FMO DATABASE

FMODB ID: 3JJRL

Calculation Name: 1KHI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KHI

Chain ID: A

ChEMBL ID:

UniProt ID: P87252

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	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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1256768.96173
FMO2-HF: Nuclear repulsion	1199571.32638
FMO2-HF: Total energy	-57197.635351
FMO2-MP2: Total energy	-57361.981656

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:27:GLY)

Summations of interaction energy for fragment #1(A:27: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.
-1.34	1.399	0.995	-1.483	-2.251	0.004

Interaction energy analysis for fragmet #1(A:27:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.018

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	29	ALA	0	0.031	0.020	3.856	-1.539	0.232	0.001	-1.073	-0.698	0.005
4	A	30	SER	0	-0.018	-0.023	6.359	0.259	0.259	0.000	0.000	0.000	0.000
5	A	31	GLN	0	0.000	0.009	7.641	0.204	0.204	0.000	0.000	0.000	0.000
6	A	32	THR	0	0.008	0.005	9.707	0.000	0.000	0.000	0.000	0.000	0.000
7	A	33	VAL	0	-0.004	0.000	13.363	0.038	0.038	0.000	0.000	0.000	0.000
8	A	34	THR	0	0.013	-0.001	17.095	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	35	ILE	0	0.008	0.013	19.871	0.031	0.031	0.000	0.000	0.000	0.000
10	A	36	PRO	0	0.030	-0.001	22.551	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	37	CYS	0	0.014	0.024	26.004	0.002	0.002	0.000	0.000	0.000	0.000
12	A	38	HIS	0	0.021	0.034	27.501	0.003	0.003	0.000	0.000	0.000	0.000
13	A	39	HIS	0	-0.079	-0.076	26.540	0.020	0.020	0.000	0.000	0.000	0.000
14	A	40	ILE	0	-0.003	0.028	23.544	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	41	ARG	1	0.845	0.920	26.175	0.082	0.082	0.000	0.000	0.000	0.000
16	A	42	LEU	0	-0.018	-0.015	26.237	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	43	GLY	0	-0.007	0.001	25.185	0.013	0.013	0.000	0.000	0.000	0.000
18	A	44	ASP	-1	-0.825	-0.893	22.551	-0.098	-0.098	0.000	0.000	0.000	0.000
19	A	45	ILE	0	-0.038	-0.030	16.308	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	46	LEU	0	-0.009	-0.009	17.970	0.013	0.013	0.000	0.000	0.000	0.000
21	A	47	ILE	0	-0.050	-0.022	12.358	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	48	LEU	0	0.007	-0.003	15.722	0.048	0.048	0.000	0.000	0.000	0.000
23	A	49	GLN	0	0.006	-0.012	16.687	-0.068	-0.068	0.000	0.000	0.000	0.000
24	A	50	GLY	0	0.012	0.013	13.918	-0.057	-0.057	0.000	0.000	0.000	0.000
25	A	51	ARG	1	0.875	0.943	11.910	0.439	0.439	0.000	0.000	0.000	0.000
26	A	52	PRO	0	0.025	0.014	10.760	0.122	0.122	0.000	0.000	0.000	0.000
27	A	53	CYS	0	-0.054	-0.001	13.773	0.013	0.013	0.000	0.000	0.000	0.000
28	A	54	GLN	0	0.041	0.035	17.467	0.023	0.023	0.000	0.000	0.000	0.000
29	A	55	VAL	0	-0.013	-0.005	20.502	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	56	ILE	0	-0.017	-0.021	23.448	0.022	0.022	0.000	0.000	0.000	0.000
31	A	57	ARG	1	0.950	0.969	26.582	0.155	0.155	0.000	0.000	0.000	0.000
