FMO DATABASE

FMODB ID: 72M6K

Calculation Name: 3KHN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KHN

Chain ID: A

ChEMBL ID:

UniProt ID: Q729W9

Base Structure: X-ray

Registration Date: 2023-06-22

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1675289.183829
FMO2-HF: Nuclear repulsion	1610453.839174
FMO2-HF: Total energy	-64835.344655
FMO2-MP2: Total energy	-65029.29242

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-77.308	-80.538	30.919	-14.907	-12.783	-0.151

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.894

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	9	GLN	0	0.049	0.024	3.021	2.059	4.227	0.059	-0.816	-1.411	0.002
4	A	10	ARG	1	1.005	1.003	3.157	32.032	33.299	0.076	-0.403	-0.941	0.002
5	A	11	GLU	-1	-0.810	-0.894	1.773	-140.107	-146.772	30.784	-13.688	-10.431	-0.155
6	A	12	LEU	0	-0.004	0.010	5.406	4.913	4.913	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.053	0.025	8.039	2.604	2.604	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.763	-0.829	8.149	-21.571	-21.571	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.020	-0.015	9.116	2.437	2.437	0.000	0.000	0.000	0.000
10	A	16	GLN	0	0.027	0.023	11.037	1.715	1.715	0.000	0.000	0.000	0.000
11	A	17	ARG	1	0.845	0.899	13.066	22.424	22.424	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.063	-0.048	12.663	2.315	2.315	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.008	-0.007	14.830	1.033	1.033	0.000	0.000	0.000	0.000
14	A	20	TYR	0	0.014	-0.006	17.254	1.213	1.213	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.017	-0.016	18.208	1.260	1.260	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.907	-0.941	19.445	-15.081	-15.081	0.000	0.000	0.000	0.000
17	A	23	MET	0	-0.059	-0.032	20.031	0.703	0.703	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.943	0.968	23.264	12.814	12.814	0.000	0.000	0.000	0.000
19	A	25	THR	0	0.020	0.021	24.602	0.555	0.555	0.000	0.000	0.000	0.000
20	A	26	TYR	0	-0.073	-0.058	25.695	0.524	0.524	0.000	0.000	0.000	0.000
21	A	27	PHE	0	0.065	0.004	25.459	0.342	0.342	0.000	0.000	0.000	0.000
22	A	28	THR	0	-0.031	-0.025	29.492	0.292	0.292	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.040	-0.013	30.166	0.368	0.368	0.000	0.000	0.000	0.000
24	A	30	ASN	0	-0.073	-0.038	30.034	0.497	0.497	0.000	0.000	0.000	0.000
25	A	31	GLY	0	0.023	0.026	33.391	0.189	0.189	0.000	0.000	0.000	0.000
26	A	32	VAL	0	-0.054	-0.046	31.535	0.273	0.273	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.846	-0.910	30.857	-10.030	-10.030	0.000	0.000	0.000	0.000
28	A	34	GLY	0	-0.033	-0.008	32.739	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.071	-0.040	34.559	0.153	0.153	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.001	0.003	28.595	-0.065	-0.065	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.013	0.033	29.237	-0.099	-0.099	0.000	0.000	0.000	0.000
32	A	38	ALA	0	0.010	-0.001	24.164	-0.215	-0.215	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.021	-0.003	22.508	0.045	0.045	0.000	0.000	0.000	0.000
34	A	40	PHE	0	-0.017	-0.021	13.342	-0.438	-0.438	0.000	0.000	0.000	0.000
35	A	41	ASP	-1	-0.913	-0.965	17.217	-14.278	-14.278	0.000	0.000	0.000	0.000
36	A	42	GLU	-1	-0.862	-0.924	11.354	-19.606	-19.606	0.000	0.000	0.000	0.000
37	A	43	GLY	0	-0.059	-0.029	12.428	-1.115	-1.115	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.000	0.006	13.409	-0.351	-0.351	0.000	0.000	0.000	0.000
