FMO DATABASE

FMODB ID: YV7G2

Calculation Name: 5GXJ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GXJ

Chain ID: B

ChEMBL ID:

UniProt ID: Q32ZE1

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	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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1533275.686674
FMO2-HF: Nuclear repulsion	1471173.691867
FMO2-HF: Total energy	-62101.994807
FMO2-MP2: Total energy	-62282.121048

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(B:48:SER)

Summations of interaction energy for fragment #1(B:48: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.
-4.34	0.156	1.308	-2.339	-3.462	-0.01

Interaction energy analysis for fragmet #1(B:48:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.004

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	B	50	ASP	-1	-0.843	-0.917	3.021	-4.729	-1.892	0.059	-1.504	-1.391	-0.006
4	B	51	MET	0	-0.022	0.031	5.065	0.397	0.445	-0.001	-0.005	-0.042	0.000
5	B	52	TYR	0	-0.018	-0.013	8.080	0.188	0.188	0.000	0.000	0.000	0.000
6	B	53	ILE	0	-0.007	-0.004	10.605	0.038	0.038	0.000	0.000	0.000	0.000
7	B	54	GLU	-1	-0.910	-0.968	14.249	-0.312	-0.312	0.000	0.000	0.000	0.000
8	B	55	ARG	1	0.776	0.876	16.284	0.110	0.110	0.000	0.000	0.000	0.000
9	B	56	ALA	0	-0.046	-0.042	20.065	0.003	0.003	0.000	0.000	0.000	0.000
10	B	57	GLY	0	0.008	-0.004	22.444	0.012	0.012	0.000	0.000	0.000	0.000
11	B	58	ASP	-1	-0.831	-0.891	25.734	-0.088	-0.088	0.000	0.000	0.000	0.000
12	B	59	ILE	0	-0.019	-0.009	26.434	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	60	THR	0	0.004	0.006	30.092	0.005	0.005	0.000	0.000	0.000	0.000
14	B	61	TRP	0	0.000	0.006	33.653	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	62	GLU	-1	-0.878	-0.938	34.478	-0.072	-0.072	0.000	0.000	0.000	0.000
16	B	63	LYS	1	0.892	0.940	38.098	0.047	0.047	0.000	0.000	0.000	0.000
17	B	64	ASP	-1	-0.953	-0.963	41.279	-0.048	-0.048	0.000	0.000	0.000	0.000
18	B	65	ALA	0	0.029	0.018	37.387	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	66	GLU	-1	-0.934	-0.967	36.723	-0.072	-0.072	0.000	0.000	0.000	0.000
20	B	67	VAL	0	-0.034	-0.019	39.013	-0.003	-0.003	0.000	0.000	0.000	0.000
21	B	68	THR	0	-0.033	-0.005	40.236	0.000	0.000	0.000	0.000	0.000	0.000
22	B	1018	THR	0	0.022	-0.019	19.572	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	1019	THR	0	-0.019	0.014	21.450	0.004	0.004	0.000	0.000	0.000	0.000
24	B	1020	ASP	-1	-0.780	-0.889	23.297	-0.092	-0.092	0.000	0.000	0.000	0.000
25	B	1021	GLY	0	0.034	0.022	24.914	0.002	0.002	0.000	0.000	0.000	0.000
