FMO DATABASE

FMODB ID: VQJZ1

Calculation Name: 3H9X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H9X

Chain ID: A

ChEMBL ID:

UniProt ID: Q880Y4

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1055509.233377
FMO2-HF: Nuclear repulsion	1007815.33886
FMO2-HF: Total energy	-47693.894517
FMO2-MP2: Total energy	-47834.81391

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:1:MET)

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

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.
-26.259	-16.434	15.568	-7.36	-18.031	-0.012

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / 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	3	ARG	1	0.821	0.870	3.582	-2.321	0.170	0.000	-1.382	-1.108	-0.001
4	A	4	GLN	0	-0.012	-0.003	5.901	0.051	0.051	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.052	0.020	2.352	-4.422	-2.399	3.423	-2.064	-3.382	-0.020
6	A	6	PHE	0	-0.015	0.000	2.368	-1.358	1.182	1.494	-1.442	-2.592	-0.011
7	A	7	ILE	0	0.029	0.018	2.961	2.311	1.600	0.150	0.932	-0.370	0.000
8	A	8	ASP	-1	-0.847	-0.920	6.423	-0.200	-0.200	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.055	-0.038	4.167	0.768	1.126	0.001	-0.040	-0.319	0.000
10	A	10	ALA	0	0.004	0.007	6.402	0.096	0.096	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.007	-0.010	7.964	0.079	0.079	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.815	0.886	9.868	-0.117	-0.117	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.829	0.913	8.861	-0.632	-0.632	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.082	-0.069	7.543	0.045	0.045	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.841	-0.897	12.421	0.025	0.025	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.061	0.000	11.670	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.882	0.934	12.187	0.294	0.294	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.014	0.016	11.809	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.784	-0.866	13.528	-0.265	-0.265	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.009	-0.018	14.091	-0.096	-0.096	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.049	-0.024	17.126	0.045	0.045	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.010	0.013	16.319	0.021	0.021	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.802	-0.893	21.114	-0.369	-0.369	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.881	0.928	23.575	0.329	0.329	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.081	-0.040	18.758	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.087	0.043	18.215	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.810	-0.889	13.381	-1.078	-1.078	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.129	-0.063	13.315	-0.158	-0.158	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.018	0.009	11.694	0.108	0.108	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.036	-0.024	12.361	-0.133	-0.133	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.040	0.015	9.545	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.812	0.865	12.339	0.325	0.325	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.824	0.924	14.695	0.163	0.163	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.043	0.014	17.399	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.811	-0.876	19.999	-0.053	-0.053	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.063	-0.049	19.997	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.800	-0.879	20.111	-0.217	-0.217	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.882	0.956	18.665	0.092	0.092	0.000	0.000	0.000	0.000
39	A	39	TRP	0	-0.002	-0.024	14.598	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.032	-0.019	8.897	0.024	0.024	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.013	0.021	8.171	-0.052	-0.052	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.017	-0.004	10.176	0.099	0.099	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.001	0.017	7.105	-0.188	-0.188	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.034	-0.012	10.182	0.361	0.361	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.756	-0.828	11.247	-1.130	-1.130	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.029	-0.010	13.713	0.170	0.170	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.040	0.014	15.281	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.011	0.005	14.955	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.722	-0.854	15.863	-0.415	-0.415	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.779	0.873	18.245	0.430	0.430	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.044	-0.016	12.545	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.019	-0.006	16.519	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.063	-0.023	12.908	0.051	0.051	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.005	-0.007	16.111	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.034	0.006	16.979	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.942	-0.967	18.649	-0.364	-0.364	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.932	0.977	12.480	0.544	0.544	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.832	0.877	14.733	0.647	0.647	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.028	-0.024	10.431	0.054	0.054	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.786	-0.867	7.946	-2.015	-2.015	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.035	-0.024	8.274	-0.277	-0.277	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.020	0.010	4.124	-0.149	0.007	0.000	-0.020	-0.136	0.000
63	A	63	ASP	-1	-0.743	-0.851	8.186	-0.754	-0.754	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.005	-0.015	6.438	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.822	0.914	10.865	0.262	0.262	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.014	-0.005	13.115	0.043	0.043	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.023	-0.021	15.497	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.042	0.021	19.120	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.824	-0.918	21.530	-0.054	-0.054	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.015	-0.009	16.781	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.010	0.011	17.309	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.001	-0.009	18.226	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.043	-0.024	19.364	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.042	0.011	13.305	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.919	0.962	14.810	0.266	0.266	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.929	0.978	16.583	0.082	0.082	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.826	0.909	12.172	-0.084	-0.084	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.023	0.010	11.075	-0.085	-0.085	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.039	0.002	8.326	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.036	-0.004	8.992	-0.322	-0.322	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.014	0.009	10.556	0.104	0.104	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.046	-0.049	14.367	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.026	0.044	15.143	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	84	TYR	0	0.055	0.020	14.958	0.132	0.132	0.000	0.000	0.000	0.000
85	A	85	HIS	1	0.848	0.916	16.224	0.506	0.506	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.035	0.056	15.433	0.043	0.043	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.021	-0.040	18.472	0.017	0.017	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.925	0.938	19.262	0.408	0.408	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.853	-0.908	20.391	-0.213	-0.213	0.000	0.000	0.000	0.000
90	A	90	HIS	0	0.023	0.014	19.206	0.025	0.025	0.000	0.000	0.000	0.000
91	A	91	TRP	0	-0.005	-0.004	12.931	0.014	0.014	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.038	-0.010	10.884	0.054	0.054	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.015	-0.019	11.174	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.035	-0.023	6.257	0.185	0.185	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.019	-0.002	6.743	-0.298	-0.298	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.020	-0.011	2.817	-1.687	-0.655	0.243	-0.299	-0.976	-0.002
97	A	97	ASN	0	-0.018	-0.036	3.221	-0.171	0.758	0.024	-0.436	-0.517	0.001
98	A	98	GLY	0	0.043	0.032	3.261	0.745	1.077	0.005	-0.073	-0.264	0.000
99	A	99	PRO	0	-0.046	-0.032	3.932	-0.389	-0.128	0.000	-0.059	-0.203	0.000
100	A	100	LEU	0	-0.019	0.016	5.556	0.358	0.358	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.054	0.020	4.380	-0.931	-0.768	-0.001	-0.019	-0.143	0.000
102	A	102	ALA	0	0.055	0.006	2.381	-1.086	-0.073	1.939	-0.883	-2.069	0.005
103	A	103	LYS	1	0.951	0.973	3.406	0.522	0.309	0.029	0.725	-0.541	-0.001
104	A	104	GLU	-1	-0.782	-0.862	7.118	0.192	0.192	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.039	0.019	2.373	-1.166	-0.753	3.532	-0.716	-3.228	-0.002
106	A	106	HIS	1	0.857	0.924	2.655	-12.937	-14.019	4.730	-1.570	-2.077	0.019
107	A	107	SER	0	0.012	0.016	5.873	-0.454	-0.454	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.029	0.018	7.625	-0.242	-0.242	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.022	-0.012	4.136	-0.430	-0.310	-0.001	-0.014	-0.106	0.000
110	A	110	GLU	-1	-0.776	-0.847	7.477	0.385	0.385	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.871	-0.944	10.518	0.176	0.176	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.026	-0.027	10.437	-0.033	-0.033	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.022	-0.005	11.199	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.017	-0.032	12.982	-0.051	-0.051	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.040	-0.013	15.590	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.031	-0.023	14.955	-0.031	-0.031	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.867	0.922	17.607	-0.030	-0.030	0.000	0.000	0.000	0.000

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