39	A	45	ILE	0	-0.030	-0.005	16.552	0.554	0.554	0.000	0.000	0.000	0.000
40	A	46	THR	0	-0.015	0.000	19.577	0.296	0.296	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.008	-0.005	22.938	0.184	0.184	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.866	0.921	25.433	11.062	11.062	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.021	0.010	29.334	0.074	0.074	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.067	0.036	32.748	0.049	0.049	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.031	-0.010	35.965	0.039	0.039	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.977	-0.968	37.672	-7.459	-7.459	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.027	-0.013	37.044	0.122	0.122	0.000	0.000	0.000	0.000
48	A	54	LEU	0	-0.036	-0.020	34.360	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	55	PHE	0	-0.012	-0.017	36.612	0.044	0.044	0.000	0.000	0.000	0.000
50	A	56	ALA	0	0.046	0.034	41.816	0.048	0.048	0.000	0.000	0.000	0.000
51	A	57	PRO	0	0.047	0.009	44.537	-0.099	-0.099	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.010	0.011	44.526	0.121	0.121	0.000	0.000	0.000	0.000
53	A	59	ALA	0	-0.038	-0.005	44.655	0.017	0.017	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.032	0.009	41.113	-0.161	-0.161	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.915	-0.936	40.850	-7.527	-7.527	0.000	0.000	0.000	0.000
56	A	62	LEU	0	-0.009	-0.003	36.939	0.012	0.012	0.000	0.000	0.000	0.000
57	A	63	ALA	0	-0.003	0.003	41.147	0.201	0.201	0.000	0.000	0.000	0.000
58	A	64	PRO	0	0.052	0.002	42.057	-0.158	-0.158	0.000	0.000	0.000	0.000
59	A	65	GLY	0	-0.018	-0.005	42.178	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	66	ALA	0	0.010	0.014	38.032	-0.183	-0.183	0.000	0.000	0.000	0.000
61	A	67	ASP	-1	-0.824	-0.907	36.935	-8.569	-8.569	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.937	0.996	36.323	8.121	8.121	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.005	0.000	32.671	-0.237	-0.237	0.000	0.000	0.000	0.000
64	A	70	LEU	0	0.019	0.000	32.365	-0.390	-0.390	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.036	0.019	31.679	-0.361	-0.361	0.000	0.000	0.000	0.000
66	A	72	THR	0	-0.012	-0.012	29.951	-0.244	-0.244	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.002	-0.003	27.235	-0.436	-0.436	0.000	0.000	0.000	0.000
68	A	74	LYS	1	0.933	0.989	27.005	9.022	9.022	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.805	-0.871	27.298	-11.559	-11.559	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.012	0.011	22.342	-0.489	-0.489	0.000	0.000	0.000	0.000
71	A	77	PHE	0	0.001	-0.007	22.916	-0.784	-0.784	0.000	0.000	0.000	0.000
72	A	78	ILE	0	-0.010	0.009	22.756	-0.516	-0.516	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.837	0.911	22.629	11.898	11.898	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.775	0.885	15.177	17.136	17.136	0.000	0.000	0.000	0.000
75	A	81	ARG	1	1.003	0.983	18.838	15.087	15.087	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.840	-0.912	13.598	-18.903	-18.903	0.000	0.000	0.000	0.000
77	A	83	GLN	0	-0.048	-0.025	15.341	-0.563	-0.563	0.000	0.000	0.000	0.000
78	A	84	ASN	0	0.042	0.023	16.448	1.270	1.270	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.011	-0.005	19.694	-0.117	-0.117	0.000	0.000	0.000	0.000
