FMO DATABASE

FMODB ID: N9MLQ

Calculation Name: 3DMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P8H7

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:

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1202313.344901
FMO2-HF: Nuclear repulsion	1146944.585132
FMO2-HF: Total energy	-55368.759769
FMO2-MP2: Total energy	-55530.838949

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-15.114	-13.549	8.784	-5.557	-4.792	-0.05

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.003

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	2	ALA	0	0.011	-0.007	3.016	-1.255	0.828	0.029	-1.063	-1.049	0.003
4	A	3	ASP	-1	-0.848	-0.910	1.919	-15.999	-16.750	8.757	-4.444	-3.562	-0.053
5	A	4	PRO	0	0.019	-0.003	4.482	0.829	0.864	-0.001	-0.014	-0.020	0.000
6	A	5	LYS	1	0.804	0.882	7.469	1.215	1.215	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.782	-0.890	4.609	-1.083	-0.885	-0.001	-0.036	-0.161	0.000
8	A	7	LEU	0	-0.032	-0.014	7.111	0.511	0.511	0.000	0.000	0.000	0.000
9	A	8	GLN	0	0.044	0.027	9.363	0.319	0.319	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.796	-0.873	10.457	-0.758	-0.758	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.824	0.917	7.027	0.979	0.979	0.000	0.000	0.000	0.000
12	A	11	PHE	0	0.014	0.012	12.786	0.111	0.111	0.000	0.000	0.000	0.000
13	A	12	TRP	0	0.006	-0.004	15.166	0.087	0.087	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.951	0.976	15.134	0.264	0.264	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.033	0.019	16.921	0.041	0.041	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.002	0.000	18.741	0.034	0.034	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.856	0.927	20.706	0.204	0.204	0.000	0.000	0.000	0.000
18	A	17	SER	0	-0.031	-0.029	21.374	0.012	0.012	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.799	-0.883	21.011	-0.069	-0.069	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.863	0.957	23.641	0.124	0.124	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.032	-0.013	25.326	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.015	0.008	23.988	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	22	MET	0	-0.011	0.004	26.358	0.007	0.007	0.000	0.000	0.000	0.000
24	A	23	LEU	0	-0.008	-0.007	27.419	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.026	0.008	29.340	0.011	0.011	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.036	-0.021	30.301	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	26	ASP	-1	-0.812	-0.896	29.485	-0.088	-0.088	0.000	0.000	0.000	0.000
28	A	27	GLY	0	-0.016	-0.005	31.515	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.078	-0.051	34.076	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.912	-0.941	36.239	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.828	-0.905	37.882	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	31	GLY	0	0.019	0.009	34.044	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	HIS	0	-0.065	-0.050	34.494	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	33	ALA	0	-0.017	0.000	32.015	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	34	ARG	1	0.889	0.928	32.514	0.057	0.057	0.000	0.000	0.000	0.000
36	A	35	PRO	0	-0.009	0.004	30.348	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	36	MET	0	-0.034	-0.009	29.988	0.003	0.003	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.002	-0.004	28.998	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.022	0.013	25.496	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.045	-0.030	26.816	0.011	0.011	0.000	0.000	0.000	0.000
41	A	40	ILE	0	0.027	0.016	21.137	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.800	-0.859	25.420	-0.131	-0.131	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.034	0.023	23.626	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.914	-0.973	19.964	-0.193	-0.193	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.048	-0.032	16.916	-0.040	-0.040	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.028	0.023	18.523	0.018	0.018	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.010	0.002	20.187	0.015	0.015	0.000	0.000	0.000	0.000
