FMO DATABASE

FMODB ID: M37YZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-668781.023175
FMO2-HF: Nuclear repulsion	629303.525207
FMO2-HF: Total energy	-39477.497967
FMO2-MP2: Total energy	-39593.201014

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.
-13.02	-9.082	2.177	-2.407	-3.708	-0.01

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 : 0.008 / q_NPA : -0.002

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	-0.055	-0.019	2.513	-9.681	-6.023	2.178	-2.387	-3.449	-0.010
4	B	10	SER	0	-0.029	-0.022	3.974	2.096	2.376	-0.001	-0.020	-0.259	0.000
5	B	11	THR	0	-0.004	-0.005	5.919	-0.060	-0.060	0.000	0.000	0.000	0.000
6	B	12	GLY	0	-0.018	0.005	8.749	0.184	0.184	0.000	0.000	0.000	0.000
7	B	13	CYS	0	-0.051	-0.012	10.576	0.090	0.090	0.000	0.000	0.000	0.000
8	B	14	THR	0	-0.015	-0.007	14.155	0.060	0.060	0.000	0.000	0.000	0.000
9	B	15	VAL	0	-0.008	-0.021	16.717	0.068	0.068	0.000	0.000	0.000	0.000
10	B	16	GLY	0	-0.015	0.039	20.114	0.022	0.022	0.000	0.000	0.000	0.000
11	B	17	GLY	0	0.020	0.008	22.958	0.034	0.034	0.000	0.000	0.000	0.000
12	B	18	SER	0	-0.014	-0.021	22.635	0.021	0.021	0.000	0.000	0.000	0.000
13	B	28	GLY	0	-0.005	-0.014	32.666	0.008	0.008	0.000	0.000	0.000	0.000
14	B	29	THR	0	-0.029	-0.011	32.880	-0.015	-0.015	0.000	0.000	0.000	0.000
15	B	30	LEU	0	0.039	0.014	35.452	0.004	0.004	0.000	0.000	0.000	0.000
16	B	31	ASN	0	0.015	0.016	38.310	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	32	PHE	0	0.014	0.032	41.459	0.005	0.005	0.000	0.000	0.000	0.000
18	B	43	LEU	0	0.067	0.017	52.686	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	44	THR	0	-0.024	-0.011	56.219	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	45	ALA	0	-0.031	-0.018	55.711	0.002	0.002	0.000	0.000	0.000	0.000
21	B	46	GLU	-1	-0.965	-0.966	54.614	-0.141	-0.141	0.000	0.000	0.000	0.000
22	B	47	VAL	0	-0.069	-0.035	55.147	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	48	ALA	0	0.057	0.037	53.454	0.004	0.004	0.000	0.000	0.000	0.000
24	B	49	SER	0	-0.066	-0.007	48.187	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	50	ALA	0	-0.016	0.013	47.119	0.000	0.000	0.000	0.000	0.000	0.000
26	B	51	ALA	0	-0.019	-0.031	42.602	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	52	THR	0	-0.021	-0.028	39.610	0.005	0.005	0.000	0.000	0.000	0.000
28	B	53	GLY	0	0.016	0.009	36.470	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	54	GLY	0	0.036	0.026	33.424	0.008	0.008	0.000	0.000	0.000	0.000
30	B	55	ASN	0	-0.072	-0.041	28.896	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	56	ILE	0	0.045	0.033	25.176	-0.018	-0.018	0.000	0.000	0.000	0.000
32	B	57	SER	0	-0.018	-0.011	22.133	0.009	0.009	0.000	0.000	0.000	0.000
33	B	58	VAL	0	0.032	0.007	18.489	-0.031	-0.031	0.000	0.000	0.000	0.000
