FMO DATABASE

FMODB ID: G6KV1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1198661.732265
FMO2-HF: Nuclear repulsion	1143293.707276
FMO2-HF: Total energy	-55368.024989
FMO2-MP2: Total energy	-55530.061148

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.
-13.549	-7.328	1.755	-4.197	-3.78	-0.029

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 : 0.034 / q_NPA : 0.016

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	-0.006	-0.006	3.104	-2.008	0.316	0.027	-1.229	-1.123	0.004
4	A	3	ASP	-1	-0.874	-0.922	2.590	-13.263	-9.370	1.729	-2.962	-2.660	-0.033
5	A	4	PRO	0	0.024	-0.008	4.710	0.608	0.612	-0.001	-0.006	0.003	0.000
6	A	5	LYS	1	0.823	0.897	7.112	1.215	1.215	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.828	-0.914	5.027	-0.723	-0.723	0.000	0.000	0.000	0.000
8	A	7	LEU	0	-0.002	-0.007	7.055	0.530	0.530	0.000	0.000	0.000	0.000
9	A	8	GLN	0	0.016	0.008	9.320	0.321	0.321	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.814	-0.889	10.187	-0.708	-0.708	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.879	0.940	8.246	0.307	0.307	0.000	0.000	0.000	0.000
12	A	11	PHE	0	0.010	0.009	12.485	0.107	0.107	0.000	0.000	0.000	0.000
13	A	12	TRP	0	0.028	0.011	15.054	0.080	0.080	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.950	0.982	14.841	0.216	0.216	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.014	0.010	16.668	0.039	0.039	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.010	0.000	18.385	0.027	0.027	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.877	0.956	20.372	0.171	0.171	0.000	0.000	0.000	0.000
18	A	17	SER	0	-0.049	-0.030	21.362	0.010	0.010	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.855	-0.934	21.338	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.902	0.966	23.683	0.095	0.095	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.024	-0.009	25.506	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.000	0.014	24.199	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	22	MET	0	-0.028	0.006	26.565	0.004	0.004	0.000	0.000	0.000	0.000
24	A	23	LEU	0	0.013	-0.006	28.091	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.023	0.019	29.808	0.008	0.008	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.032	-0.029	30.727	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	26	ASP	-1	-0.902	-0.958	29.027	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	27	GLY	0	-0.016	-0.013	31.662	0.000	0.000	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.106	-0.046	34.086	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.908	-0.940	36.391	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.881	-0.941	37.940	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	31	GLY	0	0.021	-0.006	34.694	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	32	HIS	0	-0.049	-0.031	35.151	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	33	ALA	0	-0.011	0.002	32.319	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	34	ARG	1	0.936	0.949	32.917	0.040	0.040	0.000	0.000	0.000	0.000
36	A	35	PRO	0	-0.013	0.005	30.726	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	36	MET	0	-0.023	-0.005	30.305	0.002	0.002	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.011	-0.005	29.204	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.014	0.010	25.398	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.088	-0.047	27.075	0.009	0.009	0.000	0.000	0.000	0.000
41	A	40	ILE	0	0.037	0.018	21.208	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.907	-0.960	25.638	-0.116	-0.116	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.019	0.016	23.708	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.921	-0.989	19.579	-0.177	-0.177	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.061	-0.041	17.134	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.022	0.022	18.705	0.017	0.017	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.007	0.020	20.341	0.021	0.021	0.000	0.000	0.000	0.000
