Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 1NMMZ

Calculation Name: 1J2W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J2W

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJ28

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2380663.924468
FMO2-HF: Nuclear repulsion 2302151.943148
FMO2-HF: Total energy -78511.98132
FMO2-MP2: Total energy -78743.47654


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/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.
-9.011-2.9215.652-5.369-6.376-0.025
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 : 0.067 / q_NPA : 0.012
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   
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].
3A3LEU0-0.032-0.0203.335-1.3230.3770.002-0.695-1.0080.002
4A4ALA00.0450.0313.1720.4191.2020.044-0.297-0.5310.000
5A5ALA00.0180.0064.8180.7290.857-0.001-0.011-0.1150.000
6A6HIS10.8220.9007.6981.4781.4780.0000.0000.0000.000
7A7ILE0-0.0020.0085.6440.2440.2440.0000.0000.0000.000
8A8ASP-1-0.697-0.8059.470-0.669-0.6690.0000.0000.0000.000
9A9HIS0-0.048-0.03210.4510.0050.0050.0000.0000.0000.000
10A10THR0-0.056-0.04512.1250.1070.1070.0000.0000.0000.000
11A11LEU0-0.011-0.00615.6140.0130.0130.0000.0000.0000.000
12A12LEU00.019-0.00518.3590.0210.0210.0000.0000.0000.000
13A13LYS10.7990.92021.6830.2640.2640.0000.0000.0000.000
14A14PRO00.0270.00123.771-0.002-0.0020.0000.0000.0000.000
15A15THR00.0060.00126.4120.0070.0070.0000.0000.0000.000
16A16ALA0-0.018-0.00522.5340.0020.0020.0000.0000.0000.000
17A17THR00.0520.04224.2460.0030.0030.0000.0000.0000.000
18A18LEU00.0460.01023.523-0.019-0.0190.0000.0000.0000.000
19A19GLU-1-0.935-0.95522.978-0.199-0.1990.0000.0000.0000.000
20A20GLU-1-0.773-0.88620.195-0.274-0.2740.0000.0000.0000.000
21A21VAL0-0.020-0.01918.744-0.043-0.0430.0000.0000.0000.000
22A22ALA0-0.022-0.00718.643-0.038-0.0380.0000.0000.0000.000
23A23LYS10.8490.93313.6150.4050.4050.0000.0000.0000.000
24A24ALA00.0290.00914.381-0.055-0.0550.0000.0000.0000.000
25A25ALA0-0.011-0.02513.687-0.090-0.0900.0000.0000.0000.000
26A26GLU-1-0.937-0.97514.438-0.361-0.3610.0000.0000.0000.000
27A27GLU-1-0.796-0.88410.590-0.636-0.6360.0000.0000.0000.000
28A28ALA0-0.026-0.0239.479-0.188-0.1880.0000.0000.0000.000
29A29LEU0-0.067-0.02710.015-0.134-0.1340.0000.0000.0000.000
30A30GLU-1-0.885-0.9239.077-0.576-0.5760.0000.0000.0000.000
31A31TYR0-0.061-0.0635.0400.0400.0400.0000.0000.0000.000
32A32GLY0-0.0160.0045.003-0.850-0.785-0.001-0.002-0.0620.000
33A33PHE0-0.044-0.0245.100-0.279-0.2790.0000.0000.0000.000
34A34TYR0-0.038-0.0228.0340.2410.2410.0000.0000.0000.000
35A35GLY00.0190.00410.7200.1720.1720.0000.0000.0000.000