48	A	47	PRO	0	-0.029	-0.020	23.523	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	48	ILE	0	-0.015	0.004	21.872	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	49	TRP	0	0.037	0.014	25.943	0.014	0.014	0.000	0.000	0.000	0.000
51	A	50	PHE	0	0.019	-0.005	26.525	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	51	PHE	0	0.031	0.020	31.671	0.003	0.003	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.024	-0.004	35.114	0.003	0.003	0.000	0.000	0.000	0.000
54	A	53	SER	0	0.055	0.029	37.659	0.000	0.000	0.000	0.000	0.000	0.000
55	A	54	LYS	1	0.767	0.860	41.109	0.060	0.060	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.828	-0.891	43.385	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	56	ASN	0	-0.027	-0.023	36.199	0.004	0.004	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.028	0.000	40.569	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.000	0.006	33.994	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	59	ILE	0	0.020	0.012	37.988	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.038	-0.020	39.587	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	61	MET	0	-0.034	-0.007	38.656	0.002	0.002	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.058	-0.011	34.757	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.030	0.009	37.726	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.039	-0.027	36.697	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	65	GLY	0	-0.004	0.003	34.218	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.860	0.945	33.643	0.076	0.076	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.872	0.937	26.631	0.113	0.113	0.000	0.000	0.000	0.000
69	A	68	VAL	0	0.005	-0.002	27.431	0.011	0.011	0.000	0.000	0.000	0.000
70	A	69	ILE	0	0.000	0.005	24.389	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.038	0.000	24.493	0.011	0.011	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.021	0.008	22.928	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	72	PHE	0	0.001	-0.016	18.692	0.002	0.002	0.000	0.000	0.000	0.000
74	A	73	SER	0	0.007	0.000	20.206	0.008	0.008	0.000	0.000	0.000	0.000
75	A	74	SER	0	-0.014	-0.031	17.967	0.001	0.001	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.809	0.873	20.138	0.084	0.084	0.000	0.000	0.000	0.000
77	A	76	GLY	0	0.000	0.005	20.779	0.011	0.011	0.000	0.000	0.000	0.000
78	A	77	HIS	0	-0.070	-0.037	20.032	0.030	0.030	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.823	-0.872	15.022	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	79	LEU	0	-0.023	-0.005	12.821	0.015	0.015	0.000	0.000	0.000	0.000
81	A	80	PHE	0	0.005	0.004	15.755	0.005	0.005	0.000	0.000	0.000	0.000
82	A	81	ALA	0	-0.009	-0.013	16.099	-0.036	-0.036	0.000	0.000	0.000	0.000
83	A	82	SER	0	-0.020	-0.003	18.025	0.032	0.032	0.000	0.000	0.000	0.000
84	A	83	ILE	0	-0.008	-0.003	19.803	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.031	0.022	21.329	0.034	0.034	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.058	0.020	22.931	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	86	SER	0	-0.042	-0.016	25.661	0.019	0.019	0.000	0.000	0.000	0.000
88	A	87	LEU	0	0.009	0.006	29.369	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.881	0.914	31.494	0.129	0.129	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.759	-0.853	34.429	-0.073	-0.073	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.856	-0.932	34.701	-0.112	-0.112	0.000	0.000	0.000	0.000
92	A	91	THR	0	-0.007	-0.014	36.358	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.805	-0.909	36.901	-0.091	-0.091	0.000	0.000	0.000	0.000
94	A	93	PRO	0	0.009	0.003	38.310	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	94	ALA	0	0.046	0.021	38.132	0.000	0.000	0.000	0.000	0.000	0.000
