FMO DATABASE

FMODB ID: 3Q1YL

Calculation Name: 4C9Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C9Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q96BD8

Base Structure: X-ray

Registration Date: 2023-06-20

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1107464.912493
FMO2-HF: Nuclear repulsion	1056693.010094
FMO2-HF: Total energy	-50771.902399
FMO2-MP2: Total energy	-50919.790208

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-3.324	-2	-0.011	-0.554	-0.761	0.002

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.013

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

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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	4	LYS	1	0.928	0.975	3.814	-0.882	0.262	-0.009	-0.487	-0.649	0.002
4	A	5	GLU	-1	-0.846	-0.921	6.388	1.398	1.398	0.000	0.000	0.000	0.000
5	A	6	MET	0	-0.060	-0.017	8.699	-0.225	-0.225	0.000	0.000	0.000	0.000
6	A	7	PRO	0	0.029	0.020	12.090	0.075	0.075	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.040	0.010	13.703	0.016	0.016	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.025	0.001	17.012	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.039	0.009	19.966	0.023	0.023	0.000	0.000	0.000	0.000
10	A	11	CYS	0	0.037	0.007	22.232	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.872	-0.935	25.468	-0.069	-0.069	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.770	-0.840	20.470	-0.118	-0.118	0.000	0.000	0.000	0.000
13	A	14	PHE	0	0.005	-0.005	24.886	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.006	-0.012	26.415	0.013	0.013	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.021	0.025	28.307	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.033	0.006	25.916	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.027	0.011	29.038	0.008	0.008	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.056	0.014	32.093	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.027	0.005	32.957	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	MET	0	-0.059	-0.020	27.906	0.004	0.004	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.829	0.918	29.617	0.021	0.021	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.012	0.000	31.177	0.013	0.013	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.941	0.954	32.631	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.080	-0.025	27.410	0.008	0.008	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.081	0.018	29.122	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.029	-0.044	22.335	0.011	0.011	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.045	0.010	24.275	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.044	0.048	23.771	0.010	0.010	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.000	0.005	21.576	0.018	0.018	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.048	0.024	19.668	0.013	0.013	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.836	-0.904	18.988	0.220	0.220	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.037	-0.024	19.686	0.040	0.040	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.013	-0.008	15.225	0.039	0.039	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.907	0.948	15.143	-0.178	-0.178	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.807	-0.898	15.195	0.528	0.528	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.023	-0.016	14.636	0.059	0.059	0.000	0.000	0.000	0.000
37	A	38	ASN	0	0.006	-0.011	11.221	0.008	0.008	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.852	0.931	11.377	-0.258	-0.258	0.000	0.000	0.000	0.000
39	A	40	ALA	0	-0.009	0.008	12.952	0.148	0.148	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.014	-0.008	8.916	0.072	0.072	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.009	-0.002	7.402	0.342	0.342	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.051	-0.032	9.145	0.296	0.296	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.812	0.920	11.927	-0.456	-0.456	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.014	-0.013	6.876	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.928	0.968	7.174	-2.862	-2.862	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.009	0.016	8.721	-0.172	-0.172	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.035	-0.018	9.688	-0.127	-0.127	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.027	-0.010	4.743	-0.659	-0.574	-0.001	-0.009	-0.075	0.000
49	A	50	GLN	0	-0.014	0.017	8.759	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.026	0.004	11.653	-0.148	-0.148	0.000	0.000	0.000	0.000
51	A	52	LYS	1	1.019	0.979	14.374	-0.422	-0.422	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.958	0.979	17.259	-0.321	-0.321	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.001	0.002	16.141	-0.026	-0.026	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.077	0.008	14.706	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.080	0.058	18.727	-0.050	-0.050	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.054	0.004	21.391	0.023	0.023	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.052	0.023	21.133	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.004	-0.013	16.263	0.029	0.029	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.857	0.928	18.225	-0.329	-0.329	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.013	0.009	20.194	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.011	0.014	17.604	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.016	-0.002	13.647	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	64	HIS	0	0.014	-0.011	17.178	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.867	0.925	18.910	-0.401	-0.401	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.024	-0.035	14.514	0.002	0.002	0.000	0.000	0.000	0.000
66	A	67	ILE	0	-0.040	-0.021	15.475	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.906	-0.944	18.168	0.166	0.166	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.855	-0.918	18.451	0.293	0.293	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.892	-0.913	14.053	0.188	0.188	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.032	-0.014	18.210	-0.030	-0.030	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.960	0.952	18.180	0.004	0.004	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.886	-0.926	18.370	-0.106	-0.106	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.072	-0.065	15.418	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.991	1.007	12.637	0.208	0.208	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.026	-0.015	9.851	-0.079	-0.079	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.881	0.951	9.658	0.050	0.050	0.000	0.000	0.000	0.000
77	A	78	TYR	0	0.056	0.030	4.168	0.355	0.450	-0.001	-0.058	-0.037	0.000
78	A	79	PHE	0	-0.002	-0.005	10.898	-0.098	-0.098	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.021	0.020	13.766	0.103	0.103	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.012	0.006	16.175	-0.078	-0.078	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.796	-0.916	19.839	0.183	0.183	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.002	-0.001	21.764	0.010	0.010	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.664	-0.813	16.776	0.461	0.461	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.037	-0.007	18.449	0.033	0.033	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.851	0.934	20.297	-0.197	-0.197	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.919	-0.939	18.970	0.404	0.404	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.020	0.001	15.520	0.039	0.039	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.068	-0.047	18.105	0.012	0.012	0.000	0.000	0.000	0.000
89	A	90	THR	0	0.038	0.018	20.620	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.037	-0.009	21.187	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.983	0.982	24.276	-0.179	-0.179	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.007	0.010	25.318	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.781	-0.907	26.929	0.107	0.107	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.970	0.991	29.322	-0.070	-0.070	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.956	0.974	28.862	-0.118	-0.118	0.000	0.000	0.000	0.000
96	A	97	PHE	0	0.073	0.041	21.662	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	98	HIS	1	0.846	0.891	25.469	-0.118	-0.118	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.030	-0.006	27.243	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.020	0.010	22.471	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.019	0.001	21.371	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.032	-0.007	23.290	-0.023	-0.023	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.031	0.018	23.860	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.039	0.022	18.729	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.913	0.967	20.558	0.000	0.000	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.019	-0.009	22.387	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	107	CYS	0	-0.037	-0.012	21.131	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.922	0.959	19.163	0.179	0.179	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.773	0.850	15.806	0.072	0.072	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.011	0.012	15.528	0.001	0.001	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.060	-0.028	17.514	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.832	-0.916	19.274	0.052	0.052	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.011	0.015	18.939	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.876	0.915	21.667	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.081	0.045	24.733	-0.011	-0.011	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.039	0.013	25.603	0.013	0.013	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.021	-0.005	27.732	0.009	0.009	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.006	0.018	21.875	0.008	0.008	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.041	-0.033	23.176	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.842	0.931	18.662	-0.081	-0.081	0.000	0.000	0.000	0.000
120	A	121	TYR	0	-0.024	-0.021	18.006	-0.049	-0.049	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.005	-0.009	14.052	0.043	0.043	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.009	0.003	10.693	-0.050	-0.050	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.034	-0.028	11.433	-0.174	-0.174	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)