FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 1NNQZ

Calculation Name: 3MDK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MDK

Chain ID: A

ChEMBL ID:

UniProt ID: Q88N92

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2363812.928426
FMO2-HF: Nuclear repulsion 2282589.996866
FMO2-HF: Total energy -81222.931561
FMO2-MP2: Total energy -81456.021377


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:6:ARG)


Summations of interaction energy for fragment #1(A:6: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.
-146.73-136.73714.775-9.231-15.539-0.086
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.896 / q_NPA : 0.943
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].
3A8ALA0-0.009-0.0122.682-12.066-9.4000.945-1.700-1.911-0.008
4A9CYS0-0.003-0.0125.3165.6445.740-0.001-0.006-0.0890.000
5A10TYR0-0.025-0.0038.611-1.845-1.8450.0000.0000.0000.000
6A11SER0-0.009-0.02510.8491.6211.6210.0000.0000.0000.000
7A12ASP-1-0.736-0.86812.783-16.920-16.9200.0000.0000.0000.000
8A13PRO00.0390.02113.5540.0050.0050.0000.0000.0000.000
9A14ALA00.0380.02815.0130.5020.5020.0000.0000.0000.000
10A15ASP-1-0.759-0.85217.944-15.797-15.7970.0000.0000.0000.000
11A16HIS0-0.058-0.04918.122-1.200-1.2000.0000.0000.0000.000
12A17TYR0-0.039-0.04419.415-0.366-0.3660.0000.0000.0000.000
13A18SER0-0.025-0.05414.626-1.096-1.0960.0000.0000.0000.000
14A19HIS0-0.0050.02214.712-0.553-0.5530.0000.0000.0000.000
15A20ARG10.8380.89015.87413.58813.5880.0000.0000.0000.000
16A21VAL00.0000.00411.701-0.291-0.2910.0000.0000.0000.000
17A22ARG10.7620.83410.45321.07421.0740.0000.0000.0000.000
18A23LEU0-0.0110.00011.794-1.132-1.1320.0000.0000.0000.000
19A24VAL00.0330.00213.345-0.185-0.1850.0000.0000.0000.000
20A25LEU0-0.039-0.0277.447-0.518-0.5180.0000.0000.0000.000
21A26ALA00.0010.01110.024-1.293-1.2930.0000.0000.0000.000
22A27GLU-1-0.773-0.86311.391-16.144-16.1440.0000.0000.0000.000
23A28LYS10.7170.84211.24118.81318.8130.0000.0000.0000.000
24A29GLY00.0040.01710.298-0.243-0.2430.0000.0000.0000.000
25A30VAL0-0.047-0.0106.475-1.817-1.8170.0000.0000.0000.000
26A31SER0-0.020-0.0212.836-11.643-9.6190.661-1.016-1.670-0.010
27A32VAL00.0140.0052.669-9.497-5.9361.218-1.909-2.870-0.022
28A33GLN0-0.063-0.0311.893-37.338-35.55811.838-5.156-8.462-0.047
29A34LEU00.0380.0153.7229.0138.8790.1140.556-0.5370.001
30A35ILE0-0.049-0.0275.573-3.379-3.3790.0000.0000.0000.000
31A36ASP-1-0.823-0.9018.179-23.799-23.7990.0000.0000.0000.000
32A37VAL0-0.078-0.04711.2230.1020.1020.0000.0000.0000.000
33A38ASP-1-0.816-0.90514.438-14.567-14.5670.0000.0000.0000.000
34A39PRO0-0.008-0.01517.9830.1800.1800.0000.0000.0000.000
35A40ALA0-0.042-0.01120.6590.5210.5210.0000.0000.0000.000
36A41HIS0-0.095-0.04419.4940.4390.4390.0000.0000.0000.000
37A42LEU00.0470.03518.400-0.977-0.9770.0000.0000.0000.000
38A43PRO00.0150.01214.0220.5730.5730.0000.0000.0000.000
39A44ARG10.9020.94816.46715.23715.2370.0000.0000.0000.000
40A45LYS11.0070.99511.42823.60423.6040.0000.0000.0000.000
41A46LEU0-0.0220.02513.520-1.218-1.2180.0000.0000.0000.000
42A47ALA00.014-0.00815.3050.5250.5250.0000.0000.0000.000
43A48GLU-1-0.953-0.99415.378-17.835-17.8350.0000.0000.0000.000
