FMO DATABASE

FMODB ID: 85ZQY

Calculation Name: 3DMB-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3DMB

Chain ID: A

ChEMBL ID:
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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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1199026.369085
FMO2-HF: Nuclear repulsion	1143657.879779
FMO2-HF: Total energy	-55368.489305
FMO2-MP2: Total energy	-55530.549917

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.
-16.42	-12.495	6.063	-5.23	-4.757	-0.048

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 : 0.015 / 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	-0.003	-0.007	3.050	-1.939	0.449	0.028	-1.261	-1.155	0.003
4	A	3	ASP	-1	-0.857	-0.911	2.049	-16.333	-14.974	6.037	-3.945	-3.450	-0.051
5	A	4	PRO	0	0.032	-0.007	4.669	0.712	0.721	-0.001	-0.008	0.000	0.000
6	A	5	LYS	1	0.807	0.885	7.104	1.204	1.204	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.826	-0.919	4.992	-0.848	-0.679	-0.001	-0.016	-0.152	0.000
8	A	7	LEU	0	-0.015	-0.004	7.055	0.556	0.556	0.000	0.000	0.000	0.000
9	A	8	GLN	0	0.032	0.019	9.320	0.333	0.333	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.804	-0.875	10.177	-0.713	-0.713	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.890	0.945	7.455	0.478	0.478	0.000	0.000	0.000	0.000
12	A	11	PHE	0	0.008	0.007	12.485	0.113	0.113	0.000	0.000	0.000	0.000
13	A	12	TRP	0	0.021	0.001	15.054	0.087	0.087	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.953	0.982	14.743	0.219	0.219	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.008	0.009	16.670	0.042	0.042	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.006	-0.003	18.385	0.030	0.030	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.866	0.942	20.371	0.183	0.183	0.000	0.000	0.000	0.000
18	A	17	SER	0	-0.035	-0.020	21.282	0.012	0.012	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.841	-0.923	21.295	-0.035	-0.035	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.884	0.959	23.670	0.104	0.104	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.026	-0.005	25.506	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.011	0.008	24.111	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	22	MET	0	-0.015	0.012	26.565	0.005	0.005	0.000	0.000	0.000	0.000
24	A	23	LEU	0	0.005	-0.007	27.695	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.029	0.017	29.760	0.009	0.009	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.045	-0.029	30.679	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	26	ASP	-1	-0.820	-0.906	29.619	-0.084	-0.084	0.000	0.000	0.000	0.000
28	A	27	GLY	0	-0.038	-0.024	31.619	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.100	-0.053	34.047	0.002	0.002	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.897	-0.930	36.350	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.859	-0.922	37.897	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	31	GLY	0	0.023	0.003	34.646	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	32	HIS	0	-0.054	-0.056	35.102	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	33	ALA	0	0.000	0.009	32.330	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	34	ARG	1	0.904	0.943	32.853	0.049	0.049	0.000	0.000	0.000	0.000
36	A	35	PRO	0	-0.018	0.001	30.731	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	36	MET	0	-0.017	-0.001	30.291	0.003	0.003	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.006	-0.008	29.199	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.015	0.013	25.391	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.033	-0.014	27.058	0.011	0.011	0.000	0.000	0.000	0.000
41	A	40	ILE	0	0.034	0.018	21.285	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.815	-0.860	25.638	-0.121	-0.121	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.028	0.019	23.708	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.895	-0.974	19.572	-0.177	-0.177	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.069	-0.043	17.093	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.022	0.020	18.701	0.018	0.018	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.004	0.022	20.341	0.022	0.022	0.000	0.000	0.000	0.000