32	A	58	ILE	0	0.019	0.024	27.222	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	59	SER	0	-0.084	-0.028	29.453	0.011	0.011	0.000	0.000	0.000	0.000
34	A	60	THR	0	0.033	0.008	31.128	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	61	SER	0	-0.038	-0.015	31.628	0.005	0.005	0.000	0.000	0.000	0.000
36	A	62	ALA	0	0.025	-0.001	33.578	0.004	0.004	0.000	0.000	0.000	0.000
37	A	63	ALA	0	0.001	0.011	34.963	0.005	0.005	0.000	0.000	0.000	0.000
38	A	64	THR	0	0.000	-0.001	31.763	0.001	0.001	0.000	0.000	0.000	0.000
39	A	65	GLY	0	0.006	0.011	34.694	0.001	0.001	0.000	0.000	0.000	0.000
40	A	66	GLN	0	-0.059	-0.039	28.357	0.011	0.011	0.000	0.000	0.000	0.000
41	A	67	HIS	0	0.035	0.024	28.740	0.000	0.000	0.000	0.000	0.000	0.000
42	A	68	ARG	1	0.859	0.930	26.982	0.176	0.176	0.000	0.000	0.000	0.000
43	A	69	TYR	0	0.008	-0.008	23.593	0.025	0.025	0.000	0.000	0.000	0.000
44	A	70	LEU	0	0.027	0.012	24.263	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	71	GLY	0	0.046	0.003	21.892	0.023	0.023	0.000	0.000	0.000	0.000
46	A	72	VAL	0	-0.022	0.002	20.495	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	73	ASP	-1	-0.761	-0.865	14.798	-0.522	-0.522	0.000	0.000	0.000	0.000
48	A	74	LEU	0	0.000	-0.010	14.284	0.046	0.046	0.000	0.000	0.000	0.000
49	A	75	PHE	0	-0.021	-0.012	10.026	0.034	0.034	0.000	0.000	0.000	0.000
50	A	76	THR	0	-0.031	-0.057	13.904	0.064	0.064	0.000	0.000	0.000	0.000
51	A	77	LYS	1	0.869	0.940	16.406	0.165	0.165	0.000	0.000	0.000	0.000
52	A	78	GLN	0	-0.016	0.004	18.699	0.033	0.033	0.000	0.000	0.000	0.000
53	A	79	LEU	0	0.004	0.002	20.242	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	80	HIS	0	-0.021	-0.023	18.380	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	81	GLU	-1	-0.822	-0.909	21.845	-0.178	-0.178	0.000	0.000	0.000	0.000
56	A	82	GLU	-1	-0.859	-0.923	19.017	-0.491	-0.491	0.000	0.000	0.000	0.000
57	A	83	SER	0	-0.026	-0.046	23.125	0.030	0.030	0.000	0.000	0.000	0.000
58	A	84	SER	0	0.035	0.024	24.269	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	85	PHE	0	-0.012	-0.007	22.159	0.008	0.008	0.000	0.000	0.000	0.000
60	A	86	VAL	0	-0.002	-0.002	27.353	0.004	0.004	0.000	0.000	0.000	0.000
61	A	87	SER	0	0.000	0.005	27.513	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	88	ASN	0	-0.019	-0.037	29.677	0.003	0.003	0.000	0.000	0.000	0.000
63	A	89	PRO	0	-0.001	0.003	28.622	0.002	0.002	0.000	0.000	0.000	0.000
64	A	90	ALA	0	0.039	0.025	30.947	0.005	0.005	0.000	0.000	0.000	0.000
65	A	91	PRO	0	0.045	0.008	34.675	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	92	SER	0	-0.003	-0.007	38.240	0.002	0.002	0.000	0.000	0.000	0.000
67	A	93	VAL	0	-0.027	0.018	32.466	0.000	0.000	0.000	0.000	0.000	0.000
68	A	94	VAL	0	0.002	0.002	33.250	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	95	VAL	0	-0.040	-0.014	27.821	0.005	0.005	0.000	0.000	0.000	0.000
70	A	96	GLN	0	0.065	0.036	27.681	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	97	THR	0	-0.025	-0.029	23.151	0.009	0.009	0.000	0.000	0.000	0.000