48	A	47	PRO	0	-0.012	-0.023	23.353	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	48	ILE	0	-0.032	-0.007	21.993	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	49	TRP	0	0.016	0.003	26.164	0.010	0.010	0.000	0.000	0.000	0.000
51	A	50	PHE	0	0.025	0.000	26.839	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	PHE	0	0.037	0.025	31.902	0.001	0.001	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.015	-0.008	35.298	0.004	0.004	0.000	0.000	0.000	0.000
54	A	53	SER	0	0.081	0.058	37.888	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	LYS	1	0.847	0.903	41.277	0.051	0.051	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.889	-0.943	43.452	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	56	ASN	0	0.000	-0.001	36.561	0.005	0.005	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.022	-0.001	40.163	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	58	LEU	0	-0.020	-0.011	34.310	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	59	ILE	0	0.026	0.019	38.356	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.014	-0.004	39.950	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	61	MET	0	-0.054	-0.013	38.763	0.001	0.001	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.045	-0.013	35.199	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.048	0.027	37.838	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.050	-0.029	37.017	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	65	GLY	0	-0.006	0.001	34.259	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.904	0.974	33.895	0.062	0.062	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.917	0.966	27.030	0.094	0.094	0.000	0.000	0.000	0.000
69	A	68	VAL	0	-0.007	-0.005	27.798	0.010	0.010	0.000	0.000	0.000	0.000
70	A	69	ILE	0	0.039	0.017	24.155	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	70	GLY	0	-0.009	-0.014	24.796	0.011	0.011	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.016	-0.004	23.460	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	72	PHE	0	0.010	-0.006	18.563	0.002	0.002	0.000	0.000	0.000	0.000
74	A	73	SER	0	-0.011	-0.008	20.303	0.009	0.009	0.000	0.000	0.000	0.000
75	A	74	SER	0	-0.005	-0.029	17.989	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.921	0.939	20.304	0.039	0.039	0.000	0.000	0.000	0.000
77	A	76	GLY	0	-0.026	-0.013	20.899	0.009	0.009	0.000	0.000	0.000	0.000
78	A	77	HIS	0	-0.047	-0.016	20.475	0.026	0.026	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.845	-0.882	15.263	0.066	0.066	0.000	0.000	0.000	0.000
80	A	79	LEU	0	-0.017	-0.007	12.914	0.024	0.024	0.000	0.000	0.000	0.000
81	A	80	PHE	0	0.006	0.004	15.974	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	81	ALA	0	-0.003	-0.006	16.529	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	82	SER	0	-0.023	0.008	18.303	0.019	0.019	0.000	0.000	0.000	0.000
84	A	83	ILE	0	-0.008	-0.012	19.803	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.053	0.039	21.626	0.028	0.028	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.056	0.011	23.205	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	86	SER	0	-0.043	-0.006	25.929	0.018	0.018	0.000	0.000	0.000	0.000
88	A	87	LEU	0	0.019	0.019	29.522	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.984	0.978	31.806	0.114	0.114	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.805	-0.890	34.504	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.918	-0.974	34.791	-0.096	-0.096	0.000	0.000	0.000	0.000
92	A	91	THR	0	0.016	0.008	36.367	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.860	-0.923	36.735	-0.081	-0.081	0.000	0.000	0.000	0.000
94	A	93	PRO	0	0.024	-0.004	38.157	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	94	ALA	0	0.046	0.031	37.747	0.001	0.001	0.000	0.000	0.000	0.000