80	A	86	ASN	0	-0.005	0.011	20.410	0.764	0.764	0.000	0.000	0.000	0.000
81	A	87	ILE	0	0.021	0.014	24.360	0.059	0.059	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.944	0.983	23.740	11.783	11.783	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.031	0.030	29.070	0.045	0.045	0.000	0.000	0.000	0.000
84	A	90	PHE	0	0.025	0.002	27.744	-0.064	-0.064	0.000	0.000	0.000	0.000
85	A	91	THR	0	-0.055	-0.041	33.772	0.057	0.057	0.000	0.000	0.000	0.000
86	A	92	ASP	-1	-0.788	-0.888	36.571	-7.446	-7.446	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.867	-0.953	38.992	-7.169	-7.169	0.000	0.000	0.000	0.000
88	A	94	VAL	0	-0.038	-0.007	41.121	0.182	0.182	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.031	-0.032	42.081	-0.089	-0.089	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.013	0.013	43.818	0.073	0.073	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.003	-0.020	46.364	0.137	0.137	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.066	0.029	49.634	-0.064	-0.064	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.080	-0.028	51.490	0.133	0.133	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.009	-0.014	49.004	0.002	0.002	0.000	0.000	0.000	0.000
95	A	101	ARG	1	0.945	0.972	45.258	6.764	6.764	0.000	0.000	0.000	0.000
96	A	102	PHE	0	-0.034	-0.022	44.055	-0.041	-0.041	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.866	0.920	43.533	6.983	6.983	0.000	0.000	0.000	0.000
98	A	104	ASP	-1	-0.794	-0.889	41.334	-7.170	-7.170	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.068	0.004	39.004	-0.049	-0.049	0.000	0.000	0.000	0.000
100	A	106	TRP	0	0.014	0.029	33.056	-0.305	-0.305	0.000	0.000	0.000	0.000
101	A	107	GLU	-1	-0.820	-0.896	37.620	-7.167	-7.167	0.000	0.000	0.000	0.000
102	A	108	VAL	0	0.005	0.008	39.755	-0.106	-0.106	0.000	0.000	0.000	0.000
103	A	109	SER	0	-0.038	-0.022	34.824	-0.197	-0.197	0.000	0.000	0.000	0.000
104	A	110	ALA	0	0.001	0.005	34.942	-0.265	-0.265	0.000	0.000	0.000	0.000
105	A	111	LEU	0	-0.036	-0.026	36.026	-0.128	-0.128	0.000	0.000	0.000	0.000
106	A	112	ARG	1	0.883	0.944	36.775	7.671	7.671	0.000	0.000	0.000	0.000
107	A	113	SER	0	0.013	-0.008	32.033	-0.213	-0.213	0.000	0.000	0.000	0.000
108	A	114	VAL	0	0.010	0.004	33.505	-0.234	-0.234	0.000	0.000	0.000	0.000
109	A	115	ASN	0	-0.033	-0.035	35.254	-0.115	-0.115	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.008	0.009	31.610	-0.035	-0.035	0.000	0.000	0.000	0.000
111	A	117	LEU	0	0.003	-0.007	29.664	-0.165	-0.165	0.000	0.000	0.000	0.000
112	A	118	ARG	1	0.881	0.933	32.171	7.832	7.832	0.000	0.000	0.000	0.000
113	A	119	TYR	0	-0.037	-0.014	32.636	-0.098	-0.098	0.000	0.000	0.000	0.000
114	A	120	PHE	0	0.013	-0.012	28.890	-0.101	-0.101	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.018	-0.009	29.720	-0.178	-0.178	0.000	0.000	0.000	0.000
116	A	122	GLY	0	-0.002	0.009	31.679	0.002	0.002	0.000	0.000	0.000	0.000
117	A	123	ALA	0	-0.083	-0.039	31.231	0.107	0.107	0.000	0.000	0.000	0.000
118	A	124	GLY	0	0.015	0.009	30.404	-0.138	-0.138	0.000	0.000	0.000	0.000
119	A	125	ILE	0	-0.075	-0.032	24.944	-0.489	-0.489	0.000	0.000	0.000	0.000
120	A	126	GLU	-1	-0.782	-0.863	21.723	-14.135	-14.135	0.000	0.000	0.000	0.000
121	A	127	PRO	0	0.076	0.012	25.299	-0.284	-0.284	0.000	0.000	0.000	0.000
122	A	128	ALA	0	-0.011	0.004	22.841	-0.044	-0.044	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.767	0.900	20.435	13.814	13.814	0.000	0.000	0.000	0.000