26	B	1022	VAL	0	0.004	0.012	23.617	-0.008	-0.008	0.000	0.000	0.000	0.000
27	B	1023	TYR	0	-0.080	-0.051	17.624	0.000	0.000	0.000	0.000	0.000	0.000
28	B	1024	ARG	1	0.840	0.908	16.723	0.238	0.238	0.000	0.000	0.000	0.000
29	B	1025	VAL	0	0.009	-0.009	14.015	-0.023	-0.023	0.000	0.000	0.000	0.000
30	B	1026	MET	0	0.007	0.021	11.863	0.032	0.032	0.000	0.000	0.000	0.000
31	B	1027	THR	0	-0.033	-0.025	8.802	-0.126	-0.126	0.000	0.000	0.000	0.000
32	B	1028	ARG	1	0.926	0.969	2.779	-0.863	-0.056	0.954	-0.489	-1.271	-0.004
33	B	1029	ARG	1	0.973	0.961	5.877	0.043	0.043	0.000	0.000	0.000	0.000
34	B	1030	LEU	0	0.027	0.018	2.478	-0.295	0.427	0.297	-0.335	-0.683	0.000
35	B	1031	LEU	0	0.035	0.024	4.689	0.720	0.802	-0.001	-0.006	-0.075	0.000
36	B	1032	GLY	0	0.023	0.028	8.026	0.012	0.012	0.000	0.000	0.000	0.000
37	B	1033	SER	0	-0.037	-0.037	8.761	-0.233	-0.233	0.000	0.000	0.000	0.000
38	B	1034	THR	0	-0.016	-0.010	10.993	0.108	0.108	0.000	0.000	0.000	0.000
39	B	1035	GLN	0	0.037	0.014	13.434	-0.090	-0.090	0.000	0.000	0.000	0.000
40	B	1036	VAL	0	-0.006	-0.001	14.058	0.037	0.037	0.000	0.000	0.000	0.000
41	B	1037	GLY	0	0.012	-0.009	16.497	0.040	0.040	0.000	0.000	0.000	0.000
42	B	1038	VAL	0	-0.041	0.006	18.397	-0.025	-0.025	0.000	0.000	0.000	0.000
43	B	1039	GLY	0	0.050	0.033	20.725	0.002	0.002	0.000	0.000	0.000	0.000
44	B	1040	VAL	0	-0.003	-0.003	21.951	0.004	0.004	0.000	0.000	0.000	0.000
45	B	1041	MET	0	-0.057	0.000	19.308	0.001	0.001	0.000	0.000	0.000	0.000
46	B	1042	GLN	0	-0.006	-0.029	23.705	0.003	0.003	0.000	0.000	0.000	0.000
47	B	1043	GLU	-1	-0.815	-0.894	27.174	-0.063	-0.063	0.000	0.000	0.000	0.000
48	B	1044	GLY	0	-0.005	-0.001	24.561	0.004	0.004	0.000	0.000	0.000	0.000
49	B	1045	VAL	0	-0.050	-0.006	23.530	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	1046	PHE	0	0.025	0.011	18.074	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	1047	HIS	0	0.006	0.021	21.887	0.006	0.006	0.000	0.000	0.000	0.000
52	B	1048	THR	0	0.008	-0.021	18.884	-0.017	-0.017	0.000	0.000	0.000	0.000
53	B	1049	MET	0	-0.021	0.006	21.846	0.015	0.015	0.000	0.000	0.000	0.000
54	B	1050	TRP	0	0.025	0.025	20.712	-0.031	-0.031	0.000	0.000	0.000	0.000
55	B	1051	HIS	1	0.744	0.831	19.806	0.197	0.197	0.000	0.000	0.000	0.000
56	B	1052	VAL	0	-0.065	-0.009	17.230	-0.029	-0.029	0.000	0.000	0.000	0.000
57	B	1053	THR	0	0.078	0.015	15.400	-0.051	-0.051	0.000	0.000	0.000	0.000
58	B	1054	LYS	1	0.851	0.919	15.400	0.280	0.280	0.000	0.000	0.000	0.000
59	B	1055	GLY	0	0.031	0.026	17.534	0.015	0.015	0.000	0.000	0.000	0.000
60	B	1056	SER	0	-0.051	-0.020	11.873	0.010	0.010	0.000	0.000	0.000	0.000