96	A	95	VAL	0	-0.025	-0.019	32.691	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.010	-0.005	34.983	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.859	-0.927	37.048	-0.062	-0.062	0.000	0.000	0.000	0.000
99	A	98	ARG	1	0.852	0.938	32.107	0.114	0.114	0.000	0.000	0.000	0.000
100	A	99	LEU	0	-0.023	-0.008	29.967	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	100	TRP	0	0.006	0.019	33.225	0.003	0.003	0.000	0.000	0.000	0.000
102	A	101	ASN	0	0.006	-0.007	32.484	0.003	0.003	0.000	0.000	0.000	0.000
103	A	102	PRO	0	0.044	0.010	35.900	0.002	0.002	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.015	-0.003	32.408	0.004	0.004	0.000	0.000	0.000	0.000
105	A	104	VAL	0	0.000	0.002	34.512	0.003	0.003	0.000	0.000	0.000	0.000
106	A	105	ALA	0	-0.037	-0.028	37.093	0.002	0.002	0.000	0.000	0.000	0.000
107	A	106	ALA	0	-0.008	-0.004	39.573	0.002	0.002	0.000	0.000	0.000	0.000
108	A	107	TRP	0	-0.067	-0.022	36.239	0.004	0.004	0.000	0.000	0.000	0.000
109	A	108	TYR	0	-0.054	-0.032	38.646	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.895	-0.940	43.724	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	110	GLY	0	-0.042	-0.022	47.261	0.000	0.000	0.000	0.000	0.000	0.000
112	A	111	GLY	0	-0.023	-0.008	44.240	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.826	0.878	40.200	0.057	0.057	0.000	0.000	0.000	0.000
114	A	113	ASP	-1	-0.915	-0.943	43.636	-0.044	-0.044	0.000	0.000	0.000	0.000
115	A	114	ASP	-1	-0.894	-0.939	44.886	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	115	PRO	0	0.005	-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	45.935	0.030	0.030	0.000	0.000	0.000	0.000
118	A	117	LEU	0	0.026	0.022	39.361	0.000	0.000	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.064	-0.037	39.517	0.000	0.000	0.000	0.000	0.000	0.000
120	A	119	LEU	0	0.005	0.011	33.552	0.000	0.000	0.000	0.000	0.000	0.000
121	A	120	LEU	0	-0.008	-0.010	33.223	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	121	ARG	1	0.812	0.901	29.538	0.124	0.124	0.000	0.000	0.000	0.000
123	A	122	LEU	0	0.009	0.005	25.578	0.005	0.005	0.000	0.000	0.000	0.000
124	A	123	ASP	-1	-0.857	-0.930	26.545	-0.158	-0.158	0.000	0.000	0.000	0.000
125	A	124	ALA	0	-0.038	-0.031	21.790	0.006	0.006	0.000	0.000	0.000	0.000
126	A	125	ASP	-1	-0.870	-0.914	22.473	-0.232	-0.232	0.000	0.000	0.000	0.000
127	A	126	HIS	0	-0.094	-0.072	17.798	-0.025	-0.025	0.000	0.000	0.000	0.000
128	A	127	ALA	0	0.030	0.002	16.578	0.036	0.036	0.000	0.000	0.000	0.000
129	A	128	GLN	0	-0.041	0.008	15.399	-0.050	-0.050	0.000	0.000	0.000	0.000
130	A	129	ILE	0	-0.008	-0.015	12.281	0.026	0.026	0.000	0.000	0.000	0.000
131	A	130	TRP	0	-0.019	-0.010	12.780	0.005	0.005	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.006	-0.011	8.594	-0.026	-0.026	0.000	0.000	0.000	0.000
133	A	132	ASN	0	-0.052	-0.012	13.138	0.077	0.077	0.000	0.000	0.000	0.000
134	A	133	GLY	0	0.003	0.005	13.704	0.037	0.037	0.000	0.000	0.000	0.000
135	A	134	SER	0	-0.033	-0.026	14.409	-0.077	-0.077	0.000	0.000	0.000	0.000
136	A	135	SER	0	0.017	-0.004	15.995	0.056	0.056	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.013	0.008	18.580	-0.045	-0.045	0.000	0.000	0.000	0.000
138	A	137	LEU	0	0.013	0.006	20.522	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	138	ALA	0	0.015	0.009	23.989	0.011	0.011	0.000	0.000	0.000	0.000
140	A	139	GLY	0	0.006	0.004	26.197	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	140	ILE	0	0.005	-0.004	28.016	-0.010	-0.010	0.000	0.000	0.000	0.000
142	A	141	LYS	1	0.917	0.957	31.692	-0.146	-0.146	0.000	0.000	0.000	0.000
143	A	142	VAL	0	0.033	0.020	34.070	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.011	-0.004	36.796	0.002	0.002	0.000	0.000	0.000	0.000
145	A	144	LEU	0	0.014	0.002	35.765	0.000	0.000	0.000	0.000	0.000	0.000
146	A	145	GLY	0	0.013	0.016	40.151	-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)