FMO DATABASE

FMODB ID: GN2J1

Calculation Name: 6PAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6PAX

Chain ID: A

ChEMBL ID:

UniProt ID: P26367

Base Structure: X-ray

Registration Date: 2023-06-19

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-916061.470254
FMO2-HF: Nuclear repulsion	865152.01304
FMO2-HF: Total energy	-50909.457215
FMO2-MP2: Total energy	-51057.868462

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:SER)

Summations of interaction energy for fragment #1(A:1: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.
-11.035	-6.722	2.436	-2.937	-3.812	0.007

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

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 : -0.006

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	3	SER	0	0.006	0.000	3.854	-0.828	2.077	-0.019	-1.638	-1.248	0.004
4	A	4	GLY	0	0.026	0.029	6.315	-0.511	-0.511	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.027	0.028	8.894	0.218	0.218	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.024	-0.006	12.314	-0.072	-0.072	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.027	-0.007	13.963	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.029	-0.006	16.863	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.022	0.017	16.748	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.024	0.020	14.599	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.000	-0.007	10.154	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.091	-0.047	8.169	0.228	0.228	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.046	0.016	2.326	-0.926	-0.973	2.362	-0.821	-1.494	0.000
14	A	14	ASN	0	0.010	-0.005	4.723	0.748	0.842	-0.001	-0.011	-0.081	0.000
15	A	15	GLY	0	0.077	0.049	4.245	0.009	0.290	-0.001	-0.032	-0.249	0.000
16	A	16	ARG	1	0.871	0.934	3.256	-5.870	-4.790	0.095	-0.435	-0.740	0.003
17	A	17	PRO	0	-0.047	-0.023	6.397	-0.608	-0.608	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.038	0.023	8.847	0.254	0.254	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.106	0.044	10.127	0.013	0.013	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.738	-0.860	11.984	0.746	0.746	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.054	0.040	15.129	-0.043	-0.043	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.007	-0.001	14.852	-0.054	-0.054	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.809	0.893	13.055	-0.958	-0.958	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.004	-0.015	17.705	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.922	0.968	19.841	-0.288	-0.288	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.018	-0.009	17.368	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.017	0.013	21.525	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.821	-0.899	23.856	0.254	0.254	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.034	-0.024	23.248	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.009	0.008	25.779	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.034	-0.006	27.548	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.083	-0.045	29.475	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.036	0.021	31.029	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.062	-0.011	27.553	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.953	0.935	28.610	-0.110	-0.110	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.054	0.008	24.556	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.021	0.012	24.067	0.011	0.011	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.788	-0.860	24.907	0.127	0.127	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.006	0.009	21.352	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.093	-0.051	20.045	0.004	0.004	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.914	0.934	20.442	-0.114	-0.114	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.030	-0.017	22.109	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.012	-0.009	18.409	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.013	0.011	17.221	0.047	0.047	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.009	0.013	14.990	0.050	0.050	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.033	0.021	15.217	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.124	0.032	17.291	0.038	0.038	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.031	0.024	19.127	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	CYS	0	-0.088	-0.038	13.824	0.053	0.053	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.052	0.023	16.999	0.026	0.026	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.015	0.012	19.720	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.956	0.984	14.655	-0.663	-0.663	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.052	-0.029	15.181	0.015	0.015	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.045	0.024	19.533	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.036	0.028	23.074	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.916	0.945	16.837	-0.591	-0.591	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.010	0.028	22.874	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	58	TYR	0	0.045	0.010	24.231	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.037	0.006	26.114	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.077	-0.075	24.074	0.009	0.009	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.051	0.041	26.428	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.033	-0.010	21.127	0.019	0.019	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.081	0.031	18.908	0.017	0.017	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.814	0.882	14.201	-0.693	-0.693	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.057	-0.014	12.471	-0.041	-0.041	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.972	0.969	15.155	-0.544	-0.544	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.010	0.001	13.957	0.138	0.138	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.006	-0.006	8.971	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.003	0.005	12.032	0.017	0.017	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.041	0.031	12.841	-0.082	-0.082	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.021	-0.013	15.421	-0.039	-0.039	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.995	0.996	18.697	-0.358	-0.358	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.002	-0.015	22.288	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.933	0.971	21.099	-0.284	-0.284	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.062	0.033	26.766	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.009	0.005	28.100	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.006	-0.002	29.184	0.014	0.014	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.069	0.014	29.695	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.883	-0.920	32.438	0.119	0.119	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.035	0.022	33.332	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.043	-0.029	30.825	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.005	-0.010	34.221	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.886	0.942	37.342	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.021	-0.003	34.346	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.012	-0.012	37.110	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.029	-0.027	38.857	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.048	-0.064	40.963	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.820	0.888	39.238	-0.080	-0.080	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.072	-0.028	42.202	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.812	-0.880	43.989	0.072	0.072	0.000	0.000	0.000	0.000
91	A	91	CYS	0	-0.024	-0.003	45.759	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.055	0.028	43.845	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.020	-0.002	43.639	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.021	0.019	42.192	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.021	0.000	41.782	0.004	0.004	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.027	-0.025	36.896	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	TRP	0	0.010	-0.007	38.963	0.005	0.005	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.766	-0.861	40.556	0.056	0.056	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.017	-0.015	38.216	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.851	0.907	34.844	-0.079	-0.079	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.827	-0.928	39.447	0.063	0.063	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.831	0.917	42.864	-0.073	-0.073	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.026	-0.012	37.260	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.059	-0.021	39.020	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.031	-0.023	41.755	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.784	-0.870	43.834	0.079	0.079	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.010	0.005	42.644	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.039	-0.009	37.847	0.004	0.004	0.000	0.000	0.000	0.000
109	A	109	CYS	0	-0.072	-0.044	35.875	0.009	0.009	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.049	0.001	36.830	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.030	-0.038	36.718	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.858	-0.897	33.862	0.091	0.091	0.000	0.000	0.000	0.000
113	A	113	ASN	0	-0.037	-0.018	32.088	0.004	0.004	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.015	0.037	32.954	0.008	0.008	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.002	-0.004	31.351	0.003	0.003	0.000	0.000	0.000	0.000
116	A	116	SER	0	0.054	0.034	29.517	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.138	0.040	32.399	0.007	0.007	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.011	0.011	28.962	0.006	0.006	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.020	-0.020	28.458	0.014	0.014	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.071	0.055	29.988	0.009	0.009	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.014	-0.008	32.838	0.001	0.001	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.889	0.946	25.156	-0.188	-0.188	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.004	0.005	29.796	0.009	0.009	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.030	0.014	31.115	0.003	0.003	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.932	0.966	27.949	-0.119	-0.119	0.000	0.000	0.000	0.000
126	A	126	ASN	0	-0.053	-0.040	25.734	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.042	0.020	29.734	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.036	-0.011	33.040	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.007	0.000	29.696	0.001	0.001	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.933	-0.954	30.330	0.185	0.185	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.952	0.969	31.751	-0.100	-0.100	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.046	-0.013	33.365	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.072	-0.031	28.315	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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