96	A	95	VAL	0	-0.023	-0.024	32.716	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.011	-0.006	34.990	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.848	-0.919	37.330	-0.071	-0.071	0.000	0.000	0.000	0.000
99	A	98	ARG	1	0.744	0.841	31.728	0.123	0.123	0.000	0.000	0.000	0.000
100	A	99	LEU	0	-0.018	0.000	29.967	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	100	TRP	0	0.017	0.020	33.230	0.002	0.002	0.000	0.000	0.000	0.000
102	A	101	ASN	0	-0.031	-0.029	32.820	0.004	0.004	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.032	-0.001	35.956	0.002	0.002	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.014	-0.004	32.739	0.002	0.002	0.000	0.000	0.000	0.000
105	A	104	VAL	0	-0.006	0.007	34.228	0.002	0.002	0.000	0.000	0.000	0.000
106	A	105	ALA	0	-0.014	-0.017	36.856	0.003	0.003	0.000	0.000	0.000	0.000
107	A	106	ALA	0	-0.016	-0.007	39.551	0.003	0.003	0.000	0.000	0.000	0.000
108	A	107	TRP	0	-0.070	-0.017	36.582	0.004	0.004	0.000	0.000	0.000	0.000
109	A	108	TYR	0	-0.060	-0.047	38.628	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.886	-0.932	43.873	-0.033	-0.033	0.000	0.000	0.000	0.000
111	A	110	GLY	0	-0.056	-0.032	47.210	0.001	0.001	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.015	-0.014	44.397	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.789	0.863	39.727	0.068	0.068	0.000	0.000	0.000	0.000
114	A	113	ASP	-1	-0.908	-0.946	43.453	-0.053	-0.053	0.000	0.000	0.000	0.000
115	A	114	ASP	-1	-0.846	-0.902	44.933	-0.042	-0.042	0.000	0.000	0.000	0.000
116	A	115	PRO	0	-0.003	-0.008	45.734	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.823	0.904	45.689	0.039	0.039	0.000	0.000	0.000	0.000
118	A	117	LEU	0	0.013	0.025	39.702	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.026	-0.014	39.473	0.001	0.001	0.000	0.000	0.000	0.000
120	A	119	LEU	0	-0.007	0.002	33.268	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	120	LEU	0	0.012	0.002	33.048	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	121	ARG	1	0.766	0.859	29.724	0.137	0.137	0.000	0.000	0.000	0.000
123	A	122	LEU	0	0.012	0.012	24.961	0.006	0.006	0.000	0.000	0.000	0.000
124	A	123	ASP	-1	-0.786	-0.872	26.492	-0.173	-0.173	0.000	0.000	0.000	0.000
125	A	124	ALA	0	-0.052	-0.037	21.908	0.005	0.005	0.000	0.000	0.000	0.000
126	A	125	ASP	-1	-0.886	-0.925	22.469	-0.247	-0.247	0.000	0.000	0.000	0.000
127	A	126	HIS	0	-0.070	-0.057	17.904	-0.023	-0.023	0.000	0.000	0.000	0.000
128	A	127	ALA	0	0.031	0.002	16.659	0.037	0.037	0.000	0.000	0.000	0.000
129	A	128	GLN	0	-0.026	0.015	15.307	-0.055	-0.055	0.000	0.000	0.000	0.000
130	A	129	ILE	0	-0.017	-0.023	12.257	0.019	0.019	0.000	0.000	0.000	0.000
131	A	130	TRP	0	-0.018	-0.007	12.806	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.004	-0.002	8.566	-0.044	-0.044	0.000	0.000	0.000	0.000
133	A	132	ASN	0	-0.064	-0.032	12.760	0.105	0.105	0.000	0.000	0.000	0.000
134	A	133	GLY	0	0.008	0.012	13.686	0.036	0.036	0.000	0.000	0.000	0.000
135	A	134	SER	0	-0.023	-0.017	14.278	-0.066	-0.066	0.000	0.000	0.000	0.000
136	A	135	SER	0	0.005	-0.007	15.781	0.068	0.068	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.022	-0.002	18.373	-0.047	-0.047	0.000	0.000	0.000	0.000
138	A	137	LEU	0	0.028	0.017	20.442	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	138	ALA	0	0.019	0.004	23.968	0.009	0.009	0.000	0.000	0.000	0.000
140	A	139	GLY	0	0.033	0.012	26.330	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	140	ILE	0	-0.027	-0.016	28.096	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	141	LYS	1	0.925	0.967	31.559	-0.157	-0.157	0.000	0.000	0.000	0.000
143	A	142	VAL	0	0.013	0.010	33.558	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.005	0.004	36.550	0.002	0.002	0.000	0.000	0.000	0.000
145	A	144	LEU	0	0.015	-0.003	35.364	0.000	0.000	0.000	0.000	0.000	0.000
146	A	145	GLY	0	0.011	0.017	40.000	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)