FMO DATABASE

FMODB ID: NN9GQ

Calculation Name: 3D7Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7Q

Chain ID: A

ChEMBL ID:

UniProt ID: B2JAN5

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-944315.987467
FMO2-HF: Nuclear repulsion	897585.608916
FMO2-HF: Total energy	-46730.378551
FMO2-MP2: Total energy	-46865.655671

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.
-6.366	-2.165	1.993	-2.453	-3.741	0.011

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 : 0.018 / 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	2	ASP	-1	-0.882	-0.945	2.509	0.274	2.329	0.490	-1.040	-1.504	0.001
4	A	3	LYS	1	0.881	0.959	2.748	-6.129	-4.487	0.893	-0.935	-1.600	0.010
5	A	4	LEU	0	0.015	0.021	4.226	-1.726	-1.503	0.002	-0.072	-0.153	0.000
6	A	5	ASN	0	0.051	0.009	6.158	-0.114	-0.114	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.863	-0.895	7.342	1.319	1.319	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.060	-0.068	7.982	-0.169	-0.169	0.000	0.000	0.000	0.000
9	A	8	ARG	1	0.883	0.914	10.074	0.016	0.016	0.000	0.000	0.000	0.000
10	A	9	THR	0	-0.049	-0.031	11.823	-0.100	-0.100	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.815	0.885	11.637	-0.808	-0.808	0.000	0.000	0.000	0.000
12	A	11	VAL	0	0.024	0.016	13.683	-0.056	-0.056	0.000	0.000	0.000	0.000
13	A	12	ARG	1	0.964	0.980	15.830	-0.129	-0.129	0.000	0.000	0.000	0.000
14	A	13	GLN	0	-0.028	-0.016	17.375	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.010	0.022	18.777	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	15	LEU	0	0.037	-0.009	19.509	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	16	THR	0	0.006	0.009	21.837	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.864	0.939	22.597	-0.178	-0.178	0.000	0.000	0.000	0.000
19	A	18	HIS	1	0.798	0.867	23.617	-0.137	-0.137	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.003	0.016	26.254	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	20	GLN	0	-0.034	-0.034	26.853	0.000	0.000	0.000	0.000	0.000	0.000
22	A	21	TYR	0	0.000	-0.004	27.724	0.000	0.000	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.985	1.030	31.262	-0.052	-0.052	0.000	0.000	0.000	0.000
24	A	23	PRO	0	-0.043	-0.018	33.217	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.041	-0.033	35.865	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	25	TYR	0	-0.006	-0.014	37.486	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	26	GLY	0	-0.005	-0.014	40.140	0.000	0.000	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.932	-0.940	41.711	0.023	0.023	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.043	-0.028	35.626	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.905	-0.943	34.642	0.032	0.032	0.000	0.000	0.000	0.000
31	A	30	VAL	0	-0.058	-0.049	29.258	0.001	0.001	0.000	0.000	0.000	0.000
32	A	31	GLU	-1	-0.929	-0.960	29.477	0.023	0.023	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.016	-0.021	23.730	0.000	0.000	0.000	0.000	0.000	0.000
34	A	33	ILE	0	0.005	0.003	23.806	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	34	PHE	0	-0.044	-0.033	19.324	0.013	0.013	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.847	-0.925	19.140	-0.063	-0.063	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.955	-0.998	14.017	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.975	-0.972	14.421	-0.225	-0.225	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.051	-0.029	15.044	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.812	-0.861	11.388	-0.112	-0.112	0.000	0.000	0.000	0.000
41	A	40	HIS	0	-0.060	-0.031	14.501	0.014	0.014	0.000	0.000	0.000	0.000
42	A	41	TYR	0	-0.036	-0.025	13.512	0.007	0.007	0.000	0.000	0.000	0.000
43	A	42	GLN	0	0.018	-0.011	19.174	0.011	0.011	0.000	0.000	0.000	0.000
44	A	43	ILE	0	-0.001	0.008	22.748	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	44	ILE	0	-0.011	-0.010	25.692	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	SER	0	0.013	0.026	29.067	0.000	0.000	0.000	0.000	0.000	0.000
47	A	46	VAL	0	-0.002	-0.010	32.554	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.013	0.008	35.227	0.000	0.000	0.000	0.000	0.000	0.000
49	A	48	TRP	0	-0.015	-0.002	38.930	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	49	ASN	0	0.019	0.016	42.161	0.001	0.001	0.000	0.000	0.000	0.000
51	A	50	ASN	0	0.039	0.002	43.974	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	51	GLN	0	0.007	-0.001	46.634	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	52	HIS	0	-0.008	0.008	40.832	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.918	0.977	37.607	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.029	-0.012	36.342	0.001	0.001	0.000	0.000	0.000	0.000