36A36LEU0-0.0340.00612.166-0.094-0.0940.0000.0000.0000.000
37A37CYS0-0.052-0.02014.8610.0630.0630.0000.0000.0000.000
38A38ILE00.0310.02717.4960.0080.0080.0000.0000.0000.000
39A39PRO00.0500.02520.3430.0130.0130.0000.0000.0000.000
40A40PRO00.0650.03624.204-0.003-0.0030.0000.0000.0000.000
41A41SER0-0.053-0.02826.4380.0030.0030.0000.0000.0000.000
42A42TYR0-0.020-0.03923.8510.0130.0130.0000.0000.0000.000
43A43VAL0-0.0120.01123.105-0.007-0.0070.0000.0000.0000.000
44A44ALA00.0570.02624.546-0.005-0.0050.0000.0000.0000.000
45A45TRP00.0110.01121.228-0.001-0.0010.0000.0000.0000.000
46A46VAL00.011-0.00219.320-0.001-0.0010.0000.0000.0000.000
47A47ARG10.8240.90520.1010.3330.3330.0000.0000.0000.000
48A48ALA0-0.015-0.00823.6270.0070.0070.0000.0000.0000.000
49A49ARG10.8670.94620.0690.2730.2730.0000.0000.0000.000
50A50TYR0-0.020-0.02218.0330.0050.0050.0000.0000.0000.000
51A51PRO00.0330.02620.379-0.023-0.0230.0000.0000.0000.000
52A52HIS0-0.007-0.01319.444-0.016-0.0160.0000.0000.0000.000
53A53ALA00.0050.01416.363-0.019-0.0190.0000.0000.0000.000
54A54PRO0-0.0100.00911.7000.0070.0070.0000.0000.0000.000
55A55PHE0-0.018-0.00512.300-0.037-0.0370.0000.0000.0000.000
56A56ARG10.8990.94513.6050.7340.7340.0000.0000.0000.000
57A57LEU0-0.031-0.01616.230-0.039-0.0390.0000.0000.0000.000
58A58VAL0-0.018-0.01316.5690.0410.0410.0000.0000.0000.000
59A59THR00.002-0.02619.2930.0150.0150.0000.0000.0000.000
60A60VAL0-0.071-0.03122.047-0.009-0.0090.0000.0000.0000.000
61A61VAL00.0280.01624.4510.0110.0110.0000.0000.0000.000
62A62GLY00.0540.01328.139-0.001-0.0010.0000.0000.0000.000
63A63PHE0-0.0390.00323.2710.0020.0020.0000.0000.0000.000
64A64PRO0-0.022-0.02126.8110.0080.0080.0000.0000.0000.000
65A65LEU00.030-0.01628.3630.0010.0010.0000.0000.0000.000
66A66GLY00.0550.04431.4540.0080.0080.0000.0000.0000.000
67A67TYR0-0.039-0.02632.4890.0040.0040.0000.0000.0000.000
68A68GLN0-0.011-0.01032.3820.0080.0080.0000.0000.0000.000
69A69GLU-1-0.874-0.94336.836-0.107-0.1070.0000.0000.0000.000
70A70LYS10.8780.93136.3660.1000.1000.0000.0000.0000.000
71A71GLU-1-0.773-0.88136.484-0.116-0.1160.0000.0000.0000.000
72A72VAL0-0.028-0.00635.346-0.003-0.0030.0000.0000.0000.000
73A73LYS10.7860.87732.3550.1500.1500.0000.0000.0000.000
74A74ALA00.0200.01432.360-0.011-0.0110.0000.0000.0000.000
75A75LEU00.008-0.00433.710-0.006-0.0060.0000.0000.0000.000
76A76GLU-1-0.876-0.93030.088-0.194-0.1940.0000.0000.0000.000
77A77ALA00.019-0.00129.039-0.012-0.0120.0000.0000.0000.000
78A78ALA00.0330.02129.557-0.010-0.0100.0000.0000.0000.000
79A79LEU0-0.052-0.02531.589-0.003-0.0030.0000.0000.0000.000
80A80ALA0-0.008-0.00926.491-0.005-0.0050.0000.0000.0000.000