61	B	1057	ALA	0	0.038	0.034	11.810	0.010	0.010	0.000	0.000	0.000	0.000
62	B	1058	LEU	0	-0.044	-0.011	11.272	-0.120	-0.120	0.000	0.000	0.000	0.000
63	B	1059	ARG	1	0.826	0.906	7.671	0.865	0.865	0.000	0.000	0.000	0.000
64	B	1060	SER	0	0.032	-0.007	10.984	-0.062	-0.062	0.000	0.000	0.000	0.000
65	B	1061	GLY	0	0.049	0.026	13.636	0.055	0.055	0.000	0.000	0.000	0.000
66	B	1062	GLU	-1	-0.911	-0.957	11.886	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	1063	GLY	0	-0.009	-0.005	13.332	0.066	0.066	0.000	0.000	0.000	0.000
68	B	1064	ARG	1	0.872	0.937	9.839	-0.128	-0.128	0.000	0.000	0.000	0.000
69	B	1065	LEU	0	0.005	0.009	13.357	0.029	0.029	0.000	0.000	0.000	0.000
70	B	1066	ASP	-1	-0.867	-0.940	15.097	-0.101	-0.101	0.000	0.000	0.000	0.000
71	B	1067	PRO	0	-0.042	-0.025	16.648	0.004	0.004	0.000	0.000	0.000	0.000
72	B	1068	TYR	0	-0.039	-0.017	19.494	0.019	0.019	0.000	0.000	0.000	0.000
73	B	1069	TRP	0	0.011	-0.009	23.145	0.009	0.009	0.000	0.000	0.000	0.000
74	B	1070	GLY	0	0.011	0.004	23.929	-0.018	-0.018	0.000	0.000	0.000	0.000
75	B	1071	ASP	-1	-0.818	-0.883	25.042	-0.091	-0.091	0.000	0.000	0.000	0.000
76	B	1072	VAL	0	-0.010	-0.012	24.229	-0.008	-0.008	0.000	0.000	0.000	0.000
77	B	1073	LYS	1	0.914	0.941	26.480	0.106	0.106	0.000	0.000	0.000	0.000
78	B	1074	GLN	0	-0.021	-0.006	29.428	0.002	0.002	0.000	0.000	0.000	0.000
79	B	1075	ASP	-1	-0.754	-0.832	24.314	-0.201	-0.201	0.000	0.000	0.000	0.000
80	B	1076	LEU	0	-0.031	-0.024	24.860	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	1077	VAL	0	-0.023	-0.020	20.009	0.005	0.005	0.000	0.000	0.000	0.000
82	B	1078	SER	0	-0.002	-0.012	22.918	-0.006	-0.006	0.000	0.000	0.000	0.000
83	B	1079	TYR	0	-0.009	-0.019	15.920	0.001	0.001	0.000	0.000	0.000	0.000
84	B	1080	CYS	0	-0.024	-0.029	20.001	0.001	0.001	0.000	0.000	0.000	0.000
85	B	1081	GLY	0	0.067	0.040	22.337	0.014	0.014	0.000	0.000	0.000	0.000
86	B	1082	PRO	0	-0.003	0.007	25.606	-0.012	-0.012	0.000	0.000	0.000	0.000
87	B	1083	TRP	0	-0.008	-0.016	25.504	-0.008	-0.008	0.000	0.000	0.000	0.000
88	B	1084	LYS	1	0.850	0.916	28.339	0.070	0.070	0.000	0.000	0.000	0.000
89	B	1085	LEU	0	-0.063	-0.012	27.901	0.003	0.003	0.000	0.000	0.000	0.000
90	B	1086	ASP	-1	-0.872	-0.943	32.005	-0.063	-0.063	0.000	0.000	0.000	0.000
91	B	1087	ALA	0	-0.040	-0.004	35.475	0.003	0.003	0.000	0.000	0.000	0.000
92	B	1088	ALA	0	0.044	0.020	36.061	-0.004	-0.004	0.000	0.000	0.000	0.000
93	B	1089	TRP	0	0.041	0.009	38.494	0.002	0.002	0.000	0.000	0.000	0.000
94	B	1090	ASP	-1	-0.856	-0.907	40.173	-0.051	-0.051	0.000	0.000	0.000	0.000
