FMO DATABASE

FMODB ID: MVGNZ

Calculation Name: 1ML8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ML8

Chain ID: A

ChEMBL ID:

UniProt ID: P0ADX1

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1021216.073681
FMO2-HF: Nuclear repulsion	968856.951984
FMO2-HF: Total energy	-52359.121697
FMO2-MP2: Total energy	-52506.515725

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.
-0.427	2.057	0.012	-1.069	-1.427	0.001

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 : 0.017 / 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	A	3	ALA	0	0.004	0.013	3.833	-0.629	1.510	-0.008	-0.977	-1.154	0.001
4	A	4	ARG	1	0.843	0.908	6.027	0.592	0.592	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.022	0.009	9.425	0.138	0.138	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.854	0.923	12.787	0.342	0.342	0.000	0.000	0.000	0.000
7	A	7	TRP	0	-0.021	-0.006	16.190	0.022	0.022	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.045	-0.023	19.635	0.001	0.001	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.880	-0.938	21.991	-0.160	-0.160	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.023	0.029	24.619	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.002	-0.001	23.628	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.031	0.019	21.676	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.027	-0.028	16.914	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.006	0.017	14.418	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.002	0.008	12.783	-0.067	-0.067	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.804	-0.887	9.713	-0.435	-0.435	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.025	0.000	7.414	-0.268	-0.268	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.033	0.001	3.400	-0.160	0.119	0.021	-0.090	-0.210	0.000
19	A	19	SER	0	-0.032	-0.014	5.245	0.318	0.384	-0.001	-0.002	-0.063	0.000
20	A	20	GLY	0	-0.017	0.004	7.813	0.080	0.080	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.009	0.002	10.172	0.064	0.064	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.038	-0.042	11.370	-0.064	-0.064	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.009	0.005	13.602	0.041	0.041	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.025	-0.002	16.053	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	25	MET	0	-0.025	-0.011	13.805	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.750	-0.859	19.130	-0.191	-0.191	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.007	-0.014	22.579	0.006	0.006	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.101	-0.066	23.462	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.072	-0.051	26.500	0.009	0.009	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.037	0.019	24.479	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.888	-0.900	25.378	-0.126	-0.126	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.821	0.878	26.417	0.143	0.143	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.046	-0.020	21.807	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.057	0.038	20.394	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.011	-0.034	20.906	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.005	-0.018	16.718	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.013	-0.004	17.919	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.764	-0.849	20.195	-0.165	-0.165	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.043	-0.009	15.751	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.021	-0.011	15.420	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.011	0.008	17.283	0.015	0.015	0.000	0.000	0.000	0.000
42	A	42	MET	0	0.035	0.013	19.273	0.020	0.020	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.029	-0.001	14.723	0.010	0.010	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.012	0.001	16.810	0.016	0.016	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.033	0.014	18.780	0.020	0.020	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.009	0.008	18.594	0.017	0.017	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.012	0.063	15.803	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.067	0.021	17.602	0.019	0.019	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.044	0.022	21.133	0.017	0.017	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.011	-0.003	16.466	0.015	0.015	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.866	-0.930	19.020	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.037	-0.023	21.323	0.014	0.014	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.012	-0.005	23.059	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.046	-0.029	21.306	0.012	0.012	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.070	-0.033	23.760	0.011	0.011	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.044	0.018	26.180	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.032	0.034	25.425	0.007	0.007	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.939	0.965	21.152	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.045	-0.006	28.079	0.004	0.004	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.835	0.890	30.436	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.020	0.022	32.055	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.873	-0.923	32.130	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.045	-0.030	28.655	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.048	-0.038	31.084	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.859	-0.933	29.910	-0.044	-0.044	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.115	-0.050	26.075	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.776	-0.851	27.578	-0.066	-0.066	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.015	-0.007	24.782	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.784	0.884	27.364	0.054	0.054	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.003	0.002	23.260	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.001	0.007	27.358	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.005	-0.019	26.180	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.849	-0.897	28.204	-0.067	-0.067	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.923	0.961	25.626	0.127	0.127	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.845	0.929	28.286	0.079	0.079	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.917	-0.952	30.017	-0.079	-0.079	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.014	-0.022	31.860	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.846	-0.896	30.408	-0.083	-0.083	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.047	-0.006	25.049	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.876	0.966	25.616	0.117	0.117	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.027	-0.003	21.963	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.032	0.001	20.821	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.006	-0.015	25.070	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.055	-0.042	27.330	0.009	0.009	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.005	0.009	22.198	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.017	-0.011	26.243	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.005	-0.007	22.907	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	HIS	1	0.836	0.896	27.093	0.052	0.052	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.013	-0.014	24.644	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.006	0.004	29.850	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.014	-0.006	29.853	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.055	0.026	32.135	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.045	0.004	33.405	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.808	0.914	35.752	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.814	-0.910	38.257	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.026	0.009	33.597	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.835	0.911	36.934	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.761	-0.864	36.412	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.020	0.012	36.042	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.068	-0.036	33.442	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.029	0.013	31.671	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.039	0.037	31.268	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.985	0.991	29.824	-0.029	-0.029	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.038	-0.021	27.659	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.006	-0.002	26.541	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.869	-0.939	26.716	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.069	-0.040	25.339	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.037	-0.007	22.538	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.006	-0.014	21.809	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.822	-0.876	22.924	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.841	0.919	22.152	-0.048	-0.048	0.000	0.000	0.000	0.000
112	A	112	TYR	0	-0.054	-0.042	19.411	0.018	0.018	0.000	0.000	0.000	0.000
113	A	114	SER	0	0.025	0.002	12.454	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.018	-0.016	13.346	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.048	0.010	15.396	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.011	0.010	17.366	0.004	0.004	0.000	0.000	0.000	0.000
117	A	118	MET	0	-0.056	-0.025	11.395	0.011	0.011	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.008	0.005	16.517	0.002	0.002	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.804	-0.902	18.980	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.735	0.868	19.849	0.025	0.025	0.000	0.000	0.000	0.000
121	A	122	ALA	0	-0.065	-0.035	20.823	0.004	0.004	0.000	0.000	0.000	0.000
122	A	123	VAL	0	-0.065	-0.019	21.615	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.005	0.000	24.160	0.010	0.010	0.000	0.000	0.000	0.000
124	A	125	ILE	0	0.007	0.002	21.506	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	126	THR	0	0.013	0.015	25.817	0.009	0.009	0.000	0.000	0.000	0.000
126	A	127	HIS	1	0.830	0.894	27.158	0.017	0.017	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.021	-0.001	29.073	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	TYR	0	-0.062	-0.058	31.001	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.837	-0.894	33.041	-0.032	-0.032	0.000	0.000	0.000	0.000
130	A	131	VAL	0	-0.014	-0.015	34.491	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.001	0.009	36.286	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.014	0.002	37.507	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ALA	0	-0.010	-0.005	37.304	-0.001	-0.001	0.000	0.000	0.000	0.000

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