000	0.000
37	B	63	THR	0	-0.054	-0.036	9.167	0.197	0.197	0.000	0.000	0.000	0.000
38	B	64	ASP	-1	-0.926	-0.964	11.724	-0.989	-0.989	0.000	0.000	0.000	0.000
39	B	65	PRO	0	-0.054	-0.006	13.820	-0.156	-0.156	0.000	0.000	0.000	0.000
40	B	66	VAL	0	0.008	0.000	13.308	-0.026	-0.026	0.000	0.000	0.000	0.000
41	B	67	ASP	-1	-0.803	-0.879	16.365	-0.647	-0.647	0.000	0.000	0.000	0.000
42	B	68	PHE	0	-0.045	-0.025	19.105	-0.071	-0.071	0.000	0.000	0.000	0.000
43	B	69	THR	0	-0.016	-0.028	21.352	0.082	0.082	0.000	0.000	0.000	0.000
44	B	70	VAL	0	-0.010	-0.007	24.930	-0.030	-0.030	0.000	0.000	0.000	0.000
45	B	71	ALA	0	0.021	0.020	27.194	0.032	0.032	0.000	0.000	0.000	0.000
46	B	72	ILE	0	0.002	-0.005	30.310	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	73	ASP	-1	-0.796	-0.879	33.119	-0.329	-0.329	0.000	0.000	0.000	0.000
48	B	93	TYR	0	-0.071	-0.048	43.338	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	94	ASN	0	0.048	0.007	41.009	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	95	VAL	0	-0.011	0.004	35.255	0.000	0.000	0.000	0.000	0.000	0.000
51	B	96	TYR	0	0.012	0.007	36.504	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	97	ARG	1	0.827	0.905	27.367	0.463	0.463	0.000	0.000	0.000	0.000
53	B	98	ASP	-1	-0.815	-0.899	32.762	-0.289	-0.289	0.000	0.000	0.000	0.000
54	B	99	ALA	0	0.013	0.014	35.508	0.008	0.008	0.000	0.000	0.000	0.000
55	B	100	ALA	0	-0.047	-0.022	37.303	0.013	0.013	0.000	0.000	0.000	0.000
56	B	101	ARG	1	0.879	0.943	39.057	0.236	0.236	0.000	0.000	0.000	0.000
57	B	102	THR	0	-0.042	-0.038	39.297	0.006	0.006	0.000	0.000	0.000	0.000
58	B	103	ASN	0	-0.018	-0.006	33.433	0.005	0.005	0.000	0.000	0.000	0.000
59	B	104	LEU	0	0.008	0.003	36.549	-0.010	-0.010	0.000	0.000	0.000	0.000
60	B	105	TYR	0	-0.037	-0.046	29.996	-0.020	-0.020	0.000	0.000	0.000	0.000
61	B	106	VAL	0	-0.023	-0.008	35.273	0.011	0.011	0.000	0.000	0.000	0.000
62	B	107	VAL	0	0.037	0.018	35.964	-0.016	-0.016	0.000	0.000	0.000	0.000
63	B	108	ASN	0	-0.039	-0.036	34.147	0.000	0.000	0.000	0.000	0.000	0.000
64	B	109	GLN	0	-0.040	-0.013	33.566	-0.010	-0.010	0.000	0.000	0.000	0.000
65	B	110	PRO	0	-0.028	-0.016	28.841	-0.009	-0.009	0.000	0.000	0.000	0.000
66	B	111	GLN	0	0.018	0.035	29.394	0.026	0.026	0.000	0.000	0.000	0.000
67	B	112	GLN	0	0.003	0.012	23.815	-0.010	-0.010	0.000	0.000	0.000	0.000
68	B	113	PHE	0	-0.027	-0.022	23.372	0.052	0.052	0.000	0.000	0.000	0.000
69	B	114	THR	0	0.034	0.003	20.517	-0.048	-0.048	0.000	0.000	0.000	0.000
70	B	115	THR	0	-0.006	-0.013	16.979	-0.016	-0.016	0.000	0.000	0.000	0.000
71	B	116	VAL	0	0.021	0.006	17.198	-0.013	-0.013	0.000	0.000	0.000	0.000
72	B	117	SER	0	0.047	0.017	13.364	0.137	0.137	0.000	0.000	0.000	0.000
