FMO DATABASE

FMODB ID: 94J82

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1021659.305996
FMO2-HF: Nuclear repulsion	969301.127084
FMO2-HF: Total energy	-52358.178911
FMO2-MP2: Total energy	-52505.647636

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.
-0.464	1.975	0.013	-1.047	-1.404	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 : 0.016 / 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	0.013	0.018	3.708	-0.636	1.483	-0.001	-0.961	-1.157	0.001
4	A	4	ARG	1	0.874	0.934	6.028	0.475	0.475	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.017	0.004	9.425	0.141	0.141	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.872	0.938	12.807	0.327	0.327	0.000	0.000	0.000	0.000
7	A	7	TRP	0	-0.026	-0.006	16.173	0.020	0.020	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.056	-0.033	19.650	0.000	0.000	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.878	-0.937	22.015	-0.147	-0.147	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.012	0.023	24.642	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.010	-0.003	23.642	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.021	0.019	21.741	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.021	-0.026	16.936	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.012	0.018	14.402	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.010	0.001	12.817	-0.066	-0.066	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.857	-0.934	9.946	-0.321	-0.321	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.014	-0.020	7.483	-0.240	-0.240	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.046	0.009	3.412	-0.127	0.135	0.015	-0.085	-0.191	0.000
19	A	19	SER	0	-0.047	-0.004	5.340	0.282	0.340	-0.001	-0.001	-0.056	0.000
20	A	20	GLY	0	0.011	0.014	7.867	0.046	0.046	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.010	0.005	10.257	0.026	0.026	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.033	-0.026	11.454	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.012	0.004	13.524	0.035	0.035	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.034	-0.002	16.115	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	25	MET	0	-0.034	-0.012	13.983	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.780	-0.872	19.165	-0.174	-0.174	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.007	-0.016	22.609	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.068	-0.046	23.481	0.013	0.013	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.072	-0.049	26.512	0.008	0.008	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.021	0.009	24.509	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.975	-0.966	25.410	-0.111	-0.111	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.899	0.942	26.455	0.128	0.128	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.043	-0.022	21.890	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.070	0.051	20.302	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.022	0.006	20.941	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.010	-0.013	16.863	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.010	-0.012	17.942	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.806	-0.899	20.213	-0.145	-0.145	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.028	0.001	15.669	0.010	0.010	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.026	-0.014	15.518	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.005	0.007	17.309	0.014	0.014	0.000	0.000	0.000	0.000
42	A	42	MET	0	0.036	0.009	19.499	0.020	0.020	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.020	0.005	14.758	0.011	0.011	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.019	-0.001	16.851	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.021	0.010	18.812	0.019	0.019	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.019	0.009	18.543	0.015	0.015	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.012	0.062	15.738	0.006	0.006	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.074	0.025	17.524	0.024	0.024	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.025	0.011	21.097	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.032	-0.007	16.204	0.013	0.013	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.873	-0.949	18.778	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.031	-0.018	21.230	0.013	0.013	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.001	-0.009	23.121	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.008	-0.001	21.204	0.012	0.012	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.089	-0.039	23.288	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.033	0.012	26.083	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.041	0.038	25.146	0.006	0.006	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.949	0.967	21.226	-0.052	-0.052	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.055	-0.010	27.988	0.004	0.004	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.841	0.897	30.368	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.022	0.022	31.964	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.914	-0.962	32.055	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.044	-0.028	28.612	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.035	-0.027	31.026	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.862	-0.932	29.846	-0.033	-0.033	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.122	-0.062	26.041	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.867	-0.918	27.531	-0.054	-0.054	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.008	-0.017	24.533	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.890	0.959	27.325	0.044	0.044	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.009	0.001	23.317	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.012	0.005	27.392	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.009	-0.013	26.120	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.821	-0.875	28.222	-0.061	-0.061	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.923	0.965	26.373	0.113	0.113	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.914	0.966	28.282	0.074	0.074	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.931	-0.957	30.016	-0.075	-0.075	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.029	-0.033	31.856	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.869	-0.923	29.866	-0.083	-0.083	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.009	-0.013	24.710	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.918	0.989	25.675	0.109	0.109	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.015	-0.014	22.204	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.034	0.005	20.890	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.048	-0.035	25.072	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.036	-0.036	27.348	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.004	0.010	22.236	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.019	-0.002	26.259	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.009	-0.008	23.119	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	HIS	1	0.795	0.872	27.122	0.043	0.043	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.022	-0.011	24.624	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.002	0.004	29.781	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.012	-0.003	29.966	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.055	0.025	32.066	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.032	-0.005	33.343	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.811	0.932	35.688	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.845	-0.919	38.200	0.006	0.006	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.009	0.025	34.053	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.865	0.929	36.826	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.760	-0.853	36.318	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.019	0.009	35.943	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.071	-0.034	33.294	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.039	0.020	31.658	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.043	0.037	31.170	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.977	0.991	29.340	-0.031	-0.031	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.030	-0.019	27.516	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.005	-0.003	26.438	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.897	-0.957	26.741	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.052	-0.026	25.208	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.039	-0.009	22.536	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.017	-0.008	21.831	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.796	-0.859	22.937	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.845	0.922	22.146	-0.046	-0.046	0.000	0.000	0.000	0.000
112	A	112	TYR	0	-0.088	-0.062	19.436	0.016	0.016	0.000	0.000	0.000	0.000
113	A	114	SER	0	0.021	-0.007	12.174	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.021	-0.001	13.504	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.045	0.012	15.413	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.034	0.017	17.539	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	MET	0	-0.083	-0.036	11.243	0.011	0.011	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.002	0.012	16.509	0.001	0.001	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.851	-0.942	18.977	-0.019	-0.019	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.787	0.912	19.642	0.027	0.027	0.000	0.000	0.000	0.000
121	A	122	ALA	0	-0.065	-0.040	20.882	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	VAL	0	-0.059	-0.018	21.763	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	124	ASN	0	-0.006	-0.005	24.154	0.009	0.009	0.000	0.000	0.000	0.000
124	A	125	ILE	0	0.006	0.003	21.485	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	126	THR	0	0.033	0.016	25.825	0.008	0.008	0.000	0.000	0.000	0.000
126	A	127	HIS	1	0.832	0.894	27.176	0.013	0.013	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.015	0.007	29.096	0.004	0.004	0.000	0.000	0.000	0.000
128	A	129	TYR	0	-0.068	-0.072	31.033	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.828	-0.891	33.076	-0.026	-0.026	0.000	0.000	0.000	0.000
130	A	131	VAL	0	-0.017	-0.015	34.417	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.007	0.015	36.218	0.001	0.001	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.015	0.000	37.443	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ALA	0	-0.017	-0.008	37.162	-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)