48	A	47	PRO	0	-0.007	-0.019	23.353	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	48	ILE	0	-0.032	-0.010	22.102	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	49	TRP	0	0.030	0.005	26.164	0.012	0.012	0.000	0.000	0.000	0.000
51	A	50	PHE	0	0.026	0.001	26.707	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	PHE	0	0.033	0.023	31.902	0.001	0.001	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.015	-0.009	35.298	0.004	0.004	0.000	0.000	0.000	0.000
54	A	53	SER	0	0.054	0.037	37.888	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	LYS	1	0.831	0.888	41.277	0.057	0.057	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.849	-0.900	43.452	-0.038	-0.038	0.000	0.000	0.000	0.000
57	A	56	ASN	0	-0.019	-0.009	36.600	0.004	0.004	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.027	-0.002	40.166	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	58	LEU	0	-0.009	-0.002	34.276	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	59	ILE	0	0.027	0.017	38.305	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.022	-0.008	39.899	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	61	MET	0	-0.044	-0.014	38.902	0.001	0.001	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.045	-0.014	35.048	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.038	0.020	37.792	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.046	-0.028	36.791	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	65	GLY	0	-0.007	0.001	34.213	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.895	0.970	33.862	0.073	0.073	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.883	0.937	27.093	0.109	0.109	0.000	0.000	0.000	0.000
69	A	68	VAL	0	-0.011	-0.010	27.744	0.011	0.011	0.000	0.000	0.000	0.000
70	A	69	ILE	0	0.023	0.009	24.395	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.003	-0.007	24.745	0.012	0.012	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.023	-0.007	23.409	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	72	PHE	0	0.011	-0.008	18.606	0.004	0.004	0.000	0.000	0.000	0.000
74	A	73	SER	0	0.000	0.004	20.317	0.005	0.005	0.000	0.000	0.000	0.000
75	A	74	SER	0	-0.009	-0.032	18.115	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.850	0.893	20.304	0.054	0.054	0.000	0.000	0.000	0.000
77	A	76	GLY	0	-0.018	-0.007	20.898	0.009	0.009	0.000	0.000	0.000	0.000
78	A	77	HIS	0	-0.056	-0.024	20.424	0.026	0.026	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.843	-0.885	15.321	0.045	0.045	0.000	0.000	0.000	0.000
80	A	79	LEU	0	-0.013	-0.005	12.865	0.017	0.017	0.000	0.000	0.000	0.000
81	A	80	PHE	0	0.008	0.007	15.974	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	81	ALA	0	-0.004	-0.008	16.479	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	82	SER	0	-0.021	0.010	18.252	0.024	0.024	0.000	0.000	0.000	0.000
84	A	83	ILE	0	-0.015	-0.016	19.755	-0.032	-0.032	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.045	0.035	21.576	0.031	0.031	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.056	0.011	23.159	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	86	SER	0	-0.042	-0.005	25.883	0.019	0.019	0.000	0.000	0.000	0.000
88	A	87	LEU	0	0.012	0.014	29.476	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.921	0.948	31.757	0.125	0.125	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.774	-0.852	34.504	-0.068	-0.068	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.874	-0.941	34.799	-0.107	-0.107	0.000	0.000	0.000	0.000
92	A	91	THR	0	0.016	-0.009	36.367	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.842	-0.915	36.706	-0.088	-0.088	0.000	0.000	0.000	0.000
94	A	93	PRO	0	0.026	-0.003	38.157	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	94	ALA	0	0.038	0.022	37.821	0.001	0.001	0.000	0.000	0.000	0.000