72	A	98	MET	0	0.040	0.036	20.449	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	99	LEU	0	0.016	0.011	15.023	0.022	0.022	0.000	0.000	0.000	0.000
74	A	100	GLY	0	0.067	0.038	16.668	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	101	PRO	0	-0.004	0.002	12.374	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	102	VAL	0	-0.046	-0.026	11.760	0.059	0.059	0.000	0.000	0.000	0.000
77	A	103	PHE	0	-0.010	-0.003	12.014	0.048	0.048	0.000	0.000	0.000	0.000
78	A	104	LYS	1	0.878	0.949	7.463	-0.808	-0.808	0.000	0.000	0.000	0.000
79	A	105	GLN	0	0.045	0.013	13.776	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	106	TYR	0	-0.066	-0.048	9.322	0.002	0.002	0.000	0.000	0.000	0.000
81	A	107	ARG	1	0.956	0.967	16.515	-0.364	-0.364	0.000	0.000	0.000	0.000
82	A	108	VAL	0	0.026	0.018	18.950	0.041	0.041	0.000	0.000	0.000	0.000
83	A	109	LEU	0	-0.037	-0.022	20.483	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	110	ASP	-1	-0.797	-0.917	22.407	0.176	0.176	0.000	0.000	0.000	0.000
85	A	111	MET	0	-0.080	-0.022	22.404	0.019	0.019	0.000	0.000	0.000	0.000
86	A	112	GLN	0	-0.003	-0.008	23.029	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	113	ASP	-1	-0.848	-0.908	22.698	0.145	0.145	0.000	0.000	0.000	0.000
88	A	114	GLY	0	-0.005	0.009	22.215	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	115	SER	0	-0.093	-0.037	18.100	0.016	0.016	0.000	0.000	0.000	0.000
90	A	116	ILE	0	-0.005	-0.023	17.949	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	117	VAL	0	0.006	0.034	17.886	0.053	0.053	0.000	0.000	0.000	0.000
92	A	118	ALA	0	0.021	-0.004	15.980	-0.044	-0.044	0.000	0.000	0.000	0.000
93	A	119	MET	0	-0.029	-0.003	16.229	0.051	0.051	0.000	0.000	0.000	0.000
94	A	120	THR	0	-0.010	0.002	11.929	-0.100	-0.100	0.000	0.000	0.000	0.000
95	A	121	GLU	-1	-0.976	-1.003	15.208	0.289	0.289	0.000	0.000	0.000	0.000
96	A	122	THR	0	-0.031	-0.021	14.760	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	123	GLY	0	0.034	0.015	17.166	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	124	ASP	-1	-0.898	-0.947	11.186	1.391	1.391	0.000	0.000	0.000	0.000
99	A	125	VAL	0	0.038	0.014	14.759	-0.045	-0.045	0.000	0.000	0.000	0.000
100	A	126	LYS	1	0.810	0.908	8.950	-1.532	-1.532	0.000	0.000	0.000	0.000
101	A	127	GLN	0	0.028	0.007	14.248	-0.082	-0.082	0.000	0.000	0.000	0.000
102	A	128	ASN	0	0.005	-0.011	15.504	-0.043	-0.043	0.000	0.000	0.000	0.000
103	A	129	LEU	0	-0.011	0.012	12.200	0.021	0.021	0.000	0.000	0.000	0.000
104	A	130	PRO	0	0.039	0.022	13.003	-0.062	-0.062	0.000	0.000	0.000	0.000
105	A	131	VAL	0	0.007	-0.009	15.635	0.014	0.014	0.000	0.000	0.000	0.000
106	A	132	ILE	0	-0.031	-0.010	17.226	-0.027	-0.027	0.000	0.000	0.000	0.000
107	A	133	ASP	-1	-0.926	-0.958	18.796	0.000	0.000	0.000	0.000	0.000	0.000
108	A	134	GLN	0	0.038	-0.002	21.899	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	135	SER	0	-0.014	-0.018	23.597	0.017	0.017	0.000	0.000	0.000	0.000