124	A	130	LEU	0	-0.022	0.001	22.517	-0.197	-0.197	0.000	0.000	0.000	0.000
125	A	131	THR	0	-0.021	-0.020	24.257	0.262	0.262	0.000	0.000	0.000	0.000
126	A	132	ALA	0	0.005	-0.008	26.828	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	133	THR	0	-0.062	-0.025	27.847	0.105	0.105	0.000	0.000	0.000	0.000
128	A	134	GLY	0	0.027	0.010	30.228	-0.034	-0.034	0.000	0.000	0.000	0.000
129	A	135	LEU	0	-0.021	-0.015	27.547	-0.049	-0.049	0.000	0.000	0.000	0.000
130	A	136	GLY	0	0.025	0.011	32.250	0.097	0.097	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.847	-0.905	34.958	-7.494	-7.494	0.000	0.000	0.000	0.000
132	A	138	LEU	0	-0.042	-0.017	30.060	0.077	0.077	0.000	0.000	0.000	0.000
133	A	139	ASP	-1	-0.938	-0.969	28.281	-9.838	-9.838	0.000	0.000	0.000	0.000
134	A	140	PRO	0	-0.031	0.004	30.993	-0.132	-0.132	0.000	0.000	0.000	0.000
135	A	141	LEU	0	-0.041	-0.019	28.035	-0.167	-0.167	0.000	0.000	0.000	0.000
136	A	142	PHE	0	-0.033	-0.029	31.308	-0.106	-0.106	0.000	0.000	0.000	0.000
137	A	143	PRO	0	0.046	0.030	34.310	0.079	0.079	0.000	0.000	0.000	0.000
138	A	144	ASN	0	0.071	0.043	37.180	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	145	THR	0	-0.012	-0.019	39.971	0.090	0.090	0.000	0.000	0.000	0.000
140	A	146	SER	0	-0.042	-0.042	41.993	0.114	0.114	0.000	0.000	0.000	0.000
141	A	147	ASP	-1	-0.801	-0.890	42.229	-6.721	-6.721	0.000	0.000	0.000	0.000
142	A	148	GLU	-1	-0.873	-0.913	40.476	-7.054	-7.054	0.000	0.000	0.000	0.000
143	A	149	ASN	0	-0.053	-0.040	37.770	-0.322	-0.322	0.000	0.000	0.000	0.000
144	A	150	ARG	1	0.888	0.940	37.520	6.568	6.568	0.000	0.000	0.000	0.000
145	A	151	ALA	0	-0.006	-0.012	38.812	-0.121	-0.121	0.000	0.000	0.000	0.000
146	A	152	ARG	1	0.899	0.959	34.183	8.250	8.250	0.000	0.000	0.000	0.000
147	A	153	ASN	0	-0.023	-0.029	34.139	-0.533	-0.533	0.000	0.000	0.000	0.000
148	A	154	ARG	1	0.860	0.944	35.030	7.214	7.214	0.000	0.000	0.000	0.000
149	A	155	ARG	1	0.814	0.912	28.697	9.696	9.696	0.000	0.000	0.000	0.000
150	A	156	VAL	0	0.000	-0.003	30.943	0.057	0.057	0.000	0.000	0.000	0.000
151	A	157	GLU	-1	-0.819	-0.889	26.557	-10.904	-10.904	0.000	0.000	0.000	0.000
152	A	158	PHE	0	0.007	-0.009	25.768	0.066	0.066	0.000	0.000	0.000	0.000
153	A	159	VAL	0	0.002	-0.002	20.314	-0.242	-0.242	0.000	0.000	0.000	0.000
154	A	160	LEU	0	-0.014	-0.012	19.816	-0.083	-0.083	0.000	0.000	0.000	0.000
155	A	161	GLU	-1	-0.864	-0.933	15.663	-16.563	-16.563	0.000	0.000	0.000	0.000
156	A	162	ARG	1	0.866	0.932	10.381	23.761	23.761	0.000	0.000	0.000	0.000
157	A	163	ARG	1	0.771	0.851	13.555	16.537	16.537	0.000	0.000	0.000	0.000
158	A	164	VAL	0	0.018	0.014	11.653	-1.761	-1.761	0.000	0.000	0.000	0.000
159	A	165	VAL	0	-0.001	-0.010	11.956	1.022	1.022	0.000	0.000	0.000	0.000
160	A	166	ARG	1	0.815	0.889	14.167	16.892	16.892	0.000	0.000	0.000	0.000
161	A	167	GLU	-1	-0.811	-0.903	17.847	-12.913	-12.913	0.000	0.000	0.000	0.000
162	A	168	GLY	0	0.006	0.018	21.013	-0.136	-0.136	0.000	0.000	0.000	0.000
163	A	169	HIS	0	0.005	-0.006	21.730	0.488	0.488	0.000	0.000	0.000	0.000
164	A	170	HIS	1	0.819	0.899	25.540	11.762	11.762	0.000	0.000	0.000	0.000
165	A	171	HIS	0	0.055	0.021	26.177	0.492	0.492	0.000	0.000	0.000	0.000
166	A	172	HIS	0	-0.012	0.017	29.765	0.263	0.263	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)