73	B	118	GLY	0	-0.052	-0.020	15.464	0.041	0.041	0.000	0.000	0.000	0.000
74	B	119	GLN	0	-0.091	-0.053	18.156	0.117	0.117	0.000	0.000	0.000	0.000
75	B	120	ALA	0	0.040	0.045	18.401	-0.026	-0.026	0.000	0.000	0.000	0.000
76	B	121	THR	0	-0.049	-0.035	19.342	0.043	0.043	0.000	0.000	0.000	0.000
77	B	122	ALA	0	0.015	0.011	21.995	-0.023	-0.023	0.000	0.000	0.000	0.000
78	B	123	VAL	0	0.026	0.004	24.239	-0.007	-0.007	0.000	0.000	0.000	0.000
79	B	124	PRO	0	-0.030	-0.009	26.861	0.020	0.020	0.000	0.000	0.000	0.000
80	B	125	ILE	0	0.039	0.029	29.777	0.004	0.004	0.000	0.000	0.000	0.000
81	B	126	PHE	0	0.011	0.002	32.950	0.008	0.008	0.000	0.000	0.000	0.000
82	B	127	GLY	0	0.042	0.020	36.597	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	128	ALA	0	-0.040	-0.039	39.513	0.008	0.008	0.000	0.000	0.000	0.000
84	B	129	ILE	0	-0.001	0.027	43.247	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	130	ALA	0	0.010	-0.012	46.846	0.000	0.000	0.000	0.000	0.000	0.000
86	B	131	PRO	0	0.034	0.046	50.035	0.006	0.006	0.000	0.000	0.000	0.000
87	B	132	ASN	0	0.033	-0.025	50.967	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	133	THR	0	-0.023	-0.007	49.487	0.002	0.002	0.000	0.000	0.000	0.000
89	B	134	GLY	0	0.038	-0.005	46.370	0.001	0.001	0.000	0.000	0.000	0.000
90	B	135	THR	0	-0.031	0.006	43.816	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	136	PRO	0	0.033	0.034	44.404	0.000	0.000	0.000	0.000	0.000	0.000
92	B	137	LYS	1	0.911	0.949	45.659	0.205	0.205	0.000	0.000	0.000	0.000
93	B	138	ALA	0	0.027	0.004	47.549	-0.006	-0.006	0.000	0.000	0.000	0.000
94	B	139	GLN	0	-0.020	-0.002	50.299	0.002	0.002	0.000	0.000	0.000	0.000
95	B	140	GLY	0	0.012	0.000	49.908	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	141	ASP	-1	-0.862	-0.911	47.207	-0.194	-0.194	0.000	0.000	0.000	0.000
97	B	142	TYR	0	0.015	-0.011	47.110	-0.008	-0.008	0.000	0.000	0.000	0.000
98	B	143	LYS	1	0.818	0.909	42.206	0.211	0.211	0.000	0.000	0.000	0.000
99	B	144	ASP	-1	-0.813	-0.921	40.735	-0.249	-0.249	0.000	0.000	0.000	0.000
100	B	145	THR	0	-0.121	-0.071	36.225	-0.007	-0.007	0.000	0.000	0.000	0.000
101	B	146	LEU	0	0.018	0.027	35.142	0.005	0.005	0.000	0.000	0.000	0.000
102	B	147	LEU	0	-0.002	-0.002	30.584	-0.019	-0.019	0.000	0.000	0.000	0.000
103	B	148	VAL	0	-0.036	-0.026	27.824	-0.008	-0.008	0.000	0.000	0.000	0.000
104	B	149	THR	0	-0.023	-0.004	26.816	-0.030	-0.030	0.000	0.000	0.000	0.000
105	B	150	VAL	0	-0.021	-0.011	21.643	0.013	0.013	0.000	0.000	0.000	0.000
106	B	151	ASN	0	-0.050	-0.021	22.288	-0.019	-0.019	0.000	0.000	0.000	0.000
107	B	152	PHE	0	0.053	0.024	17.404	-0.032	-0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:7:HIS)