110	A	136	SER	0	0.001	0.001	26.845	0.010	0.010	0.000	0.000	0.000	0.000
111	A	137	LEU	0	-0.022	0.011	19.869	0.011	0.011	0.000	0.000	0.000	0.000
112	A	138	TRP	0	0.057	0.028	21.728	0.013	0.013	0.000	0.000	0.000	0.000
113	A	139	ASN	0	0.054	0.016	24.720	0.016	0.016	0.000	0.000	0.000	0.000
114	A	140	ARG	1	0.753	0.866	23.831	-0.028	-0.028	0.000	0.000	0.000	0.000
115	A	141	LEU	0	0.034	0.004	21.418	0.005	0.005	0.000	0.000	0.000	0.000
116	A	142	GLN	0	0.010	-0.012	25.552	0.006	0.006	0.000	0.000	0.000	0.000
117	A	143	LYS	1	0.969	0.993	27.717	-0.051	-0.051	0.000	0.000	0.000	0.000
118	A	144	ALA	0	-0.006	0.007	27.550	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	145	PHE	0	-0.039	-0.012	25.040	0.006	0.006	0.000	0.000	0.000	0.000
120	A	146	GLU	-1	-0.885	-0.950	28.109	0.110	0.110	0.000	0.000	0.000	0.000
121	A	147	SER	0	-0.071	-0.042	31.455	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	148	GLY	0	0.039	0.021	30.977	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	149	ARG	1	0.858	0.940	27.408	-0.171	-0.171	0.000	0.000	0.000	0.000
124	A	150	GLY	0	0.047	0.034	26.231	0.012	0.012	0.000	0.000	0.000	0.000
125	A	151	SER	0	-0.067	-0.036	26.285	0.010	0.010	0.000	0.000	0.000	0.000
126	A	152	VAL	0	0.025	0.014	23.269	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	153	ARG	1	0.801	0.887	20.117	-0.185	-0.185	0.000	0.000	0.000	0.000
128	A	154	VAL	0	0.047	0.021	16.673	-0.031	-0.031	0.000	0.000	0.000	0.000
129	A	155	LEU	0	-0.022	-0.011	16.876	0.038	0.038	0.000	0.000	0.000	0.000
130	A	156	VAL	0	-0.008	-0.013	10.873	-0.030	-0.030	0.000	0.000	0.000	0.000
131	A	157	VAL	0	0.019	0.017	10.117	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	158	SER	0	0.002	-0.030	5.767	0.051	0.051	0.000	0.000	0.000	0.000
133	A	159	ASP	-1	-0.776	-0.881	6.029	-1.743	-1.743	0.000	0.000	0.000	0.000
134	A	160	HIS	0	-0.042	-0.012	4.274	0.317	0.470	-0.001	-0.055	-0.098	0.000
135	A	161	GLY	0	-0.008	0.003	2.599	-2.030	-0.699	0.869	-1.079	-1.121	-0.001
136	A	162	ARG	1	0.837	0.911	2.944	3.177	2.661	0.126	0.724	-0.334	0.000
137	A	163	GLU	-1	-0.753	-0.845	6.538	1.353	1.353	0.000	0.000	0.000	0.000
138	A	164	MET	0	-0.035	-0.012	8.860	-0.033	-0.033	0.000	0.000	0.000	0.000
139	A	165	ALA	0	0.005	0.013	12.577	-0.021	-0.021	0.000	0.000	0.000	0.000
140	A	166	VAL	0	-0.019	-0.032	14.502	-0.042	-0.042	0.000	0.000	0.000	0.000
141	A	167	ASP	-1	-0.761	-0.880	17.215	0.013	0.013	0.000	0.000	0.000	0.000
142	A	168	MET	0	-0.066	-0.007	19.517	0.034	0.034	0.000	0.000	0.000	0.000
143	A	169	LYS	1	0.863	0.936	21.949	-0.143	-0.143	0.000	0.000	0.000	0.000
144	A	170	VAL	0	0.040	0.033	23.957	0.019	0.019	0.000	0.000	0.000	0.000
145	A	171	VAL	0	-0.074	-0.050	25.109	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	172	HIS	0	0.029	0.020	26.367	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	173	GLY	0	0.035	0.024	29.885	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:GLY)