81A81CYS0-0.004-0.01025.836-0.011-0.0110.0000.0000.0000.000
82A82ALA0-0.0190.00527.827-0.003-0.0030.0000.0000.0000.000
83A83ARG10.8800.94028.3700.1800.1800.0000.0000.0000.000
84A84GLY00.0380.01925.547-0.006-0.0060.0000.0000.0000.000
85A85ALA0-0.010-0.00622.772-0.026-0.0260.0000.0000.0000.000
86A86ASP-1-0.775-0.86819.708-0.388-0.3880.0000.0000.0000.000
87A87GLU-1-0.762-0.85318.018-0.522-0.5220.0000.0000.0000.000
88A88VAL00.002-0.00121.772-0.001-0.0010.0000.0000.0000.000
89A89ASP-1-0.721-0.83819.756-0.417-0.4170.0000.0000.0000.000
90A90MET00.0170.02523.0870.0090.0090.0000.0000.0000.000
91A91VAL0-0.038-0.01626.440-0.010-0.0100.0000.0000.0000.000
92A92LEU00.0320.03328.6860.0110.0110.0000.0000.0000.000
93A93HIS00.0130.00731.650-0.002-0.0020.0000.0000.0000.000
94A94LEU00.0140.00030.4730.0070.0070.0000.0000.0000.000
95A95GLY00.0150.01634.5820.0060.0060.0000.0000.0000.000
96A96ARG10.8780.92938.0210.1020.1020.0000.0000.0000.000
97A97ALA00.0210.00934.8340.0040.0040.0000.0000.0000.000
98A98LYS10.7540.85635.8010.1090.1090.0000.0000.0000.000
99A99ALA0-0.030-0.01138.4740.0050.0050.0000.0000.0000.000
100A100GLY0-0.0150.00039.9100.0050.0050.0000.0000.0000.000
101A101ASP-1-0.849-0.91840.690-0.093-0.0930.0000.0000.0000.000
102A102LEU00.006-0.02336.918-0.006-0.0060.0000.0000.0000.000
103A103ASP-1-0.866-0.92138.431-0.095-0.0950.0000.0000.0000.000
104A104TYR0-0.037-0.02637.195-0.001-0.0010.0000.0000.0000.000
105A105LEU0-0.045-0.02634.474-0.006-0.0060.0000.0000.0000.000
106A106GLU-1-0.850-0.93935.209-0.119-0.1190.0000.0000.0000.000
107A107ALA00.0180.00636.291-0.005-0.0050.0000.0000.0000.000
108A108GLU-1-0.791-0.88934.246-0.148-0.1480.0000.0000.0000.000
109A109VAL0-0.035-0.01830.434-0.008-0.0080.0000.0000.0000.000
110A110ARG10.8330.91832.7350.1240.1240.0000.0000.0000.000
111A111ALA0-0.012-0.00435.341-0.002-0.0020.0000.0000.0000.000
112A112VAL0-0.012-0.02229.674-0.002-0.0020.0000.0000.0000.000
113A113ARG10.7430.85327.0610.2070.2070.0000.0000.0000.000
114A114GLU-1-0.871-0.93531.917-0.128-0.1280.0000.0000.0000.000
115A115ALA0-0.0300.00233.4270.0040.0040.0000.0000.0000.000
116A116VAL0-0.050-0.02228.201-0.004-0.0040.0000.0000.0000.000
117A117PRO00.0180.01629.364-0.014-0.0140.0000.0000.0000.000
118A118GLN0-0.054-0.03228.2640.0050.0050.0000.0000.0000.000
119A119ALA00.0270.02724.759-0.015-0.0150.0000.0000.0000.000
120A120VAL0-0.038-0.01420.2370.0120.0120.0000.0000.0000.000
121A121LEU00.0060.00523.075-0.014-0.0140.0000.0000.0000.000
122A122LYS10.7490.84917.4560.4750.4750.0000.0000.0000.000
123A123VAL00.010-0.00223.3870.0090.0090.0000.0000.0000.000
124A124ILE0-0.056-0.03423.312-0.007-0.0070.0000.0000.0000.000
