FMO DATABASE

FMODB ID: 72L6K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1021677.93734
FMO2-HF: Nuclear repulsion	969318.40967
FMO2-HF: Total energy	-52359.52767
FMO2-MP2: Total energy	-52506.868734

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.
-0.421	1.966	0.057	-1.026	-1.418	0.002

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 : 0.027 / q_NPA : -0.001

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	0.000	0.004	3.872	-0.466	1.441	-0.003	-0.881	-1.023	0.002
4	A	4	ARG	1	0.824	0.897	5.906	0.604	0.604	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.039	0.011	9.323	0.133	0.133	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.837	0.909	12.948	0.320	0.320	0.000	0.000	0.000	0.000
7	A	7	TRP	0	-0.007	0.010	16.292	0.022	0.022	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.049	-0.027	19.797	0.000	0.000	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.855	-0.932	22.227	-0.161	-0.161	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.016	0.004	24.685	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.011	0.007	23.939	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.040	0.041	21.905	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.033	-0.031	17.087	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.000	0.023	14.464	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.004	-0.001	12.937	-0.055	-0.055	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.793	-0.881	9.710	-0.502	-0.502	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.002	0.001	6.976	-0.278	-0.278	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.034	0.003	3.185	-0.208	0.186	0.061	-0.142	-0.313	0.000
19	A	19	SER	0	-0.057	-0.019	5.001	0.318	0.404	-0.001	-0.003	-0.082	0.000
20	A	20	GLY	0	0.022	0.020	7.752	0.098	0.098	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.025	-0.007	10.018	0.056	0.056	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.048	-0.050	11.035	-0.084	-0.084	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.001	0.006	13.472	0.042	0.042	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.025	0.004	16.010	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	25	MET	0	-0.009	-0.005	14.075	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.741	-0.859	19.425	-0.188	-0.188	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.003	-0.008	22.663	0.004	0.004	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.090	-0.054	23.695	0.022	0.022	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.085	-0.063	26.391	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.036	0.024	24.602	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.894	-0.911	25.657	-0.131	-0.131	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.797	0.875	26.097	0.140	0.140	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.017	-0.007	21.447	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.051	0.026	20.570	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.007	-0.037	20.492	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.016	-0.022	16.511	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.003	0.017	17.678	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.771	-0.849	20.259	-0.170	-0.170	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.039	-0.011	15.846	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.001	0.001	15.023	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.006	0.006	16.972	0.014	0.014	0.000	0.000	0.000	0.000
42	A	42	MET	0	0.013	-0.004	19.207	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.026	0.000	14.462	0.010	0.010	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.009	-0.006	16.530	0.014	0.014	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.032	0.013	18.477	0.019	0.019	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.012	0.004	18.805	0.016	0.016	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.030	0.035	15.851	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.052	0.005	17.531	0.016	0.016	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.003	0.009	21.014	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.002	0.003	16.511	0.014	0.014	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.788	-0.866	19.397	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.005	0.000	21.538	0.014	0.014	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.030	0.008	23.129	0.009	0.009	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.052	-0.030	21.230	0.013	0.013	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.057	-0.033	23.752	0.011	0.011	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.032	0.021	26.222	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.038	0.024	25.496	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.905	0.959	20.944	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.022	-0.005	27.933	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.840	0.899	30.211	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.006	0.008	32.068	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.861	-0.915	32.229	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.039	-0.022	28.872	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.042	-0.033	31.131	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.872	-0.934	29.632	-0.053	-0.053	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.117	-0.060	26.335	0.004	0.004	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.765	-0.839	27.190	-0.074	-0.074	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.011	-0.018	24.478	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.811	0.892	27.429	0.059	0.059	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.015	0.003	23.080	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.013	-0.004	27.111	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.000	-0.009	26.140	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.855	-0.897	28.207	-0.066	-0.066	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.925	0.942	25.368	0.125	0.125	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.854	0.933	28.350	0.071	0.071	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.907	-0.950	29.984	-0.073	-0.073	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.008	-0.010	32.324	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.840	-0.891	30.570	-0.075	-0.075	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.038	-0.006	25.146	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.869	0.940	25.630	0.109	0.109	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.017	0.006	21.740	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.009	-0.007	20.951	0.009	0.009	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.010	-0.014	25.172	0.003	0.003	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.050	-0.039	27.492	0.011	0.011	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.000	0.003	22.420	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.006	0.012	26.540	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.001	-0.008	22.610	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	88	HIS	1	0.838	0.896	26.819	0.052	0.052	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.016	-0.009	24.247	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.025	-0.008	29.456	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.004	-0.004	29.862	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.056	0.030	32.147	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.043	-0.002	33.276	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.784	0.898	35.635	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.799	-0.903	37.823	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.019	0.011	33.526	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.846	0.923	36.779	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.779	-0.874	36.267	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.032	0.016	35.521	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.053	-0.030	33.127	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.017	0.008	31.514	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.048	0.037	30.790	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.959	0.981	29.806	-0.023	-0.023	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.043	-0.026	27.405	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.005	0.002	26.068	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.870	-0.937	26.156	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.056	-0.037	25.208	0.003	0.003	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.064	-0.041	21.231	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.009	-0.009	21.550	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.823	-0.880	22.469	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.820	0.909	21.918	-0.041	-0.041	0.000	0.000	0.000	0.000
112	A	112	TYR	0	-0.049	-0.021	18.961	0.020	0.020	0.000	0.000	0.000	0.000
113	A	114	SER	0	0.014	-0.005	12.390	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.014	-0.008	13.024	0.000	0.000	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.056	0.006	15.146	0.002	0.002	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.018	0.018	17.151	0.007	0.007	0.000	0.000	0.000	0.000
117	A	118	MET	0	-0.070	-0.024	11.306	0.019	0.019	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.008	0.001	16.559	0.006	0.006	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.807	-0.907	18.927	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.735	0.856	19.840	0.012	0.012	0.000	0.000	0.000	0.000
121	A	122	ALA	0	-0.053	-0.022	20.832	0.005	0.005	0.000	0.000	0.000	0.000
122	A	123	VAL	0	-0.043	-0.008	21.732	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.006	0.006	24.202	0.008	0.008	0.000	0.000	0.000	0.000
124	A	125	ILE	0	-0.009	-0.002	21.034	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	126	THR	0	0.005	0.007	25.407	0.009	0.009	0.000	0.000	0.000	0.000
126	A	127	HIS	1	0.825	0.894	26.851	0.016	0.016	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.039	-0.011	28.703	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	TYR	0	-0.060	-0.059	30.610	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.836	-0.890	32.740	-0.035	-0.035	0.000	0.000	0.000	0.000
130	A	131	VAL	0	-0.011	-0.013	34.239	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.003	0.004	36.258	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.014	0.008	37.446	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ALA	0	-0.019	-0.010	36.996	-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)