44A49VAL0-0.031-0.01112.7720.1950.1950.0000.0000.0000.000
45A50ASN0-0.020-0.02116.0391.0161.0160.0000.0000.0000.000
46A51PRO00.0000.01118.4130.0610.0610.0000.0000.0000.000
47A52TYR0-0.027-0.01921.6340.7960.7960.0000.0000.0000.000
48A53GLY0-0.026-0.00819.5340.1860.1860.0000.0000.0000.000
49A54SER00.0260.02118.710-0.161-0.1610.0000.0000.0000.000
50A55VAL0-0.0170.00615.061-1.141-1.1410.0000.0000.0000.000
51A56PRO00.0280.00913.9440.9240.9240.0000.0000.0000.000
52A57THR0-0.070-0.04412.9701.6791.6790.0000.0000.0000.000
53A58LEU0-0.0060.0077.950-2.091-2.0910.0000.0000.0000.000
54A59VAL0-0.021-0.0208.2492.4172.4170.0000.0000.0000.000
55A60ASP-1-0.808-0.8876.443-34.351-34.3510.0000.0000.0000.000
56A61ARG10.8500.9036.94023.11923.1190.0000.0000.0000.000
57A62ASP-1-0.891-0.9438.322-18.820-18.8200.0000.0000.0000.000
58A63LEU0-0.0190.00911.0721.3941.3940.0000.0000.0000.000
59A64ALA00.0100.00311.185-1.979-1.9790.0000.0000.0000.000
60A65LEU0-0.027-0.00513.2781.4861.4860.0000.0000.0000.000
61A66TYR00.031-0.00414.199-0.895-0.8950.0000.0000.0000.000
62A67GLU-1-0.715-0.81116.877-13.690-13.6900.0000.0000.0000.000
63A68SER0-0.014-0.01117.256-0.469-0.4690.0000.0000.0000.000
64A69THR0-0.042-0.05917.599-0.432-0.4320.0000.0000.0000.000
65A70VAL00.0160.00917.758-0.203-0.2030.0000.0000.0000.000
66A71VAL0-0.0030.00112.545-0.518-0.5180.0000.0000.0000.000
67A72MET0-0.019-0.01014.290-0.808-0.8080.0000.0000.0000.000
68A73GLU-1-0.759-0.84416.190-13.513-13.5130.0000.0000.0000.000
69A74TYR00.0160.0179.8940.3260.3260.0000.0000.0000.000
70A75LEU0-0.022-0.0279.524-0.529-0.5290.0000.0000.0000.000
71A76GLU-1-0.765-0.87513.248-15.676-15.6760.0000.0000.0000.000
72A77GLU-1-0.894-0.94516.530-13.283-13.2830.0000.0000.0000.000
73A78ARG10.8070.9068.56123.63823.6380.0000.0000.0000.000
74A79TYR0-0.021-0.0197.490-1.009-1.0090.0000.0000.0000.000
75A80PRO00.0150.01813.4100.0220.0220.0000.0000.0000.000
76A81HIS0-0.049-0.00215.7080.9660.9660.0000.0000.0000.000
77A82PRO00.0560.02515.110-1.034-1.0340.0000.0000.0000.000
78A83PRO00.0080.01217.708-0.688-0.6880.0000.0000.0000.000
79A84LEU00.0150.00316.347-0.066-0.0660.0000.0000.0000.000
80A85MET0-0.073-0.02720.5750.5100.5100.0000.0000.0000.000
81A86PRO00.0780.04323.3060.0320.0320.0000.0000.0000.000
82A87VAL00.0240.01725.617-0.030-0.0300.0000.0000.0000.000
83A88TYR00.0180.00927.1930.0700.0700.0000.0000.0000.000
84A89PRO00.0380.00530.200-0.082-0.0820.0000.0000.0000.000
85A90VAL00.0340.01631.190-0.123-0.1230.0000.0000.0000.000
86A91ALA00.0180.02530.4090.0210.0210.0000.0000.0000.000
87A92ARG10.8530.91821.85812.39412.3940.0000.0000.0000.000
88A93GLY00.0080.00428.118-0.216-0.2160.0000.0000.0000.000
89A94ASN0-0.042-0.03430.7170.0750.0750.0000.0000.0000.000
90A95SER00.0540.02626.1740.0040.0040.0000.0000.0000.000
91A96ARG10.8300.87122.69712.19612.1960.0000.0000.0000.000
92A97LEU0-0.036-0.00627.354-0.053-0.0530.0000.0000.0000.000
93A98LEU00.0000.00329.3800.1150.1150.0000.0000.0000.000
94A99MET00.0320.01222.063-0.018-0.0180.0000.0000.0000.000
95A100HIS0-0.013-0.00326.7760.2100.2100.0000.0000.0000.000
96A101ARG10.8580.89928.9288.9588.9580.0000.0000.0000.000