95	B	1091	GLY	0	0.038	0.017	42.955	0.003	0.003	0.000	0.000	0.000	0.000
96	B	1092	HIS	1	0.875	0.931	44.383	0.048	0.048	0.000	0.000	0.000	0.000
97	B	1093	SER	0	-0.120	-0.086	43.504	0.002	0.002	0.000	0.000	0.000	0.000
98	B	1094	GLU	-1	-0.818	-0.902	41.922	-0.061	-0.061	0.000	0.000	0.000	0.000
99	B	1095	VAL	0	-0.078	-0.038	36.617	0.001	0.001	0.000	0.000	0.000	0.000
100	B	1096	GLN	0	0.040	0.001	35.204	0.000	0.000	0.000	0.000	0.000	0.000
101	B	1097	LEU	0	-0.046	-0.008	29.340	-0.004	-0.004	0.000	0.000	0.000	0.000
102	B	1098	LEU	0	0.052	0.039	27.940	0.001	0.001	0.000	0.000	0.000	0.000
103	B	1099	ALA	0	-0.011	0.000	27.635	-0.012	-0.012	0.000	0.000	0.000	0.000
104	B	1100	VAL	0	0.043	-0.010	21.964	0.006	0.006	0.000	0.000	0.000	0.000
105	B	1101	PRO	0	0.025	0.013	23.092	-0.023	-0.023	0.000	0.000	0.000	0.000
106	B	1102	PRO	0	-0.023	-0.006	19.645	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	1103	GLY	0	-0.013	-0.020	19.806	0.017	0.017	0.000	0.000	0.000	0.000
108	B	1104	GLU	-1	-0.859	-0.894	21.034	-0.114	-0.114	0.000	0.000	0.000	0.000
109	B	1105	ARG	1	0.978	0.997	23.773	0.075	0.075	0.000	0.000	0.000	0.000
110	B	1106	ALA	0	0.048	0.016	25.576	0.001	0.001	0.000	0.000	0.000	0.000
111	B	1107	ARG	1	0.800	0.874	27.047	0.130	0.130	0.000	0.000	0.000	0.000
112	B	1108	ASN	0	-0.024	-0.012	30.571	-0.011	-0.011	0.000	0.000	0.000	0.000
113	B	1109	ILE	0	-0.011	0.000	31.890	0.003	0.003	0.000	0.000	0.000	0.000
114	B	1110	GLN	0	-0.034	-0.019	35.446	-0.003	-0.003	0.000	0.000	0.000	0.000
115	B	1111	THR	0	-0.008	-0.006	36.609	0.001	0.001	0.000	0.000	0.000	0.000
116	B	1112	LEU	0	0.014	0.011	39.646	0.000	0.000	0.000	0.000	0.000	0.000
117	B	1113	PRO	0	-0.048	-0.011	37.974	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	1114	GLY	0	0.038	0.028	39.626	0.005	0.005	0.000	0.000	0.000	0.000
119	B	1115	ILE	0	-0.021	-0.018	40.338	-0.003	-0.003	0.000	0.000	0.000	0.000
120	B	1116	PHE	0	-0.006	-0.006	38.853	0.001	0.001	0.000	0.000	0.000	0.000
121	B	1117	LYS	1	0.803	0.889	41.481	0.055	0.055	0.000	0.000	0.000	0.000
122	B	1118	THR	0	-0.041	-0.025	38.398	-0.004	-0.004	0.000	0.000	0.000	0.000
123	B	1119	LYS	1	0.934	0.968	40.477	0.059	0.059	0.000	0.000	0.000	0.000
124	B	1120	ASP	-1	-0.928	-0.975	39.992	-0.063	-0.063	0.000	0.000	0.000	0.000
125	B	1121	GLY	0	0.050	0.029	41.150	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	1122	ASP	-1	-0.809	-0.905	42.024	-0.056	-0.056	0.000	0.000	0.000	0.000
127	B	1123	ILE	0	-0.032	0.010	36.242	0.001	0.001	0.000	0.000	0.000	0.000
128	B	1124	GLY	0	0.030	0.021	38.859	0.001	0.001	0.000	0.000	0.000	0.000