125A125LEU00.021-0.00425.6260.0160.0160.0000.0000.0000.000
126A126GLU-1-0.771-0.84626.204-0.206-0.2060.0000.0000.0000.000
127A127THR0-0.039-0.04724.7810.0120.0120.0000.0000.0000.000
128A128GLY0-0.027-0.00827.6220.0100.0100.0000.0000.0000.000
129A129TYR00.000-0.00128.7800.0120.0120.0000.0000.0000.000
130A130PHE0-0.076-0.02630.7330.0110.0110.0000.0000.0000.000
131A131SER00.028-0.00431.575-0.002-0.0020.0000.0000.0000.000
132A132PRO00.024-0.00530.691-0.007-0.0070.0000.0000.0000.000
133A133GLU-1-0.847-0.94131.884-0.094-0.0940.0000.0000.0000.000
134A134GLU-1-0.795-0.85634.400-0.104-0.1040.0000.0000.0000.000
135A135ILE00.0040.00727.929-0.005-0.0050.0000.0000.0000.000
136A136ALA0-0.003-0.00430.939-0.008-0.0080.0000.0000.0000.000
137A137ARG10.9530.98132.1530.0930.0930.0000.0000.0000.000
138A138LEU0-0.0010.00131.315-0.001-0.0010.0000.0000.0000.000
139A139ALA00.007-0.00228.921-0.006-0.0060.0000.0000.0000.000
140A140GLU-1-0.776-0.85630.270-0.122-0.1220.0000.0000.0000.000
141A141ALA00.0170.01433.1530.0000.0000.0000.0000.0000.000
142A142ALA00.0280.00529.173-0.002-0.0020.0000.0000.0000.000
143A143ILE0-0.010-0.00928.626-0.006-0.0060.0000.0000.0000.000
144A144ARG10.7850.90430.7530.1050.1050.0000.0000.0000.000
145A145GLY00.0330.01933.4270.0040.0040.0000.0000.0000.000
146A146GLY0-0.004-0.01131.1270.0020.0020.0000.0000.0000.000
147A147ALA0-0.051-0.02326.575-0.012-0.0120.0000.0000.0000.000
148A148ASP-1-0.766-0.85023.360-0.250-0.2500.0000.0000.0000.000
149A149PHE0-0.061-0.04217.240-0.020-0.0200.0000.0000.0000.000
150A150LEU00.0240.03022.7850.0140.0140.0000.0000.0000.000
151A151LYS10.8250.89819.7070.3360.3360.0000.0000.0000.000
152A152THR00.012-0.00420.7790.0100.0100.0000.0000.0000.000
153A153SER00.0270.01421.4640.0260.0260.0000.0000.0000.000
154A154THR0-0.044-0.07222.045-0.034-0.0340.0000.0000.0000.000
155A155GLY0-0.059-0.03121.637-0.029-0.0290.0000.0000.0000.000
156A156PHE0-0.067-0.04022.2860.0030.0030.0000.0000.0000.000
157A157GLY00.0480.04525.9530.0160.0160.0000.0000.0000.000
158A158PRO0-0.050-0.02927.058-0.005-0.0050.0000.0000.0000.000
159A159ARG10.8090.87924.2010.1870.1870.0000.0000.0000.000
160A160GLY0-0.0190.00020.808-0.011-0.0110.0000.0000.0000.000
161A161ALA0-0.019-0.00318.3750.0230.0230.0000.0000.0000.000
162A162SER0-0.013-0.03220.3980.0030.0030.0000.0000.0000.000
163A163LEU00.029-0.00117.268-0.016-0.0160.0000.0000.0000.000
164A164GLU-1-0.826-0.89920.533-0.139-0.1390.0000.0000.0000.000
165A165ASP-1-0.747-0.82122.415-0.192-0.1920.0000.0000.0000.000
166A166VAL0-0.031-0.01218.0890.0000.0000.0000.0000.0000.000
167A167ALA00.0640.03021.3080.0050.0050.0000.0000.0000.000
168A168LEU0-0.101-0.04123.2150.0130.0130.0000.0000.0000.000