97A102ILE00.0230.02526.5430.1670.1670.0000.0000.0000.000
98A103GLN00.0320.01825.353-0.479-0.4790.0000.0000.0000.000
99A104ARG10.8520.90828.1739.0539.0530.0000.0000.0000.000
100A105ASP-1-0.813-0.87931.845-8.822-8.8220.0000.0000.0000.000
101A106TRP0-0.022-0.02130.0120.0840.0840.0000.0000.0000.000
102A107CYS0-0.0290.02026.163-0.143-0.1430.0000.0000.0000.000
103A108ALA00.0570.04228.544-0.047-0.0470.0000.0000.0000.000
104A109LEU0-0.028-0.00631.0650.1510.1510.0000.0000.0000.000
105A110ALA00.0450.01027.8790.0990.0990.0000.0000.0000.000
106A111ASP-1-0.757-0.84726.511-12.274-12.2740.0000.0000.0000.000
107A112THR0-0.057-0.03828.9400.1690.1690.0000.0000.0000.000
108A113VAL0-0.059-0.01831.2410.2740.2740.0000.0000.0000.000
109A114LEU00.004-0.01025.1880.0810.0810.0000.0000.0000.000
110A115ASP-1-0.811-0.89628.770-10.512-10.5120.0000.0000.0000.000
111A116PRO0-0.012-0.01028.2750.4290.4290.0000.0000.0000.000
112A117ARG10.8590.93031.2159.8599.8590.0000.0000.0000.000
113A118SER0-0.0130.00633.4840.4780.4780.0000.0000.0000.000
114A119SER00.0090.01035.4520.0990.0990.0000.0000.0000.000
115A120GLU-1-0.807-0.91837.815-8.636-8.6360.0000.0000.0000.000
116A121ALA0-0.0260.01339.7000.0030.0030.0000.0000.0000.000
117A122ALA00.0820.04537.637-0.023-0.0230.0000.0000.0000.000
118A123ARG10.7790.87333.2479.2119.2110.0000.0000.0000.000
119A124THR0-0.062-0.04136.333-0.127-0.1270.0000.0000.0000.000
120A125GLU-1-0.945-0.98339.102-7.750-7.7500.0000.0000.0000.000
121A126ALA00.0290.02435.0180.0060.0060.0000.0000.0000.000
122A127ARG10.9100.94733.4029.0149.0140.0000.0000.0000.000
123A128LYS10.7810.87435.9707.3687.3680.0000.0000.0000.000
124A129ALA00.0460.01738.0050.0140.0140.0000.0000.0000.000
125A130LEU00.0240.03330.501-0.006-0.0060.0000.0000.0000.000
126A131ARG10.9130.95034.9958.0088.0080.0000.0000.0000.000
127A132GLU-1-0.811-0.87136.150-7.516-7.5160.0000.0000.0000.000
128A133SER0-0.017-0.01735.9780.1330.1330.0000.0000.0000.000
129A134LEU0-0.0040.00030.962-0.006-0.0060.0000.0000.0000.000
130A135THR0-0.041-0.03934.8880.0280.0280.0000.0000.0000.000
131A136GLY0-0.040-0.01437.7950.0980.0980.0000.0000.0000.000
132A137VAL00.0040.00134.0240.1210.1210.0000.0000.0000.000
133A138SER00.0130.00335.574-0.119-0.1190.0000.0000.0000.000
134A139PRO0-0.022-0.01436.560-0.107-0.1070.0000.0000.0000.000
135A140LEU00.0610.04635.4740.0060.0060.0000.0000.0000.000
136A141PHE0-0.036-0.01329.633-0.126-0.1260.0000.0000.0000.000
137A142SER0-0.060-0.05833.886-0.128-0.1280.0000.0000.0000.000
138A143GLU-1-0.985-0.98936.459-8.060-8.0600.0000.0000.0000.000
139A144PHE0-0.0210.00931.9920.0690.0690.0000.0000.0000.000
140A145ALA0-0.005-0.00229.208-0.093-0.0930.0000.0000.0000.000
141A146CYS0-0.073-0.03624.836-0.306-0.3060.0000.0000.0000.000
142A147PHE00.020-0.01827.5180.4910.4910.0000.0000.0000.000
143A148MET0-0.041-0.00729.351-0.055-0.0550.0000.0000.0000.000
144A149SER0-0.023-0.01527.0120.1590.1590.0000.0000.0000.000
145A150ASP-1-0.853-0.92829.727-9.753-9.7530.0000.0000.0000.000
146A151GLU-1-0.952-0.98024.408-12.061-12.0610.0000.0000.0000.000
147A152GLN00.0210.02020.1390.8050.8050.0000.0000.0000.000
148A153SER00.030-0.01322.155-0.258-0.2580.0000.0000.0000.000