96	A	95	VAL	0	-0.033	-0.020	32.715	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.009	-0.008	34.983	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.852	-0.917	37.048	-0.065	-0.065	0.000	0.000	0.000	0.000
99	A	98	ARG	1	0.761	0.846	31.765	0.116	0.116	0.000	0.000	0.000	0.000
100	A	99	LEU	0	-0.018	-0.004	29.882	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	100	TRP	0	0.021	0.022	33.225	0.003	0.003	0.000	0.000	0.000	0.000
102	A	101	ASN	0	-0.031	-0.026	32.877	0.004	0.004	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.044	0.006	35.976	0.002	0.002	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.010	0.004	32.557	0.002	0.002	0.000	0.000	0.000	0.000
105	A	104	VAL	0	-0.016	-0.008	34.444	0.003	0.003	0.000	0.000	0.000	0.000
106	A	105	ALA	0	-0.033	-0.025	37.093	0.002	0.002	0.000	0.000	0.000	0.000
107	A	106	ALA	0	-0.007	-0.003	39.586	0.002	0.002	0.000	0.000	0.000	0.000
108	A	107	TRP	0	-0.069	-0.024	36.340	0.004	0.004	0.000	0.000	0.000	0.000
109	A	108	TYR	0	-0.063	-0.038	38.733	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.898	-0.942	43.724	-0.027	-0.027	0.000	0.000	0.000	0.000
111	A	110	GLY	0	-0.037	-0.020	47.284	0.001	0.001	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.029	-0.012	44.241	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.815	0.870	39.975	0.061	0.061	0.000	0.000	0.000	0.000
114	A	113	ASP	-1	-0.919	-0.949	43.636	-0.048	-0.048	0.000	0.000	0.000	0.000
115	A	114	ASP	-1	-0.888	-0.936	44.959	-0.038	-0.038	0.000	0.000	0.000	0.000
116	A	115	PRO	0	0.002	-0.008	45.707	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.784	0.893	45.961	0.034	0.034	0.000	0.000	0.000	0.000
118	A	117	LEU	0	0.027	0.020	39.834	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.055	-0.032	39.684	0.000	0.000	0.000	0.000	0.000	0.000
120	A	119	LEU	0	0.001	0.010	33.488	0.000	0.000	0.000	0.000	0.000	0.000
121	A	120	LEU	0	0.002	-0.008	33.153	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	121	ARG	1	0.772	0.860	29.570	0.134	0.134	0.000	0.000	0.000	0.000
123	A	122	LEU	0	0.018	0.012	25.252	0.004	0.004	0.000	0.000	0.000	0.000
124	A	123	ASP	-1	-0.837	-0.903	26.544	-0.168	-0.168	0.000	0.000	0.000	0.000
125	A	124	ALA	0	-0.030	-0.029	21.817	0.006	0.006	0.000	0.000	0.000	0.000
126	A	125	ASP	-1	-0.872	-0.919	22.430	-0.254	-0.254	0.000	0.000	0.000	0.000
127	A	126	HIS	0	-0.087	-0.064	17.850	-0.027	-0.027	0.000	0.000	0.000	0.000
128	A	127	ALA	0	0.026	-0.004	16.609	0.040	0.040	0.000	0.000	0.000	0.000
129	A	128	GLN	0	-0.037	0.011	15.360	-0.055	-0.055	0.000	0.000	0.000	0.000
130	A	129	ILE	0	-0.010	-0.020	12.367	0.031	0.031	0.000	0.000	0.000	0.000
131	A	130	TRP	0	-0.016	-0.008	12.736	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.002	-0.004	8.752	-0.025	-0.025	0.000	0.000	0.000	0.000
133	A	132	ASN	0	-0.058	-0.016	13.138	0.077	0.077	0.000	0.000	0.000	0.000
134	A	133	GLY	0	0.008	0.007	13.704	0.038	0.038	0.000	0.000	0.000	0.000
135	A	134	SER	0	-0.024	-0.024	14.409	-0.068	-0.068	0.000	0.000	0.000	0.000
136	A	135	SER	0	0.011	0.002	15.995	0.058	0.058	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.031	-0.002	18.580	-0.044	-0.044	0.000	0.000	0.000	0.000
138	A	137	LEU	0	0.019	0.008	20.522	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	138	ALA	0	0.016	0.006	23.989	0.012	0.012	0.000	0.000	0.000	0.000
140	A	139	GLY	0	0.015	0.009	26.197	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	140	ILE	0	0.000	-0.007	28.016	-0.010	-0.010	0.000	0.000	0.000	0.000
142	A	141	LYS	1	0.917	0.960	31.692	-0.151	-0.151	0.000	0.000	0.000	0.000
143	A	142	VAL	0	0.030	0.015	34.070	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.005	0.003	36.795	0.002	0.002	0.000	0.000	0.000	0.000
145	A	144	LEU	0	0.010	-0.002	35.627	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	145	GLY	0	0.017	0.018	40.150	-0.005	-0.005	0.000	0.000	0.000	0.000

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