34	B	59	THR	0	-0.022	-0.011	15.827	0.097	0.097	0.000	0.000	0.000	0.000
35	B	61	ASP	-1	-0.770	-0.896	8.296	-3.746	-3.746	0.000	0.000	0.000	0.000
36	B	62	GLY	0	0.069	0.048	9.306	-0.467	-0.467	0.000	0.000	0.000	0.000
37	B	63	THR	0	-0.111	-0.065	8.834	0.149	0.149	0.000	0.000	0.000	0.000
38	B	64	ASP	-1	-0.955	-0.984	11.528	-0.851	-0.851	0.000	0.000	0.000	0.000
39	B	65	PRO	0	-0.027	-0.005	14.143	-0.153	-0.153	0.000	0.000	0.000	0.000
40	B	66	VAL	0	0.006	0.015	13.987	-0.069	-0.069	0.000	0.000	0.000	0.000
41	B	67	ASP	-1	-0.873	-0.943	16.959	-0.625	-0.625	0.000	0.000	0.000	0.000
42	B	68	PHE	0	-0.047	-0.043	19.485	-0.076	-0.076	0.000	0.000	0.000	0.000
43	B	69	THR	0	-0.051	-0.017	21.704	0.087	0.087	0.000	0.000	0.000	0.000
44	B	70	VAL	0	0.005	0.004	25.086	-0.033	-0.033	0.000	0.000	0.000	0.000
45	B	71	ALA	0	-0.002	-0.002	27.493	0.035	0.035	0.000	0.000	0.000	0.000
46	B	72	ILE	0	-0.010	-0.003	30.661	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	73	ASP	-1	-0.852	-0.920	33.232	-0.329	-0.329	0.000	0.000	0.000	0.000
48	B	93	TYR	0	-0.087	0.032	44.079	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	94	ASN	0	0.057	0.013	41.079	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	95	VAL	0	-0.001	0.012	35.483	0.001	0.001	0.000	0.000	0.000	0.000
51	B	96	TYR	0	0.000	0.001	36.705	0.000	0.000	0.000	0.000	0.000	0.000
52	B	97	ARG	1	0.855	0.896	27.744	0.441	0.441	0.000	0.000	0.000	0.000
53	B	98	ASP	-1	-0.855	-0.920	33.426	-0.273	-0.273	0.000	0.000	0.000	0.000
54	B	99	ALA	0	0.040	0.028	36.121	0.007	0.007	0.000	0.000	0.000	0.000
55	B	100	ALA	0	-0.033	-0.025	37.706	0.007	0.007	0.000	0.000	0.000	0.000
56	B	101	ARG	1	0.879	0.938	39.512	0.229	0.229	0.000	0.000	0.000	0.000
57	B	102	THR	0	-0.020	-0.017	39.902	0.009	0.009	0.000	0.000	0.000	0.000
58	B	103	ASN	0	-0.011	-0.014	34.123	0.005	0.005	0.000	0.000	0.000	0.000
59	B	104	LEU	0	-0.008	-0.002	36.871	-0.012	-0.012	0.000	0.000	0.000	0.000
60	B	105	TYR	0	-0.017	-0.008	30.781	-0.019	-0.019	0.000	0.000	0.000	0.000
61	B	106	VAL	0	-0.030	-0.014	35.851	0.010	0.010	0.000	0.000	0.000	0.000
62	B	107	VAL	0	0.047	0.021	36.128	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	108	ASN	0	-0.026	-0.024	34.295	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	109	GLN	0	-0.025	-0.006	34.210	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	110	PRO	0	-0.023	-0.013	28.962	-0.009	-0.009	0.000	0.000	0.000	0.000
66	B	111	GLN	0	0.024	0.056	29.434	0.021	0.021	0.000	0.000	0.000	0.000
67	B	112	GLN	0	0.038	0.010	24.763	-0.081	-0.081	0.000	0.000	0.000	0.000
68	B	113	PHE	0	-0.016	-0.002	23.755	0.052	0.052	0.000	0.000	0.000	0.000
69	B	114	THR	0	0.066	0.053	20.498	-0.033	-0.033	0.000	0.000	0.000	0.000
70	B	115	THR	0	-0.017	-0.011	17.464	-0.019	-0.019	0.000	0.000	0.000	0.000