149A154LEU00.0650.00717.760-0.439-0.4390.0000.0000.0000.000
150A155VAL00.0160.00621.171-0.044-0.0440.0000.0000.0000.000
151A156ASP-1-0.723-0.81122.766-12.264-12.2640.0000.0000.0000.000
152A157CYS0-0.057-0.02718.683-0.402-0.4020.0000.0000.0000.000
153A158CYS0-0.048-0.02020.657-0.391-0.3910.0000.0000.0000.000
154A159LEU0-0.0060.00722.9250.1430.1430.0000.0000.0000.000
155A160LEU00.0080.00321.5930.1720.1720.0000.0000.0000.000
156A161PRO00.0300.01719.3050.2320.2320.0000.0000.0000.000
157A162ILE0-0.005-0.00721.5860.1730.1730.0000.0000.0000.000
158A163LEU00.0290.00025.2800.3200.3200.0000.0000.0000.000
159A164TRP0-0.030-0.02520.6960.4470.4470.0000.0000.0000.000
160A165ARG10.7860.85318.43815.76815.7680.0000.0000.0000.000
161A166LEU0-0.0240.00525.1640.3530.3530.0000.0000.0000.000
162A167PRO00.0350.01127.0550.3550.3550.0000.0000.0000.000
163A168VAL00.0220.01424.9800.3150.3150.0000.0000.0000.000
164A169LEU0-0.0090.01827.7890.1830.1830.0000.0000.0000.000
165A170GLY0-0.0020.01730.2340.3790.3790.0000.0000.0000.000
166A171ILE0-0.084-0.05432.0720.3870.3870.0000.0000.0000.000
167A172GLU-1-0.762-0.83732.431-9.010-9.0100.0000.0000.0000.000
168A173LEU0-0.012-0.01632.1780.1540.1540.0000.0000.0000.000
169A174PRO00.0040.01036.0890.1170.1170.0000.0000.0000.000
170A175ARG10.8460.86936.2548.3928.3920.0000.0000.0000.000
171A176GLN00.0100.00339.732-0.067-0.0670.0000.0000.0000.000
172A177ALA0-0.0040.00536.3570.0210.0210.0000.0000.0000.000
173A178LYS10.8280.89435.8028.3918.3910.0000.0000.0000.000
174A179PRO00.0440.02335.003-0.238-0.2380.0000.0000.0000.000
175A180LEU00.0070.01330.720-0.299-0.2990.0000.0000.0000.000
176A181LEU0-0.003-0.01530.899-0.379-0.3790.0000.0000.0000.000
177A182ASP-1-0.749-0.85630.558-9.310-9.3100.0000.0000.0000.000
178A183TYR0-0.091-0.07225.949-0.286-0.2860.0000.0000.0000.000
179A184MET0-0.043-0.02526.573-0.317-0.3170.0000.0000.0000.000
180A185GLU-1-0.979-0.97725.749-10.613-10.6130.0000.0000.0000.000
181A186ARG10.8080.90825.8639.9769.9760.0000.0000.0000.000
182A187GLN0-0.001-0.00922.685-1.002-1.0020.0000.0000.0000.000
183A188PHE0-0.007-0.02021.309-0.631-0.6310.0000.0000.0000.000
184A189ALA0-0.0020.00720.664-0.655-0.6550.0000.0000.0000.000
185A190ARG10.7540.86018.88314.97714.9770.0000.0000.0000.000
186A191GLU-1-0.905-0.95815.331-17.246-17.2460.0000.0000.0000.000
187A192PRO00.0070.00513.812-0.997-0.9970.0000.0000.0000.000
188A193PHE00.0570.03114.258-0.938-0.9380.0000.0000.0000.000
189A194GLN00.0210.01815.731-0.911-0.9110.0000.0000.0000.000
190A195ALA0-0.016-0.01010.441-0.569-0.5690.0000.0000.0000.000
191A196SER0-0.052-0.02510.672-1.582-1.5820.0000.0000.0000.000
192A197LEU0-0.053-0.00412.870-0.175-0.1750.0000.0000.0000.000
193A198SER0-0.001-0.03512.521-0.751-0.7510.0000.0000.0000.000
194A199SER00.003-0.00813.5550.6030.6030.0000.0000.0000.000
195A200VAL00.0740.03815.6280.9640.9640.0000.0000.0000.000
196A201GLU-1-0.722-0.83115.579-18.241-18.2410.0000.0000.0000.000
197A202ARG10.8170.91314.56719.34319.3430.0000.0000.0000.000
198A203GLU-1-0.894-0.94619.337-14.361-14.3610.0000.0000.0000.000
199A204MET0-0.099-0.02120.2020.7840.7840.0000.0000.0000.000
200A205ARG10.7690.89323.11312.71512.7150.0000.0000.0000.000