129	B	1125	ALA	0	0.015	-0.006	35.634	-0.005	-0.005	0.000	0.000	0.000	0.000
130	B	1126	VAL	0	0.017	-0.003	33.503	0.005	0.005	0.000	0.000	0.000	0.000
131	B	1127	ALA	0	0.005	0.009	34.518	-0.006	-0.006	0.000	0.000	0.000	0.000
132	B	1128	LEU	0	0.023	0.006	33.463	0.003	0.003	0.000	0.000	0.000	0.000
133	B	1129	ASP	-1	-0.896	-0.915	31.517	-0.118	-0.118	0.000	0.000	0.000	0.000
134	B	1130	TYR	0	0.018	-0.012	27.323	0.001	0.001	0.000	0.000	0.000	0.000
135	B	1131	PRO	0	0.009	0.009	24.097	-0.007	-0.007	0.000	0.000	0.000	0.000
136	B	1132	ALA	0	0.029	0.028	22.330	-0.003	-0.003	0.000	0.000	0.000	0.000
137	B	1133	GLY	0	0.039	0.019	20.029	-0.017	-0.017	0.000	0.000	0.000	0.000
138	B	1134	THR	0	0.016	-0.004	20.758	-0.010	-0.010	0.000	0.000	0.000	0.000
139	B	1135	SER	0	-0.050	-0.004	22.601	0.012	0.012	0.000	0.000	0.000	0.000
140	B	1136	GLY	0	0.023	-0.007	22.511	-0.023	-0.023	0.000	0.000	0.000	0.000
141	B	1137	SER	0	-0.018	-0.014	24.275	0.005	0.005	0.000	0.000	0.000	0.000
142	B	1138	PRO	0	0.011	0.022	25.734	0.007	0.007	0.000	0.000	0.000	0.000
143	B	1139	ILE	0	0.029	0.013	28.538	0.004	0.004	0.000	0.000	0.000	0.000
144	B	1140	LEU	0	0.015	0.006	31.200	0.003	0.003	0.000	0.000	0.000	0.000
145	B	1141	ASP	-1	-0.757	-0.868	34.641	-0.059	-0.059	0.000	0.000	0.000	0.000
146	B	1142	LYS	1	0.929	0.940	37.959	0.051	0.051	0.000	0.000	0.000	0.000
147	B	1143	CYS	0	-0.132	-0.056	39.974	0.003	0.003	0.000	0.000	0.000	0.000
148	B	1144	GLY	0	0.044	0.032	36.172	0.002	0.002	0.000	0.000	0.000	0.000
149	B	1145	ARG	1	0.843	0.915	34.330	0.052	0.052	0.000	0.000	0.000	0.000
150	B	1146	VAL	0	0.030	0.005	29.383	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	1147	ILE	0	-0.037	-0.011	32.711	0.002	0.002	0.000	0.000	0.000	0.000
152	B	1148	GLY	0	0.023	0.006	31.786	0.002	0.002	0.000	0.000	0.000	0.000
153	B	1149	LEU	0	-0.042	-0.009	25.134	-0.004	-0.004	0.000	0.000	0.000	0.000
154	B	1150	TYR	0	0.017	-0.021	26.865	-0.002	-0.002	0.000	0.000	0.000	0.000
155	B	1151	GLY	0	-0.003	-0.009	27.182	-0.015	-0.015	0.000	0.000	0.000	0.000
156	B	1152	ASN	0	-0.030	-0.020	27.797	0.005	0.005	0.000	0.000	0.000	0.000
157	B	1153	GLY	0	-0.003	0.003	30.242	0.005	0.005	0.000	0.000	0.000	0.000
158	B	1154	VAL	0	-0.034	-0.013	33.038	-0.003	-0.003	0.000	0.000	0.000	0.000
159	B	1155	VAL	0	0.051	0.022	35.533	0.004	0.004	0.000	0.000	0.000	0.000
160	B	1156	ILE	0	-0.007	0.002	37.911	0.001	0.001	0.000	0.000	0.000	0.000
161	B	1157	LYS	1	0.858	0.920	41.453	0.057	0.057	0.000	0.000	0.000	0.000
162	B	1158	ASN	0	0.003	0.013	43.620	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:48:SER)