71	B	116	VAL	0	0.042	0.014	17.659	0.018	0.018	0.000	0.000	0.000	0.000
72	B	117	SER	0	0.069	0.028	14.106	0.038	0.038	0.000	0.000	0.000	0.000
73	B	118	GLY	0	-0.012	-0.007	16.089	0.013	0.013	0.000	0.000	0.000	0.000
74	B	119	GLN	0	-0.109	-0.054	18.675	0.113	0.113	0.000	0.000	0.000	0.000
75	B	120	ALA	0	0.055	0.059	18.851	-0.036	-0.036	0.000	0.000	0.000	0.000
76	B	121	THR	0	-0.001	-0.031	19.860	0.042	0.042	0.000	0.000	0.000	0.000
77	B	122	ALA	0	-0.037	-0.003	22.540	-0.032	-0.032	0.000	0.000	0.000	0.000
78	B	123	VAL	0	0.035	0.011	24.488	0.003	0.003	0.000	0.000	0.000	0.000
79	B	124	PRO	0	-0.042	-0.017	27.134	0.016	0.016	0.000	0.000	0.000	0.000
80	B	125	ILE	0	0.034	0.013	30.060	0.004	0.004	0.000	0.000	0.000	0.000
81	B	126	PHE	0	-0.035	-0.022	33.405	0.013	0.013	0.000	0.000	0.000	0.000
82	B	127	GLY	0	0.059	0.032	37.075	0.003	0.003	0.000	0.000	0.000	0.000
83	B	128	ALA	0	-0.055	-0.047	39.898	0.010	0.010	0.000	0.000	0.000	0.000
84	B	129	ILE	0	0.084	0.099	43.581	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	130	ALA	0	0.051	0.021	47.010	0.005	0.005	0.000	0.000	0.000	0.000
86	B	131	PRO	0	-0.003	-0.040	50.227	0.010	0.010	0.000	0.000	0.000	0.000
87	B	132	ASN	0	0.020	-0.006	50.985	-0.006	-0.006	0.000	0.000	0.000	0.000
88	B	133	THR	0	0.017	-0.046	49.332	0.001	0.001	0.000	0.000	0.000	0.000
89	B	134	GLY	0	-0.033	-0.085	45.773	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	135	THR	0	-0.039	-0.028	43.476	-0.008	-0.008	0.000	0.000	0.000	0.000
91	B	136	PRO	0	0.016	0.022	44.722	0.001	0.001	0.000	0.000	0.000	0.000
92	B	137	LYS	1	0.960	0.970	45.852	0.203	0.203	0.000	0.000	0.000	0.000
93	B	138	ALA	0	0.011	0.018	47.674	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	139	GLN	0	-0.011	-0.001	50.372	0.003	0.003	0.000	0.000	0.000	0.000
95	B	140	GLY	0	-0.014	-0.006	49.747	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	141	ASP	-1	-0.871	-0.942	46.964	-0.202	-0.202	0.000	0.000	0.000	0.000
97	B	142	TYR	0	-0.039	-0.042	47.161	-0.008	-0.008	0.000	0.000	0.000	0.000
98	B	143	LYS	1	0.873	0.948	42.367	0.225	0.225	0.000	0.000	0.000	0.000
99	B	144	ASP	-1	-0.873	-0.941	40.869	-0.269	-0.269	0.000	0.000	0.000	0.000
100	B	145	THR	0	-0.105	-0.053	36.108	-0.011	-0.011	0.000	0.000	0.000	0.000
101	B	146	LEU	0	0.020	0.022	35.212	0.002	0.002	0.000	0.000	0.000	0.000
102	B	147	LEU	0	-0.009	0.007	31.015	-0.022	-0.022	0.000	0.000	0.000	0.000
103	B	148	VAL	0	-0.020	-0.020	27.954	0.007	0.007	0.000	0.000	0.000	0.000
104	B	149	THR	0	-0.020	-0.001	26.544	-0.030	-0.030	0.000	0.000	0.000	0.000
105	B	150	VAL	0	-0.003	-0.006	21.737	0.019	0.019	0.000	0.000	0.000	0.000
106	B	151	ASN	0	-0.050	-0.033	22.805	-0.051	-0.051	0.000	0.000	0.000	0.000
107	B	152	PHE	0	0.072	0.034	17.680	-0.020	-0.020	0.000	0.000	0.000	0.000

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