169A169LEU00.019-0.00222.9250.0060.0060.0000.0000.0000.000
170A170VAL00.0210.01621.0120.0030.0030.0000.0000.0000.000
171A171ARG10.9110.96724.3030.1230.1230.0000.0000.0000.000
172A172VAL00.0000.01427.5370.0120.0120.0000.0000.0000.000
173A173ALA00.0210.01925.7600.0070.0070.0000.0000.0000.000
174A174GLN0-0.079-0.04727.7280.0080.0080.0000.0000.0000.000
175A175GLY0-0.003-0.00125.3920.0070.0070.0000.0000.0000.000
176A176ARG10.7670.85626.3050.1210.1210.0000.0000.0000.000
177A177ALA00.0330.03025.160-0.003-0.0030.0000.0000.0000.000
178A178GLN00.0030.02418.547-0.033-0.0330.0000.0000.0000.000
179A179VAL00.0200.00519.6010.0150.0150.0000.0000.0000.000
180A180LYS10.7650.85815.5060.4830.4830.0000.0000.0000.000
181A181ALA00.0360.02615.5820.0410.0410.0000.0000.0000.000
182A182ALA00.000-0.01516.159-0.072-0.0720.0000.0000.0000.000
183A183GLY00.0780.05017.4230.0490.0490.0000.0000.0000.000
184A184GLY0-0.001-0.00917.979-0.001-0.0010.0000.0000.0000.000
185A185ILE0-0.010-0.00811.7300.0130.0130.0000.0000.0000.000
186A186ARG10.8860.94413.5370.3820.3820.0000.0000.0000.000
187A187ASP-1-0.761-0.83910.189-0.369-0.3690.0000.0000.0000.000
188A188ARG10.9000.9023.882-0.487-0.344-0.001-0.018-0.1240.000
189A189GLU-1-0.816-0.8877.718-0.041-0.0410.0000.0000.0000.000
190A190THR0-0.038-0.07110.7300.0300.0300.0000.0000.0000.000
191A191ALA0-0.014-0.0088.6480.0180.0180.0000.0000.0000.000
192A192LEU00.0100.0057.4360.0050.0050.0000.0000.0000.000
193A193ARG10.8070.89210.4770.2280.2280.0000.0000.0000.000
194A194MET0-0.0130.00213.4570.0330.0330.0000.0000.0000.000
195A195LEU0-0.015-0.0079.435-0.001-0.0010.0000.0000.0000.000
196A196LYS10.9290.97113.5830.0500.0500.0000.0000.0000.000
197A197ALA0-0.034-0.01115.5090.0340.0340.0000.0000.0000.000
198A198GLY00.0110.00017.1250.0200.0200.0000.0000.0000.000
199A199ALA0-0.049-0.00915.319-0.007-0.0070.0000.0000.0000.000
200A200SER0-0.014-0.02514.894-0.026-0.0260.0000.0000.0000.000
201A201ARG10.7400.83512.9150.5260.5260.0000.0000.0000.000
202A202LEU00.0340.0099.3860.0790.0790.0000.0000.0000.000
203A203GLY00.0240.00513.030-0.051-0.0510.0000.0000.0000.000
204A204THR0-0.037-0.04511.3720.0760.0760.0000.0000.0000.000
205A205SER00.0880.05912.975-0.064-0.0640.0000.0000.0000.000
206A206SER0-0.027-0.00811.2690.0330.0330.0000.0000.0000.000
207A207GLY00.0300.0278.500-0.078-0.0780.0000.0000.0000.000
208A208VAL00.0770.0326.733-0.345-0.3450.0000.0000.0000.000
209A209ALA00.0090.0056.791-0.221-0.2210.0000.0000.0000.000
210A210LEU0-0.092-0.0326.0730.1000.1000.0000.0000.0000.000
211A211VAL0-0.049-0.0262.077-2.187-1.2184.579-3.051-2.498-0.001
212A212ALA00.0100.0262.437-5.877-3.5751.030-1.295-2.038-0.026