56	A	55	TYR	0	0.003	-0.022	31.482	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	56	GLY	0	0.017	0.006	32.089	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	57	PRO	0	-0.035	-0.012	26.573	0.003	0.003	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.002	0.020	27.661	0.000	0.000	0.000	0.000	0.000	0.000
60	A	59	MET	0	-0.045	-0.021	22.701	0.011	0.011	0.000	0.000	0.000	0.000
61	A	60	HIS	0	0.000	-0.002	19.852	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.034	-0.011	16.684	0.010	0.010	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.752	-0.851	15.555	0.022	0.022	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.023	-0.004	8.928	0.060	0.060	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.952	0.973	11.262	-0.057	-0.057	0.000	0.000	0.000	0.000
66	A	65	ASN	0	-0.017	-0.012	8.212	0.002	0.002	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.024	-0.034	2.652	0.573	0.854	0.608	-0.406	-0.484	0.000
68	A	67	LYS	1	0.860	0.960	6.622	-0.087	-0.087	0.000	0.000	0.000	0.000
69	A	68	ILE	0	0.041	0.025	10.061	-0.083	-0.083	0.000	0.000	0.000	0.000
70	A	69	TRP	0	-0.024	-0.011	12.878	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	70	ILE	0	0.017	-0.006	16.061	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	71	GLN	0	-0.081	-0.071	18.669	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	72	GLN	0	0.017	-0.002	21.580	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	73	ASN	0	0.033	0.035	23.771	0.007	0.007	0.000	0.000	0.000	0.000
75	A	74	THR	0	-0.017	0.012	26.146	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.078	-0.071	27.559	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	76	GLU	-1	-0.919	-0.972	29.705	0.079	0.079	0.000	0.000	0.000	0.000
78	A	77	ALA	0	-0.031	0.001	26.035	0.004	0.004	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.858	-0.941	23.979	0.136	0.136	0.000	0.000	0.000	0.000
80	A	79	ILE	0	0.018	-0.009	19.537	0.012	0.012	0.000	0.000	0.000	0.000
81	A	80	ALA	0	0.027	0.018	19.004	0.026	0.026	0.000	0.000	0.000	0.000
82	A	81	LEU	0	0.004	0.003	19.276	0.031	0.031	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.779	-0.869	21.192	0.168	0.168	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.029	-0.015	15.242	0.019	0.019	0.000	0.000	0.000	0.000
85	A	84	MET	0	-0.045	-0.026	16.537	0.035	0.035	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.936	-0.950	17.720	0.223	0.223	0.000	0.000	0.000	0.000
87	A	86	MET	0	-0.090	-0.033	16.243	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	87	GLY	0	0.001	0.004	14.564	0.073	0.073	0.000	0.000	0.000	0.000
89	A	88	ILE	0	-0.047	-0.008	11.388	0.124	0.124	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.838	-0.931	11.802	0.294	0.294	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.965	0.964	13.406	-0.200	-0.200	0.000	0.000	0.000	0.000
92	A	91	GLN	0	-0.025	-0.017	13.559	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.831	-0.914	8.543	0.840	0.840	0.000	0.000	0.000	0.000
94	A	93	ILE	0	0.019	0.025	11.492	0.004	0.004	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.009	-0.006	14.137	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	95	ILE	0	0.030	0.015	16.711	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.033	0.018	20.130	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	97	PHE	0	-0.002	0.003	20.900	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	98	HIS	0	0.006	0.026	23.418	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	99	THR	0	0.038	-0.018	23.723	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	100	PRO	0	0.078	0.020	22.561	0.007	0.007	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.926	0.981	23.585	-0.046	-0.046	0.000	0.000	0.000	0.000
103	A	102	MET	0	0.001	0.004	26.481	0.003	0.003	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.903	0.968	19.628	-0.067	-0.067	0.000	0.000	0.000	0.000
105	A	104	GLN	0	-0.035	-0.017	22.274	0.008	0.008	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.068	-0.039	23.806	0.000	0.000	0.000	0.000	0.000	0.000
107	A	106	SER	0	-0.043	-0.029	23.785	0.004	0.004	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.046	0.031	22.636	0.005	0.005	0.000	0.000	0.000	0.000
109	A	108	PHE	0	-0.037	-0.020	17.754	0.017	0.017	0.000	0.000	0.000	0.000
110	A	109	ALA	0	-0.030	0.005	14.683	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	110	VAL	0	0.006	-0.011	16.643	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.942	-0.971	12.617	0.018	0.018	0.000	0.000	0.000	0.000

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